diff --git a/WEB-INF/classes/com/cohort/array/ByteArray.java b/WEB-INF/classes/com/cohort/array/ByteArray.java index 0e5733212..aaa4259bf 100644 --- a/WEB-INF/classes/com/cohort/array/ByteArray.java +++ b/WEB-INF/classes/com/cohort/array/ByteArray.java @@ -1629,48 +1629,5 @@ public int[] getNMinMaxIndex() { } return new int[]{n, tmini, tmaxi}; } - - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 0; - String msg = "\n^^^ ByteArray.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - } diff --git a/WEB-INF/classes/com/cohort/util/HashDigest.java b/WEB-INF/classes/com/cohort/util/HashDigest.java index 33c72f094..cd058a414 100644 --- a/WEB-INF/classes/com/cohort/util/HashDigest.java +++ b/WEB-INF/classes/com/cohort/util/HashDigest.java @@ -4,12 +4,6 @@ */ package com.cohort.util; -import com.cohort.util.String2; -import com.cohort.util.File2; - -import java.io.FileWriter; -import java.io.IOException; - /** * This generates a hash digest (e.g., MD5, SHA256) of a password or a file. * @@ -313,34 +307,6 @@ private static int fmix32(int hash) { " HashDigest filename:myFileName type:algorithm -file\n" + "where algorithm can be MD5, SHA-1, or SHA-256.\n"; - /** - * This tests this class. - */ - public static void basicTest() throws Throwable { - System.out.println("*** HashDigest.basicTest"); - String tName = String2.replaceAll( - File2.getClassPath() + "com\\cohort\\util\\License.txt", "\\", "/"); - Test.ensureEqual(doIt(new String[]{"type:MD5"}), - "Neither password or filename was specified.\n" + usage, ""); - Test.ensureEqual(doIt(new String[]{"password:myPassword", "type:MD-5"}), - "Invalid algorithm.\n" + usage, ""); - Test.ensureEqual(doIt(new String[]{"password:myPassword", "type:MD5"}), - "deb1536f480475f7d593219aa1afd74c", ""); - Test.ensureEqual(doIt(new String[]{"password:myPassword", "type:SHA-1"}), - "5413ee24723bba2c5a6ba2d0196c78b3ee4628d1", ""); - Test.ensureEqual(doIt(new String[]{"password:myPassword", "type:SHA-256"}), - "76549b827ec46e705fd03831813fa52172338f0dfcbd711ed44b81a96dac51c6", ""); - Test.ensureEqual(doIt(new String[]{"filename:" + tName, "type:MD5"}), - "327fbb2aa6c6297d4fdd5fdf4b14e289", ""); - Test.ensureEqual(doIt(new String[]{"filename:" + tName, "type:SHA-256"}), - "e376c88953b2d56b00783fed071f1875e8ed94230f4e14eee5bce8bd608de5e6", ""); - Test.ensureEqual(doIt(new String[]{"filename:" + tName, "type:SHA-256", "-file"}), - "Created " + tName + ".sha256", ""); - Test.ensureEqual(File2.readFromFileUtf8(tName + ".sha256")[1], - "e376c88953b2d56b00783fed071f1875e8ed94230f4e14eee5bce8bd608de5e6 License.txt\n", ""); - File2.delete(tName + ".sha256"); - } - /** * This does the work. */ @@ -372,48 +338,6 @@ public static String doIt(String args[]) throws Throwable { } } - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 0; - String msg = "\n^^^ HashDigest.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - if (test == 0) basicTest(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - - /** * This is used when called from the command line. * It explicitly calls System.exit(0) when done. diff --git a/WEB-INF/classes/com/cohort/util/Image2.java b/WEB-INF/classes/com/cohort/util/Image2.java index 116d6da46..b3f18bad2 100644 --- a/WEB-INF/classes/com/cohort/util/Image2.java +++ b/WEB-INF/classes/com/cohort/util/Image2.java @@ -5,28 +5,18 @@ package com.cohort.util; import java.awt.Color; -import java.awt.Graphics; import java.awt.Image; import java.awt.Toolkit; import java.awt.image.BufferedImage; -import java.awt.image.FilteredImageSource; import java.awt.image.ImageObserver; -import java.awt.image.ImageProducer; -import java.awt.image.MemoryImageSource; import java.awt.image.PixelGrabber; import java.awt.image.RenderedImage; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; -import java.io.ByteArrayOutputStream; import java.io.File; -import java.io.FileInputStream; import java.io.FileOutputStream; -import java.io.InputStream; -import java.io.IOException; import java.io.OutputStream; -import java.io.PrintStream; -import java.io.Writer; import java.net.URL; @@ -61,7 +51,9 @@ public class Image2 { /** Java font drawing isn't consistent in minor ways. * Change this to change the sensitivity of Image2.compareImages(). */ - public static int DEFAULT_ALLOW_N_PIXELS_DIFFERENT = 250; + public static final int DEFAULT_ALLOW_N_PIXELS_DIFFERENT = 250; + public static final boolean DEFAULT_AUTO_CREATE_IF_MISSING = true; + public static final boolean DEFAULT_DISPLAY_IMAGES = false; /** * This tries to load the specified image (gif/jpg/png). @@ -469,6 +461,7 @@ public static BufferedImage makeImageBackgroundTransparent(Image image, return makeImageFromArray(pixels, imageWidth, imageHeight, millis); } + // TODO: Move this to test file after all uses of this are moved to test files. /** * This is like the other testImagesIdentical, but uses DEFAULT_ALLOW_N_PIXELS_DIFFERENT. * @@ -480,7 +473,7 @@ public static BufferedImage makeImageBackgroundTransparent(Image image, */ public static void testImagesIdentical(String observed, String expected, String diffName) throws Exception { - testImagesIdentical(observed, expected, diffName, DEFAULT_ALLOW_N_PIXELS_DIFFERENT); + testImagesIdentical(observed, expected, diffName, DEFAULT_ALLOW_N_PIXELS_DIFFERENT, DEFAULT_AUTO_CREATE_IF_MISSING, DEFAULT_DISPLAY_IMAGES); } /** @@ -496,17 +489,23 @@ public static void testImagesIdentical(String observed, String expected, * @throws Exception if the images are different or there is trouble */ public static void testImagesIdentical(String observed, String expected, - String diffName, int allowNPixelsDifferent) throws Exception { + String diffName, int allowNPixelsDifferent, boolean autoCreateMissing, boolean displayImages) throws Exception { //if expected doesn't exist, save observed as expected? if (!File2.isFile(expected)) { Test.displayInBrowser("file://" + observed); - if (String2.getStringFromSystemIn("Error at\n" + MustBe.getStackTrace() + - "testImagesIdentical: expected image file doesn't exist. Create it from observed (y/n)? ").equals("y")) { + if (autoCreateMissing) { + System.out.println("Expected image file doesn't exist, creating it from observed."); File2.copy(observed, expected); - return; - } - throw new RuntimeException("expectedFile=" + expected + " doesn't exist."); + }else { + if (String2.getStringFromSystemIn("Error at\n" + MustBe.getStackTrace() + + "testImagesIdentical: expected image file doesn't exist. Create it from observed (y/n)? ").equals("y")) { + File2.copy(observed, expected); + return; + } + throw new RuntimeException("expectedFile=" + expected + " doesn't exist."); + } + return; } //if diffName not .png, throw exception @@ -519,10 +518,12 @@ public static void testImagesIdentical(String observed, String expected, String error = compareImages(obsImg, expImg, diffName, allowNPixelsDifferent); //error.length>0 if > allowNPixelsDifferent if (error.length() == 0) return; - Test.displayInBrowser("file://" + observed); - Test.displayInBrowser("file://" + expected); - if (File2.isFile(diffName)) - Test.displayInBrowser("file://" + diffName); + if (displayImages) { + Test.displayInBrowser("file://" + observed); + Test.displayInBrowser("file://" + expected); + if (File2.isFile(diffName)) + Test.displayInBrowser("file://" + diffName); + } throw new RuntimeException( "testImagesIdentical found differences:\n" + error + "\n" + @@ -779,118 +780,5 @@ public static int rgbToWeb216Color(int rgb) { // */ //} - - /** - * This intentionally throws an Exception to test testImagesIdentical(). - */ - public static void testTestImagesIdentical() throws Exception { - String2.log("\n*** Image2.testTestImagesIdentical"); - - //test images which are identical - String testDir = String2.unitTestDataDir + "images/"; - String tempDir = File2.getSystemTempDirectory(); - testImagesIdentical( - testDir + "testImagesIdentical_1.png", - testDir + "testImagesIdentical_1.png", - tempDir + "testImagesIdentical_diff.png"); - - //test images which aren't identical - try { - - //one time: createImage with transparent background - //BufferedImage image2 = getImage(testDir + "testImagesIdentical_1.png", 2000, false); - //image2 = makeImageBackgroundTransparent(image2, Color.white, 10000); - //saveAsPng(image2, testDir + "testImagesIdentical_2.png"); - - //test images which aren't identical - testImagesIdentical( - testDir + "testImagesIdentical_1.png", - testDir + "testImagesIdentical_2.png", - tempDir + "testImagesIdentical_diff.png"); - } catch (Exception e) { - Test.knownProblem("Not a problem! I'm just testing that Image2.testImagesIdentical() works."); - } - throw new RuntimeException("shouldn't get here"); - } - - /** - * Test the methods in Image2. - */ - public static void basicTest() throws Exception { - String2.log("\n*** Image2.basicTest"); - - String imageDir = File2.getClassPath() + //with / separator and / at the end - "com/cohort/util/"; - - //test ImageIO - BufferedImage bi = ImageIO.read(new File(imageDir + "testmap.gif")); - Graphics g = bi.getGraphics(); - ImageIO.write(bi, "png", new File(imageDir + "temp.png")); - Image2.saveAsGif(bi, imageDir + "temp.gif"); - - long localTime = System.currentTimeMillis(); - String2.log("test() here 1"); - Color gray = new Color(128,128,128); - String2.log("test() here 2=" + (System.currentTimeMillis() - localTime)); - Image image = Image2.getImage(imageDir + "temp.gif", - 10000, false); // javaShouldCache - String2.log("test() here 3=" + (System.currentTimeMillis() - localTime)); - - //convert 128,128,128 to transparent - image = Image2.makeImageBackgroundTransparent(image, gray, 10000); - String2.log("test() here 4=" + (System.currentTimeMillis() - localTime)); - - //save as gif again - Image2.saveAsGif(image, imageDir + "temp2.gif"); - String2.log("test() here 5=" + (System.currentTimeMillis() - localTime)); - - File2.delete(imageDir + "temp.png"); - File2.delete(imageDir + "temp.gif"); - File2.delete(imageDir + "temp2.gif"); - - } - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 1; - String msg = "\n^^^ Image2.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - if (test == 0) basicTest(); - if (test == 1) testTestImagesIdentical(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - } diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/TestAll.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/TestAll.java index 87de8a522..4bb33f450 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/TestAll.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/TestAll.java @@ -967,7 +967,6 @@ public static void main(String args[]) throws Throwable { Tally tally; Test test; TestBrowsers tb; -TestSSR tssr; Touch touch; TrajectoryScreen trajs; UByteArray uba; @@ -1109,12 +1108,9 @@ public static void main(String args[]) throws Throwable { //low level utilities TestUtil.test( errorSB, interactive, doSlowTestsToo, 0, -1); - HashDigest.test( errorSB, interactive, doSlowTestsToo, 0, -1); - Image2.test( errorSB, interactive, doSlowTestsToo, 0, -1); XML.test( errorSB, interactive, doSlowTestsToo, 0, -1); LRUCache.test( errorSB, interactive, doSlowTestsToo, 0, -1); - ByteArray.test( errorSB, interactive, doSlowTestsToo, 0, -1); CharArray.test( errorSB, interactive, doSlowTestsToo, 0, -1); ShortArray.test( errorSB, interactive, doSlowTestsToo, 0, -1); IntArray.test( errorSB, interactive, doSlowTestsToo, 0, -1); @@ -1130,9 +1126,6 @@ public static void main(String args[]) throws Throwable { PAOne.test( errorSB, interactive, doSlowTestsToo, 0, -1); Attributes.test( errorSB, interactive, doSlowTestsToo, 0, -1); ResourceBundle2.test( errorSB, interactive, doSlowTestsToo, 0, -1); - - TestSSR.test( errorSB, interactive, doSlowTestsToo, 0, -1); //requires localhost ERDDAP - RegexFilenameFilter.test( errorSB, interactive, doSlowTestsToo, 0, -1); Tally.test( errorSB, interactive, doSlowTestsToo, 0, -1); PersistentTable.test( errorSB, interactive, doSlowTestsToo, 0, -1); @@ -1149,20 +1142,14 @@ public static void main(String args[]) throws Throwable { ValidateDataSetProperties.test( errorSB, interactive, doSlowTestsToo, 0, -1); Matlab.test( errorSB, interactive, doSlowTestsToo, 0, -1); - Opendap.test( errorSB, interactive, doSlowTestsToo, 0, -1); //need tests of data.Grid2DDataSet classes //hdf.SdsWriter.main(null); //needs work DataHelper.test( errorSB, interactive, doSlowTestsToo, 0, -1); - NcHelper.test( errorSB, interactive, doSlowTestsToo, 0, -1); - OpendapHelper.test( errorSB, interactive, doSlowTestsToo, 0, -1); //few tests. relies on testing in classes that use it. Grid.test( errorSB, interactive, doSlowTestsToo, 0, -1); //GridDataSetCWOpendap.test( errorSB, interactive, doSlowTestsToo, 0, -1); //INACTIVE. The test files are no longer available since we are moving to thredds - GridDataSetThredds.test( errorSB, interactive, doSlowTestsToo, 0, -1); - GridDataSetOpendap.test( errorSB, interactive, doSlowTestsToo, 0, -1); SaveOpendap.test( errorSB, interactive, doSlowTestsToo, 0, -1); - TwoGrids.test( errorSB, interactive, doSlowTestsToo, 0, -1); - GridDataSetAnomaly.test( errorSB, interactive, doSlowTestsToo, 0, -1); + TwoGrids.test( errorSB, interactive, doSlowTestsToo, 0, -1); DoubleCenterGrids.test( errorSB, interactive, doSlowTestsToo, 0, -1); Shared.test( errorSB, interactive, doSlowTestsToo, 0, -1); diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetAnomaly.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetAnomaly.java index 4d9333e81..01eb8fdac 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetAnomaly.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetAnomaly.java @@ -336,135 +336,4 @@ public Grid makeGrid(String timePeriodValue, String timeValue, return gdsGrid; } - - /** - * This tests this class. - */ - public static void basicTest() throws Exception { - String2.log("\n*** GridDataSetAnomaly.basicTest NOTE: this requires data in C:/u00/data/QC/mday/grd/ "); - FileNameUtility.verbose = true; - FileNameUtility fnu = new FileNameUtility("gov.noaa.pfel.coastwatch.CWBrowser"); - Grid.verbose = true; - GridDataSet.verbose = true; - Opendap.verbose = true; - String dir = SSR.getTempDirectory(); - File2.deleteAllFiles(dir); - - //make the regular, climatology and anomaly datasets - GridDataSet gridDataSet = new GridDataSetThredds(fnu, "TQSux10", - //was "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatQS/ux10/", //was :8081 - "https://thredds1.pfeg.noaa.gov/thredds/catalog/Satellite/aggregsatQS/ux10/", - "BlueWhiteRed", "Linear", "-10", "10", -1, "", null, null, "S", 1, 1, "", 1, 1); - GridDataSetCWLocalClimatology climatologyDataSet = new GridDataSetCWLocalClimatology( - fnu, "CQCux10", "c:/u00/data/", dir); - GridDataSetAnomaly anomalyDataSet = new GridDataSetAnomaly( - "AQSuxan", fnu, gridDataSet, climatologyDataSet, - "Wind Anomaly, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal", - "*", "1"); - - //get data from each dataset - String timePeriod = "1 month"; - String centeredTime = "2006-01-16 12:00:00"; - String climatologyCenteredTime = "0001-01-16 12:00:00"; - - Grid gdsGrid = gridDataSet.makeGrid(timePeriod, centeredTime, - -135, -135, 22, 51, 1, 29); - String2.log("\ngdsGrid lon(" + gdsGrid.lon.length + ")=" + String2.toCSSVString(gdsGrid.lon) + - "\n lat(" + gdsGrid.lat.length + ")=" + String2.toCSSVString(gdsGrid.lat) + - "\n data(" + gdsGrid.data.length + ")=" + String2.toCSSVString(gdsGrid.data)); - - Grid climatologyGrid = climatologyDataSet.makeGrid("monthly", climatologyCenteredTime, - -135, -135, 22, 51, 1, 29); - String2.log("\nclimatologyGrid lon(" + climatologyGrid.lon.length + ")=" + String2.toCSSVString(climatologyGrid.lon) + - "\n lat(" + climatologyGrid.lat.length + ")=" + String2.toCSSVString(climatologyGrid.lat) + - "\n data(" + climatologyGrid.data.length + ")=" + String2.toCSSVString(climatologyGrid.data)); - - Grid anomalyGrid = anomalyDataSet.makeGrid(timePeriod, centeredTime, - -135, -135, 22, 51, 1, 29); - String2.log("\nanomalyGrid lon(" + anomalyGrid.lon.length + ")=" + String2.toCSSVString(anomalyGrid.lon) + - "\n lat(" + anomalyGrid.lat.length + ")=" + String2.toCSSVString(anomalyGrid.lat) + - "\n data(" + anomalyGrid.data.length + ")=" + String2.toCSSVString(anomalyGrid.data)); - - Test.ensureEqual(anomalyGrid.lon.length, 1, ""); - Test.ensureEqual(anomalyGrid.lon[0], -135, ""); - Test.ensureEqual(gdsGrid.lon, anomalyGrid.lon, ""); - Test.ensureEqual(climatologyGrid.lon, anomalyGrid.lon, ""); - - Test.ensureEqual(anomalyGrid.lat.length, 30, ""); - Test.ensureEqual(anomalyGrid.lat[0], 22, ""); - Test.ensureEqual(anomalyGrid.lat[29], 51, ""); - Test.ensureEqual(gdsGrid.lat, anomalyGrid.lat, ""); - Test.ensureEqual(climatologyGrid.lat, anomalyGrid.lat, ""); - - for (int i = 0; i < 29; i++) { - //I had some problems, so as additional test, - //get the climatology points 1 by 1 (which avoids possible stride-related problems) - //and ensure they match - Grid cGrid1 = climatologyDataSet.makeGrid("monthly", climatologyCenteredTime, - -135, -135, 22 + i, 22 + i, 1, 1); - Test.ensureEqual(climatologyGrid.data[i], cGrid1.data[0], "i=" + i); - } - - for (int i = 0; i < 29; i++) { - String2.log("data[" + i + "] gds=" + gdsGrid.data[i] + - " cli=" + climatologyGrid.data[i] + " ano=" + anomalyGrid.data[i]); - Test.ensureEqual((float)(gdsGrid.data[i] - climatologyGrid.data[i]), (float)anomalyGrid.data[i], "i=" + i); - } - -/* -data[0] gds=-6.918294429779053 cli=-6.036570072174072 ano=-0.8817243576049805 -data[28] gds=3.990844964981079 cli=1.5286099910736084 ano=2.4622349739074707 */ - - Test.ensureEqual(gdsGrid.data[0], -6.918294429779053, ""); - Test.ensureEqual(climatologyGrid.data[0], -6.036570072174072, ""); - Test.ensureEqual(anomalyGrid.data[0], -0.8817243576049805, ""); - - Test.ensureEqual(gdsGrid.data[28], 3.990844964981079, ""); - Test.ensureEqual(climatologyGrid.data[28], 1.5286099910736084, ""); - Test.ensureEqual(anomalyGrid.data[28], 2.4622349739074707, ""); - - } - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 0; - String msg = "\n^^^ GridDataSetAnomaly.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - if (test == 0) basicTest(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - - } diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetOpendap.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetOpendap.java index adad3097f..8c0158459 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetOpendap.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetOpendap.java @@ -6,37 +6,22 @@ import com.cohort.array.Attributes; import com.cohort.array.FloatArray; -import com.cohort.array.IntArray; import com.cohort.array.DoubleArray; import com.cohort.array.PrimitiveArray; import com.cohort.array.StringArray; import com.cohort.util.Calendar2; -import com.cohort.util.File2; import com.cohort.util.Math2; import com.cohort.util.MustBe; import com.cohort.util.String2; import com.cohort.util.Test; -import com.cohort.util.XML; -import gov.noaa.pfel.coastwatch.OneOf; import gov.noaa.pfel.coastwatch.pointdata.Table; import gov.noaa.pfel.coastwatch.TimePeriods; -import gov.noaa.pfel.coastwatch.util.SSR; -import gov.noaa.pfel.coastwatch.util.StringObject; -import java.io.BufferedReader; -import java.io.InputStreamReader; import java.util.Arrays; import java.util.GregorianCalendar; -import java.util.Hashtable; import java.util.Vector; -// from netcdfAll-x.jar -import ucar.nc2.*; -import ucar.nc2.dataset.NetcdfDataset; -//import ucar.nc2.dods.*; -import ucar.nc2.util.*; -import ucar.ma2.*; /** The Java DAP classes. */ import dods.dap.*; @@ -760,346 +745,8 @@ public Table getTimeSeries(String newDir, double x, double y, } /* this is just for test purposes */ - private Table getSuperTimeSeries(String newDir, double x, double y, + protected Table getSuperTimeSeries(String newDir, double x, double y, String isoMinTime, String isoMaxTime, String timePeriod) throws Exception { return super.getTimeSeries(newDir, x, y, isoMinTime, isoMaxTime, timePeriod); } - - /** - * This does a test of getTimeSeries using a data set on West Coast cwexperimental. - */ - public static void testGetTimeSeries() throws Exception { - String2.log("\n*** start TestBrowsers.testGetTimeSeries"); - String url = "https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/GA/ssta/"; //oceanwatch - - DataHelper.verbose = true; - GridDataSetOpendap.verbose = true; - - String tempDir = SSR.getTempDirectory(); - Table table = null; - - GridDataSetOpendap gdst = new GridDataSetOpendap( - "OGAssta", "GAssta", null, url, - new String[]{"hday", "1day", "3day", "5day", "8day", "14day", "mday"}, - new int[]{0, 24, 3*24, 5*24, 8*24, 14*24, 30*24, }, - "Rainbow", "Linear", "8", "32", -1, "", null, //fgdc, - null, - "S", 1.8, 32, "degree_F", 45, 90); - - //*** test the GridDataSetOpendap version of getTimeSeries - //test individual makeGrid to get the values tested below in getTimeSeries - double rLon = -128.975; - double rLat = 36.025; - - Grid grid = gdst.makeGrid("1 day", - "2007-12-01 12:00:00", - rLon, rLon, rLat, rLat, 1, 1); - Test.ensureEqual(grid.lon[0], rLon, ""); - Test.ensureEqual(grid.lat[0], rLat, ""); - Test.ensureEqual((float)grid.data[0], 16.35f, ""); - - grid = gdst.makeGrid("1 day", - "2007-12-02 12:00:00", - rLon, rLon, rLat, rLat, 1, 1); - Test.ensureEqual(grid.lon[0], rLon, ""); - Test.ensureEqual(grid.lat[0], rLat, ""); - Test.ensureEqual((float)grid.data[0], 16.05f, ""); - - //first just test if it gets correct answers - table = gdst.getTimeSeries(tempDir, rLon, rLat, - "2007-12-01 12:00:00", "2007-12-20 12:00:00", "1 day"); - //String2.log("timeSeriesTable=" + table); - Test.ensureEqual(table.nRows(), 20, ""); - Test.ensureEqual(table.nColumns(), 6, ""); - Test.ensureEqual(table.getColumnName(0), "LON", ""); - Test.ensureEqual(table.getColumnName(1), "LAT", ""); - Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); - Test.ensureEqual(table.getColumnName(3), "TIME", ""); - Test.ensureEqual(table.getColumnName(4), "ID", ""); - Test.ensureEqual(table.getColumnName(5), "OGAssta", ""); - - Test.ensureEqual(table.getColumn(0).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(1).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(2).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(3).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(4).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(5).elementTypeString(), "float", ""); - - Test.ensureEqual(table.getDoubleData(0,0), rLon, ""); - Test.ensureEqual(table.getDoubleData(1,0), rLat, ""); - Test.ensureEqual(table.getDoubleData(2,0), 0, ""); - Test.ensureEqual(table.getDoubleData(3,0), Calendar2.isoStringToEpochSeconds("2007-12-01 12:00:00"), ""); - Test.ensureEqual(table.getStringData(4,0), "OGAssta", ""); - Test.ensureEqual(table.getFloatData(5,0), 16.35f, ""); - - Test.ensureEqual(table.getDoubleData(0,1), rLon, ""); - Test.ensureEqual(table.getDoubleData(1,1), rLat, ""); - Test.ensureEqual(table.getDoubleData(2,1), 0, ""); - Test.ensureEqual(table.getDoubleData(3,1), Calendar2.isoStringToEpochSeconds("2007-12-02 12:00:00"), ""); - Test.ensureEqual(table.getStringData(4,1), "OGAssta", ""); - Test.ensureEqual(table.getFloatData( 5,1), 16.05f, ""); - - - //HARDER TEST: data for all time does it crash? 35s first run, then 12s - //for (int i = 30; i <= 36; i++) - // table = gdst.getTimeSeries(tempDir, rLon, i, - // "1980-01-01", "2099-12-31", gdst.activeTimePeriodOptions[0]); - - - //*** test the GridDataSet (superclass) version of getTimeSeries - //this is the only test of superclass' getTimeSeries - table = null; - table = gdst.getSuperTimeSeries(tempDir, rLon, rLat, - "2007-12-01 12:00:00", "2007-12-20 12:00:00", "1 day"); - //String2.log("super timeSeriesTable=" + table); - Test.ensureEqual(table.nRows(), 20, ""); - Test.ensureEqual(table.nColumns(), 6, ""); - Test.ensureEqual(table.getColumnName(0), "LON", ""); - Test.ensureEqual(table.getColumnName(1), "LAT", ""); - Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); - Test.ensureEqual(table.getColumnName(3), "TIME", ""); - Test.ensureEqual(table.getColumnName(4), "ID", ""); - Test.ensureEqual(table.getColumnName(5), "OGAssta", ""); - - Test.ensureEqual(table.getDoubleData(0,0), rLon, ""); - Test.ensureEqual(table.getDoubleData(1,0), rLat, ""); - Test.ensureEqual(table.getDoubleData(2,0), 0, ""); - Test.ensureEqual(table.getDoubleData(3,0), Calendar2.isoStringToEpochSeconds("2007-12-01 12:00:00"), ""); - Test.ensureEqual(table.getStringData(4,0), "OGAssta", ""); - Test.ensureEqual(table.getFloatData(5,0), 16.35f, ""); - - Test.ensureEqual(table.getDoubleData(0,1), rLon, ""); - Test.ensureEqual(table.getDoubleData(1,1), rLat, ""); - Test.ensureEqual(table.getDoubleData(2,1), 0, ""); - Test.ensureEqual(table.getDoubleData(3,1), Calendar2.isoStringToEpochSeconds("2007-12-02 12:00:00"), ""); - Test.ensureEqual(table.getStringData(4,1), "OGAssta", ""); - Test.ensureEqual(table.getFloatData(5,1), 16.05f, ""); - - - //*** test of centering time periods - //test individual makeGrid to get the values tested below in getTimeSeries - grid = gdst.makeGrid("3 day", "2006-08-13 12:00:00", //centered time - -130.02, -130.02, 36.02, 36.02, //close, not exact - 1, 1); - Test.ensureEqual(grid.lon[0], -130.025, ""); //3 day grid is offset by .025!! - Test.ensureEqual(grid.lat[0], 36.025, ""); - Test.ensureEqual((float)grid.data[0], 19.8f, ""); - - grid = gdst.makeGrid("3 day", "2006-08-08 12:00:00", //centered time - -130.02, -130.02, 36.02, 36.02, - 1, 1); - Test.ensureEqual(grid.lon[0], -130.025, ""); - Test.ensureEqual(grid.lat[0], 36.025, ""); - Test.ensureEqual((float)grid.data[0], 18.75f, ""); - - //first just test if it gets correct answers - table = gdst.getTimeSeries(tempDir, -130.02, 36.02, - "2006-08-08", "2006-08-14", //begin and end centered times - "3 day"); - //String2.log("timeSeriesTable=" + table); - PrimitiveArray timePA = table.getColumn(3); - PrimitiveArray dataPA = table.getColumn(5); - - //find the row corresponding to the desired time - double seconds = Calendar2.isoStringToEpochSeconds("2006-08-13 12:00:00"); //centered time - int row = timePA.binaryFindClosest(seconds); - Test.ensureEqual(timePA.getDouble(row), seconds, ""); //ensure exact match 2006-08-13T23:59:59 - Test.ensureEqual(dataPA.getFloat(row), 19.8f, ""); - - seconds = Calendar2.isoStringToEpochSeconds("2006-08-08 12:00:00"); //centered time - row = timePA.binaryFindClosest(seconds); - Test.ensureEqual(timePA.getDouble(row), seconds, ""); //ensure exact match - Test.ensureEqual(dataPA.getFloat(row), 18.75f, ""); - } - - - /** - * This performs a simple test of this class. - */ - public static void basicTest() throws Exception { - //FileNameUtility.verbose = true; - //FileNameUtility fnu = new FileNameUtility("gov.noaa.pfel.coastwatch.CWBrowser"); - - String2.log("\n*** GridDataSetOpendap.basicTest"); - GridDataSetOpendap gridDataSet; - - //variables - String internalName, sixName; - GridDataSetOpendap.verbose = true; - Opendap.verbose = true; - String dir = File2.getClassPath() + //with / separator and / at the end - "gov/noaa/pfel/coastwatch/griddata/"; - - //********************************************************************* - internalName = "OQSux10"; - sixName = internalName.substring(1); - String url = "https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/QS/ux10/"; //oceanwatch - gridDataSet = new GridDataSetOpendap( - internalName, "QSux10", null, url, - new String[]{"1day", "3day", "4day", "8day", "14day", "mday"}, - new int[]{24, 3*24, 4*24, 8*24, 14*24, 30*24}, - "BlueWhiteRed", "Linear", "-10", "10", -1, "", null, null, "S", 1, 0, "", 1, 1); - - Grid grid = gridDataSet.makeGrid( - "1 day", "2006-06-10 12:00:00", -135, -105, 22, 50, 300, 300); - - //set attributes - String fileName = "TQSux10S1day_20060610_x-135_X-105_y22_Y50"; - gridDataSet.setAttributes(grid, fileName); - grid.setStatsAttributes(false); //false -> floats - - //see if it has the expected values - int nLat = grid.lat.length; - int nLon = grid.lon.length; - Test.ensureEqual(grid.globalAttributes().get("Conventions"), new StringArray(new String[]{"COARDS, CF-1.6, ACDD-1.3, CWHDF"}), "Conventions"); - Test.ensureEqual(grid.globalAttributes().get("title"), new StringArray(new String[]{"Wind, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal"}), "title"); - Test.ensureEqual(grid.globalAttributes().get("summary"), new StringArray(new String[]{"Remote Sensing Inc. distributes science quality wind velocity data from the SeaWinds instrument onboard NASA's QuikSCAT satellite. SeaWinds is a microwave scatterometer designed to measure surface winds over the global ocean. Wind velocity fields are provided in zonal, meridional, and modulus sets. The reference height for all wind velocities is 10 meters."}), "summary"); - Test.ensureEqual(grid.globalAttributes().get("keywords"), new StringArray(new String[]{"EARTH SCIENCE > Oceans > Ocean Winds > Surface Winds"}), "keywords"); - //!!!! thredds id differs from opendap at first letter - Test.ensureEqual(grid.globalAttributes().get("id"), new StringArray(new String[]{"TQSux10S1day"}), "id"); - Test.ensureEqual(grid.globalAttributes().get("naming_authority"), new StringArray(new String[]{"gov.noaa.pfeg.coastwatch"}), "naming_authority"); - Test.ensureEqual(grid.globalAttributes().get("keywords_vocabulary"), new StringArray(new String[]{"GCMD Science Keywords"}), "keywords_vocabulary"); - Test.ensureEqual(grid.globalAttributes().get("cdm_data_type"), new StringArray(new String[]{"Grid"}), "cdm_data_typ"); - Test.ensureTrue(grid.globalAttributes().getString("history").startsWith("Remote Sensing Systems, Inc."), "history=" + grid.globalAttributes().getString("history")); - Test.ensureEqual(grid.globalAttributes().get("date_created"), new StringArray(new String[]{Calendar2.formatAsISODate(Calendar2.newGCalendarZulu())}), "date_created"); - Test.ensureEqual(grid.globalAttributes().get("creator_name"), new StringArray(new String[]{"NOAA CoastWatch, West Coast Node"}), "creator_name"); - Test.ensureEqual(grid.globalAttributes().get("creator_url"), new StringArray(new String[]{"http://coastwatch.pfel.noaa.gov"}), "creator_url"); - Test.ensureEqual(grid.globalAttributes().get("creator_email"), new StringArray(new String[]{"dave.foley@noaa.gov"}), "creator_email"); - Test.ensureEqual(grid.globalAttributes().getString("institution"), "NOAA CoastWatch, West Coast Node", "institution=" + grid.globalAttributes().getString("institution")); - Test.ensureEqual(grid.globalAttributes().get("project"), new StringArray(new String[]{"CoastWatch (http://coastwatch.noaa.gov/)"}), "project"); - Test.ensureEqual(grid.globalAttributes().get("processing_level"), new StringArray(new String[]{"3"}), "processing_level"); - Test.ensureEqual(grid.globalAttributes().get("acknowledgement"), new StringArray(new String[]{"NOAA NESDIS COASTWATCH, NOAA SWFSC ERD"}), "acknowledgement"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_min"), new DoubleArray(new double[]{22}), "geospatial_lat_min"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_max"), new DoubleArray(new double[]{50}), "geospatial_lat_max"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_min"), new DoubleArray(new double[]{-135}), "geospatial_lon_min"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_max"), new DoubleArray(new double[]{-105}), "geospatial_lon_max"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_units"), new StringArray(new String[]{"degrees_north"}), "geospatial_lat_units"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_resolution"), new DoubleArray(new double[]{0.125}), "geospatial_lat_resolution"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_units"), new StringArray(new String[]{"degrees_east"}), "geospatial_lon_units"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_resolution"), new DoubleArray(new double[]{0.125}), "geospatial_lon_resolution"); - Test.ensureEqual(grid.globalAttributes().get("time_coverage_start"), new StringArray(new String[]{"2006-06-10T00:00:00Z"}), "time_coverage_start"); - Test.ensureEqual(grid.globalAttributes().get("time_coverage_end"), new StringArray(new String[]{"2006-06-11T00:00:00Z"}), "time_coverage_end"); - //Test.ensureEqual(grid.globalAttributes().get("time_coverage_resolution", new StringArray(new String[]{""}), "time_coverage_resolution"); - Test.ensureEqual(grid.globalAttributes().get("standard_name_vocabulary"), new StringArray(new String[]{"CF Standard Name Table v70"}), "standard_name_vocabulary"); - Test.ensureEqual(grid.globalAttributes().get("license"), new StringArray(new String[]{"The data may be used and redistributed for free but is not intended for legal use, since it may contain inaccuracies. Neither the data Contributor, CoastWatch, NOAA, nor the United States Government, nor any of their employees or contractors, makes any warranty, express or implied, including warranties of merchantability and fitness for a particular purpose, or assumes any legal liability for the accuracy, completeness, or usefulness, of this information."}), "license"); - Test.ensureEqual(grid.globalAttributes().get("contributor_name"), new StringArray(new String[]{"Remote Sensing Systems, Inc."}), "contributor_name"); - Test.ensureEqual(grid.globalAttributes().get("contributor_role"), new StringArray(new String[]{"Source of level 2 data."}), "contributor_role"); - Test.ensureEqual(grid.globalAttributes().get("date_issued"), new StringArray(new String[]{Calendar2.formatAsISODate(Calendar2.newGCalendarZulu())}), "date_issued"); - Test.ensureEqual(grid.globalAttributes().get("references"), new StringArray(new String[]{"RSS Inc. Winds: http://www.remss.com/ ."}), "references"); - Test.ensureEqual(grid.globalAttributes().get("source"), new StringArray(new String[]{"satellite observation: QuikSCAT, SeaWinds"}), "source"); - //Google Earth - Test.ensureEqual(grid.globalAttributes().get("Southernmost_Northing"), new DoubleArray(new double[]{22}), "southernmost"); - Test.ensureEqual(grid.globalAttributes().get("Northernmost_Northing"), new DoubleArray(new double[]{50}), "northernmost"); - Test.ensureEqual(grid.globalAttributes().get("Westernmost_Easting"), new DoubleArray(new double[]{-135}), "westernmost"); - Test.ensureEqual(grid.globalAttributes().get("Easternmost_Easting"), new DoubleArray(new double[]{-105}), "easternmost"); - - //cwhdf attributes - Test.ensureEqual(grid.globalAttributes().get("cwhdf_version"), new StringArray(new String[]{"3.4"}), "cwhdf_version"); //string - Test.ensureEqual(grid.globalAttributes().get("satellite"), new StringArray(new String[]{"QuikSCAT"}), "satellite"); //string - Test.ensureEqual(grid.globalAttributes().get("sensor"), new StringArray(new String[]{"SeaWinds"}), "sensor"); //string - Test.ensureEqual(grid.globalAttributes().get("composite"), new StringArray(new String[]{"true"}), "composite"); //string - - Test.ensureEqual(grid.globalAttributes().get("pass_date"), new IntArray(new int[]{13309}), "pass_date"); //int32[nDays] - Test.ensureEqual(grid.globalAttributes().get("start_time"), new DoubleArray(new double[]{0}), "start_time"); //float64[nDays] - Test.ensureEqual(grid.globalAttributes().get("origin"), new StringArray(new String[]{"Remote Sensing Systems, Inc."}), "origin"); //string - //Test.ensureEqual(grid.globalAttributes().get("history"), new StringArray(new String[]{"unknown"}), "history"); //string - - Test.ensureEqual(grid.globalAttributes().get("projection_type"), new StringArray(new String[]{"mapped"}), "projection_type"); //string - Test.ensureEqual(grid.globalAttributes().get("projection"), new StringArray(new String[]{"geographic"}), "projection"); //string - Test.ensureEqual(grid.globalAttributes().get("gctp_sys"), new IntArray(new int[]{0}), "gctp_sys"); //int32 - Test.ensureEqual(grid.globalAttributes().get("gctp_zone"), new IntArray(new int[]{0}), "gctp_zone"); //int32 - Test.ensureEqual(grid.globalAttributes().get("gctp_parm"), new DoubleArray(new double[15]), "gctp_parm"); //float64[15 0's] - Test.ensureEqual(grid.globalAttributes().get("gctp_datum"), new IntArray(new int[]{12}), "gctp_datum");//int32 12=WGS84 - - double matrix[] = {0, -grid.latSpacing, grid.lonSpacing, 0, grid.lon[0], grid.lat[nLat-1]}; //up side down - Test.ensureEqual(grid.globalAttributes().get("et_affine"), new DoubleArray(matrix), "et_affine"); //right side up - - Test.ensureEqual(grid.globalAttributes().get("rows"), new IntArray(new int[]{grid.lat.length}), "rows");//int32 number of rows - Test.ensureEqual(grid.globalAttributes().get("cols"), new IntArray(new int[]{grid.lon.length}), "cols");//int32 number of columns - Test.ensureEqual(grid.globalAttributes().get("polygon_latitude"), new DoubleArray(new double[]{ - grid.lat[0], grid.lat[nLat - 1], grid.lat[nLat - 1], grid.lat[0], grid.lat[0]}), "polygon_latitude"); - Test.ensureEqual(grid.globalAttributes().get("polygon_longitude"), new DoubleArray(new double[]{ - grid.lon[0], grid.lon[0], grid.lon[nLon - 1], grid.lon[nLon - 1], grid.lon[0]}), "polygon_longitude"); - - //lat attributes - Test.ensureEqual(grid.latAttributes().get("long_name"), new StringArray(new String[]{"Latitude"}), "lat long_name"); - Test.ensureEqual(grid.latAttributes().get("standard_name"), new StringArray(new String[]{"latitude"}), "lat standard_name"); - Test.ensureEqual(grid.latAttributes().get("units"), new StringArray(new String[]{"degrees_north"}), "lat units"); - Test.ensureEqual(grid.latAttributes().get("point_spacing"), new StringArray(new String[]{"even"}), "lat point_spacing"); - Test.ensureEqual(grid.latAttributes().get("actual_range"), new DoubleArray(new double[]{22, 50}), "lat actual_range"); - - //CWHDF metadata/attributes for Latitude - Test.ensureEqual(grid.latAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys");//string - Test.ensureEqual(grid.latAttributes().get("fraction_digits"), new IntArray(new int[]{2}), "fraction_digits"); //int32 - - - //lon attributes - Test.ensureEqual(grid.lonAttributes().get("long_name"), new StringArray(new String[]{"Longitude"}), "lon long_name"); - Test.ensureEqual(grid.lonAttributes().get("standard_name"), new StringArray(new String[]{"longitude"}), "lon standard_name"); - Test.ensureEqual(grid.lonAttributes().get("units"), new StringArray(new String[]{"degrees_east"}), "lon units"); - Test.ensureEqual(grid.lonAttributes().get("point_spacing"), new StringArray(new String[]{"even"}), "lon point_spacing"); - Test.ensureEqual(grid.lonAttributes().get("actual_range"), new DoubleArray(new double[]{-135, -105}), "lon actual_range"); - - //CWHDF metadata/attributes for Longitude - Test.ensureEqual(grid.lonAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys"); //string - Test.ensureEqual(grid.lonAttributes().get("fraction_digits"), new IntArray(new int[]{2}), "fraction_digits"); //int32 - - - //data attributes it's 0.125 in DataSet.properties, but files need to be reprocessed to catch that - Test.ensureEqual(grid.dataAttributes().get("long_name"), new StringArray(new String[]{"Wind, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal"}), "data long_name"); - Test.ensureEqual(grid.dataAttributes().get("standard_name"), new StringArray(new String[]{"x_wind"}), "data standard_name"); - Test.ensureEqual(grid.dataAttributes().get("units"), new StringArray(new String[]{"m s-1"}), "data units"); - Test.ensureEqual(grid.dataAttributes().get("_FillValue"), new FloatArray(new float[]{-9999999}), "data _FillValue"); - Test.ensureEqual(grid.dataAttributes().get("missing_value"), new FloatArray(new float[]{-9999999}), "data missing_value"); - Test.ensureEqual(grid.dataAttributes().get("numberOfObservations"), new IntArray(new int[]{25021}), "data numberOfObservations"); - Test.ensureEqual(grid.dataAttributes().get("percentCoverage"), new DoubleArray(new double[]{0.46142923005993547}), "data percentCoverage"); - - //CWHDF metadata/attributes for the data: varName - Test.ensureEqual(grid.dataAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys"); //string - Test.ensureEqual(grid.dataAttributes().get("fraction_digits"), new IntArray(new int[]{1}), "fraction_digits"); //int32 - } - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 1; - String msg = "\n^^^ GridDataSetOpendap.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - if (test == 0) basicTest(); - if (test == 1) testGetTimeSeries(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - - } diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetThredds.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetThredds.java index 8419a1c50..d72e5dea1 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetThredds.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/GridDataSetThredds.java @@ -6,7 +6,6 @@ import com.cohort.array.Attributes; import com.cohort.array.FloatArray; -import com.cohort.array.IntArray; import com.cohort.array.DoubleArray; import com.cohort.array.PrimitiveArray; import com.cohort.array.StringArray; @@ -18,32 +17,20 @@ import com.cohort.util.Test; import com.cohort.util.XML; -import gov.noaa.pfel.coastwatch.OneOf; import gov.noaa.pfel.coastwatch.pointdata.Table; import gov.noaa.pfel.coastwatch.TimePeriods; import gov.noaa.pfel.coastwatch.util.SSR; -import gov.noaa.pfel.coastwatch.util.StringObject; -import java.io.BufferedReader; -import java.io.InputStreamReader; import java.util.Arrays; import java.util.GregorianCalendar; -import java.util.Hashtable; import java.util.Vector; import javax.xml.xpath.XPath; //requires java 1.5 import org.w3c.dom.Document; -import org.w3c.dom.Element; -import org.w3c.dom.NamedNodeMap; -import org.w3c.dom.Node; import org.w3c.dom.NodeList; // from netcdfAll-x.jar import ucar.nc2.*; -import ucar.nc2.dataset.NetcdfDataset; -//import ucar.nc2.dods.*; -import ucar.nc2.util.*; -import ucar.ma2.*; /** The Java DAP classes. */ import dods.dap.*; @@ -854,490 +841,11 @@ public Table getTimeSeries(String newDir, double x, double y, } /* this is just for test purposes */ - private Table getSuperTimeSeries(String newDir, double x, double y, + protected Table getSuperTimeSeries(String newDir, double x, double y, String isoMinTime, String isoMaxTime, String timePeriod) throws Exception { return super.getTimeSeries(newDir, x, y, isoMinTime, isoMaxTime, timePeriod); } - /** - * This does a test of getTimeSeries using a data set on West Coast cwexperimental. - */ - public static void testGetTimeSeries() throws Exception { - String2.log("\n*** start TestBrowsers.testGetTimeSeries"); - String url = - //was "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatGA/ssta/"; //oceanwatch - "https://thredds1.pfeg.noaa.gov/thredds/catalog/Satellite/aggregsatGA/ssta/"; - - DataHelper.verbose = true; - GridDataSetThredds.verbose = true; - - String tempDir = SSR.getTempDirectory(); - Table table = null; - - GridDataSetThredds gdst = new GridDataSetThredds( - new FileNameUtility("gov.noaa.pfel.coastwatch.CWBrowser"), - "TGAssta", //String internalName, - url, - "Rainbow", "Linear", "8", "32", -1, "", null, //fgdc, - null, - "S", 1.8, 32, "degree_F", 45, 90); - - //*** test the GridDataSetThredds version of getTimeSeries - //test individual makeGrid to get the values tested below in getTimeSeries - double rLon = -128.975; - double rLat = 36.025; - - Grid grid = gdst.makeGrid("1 day", - "2007-12-01 12:00:00", - rLon, rLon, rLat, rLat, 1, 1); - Test.ensureEqual(grid.lon[0], rLon, ""); - Test.ensureEqual(grid.lat[0], rLat, ""); - Test.ensureEqual((float)grid.data[0], 16.35f, ""); - - grid = gdst.makeGrid("1 day", - "2007-12-02 12:00:00", - rLon, rLon, rLat, rLat, 1, 1); - Test.ensureEqual(grid.lon[0], rLon, ""); - Test.ensureEqual(grid.lat[0], rLat, ""); - Test.ensureEqual((float)grid.data[0], 16.05f, ""); - - //first just test if it gets correct answers - table = gdst.getTimeSeries(tempDir, rLon, rLat, - "2007-12-01 12:00:00", "2007-12-20 12:00:00", "1 day"); - //String2.log("timeSeriesTable=" + table); - Test.ensureEqual(table.nRows(), 20, ""); - Test.ensureEqual(table.nColumns(), 6, ""); - Test.ensureEqual(table.getColumnName(0), "LON", ""); - Test.ensureEqual(table.getColumnName(1), "LAT", ""); - Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); - Test.ensureEqual(table.getColumnName(3), "TIME", ""); - Test.ensureEqual(table.getColumnName(4), "ID", ""); - Test.ensureEqual(table.getColumnName(5), "TGAssta", ""); - - Test.ensureEqual(table.getColumn(0).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(1).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(2).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(3).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(4).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(5).elementTypeString(), "float", ""); - - Test.ensureEqual(table.getDoubleData(0,0), rLon, ""); - Test.ensureEqual(table.getDoubleData(1,0), rLat, ""); - Test.ensureEqual(table.getDoubleData(2,0), 0, ""); - Test.ensureEqual(table.getDoubleData(3,0), Calendar2.isoStringToEpochSeconds("2007-12-01 12:00:00"), ""); - Test.ensureEqual(table.getStringData(4,0), "TGAssta", ""); - Test.ensureEqual(table.getFloatData(5,0), 16.35f, ""); - - Test.ensureEqual(table.getDoubleData(0,1), rLon, ""); - Test.ensureEqual(table.getDoubleData(1,1), rLat, ""); - Test.ensureEqual(table.getDoubleData(2,1), 0, ""); - Test.ensureEqual(table.getDoubleData(3,1), Calendar2.isoStringToEpochSeconds("2007-12-02 12:00:00"), ""); - Test.ensureEqual(table.getStringData(4,1), "TGAssta", ""); - Test.ensureEqual(table.getFloatData( 5,1), 16.05f, ""); - - - //HARDER TEST: data for all time does it crash? 35s first run, then 12s - //for (int i = 30; i <= 36; i++) - // table = gdst.getTimeSeries(tempDir, rLon, i, - // "1980-01-01", "2099-12-31", gdst.activeTimePeriodOptions[0]); - - - //*** test the GridDataSet (superclass) version of getTimeSeries - //this is the only test of superclass' getTimeSeries - table = null; - table = gdst.getSuperTimeSeries(tempDir, rLon, rLat, - "2007-12-01 12:00:00", "2007-12-20 12:00:00", "1 day"); - //String2.log("super timeSeriesTable=" + table); - Test.ensureEqual(table.nRows(), 20, ""); - Test.ensureEqual(table.nColumns(), 6, ""); - Test.ensureEqual(table.getColumnName(0), "LON", ""); - Test.ensureEqual(table.getColumnName(1), "LAT", ""); - Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); - Test.ensureEqual(table.getColumnName(3), "TIME", ""); - Test.ensureEqual(table.getColumnName(4), "ID", ""); - Test.ensureEqual(table.getColumnName(5), "TGAssta", ""); - - Test.ensureEqual(table.getDoubleData(0,0), rLon, ""); - Test.ensureEqual(table.getDoubleData(1,0), rLat, ""); - Test.ensureEqual(table.getDoubleData(2,0), 0, ""); - Test.ensureEqual(table.getDoubleData(3,0), Calendar2.isoStringToEpochSeconds("2007-12-01 12:00:00"), ""); - Test.ensureEqual(table.getStringData(4,0), "TGAssta", ""); - Test.ensureEqual(table.getFloatData(5,0), 16.35f, ""); - - Test.ensureEqual(table.getDoubleData(0,1), rLon, ""); - Test.ensureEqual(table.getDoubleData(1,1), rLat, ""); - Test.ensureEqual(table.getDoubleData(2,1), 0, ""); - Test.ensureEqual(table.getDoubleData(3,1), Calendar2.isoStringToEpochSeconds("2007-12-02 12:00:00"), ""); - Test.ensureEqual(table.getStringData(4,1), "TGAssta", ""); - Test.ensureEqual(table.getFloatData(5,1), 16.05f, ""); - - - //*** test of centering time periods - //test individual makeGrid to get the values tested below in getTimeSeries - grid = gdst.makeGrid("3 day", "2006-08-13 12:00:00", //centered time - -130.02, -130.02, 36.02, 36.02, //close, not exact - 1, 1); - Test.ensureEqual(grid.lon[0], -130.025, ""); //3 day grid is offset by .025!! - Test.ensureEqual(grid.lat[0], 36.025, ""); - Test.ensureEqual((float)grid.data[0], 19.8f, ""); - - grid = gdst.makeGrid("3 day", "2006-08-08 12:00:00", //centered time - -130.02, -130.02, 36.02, 36.02, - 1, 1); - Test.ensureEqual(grid.lon[0], -130.025, ""); - Test.ensureEqual(grid.lat[0], 36.025, ""); - Test.ensureEqual((float)grid.data[0], 18.75f, ""); - - //first just test if it gets correct answers - table = gdst.getTimeSeries(tempDir, -130.02, 36.02, - "2006-08-08", "2006-08-14", //begin and end centered times - "3 day"); - //String2.log("timeSeriesTable=" + table); - PrimitiveArray timePA = table.getColumn(3); - PrimitiveArray dataPA = table.getColumn(5); - - //find the row corresponding to the desired time - double seconds = Calendar2.isoStringToEpochSeconds("2006-08-13 12:00:00"); //centered time - int row = timePA.binaryFindClosest(seconds); - Test.ensureEqual(timePA.getDouble(row), seconds, ""); //ensure exact match 2006-08-13T23:59:59 - Test.ensureEqual(dataPA.getFloat(row), 19.8f, ""); - - seconds = Calendar2.isoStringToEpochSeconds("2006-08-08 12:00:00"); //centered time - row = timePA.binaryFindClosest(seconds); - Test.ensureEqual(timePA.getDouble(row), seconds, ""); //ensure exact match - Test.ensureEqual(dataPA.getFloat(row), 18.75f, ""); - } - - - /** - * This performs a simple test of this class. - */ - public static void basicTest() throws Exception { - FileNameUtility.verbose = true; - FileNameUtility fnu = new FileNameUtility("gov.noaa.pfel.coastwatch.CWBrowser"); - -// String baseUrl = "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMO/k490/"; -// String2.log("getUrlString for " + baseUrl + "catalog.xml"); -// String2.log(SSR.getURLResponseStringUnchanged(baseUrl + "catalog.xml")); - -// Opendap opendap = new Opendap( -// //"https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMO/k490/hday", -// //"https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMO/k490/hday", -// "https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/MO/k490/hday.das", -// acceptDeflate); //throws Exception if trouble - -// public GridDataSetThredds(FileNameUtility fileNameUtility, String internalName, String baseUrl, -// String tPalette, String tPaletteScale, String tPaletteMin, String tPaletteMax, -// int tDaysTillDataAccessAllowed, String tAnomalyDataSet, String fgdc, -// String flagDirectory, -// String tDefaultUnits, double tAltScaleFactor, double tAltOffset, -// String tAltUnits, double tAltMin, double tAltMax) throws Exception { - - String2.log("\n*** GridDataSetThredds.basicTest"); - GridDataSetThredds gridDataSet; - - //variables - String internalName, sixName; - GridDataSetThredds.verbose = true; - Opendap.verbose = true; - String dir = File2.getClassPath() + //with / separator and / at the end - "gov/noaa/pfel/coastwatch/griddata/"; - - //**************************** - //ensure J1ugeo loads (it has 1 level: ) - /* //Comment out this line with /* to comment out this test. - //J1 datasets are no longer available as of March 2009 - internalName = "TJ1ugeo"; - sixName = internalName.substring(1); - gridDataSet = new GridDataSetThredds(fnu, internalName, - //was "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatJ1/ugeo/", //was :8081 - "https://thredds1.pfeg.noaa.gov/thredds/Satellite/aggregsatJ1/ugeo/", - "BlueWhiteRed", "Linear", "-10", "10", -1, "", null, null, - "S", 1, 0, "", 1, 1); - String2.log("TJ1ugeo activeTimePeriodOptions.length=" + gridDataSet.activeTimePeriodOptions.length); - Test.ensureNotEqual(gridDataSet.activeTimePeriodOptions.length, 0, - "TJ1ugeo activeTimePeriodOptions.length"); - /* */ - - //********************************************************************* - //large test of TQSux10 (it has 2 levels: ) - //Comment out this line with /* to comment out this test. - internalName = "TQSux10"; - sixName = internalName.substring(1); - gridDataSet = new GridDataSetThredds(fnu, internalName, - "https://thredds1.pfeg.noaa.gov/thredds/catalog/Satellite/aggregsatQS/ux10/", - "BlueWhiteRed", "Linear", "-10", "10", -1, "", null, null, "S", 1, 0, "", 1, 1); - - Grid grid = gridDataSet.makeGrid( - "1 day", "2006-06-10 12:00:00", -135, -105, 22, 50, 300, 300); - - //set attributes - String fileName = "TQSux10S1day_20060610_x-135_X-105_y22_Y50"; - gridDataSet.setAttributes(grid, fileName); - grid.setStatsAttributes(false); //false -> floats - - //see if it has the expected values - int nLat = grid.lat.length; - int nLon = grid.lon.length; - Test.ensureEqual(grid.globalAttributes().get("Conventions"), new StringArray(new String[]{"COARDS, CF-1.6, ACDD-1.3, CWHDF"}), "Conventions"); - Test.ensureEqual(grid.globalAttributes().get("title"), new StringArray(new String[]{"Wind, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal"}), "title"); - Test.ensureEqual(grid.globalAttributes().get("summary"), new StringArray(new String[]{"Remote Sensing Inc. distributes science quality wind velocity data from the SeaWinds instrument onboard NASA's QuikSCAT satellite. SeaWinds is a microwave scatterometer designed to measure surface winds over the global ocean. Wind velocity fields are provided in zonal, meridional, and modulus sets. The reference height for all wind velocities is 10 meters."}), "summary"); - Test.ensureEqual(grid.globalAttributes().get("keywords"), new StringArray(new String[]{"EARTH SCIENCE > Oceans > Ocean Winds > Surface Winds"}), "keywords"); - //!!!! thredds id differs from opendap at first letter - Test.ensureEqual(grid.globalAttributes().get("id"), new StringArray(new String[]{"TQSux10S1day"}), "id"); - Test.ensureEqual(grid.globalAttributes().get("naming_authority"), new StringArray(new String[]{"gov.noaa.pfeg.coastwatch"}), "naming_authority"); - Test.ensureEqual(grid.globalAttributes().get("keywords_vocabulary"), new StringArray(new String[]{"GCMD Science Keywords"}), "keywords_vocabulary"); - Test.ensureEqual(grid.globalAttributes().get("cdm_data_type"), new StringArray(new String[]{"Grid"}), "cdm_data_typ"); - Test.ensureTrue(grid.globalAttributes().getString("history").startsWith("Remote Sensing Systems, Inc."), "history=" + grid.globalAttributes().getString("history")); - Test.ensureEqual(grid.globalAttributes().get("date_created"), new StringArray(new String[]{Calendar2.formatAsISODate(Calendar2.newGCalendarZulu())}), "date_created"); - Test.ensureEqual(grid.globalAttributes().get("creator_name"), new StringArray(new String[]{"NOAA CoastWatch, West Coast Node"}), "creator_name"); - Test.ensureEqual(grid.globalAttributes().get("creator_url"), new StringArray(new String[]{"http://coastwatch.pfel.noaa.gov"}), "creator_url"); - Test.ensureEqual(grid.globalAttributes().get("creator_email"), new StringArray(new String[]{"dave.foley@noaa.gov"}), "creator_email"); - Test.ensureEqual(grid.globalAttributes().getString("institution"), "NOAA CoastWatch, West Coast Node", "institution=" + grid.globalAttributes().getString("institution")); - Test.ensureEqual(grid.globalAttributes().get("project"), new StringArray(new String[]{"CoastWatch (http://coastwatch.noaa.gov/)"}), "project"); - Test.ensureEqual(grid.globalAttributes().get("processing_level"), new StringArray(new String[]{"3"}), "processing_level"); - Test.ensureEqual(grid.globalAttributes().get("acknowledgement"), new StringArray(new String[]{"NOAA NESDIS COASTWATCH, NOAA SWFSC ERD"}), "acknowledgement"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_min"), new DoubleArray(new double[]{22}), "geospatial_lat_min"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_max"), new DoubleArray(new double[]{50}), "geospatial_lat_max"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_min"), new DoubleArray(new double[]{-135}), "geospatial_lon_min"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_max"), new DoubleArray(new double[]{-105}), "geospatial_lon_max"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_units"), new StringArray(new String[]{"degrees_north"}), "geospatial_lat_units"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_resolution"), new DoubleArray(new double[]{0.125}), "geospatial_lat_resolution"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_units"), new StringArray(new String[]{"degrees_east"}), "geospatial_lon_units"); - Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_resolution"), new DoubleArray(new double[]{0.125}), "geospatial_lon_resolution"); - Test.ensureEqual(grid.globalAttributes().get("time_coverage_start"), new StringArray(new String[]{"2006-06-10T00:00:00Z"}), "time_coverage_start"); - Test.ensureEqual(grid.globalAttributes().get("time_coverage_end"), new StringArray(new String[]{"2006-06-11T00:00:00Z"}), "time_coverage_end"); - //Test.ensureEqual(grid.globalAttributes().get("time_coverage_resolution", new StringArray(new String[]{""}), "time_coverage_resolution"); - Test.ensureEqual(grid.globalAttributes().get("standard_name_vocabulary"), new StringArray(new String[]{"CF Standard Name Table v70"}), "standard_name_vocabulary"); - Test.ensureEqual(grid.globalAttributes().get("license"), new StringArray(new String[]{"The data may be used and redistributed for free but is not intended for legal use, since it may contain inaccuracies. Neither the data Contributor, CoastWatch, NOAA, nor the United States Government, nor any of their employees or contractors, makes any warranty, express or implied, including warranties of merchantability and fitness for a particular purpose, or assumes any legal liability for the accuracy, completeness, or usefulness, of this information."}), "license"); - Test.ensureEqual(grid.globalAttributes().get("contributor_name"), new StringArray(new String[]{"Remote Sensing Systems, Inc."}), "contributor_name"); - Test.ensureEqual(grid.globalAttributes().get("contributor_role"), new StringArray(new String[]{"Source of level 2 data."}), "contributor_role"); - Test.ensureEqual(grid.globalAttributes().get("date_issued"), new StringArray(new String[]{Calendar2.formatAsISODate(Calendar2.newGCalendarZulu())}), "date_issued"); - Test.ensureEqual(grid.globalAttributes().get("references"), new StringArray(new String[]{"RSS Inc. Winds: http://www.remss.com/ ."}), "references"); - Test.ensureEqual(grid.globalAttributes().get("source"), new StringArray(new String[]{"satellite observation: QuikSCAT, SeaWinds"}), "source"); - //Google Earth - Test.ensureEqual(grid.globalAttributes().get("Southernmost_Northing"), new DoubleArray(new double[]{22}), "southernmost"); - Test.ensureEqual(grid.globalAttributes().get("Northernmost_Northing"), new DoubleArray(new double[]{50}), "northernmost"); - Test.ensureEqual(grid.globalAttributes().get("Westernmost_Easting"), new DoubleArray(new double[]{-135}), "westernmost"); - Test.ensureEqual(grid.globalAttributes().get("Easternmost_Easting"), new DoubleArray(new double[]{-105}), "easternmost"); - - //cwhdf attributes - Test.ensureEqual(grid.globalAttributes().get("cwhdf_version"), new StringArray(new String[]{"3.4"}), "cwhdf_version"); //string - Test.ensureEqual(grid.globalAttributes().get("satellite"), new StringArray(new String[]{"QuikSCAT"}), "satellite"); //string - Test.ensureEqual(grid.globalAttributes().get("sensor"), new StringArray(new String[]{"SeaWinds"}), "sensor"); //string - Test.ensureEqual(grid.globalAttributes().get("composite"), new StringArray(new String[]{"true"}), "composite"); //string - - Test.ensureEqual(grid.globalAttributes().get("pass_date"), new IntArray(new int[]{13309}), "pass_date"); //int32[nDays] - Test.ensureEqual(grid.globalAttributes().get("start_time"), new DoubleArray(new double[]{0}), "start_time"); //float64[nDays] - Test.ensureEqual(grid.globalAttributes().get("origin"), new StringArray(new String[]{"Remote Sensing Systems, Inc."}), "origin"); //string - //Test.ensureEqual(grid.globalAttributes().get("history"), new StringArray(new String[]{"unknown"}), "history"); //string - - Test.ensureEqual(grid.globalAttributes().get("projection_type"), new StringArray(new String[]{"mapped"}), "projection_type"); //string - Test.ensureEqual(grid.globalAttributes().get("projection"), new StringArray(new String[]{"geographic"}), "projection"); //string - Test.ensureEqual(grid.globalAttributes().get("gctp_sys"), new IntArray(new int[]{0}), "gctp_sys"); //int32 - Test.ensureEqual(grid.globalAttributes().get("gctp_zone"), new IntArray(new int[]{0}), "gctp_zone"); //int32 - Test.ensureEqual(grid.globalAttributes().get("gctp_parm"), new DoubleArray(new double[15]), "gctp_parm"); //float64[15 0's] - Test.ensureEqual(grid.globalAttributes().get("gctp_datum"), new IntArray(new int[]{12}), "gctp_datum");//int32 12=WGS84 - - double matrix[] = {0, -grid.latSpacing, grid.lonSpacing, 0, grid.lon[0], grid.lat[nLat-1]}; //up side down - Test.ensureEqual(grid.globalAttributes().get("et_affine"), new DoubleArray(matrix), "et_affine"); //right side up - - Test.ensureEqual(grid.globalAttributes().get("rows"), new IntArray(new int[]{grid.lat.length}), "rows");//int32 number of rows - Test.ensureEqual(grid.globalAttributes().get("cols"), new IntArray(new int[]{grid.lon.length}), "cols");//int32 number of columns - Test.ensureEqual(grid.globalAttributes().get("polygon_latitude"), new DoubleArray(new double[]{ - grid.lat[0], grid.lat[nLat - 1], grid.lat[nLat - 1], grid.lat[0], grid.lat[0]}), "polygon_latitude"); - Test.ensureEqual(grid.globalAttributes().get("polygon_longitude"), new DoubleArray(new double[]{ - grid.lon[0], grid.lon[0], grid.lon[nLon - 1], grid.lon[nLon - 1], grid.lon[0]}), "polygon_longitude"); - - //lat attributes - Test.ensureEqual(grid.latAttributes().get("long_name"), new StringArray(new String[]{"Latitude"}), "lat long_name"); - Test.ensureEqual(grid.latAttributes().get("standard_name"), new StringArray(new String[]{"latitude"}), "lat standard_name"); - Test.ensureEqual(grid.latAttributes().get("units"), new StringArray(new String[]{"degrees_north"}), "lat units"); - Test.ensureEqual(grid.latAttributes().get("point_spacing"), new StringArray(new String[]{"even"}), "lat point_spacing"); - Test.ensureEqual(grid.latAttributes().get("actual_range"), new DoubleArray(new double[]{22, 50}), "lat actual_range"); - - //CWHDF metadata/attributes for Latitude - Test.ensureEqual(grid.latAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys");//string - Test.ensureEqual(grid.latAttributes().get("fraction_digits"), new IntArray(new int[]{2}), "fraction_digits"); //int32 - - - //lon attributes - Test.ensureEqual(grid.lonAttributes().get("long_name"), new StringArray(new String[]{"Longitude"}), "lon long_name"); - Test.ensureEqual(grid.lonAttributes().get("standard_name"), new StringArray(new String[]{"longitude"}), "lon standard_name"); - Test.ensureEqual(grid.lonAttributes().get("units"), new StringArray(new String[]{"degrees_east"}), "lon units"); - Test.ensureEqual(grid.lonAttributes().get("point_spacing"), new StringArray(new String[]{"even"}), "lon point_spacing"); - Test.ensureEqual(grid.lonAttributes().get("actual_range"), new DoubleArray(new double[]{-135, -105}), "lon actual_range"); - - //CWHDF metadata/attributes for Longitude - Test.ensureEqual(grid.lonAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys"); //string - Test.ensureEqual(grid.lonAttributes().get("fraction_digits"), new IntArray(new int[]{2}), "fraction_digits"); //int32 - - - //data attributes DataSet.properties has 0.125, but files need to be reprocessed to catch that - Test.ensureEqual(grid.dataAttributes().get("long_name"), new StringArray(new String[]{"Wind, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal"}), "data long_name"); - Test.ensureEqual(grid.dataAttributes().get("standard_name"), new StringArray(new String[]{"x_wind"}), "data standard_name"); - Test.ensureEqual(grid.dataAttributes().get("units"), new StringArray(new String[]{"m s-1"}), "data units"); - Test.ensureEqual(grid.dataAttributes().get("_FillValue"), new FloatArray(new float[]{-9999999}), "data _FillValue"); - Test.ensureEqual(grid.dataAttributes().get("missing_value"), new FloatArray(new float[]{-9999999}), "data missing_value"); - Test.ensureEqual(grid.dataAttributes().get("numberOfObservations"), new IntArray(new int[]{25021}), "data numberOfObservations"); - Test.ensureEqual(grid.dataAttributes().get("percentCoverage"), new DoubleArray(new double[]{0.46142923005993547}), "data percentCoverage"); - - //CWHDF metadata/attributes for the data: varName - Test.ensureEqual(grid.dataAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys"); //string - Test.ensureEqual(grid.dataAttributes().get("fraction_digits"), new IntArray(new int[]{1}), "fraction_digits"); //int32 - - /* */ - - //*************************************** - //large test of TMBchla which covers has odd x range ~ 110 to 320 - //actual dataset minX=120.0 maxX=320.0 minY=-45.0 maxY=65.0 xInc=0.025 yInc=0.025 - //These mimic tests in Grid.testReadGrdSubset(). - //Comment out this line with /* to comment out this test. - gridDataSet = new GridDataSetThredds(fnu, "TMBchla", - //was "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMB/chla/", //was :8081 - "https://thredds1.pfeg.noaa.gov/thredds/catalog/Satellite/aggregsatMB/chla/", - "Rainbow", "Log", ".001", "30", -1, "", null, null, "S", 1, 0, "", 1, 1); - fileName = "temp"; - - //get 4 points individually - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315, 315, 30, 30, 1, 1); - Test.ensureEqual(grid.lon, new double[]{315}, ""); - Test.ensureEqual(grid.lat, new double[]{30}, ""); - Test.ensureEqual((float)grid.data[0], (float)0.039, ""); - - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 135, 30, 30, 1, 1); - Test.ensureEqual(grid.lon, new double[]{135}, ""); - Test.ensureEqual(grid.lat, new double[]{30}, ""); - Test.ensureEqual((float)grid.data[0], (float)0.200333, ""); - - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315, 315, -41, -41, 1, 1); - Test.ensureEqual(grid.lon, new double[]{315}, ""); - Test.ensureEqual(grid.lat, new double[]{-41}, ""); - Test.ensureEqual((float)grid.data[0], (float)0.968, ""); - - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 135, -41, -41, 1, 1); - Test.ensureEqual(grid.lon, new double[]{135}, ""); - Test.ensureEqual(grid.lat, new double[]{-41}, ""); - Test.ensureEqual((float)grid.data[0], (float) 0.431, ""); - - //test 2 wide, 1 high - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 315, 30, 30, 2, 1); - Test.ensureEqual(grid.lon, new double[]{135, 315}, ""); - Test.ensureEqual(grid.lat, new double[]{30}, ""); - Test.ensureEqual((float)grid.data[0], (float)0.200333, ""); - Test.ensureEqual((float)grid.data[1], (float)0.039, ""); - - //test 37 wide, 1 high test most of the data rotated around to right - //This is a little contrived: getting every 5 degrees of lon allows it to - // cleanly align at 0 and still get my two test points exactly. - // But that is part of the nature of having to move the data columns around. - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", -45, 135, 30, 30, 37, 1); //180 range / 5 = 36 + 1 - String2.log("lon=" + String2.toCSSVString(grid.lon)); - Test.ensureEqual(grid.lon, DataHelper.getRegularArray(37, -45, 5), ""); - Test.ensureEqual(grid.lat, new double[]{30}, ""); - Test.ensureEqual((float)grid.data[0], (float)0.039, ""); - Test.ensureEqual((float)grid.data[36], (float)0.200333, ""); - - //test 1 wide, 2 high x in 0.. 180 - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 135, -41, 30, 1, 2); - Test.ensureEqual(grid.lon, new double[]{135}, ""); - Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); - Test.ensureEqual((float)grid.data[0], (float) 0.431, ""); - Test.ensureEqual((float)grid.data[1], (float)0.200333, ""); - - //test 1 wide, 2 high in x>180 - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315, 315, -41, 30, 1, 2); - Test.ensureEqual(grid.lon, new double[]{315}, ""); - Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); - Test.ensureEqual((float)grid.data[0], (float)0.968, ""); - Test.ensureEqual((float)grid.data[1], (float)0.039, ""); - - //test 1 wide, 2 high in x<0 - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315-360, 315-360, -41, 30, 1, 2); - Test.ensureEqual(grid.lon, new double[]{315-360}, ""); - Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); - Test.ensureEqual((float)grid.data[0], (float)0.968, ""); - Test.ensureEqual((float)grid.data[1], (float)0.039, ""); - - //test 2 wide, 2 high in x<0 - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 315, -41, 30, 2, 2); - Test.ensureEqual(grid.lon, new double[]{135, 315}, ""); - Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); - Test.ensureEqual((float)grid.data[0], (float) 0.431, ""); - Test.ensureEqual((float)grid.data[1], (float)0.200333, ""); - Test.ensureEqual((float)grid.data[2], (float)0.968, ""); - Test.ensureEqual((float)grid.data[3], (float)0.039, ""); - - //test 37 wide, 2 high in x<0 - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315-360, 135, -41, 30, 37, 2); - Test.ensureEqual(grid.lon, DataHelper.getRegularArray(37, -45, 5), ""); - Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); - Test.ensureEqual((float)grid.data[0], (float)0.968, ""); - Test.ensureEqual((float)grid.data[1], (float)0.039, ""); - Test.ensureEqual((float)grid.data[72], (float)0.431, ""); - Test.ensureEqual((float)grid.data[73], (float)0.200333, ""); - - /* */ - - /* - //*************************************** - //one time only: get one of these files for testing readGrd - //actual dataset minX=120.0 maxX=320.0 minY=-45.0 maxY=65.0 xInc=0.025 yInc=0.025 - gridDataSet = new GridDataSetThredds(fnu, "TMBchla", - "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMB/chla/", //was :8081 - "Rainbow", "Log", ".001", "30", -1, "", null, null); - fileName = "TestReadGrgTMBchla"; - - //get 4 points individually - grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 120, 320, -45, 65, 201, 111); //1 x 1 degree - String2.log("resultingFileName=" + resultingFileName); - //result is TestReadGrgTMBchla_x120_X320_y-45_Y65_nx201_ny111.grd - */ - } - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 1; - String msg = "\n^^^ GridDatasetThredds.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - if (test == 0) basicTest(); - if (test == 1) testGetTimeSeries(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - - /** * This performs a quick test of a dataset (e.g. to see why it isn't loading in * a CWBrowser). diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/NcHelper.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/NcHelper.java index 6ebcc02b8..f26466918 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/NcHelper.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/NcHelper.java @@ -13,11 +13,9 @@ import com.cohort.util.Test; import java.io.StringWriter; -import java.net.URL; import java.util.ArrayList; import java.util.Arrays; import java.util.BitSet; -import java.util.Enumeration; import java.util.Iterator; import java.util.List; @@ -26,8 +24,6 @@ import ucar.nc2.*; import ucar.nc2.dataset.NetcdfDataset; import ucar.nc2.dataset.NetcdfDatasets; -//import ucar.nc2.dods.*; -import ucar.nc2.util.*; import ucar.nc2.write.*; @@ -2380,204 +2376,6 @@ public static void testJplG1SST() throws Exception { String2.log("diffString=\n" + pas14.diffString(pas13)); } - /** - * Test findAllVariablesWithDims. - * @throws Exception if trouble - */ - public static void testFindAllVariablesWithDims() throws Exception { - StringArray sa = new StringArray(); - NetcdfFile ncFile = openFile("c:/data/nodcTemplates/ncCFMA2a.nc"); - try { - Variable vars[] = findAllVariablesWithDims(ncFile); - for (int v = 0; v < vars.length; v++) - sa.add(vars[v].getFullName()); - sa.sort(); - } finally { - ncFile.close(); - } - String results = sa.toString(); - String expected = - "bottle_posn, cast, cruise_id, latitude, longitude, ship, temperature0, time"; - Test.ensureEqual(results, expected, "results=" + results); - - } - - - - /** This is a test of unlimitedDimension - */ - public static void testUnlimited() throws Exception { - String testUnlimitedFileName = "/temp/unlimited.nc"; - String2.log("\n* Projects.testUnlimited() " + testUnlimitedFileName); - int strlen = 6; - int row = -1; - String results, expected; - NetcdfFormatWriter ncWriter = null; - try { - NetcdfFormatWriter.Builder file = NetcdfFormatWriter.createNewNetcdf3( - testUnlimitedFileName); - Group.Builder rootGroup = file.getRootGroup(); - - //add the unlimited time dimension - //Dimension timeDim = file.addUnlimitedDimension("time"); - - //alternative way to add the unlimited dimension - Dimension timeDim = Dimension.builder().setName("time").setIsUnlimited(true).setLength(0).build(); - rootGroup.addDimension(timeDim); - - ArrayList dims = new ArrayList(); - dims.add(timeDim); - - // define Variables - Variable.Builder timeVar = NcHelper.addVariable(rootGroup, "time", DataType.DOUBLE, dims); - timeVar.addAttribute(new Attribute("units", "seconds since 1970-01-01")); - - Variable.Builder latVar = NcHelper.addVariable(rootGroup, "lat", DataType.DOUBLE, dims); - latVar.addAttribute(new Attribute("units", "degrees_north")); - - Variable.Builder lonVar = NcHelper.addVariable(rootGroup, "lon", DataType.DOUBLE, dims); - lonVar.addAttribute(new Attribute("units", "degrees_east")); - - Variable.Builder sstVar = NcHelper.addVariable(rootGroup, "sst", DataType.DOUBLE, dims); - sstVar.addAttribute(new Attribute("units", "degree_C")); - - Variable.Builder commentVar = NcHelper.addNc3StringVariable(rootGroup, "comment", dims, strlen); - - // create the file - ncWriter = file.build(); - - //optional - ncWriter.close(); - ncWriter = null; - - //ncdump it - String2.log("\nInitially:\n" + NcHelper.ncdump(testUnlimitedFileName, "")); - - //write 1 row at a time to the file - for (row = 0; row < 5; row++) { - Math2.sleep(20); - if (ncWriter == null) - ncWriter = NetcdfFormatWriter.openExisting(testUnlimitedFileName).build(); - String2.log("writing row=" + row); - - int[] origin1 = new int[] {row}; - int[] origin2 = new int[] {row, 0}; - Array array; - ArrayChar.D2 ac = new ArrayChar.D2(1, strlen); - - double cTime = System.currentTimeMillis() / 1000.0; - array = get1DArray(new double[] {row}, false); ncWriter.write(ncWriter.findVariable("time"), origin1, array); - String2.log(">> array=" + array.toString()); - array = get1DArray(new double[] {33.33}, false); ncWriter.write(ncWriter.findVariable("lat"), origin1, array); - array = get1DArray(new double[] {-123.45}, false); ncWriter.write(ncWriter.findVariable("lon"), origin1, array); - array = get1DArray(new double[] {10 + row / 10.0}, false); ncWriter.write(ncWriter.findVariable("sst"), origin1, array); - ac.setString(0, row + " comment"); ncWriter.write(ncWriter.findVariable("comment"), origin2, ac); - ncWriter.close(); - ncWriter = null; - - String2.log("\nrow=" + row + ":\n" + NcHelper.ncdump(testUnlimitedFileName, "")); - - /* - if (row == 1) { - results = NcHelper.ncdump(testUnlimitedFileName, ""); - String2.log(results); - expected = -"netcdf unlimited.nc {\n" + //2013-09-03 netcdf-java 4.3 added blank lines -" dimensions:\n" + -" time = UNLIMITED; // (2 currently)\n" + -" comment_strlen = 6;\n" + -" variables:\n" + -" double time(time=2);\n" + -" :units = \"seconds since 1970-01-01\";\n" + -"\n" + -" double lat(time=2);\n" + -" :units = \"degrees_north\";\n" + -"\n" + -" double lon(time=2);\n" + -" :units = \"degrees_east\";\n" + -"\n" + -" double sst(time=2);\n" + -" :units = \"degree_C\";\n" + -"\n" + -" char comment(time=2, comment_strlen=6);\n" + -"\n" + -"\n" + -" data:\n" + -" time = \n" + -" {0.0, 1.0}\n" + -" lat = \n" + -" {33.33, 33.33}\n" + -" lon = \n" + -" {-123.45, -123.45}\n" + -" sst = \n" + -" {10.0, 10.1}\n" + -" comment = \"0 comm\", \"1 comm\"\n" + -"}\n"; - if (!results.equals(expected)) { - ncWriter.close(); - ncWriter = null; - Test.ensureEqual(results, expected, "trouble when i==1"); - } - } - */ - } - - - //NOTE: instead of closing the ncWriter to write changes to disk, you can use ncWriter.flush(). - if (ncWriter != null) { - try {ncWriter.abort(); } catch (Exception e9) {} - File2.delete(testUnlimitedFileName); - ncWriter = null; - } - } catch (Exception e9) { - String2.log("row=" + row + " " + NcHelper.ERROR_WHILE_CREATING_NC_FILE + MustBe.throwableToString(e9)); - if (ncWriter != null) { - try {ncWriter.abort(); } catch (Exception e8) {} - File2.delete(testUnlimitedFileName); - ncWriter = null; - } - throw e9; - } - - results = NcHelper.ncdump(testUnlimitedFileName, ""); - String2.log(results); - expected = -"netcdf unlimited.nc {\n" + //2013-09-03 netcdf-java 4.3 added blank lines -" dimensions:\n" + -" time = UNLIMITED; // (5 currently)\n" + -" comment_strlen = 6;\n" + -" variables:\n" + -" double time(time=5);\n" + -" :units = \"seconds since 1970-01-01\";\n" + -"\n" + -" double lat(time=5);\n" + -" :units = \"degrees_north\";\n" + -"\n" + -" double lon(time=5);\n" + -" :units = \"degrees_east\";\n" + -"\n" + -" double sst(time=5);\n" + -" :units = \"degree_C\";\n" + -"\n" + -" char comment(time=5, comment_strlen=6);\n" + -"\n" + -"\n" + -" data:\n" + -" time = \n" + -" {0.0, 1.0, 2.0, 3.0, 4.0}\n" + -" lat = \n" + -" {33.33, 33.33, 33.33, 33.33, 33.33}\n" + -" lon = \n" + -" {-123.45, -123.45, -123.45, -123.45, -123.45}\n" + -" sst = \n" + -" {10.0, 10.1, 10.2, 10.3, 10.4}\n" + -" comment = \"0 comm\", \"1 comm\", \"2 comm\", \"3 comm\", \"4 comm\"\n" + -"}\n"; - Test.ensureEqual(results, expected, ""); - - } - - /** * An experiment with NetcdfDataset accessing a DAP sequence dataset. */ @@ -2591,380 +2389,6 @@ public static void testSequence() throws Throwable { } } - - /** - * This tests the methods in this class. - */ - public static void testBasic() throws Throwable { - String2.log("\n*** NcHelper.testBasic..."); - String fullName; - - - //getArray get1DArray, get1DArrayLength - Object o; - o = new String[]{"5.5", "7.77"}; - Array array = get1DArray(o, false); - Test.ensureTrue(array instanceof ArrayChar.D2, "get1DArray a"); - Test.ensureEqual(get1DArrayLength(array), 2, "get1DArrayLength a"); - o = getPrimitiveArray(array); - Test.ensureTrue(o instanceof StringArray, "getArray a; o=" + o.toString()); - StringArray sar = (StringArray)o; - Test.ensureEqual(sar.size(), 2, ""); - Test.ensureEqual(sar.get(0), "5.5", ""); - Test.ensureEqual(sar.get(1), "7.77", ""); - - /* - ArrayChar.D3 ac3 = new ArrayChar.D3(2, 3, 5); - Index index = ac3.getIndex(); - index.set(0, 0); ac3.setString(index, "a"); - index.set(0, 1); ac3.setString(index, "bb"); - index.set(0, 2); ac3.setString(index, "ccc"); - index.set(1, 0); ac3.setString(index, "dddd"); - index.set(1, 1); ac3.setString(index, "e"); - index.set(1, 2); ac3.setString(index, "f"); - o = getArray(ac3); - Test.ensureTrue(o instanceof String[], "getArray a; o=" + o.toString()); - sar = (String[])o; - Test.ensureEqual(sar.length, 6, ""); - Test.ensureEqual(sar[0], "a", ""); - Test.ensureEqual(sar[1], "bb", ""); - Test.ensureEqual(sar[2], "ccc", ""); - Test.ensureEqual(sar[3], "dddd", ""); - Test.ensureEqual(sar[4], "e", ""); - Test.ensureEqual(sar[5], "f", ""); - */ - - o = new byte[]{(byte)2, (byte)9}; - array = get1DArray(o, false); - Test.ensureTrue(array instanceof ArrayByte.D1, "get1DArray b"); - Test.ensureEqual(get1DArrayLength(array), 2, "get1DArrayLength a"); - o = getPrimitiveArray(array); - Test.ensureTrue(o instanceof ByteArray, "getArray b"); - ByteArray bar = (ByteArray)o; - Test.ensureEqual(bar.size(), 2, ""); - Test.ensureEqual(bar.get(0), 2, ""); - Test.ensureEqual(bar.get(1), 9, ""); - - o = new double[]{2.2, 9.9}; - array = get1DArray(o, false); - Test.ensureTrue(array instanceof ArrayDouble.D1, "get1DArray c"); - Test.ensureEqual(get1DArrayLength(array), 2, "get1DArrayLength a"); - o = getPrimitiveArray(array); - Test.ensureTrue(o instanceof DoubleArray, "getArray c"); - DoubleArray dar = (DoubleArray)o; - Test.ensureEqual(dar.size(), 2, ""); - Test.ensureEqual(dar.get(0), 2.2, ""); - Test.ensureEqual(dar.get(1), 9.9, ""); - - //test readWritePAsInNc - ByteArray ba = new ByteArray(new byte[]{1,2,4,7}); - ShortArray sha = new ShortArray(new short[]{100,200,400,700}); - IntArray ia = new IntArray(new int[]{-1, 0, 1}); - LongArray la = new LongArray(new long[]{-10L, 0, 10L}); - char charAr[] = new char[65536]; - for (int i = 0; i < 65536; i++) - charAr[i] = (char)i; - CharArray ca = new CharArray(charAr); - FloatArray fa = new FloatArray(new float[]{-1.1f, 2.2f, 5.5f, Float.NaN}); - DoubleArray da = new DoubleArray(new double[]{1.1, 2.2, 9.9, Double.NaN}); - StringArray sa = new StringArray(); - for (int i = 0; i < 65536; i++) - sa.add("a" + (i==8?" " : (char)i) + "z"); //backspace not saved - //write to file - fullName = "c:/temp/PAsInNc.nc"; - File2.delete(fullName); //for test, make double sure it doesn't already exist - StringArray varNames = new StringArray(new String[]{ - "ba", "sha", "ia", "la", "ca", "fa", "da", "sa"}); - PrimitiveArray pas[] = new PrimitiveArray[]{ - ba, sha, ia, la, ca, fa, da, sa}; - writePAsInNc3(fullName, varNames, pas); - //read from file - StringArray varNames2 = new StringArray(); - PrimitiveArray pas2[] = readPAsInNc3(fullName, null, varNames2); - Test.ensureEqual(varNames, varNames2, ""); - Test.ensureEqual(pas.length, pas2.length, ""); - for (int i = 0; i < pas.length; i++) { - int which = varNames2.indexOf(varNames.get(i)); - PrimitiveArray pa2 = pas2[which]; - Test.ensureEqual(pas[i].elementTypeString(), pa2.elementTypeString(), "i=" + i); - if (pas[i].elementType() == PAType.STRING) { - for (int j = 0; j < pas[i].size(); j++) - Test.ensureEqual(String2.toJson(pas[i].getString(j)), - String2.toJson( pa2.getString(j)), "i=" + i + " j=" + j); - } else { - Test.ensureEqual(pas[i].toJsonCsvString(),pa2.toJsonCsvString(), "i=" + i); - } - } - - pas2 = readPAsInNc3(fullName, new String[]{"sa"}, varNames2); - Test.ensureEqual(varNames2.size(), 1, ""); - Test.ensureEqual(varNames2.get(0), "sa", ""); - Test.ensureEqual(pas2.length, 1, ""); - Test.ensureEqual(pas[varNames.indexOf("sa")].toJsonCsvString(), pas2[0].toJsonCsvString(), ""); - - //test writeAttributesToNc - fullName = "c:/temp/AttsInNc.nc"; - Attributes atts = new Attributes(); - for (int i = 0; i < pas.length; i++) - atts.set(varNames.get(i), pas[i]); - writeAttributesToNc3(fullName, atts); - //read 1 - PrimitiveArray pa = readAttributeFromNc(fullName, "sa"); - Test.ensureEqual(sa.elementTypeString(), pa.elementTypeString(), ""); - Test.ensureEqual(sa, pa, ""); - pa = readAttributeFromNc(fullName, "ia"); - Test.ensureEqual(ia.elementTypeString(), pa.elementTypeString(), ""); - Test.ensureEqual(ia, pa, ""); - //read many - pas2 = readAttributesFromNc3(fullName, varNames.toArray()); - for (int i = 0; i < pas.length; i++) { - Test.ensureEqual(pas[i].elementTypeString(), pas2[i].elementTypeString(), "i=" + i); - Test.ensureEqual(pas[i].toJsonCsvString(), pas2[i].toJsonCsvString(), "i=" + i); - } - //read all - atts = readAttributesFromNc3(fullName); - for (int i = 0; i < varNames.size(); i++) { - pa = atts.get(varNames.get(i)); - Test.ensureEqual(pas[i].elementTypeString(), pa.elementTypeString(), "i=" + i); - Test.ensureEqual(pas[i].toJsonCsvString(), pa.toJsonCsvString(), "i=" + i); - } - //test fail to read non-existent file - try { - pa = readAttributeFromNc(fullName + "zztop", "sa"); - throw new RuntimeException("shouldn't get here"); - } catch (Exception e) { - if (e.toString().indexOf( - "java.io.FileNotFoundException: c:\\temp\\AttsInNc.nczztop " + - "(The system cannot find the file specified)") < 0) - throw e; - } - - try { - pas2 = readAttributesFromNc3(fullName + "zztop", varNames.toArray()); - throw new RuntimeException("shouldn't get here"); - } catch (Exception e) { - if (e.toString().indexOf( - "java.io.FileNotFoundException: c:\\temp\\AttsInNc.nczztop " + - "(The system cannot find the file specified)") < 0) - throw e; - } - - try { - atts = readAttributesFromNc3(fullName + "zztop"); - throw new RuntimeException("shouldn't get here"); - } catch (Exception e) { - if (e.toString().indexOf( - "java.io.FileNotFoundException: c:\\temp\\AttsInNc.nczztop " + - "(The system cannot find the file specified)") < 0) - throw e; - } - - //test fail to read non-existent var - try { - pa = readAttributeFromNc(fullName, "zztop"); - throw new RuntimeException("shouldn't get here"); - } catch (Exception e) { - if (e.toString().indexOf( - String2.ERROR + ": Expected variable #0 not found while reading " + - "c:/temp/AttsInNc.nc (loadVarNames=zztop).") < 0) - throw e; - } - - try { - pas2 = readAttributesFromNc3(fullName, new String[]{"zztop"}); - throw new RuntimeException("shouldn't get here"); - } catch (Exception e) { - if (e.toString().indexOf( - String2.ERROR + ": Expected variable #0 not found while reading " + - "c:/temp/AttsInNc.nc (loadVarNames=zztop).") < 0) - throw e; - } - - //test if defining >2GB throws exception - fullName = "c:/temp/TooBig.nc"; - File2.delete(fullName); - NetcdfFormatWriter ncWriter = null; - - //*** test writing Strings to nc files - fullName = "c:/temp/StringsInNc.nc"; - File2.delete(fullName); - ncWriter = null; - try { - NetcdfFormatWriter.Builder ncOut = NetcdfFormatWriter.createNewNetcdf3(fullName); - //"define" mode - Group.Builder rootGroup = ncOut.getRootGroup(); - ncOut.setFill(false); - Dimension dim0 = NcHelper.addDimension(rootGroup, "dim0", 2); - Dimension dim1 = NcHelper.addDimension(rootGroup, "dim1", 3); - ArrayList dims = new ArrayList(); - dims.add(dim0); - dims.add(dim1); - NcHelper.addNc3StringVariable(rootGroup, "s1", dims, 4); //test strLength not long enough for all strings! - Array ar; - - //"create" mode - ncWriter = ncOut.build(); - String sa6[] = {"", "a", "abcd", "abc", "abcd", "abcd"}; - Variable s1Var = ncWriter.findVariable("s1"); - - //this fails (as expected and desired): - // so origin and ar must be correct nDimensions and size - //ar = Array.factory(DataType.STRING, new int[]{6}, sa6); - //ncOut.writeStringDataToChar(s1, new int[]{0}, ar); - - ar = Array.factory(DataType.STRING, new int[]{2,3}, sa6); - ncWriter.writeStringDataToChar(s1Var, new int[]{0, 0}, ar); - ncWriter.close(); - ncWriter = null; - } catch (Exception e) { - String2.log(NcHelper.ERROR_WHILE_CREATING_NC_FILE + MustBe.throwableToString(e)); - if (ncWriter != null) { - try {ncWriter.abort(); } catch (Exception e9) {} - File2.delete(fullName); - ncWriter = null; - } - } - - //Strings are truncated to maxCharLength specified in "define" mode. - String results = ncdump(fullName, ""); - String expected = -"netcdf StringsInNc.nc {\n" + -" dimensions:\n" + -" dim0 = 2;\n" + -" dim1 = 3;\n" + -" s1_strlen = 4;\n" + -" variables:\n" + -" char s1(dim0=2, dim1=3, s1_strlen=4);\n" + -"\n" + -"\n" + -" data:\n" + -" s1 = \n" + -" { \"\", \"a\", \"abcd\", \"abc\", \"abcd\", \"abcd\"\n" + -" }\n" + -"}\n"; - String2.log("results=\n" + results); - Test.ensureEqual(results, expected, ""); - File2.delete(fullName); - - - //*** test writing too-long Strings to nc files - //Must the char[][] be the exact right size? What if too long? - fullName = "c:/temp/StringsInNc2.nc"; - File2.delete(fullName); - ncWriter = null; - try { - NetcdfFormatWriter.Builder ncOut = NetcdfFormatWriter.createNewNetcdf3(fullName); - //"define" mode - Group.Builder rootGroup = ncOut.getRootGroup(); - ncOut.setFill(false); - Dimension dim0 = NcHelper.addDimension(rootGroup, "dim0", 2); - Dimension dim1 = NcHelper.addDimension(rootGroup, "dim1", 3); - ArrayList dims = new ArrayList(); - dims.add(dim0); - dims.add(dim1); - NcHelper.addNc3StringVariable(rootGroup, "s1", dims, 4); //test strLength not long enough for all strings! - Array ar; - - //"create" mode - ncWriter = ncOut.build(); - String sa6[] = {"", "a", "abcde", "abc", "abcd", "abcde"}; - Variable s1Var = ncWriter.findVariable("s1"); - - //this fails (as expected and desired): - // so origin and ar must be correct nDimensions and size - //ar = Array.factory(DataType.STRING, new int[]{6}, sa6); - //ncOut.writeStringDataToChar(s1, new int[]{0}, ar); - - ar = Array.factory(DataType.STRING, new int[]{2,3}, sa6); - ncWriter.writeStringDataToChar(s1Var, new int[]{0, 0}, ar); - ncWriter.close(); - ncWriter = null; - } catch (Exception e) { - String2.log(NcHelper.ERROR_WHILE_CREATING_NC_FILE + MustBe.throwableToString(e)); - if (ncWriter != null) { - try {ncWriter.abort(); } catch (Exception e9) {} - File2.delete(fullName); - ncWriter = null; - } - } - - //Strings are truncated to maxCharLength specified in "define" mode. - results = ncdump(fullName, ""); - expected = -"netcdf StringsInNc2.nc {\n" + -" dimensions:\n" + -" dim0 = 2;\n" + -" dim1 = 3;\n" + -" s1_strlen = 4;\n" + -" variables:\n" + -" char s1(dim0=2, dim1=3, s1_strlen=4);\n" + -"\n" + -"\n" + -" data:\n" + -" s1 = \n" + -" { \"\", \"a\", \"abcd\", \"abc\", \"abcd\", \"abcd\"\n" + -" }\n" + -"}\n"; - String2.log("results=\n" + results); - Test.ensureEqual(results, expected, ""); - - - //nc chars are essentially unsigned bytes! - String2.log(File2.hexDump(fullName, 1000000)); - File2.delete(fullName); - - //2021-01-06 This worked (ie netcdf-java refused to create the file) - // until netcdf-java v5.4.1. I reported to Sean Arms. - if (true) { //this is normally true - try { - NetcdfFormatWriter.Builder ncOut = NetcdfFormatWriter.createNewNetcdf3( - fullName) - .setFormat(NetcdfFileFormat.NETCDF3) //this is default. I'm just testing. - .setFill(false); - - //"define" mode 2vars * 3000*50000*8bytes = 2,400,000,000 - Group.Builder rootGroup = ncOut.getRootGroup(); - - Dimension dim0 = NcHelper.addDimension(rootGroup, "dim0", 3000); - Dimension dim1 = NcHelper.addDimension(rootGroup, "dim1", 50000); - List dims = Arrays.asList(dim0, dim1); - NcHelper.addVariable(rootGroup, "d1", DataType.DOUBLE, dims); - NcHelper.addVariable(rootGroup, "d2", DataType.DOUBLE, dims); - - //define a var above 2GB (This causes the exception.) - NcHelper.addVariable(rootGroup, "b3", DataType.BYTE, Arrays.asList(dim0)); - - //"create" mode (and error isn't triggered till here) - ncWriter = ncOut.build(); - - ncWriter.close(); //it calls flush() and doesn't like flush called separately - ncWriter = null; - if (true) - throw new RuntimeException("Shouldn't get here (It let me create nc3 file >2GB!) . fileSize=" + File2.length(fullName)); - - } catch (Throwable t) { - String2.log(NcHelper.ERROR_WHILE_CREATING_NC_FILE + MustBe.throwableToString(t)); - if (ncWriter != null) { - try {ncWriter.abort(); } catch (Exception e9) {} - File2.delete(fullName); - ncWriter = null; - } - - String msg = t.toString(); - String2.log("Intentional error (should be: not allowed to create nc3 file >2GB):\n" + msg); - - if (!msg.equals( - "java.lang.IllegalArgumentException: Variable starting pos=2400000172 " + - "may not exceed 2147483647")) - Test.knownProblem("netcdf-java 5.4.1+ allows creation of nc3 files >2GB!\n" + - "I reported this to Sean Arms 2021-01-06.", t); - } finally { - File2.delete(fullName); - } - } - - } - /** * This reads the specified data from a multidimensional structure. * @@ -3048,124 +2472,4 @@ public static PrimitiveArray[] readStructure(NetcdfFile nc, String structureName return pa; } - - /** - * This is the test that I sent to Sean. It only uses netcdf-java methods, not NcHelper. - */ - public static void testReadStructure() throws Throwable { - String fileName = String2.unitTestDataDir + "nc/SDScompound.h5"; - System.out.println(ncdump(fileName, "-v ArrayOfStructures")); - NetcdfFile nc = NetcdfFiles.open(fileName); - try { - System.out.println(nc.toString()); - Variable v = nc.findVariable("ArrayOfStructures"); - if (v instanceof Structure s) { - System.out.println("v=" + v); - StructureMembers sm = s.makeStructureMembers(); - System.out.println("sm=" + sm); - StructureMembers.Member smma = sm.findMember("a_name"); - StructureMembers.Member smmb = sm.findMember("b_name"); - StructureMembers.Member smmc = sm.findMember("c_name"); - //boolean buildStringsFromChars = false; - //boolean isUnsigned = false; - StructureDataIterator it = s.getStructureIterator(); - int recNo = 0; - try { - while (it.hasNext()) { - StructureData sd = it.next(); - System.out.println("byName recNo=" + recNo + - " a_name=" + sd.getScalarInt( "a_name") + - " b_name=" + sd.getScalarFloat( "b_name") + - " c_name=" + sd.getScalarDouble("c_name")); - System.out.println("byMem recNo=" + recNo + - " a_name=" + sd.getScalarInt( smma) + - " b_name=" + sd.getScalarFloat( smmb) + - " c_name=" + sd.getScalarDouble(smmc)); - recNo++; - } - } finally { - it.close(); - } - } - - } finally { - nc.close(); - } - } - - /** - * ERDDAP: require that all vars be in same structure - */ - public static void testReadStructure2() throws Throwable { - String fileName = String2.unitTestDataDir + "nc/SDScompound.h5"; - System.out.println(ncdump(fileName, "-v ArrayOfStructures")); - NetcdfFile nc = NetcdfFiles.open(fileName); - try { - String memberNames[] = new String[]{"a_name", "b_name", "c_name"}; - PrimitiveArray pa[] = readStructure(nc, "ArrayOfStructures", - memberNames, IntArray.fromCSV("0,1,9")); - Test.ensureEqual(pa[0].toString(), "0, 1, 2, 3, 4, 5, 6, 7, 8, 9", "a_name"); - Test.ensureEqual(pa[1].toString(), "0.0, 1.0, 4.0, 9.0, 16.0, 25.0, 36.0, 49.0, 64.0, 81.0", "b_name"); - Test.ensureEqual(pa[2].toString(), "1.0, 0.5, 0.3333333333333333, 0.25, 0.2, 0.16666666666666666, 0.14285714285714285, 0.125, 0.1111111111111111, 0.1", "c_name"); - - pa = readStructure(nc, "ArrayOfStructures", memberNames, IntArray.fromCSV("2,3,9")); - Test.ensureEqual(pa[0].toString(), "2, 5, 8", "a_name"); - Test.ensureEqual(pa[1].toString(), "4.0, 25.0, 64.0", "b_name"); - Test.ensureEqual(pa[2].toString(), "0.3333333333333333, 0.16666666666666666, 0.1111111111111111", "c_name"); - - pa = readStructure(nc, "ArrayOfStructures", memberNames, IntArray.fromCSV("2,3,8")); - Test.ensureEqual(pa[0].toString(), "2, 5, 8", "a_name"); - Test.ensureEqual(pa[1].toString(), "4.0, 25.0, 64.0", "b_name"); - Test.ensureEqual(pa[2].toString(), "0.3333333333333333, 0.16666666666666666, 0.1111111111111111", "c_name"); - } finally { - nc.close(); - } - } - - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 3; - String msg = "\n^^^ NcHelper.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - if (test == 0) testBasic(); - if (test == 1) testFindAllVariablesWithDims(); - if (test == 2) testUnlimited(); - if (test == 3) testReadStructure2(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - - } diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/Opendap.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/Opendap.java index 7b1a8ef60..c81808d9b 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/Opendap.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/Opendap.java @@ -19,21 +19,9 @@ import gov.noaa.pfel.coastwatch.TimePeriods; import gov.noaa.pfel.coastwatch.util.SSR; -//import java.net.URL; -//import java.net.URLConnection; -//import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.ByteArrayOutputStream; -//import java.io.InputStream; -//import java.io.InputStreamReader; -import java.io.FileWriter; -import java.text.SimpleDateFormat; import java.util.Arrays; -import java.util.Calendar; import java.util.Enumeration; -import java.util.Date; import java.util.GregorianCalendar; -import java.util.Vector; /** The Java DAP classes. */ import dods.dap.*; @@ -1382,133 +1370,6 @@ public static void doOtterSpeedTests(boolean doDotTestToo, boolean doAsciiTestTo * @throws Exception if troube */ public static void main(String args[]) throws Exception { - basicTest(); + // basicTest(); } - - public static void basicTest() throws Exception { - - Grid.verbose = true; - Opendap.verbose = true; - Opendap opendap; - - - /* - //test Oceanwatch Opendap no longer active - opendap = new Opendap( - //"http://las.pfeg.noaa.gov/cgi-bin/nph-dods/data/oceanwatch/nrt/gac/AG1day.nc", - "http://192.168.31.13/cgi-bin/nph-dods/data/oceanwatch/nrt/qscat/QNuy108day.nc", - true, null); - //opendap.getGridInfo("ssta", "-1.0e34"); - opendap.getGridInfo("uy10", "-1.0e34"); - opendap.numberOfObservations = - DataHelper.getDoubleArray(opendap.dConnect, - "?numberOfObservations.numberOfObservations"); - opendap.getTimeOptions(true, Calendar2.SECONDS_PER_DAY, Calendar2.isoStringToEpochSeconds("1985-01-01")); - File2.delete(SSR.getTempDirectory() + "OpendapTest.grd"); - opendap.makeGrid(SSR.getTempDirectory(), "OpendapTest.grd", - opendap.timeOptions[0], - -135 + 360, -105 + 360, 22, 50, //US+Mexico - Integer.MAX_VALUE, Integer.MAX_VALUE, null); - */ - - - //test THREDDS //was :8081 - opendap = new Opendap("https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/GA/ssta/3day", true, null); - DConnect dConnect = new DConnect(opendap.url, opendap.acceptDeflate, 1, 1); - opendap.getGridInfo(dConnect.getDAS(OpendapHelper.DEFAULT_TIMEOUT), - dConnect.getDDS(OpendapHelper.DEFAULT_TIMEOUT), "GAssta", "-1.0e34"); - Test.ensureEqual(opendap.getLat(0), -44.975, ""); //I'm not sure about exact range, should be global data - Test.ensureEqual(opendap.getLat(opendap.gridNLatValues - 1), 59.975, ""); - Test.ensureEqual(opendap.gridLatIncrement, .05, ""); - Test.ensureEqual(opendap.getLon(0), 180.025, ""); - Test.ensureEqual(opendap.getLon(opendap.gridNLonValues - 1), 329.975, ""); - Test.ensureEqual(opendap.gridLonIncrement, .05, ""); - - //test THREDDS - opendap = new Opendap( //was :8081 - "https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/AG/ssta/3day", - true, null); - dConnect = new DConnect(opendap.url, opendap.acceptDeflate, 1, 1); - opendap.getGridInfo(dConnect.getDAS(60000), dConnect.getDDS(60000), "AGssta", "-1.0e34"); - Test.ensureEqual(opendap.getLat(0), -75, ""); - Test.ensureEqual(opendap.getLat(opendap.gridNLatValues - 1), 75, ""); - Test.ensureEqual(opendap.gridLatIncrement, .1, ""); - Test.ensureEqual(opendap.getLon(0), 0, ""); - Test.ensureEqual(opendap.getLon(opendap.gridNLonValues - 1), 360, ""); - Test.ensureEqual(opendap.gridLonIncrement, .1, ""); - opendap.getTimeOptions(false, - opendap.gridTimeFactorToGetSeconds, - opendap.gridTimeBaseSeconds, - 3 * 24); - - //ensure not oddly spaced after makeLonPM180 - //data is 0..360, so ask for ~-180 to ~180 - String dir = SSR.getTempDirectory(); - Grid grid = opendap.makeGrid(opendap.timeOptions[0], - -170, 170, 22, 50, 53, 37); - String2.log("lon values: " + String2.toCSSVString(grid.lon)); - DataHelper.ensureEvenlySpaced(grid.lon, "The lon values aren't evenly spaced:\n"); - DataHelper.ensureEvenlySpaced(grid.lat, "The lat values aren't evenly spaced:\n"); - int nLon = grid.lon.length; - int nLat = grid.lat.length; - String lonString = "lon values: " + String2.toCSSVString(grid.lon); - String latString = "lat values: " + String2.toCSSVString(grid.lat); -//???the results seem to flip flop, perhaps based on some intermediate file that isn't being deleted every time -//but both answers are ok (179.2 is preferred?) -// if (nLon == 55) { - Test.ensureEqual(grid.lon[0], -172.8, lonString); - Test.ensureEqual(grid.lon[nLon-1], 172.8, lonString); -// } else if (nLon == 57) { -// Test.ensureEqual(grid.lon[0], -179.2, lonString); -// Test.ensureEqual(grid.lon[nLon-1], 179.2, lonString); -// } else -// Test.error(grid.lonInfoString()); - Test.ensureEqual(nLat, 41, latString); - Test.ensureEqual(grid.lat[0], 22, latString); - Test.ensureEqual(grid.lat[nLat-1], 50, latString); - - } - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 0; - String msg = "\n^^^ Opendap.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - if (test == 0) basicTest(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - - } diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/OpendapHelper.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/OpendapHelper.java index d7738d0eb..6d5ed5d0a 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/OpendapHelper.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/griddata/OpendapHelper.java @@ -21,17 +21,12 @@ import java.io.ByteArrayOutputStream; import java.io.Writer; -import java.net.URL; import java.util.ArrayList; import java.util.Arrays; -import java.util.BitSet; import java.util.Enumeration; -import java.util.HashMap; -import java.util.List; import ucar.ma2.Array; import ucar.ma2.ArrayObject; -import ucar.ma2.ArrayString; import ucar.ma2.DataType; import ucar.nc2.Dimension; import ucar.nc2.Group; @@ -1104,53 +1099,6 @@ public static String[] findVarsWithSharedDimensions(DDS dds) return varNames.toArray(); } - /** This tests findVarsWithSharedDimensions. */ - public static void testFindVarsWithSharedDimensions() throws Throwable { - String2.log("\n\n*** OpendapHelper.findVarsWithSharedDimensions"); - String expected, results; - DConnect dConnect; - DDS dds; - - /* - //test of Sequence DAP dataset - String2.log("\n*** test of Sequence DAP dataset"); - String sequenceUrl = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1"; - dConnect = new DConnect(sequenceUrl, true, 1, 1); - dds = dConnect.getDDS(DEFAULT_TIMEOUT); - results = String2.toCSSVString(findVarsWithSharedDimensions(dds)); - expected = -"zztop"; - Test.ensureEqual(results, expected, "results=" + results); - */ - - - //test of DArray DAP dataset -//2018-09-13 https: works in browser by not yet in Java - String dArrayUrl = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; - String2.log("\n*** test of DArray DAP dataset\n" + dArrayUrl); - dConnect = new DConnect(dArrayUrl, true, 1, 1); - dds = dConnect.getDDS(DEFAULT_TIMEOUT); - results = String2.toCSSVString(findVarsWithSharedDimensions(dds)); - expected = -"time, lat, lon, PL_HD, PL_CRS, DIR, PL_WDIR, PL_SPD, SPD, PL_WSPD, P, T, RH, date, time_of_day, flag"; - Test.ensureEqual(results, expected, "results=" + results); - - - //***** test of DGrid DAP dataset - String2.log("\n*** test of DGrid DAP dataset"); - String dGridUrl = "https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday"; - dConnect = new DConnect(dGridUrl, true, 1, 1); - dds = dConnect.getDDS(DEFAULT_TIMEOUT); - results = String2.toCSSVString(findVarsWithSharedDimensions(dds)); - expected = "x_wind, y_wind"; - Test.ensureEqual(results, expected, "results=" + results); - - - /* */ - String2.log("\n*** OpendapHelper.testFindVarsWithSharedDimensions finished."); - - } - /** * This tests if baseType is an instanceof a * scalar (DBoolean, DByte, DFloat32, DFloat64, DInt16, DInt32, DString) @@ -1199,81 +1147,6 @@ public static String[] findAllScalarOrMultiDimVars(DDS dds) return varNames.toArray(); } - /** This tests findAllVars. */ - public static void testFindAllScalarOrMultiDimVars() throws Throwable { - String2.log("\n\n*** OpendapHelper.testFindAllScalarOrMultiDimVars"); - String expected, results; - DConnect dConnect; - DDS dds; - String url; - - /* - //test of Sequence DAP dataset - String2.log("\n*** test of Sequence DAP dataset"); - url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1"; - dConnect = new DConnect(url, true, 1, 1); - dds = dConnect.getDDS(DEFAULT_TIMEOUT); - results = String2.toCSSVString(findVarsWithSharedDimensions(dds)); - expected = -"zztop"; - Test.ensureEqual(results, expected, "results=" + results); - */ - - - //test of DArray DAP dataset - //2018-09-13 https: works in browser by not yet in Java. 2019-06-28 https works in Java - url = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; - String2.log("\n*** test of DArray DAP dataset\n" + url); - dConnect = new DConnect(url, true, 1, 1); - dds = dConnect.getDDS(DEFAULT_TIMEOUT); - results = String2.toCSSVString(findAllScalarOrMultiDimVars(dds)); - expected = -"time, lat, lon, PL_HD, PL_CRS, DIR, PL_WDIR, PL_SPD, SPD, PL_WSPD, P, T, RH, date, time_of_day, flag, history"; - Test.ensureEqual(results, expected, "results=" + results); - - - //***** test of DGrid DAP dataset - String2.log("\n*** test of DGrid DAP dataset"); - url = "https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday"; - dConnect = new DConnect(url, true, 1, 1); - dds = dConnect.getDDS(DEFAULT_TIMEOUT); - results = String2.toCSSVString(findAllScalarOrMultiDimVars(dds)); - expected = -"time, altitude, latitude, longitude, x_wind, y_wind"; - Test.ensureEqual(results, expected, "results=" + results); - - //***** test of NODC template dataset -/** 2020-10-26 disabled because source is unreliable - String2.log("\n*** test of NODC template dataset"); - url = "https://data.nodc.noaa.gov/thredds/dodsC/testdata/netCDFTemplateExamples/timeSeries/BodegaMarineLabBuoyCombined.nc"; - dConnect = new DConnect(url, true, 1, 1); - dds = dConnect.getDDS(DEFAULT_TIMEOUT); - results = String2.toCSSVString(findAllScalarOrMultiDimVars(dds)); - expected = -"time, lat, lon, alt, station_name, temperature, salinity, density, conductivity, " + -"turbidity, fluorescence, platform1, temperature_qc, salinity_qc, density_qc, " + -"conductivity_qc, turbidity_qc, fluorescence_qc, instrument1, instrument2, " + -"instrument3, ht_wgs84, ht_mllw, crs"; - Test.ensureEqual(results, expected, "results=" + results); -*/ - - //***** test of sequence dataset (no vars should be found - String2.log("\n*** test of sequence dataset"); - url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCAMarCatLY"; - dConnect = new DConnect(url, true, 1, 1); - dds = dConnect.getDDS(DEFAULT_TIMEOUT); - results = String2.toCSSVString(findAllScalarOrMultiDimVars(dds)); - expected = ""; - Test.ensureEqual(results, expected, "results=" + results); - - - /* */ - String2.log("\n*** OpendapHelper.testFindAllScalarOrMultiDimVars finished."); - - } - - - /** * Get all of the data from allScalarOrMultiDimVars in an Opendap dataset * and save in .nc file. @@ -1535,207 +1408,6 @@ public static void allDapToNc(String dapUrl, String fullFileName) throws Throwab } } - /** - * Test allDapToNc. - * @param whichTests -1 for all, or 0.. for specific ones - */ - public static void testAllDapToNc(int whichTests) throws Throwable { - //tests from nodc template examples https://www.ncei.noaa.gov/netcdf-templates - String2.log("\n*** OpendapHelper.testAllDapToNc(" + whichTests + ")"); - String dir = "c:/data/nodcTemplates/"; - //2023-02-15 This method hadn't been run since 2020 because tdsUrl often stalled, so I had commented it out. - //tdsUrl was "https://data.nodc.noaa.gov/thredds/dodsC/testdata/netCDFTemplateExamples/"; //+e.g., point/KachemakBay.nc"; - String tdsUrl = "https://www.ncei.noaa.gov/thredds-ocean/dodsC/example/v1.0/"; //+e.g., point/KachemakBay.nc"; - String fileName; - String url, results, expected; - - if (whichTests == -1 || whichTests == 0) { - //this tests numeric scalars, and numeric and String 1D arrays - fileName = "pointKachemakBay.nc"; - url = tdsUrl + "point/KachemakBay.nc"; - allDapToNc(url, dir + fileName); - results = NcHelper.dds(dir + fileName); - String2.log(results); - //expected = "zztop"; - //Test.ensureEqual(results, expected, ""); - } - - if (whichTests == -1 || whichTests == 1) { - //this tests numeric and String scalars, and numeric 1D arrays - fileName = "timeSeriesBodegaMarineLabBuoy.nc"; - url = tdsUrl + "timeSeries/BodegaMarineLabBuoy.nc"; - allDapToNc(url, dir + fileName); - results = NcHelper.dds(dir + fileName); - expected = -"netcdf c:/data/nodcTemplates/timeSeriesBodegaMarineLabBuoy.nc {\n" + -" dimensions:\n" + -" time = 63242;\n" + -" string1 = 1;\n" + -" station_name_strlen = 17;\n" + -" variables:\n" + -" double time(time=63242);\n" + -" float lat;\n" + -" float lon;\n" + -" double alt;\n" + -" char station_name(string1=1, station_name_strlen=17);\n" + -" double temperature(time=63242);\n" + -" double salinity(time=63242);\n" + -" double density(time=63242);\n" + -" double conductivity(time=63242);\n" + -" int platform1;\n" + -" int temperature_qc(time=63242);\n" + -" int salinity_qc(time=63242);\n" + -" int density_qc(time=63242);\n" + -" int conductivity_qc(time=63242);\n" + -" int instrument1;\n" + -" int instrument2;\n" + -" double ht_wgs84;\n" + -" double ht_mllw;\n" + -" int crs;\n" + -" // global attributes:\n" + -"}\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } - - if (whichTests == -1 || whichTests == 2) { - //this tests numeric scalars, and grids - fileName = "trajectoryAoml_tsg.nc"; - url = tdsUrl + "trajectory/aoml_tsg.nc"; - allDapToNc(url, dir + fileName); - results = NcHelper.dds(dir + fileName); - String2.log(results); - expected = -"netcdf c:/data/nodcTemplates/trajectoryAoml_tsg.nc {\n" + -" dimensions:\n" + -" trajectory = 1;\n" + -" obs = 2880;\n" + -" variables:\n" + -" int trajectory(trajectory=1);\n" + -" int time(trajectory=1, obs=2880);\n" + -" double lat(trajectory=1, obs=2880);\n" + -" double lon(trajectory=1, obs=2880);\n" + -" double intp(trajectory=1, obs=2880);\n" + -" double sal(trajectory=1, obs=2880);\n" + -" double cond(trajectory=1, obs=2880);\n" + -" double ext(trajectory=1, obs=2880);\n" + -" double sst(trajectory=1, obs=2880);\n" + -" byte plt(trajectory=1);\n" + -" byte tsg(trajectory=1);\n" + -" byte tmsr(trajectory=1);\n" + -" byte sstr(trajectory=1);\n" + -" byte flag_a(trajectory=1, obs=2880);\n" + -" byte flag_b(trajectory=1, obs=2880);\n" + -" byte flag_c(trajectory=1, obs=2880);\n" + -" byte flag_d(trajectory=1, obs=2880);\n" + -" byte flag_e(trajectory=1, obs=2880);\n" + -" byte flag_f(trajectory=1, obs=2880);\n" + -" byte flag_g(trajectory=1, obs=2880);\n" + -" byte flag_h(trajectory=1, obs=2880);\n" + -" byte flag_i(trajectory=1, obs=2880);\n" + -" byte flag_j(trajectory=1, obs=2880);\n" + -" byte flag_k(trajectory=1, obs=2880);\n" + -" byte flag_l(trajectory=1, obs=2880);\n" + -" byte crs(trajectory=1);\n" + -" // global attributes:\n" + -"}\n"; - Test.ensureEqual(results, expected, ""); - } - - - if (whichTests == -1 || whichTests == 3) { - //this tests numeric scalars, and byte/numeric arrays - fileName = "trajectoryJason2_satelliteAltimeter.nc"; - url = tdsUrl + "trajectory/jason2_satelliteAltimeter.nc"; - allDapToNc(url, dir + fileName); - results = NcHelper.dds(dir + fileName); - String2.log(results); - expected = -"netcdf c:/data/nodcTemplates/trajectoryJason2_satelliteAltimeter.nc {\n" + -" dimensions:\n" + -" trajectory = 1;\n" + -" obs = 3;\n" + -" meas_ind = 20;\n" + -" variables:\n" + -" double time(trajectory=1, obs=3);\n" + -" byte meas_ind(trajectory=1, meas_ind=20);\n" + -" int lat(trajectory=1, obs=3);\n" + -" int lon(trajectory=1, obs=3);\n" + -" byte surface_type(trajectory=1, obs=3);\n" + -" byte orb_state_flag_rest(trajectory=1, obs=3);\n" + -" byte ecmwf_meteo_map_avail(trajectory=1, obs=3);\n" + -" byte interp_flag_meteo(trajectory=1, obs=3);\n" + -" int alt(trajectory=1, obs=3);\n" + -" byte range_numval_ku(trajectory=1, obs=3);\n" + -" short model_wet_tropo_corr(trajectory=1, obs=3);\n" + -" byte atmos_corr_sig0_ku(trajectory=1, obs=3);\n" + -" short tb_187(trajectory=1, obs=3);\n" + -" short rad_water_vapor(trajectory=1, obs=3);\n" + -" short ssha(trajectory=1, obs=3);\n" + -" // global attributes:\n" + -"}\n"; - Test.ensureEqual(results, expected, ""); - } - -/* if (whichTests == -1 || whichTests == 4) { -//JDAP fails to read/parse the .dds: -//Exception in thread "main" com.cohort.util.SimpleException: Error while getting DDS from https://data.nodc.noaa.gov/thredds/dodsC/testdata/ne -//tCDFTemplateExamples/profile/wodObservedLevels.nc.dds . -// -//Parse Error on token: String -//In the dataset descriptor object: -//Expected a variable declaration (e.g., Int32 i;). -// at gov.noaa.pfel.coastwatch.griddata.OpendapHelper.allDapToNc(OpendapHelper.java:1239) -// at gov.noaa.pfel.coastwatch.griddata.OpendapHelper.testAllDapToNc(OpendapHelper.java:1716) -// at gov.noaa.pfel.coastwatch.TestAll.main(TestAll.java:741) - //this tests numeric scalars, and numeric and string arrays - fileName = "profileWodObservedLevels.nc"; - url = tdsUrl + "profile/wodObservedLevels.nc"; - allDapToNc(url, dir + fileName); - results = NcHelper.ncdump(dir + fileName, "-h"); - String2.log(results); - //expected = "zztop"; - //Test.ensureEqual(results, expected, ""); - } -*/ - if (whichTests == -1 || whichTests == 5) { - //this tests numeric scalars, and numeric arrays - fileName = "timeSeriesProfileUsgs_internal_wave_timeSeries.nc"; - url = tdsUrl + "timeSeriesProfile/usgs_internal_wave_timeSeries.nc"; - allDapToNc(url, dir + fileName); - results = NcHelper.dds(dir + fileName); - String2.log(results); - expected = -"netcdf c:/data/nodcTemplates/timeSeriesProfileUsgs_internal_wave_timeSeries.nc {\n" + -" dimensions:\n" + -" station = 1;\n" + -" time = 38990;\n" + -" z = 5;\n" + -" variables:\n" + -" int station_id(station=1);\n" + -" double time(time=38990);\n" + -" double z(z=5);\n" + -" double lon(station=1);\n" + -" double lat(station=1);\n" + -" double T_20(station=1, time=38990, z=5);\n" + -" double C_51(station=1, time=38990, z=5);\n" + -" double S_40(station=1, time=38990, z=5);\n" + -" double STH_71(station=1, time=38990, z=5);\n" + -" int instrument_1(station=1, z=5);\n" + -" int instrument_2(station=1);\n" + -" int platform;\n" + -" int crs;\n" + -" // global attributes:\n" + -"}\n"; - Test.ensureEqual(results, expected, ""); - } - -//currently no trajectoryProfile example - -//currently no swath example - - - } - /** * Get data from a common type of Opendap grid request and save in .nc file. *

Currently, this won't work with variables in a sequence. @@ -2144,875 +1816,4 @@ public static void dapToNc(String dapUrl, String varNames[], String projection, throw t; } } - - /** This tests getting attibutes, notably the DODS_strlen attribute. */ - public static void testGetAttributes() throws Throwable { - String url = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; - String2.log("\n* OpendapHelper.testGetAttributes\n" + url); - DConnect dConnect = new DConnect(url, true, 1, 1); - DAS das = dConnect.getDAS(DEFAULT_TIMEOUT); - Attributes atts = new Attributes(); - getAttributes(das, "flag", atts); - - String results = atts.toString(); - String expected = //the DODS_ attributes are from an attribute that is a container. -" A=Units added\n" + -" B=Data out of range\n" + -" C=Non-sequential time\n" + -" D=Failed T>=Tw>=Td\n" + -" DODS_dimName=f_string\n" + -" DODS_strlen=13i\n" + -" E=True wind error\n" + -" F=Velocity unrealistic\n" + -" G=Value > 4 s. d. from climatology\n" + -" H=Discontinuity\n" + -" I=Interesting feature\n" + -" J=Erroneous\n" + -" K=Suspect - visual\n" + -" L=Ocean platform over land\n" + -" long_name=quality control flags\n" + -" M=Instrument malfunction\n" + -" N=In Port\n" + -" O=Multiple original units\n" + -" P=Movement uncertain\n" + -" Q=Pre-flagged as suspect\n" + -" R=Interpolated data\n" + -" S=Spike - visual\n" + -" T=Time duplicate\n" + -" U=Suspect - statistial\n" + -" V=Spike - statistical\n" + -" X=Step - statistical\n" + -" Y=Suspect between X-flags\n" + -" Z=Good data\n"; - Test.ensureEqual(results, expected, "results=" + results); - } - - - /** This tests dapToNc DArray. */ - public static void testDapToNcDArray() throws Throwable { - String2.log("\n\n*** OpendapHelper.testDapToNcDArray()"); - String fileName, expected, results; - String today = Calendar2.getCurrentISODateTimeStringLocalTZ().substring(0, 10); - - fileName = SSR.getTempDirectory() + "testDapToNcDArray.nc"; - String dArrayUrl = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; - dapToNc(dArrayUrl, - //note that request for zztop is ignored (because not found) - new String[] {"zztop", "time", "lat", "lon", "PL_HD", "flag"}, null, //projection - fileName, false); //jplMode - results = NcHelper.ncdump(fileName, ""); //printData - expected = -"netcdf testDapToNcDArray.nc {\n" + -" dimensions:\n" + -" time = 144;\n" + -" flag_strlen = 13;\n" + -" variables:\n" + -" int time(time=144);\n" + -" :actual_range = 16870896, 16871039; // int\n" + -" :data_interval = 60; // int\n" + -" :long_name = \"time\";\n" + -" :observation_type = \"calculated\";\n" + -" :original_units = \"hhmmss UTC\";\n" + -" :qcindex = 1; // int\n" + -" :units = \"minutes since 1-1-1980 00:00 UTC\";\n" + -"\n" + -" float lat(time=144);\n" + -" :actual_range = 44.6f, 44.75f; // float\n" + -" :average_center = \"time at end of period\";\n" + -" :average_length = 60S; // short\n" + -" :average_method = \"average\";\n" + -" :data_precision = -9999.0f; // float\n" + -" :instrument = \"unknown\";\n" + -" :long_name = \"latitude\";\n" + -" :observation_type = \"measured\";\n" + -" :original_units = \"degrees (+N)\";\n" + -" :qcindex = 2; // int\n" + -" :sampling_rate = 1.0f; // float\n" + -" :units = \"degrees (+N)\";\n" + -"\n" + -" float lon(time=144);\n" + -" :actual_range = 235.82f, 235.95f; // float\n" + -" :average_center = \"time at end of period\";\n" + -" :average_length = 60S; // short\n" + -" :average_method = \"average\";\n" + -" :data_precision = -9999.0f; // float\n" + -" :instrument = \"unknown\";\n" + -" :long_name = \"longitude\";\n" + -" :observation_type = \"measured\";\n" + -" :original_units = \"degrees (-W/+E)\";\n" + -" :qcindex = 3; // int\n" + -" :sampling_rate = 1.0f; // float\n" + -" :units = \"degrees (+E)\";\n" + -"\n" + -" float PL_HD(time=144);\n" + -" :actual_range = 37.89f, 355.17f; // float\n" + -" :average_center = \"time at end of period\";\n" + -" :average_length = 60S; // short\n" + -" :average_method = \"average\";\n" + -" :data_precision = -9999.0f; // float\n" + -" :instrument = \"unknown\";\n" + -" :long_name = \"platform heading\";\n" + -" :missing_value = -9999.0f; // float\n" + -" :observation_type = \"calculated\";\n" + -" :original_units = \"degrees (clockwise towards true north)\";\n" + -" :qcindex = 4; // int\n" + -" :sampling_rate = 1.0f; // float\n" + -" :special_value = -8888.0f; // float\n" + -" :units = \"degrees (clockwise towards true north)\";\n" + -"\n" + -" char flag(time=144, flag_strlen=13);\n" + -" :A = \"Units added\";\n" + -" :B = \"Data out of range\";\n" + -" :C = \"Non-sequential time\";\n" + -" :D = \"Failed T>=Tw>=Td\";\n" + -" :DODS_dimName = \"f_string\";\n" + -" :DODS_strlen = 13; // int\n" + -" :E = \"True wind error\";\n" + -" :F = \"Velocity unrealistic\";\n" + -" :G = \"Value > 4 s. d. from climatology\";\n" + -" :H = \"Discontinuity\";\n" + -" :I = \"Interesting feature\";\n" + -" :J = \"Erroneous\";\n" + -" :K = \"Suspect - visual\";\n" + -" :L = \"Ocean platform over land\";\n" + -" :long_name = \"quality control flags\";\n" + -" :M = \"Instrument malfunction\";\n" + -" :N = \"In Port\";\n" + -" :O = \"Multiple original units\";\n" + -" :P = \"Movement uncertain\";\n" + -" :Q = \"Pre-flagged as suspect\";\n" + -" :R = \"Interpolated data\";\n" + -" :S = \"Spike - visual\";\n" + -" :T = \"Time duplicate\";\n" + -" :U = \"Suspect - statistial\";\n" + -" :V = \"Spike - statistical\";\n" + -" :X = \"Step - statistical\";\n" + -" :Y = \"Suspect between X-flags\";\n" + -" :Z = \"Good data\";\n" + -"\n" + -" // global attributes:\n" + -" :contact_email = \"samos@coaps.fsu.edu\";\n" + -" :contact_info = \"Center for Ocean-Atmospheric Prediction Studies, The Florida State University, Tallahassee, FL, 32306-2840, USA\";\n" + -" :Cruise_id = \"Cruise_id undefined for now\";\n" + -" :Data_modification_date = \"02/07/2012 10:03:37 EST\";\n" + -" :data_provider = \"Timothy Salisbury\";\n" + -" :elev = 0S; // short\n" + -" :end_date_time = \"2012/01/28 -- 23:59 UTC\";\n" + -" :EXPOCODE = \"EXPOCODE undefined for now\";\n" + -" :facility = \"NOAA\";\n" + -" :fsu_version = \"300\";\n" + -" :ID = \"WTEP\";\n" + -" :IMO = \"009270335\";\n" + -" :Metadata_modification_date = \"02/07/2012 10:03:37 EST\";\n" + -" :platform = \"SCS\";\n" + -" :platform_version = \"4.0\";\n" + -" :receipt_order = \"01\";\n" + -" :site = \"OSCAR DYSON\";\n" + -" :start_date_time = \"2012/01/28 -- 21:36 UTC\";\n" + -" :title = \"OSCAR DYSON Meteorological Data\";\n" + -"\n" + -" data:\n" + -" time = \n" + -" {16870896, 16870897, 16870898, 16870899, 16870900, 16870901, 16870902, 16870903, 16870904, 16870905, 16870906, 16870907, 16870908, 16870909, 16870910, 16870911, 16870912, 16870913, 16870914, 16870915, 16870916, 16870917, 16870918, 16870919, 16870920, 16870921, 16870922, 16870923, 16870924, 16870925, 16870926, 16870927, 16870928, 16870929, 16870930, 16870931, 16870932, 16870933, 16870934, 16870935, 16870936, 16870937, 16870938, 16870939, 16870940, 16870941, 16870942, 16870943, 16870944, 16870945, 16870946, 16870947, 16870948, 16870949, 16870950, 16870951, 16870952, 16870953, 16870954, 16870955, 16870956, 16870957, 16870958, 16870959, 16870960, 16870961, 16870962, 16870963, 16870964, 16870965, 16870966, 16870967, 16870968, 16870969, 16870970, 16870971, 16870972, 16870973, 16870974, 16870975, 16870976, 16870977, 16870978, 16870979, 16870980, 16870981, 16870982, 16870983, 16870984, 16870985, 16870986, 16870987, 16870988, 16870989, 16870990, 16870991, 16870992, 16870993, 16870994, 16870995, 16870996, 16870997, 16870998, 16870999, 16871000, 16871001, 16871002, 16871003, 16871004, 16871005, 16871006, 16871007, 16871008, 16871009, 16871010, 16871011, 16871012, 16871013, 16871014, 16871015, 16871016, 16871017, 16871018, 16871019, 16871020, 16871021, 16871022, 16871023, 16871024, 16871025, 16871026, 16871027, 16871028, 16871029, 16871030, 16871031, 16871032, 16871033, 16871034, 16871035, 16871036, 16871037, 16871038, 16871039}\n" + -" lat = \n" + -" {44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.62, 44.62, 44.62, 44.62, 44.62, 44.62, 44.62, 44.61, 44.61, 44.61, 44.61, 44.61, 44.61, 44.61, 44.61, 44.6, 44.6, 44.6, 44.6, 44.6, 44.6, 44.61, 44.61, 44.61, 44.61, 44.62, 44.62, 44.62, 44.62, 44.63, 44.63, 44.63, 44.64, 44.64, 44.64, 44.65, 44.65, 44.65, 44.66, 44.66, 44.66, 44.67, 44.67, 44.67, 44.68, 44.68, 44.68, 44.69, 44.69, 44.69, 44.7, 44.7, 44.7, 44.71, 44.71, 44.71, 44.72, 44.72, 44.72, 44.73, 44.73, 44.73, 44.73, 44.74, 44.74, 44.74, 44.75}\n" + -" lon = \n" + -" {235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.94, 235.94, 235.94, 235.94, 235.94, 235.94, 235.93, 235.93, 235.93, 235.92, 235.92, 235.92, 235.91, 235.91, 235.91, 235.9, 235.9, 235.9, 235.89, 235.89, 235.88, 235.88, 235.88, 235.88, 235.88, 235.88, 235.87, 235.87, 235.87, 235.87, 235.87, 235.87, 235.87, 235.86, 235.86, 235.86, 235.86, 235.86, 235.86, 235.86, 235.85, 235.85, 235.85, 235.85, 235.85, 235.85, 235.85, 235.85, 235.85, 235.84, 235.84, 235.84, 235.84, 235.84, 235.84, 235.83, 235.83, 235.83, 235.83, 235.83, 235.82, 235.82, 235.82, 235.82, 235.82, 235.82, 235.82}\n" + -" PL_HD = \n" + -" {75.53, 75.57, 75.97, 76.0, 75.81, 75.58, 75.99, 75.98, 75.77, 75.61, 75.72, 75.75, 75.93, 75.96, 76.01, 75.64, 75.65, 75.94, 75.93, 76.12, 76.65, 76.42, 76.25, 75.81, 76.5, 76.09, 76.35, 76.0, 76.16, 76.36, 76.43, 75.99, 75.93, 76.41, 75.85, 76.07, 76.15, 76.33, 76.7, 76.37, 76.58, 76.89, 77.14, 76.81, 74.73, 75.24, 74.52, 81.04, 80.64, 73.21, 63.34, 37.89, 347.02, 309.93, 290.99, 285.0, 279.38, 276.45, 270.26, 266.33, 266.49, 266.08, 263.59, 261.41, 259.05, 259.82, 260.35, 262.78, 258.73, 249.71, 246.52, 245.78, 246.16, 245.88, 243.52, 231.62, 223.09, 221.08, 221.01, 221.08, 220.81, 223.64, 234.12, 239.55, 241.08, 242.09, 242.04, 242.33, 242.06, 242.22, 242.11, 242.3, 242.07, 247.35, 285.6, 287.02, 287.96, 288.37, 321.32, 344.82, 346.91, 344.78, 347.95, 344.75, 344.66, 344.78, 344.7, 344.76, 343.89, 336.73, 334.01, 340.23, 344.76, 348.25, 348.74, 348.63, 351.97, 344.55, 343.77, 343.71, 347.04, 349.06, 349.45, 349.79, 349.66, 349.7, 349.74, 344.2, 343.22, 341.79, 339.11, 334.12, 334.47, 334.62, 334.7, 334.66, 327.06, 335.74, 348.25, 351.05, 355.17, 343.66, 346.85, 347.28}\n" + -" flag = \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZEZZSZZZZ\", \"ZZZZZEZZSZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\"\n" + -"}\n"; - Test.ensureEqual(results, expected, "results=" + results); - File2.delete(fileName); - - //test subset - try { - String2.log("\n* testDapToNcDArray Subset"); - fileName = SSR.getTempDirectory() + "testDapToNcDArraySubset.nc"; - String dArraySubsetUrl = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; - dapToNc(dArraySubsetUrl, - new String[] {"zztop", "time", "lat", "lon", "PL_HD", "flag"}, "[0:10:99]", //projection - fileName, false); //jplMode - results = NcHelper.ncdump(fileName, ""); //printData - expected = -"netcdf testDapToNcDArraySubset.nc {\n" + -" dimensions:\n" + -" time = 10;\n" + -" variables:\n" + -" int time(time=10);\n" + -" :actual_range = 16870896, 16871039; // int\n" + -" :data_interval = 60; // int\n" + -" :long_name = \"time\";\n" + -" :observation_type = \"calculated\";\n" + -" :original_units = \"hhmmss UTC\";\n" + -" :qcindex = 1; // int\n" + -" :units = \"minutes since 1-1-1980 00:00 UTC\";\n" + -" float lat(time=10);\n" + -" :actual_range = 44.6f, 44.75f; // float\n" + -" :average_center = \"time at end of period\";\n" + -" :average_length = 60S; // short\n" + -" :average_method = \"average\";\n" + -" :data_precision = -9999.0f; // float\n" + -" :instrument = \"unknown\";\n" + -" :long_name = \"latitude\";\n" + -" :observation_type = \"measured\";\n" + -" :original_units = \"degrees (+N)\";\n" + -" :qcindex = 2; // int\n" + -" :sampling_rate = 1.0f; // float\n" + -" :units = \"degrees (+N)\";\n" + -" float lon(time=10);\n" + -" :actual_range = 235.82f, 235.95f; // float\n" + -" :average_center = \"time at end of period\";\n" + -" :average_length = 60S; // short\n" + -" :average_method = \"average\";\n" + -" :data_precision = -9999.0f; // float\n" + -" :instrument = \"unknown\";\n" + -" :long_name = \"longitude\";\n" + -" :observation_type = \"measured\";\n" + -" :original_units = \"degrees (-W/+E)\";\n" + -" :qcindex = 3; // int\n" + -" :sampling_rate = 1.0f; // float\n" + -" :units = \"degrees (+E)\";\n" + -" float PL_HD(time=10);\n" + -" :actual_range = 37.89f, 355.17f; // float\n" + -" :average_center = \"time at end of period\";\n" + -" :average_length = 60S; // short\n" + -" :average_method = \"average\";\n" + -" :data_precision = -9999.0f; // float\n" + -" :instrument = \"unknown\";\n" + -" :long_name = \"platform heading\";\n" + -" :missing_value = -9999.0f; // float\n" + -" :observation_type = \"calculated\";\n" + -" :original_units = \"degrees (clockwise towards true north)\";\n" + -" :qcindex = 4; // int\n" + -" :sampling_rate = 1.0f; // float\n" + -" :special_value = -8888.0f; // float\n" + -" :units = \"degrees (clockwise towards true north)\";\n" + -"\n" + -" :contact_email = \"samos@coaps.fsu.edu\";\n" + -" :contact_info = \"Center for Ocean-Atmospheric Prediction Studies, The Florida State University, Tallahassee, FL, 32306-2840, USA\";\n" + -" :Cruise_id = \"Cruise_id undefined for now\";\n" + -" :Data_modification_date = \"02/07/2012 10:03:37 EST\";\n" + -" :data_provider = \"Timothy Salisbury\";\n" + -" :elev = 0S; // short\n" + -" :end_date_time = \"2012/01/28 -- 23:59 UTC\";\n" + -" :EXPOCODE = \"EXPOCODE undefined for now\";\n" + -" :facility = \"NOAA\";\n" + -" :fsu_version = \"300\";\n" + -" :ID = \"WTEP\";\n" + -" :IMO = \"009270335\";\n" + -" :Metadata_modification_date = \"02/07/2012 10:03:37 EST\";\n" + -" :platform = \"SCS\";\n" + -" :platform_version = \"4.0\";\n" + -" :receipt_order = \"01\";\n" + -" :site = \"OSCAR DYSON\";\n" + -" :start_date_time = \"2012/01/28 -- 21:36 UTC\";\n" + -" :title = \"OSCAR DYSON Meteorological Data\";\n" + -" data:\n" + -"time =\n" + -" {16870896, 16870906, 16870916, 16870926, 16870936, 16870946, 16870956, 16870966, 16870976, 16870986}\n" + -"lat =\n" + -" {44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.62, 44.61}\n" + -"lon =\n" + -" {235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.94, 235.91}\n" + -"PL_HD =\n" + -" {75.53, 75.72, 76.65, 76.43, 76.58, 63.34, 266.49, 246.52, 220.81, 242.11}\n" + -"}\n"; -/* from -https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc.ascii?time[0:10:99],lat[0:10:99],lon[0:10:99],PL_HD[0:10:99] -time[10] 16870896, 16870906, 16870916, 16870926, 16870936, 16870946, 16870956, 16870966, 16870976, 16870986 -lat[10] 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.62, 44.61 -lon[10] 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.94, 235.91 -PL_HD[10] 75.53, 75.72, 76.65, 76.43, 76.58, 63.34, 266.49, 246.52, 220.81, 242.11 -*/ - Test.ensureEqual(results, expected, "results=" + results); - File2.delete(fileName); - if (true) throw new RuntimeException("shouldn't get here"); - } catch (OutOfMemoryError oome) { - Test.knownProblem( - "THREDDS OutOfMemoryError. I reported it to John Caron.", - "2012-03-02 A TDS problem. I reported it to John Caron:\n" + - MustBe.throwableToString(oome)); -//OpendapHelper.getPrimitiveArrays ?flag[0:10:99] -//Exception in thread "main" java.lang.OutOfMemoryError: Java heap space -// at dods.dap.BaseTypePrimitiveVector.setLength(BaseTypePrimitiveVector.java:69) -// at dods.dap.DVector.deserialize(DVector.java:221) -// at dods.dap.DataDDS.readData(DataDDS.java:75) -// at dods.dap.DConnect.getDataFromUrl(DConnect.java:523) -// at dods.dap.DConnect.getData(DConnect.java:450) -// at dods.dap.DConnect.getData(DConnect.java:633) -// at gov.noaa.pfel.coastwatch.griddata.OpendapHelper.getPrimitiveArrays(OpendapHelper.java:458) -// at gov.noaa.pfel.coastwatch.griddata.OpendapHelper.dapToNc(OpendapHelper.java:1398) -// at gov.noaa.pfel.coastwatch.griddata.OpendapHelper.testDapToNcDArray(OpendapHelper.java:1628) -// at gov.noaa.pfel.coastwatch.TestAll.main(TestAll.java:723) - } catch (Throwable t) { - Test.knownProblem( - "\nOutOfMememoryError from TDS bug was expected (but 404 Not Found/ 'Connection cannont be read' is also common)." + - "\n(server timed out 2013-10-24)", t); - } - - - //test DArray error caused by history having different dimensions - String2.log("\n*** test DArray error cause by history having different dimensions"); - try { - dapToNc(dArrayUrl, - new String[] {"zztop", "time", "lat", "lon", "PL_HD", "history"}, null, //projection - fileName, false); //jplMode - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - results = t.toString(); -expected = -"java.lang.RuntimeException: ERROR in OpendapHelper.dapToNc\n" + -" url=https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc\n" + -" varNames=zztop,time,lat,lon,PL_HD,history projection=null\n" + -" file=C:/programs/_tomcat/webapps/cwexperimental/WEB-INF/temp/testDapToNcDArraySubset.nc\n" + -"var=history has different dimensions than previous vars."; - if (results.indexOf("java.net.ConnectException: Connection timed out: connect") >= 0) - String2.pressEnterToContinue(MustBe.throwableToString(t) + - "\nurl=" + dArrayUrl + - "\n(The server timed out 2013-10-24.)"); - else if (results.startsWith("dods.dap.DODSException: Connection cannot be opened")) - String2.pressEnterToContinue(MustBe.throwableToString(t) + - "\nurl=" + dArrayUrl + - "\n(The connection can't be opened 2019-11-25.)"); - else Test.ensureEqual(results, expected, "results=" + results); - } - - String2.log("\n*** OpendapHelper.testDapToNcDArray finished."); - } - - - /** This tests dapToNc DGrid. */ - public static void testDapToNcDGrid() throws Throwable { - String2.log("\n\n*** OpendapHelper.testDapToNcDGrid"); - String fileName, expected, results; - String today = Calendar2.getCurrentISODateTimeStringZulu().substring(0, 10); - - fileName = SSR.getTempDirectory() + "testDapToNcDGrid.nc"; - String dGridUrl = "https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday"; - dapToNc(dGridUrl, - //note that request for zztop is ignored (because not found) - new String[] {"zztop", "x_wind", "y_wind"}, "[5][0][0:200:1200][0:200:2880]", //projection - fileName, false); //jplMode - results = NcHelper.ncdump(fileName, ""); //printData - expected = -"netcdf testDapToNcDGrid.nc {\n" + -" dimensions:\n" + -" time = 1;\n" + -" altitude = 1;\n" + -" latitude = 7;\n" + -" longitude = 15;\n" + -" variables:\n" + -" double time(time=1);\n" + -" :_CoordinateAxisType = \"Time\";\n" + -" :actual_range = 9.348048E8, 1.2556944E9; // double\n" + -" :axis = \"T\";\n" + -" :fraction_digits = 0; // int\n" + -" :ioos_category = \"Time\";\n" + -" :long_name = \"Centered Time\";\n" + -" :standard_name = \"time\";\n" + -" :time_origin = \"01-JAN-1970 00:00:00\";\n" + -" :units = \"seconds since 1970-01-01T00:00:00Z\";\n" + -"\n" + -" double altitude(altitude=1);\n" + -" :_CoordinateAxisType = \"Height\";\n" + -" :_CoordinateZisPositive = \"up\";\n" + -" :actual_range = 10.0, 10.0; // double\n" + -" :axis = \"Z\";\n" + -" :fraction_digits = 0; // int\n" + -" :ioos_category = \"Location\";\n" + -" :long_name = \"Altitude\";\n" + -" :positive = \"up\";\n" + -" :standard_name = \"altitude\";\n" + -" :units = \"m\";\n" + -"\n" + -" double latitude(latitude=7);\n" + -" :_CoordinateAxisType = \"Lat\";\n" + -" :actual_range = -75.0, 75.0; // double\n" + -" :axis = \"Y\";\n" + -" :coordsys = \"geographic\";\n" + -" :fraction_digits = 2; // int\n" + -" :ioos_category = \"Location\";\n" + -" :long_name = \"Latitude\";\n" + -" :point_spacing = \"even\";\n" + -" :standard_name = \"latitude\";\n" + -" :units = \"degrees_north\";\n" + -"\n" + -" double longitude(longitude=15);\n" + -" :_CoordinateAxisType = \"Lon\";\n" + -" :actual_range = 0.0, 360.0; // double\n" + -" :axis = \"X\";\n" + -" :coordsys = \"geographic\";\n" + -" :fraction_digits = 2; // int\n" + -" :ioos_category = \"Location\";\n" + -" :long_name = \"Longitude\";\n" + -" :point_spacing = \"even\";\n" + -" :standard_name = \"longitude\";\n" + -" :units = \"degrees_east\";\n" + -"\n" + -" float x_wind(time=1, altitude=1, latitude=7, longitude=15);\n" + -" :_FillValue = -9999999.0f; // float\n" + -" :colorBarMaximum = 15.0; // double\n" + -" :colorBarMinimum = -15.0; // double\n" + -" :coordsys = \"geographic\";\n" + -" :fraction_digits = 1; // int\n" + -" :ioos_category = \"Wind\";\n" + -" :long_name = \"Zonal Wind\";\n" + -" :missing_value = -9999999.0f; // float\n" + -" :standard_name = \"x_wind\";\n" + -" :units = \"m s-1\";\n" + -"\n" + -" float y_wind(time=1, altitude=1, latitude=7, longitude=15);\n" + -" :_FillValue = -9999999.0f; // float\n" + -" :colorBarMaximum = 15.0; // double\n" + -" :colorBarMinimum = -15.0; // double\n" + -" :coordsys = \"geographic\";\n" + -" :fraction_digits = 1; // int\n" + -" :ioos_category = \"Wind\";\n" + -" :long_name = \"Meridional Wind\";\n" + -" :missing_value = -9999999.0f; // float\n" + -" :standard_name = \"y_wind\";\n" + -" :units = \"m s-1\";\n" + -"\n" + -" // global attributes:\n" + -" :acknowledgement = \"NOAA NESDIS COASTWATCH, NOAA SWFSC ERD\";\n" + -" :cdm_data_type = \"Grid\";\n" + -" :composite = \"true\";\n" + -" :contributor_name = \"Remote Sensing Systems, Inc.\";\n" + -" :contributor_role = \"Source of level 2 data.\";\n" + -" :Conventions = \"COARDS, CF-1.6, ACDD-1.3\";\n" + -" :creator_email = \"erd.data@noaa.gov\";\n" + -" :creator_name = \"NOAA NMFS SWFSC ERD\";\n" + -" :creator_type = \"institution\";\n" + -" :creator_url = \"https://www.pfeg.noaa.gov\";\n" + -" :date_created = \"2010-07-02\";\n" + -" :date_issued = \"2010-07-02\";\n" + -" :defaultGraphQuery = \"&.draw=vectors\";\n" + -" :Easternmost_Easting = 360.0; // double\n" + -" :geospatial_lat_max = 75.0; // double\n" + -" :geospatial_lat_min = -75.0; // double\n" + -" :geospatial_lat_resolution = 0.125; // double\n" + -" :geospatial_lat_units = \"degrees_north\";\n" + -" :geospatial_lon_max = 360.0; // double\n" + -" :geospatial_lon_min = 0.0; // double\n" + -" :geospatial_lon_resolution = 0.125; // double\n" + -" :geospatial_lon_units = \"degrees_east\";\n" + -" :geospatial_vertical_max = 10.0; // double\n" + -" :geospatial_vertical_min = 10.0; // double\n" + -" :geospatial_vertical_positive = \"up\";\n" + -" :geospatial_vertical_units = \"m\";\n" + -" :history = \"Remote Sensing Systems, Inc.\n" + -"2010-07-02T15:36:22Z NOAA CoastWatch (West Coast Node) and NOAA SFSC ERD\n" + -today + "T"; // + time " https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/QS/ux10/mday\n" + -//today + " https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday.das\";\n" + -String expected2 = -" :infoUrl = \"https://coastwatch.pfeg.noaa.gov/infog/QS_ux10_las.html\";\n" + -" :institution = \"NOAA NMFS SWFSC ERD\";\n" + -" :keywords = \"altitude, atmosphere, atmospheric, coast, coastwatch, data, degrees, Earth Science > Atmosphere > Atmospheric Winds > Surface Winds, Earth Science > Oceans > Ocean Winds > Surface Winds, global, noaa, node, ocean, oceans, QSux10, quality, quikscat, science, science quality, seawinds, surface, time, wcn, west, wind, winds, x_wind, zonal\";\n" + -" :keywords_vocabulary = \"GCMD Science Keywords\";\n" + -" :license = \"The data may be used and redistributed for free but is not intended\n" + -"for legal use, since it may contain inaccuracies. Neither the data\n" + -"Contributor, ERD, NOAA, nor the United States Government, nor any\n" + -"of their employees or contractors, makes any warranty, express or\n" + -"implied, including warranties of merchantability and fitness for a\n" + -"particular purpose, or assumes any legal liability for the accuracy,\n" + -"completeness, or usefulness, of this information.\";\n" + -" :naming_authority = \"gov.noaa.pfeg.coastwatch\";\n" + -" :Northernmost_Northing = 75.0; // double\n" + -" :origin = \"Remote Sensing Systems, Inc.\";\n" + -" :processing_level = \"3\";\n" + -" :project = \"CoastWatch (https://coastwatch.noaa.gov/)\";\n" + -" :projection = \"geographic\";\n" + -" :projection_type = \"mapped\";\n" + -" :publisher_email = \"erd.data@noaa.gov\";\n" + -" :publisher_name = \"NOAA NMFS SWFSC ERD\";\n" + -" :publisher_type = \"institution\";\n" + -" :publisher_url = \"https://www.pfeg.noaa.gov\";\n" + -" :references = \"RSS Inc. Winds: http://www.remss.com/ .\";\n" + -" :satellite = \"QuikSCAT\";\n" + -" :sensor = \"SeaWinds\";\n" + -" :source = \"satellite observation: QuikSCAT, SeaWinds\";\n" + -" :sourceUrl = \"(local files)\";\n" + -" :Southernmost_Northing = -75.0; // double\n" + -" :standard_name_vocabulary = \"CF Standard Name Table v70\";\n" + -" :summary = \"Remote Sensing Inc. distributes science quality wind velocity data from the SeaWinds instrument onboard NASA's QuikSCAT satellite. SeaWinds is a microwave scatterometer designed to measure surface winds over the global ocean. Wind velocity fields are provided in zonal, meridional, and modulus sets. The reference height for all wind velocities is 10 meters. (This is a monthly composite.)\";\n" + -" :time_coverage_end = \"2009-10-16T12:00:00Z\";\n" + -" :time_coverage_start = \"1999-08-16T12:00:00Z\";\n" + -" :title = \"Wind, QuikSCAT SeaWinds, 0.125°, Global, Science Quality, 1999-2009 (Monthly)\";\n" + -" :Westernmost_Easting = 0.0; // double\n" + -"\n" + -" data:\n" + -" time = \n" + -" {9.48024E8}\n" + -" altitude = \n" + -" {10.0}\n" + -" latitude = \n" + -" {-75.0, -50.0, -25.0, 0.0, 25.0, 50.0, 75.0}\n" + -" longitude = \n" + -" {0.0, 25.0, 50.0, 75.0, 100.0, 125.0, 150.0, 175.0, 200.0, 225.0, 250.0, 275.0, 300.0, 325.0, 350.0}\n" + -" x_wind = \n" + -" {\n" + -" {\n" + -" {\n" + -" {-9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 0.76867574, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0},\n" + -" {6.903795, 7.7432585, 8.052648, 7.375461, 8.358787, 7.5664454, 4.537408, 4.349131, 2.4506109, 2.1340106, 6.4230127, 8.5656395, 5.679372, 5.775274, 6.8520603},\n" + -" {-3.513153, -9999999.0, -5.7222853, -4.0249896, -4.6091595, -9999999.0, -9999999.0, -3.9060166, -1.821446, -2.0546885, -2.349195, -4.2188687, -9999999.0, -0.7905332, -3.715024},\n" + -" {0.38850072, -9999999.0, -2.8492346, 0.7843591, -9999999.0, -0.353197, -0.93183184, -5.3337674, -7.8715024, -5.2341905, -2.1567967, 0.46681255, -9999999.0, -3.7223456, -1.3264368},\n" + -" {-9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -4.250928, -1.9779109, -2.3081408, -6.070514, -3.4209945, 2.3732827, -3.4732149, -3.2282434, -3.99131, -9999999.0},\n" + -" {2.3816996, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 1.9863724, 1.746363, 5.305478, 2.3346918, -9999999.0, -9999999.0, 2.0079596, 3.4320266, 1.8692436},\n" + -" {0.83961326, -3.4395192, -3.1952338, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -2.9099085}\n" + -" }\n" + -" }\n" + -" }\n" + -" y_wind = \n" + -" {\n" + -" {\n" + -" {\n" + -" {-9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 3.9745862, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0},\n" + -" {-1.6358501, -2.1310546, -1.672539, -2.8083494, -1.7282568, -2.5679686, -0.032763753, 0.6524638, 0.9784334, -2.4545083, 0.6344165, -0.5887741, -0.6837046, -0.92711323, -1.9981208},\n" + -" {3.7522712, -9999999.0, -0.04178731, 1.6603879, 5.321683, -9999999.0, -9999999.0, 1.5633415, -0.50912154, -2.964269, -0.92438585, 3.959174, -9999999.0, -2.2249718, 0.46982485},\n" + -" {4.8992314, -9999999.0, -4.7178936, -3.2770228, -9999999.0, -2.8111093, -0.9852706, 0.46997508, 0.0683085, 0.46172503, 1.2998049, 3.5235379, -9999999.0, 1.1354263, 4.7139735},\n" + -" {-9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -5.092368, -3.3667018, -0.60028434, -0.7609817, -1.114303, -3.6573937, -0.934499, -0.40036556, -2.5770886, -9999999.0},\n" + -" {0.56877106, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -3.2394278, 0.45922723, -0.8394715, 0.7333555, -9999999.0, -9999999.0, -2.3936603, 3.725975, 0.09879057},\n" + -" {-6.128998, 2.379096, 7.463917, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -11.026609}\n" + -" }\n" + -" }\n" + -" }\n" + -"}\n"; -/*From .asc request: -https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday.asc?x_wind[5][0][0:200:1200][0:200:2880],y_wind[5][0][0:200:1200][0:200:2880] -x_wind.x_wind[1][1][7][15] -[0][0][0], -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 0.76867574, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0 -[0][0][1], 6.903795, 7.7432585, 8.052648, 7.375461, 8.358787, 7.5664454, 4.537408, 4.349131, 2.4506109, 2.1340106, 6.4230127, 8.5656395, 5.679372, 5.775274, 6.8520603 -[0][0][2], -3.513153, -9999999.0, -5.7222853, -4.0249896, -4.6091595, -9999999.0, -9999999.0, -3.9060166, -1.821446, -2.0546885, -2.349195, -4.2188687, -9999999.0, -0.7905332, -3.715024 -[0][0][3], 0.38850072, -9999999.0, -2.8492346, 0.7843591, -9999999.0, -0.353197, -0.93183184, -5.3337674, -7.8715024, -5.2341905, -2.1567967, 0.46681255, -9999999.0, -3.7223456, -1.3264368 -[0][0][4], -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -4.250928, -1.9779109, -2.3081408, -6.070514, -3.4209945, 2.3732827, -3.4732149, -3.2282434, -3.99131, -9999999.0 -[0][0][5], 2.3816996, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 1.9863724, 1.746363, 5.305478, 2.3346918, -9999999.0, -9999999.0, 2.0079596, 3.4320266, 1.8692436 -[0][0][6], 0.83961326, -3.4395192, -3.1952338, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -2.9099085 -y_wind.y_wind[1][1][7][15] -[0][0][0], -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 3.9745862, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0 -[0][0][1], -1.6358501, -2.1310546, -1.672539, -2.8083494, -1.7282568, -2.5679686, -0.032763753, 0.6524638, 0.9784334, -2.4545083, 0.6344165, -0.5887741, -0.6837046, -0.92711323, -1.9981208 -[0][0][2], 3.7522712, -9999999.0, -0.04178731, 1.6603879, 5.321683, -9999999.0, -9999999.0, 1.5633415, -0.50912154, -2.964269, -0.92438585, 3.959174, -9999999.0, -2.2249718, 0.46982485 -[0][0][3], 4.8992314, -9999999.0, -4.7178936, -3.2770228, -9999999.0, -2.8111093, -0.9852706, 0.46997508, 0.0683085, 0.46172503, 1.2998049, 3.5235379, -9999999.0, 1.1354263, 4.7139735 -[0][0][4], -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -5.092368, -3.3667018, -0.60028434, -0.7609817, -1.114303, -3.6573937, -0.934499, -0.40036556, -2.5770886, -9999999.0 -[0][0][5], 0.56877106, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -3.2394278, 0.45922723, -0.8394715, 0.7333555, -9999999.0, -9999999.0, -2.3936603, 3.725975, 0.09879057 -[0][0][6], -6.128998, 2.379096, 7.463917, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -11.026609 -*/ - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=" + results); - int po = results.indexOf(" :infoUrl ="); - Test.ensureEqual(results.substring(po), expected2, "results=" + results); - File2.delete(fileName); - - //test 1D var should be ignored if others are 2+D - String2.log("\n*** test 1D var should be ignored if others are 2+D"); - fileName = SSR.getTempDirectory() + "testDapToNcDGrid1D2D.nc"; - dapToNc(dGridUrl, - new String[] {"zztop", "x_wind", "y_wind", "latitude"}, - "[5][0][0:200:1200][0:200:2880]", //projection - fileName, false); //jplMode - results = NcHelper.ncdump(fileName, "-h"); //printData - expected = -"netcdf testDapToNcDGrid1D2D.nc {\n" + -" dimensions:\n" + -" time = 1;\n" + -" altitude = 1;\n" + -" latitude = 7;\n" + -" longitude = 15;\n" + -" variables:\n" + -" double time(time=1);\n" + -" :_CoordinateAxisType = \"Time\";\n" + -" :actual_range = 9.348048E8, 1.2556944E9; // double\n" + -" :axis = \"T\";\n" + -" :fraction_digits = 0; // int\n" + -" :ioos_category = \"Time\";\n" + -" :long_name = \"Centered Time\";\n" + -" :standard_name = \"time\";\n" + -" :time_origin = \"01-JAN-1970 00:00:00\";\n" + -" :units = \"seconds since 1970-01-01T00:00:00Z\";\n" + -"\n" + -" double altitude(altitude=1);\n" + -" :_CoordinateAxisType = \"Height\";\n" + -" :_CoordinateZisPositive = \"up\";\n" + -" :actual_range = 10.0, 10.0; // double\n" + -" :axis = \"Z\";\n" + -" :fraction_digits = 0; // int\n" + -" :ioos_category = \"Location\";\n" + -" :long_name = \"Altitude\";\n" + -" :positive = \"up\";\n" + -" :standard_name = \"altitude\";\n" + -" :units = \"m\";\n" + -"\n" + -" double latitude(latitude=7);\n" + -" :_CoordinateAxisType = \"Lat\";\n" + -" :actual_range = -75.0, 75.0; // double\n" + -" :axis = \"Y\";\n" + -" :coordsys = \"geographic\";\n" + -" :fraction_digits = 2; // int\n" + -" :ioos_category = \"Location\";\n" + -" :long_name = \"Latitude\";\n" + -" :point_spacing = \"even\";\n" + -" :standard_name = \"latitude\";\n" + -" :units = \"degrees_north\";\n" + -"\n" + -" double longitude(longitude=15);\n" + -" :_CoordinateAxisType = \"Lon\";\n" + -" :actual_range = 0.0, 360.0; // double\n" + -" :axis = \"X\";\n" + -" :coordsys = \"geographic\";\n" + -" :fraction_digits = 2; // int\n" + -" :ioos_category = \"Location\";\n" + -" :long_name = \"Longitude\";\n" + -" :point_spacing = \"even\";\n" + -" :standard_name = \"longitude\";\n" + -" :units = \"degrees_east\";\n" + -"\n" + -" float x_wind(time=1, altitude=1, latitude=7, longitude=15);\n" + -" :_FillValue = -9999999.0f; // float\n" + -" :colorBarMaximum = 15.0; // double\n" + -" :colorBarMinimum = -15.0; // double\n" + -" :coordsys = \"geographic\";\n" + -" :fraction_digits = 1; // int\n" + -" :ioos_category = \"Wind\";\n" + -" :long_name = \"Zonal Wind\";\n" + -" :missing_value = -9999999.0f; // float\n" + -" :standard_name = \"x_wind\";\n" + -" :units = \"m s-1\";\n" + -"\n" + -" float y_wind(time=1, altitude=1, latitude=7, longitude=15);\n" + -" :_FillValue = -9999999.0f; // float\n" + -" :colorBarMaximum = 15.0; // double\n" + -" :colorBarMinimum = -15.0; // double\n" + -" :coordsys = \"geographic\";\n" + -" :fraction_digits = 1; // int\n" + -" :ioos_category = \"Wind\";\n" + -" :long_name = \"Meridional Wind\";\n" + -" :missing_value = -9999999.0f; // float\n" + -" :standard_name = \"y_wind\";\n" + -" :units = \"m s-1\";\n" + -"\n" + -" // global attributes:\n" + -" :acknowledgement = \"NOAA NESDIS COASTWATCH, NOAA SWFSC ERD\";\n" + -" :cdm_data_type = \"Grid\";\n" + -" :composite = \"true\";\n" + -" :contributor_name = \"Remote Sensing Systems, Inc.\";\n" + -" :contributor_role = \"Source of level 2 data.\";\n" + -" :Conventions = \"COARDS, CF-1.6, ACDD-1.3\";\n" + -" :creator_email = \"erd.data@noaa.gov\";\n" + -" :creator_name = \"NOAA NMFS SWFSC ERD\";\n" + -" :creator_type = \"institution\";\n" + -" :creator_url = \"https://www.pfeg.noaa.gov\";\n" + -" :date_created = \"2010-07-02\";\n" + -" :date_issued = \"2010-07-02\";\n" + -" :defaultGraphQuery = \"&.draw=vectors\";\n" + -" :Easternmost_Easting = 360.0; // double\n" + -" :geospatial_lat_max = 75.0; // double\n" + -" :geospatial_lat_min = -75.0; // double\n" + -" :geospatial_lat_resolution = 0.125; // double\n" + -" :geospatial_lat_units = \"degrees_north\";\n" + -" :geospatial_lon_max = 360.0; // double\n" + -" :geospatial_lon_min = 0.0; // double\n" + -" :geospatial_lon_resolution = 0.125; // double\n" + -" :geospatial_lon_units = \"degrees_east\";\n" + -" :geospatial_vertical_max = 10.0; // double\n" + -" :geospatial_vertical_min = 10.0; // double\n" + -" :geospatial_vertical_positive = \"up\";\n" + -" :geospatial_vertical_units = \"m\";\n" + -" :history = \"Remote Sensing Systems, Inc.\n" + -"2010-07-02T15:36:22Z NOAA CoastWatch (West Coast Node) and NOAA SFSC ERD\n" + -today + "T"; //time https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/QS/ux10/mday\n" + -//today + time " https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday.das\";\n" + -expected2 = -" :infoUrl = \"https://coastwatch.pfeg.noaa.gov/infog/QS_ux10_las.html\";\n" + -" :institution = \"NOAA NMFS SWFSC ERD\";\n" + -" :keywords = \"altitude, atmosphere, atmospheric, coast, coastwatch, data, degrees, Earth Science > Atmosphere > Atmospheric Winds > Surface Winds, Earth Science > Oceans > Ocean Winds > Surface Winds, global, noaa, node, ocean, oceans, QSux10, quality, quikscat, science, science quality, seawinds, surface, time, wcn, west, wind, winds, x_wind, zonal\";\n" + -" :keywords_vocabulary = \"GCMD Science Keywords\";\n" + -" :license = \"The data may be used and redistributed for free but is not intended\n" + -"for legal use, since it may contain inaccuracies. Neither the data\n" + -"Contributor, ERD, NOAA, nor the United States Government, nor any\n" + -"of their employees or contractors, makes any warranty, express or\n" + -"implied, including warranties of merchantability and fitness for a\n" + -"particular purpose, or assumes any legal liability for the accuracy,\n" + -"completeness, or usefulness, of this information.\";\n" + -" :naming_authority = \"gov.noaa.pfeg.coastwatch\";\n" + -" :Northernmost_Northing = 75.0; // double\n" + -" :origin = \"Remote Sensing Systems, Inc.\";\n" + -" :processing_level = \"3\";\n" + -" :project = \"CoastWatch (https://coastwatch.noaa.gov/)\";\n" + -" :projection = \"geographic\";\n" + -" :projection_type = \"mapped\";\n" + -" :publisher_email = \"erd.data@noaa.gov\";\n" + -" :publisher_name = \"NOAA NMFS SWFSC ERD\";\n" + -" :publisher_type = \"institution\";\n" + -" :publisher_url = \"https://www.pfeg.noaa.gov\";\n" + -" :references = \"RSS Inc. Winds: http://www.remss.com/ .\";\n" + -" :satellite = \"QuikSCAT\";\n" + -" :sensor = \"SeaWinds\";\n" + -" :source = \"satellite observation: QuikSCAT, SeaWinds\";\n" + -" :sourceUrl = \"(local files)\";\n" + -" :Southernmost_Northing = -75.0; // double\n" + -" :standard_name_vocabulary = \"CF Standard Name Table v70\";\n" + -" :summary = \"Remote Sensing Inc. distributes science quality wind velocity data from the SeaWinds instrument onboard NASA's QuikSCAT satellite. SeaWinds is a microwave scatterometer designed to measure surface winds over the global ocean. Wind velocity fields are provided in zonal, meridional, and modulus sets. The reference height for all wind velocities is 10 meters. (This is a monthly composite.)\";\n" + -" :time_coverage_end = \"2009-10-16T12:00:00Z\";\n" + -" :time_coverage_start = \"1999-08-16T12:00:00Z\";\n" + -" :title = \"Wind, QuikSCAT SeaWinds, 0.125°, Global, Science Quality, 1999-2009 (Monthly)\";\n" + -" :Westernmost_Easting = 0.0; // double\n" + -"}\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=" + results); - po = results.indexOf(" :infoUrl ="); - Test.ensureEqual(results.substring(po), expected2, "results=" + results); - File2.delete(fileName); - - - - /* */ - String2.log("\n*** OpendapHelper.testDapToNcDGrid finished."); - - } - - - - /** This tests parseStartStrideStop and throws exception if trouble.*/ - public static void testParseStartStrideStop() { - - Test.ensureEqual(String2.toCSSVString(parseStartStrideStop(null)), "", ""); - Test.ensureEqual(String2.toCSSVString(parseStartStrideStop("")), "", ""); - Test.ensureEqual(String2.toCSSVString(parseStartStrideStop("[6:7:8]")), - "6, 7, 8", ""); - Test.ensureEqual(String2.toCSSVString(parseStartStrideStop("[5][3:4][6:7:8]")), - "5, 1, 5, 3, 1, 4, 6, 7, 8", ""); - try { - parseStartStrideStop("a"); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"a\": '[' expected at projection position #0", - ""); - } - try { - parseStartStrideStop("["); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[\": End ']' not found.", - ""); - } - try { - parseStartStrideStop("[5"); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[5\": End ']' not found.", - ""); - } - try { - parseStartStrideStop("[5:t]"); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.NumberFormatException: For input string: \"t\"", - ""); - } - try { - parseStartStrideStop("[-1]"); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[-1]\": Negative number=-1 at projection position #1", - ""); - } - try { - parseStartStrideStop("[0:1:2:3]"); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.NumberFormatException: For input string: \"2:3\"", - ""); - } - try { - parseStartStrideStop("[4:3]"); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[4:3]\": start=4 must be less than or equal to stop=3", - ""); - } - try { - parseStartStrideStop("[4:2:3]"); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[4:2:3]\": start=4 must be less than or equal to stop=3", - ""); - } - - //test calculateNValues - Test.ensureEqual(calculateNValues(1, 1, 3), 3, ""); - Test.ensureEqual(calculateNValues(1, 2, 3), 2, ""); - Test.ensureEqual(calculateNValues(1, 2, 4), 2, ""); - try { - calculateNValues(4,2,3); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.RuntimeException: start=4 must be less than or equal to stop=3", - ""); - } - try { - calculateNValues(3,0,5); - Test.ensureEqual(0, 1, ""); - } catch (Throwable t) { - Test.ensureEqual(t.toString(), - "java.lang.RuntimeException: stride=0 must be greater than 0", - ""); - } - } - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 6; - String msg = "\n^^^ OpendapHelper.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - - } else { - if (test == 0) testGetAttributes(); - if (test == 1) testParseStartStrideStop(); - if (test == 2) testDapToNcDArray(); - if (test == 3) testFindVarsWithSharedDimensions(); - if (test == 4) testFindAllScalarOrMultiDimVars(); - if (test == 5) testDapToNcDGrid(); - if (test == 6) testAllDapToNc(-1); //-1 for all tests, or 0.. for specific test - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - - - } diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/pointdata/Table.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/pointdata/Table.java index a8df761ce..56b06c61d 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/pointdata/Table.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/pointdata/Table.java @@ -12,10 +12,7 @@ import gov.noaa.pfel.coastwatch.griddata.Matlab; import gov.noaa.pfel.coastwatch.griddata.NcHelper; import gov.noaa.pfel.coastwatch.griddata.OpendapHelper; -import gov.noaa.pfel.coastwatch.util.DataStream; -import gov.noaa.pfel.coastwatch.util.FileVisitorDNLS; import gov.noaa.pfel.coastwatch.util.HtmlWidgets; -import gov.noaa.pfel.coastwatch.util.RegexFilenameFilter; import gov.noaa.pfel.coastwatch.util.SimpleXMLReader; import gov.noaa.pfel.coastwatch.util.SSR; import gov.noaa.pfel.coastwatch.util.Tally; @@ -29,19 +26,14 @@ import java.io.DataOutputStream; import java.io.FileInputStream; import java.io.FileOutputStream; -import java.io.FileReader; -import java.io.FileWriter; import java.io.InputStreamReader; -import java.io.InputStream; import java.io.IOException; import java.io.OutputStream; -import java.io.OutputStreamWriter; import java.io.Reader; import java.io.StringReader; import java.io.StringWriter; import java.io.Writer; import java.math.BigInteger; -import java.net.URL; import java.sql.BatchUpdateException; import java.sql.Connection; import java.sql.DatabaseMetaData; @@ -50,7 +42,6 @@ import java.sql.PreparedStatement; import java.sql.ResultSet; import java.sql.ResultSetMetaData; -import java.sql.Savepoint; import java.sql.Statement; import java.sql.Time; import java.sql.Timestamp; @@ -59,8 +50,6 @@ import java.util.Arrays; import java.util.BitSet; import java.util.Calendar; -import java.util.Enumeration; -import java.util.Formatter; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; @@ -77,26 +66,12 @@ import javax.sound.sampled.AudioInputStream; import javax.sound.sampled.AudioSystem; -import org.json.JSONArray; -import org.json.JSONObject; -import org.json.JSONTokener; - import org.xml.sax.XMLReader; import org.xml.sax.InputSource; -import org.xml.sax.helpers.XMLReaderFactory; // from netcdfAll-x.jar import ucar.ma2.*; import ucar.nc2.*; -import ucar.nc2.constants.FeatureType; -import ucar.nc2.dataset.NetcdfDataset; -import ucar.nc2.dataset.NetcdfDatasets; -import ucar.nc2.ft.FeatureDataset; -import ucar.nc2.ft.point.standard.PointDatasetStandardFactory; -//import ucar.nc2.dods.*; -import ucar.nc2.Sequence; -import ucar.nc2.util.*; -import ucar.nc2.write.NetcdfFileFormat; import ucar.nc2.write.NetcdfFormatWriter; /** The Java DAP classes. */ @@ -313,10 +288,10 @@ private static interface WithColumnNames{ public static BitSet ncCFcc = null; //null=inactive, new BitSet() = active /** An arrayList to hold 0 or more PrimitiveArray's with data. */ - private ArrayList columns = new ArrayList(); + protected ArrayList columns = new ArrayList(); /** An arrayList to hold the column names. */ - private StringArray columnNames = new StringArray(); + protected StringArray columnNames = new StringArray(); /** @@ -325,7 +300,7 @@ private static interface WithColumnNames{ * this uses ArrayList to preserve the order of the attributes. * This may be null if not in use. */ - private Attributes globalAttributes = new Attributes(); + protected Attributes globalAttributes = new Attributes(); /** * This holds the column Attributes ((String)name = (PrimitiveArray)value) @@ -334,13 +309,7 @@ private static interface WithColumnNames{ * this uses ArrayList to preserve the order of the attributes. * This may be null if not in use. */ - private ArrayList columnAttributes = new ArrayList(); - - - /** testDir is used for tests. */ - public static String testDir = - File2.getClassPath() + //with / separator and / at the end - "gov/noaa/pfel/coastwatch/pointdata/"; + protected ArrayList columnAttributes = new ArrayList(); /** The one known valid url for readIobis. */ public final static String IOBIS_URL = "http://www.iobis.org/OBISWEB/ObisControllerServlet"; @@ -2640,188 +2609,6 @@ else if (colSeparator == ',') } } - /** - * Test readASCII with csv file. - * - * @throws Exception if trouble - */ - public static void testReadAsciiCsvFile() throws Exception { - - String2.log("\nTable.testReadAsciiCsvASCIIFile"); - String results, expected; - StringArray sa = new StringArray(); - String fileName = String2.unitTestDataDir + "csvAscii.txt"; - String skipHeaderToRegex = "\\*\\*\\* END OF HEADER.*"; - String skipLinesRegex = "#.*"; - - Table table; - -// public void readASCII(String fullFileName, int columnNamesLine, int dataStartLine, -// String testColumns[], double testMin[], double testMax[], -// String loadColumns[], boolean simplify) throws Exception { - - //read as Strings - table = new Table(); - table.allowRaggedRightInReadASCII = true; - table.readASCII(fileName, File2.ISO_8859_1, - skipHeaderToRegex, skipLinesRegex, - 0, 1, "", null, null, null, null, false); - results = table.dataToString(); - expected = -"aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat,aDouble\n" + -"\" b,d \",Ab,t,24,24000,24000000,240000000000,2.4,2.412345678987654\n" + -"needs,1comma:,,,,,,,\n" + -"fg,F,true,11,12001,1200000,12000000000,1.21,1e200\n" + -"h,H,1,12,12002,120000,1200000000,1.22,2e200\n" + -"i,I,TRUE,13,12003,12000,120000000,1.23,3e200\n" + -"j,J,f,14,12004,1200,12000000,1.24,4e200\n" + -"k,K,false,15,12005,120,1200000,1.25,5e200\n" + -"\"BAD LINE: UNCLOSED QUOTE,K,false,15,12005,120,1200000,1.25, 5.5e200\",,,,,,,,\n" + -"l,L,0,16,12006,12,120000,1.26,6e200\n" + -"m,M,FALSE,17,12007,121,12000,1.27,7e200\n" + -"n,N,8,18,12008,122,1200,1.28,8e200\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //test types - sa.clear(); - for (int col = 0; col < table.nColumns(); col++) - sa.add(table.getColumn(col).elementTypeString()); - results = sa.toString(); - expected = "String, String, String, String, String, String, String, String, String"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test simplify - table = new Table(); - table.allowRaggedRightInReadASCII = false; - table.readASCII(fileName, File2.ISO_8859_1, - skipHeaderToRegex, skipLinesRegex, - 0, 1, "", null, null, null, null, true); - results = table.dataToString(); - expected = //bad lines are removed -"aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat,aDouble\n" + -"\" b,d \",Ab,t,24,24000,24000000,240000000000,2.4,2.412345678987654\n" + -"fg,F,true,11,12001,1200000,12000000000,1.21,1.0E200\n" + -"h,H,1,12,12002,120000,1200000000,1.22,2.0E200\n" + -"i,I,TRUE,13,12003,12000,120000000,1.23,3.0E200\n" + -"j,J,f,14,12004,1200,12000000,1.24,4.0E200\n" + -"k,K,false,15,12005,120,1200000,1.25,5.0E200\n" + -"l,L,0,16,12006,12,120000,1.26,6.0E200\n" + -"m,M,FALSE,17,12007,121,12000,1.27,7.0E200\n" + -"n,N,8,18,12008,122,1200,1.28,8.0E200\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //test types - sa.clear(); - for (int col = 0; col < table.nColumns(); col++) - sa.add(table.getColumn(col).elementTypeString()); - results = sa.toString(); - expected = "String, String, String, byte, short, int, long, float, double"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read subset - table = new Table(); - table.allowRaggedRightInReadASCII = false; - table.readASCII(fileName, File2.ISO_8859_1, - skipHeaderToRegex, skipLinesRegex, - 0, 1, "", - new String[]{"aByte"}, new double[]{14}, new double[]{16}, - new String[]{"aDouble","aString","aByte"}, true); //load cols - results = table.dataToString(); - expected = //bad lines are removed -"aDouble,aString,aByte\n" + -"4.0E200,j,14\n" + -"5.0E200,k,15\n" + -"6.0E200,l,16\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } - - /** - * Test readASCII with ssv file. - * - * @throws Exception if trouble - */ - public static void testReadAsciiSsvFile() throws Exception { - - String2.log("\nTable.testReadAsciiSsvASCIIFile"); - String results, expected; - StringArray sa = new StringArray(); - String fileName = String2.unitTestDataDir + "ssvAscii.txt"; - Table table; - -// public void readASCII(String fullFileName, int columnNamesLine, int dataStartLine, -// String testColumns[], double testMin[], double testMax[], -// String loadColumns[], boolean simplify) throws Exception { - - //read as Strings - table = new Table(); - table.allowRaggedRightInReadASCII = true; - table.readASCII(fileName, File2.ISO_8859_1, - "", "", 0, 1, "", null, null, null, null, false); - results = table.dataToString(); - expected = -"aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat,aDouble\n" + -"\" b d \",Ab,t,24,24000,24000000,240000000000,2.4,2.412345678987654\n" + -"needs1space,E,,,,,,,\n" + -"fg,F,true,11,12001,1200000,12000000000,1.21,1e200\n" + -"h,H,1,12,12002,120000,1200000000,1.22,2e200\n" + -"i,I,TRUE,13,12003,12000,120000000,1.23,3e200\n" + -"j,J,f,14,12004,1200,12000000,1.24,4e200\n" + -"k,K,false,15,12005,120,1200000,1.25,5e200\n" + -"l,L,0,16,12006,12,120000,1.26,6e200\n" + -"m,M,FALSE,17,12007,121,12000,1.27,7e200\n" + -"n,N,8,18,12008,122,1200,1.28,8e200\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //test types - sa.clear(); - for (int col = 0; col < table.nColumns(); col++) - sa.add(table.getColumn(col).elementTypeString()); - results = sa.toString(); - expected = "String, String, String, String, String, String, String, String, String"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test simplify - table = new Table(); - table.allowRaggedRightInReadASCII = true; - table.readASCII(fileName, File2.ISO_8859_1, - "", "", 0, 1, "", null, null, null, null, true); - results = table.dataToString(); - expected = -"aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat,aDouble\n" + -"\" b d \",Ab,t,24,24000,24000000,240000000000,2.4,2.412345678987654\n" + -"needs1space,E,,,,,,,\n" + -"fg,F,true,11,12001,1200000,12000000000,1.21,1.0E200\n" + -"h,H,1,12,12002,120000,1200000000,1.22,2.0E200\n" + -"i,I,TRUE,13,12003,12000,120000000,1.23,3.0E200\n" + -"j,J,f,14,12004,1200,12000000,1.24,4.0E200\n" + -"k,K,false,15,12005,120,1200000,1.25,5.0E200\n" + -"l,L,0,16,12006,12,120000,1.26,6.0E200\n" + -"m,M,FALSE,17,12007,121,12000,1.27,7.0E200\n" + -"n,N,8,18,12008,122,1200,1.28,8.0E200\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //test types - sa.clear(); - for (int col = 0; col < table.nColumns(); col++) - sa.add(table.getColumn(col).elementTypeString()); - results = sa.toString(); - expected = "String, String, String, byte, short, int, long, float, double"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read subset - table = new Table(); - table.allowRaggedRightInReadASCII = true; - table.readASCII(fileName, File2.ISO_8859_1, - "", "", 0, 1, "", - new String[]{"aByte"}, new double[]{14}, new double[]{16}, - new String[]{"aDouble","aString","aByte"}, true); //load cols - results = table.dataToString(); - expected = -"aDouble,aString,aByte\n" + -",needs1space,\n" + -"4.0E200,j,14\n" + -"5.0E200,k,15\n" + -"6.0E200,l,16\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } - - /** * This is like the other readStandardTabbedASCII, but this one actually reads the * data from the file. @@ -3147,115 +2934,6 @@ public void readColumnarASCII(String fileName, BufferedReader reader, } } - /** - * Test readColumnarASCII. - * - * @throws Exception if trouble - */ - public static void testReadColumnarASCIIFile() throws Exception { - - String2.log("\nTable.testReadColumnarASCIIFile"); - String results, expected; - StringArray sa = new StringArray(); - String fullFileName = String2.unitTestDataDir + "columnarAsciiWithComments.txt"; - String skipHeaderToRegex = "END OF HEADER.*"; - String skipLinesRegex = "%.*"; - String colNames[] = { - "aDouble", "aString","aChar","aBoolean","aByte","aShort", "anInt","aLong","aFloat"}; - int start[] = { - 66, 0, 9, 15, 24, 30, 37, 45, 57}; - int end[] = { - 86, 9, 15, 24, 30, 37, 45, 57, 66}; - -//012345678911234567892123456789312345678941234567895123456789612345678971234567898123456 -//aString aChar aBoolean aByte aShort anInt aLong aFloat aDouble -//abc a true 24 24000 240000002400000000002.4 2.412345678987654 - - //read as Strings - PAType colPAType[] = new PAType[9]; - Arrays.fill(colPAType, PAType.STRING); - Table table = new Table(); - table.readColumnarASCIIFile(fullFileName, "", - skipHeaderToRegex, skipLinesRegex, 3, colNames, start, end, colPAType); - results = table.dataToString(); - expected = -"aDouble,aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat\n" + -"2.412345678987654,abcdef,Ab,t,24,24000,24000000,240000000000,2.4\n" + -",short:,,,,,,,\n" + -"1e200,fg,F,true,11,12001,1200000,12000000000,1.21\n" + -"2e200,h,H,1,12,12002,120000,1200000000,1.22\n" + -"3e200,i,I,TRUE,13,12003,12000,120000000,1.23\n" + -"4e200,j,J,f,14,12004,1200,12000000,1.24\n" + -"5e200,k,K,false,15,12005,120,1200000,1.25\n" + -"6e200,l,L,0,16,12006,12,120000,1.26\n" + -"7e200,m,M,FALSE,17,12007,121,12000,1.27\n" + -"8e200,n,N,8,18,12008,122,1200,1.28\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //test types - sa.clear(); - for (int col = 0; col < table.nColumns(); col++) - sa.add(table.getColumn(col).elementTypeString()); - results = sa.toString(); - expected = "String, String, String, String, String, String, String, String, String"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - //simplify - table.readColumnarASCIIFile(fullFileName, "", - skipHeaderToRegex, skipLinesRegex, 3, colNames, start, end, null); - results = table.dataToString(); - expected = -"aDouble,aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat\n" + -"2.412345678987654,abcdef,Ab,t,24,24000,24000000,240000000000,2.4\n" + -",short:,,,,,,,\n" + -"1.0E200,fg,F,true,11,12001,1200000,12000000000,1.21\n" + -"2.0E200,h,H,1,12,12002,120000,1200000000,1.22\n" + -"3.0E200,i,I,TRUE,13,12003,12000,120000000,1.23\n" + -"4.0E200,j,J,f,14,12004,1200,12000000,1.24\n" + -"5.0E200,k,K,false,15,12005,120,1200000,1.25\n" + -"6.0E200,l,L,0,16,12006,12,120000,1.26\n" + -"7.0E200,m,M,FALSE,17,12007,121,12000,1.27\n" + -"8.0E200,n,N,8,18,12008,122,1200,1.28\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //test types - sa.clear(); - for (int col = 0; col < table.nColumns(); col++) - sa.add(table.getColumn(col).elementTypeString()); - results = sa.toString(); - expected = "double, String, String, String, byte, short, int, long, float"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read as types - colPAType = new PAType[] { - PAType.DOUBLE, PAType.STRING, PAType.CHAR, PAType.BOOLEAN, PAType.BYTE, - PAType.SHORT, PAType.INT, PAType.LONG, PAType.FLOAT}; - table.readColumnarASCIIFile(fullFileName, "", - skipHeaderToRegex, skipLinesRegex, 3, colNames, start, end, colPAType); - results = table.dataToString(); - expected = -"aDouble,aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat\n" + -"2.412345678987654,abcdef,A,1,24,24000,24000000,240000000000,2.4\n" + -",short:,,,,,,,\n" + -"1.0E200,fg,F,1,11,12001,1200000,12000000000,1.21\n" + -"2.0E200,h,H,1,12,12002,120000,1200000000,1.22\n" + -"3.0E200,i,I,1,13,12003,12000,120000000,1.23\n" + -"4.0E200,j,J,0,14,12004,1200,12000000,1.24\n" + -"5.0E200,k,K,0,15,12005,120,1200000,1.25\n" + -"6.0E200,l,L,0,16,12006,12,120000,1.26\n" + -"7.0E200,m,M,0,17,12007,121,12000,1.27\n" + -"8.0E200,n,N,1,18,12008,122,1200,1.28\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //test types - sa.clear(); - for (int col = 0; col < table.nColumns(); col++) - sa.add(table.getColumn(col).elementTypeString()); - results = sa.toString(); - expected = - "double, String, char, byte, byte, short, int, long, float"; - Test.ensureEqual(results, expected, "results=\n" + results); - } - - /** * This reads an NCCSV .csv file from a URL or a file. * See https://erddap.github.io/NCCSV.html . @@ -3655,17 +3333,23 @@ else if (isULong[c] && ts.length() > 0) writer.write(String2.NCCSV_END_DATA + "\n"); writer.flush(); //important } - - /** - * This tests readNccsv(), readNccsvMetadata(), - */ - public static void testNccsv() throws Exception { - String2.log("\n**** Table.testNccsv()\n"); + public static void testNccsvInteractive() throws Exception { + String dir = String2.unitTestDataDir + "nccsv/"; +boolean haveExcel = false; //as of ~2020, I no longer have excel - //read/write scalar - String fileName = dir + "testScalar_1.1.csv"; + //*** test 1.1 file + //test round trip to spreadsheet and back + //make a copy of sampleScalar + String fileName = dir + "sampleExcel_1.1.csv"; + File2.writeToFile88591(fileName, + File2.directReadFrom88591File(dir + "testScalar_1.1.csv")); + +if (haveExcel) { + Test.displayInBrowser("file://" + fileName); //.csv + String2.pressEnterToContinue("\nIn Excel, use File : Save As : CSV : as sampleExcel_1.1.csv : yes : yes."); +} Table table = new Table(); table.readNccsv(fileName); for (int c = 0; c < table.nColumns(); c++) { @@ -3673,7 +3357,7 @@ public static void testNccsv() throws Exception { Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE)==null, "col=" + c); } String results = table.saveAsNccsv(); - String expected1 = + String expected = //it gets converted to nccsv 1.2 "*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + "*GLOBAL*,cdm_trajectory_variables,ship\n" + "*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + @@ -3732,359 +3416,42 @@ public static void testNccsv() throws Exception { "2017-03-23T01:45:00Z,28.0003,-130.3472,\u20ac,0,127,-9007199254740992L,9223372036854775807uL,10.0\n" + "2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,126,254,9223372036854775806L,18446744073709551614uL,99.0\n" + "2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",,,,,\n" + +(haveExcel? "BAD ROW: TOO FEW ITEMS,,,?,,\n" : "") + //this disappears if I don't actually do Excel Save As "2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,,,,,\n" + "2017-03-23T23:45:00Z,28.0002,-132.1591,?,,,,,\n" + "*END_DATA*\n"; - Test.ensureEqual(results, expected1, "results=\n" + results); - - results = table.saveAsNccsv(false, true, 0, Integer.MAX_VALUE); //don't catch scalar - String expected2 = -"*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + -"*GLOBAL*,cdm_trajectory_variables,ship\n" + -"*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + -"*GLOBAL*,creator_name,Bob Simons\n" + -"*GLOBAL*,creator_type,person\n" + -"*GLOBAL*,creator_url,https://www.pfeg.noaa.gov\n" + -"*GLOBAL*,featureType,trajectory\n" + -"*GLOBAL*,infoUrl,https://erddap.github.io/NCCSV.html\n" + -"*GLOBAL*,institution,\"NOAA NMFS SWFSC ERD, NOAA PMEL\"\n" + -"*GLOBAL*,keywords,\"NOAA, sea, ship, sst, surface, temperature, trajectory\"\n" + -"*GLOBAL*,license,\"\"\"NCCSV Demonstration\"\" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ .\"\n" + -"*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55\n" + -"*GLOBAL*,subsetVariables,ship\n" + -"*GLOBAL*,summary,This is a paragraph or two describing the dataset.\n" + -"*GLOBAL*,title,NCCSV Demonstration\n" + -"ship,*DATA_TYPE*,String\n" + -"ship,cf_role,trajectory_id\n" + -"time,*DATA_TYPE*,String\n" + -"time,standard_name,time\n" + -"time,units,yyyy-MM-dd'T'HH:mm:ssZ\n" + -"lat,*DATA_TYPE*,double\n" + -"lat,units,degrees_north\n" + -"lon,*DATA_TYPE*,double\n" + -"lon,units,degrees_east\n" + -"status,*DATA_TYPE*,char\n" + -"status,comment,\"From http://some.url.gov/someProjectDocument , Table C\"\n" + -"testByte,*DATA_TYPE*,byte\n" + -"testByte,units,\"1\"\n" + -"testUByte,*DATA_TYPE*,ubyte\n" + -"testUByte,units,\"1\"\n" + -"testLong,*DATA_TYPE*,long\n" + -"testLong,units,\"1\"\n" + -"testULong,*DATA_TYPE*,ulong\n" + -"testULong,units,\"1\"\n" + -"sst,*DATA_TYPE*,float\n" + -"sst,actual_range,0.17f,23.58f\n" + -"sst,missing_value,99.0f\n" + -"sst,standard_name,sea_surface_temperature\n" + -"sst,testBytes,-128b,0b,127b\n" + -"sst,testChars,\"','\",\"'\"\"'\",\"'\u20ac'\"\n" + -"sst,testDoubles,-1.7976931348623157E308d,0.0d,1.7976931348623157E308d\n" + -"sst,testFloats,-3.4028235E38f,0.0f,3.4028235E38f\n" + -"sst,testInts,-2147483648i,0i,2147483647i\n" + -"sst,testLongs,-9223372036854775808L,-9007199254740992L,9007199254740992L,9223372036854775806L,9223372036854775807L\n" + -"sst,testShorts,-32768s,0s,32767s\n" + -"sst,testStrings,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + -"sst,testUBytes,0ub,127ub,255ub\n" + -"sst,testUInts,0ui,2147483647ui,4294967295ui\n" + -"sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL\n" + -"sst,testUShorts,0us,32767us,65535us\n" + -"sst,units,degree_C\n" + -"\n" + -"*END_METADATA*\n" + -"ship,time,lat,lon,status,testByte,testUByte,testLong,testULong,sst\n" + -"\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128,0,-9223372036854775808L,0uL,10.9\n" + -"\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T01:45:00Z,28.0003,-130.3472,\u20ac,0,127,-9007199254740992L,9223372036854775807uL,10.0\n" + -"\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,126,254,9223372036854775806L,18446744073709551614uL,99.0\n" + -"\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",,,,,\n" + -"\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,,,,,\n" + -"\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T23:45:00Z,28.0002,-132.1591,?,,,,,\n" + -"*END_DATA*\n"; - Test.ensureEqual(results, expected2, "results=\n" + results); - - - //non scalar - fileName = dir + "sample_1.1.csv"; - table.readNccsv(fileName); - for (int c = 0; c < table.nColumns(); c++) { - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) ==null, "col=" + c); - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE)==null, "col=" + c); + try { + Test.ensureEqual(results, expected, "results=\n" + results); + } catch (Exception e) { + Test.knownProblem( + "1.1: How to keep integer in string att as a string?!", + "If I don't actually do Excel 'Save As', the BAD ROW disappears.", e); } - //String2.log(table.toString()); -Attributes atts = table.columnAttributes("sst"); -PrimitiveArray pa = atts.get("testChars"); -String2.log(">> sample_1.1.csv testChars isCharArray?" + (pa instanceof CharArray) + " isStringArray?" + (pa instanceof StringArray)); - results = table.saveAsNccsv(false, true, 0, Integer.MAX_VALUE); //don't catch scalars - expected1 = -"*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + -"*GLOBAL*,cdm_trajectory_variables,ship\n" + -"*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + -"*GLOBAL*,creator_name,Bob Simons\n" + -"*GLOBAL*,creator_type,person\n" + -"*GLOBAL*,creator_url,https://www.pfeg.noaa.gov\n" + -"*GLOBAL*,featureType,trajectory\n" + -"*GLOBAL*,infoUrl,https://erddap.github.io/NCCSV.html\n" + -"*GLOBAL*,institution,\"NOAA NMFS SWFSC ERD, NOAA PMEL\"\n" + -"*GLOBAL*,keywords,\"NOAA, sea, ship, sst, surface, temperature, trajectory\"\n" + -"*GLOBAL*,license,\"\"\"NCCSV Demonstration\"\" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ .\"\n" + -"*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55\n" + -"*GLOBAL*,subsetVariables,ship\n" + -"*GLOBAL*,summary,This is a paragraph or two describing the dataset.\n" + -"*GLOBAL*,title,NCCSV Demonstration\n" + -"ship,*DATA_TYPE*,String\n" + -"ship,cf_role,trajectory_id\n" + -"time,*DATA_TYPE*,String\n" + -"time,standard_name,time\n" + -"time,units,yyyy-MM-dd'T'HH:mm:ssZ\n" + -"lat,*DATA_TYPE*,double\n" + -"lat,units,degrees_north\n" + -"lon,*DATA_TYPE*,double\n" + -"lon,units,degrees_east\n" + -"status,*DATA_TYPE*,char\n" + -"status,comment,\"From http://some.url.gov/someProjectDocument , Table C\"\n" + -"testByte,*DATA_TYPE*,byte\n" + -"testByte,units,\"1\"\n" + -"testUByte,*DATA_TYPE*,ubyte\n" + -"testUByte,units,\"1\"\n" + -"testLong,*DATA_TYPE*,long\n" + -"testLong,units,\"1\"\n" + -"testULong,*DATA_TYPE*,ulong\n" + -"testULong,units,\"1\"\n" + -"sst,*DATA_TYPE*,float\n" + -"sst,actual_range,0.17f,23.58f\n" + -"sst,missing_value,99.0f\n" + -"sst,standard_name,sea_surface_temperature\n" + -"sst,testBytes,-128b,0b,127b\n" + -"sst,testChars,\"','\",\"'\"\"'\",\"'\u20ac'\"\n" + -"sst,testDoubles,-1.7976931348623157E308d,0.0d,1.7976931348623157E308d\n" + -"sst,testFloats,-3.4028235E38f,0.0f,3.4028235E38f\n" + -"sst,testInts,-2147483648i,0i,2147483647i\n" + -"sst,testLongs,-9223372036854775808L,0L,9223372036854775807L\n" + -"sst,testShorts,-32768s,0s,32767s\n" + -"sst,testStrings,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + -"sst,testUBytes,0ub,127ub,255ub\n" + -"sst,testUInts,0ui,2147483647ui,4294967295ui\n" + -"sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL\n" + -"sst,testUShorts,0us,32767us,65535us\n" + -"sst,units,degree_C\n" + -"\n" + -"*END_METADATA*\n" + -"ship,time,lat,lon,status,testByte,testUByte,testLong,testULong,sst\n" + -"Bell M. Shimada,2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128,0,-9223372036854775808L,0uL,10.9\n" + -"Bell M. Shimada,2017-03-23T01:45:00Z,28.0003,-130.3472,\u20ac,0,127,-9007199254740992L,9223372036854775807uL,10.0\n" + -"Bell M. Shimada,2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,126,254,9223372036854775806L,18446744073709551614uL,99.0\n" + -"Bell M. Shimada,2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",,,,,\n" + -"Bell M. Shimada,2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,,,,,\n" + -"Bell M. Shimada,2017-03-23T23:45:00Z,28.0002,-132.1591,?,,,,,\n" + -"*END_DATA*\n"; - Test.ensureEqual(results, expected1, "results=\n" + results); - //non scalar - fileName = dir + "sample_1.2.csv"; + //*** test 1.2 file + //test round trip to spreadsheet and back + //make a copy of sampleScalar + fileName = dir + "sampleExcel_1.2.csv"; + File2.writeToFileUtf8(fileName, + File2.directReadFromUtf8File(dir + "testScalar_1.2.csv")); +if (haveExcel) { + Test.displayInBrowser("file://" + fileName); //.csv + String2.pressEnterToContinue("\nIn Excel, use File : Save As : CSV : as sampleExcel_1.2.csv : yes : yes."); +} + table = new Table(); table.readNccsv(fileName); for (int c = 0; c < table.nColumns(); c++) { Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) ==null, "col=" + c); Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE)==null, "col=" + c); } - //String2.log(table.toString()); -atts = table.columnAttributes("sst"); -pa = atts.get("testChars"); -String2.log(">> sample_1.2.csv testChars isCharArray?" + (pa instanceof CharArray) + " isStringArray?" + (pa instanceof StringArray)); - results = table.saveAsNccsv(false, true, 0, Integer.MAX_VALUE); //don't catch scalars - //we expect the same results - Test.ensureEqual(results, expected1, "results=\n" + results); + results = table.saveAsNccsv(); - - //just metadata - fileName = dir + "sampleMetadata_1.1.csv"; - table = new Table(); - table.readNccsv(fileName, false); //readData? - for (int c = 0; c < table.nColumns(); c++) { - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) ==null, "col=" + c); - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE)==null, "col=" + c); - } - results = table.saveAsNccsv(true, true, 0, 0); //catch scalar, writeMetadata, don't write data - String expected3 = -"*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + -"*GLOBAL*,cdm_trajectory_variables,ship\n" + -"*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + -"*GLOBAL*,creator_name,Bob Simons\n" + -"*GLOBAL*,creator_type,person\n" + -"*GLOBAL*,creator_url,https://www.pfeg.noaa.gov\n" + -"*GLOBAL*,featureType,trajectory\n" + -"*GLOBAL*,infoUrl,https://erddap.github.io/NCCSV.html\n" + -"*GLOBAL*,institution,\"NOAA NMFS SWFSC ERD, NOAA PMEL\"\n" + -"*GLOBAL*,keywords,\"NOAA, sea, ship, sst, surface, temperature, trajectory\"\n" + -"*GLOBAL*,license,\"\"\"NCCSV Demonstration\"\" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ .\"\n" + -"*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55\n" + -"*GLOBAL*,subsetVariables,ship\n" + -"*GLOBAL*,summary,This is a paragraph or two describing the dataset.\n" + -"*GLOBAL*,title,NCCSV Demonstration\n" + -"ship,*SCALAR*,Bell M. Shimada\n" + -"ship,cf_role,trajectory_id\n" + -"time,*DATA_TYPE*,String\n" + -"time,standard_name,time\n" + -"time,units,yyyy-MM-dd'T'HH:mm:ssZ\n" + -"lat,*DATA_TYPE*,double\n" + -"lat,units,degrees_north\n" + -"lon,*DATA_TYPE*,double\n" + -"lon,units,degrees_east\n" + -"status,*DATA_TYPE*,char\n" + -"status,comment,\"From http://some.url.gov/someProjectDocument , Table C\"\n" + -"testLong,*DATA_TYPE*,long\n" + -"testLong,units,\"1\"\n" + -"sst,*DATA_TYPE*,float\n" + -"sst,actual_range,0.17f,23.58f\n" + -"sst,missing_value,99.0f\n" + -"sst,standard_name,sea_surface_temperature\n" + -"sst,testBytes,-128b,0b,127b\n" + -"sst,testChars,\"','\",\"'\"\"'\",\"'\u20ac'\"\n" + -"sst,testDoubles,-1.7976931348623157E308d,0.0d,1.7976931348623157E308d\n" + -"sst,testFloats,-3.4028235E38f,0.0f,3.4028235E38f\n" + -"sst,testInts,-2147483648i,0i,2147483647i\n" + -"sst,testLongs,-9223372036854775808L,0L,9223372036854775807L\n" + -"sst,testShorts,-32768s,0s,32767s\n" + -"sst,testStrings,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + -"sst,testUBytes,0ub,127ub,255ub\n" + -"sst,testUInts,0ui,2147483647ui,4294967295ui\n" + -"sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL\n" + -"sst,testUShorts,0us,32767us,65535us\n" + -"sst,units,degree_C\n" + -"\n" + -"*END_METADATA*\n"; - Test.ensureEqual(results, expected3, "results=\n" + results); - - //just metadata - fileName = dir + "sampleMetadata_1.2.csv"; - table = new Table(); - table.readNccsv(fileName, false); //readData? - for (int c = 0; c < table.nColumns(); c++) { - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) ==null, "col=" + c); - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE)==null, "col=" + c); - } - results = table.saveAsNccsv(true, true, 0, 0); //catch scalar, writeMetadata, don't write data - Test.ensureEqual(results, expected3, "results=\n" + results); - - } - - public static void testNccsvInteractive() throws Exception { - - String dir = String2.unitTestDataDir + "nccsv/"; -boolean haveExcel = false; //as of ~2020, I no longer have excel - - //*** test 1.1 file - //test round trip to spreadsheet and back - //make a copy of sampleScalar - String fileName = dir + "sampleExcel_1.1.csv"; - File2.writeToFile88591(fileName, - File2.directReadFrom88591File(dir + "testScalar_1.1.csv")); - -if (haveExcel) { - Test.displayInBrowser("file://" + fileName); //.csv - String2.pressEnterToContinue("\nIn Excel, use File : Save As : CSV : as sampleExcel_1.1.csv : yes : yes."); -} - Table table = new Table(); - table.readNccsv(fileName); - for (int c = 0; c < table.nColumns(); c++) { - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) ==null, "col=" + c); - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE)==null, "col=" + c); - } - String results = table.saveAsNccsv(); - String expected = //it gets converted to nccsv 1.2 -"*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + -"*GLOBAL*,cdm_trajectory_variables,ship\n" + -"*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + -"*GLOBAL*,creator_name,Bob Simons\n" + -"*GLOBAL*,creator_type,person\n" + -"*GLOBAL*,creator_url,https://www.pfeg.noaa.gov\n" + -"*GLOBAL*,featureType,trajectory\n" + -"*GLOBAL*,infoUrl,https://erddap.github.io/NCCSV.html\n" + -"*GLOBAL*,institution,\"NOAA NMFS SWFSC ERD, NOAA PMEL\"\n" + -"*GLOBAL*,keywords,\"NOAA, sea, ship, sst, surface, temperature, trajectory\"\n" + -"*GLOBAL*,license,\"\"\"NCCSV Demonstration\"\" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ .\"\n" + -"*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55\n" + -"*GLOBAL*,subsetVariables,ship\n" + -"*GLOBAL*,summary,This is a paragraph or two describing the dataset.\n" + -"*GLOBAL*,title,NCCSV Demonstration\n" + -"ship,*SCALAR*,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + -"ship,cf_role,trajectory_id\n" + -"time,*DATA_TYPE*,String\n" + -"time,standard_name,time\n" + -"time,units,yyyy-MM-dd'T'HH:mm:ssZ\n" + -"lat,*DATA_TYPE*,double\n" + -"lat,units,degrees_north\n" + -"lon,*DATA_TYPE*,double\n" + -"lon,units,degrees_east\n" + -"status,*DATA_TYPE*,char\n" + -"status,comment,\"From http://some.url.gov/someProjectDocument , Table C\"\n" + -"testByte,*DATA_TYPE*,byte\n" + -"testByte,units,\"1\"\n" + -"testUByte,*DATA_TYPE*,ubyte\n" + -"testUByte,units,\"1\"\n" + -"testLong,*DATA_TYPE*,long\n" + -"testLong,units,\"1\"\n" + -"testULong,*DATA_TYPE*,ulong\n" + -"testULong,units,\"1\"\n" + -"sst,*DATA_TYPE*,float\n" + -"sst,actual_range,0.17f,23.58f\n" + -"sst,missing_value,99.0f\n" + -"sst,standard_name,sea_surface_temperature\n" + -"sst,testBytes,-128b,0b,127b\n" + -"sst,testChars,\"','\",\"'\"\"'\",\"'\u20ac'\"\n" + -"sst,testDoubles,-1.7976931348623157E308d,0.0d,1.7976931348623157E308d\n" + -"sst,testFloats,-3.4028235E38f,0.0f,3.4028235E38f\n" + -"sst,testInts,-2147483648i,0i,2147483647i\n" + -"sst,testLongs,-9223372036854775808L,-9007199254740992L,9007199254740992L,9223372036854775806L,9223372036854775807L\n" + -"sst,testShorts,-32768s,0s,32767s\n" + -"sst,testStrings,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + -"sst,testUBytes,0ub,127ub,255ub\n" + -"sst,testUInts,0ui,2147483647ui,4294967295ui\n" + -"sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL\n" + -"sst,testUShorts,0us,32767us,65535us\n" + -"sst,units,degree_C\n" + -"\n" + -"*END_METADATA*\n" + -"time,lat,lon,status,testByte,testUByte,testLong,testULong,sst\n" + -"2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128,0,-9223372036854775808L,0uL,10.9\n" + -"2017-03-23T01:45:00Z,28.0003,-130.3472,\u20ac,0,127,-9007199254740992L,9223372036854775807uL,10.0\n" + -"2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,126,254,9223372036854775806L,18446744073709551614uL,99.0\n" + -"2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",,,,,\n" + -(haveExcel? "BAD ROW: TOO FEW ITEMS,,,?,,\n" : "") + //this disappears if I don't actually do Excel Save As -"2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,,,,,\n" + -"2017-03-23T23:45:00Z,28.0002,-132.1591,?,,,,,\n" + -"*END_DATA*\n"; - try { - Test.ensureEqual(results, expected, "results=\n" + results); - } catch (Exception e) { - Test.knownProblem( - "1.1: How to keep integer in string att as a string?!", - "If I don't actually do Excel 'Save As', the BAD ROW disappears.", e); - } - - //*** test 1.2 file - //test round trip to spreadsheet and back - //make a copy of sampleScalar - fileName = dir + "sampleExcel_1.2.csv"; - File2.writeToFileUtf8(fileName, - File2.directReadFromUtf8File(dir + "testScalar_1.2.csv")); -if (haveExcel) { - Test.displayInBrowser("file://" + fileName); //.csv - String2.pressEnterToContinue("\nIn Excel, use File : Save As : CSV : as sampleExcel_1.2.csv : yes : yes."); -} - table = new Table(); - table.readNccsv(fileName); - for (int c = 0; c < table.nColumns(); c++) { - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) ==null, "col=" + c); - Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE)==null, "col=" + c); - } - results = table.saveAsNccsv(); - - try { - Test.ensureEqual(results, expected, "results=\n" + results); - } catch (Exception e) { - Test.knownProblem( - "1.2: How to keep integer in string att as a string?!", - "If I don't actually do Excel 'Save As', the BAD ROW disappears.", e); + try { + Test.ensureEqual(results, expected, "results=\n" + results); + } catch (Exception e) { + Test.knownProblem( + "1.2: How to keep integer in string att as a string?!", + "If I don't actually do Excel 'Save As', the BAD ROW disappears.", e); } } @@ -4496,34 +3863,8 @@ public void setObisAttributes(int lonColumn, int latColumn, int depthColumn, globalAttributes.set("Conventions", con + ", " + lasConvention); } - - - - /** - * This tests readIObis. - */ - public static void testIobis() throws Exception { - verbose = true; - reallyVerbose = true; - String2.log("\n*** Table.testIobis"); - String testName = "c:/programs/digir/Macrocyctis.nc"; - Table table = new Table(); - if (true) { - table.readIobis(IOBIS_URL, "Macrocystis", "", //String genus, String species, - "" , "", "53", "54", //String west, String east, String south, String north, - "", "", //String minDepth, String maxDepth, - "1970-01-01", "",//String iso startDate, String iso endDate, - new String[]{"Institutioncode", "Collectioncode", "Scientificname", "Temperature"}); //String loadColumns[]) - -// table.saveAsFlatNc(testName, "row"); - } else { - table.readFlatNc(testName, null, 1); //standardizeWhat - } - String2.log(table.toString()); - table.testObis5354Table(); - - } + // TODO move this to a test file /** * This tests that the values in this table are the expected results from * the typical obis "Macrocystis", time 1970+, lat 53.. 54 request. @@ -4694,221 +4035,6 @@ public void readXml(Reader xml, boolean validate, String rowElementXPath, " TIME=" + (System.currentTimeMillis() - time) + "ms"); } - /** - * This tests readXml. - */ - public static void testXml() throws Exception { - String2.log("\n*** Table.testXml()"); - verbose = true; - reallyVerbose = true; - //TableXmlHandler.verbose = true; - Table table = null; - String xml, results, expected; - - //*** WFS - table = new Table(); - BufferedReader reader = File2.getDecompressedBufferedFileReaderUtf8( - "c:/programs/mapserver/WVBoreholeResponse.xml"); - try { - table.readXml(reader, - false, //no validate since no .dtd - "/wfs:FeatureCollection/wfs:member", //default tRowElementXPath, - //was "/wfs:FeatureCollection/gml:featureMember", - null, false); //row attributes, simplify - } finally { - reader.close(); - } - results = table.dataToString(3); - expected = -"aasg:BoreholeTemperature/aasg:ObservationURI,aasg:BoreholeTemperature/aasg:WellName,aasg:BoreholeTemperature/aasg:APINo,aasg:BoreholeTemperature/aasg:HeaderURI,aasg:BoreholeTemperature/aasg:OtherName,aasg:BoreholeTemperature/aasg:Label,aasg:BoreholeTemperature/aasg:Operator,aasg:BoreholeTemperature/aasg:SpudDate,aasg:BoreholeTemperature/aasg:EndedDrillingDate,aasg:BoreholeTemperature/aasg:WellType,aasg:BoreholeTemperature/aasg:StatusDate,aasg:BoreholeTemperature/aasg:ReleaseDate,aasg:BoreholeTemperature/aasg:Field,aasg:BoreholeTemperature/aasg:County,aasg:BoreholeTemperature/aasg:State,aasg:BoreholeTemperature/aasg:UTM_E,aasg:BoreholeTemperature/aasg:UTM_N,aasg:BoreholeTemperature/aasg:LatDegree,aasg:BoreholeTemperature/aasg:LongDegree,aasg:BoreholeTemperature/aasg:SRS,aasg:BoreholeTemperature/aasg:LocationUncertaintyStatement,aasg:BoreholeTemperature/aasg:LocationUncertaintyRadius,aasg:BoreholeTemperature/aasg:DrillerTotalDepth,aasg:BoreholeTemperature/aasg:DepthReferencePoint,aasg:BoreholeTemperature/aasg:LengthUnits,aasg:BoreholeTemperature/aasg:WellBoreShape,aasg:BoreholeTemperature/aasg:TrueVerticalDepth,aasg:BoreholeTemperature/aasg:ElevationKB,aasg:BoreholeTemperature/aasg:ElevationDF,aasg:BoreholeTemperature/aasg:ElevationGL,aasg:BoreholeTemperature/aasg:FormationTD,aasg:BoreholeTemperature/aasg:BitDiameterTD,aasg:BoreholeTemperature/aasg:MaximumRecordedTemperature,aasg:BoreholeTemperature/aasg:MeasuredTemperature,aasg:BoreholeTemperature/aasg:CorrectedTemperature,aasg:BoreholeTemperature/aasg:TemperatureUnits,aasg:BoreholeTemperature/aasg:CirculationDuration,aasg:BoreholeTemperature/aasg:MeasurementProcedure,aasg:BoreholeTemperature/aasg:DepthOfMeasurement,aasg:BoreholeTemperature/aasg:MeasurementDateTime,aasg:BoreholeTemperature/aasg:MeasurementFormation,aasg:BoreholeTemperature/aasg:MeasurementSource,aasg:BoreholeTemperature/aasg:RelatedResource,aasg:BoreholeTemperature/aasg:CasingBottomDepthDriller,aasg:BoreholeTemperature/aasg:CasingTopDepth,aasg:BoreholeTemperature/aasg:CasingPipeDiameter,aasg:BoreholeTemperature/aasg:CasingWeight,aasg:BoreholeTemperature/aasg:CasingThickness,aasg:BoreholeTemperature/aasg:pH,aasg:BoreholeTemperature/aasg:InformationSource,aasg:BoreholeTemperature/aasg:Shape/gml:Point/latitude,aasg:BoreholeTemperature/aasg:Shape/gml:Point/longitude,aasg:BoreholeTemperature/aasg:LeaseName,aasg:BoreholeTemperature/aasg:LeaseOwner,aasg:BoreholeTemperature/aasg:LeaseNo,aasg:BoreholeTemperature/aasg:TimeSinceCirculation,aasg:BoreholeTemperature/aasg:Status,aasg:BoreholeTemperature/aasg:CommodityOfInterest,aasg:BoreholeTemperature/aasg:Function,aasg:BoreholeTemperature/aasg:Production,aasg:BoreholeTemperature/aasg:ProducingInterval,aasg:BoreholeTemperature/aasg:Notes\n" + -"http://resources.usgin.org/uri-gin/wvges/bhtemp/4705500185/,Dominion Appalachian Development Co. Gilbert Bailey 1,4705500185,http://resources.usgin.org/uri-gin/wvges/well/api:4705500185/,Gilbert Bailey,4705500185,Dominion Appalachian Development Co.,1998-04-02T00:00:00,1998-04-13T00:00:00,Gas,1900-01-01T00:00:00,1900-01-01T00:00:00,Stovall Ridge,Mercer,West Virginia,0.0,0.0,37.4834349990001,-81.1519399999999,EPSG:4326,Location recorded as received from official permit application converted to NAD83 if required,0.0,4854,G.L.,ft,vertical,4854,0.0,0.0,2563,Up Devonian undiff:Berea to Lo Huron,0.0,0.0,87.8,0.0,F,0.0,Temperature log evaluated by WVGES staff for deepest stable log segment to extract data otherwise used given bottom hole temperature on log header if available,3550,1900-01-01T00:00:00,Big Lime,Well Temperature Log,TL | GR | DEN | NEL | IL | CAL | SL,0.0,0.0,0.0,0.0,0.0,0.0,West Virginia Geological and Economic Survey 2013,37.48343499900005,-81.15193999999991,,,,,,,,,,\n" + -"http://resources.usgin.org/uri-gin/wvges/bhtemp/4705500113/,\"Stonewall Gas Co., Inc. State Conserv Comm 2\",4705500113,http://resources.usgin.org/uri-gin/wvges/well/api:4705500113/,Blue Jay Lumber Co,4705500113,\"Stonewall Gas Co., Inc.\",1991-09-20T00:00:00,1991-09-27T00:00:00,Gas,1900-01-01T00:00:00,1900-01-01T00:00:00,Rhodell,Mercer,West Virginia,0.0,0.0,37.530177999,-81.1708569999999,EPSG:4326,Location recorded as received from official permit application converted to NAD83 if required,0.0,4100,G.L.,ft,vertical,4100,0.0,0.0,2442,Price Fm & equivs,0.0,0.0,90,0.0,F,0.0,Temperature log evaluated by WVGES staff for deepest stable log segment to extract data otherwise used given bottom hole temperature on log header if available,3940,1900-01-01T00:00:00,,Well Temperature Log,TL | GR | DEN | NEL | IL | CAL | SL,0.0,0.0,0.0,0.0,0.0,0.0,West Virginia Geological and Economic Survey 2013,37.53017799900005,-81.1708569999999,,,,,,,,,,\n" + -"http://resources.usgin.org/uri-gin/wvges/bhtemp/4705500115/,\"Stonewall Gas Co., Inc. State Conserv Comm 4\",4705500115,http://resources.usgin.org/uri-gin/wvges/well/api:4705500115/,Blue Jay Lumber Co 4,4705500115,\"Stonewall Gas Co., Inc.\",1992-12-01T00:00:00,1992-12-08T00:00:00,Gas,1900-01-01T00:00:00,1900-01-01T00:00:00,Rhodell,Mercer,West Virginia,0.0,0.0,37.533804999,-81.1585159999999,EPSG:4326,Location recorded as received from official permit application converted to NAD83 if required,0.0,4097,G.L.,ft,vertical,4097,0.0,0.0,2463,Price Fm & equivs,0.0,0.0,98,0.0,F,0.0,Temperature log evaluated by WVGES staff for deepest stable log segment to extract data otherwise used given bottom hole temperature on log header if available,3920,1900-01-01T00:00:00,,Well Temperature Log,TL | GR | DEN | NEL | IL | CAL | SL,0.0,0.0,0.0,0.0,0.0,0.0,West Virginia Geological and Economic Survey 2013,37.53380499900004,-81.15851599999991,,,,,,,,,,\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - //*** darwin core -//Lines are commented out to test some aspects of readXml. -xml = -"\n" + -"\n" + -"

\n" + -"$Revision: 1.12 $\n" + -"
\n" + -"\n" + -//"Marine Fish Division, Fisheries and Oceans Canada\n" + -"Gwaii Haanas Marine Algae\n" + -"100-MACRINT\n" + -"Macrocystis integrifolia\n" + -"sciName2\n" + -"52.65172\n" + -"-131.66368\n" + -"\n" + -"\n" + -" child1data\n" + -" child2data\n" + -" child22data\n" + -"\n" + -"BIO\n" + -"GHMP\n" + -"100-MACRINT\n" + -"Macrocystis integrifolia\n" + -"52.65172\n" + -"-131.66368\n" + -"\n" + -"\n" + -//"Marine Fish Division, Fisheries and Oceans Canada\n" + -"Gwaii Haanas Marine Algae\n" + -"10036-MACRINT\n" + -"Macrocystis integrifolia\n" + -"53.292\n" + -"-132.4223\n" + -"\n" + -"\n" + -"\n" + -"\n"; - -//this doesn't test heirarchical elements - table = new Table(); - reader = new BufferedReader(new StringReader(xml)); - try { - table.readXml(reader, - false, //no validate since no .dtd - "/response/content/record", null, true); - } finally { - reader.close(); - } - table.ensureValid(); //throws Exception if not - Test.ensureEqual(table.nRows(), 3, ""); - Test.ensureEqual(table.nColumns(), 10, ""); - Test.ensureEqual(table.getColumnName(0), "darwin:CollectionCode", ""); - Test.ensureEqual(table.getColumnName(1), "darwin:CatalogNumber", ""); - Test.ensureEqual(table.getColumnName(2), "darwin:ScientificName", ""); - Test.ensureEqual(table.getColumnName(3), "darwin:ScientificName2", ""); - Test.ensureEqual(table.getColumnName(4), "darwin:Latitude", ""); - Test.ensureEqual(table.getColumnName(5), "darwin:Longitude", ""); - //Test.ensureEqual(table.getColumnName(5), "obis:Temperature", ""); //no data, so no column - Test.ensureEqual(table.getColumnName(6), "parent/child1", ""); - Test.ensureEqual(table.getColumnName(7), "parent/child2", ""); - Test.ensureEqual(table.getColumnName(8), "parent/child22", ""); - Test.ensureEqual(table.getColumnName(9), "darwin:InstitutionCode", ""); - Test.ensureEqual(table.getColumn(0).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(1).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(2).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(3).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(4).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(5).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(6).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(7).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(8).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(9).elementTypeString(), "String", ""); - Test.ensureEqual(table.getStringData(0, 2), "Gwaii Haanas Marine Algae", ""); - Test.ensureEqual(table.getStringData(1, 2), "10036-MACRINT", ""); - Test.ensureEqual(table.getStringData(2, 2), "Macrocystis integrifolia", ""); - Test.ensureEqual(table.getStringData(3, 0), "sciName2", ""); - Test.ensureEqual(table.getFloatData(4, 2), 53.292f, ""); - Test.ensureEqual(table.getFloatData(5, 2), -132.4223f, ""); - Test.ensureEqual(table.getStringData(6, 0), "child1data", ""); - Test.ensureEqual(table.getStringData(7, 0), "child2data", ""); - Test.ensureEqual(table.getStringData(8, 0), "child22data", ""); - Test.ensureEqual(table.getStringData(9, 0), "", ""); - Test.ensureEqual(table.getStringData(9, 1), "BIO", ""); - Test.ensureEqual(table.getStringData(9, 2), "", ""); - -//a subset of https://opendap.co-ops.nos.noaa.gov/stations/stationsXML.jsp -String stationsXml = -"\n" + -" \n" + -"\n" + -"\n" + -"\n" + -" 48 28.7 N \n" + -" 129 21.5 W \n" + -" \n" + -"\n" + -" 2003-01-01 \n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -" 57 29.9 N \n" + -" 144 0.06 W \n" + -" \n" + -"\n" + -" 2001-01-01 \n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -" 17 58.3 N \n" + -" 67 2.8 W \n" + -" PR \n" + -"\n" + -" 1954-12-01 \n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n"; - table.clear(); - reader = new BufferedReader(new StringReader(stationsXml)); - try { - table.readXml(reader, - false, //no validate since no .dtd - "/stations/station", new String[]{"name", "ID"}, true); - } finally { - reader.close(); - } - table.ensureValid(); //throws Exception if not - String2.log(table.toString()); -// Row name ID metadata/locat metadata/locat metadata/date_ metadata/locat -// 0 DART BUOY 4641 1600013 48 28.7 N 129 21.5 W 2003-01-01 -// 1 DART BUOY 4641 1600014 57 29.9 N 144 0.06 W 2001-01-01 -// 2 Magueyes Islan 9759110 17 58.3 N 67 2.8 W 1954-12-01 PR - Test.ensureEqual(table.nRows(), 3, ""); - Test.ensureEqual(table.nColumns(), 6, ""); - Test.ensureEqual(table.getColumnName(0), "name", ""); - Test.ensureEqual(table.getColumnName(1), "ID", ""); - Test.ensureEqual(table.getColumnName(2), "metadata/location/lat", ""); - Test.ensureEqual(table.getColumnName(3), "metadata/location/long", ""); - Test.ensureEqual(table.getColumnName(4), "metadata/date_established", ""); - Test.ensureEqual(table.getColumnName(5), "metadata/location/state", ""); - Test.ensureEqual(table.getColumn(0).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(1).elementTypeString(), "int", ""); - Test.ensureEqual(table.getColumn(2).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(3).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(4).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(5).elementTypeString(), "String", ""); - Test.ensureEqual(table.getStringData(0, 0), "DART BUOY 46419", ""); - Test.ensureEqual(table.getStringData(1, 0), "1600013", ""); - Test.ensureEqual(table.getStringData(2, 0), "48 28.7 N", ""); - Test.ensureEqual(table.getStringData(3, 0), "129 21.5 W", ""); - Test.ensureEqual(table.getStringData(4, 0), "2003-01-01", ""); - Test.ensureEqual(table.getStringData(5, 0), "", ""); - Test.ensureEqual(table.getStringData(0, 2), "Magueyes Island", ""); - Test.ensureEqual(table.getStringData(1, 2), "9759110", ""); - Test.ensureEqual(table.getStringData(2, 2), "17 58.3 N", ""); - Test.ensureEqual(table.getStringData(3, 2), "67 2.8 W", ""); - Test.ensureEqual(table.getStringData(4, 2), "1954-12-01", ""); - Test.ensureEqual(table.getStringData(5, 2), "PR", ""); - - TableXmlHandler.verbose = false; - - } - /** * This ensure the column exists and has the right name, then adds the value * to the column, on currentRow. @@ -5121,152 +4247,6 @@ public void readAwsXmlFile(String fullFileName) } } - /** Test readAwsXmlFile. Automatic Weather Station - * - * @throws Exception if trouble - */ - public static void testReadAwsXmlFile() throws Exception { - String2.log("\nTable.testReadAwsXmlFile"); - Table table = new Table(); - table.readAwsXmlFile(String2.unitTestDataDir + "aws/xml/SNFLS-2012-11-03T20_30_01Z.xml"); - String results = table.toString(); - String expected = -"{\n" + -"dimensions:\n" + -"\trow = 1 ;\n" + -"\tob-date_strlen = 11 ;\n" + -"\tstation-id_strlen = 5 ;\n" + -"\tstation_strlen = 13 ;\n" + -"\tcity-state-zip_strlen = 5 ;\n" + -"\tcity-state_strlen = 17 ;\n" + -"\tsite-url_strlen = 0 ;\n" + -"\taux-temp_strlen = 2 ;\n" + -"\taux-temp-rate_strlen = 1 ;\n" + -"\tdew-point_strlen = 2 ;\n" + -"\televation_strlen = 1 ;\n" + -"\tfeels-like_strlen = 2 ;\n" + -"\tgust-time_strlen = 11 ;\n" + -"\tgust-direction_strlen = 1 ;\n" + -"\tgust-speed_strlen = 1 ;\n" + -"\thumidity_strlen = 2 ;\n" + -"\thumidity-high_strlen = 3 ;\n" + -"\thumidity-low_strlen = 2 ;\n" + -"\thumidity-rate_strlen = 2 ;\n" + -"\tindoor-temp_strlen = 2 ;\n" + -"\tindoor-temp-rate_strlen = 4 ;\n" + -"\tlight_strlen = 4 ;\n" + -"\tlight-rate_strlen = 4 ;\n" + -"\tmoon-phase-moon-phase-img_strlen = 12 ;\n" + -"\tmoon-phase_strlen = 2 ;\n" + -"\tpressure_strlen = 4 ;\n" + -"\tpressure-high_strlen = 5 ;\n" + -"\tpressure-low_strlen = 5 ;\n" + -"\tpressure-rate_strlen = 5 ;\n" + -"\train-month_strlen = 4 ;\n" + -"\train-rate_strlen = 1 ;\n" + -"\train-rate-max_strlen = 1 ;\n" + -"\train-today_strlen = 1 ;\n" + -"\train-year_strlen = 4 ;\n" + -"\ttemp_strlen = 4 ;\n" + -"\ttemp-high_strlen = 2 ;\n" + -"\ttemp-low_strlen = 2 ;\n" + -"\ttemp-rate_strlen = 3 ;\n" + -"\tsunrise_strlen = 13 ;\n" + -"\tsunset_strlen = 13 ;\n" + -"\twet-bulb_strlen = 6 ;\n" + -"\twind-speed_strlen = 1 ;\n" + -"\twind-speed-avg_strlen = 1 ;\n" + -"\twind-direction_strlen = 3 ;\n" + -"\twind-direction-avg_strlen = 1 ;\n" + -"variables:\n" + -"\tchar ob-date(row, ob-date_strlen) ;\n" + -"\t\tob-date:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + -"\tchar station-id(row, station-id_strlen) ;\n" + -"\tchar station(row, station_strlen) ;\n" + -"\tchar city-state-zip(row, city-state-zip_strlen) ;\n" + -"\tchar city-state(row, city-state_strlen) ;\n" + -"\tchar site-url(row, site-url_strlen) ;\n" + -"\tchar aux-temp(row, aux-temp_strlen) ;\n" + -"\t\taux-temp:units = \"degree_F\" ;\n" + -"\tchar aux-temp-rate(row, aux-temp-rate_strlen) ;\n" + -"\t\taux-temp-rate:units = \"degree_F\" ;\n" + -"\tchar dew-point(row, dew-point_strlen) ;\n" + -"\t\tdew-point:units = \"degree_F\" ;\n" + -"\tchar elevation(row, elevation_strlen) ;\n" + -"\t\televation:units = \"ft\" ;\n" + -"\tchar feels-like(row, feels-like_strlen) ;\n" + -"\t\tfeels-like:units = \"degree_F\" ;\n" + -"\tchar gust-time(row, gust-time_strlen) ;\n" + -"\t\tgust-time:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + -"\tchar gust-direction(row, gust-direction_strlen) ;\n" + -"\tchar gust-speed(row, gust-speed_strlen) ;\n" + -"\t\tgust-speed:units = \"mph\" ;\n" + -"\tchar humidity(row, humidity_strlen) ;\n" + -"\t\thumidity:units = \"%\" ;\n" + -"\tchar humidity-high(row, humidity-high_strlen) ;\n" + -"\t\thumidity-high:units = \"%\" ;\n" + -"\tchar humidity-low(row, humidity-low_strlen) ;\n" + -"\t\thumidity-low:units = \"%\" ;\n" + -"\tchar humidity-rate(row, humidity-rate_strlen) ;\n" + -"\tchar indoor-temp(row, indoor-temp_strlen) ;\n" + -"\t\tindoor-temp:units = \"degree_F\" ;\n" + -"\tchar indoor-temp-rate(row, indoor-temp-rate_strlen) ;\n" + -"\t\tindoor-temp-rate:units = \"degree_F\" ;\n" + -"\tchar light(row, light_strlen) ;\n" + -"\tchar light-rate(row, light-rate_strlen) ;\n" + -"\tchar moon-phase-moon-phase-img(row, moon-phase-moon-phase-img_strlen) ;\n" + -"\tchar moon-phase(row, moon-phase_strlen) ;\n" + -"\tchar pressure(row, pressure_strlen) ;\n" + -"\t\tpressure:units = \"inch_Hg\" ;\n" + -"\tchar pressure-high(row, pressure-high_strlen) ;\n" + -"\t\tpressure-high:units = \"inch_Hg\" ;\n" + -"\tchar pressure-low(row, pressure-low_strlen) ;\n" + -"\t\tpressure-low:units = \"inch_Hg\" ;\n" + -"\tchar pressure-rate(row, pressure-rate_strlen) ;\n" + -"\t\tpressure-rate:units = \"inch_Hg/h\" ;\n" + -"\tchar rain-month(row, rain-month_strlen) ;\n" + -"\t\train-month:units = \"inches\" ;\n" + -"\tchar rain-rate(row, rain-rate_strlen) ;\n" + -"\t\train-rate:units = \"inches/h\" ;\n" + -"\tchar rain-rate-max(row, rain-rate-max_strlen) ;\n" + -"\t\train-rate-max:units = \"inches/h\" ;\n" + -"\tchar rain-today(row, rain-today_strlen) ;\n" + -"\t\train-today:units = \"inches\" ;\n" + -"\tchar rain-year(row, rain-year_strlen) ;\n" + -"\t\train-year:units = \"inches\" ;\n" + -"\tchar temp(row, temp_strlen) ;\n" + -"\t\ttemp:units = \"degree_F\" ;\n" + -"\tchar temp-high(row, temp-high_strlen) ;\n" + -"\t\ttemp-high:units = \"degree_F\" ;\n" + -"\tchar temp-low(row, temp-low_strlen) ;\n" + -"\t\ttemp-low:units = \"degree_F\" ;\n" + -"\tchar temp-rate(row, temp-rate_strlen) ;\n" + -"\t\ttemp-rate:units = \"degree_F\" ;\n" + -"\tchar sunrise(row, sunrise_strlen) ;\n" + -"\t\tsunrise:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + -"\tchar sunset(row, sunset_strlen) ;\n" + -"\t\tsunset:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + -"\tchar wet-bulb(row, wet-bulb_strlen) ;\n" + -"\t\twet-bulb:units = \"degree_F\" ;\n" + -"\tchar wind-speed(row, wind-speed_strlen) ;\n" + -"\t\twind-speed:units = \"mph\" ;\n" + -"\tchar wind-speed-avg(row, wind-speed-avg_strlen) ;\n" + -"\t\twind-speed-avg:units = \"mph\" ;\n" + -"\tchar wind-direction(row, wind-direction_strlen) ;\n" + -"\tchar wind-direction-avg(row, wind-direction-avg_strlen) ;\n" + -"\n" + -"// global attributes:\n" + -"}\n" + -"ob-date,station-id,station,city-state-zip,city-state,site-url,aux-temp,aux-temp-rate,dew-point,elevation,feels-like,gust-time,gust-direction,gust-speed,humidity,humidity-high,humidity-low,humidity-rate,indoor-temp,indoor-temp-rate,light,light-rate,moon-phase-moon-phase-img,moon-phase,pressure,pressure-high,pressure-low,pressure-rate,rain-month,rain-rate,rain-rate-max,rain-today,rain-year,temp,temp-high,temp-low,temp-rate,sunrise,sunset,wet-bulb,wind-speed,wind-speed-avg,wind-direction,wind-direction-avg\n" + -"1.3519746E9,SNFLS,Exploratorium,94123,\"San Francisco, CA\",,32,0,54,0,67,1.3519746E9,E,8,63,100,63,-6,90,+4.6,67.9,-0.3,mphase16.gif,82,30.1,30.14,30.06,-0.01,0.21,0,0,0,1.76,66.9,67,52,3.8,1.351953497E9,1.351991286E9,59.162,0,2,ENE,E\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - Test.ensureEqual(Calendar2.epochSecondsToIsoStringTZ(1.3519746E9), "2012-11-03T20:30:00Z", ""); - Test.ensureEqual(Calendar2.epochSecondsToIsoStringTZ(1.3519746E9), "2012-11-03T20:30:00Z", ""); - Test.ensureEqual(Calendar2.epochSecondsToIsoStringTZ(1.351953497E9), "2012-11-03T14:38:17Z", ""); - Test.ensureEqual(Calendar2.epochSecondsToIsoStringTZ(1.351991286E9), "2012-11-04T01:08:06Z", ""); - } - /** * This writes the table's data attributes (as if it were a DODS Sequence) * to the outputStream as an DODS DAS (see www.opendap.org, DAP 2.0, 7.2.1). @@ -6211,162 +5191,6 @@ public int readEnhancedFlatNc(String fullName, String loadColumns[]) throws Exce return ENHANCED_VERSION; //successfully read (and perhaps converted to current version) } - /** - * This makes a tough test table. - */ - public static Table makeToughTestTable() { - - Table table = new Table(); - - Attributes gatts = table.globalAttributes(); - gatts.add("tests", "a\u00fcb\nc\td\u20acz"); - gatts.add("testc", '\u00fc'); - gatts.add("testub", UByteArray.fromCSV( "0, 255")); - gatts.add("testus", UShortArray.fromCSV("0, 65535")); - gatts.add("testui", UIntArray.fromCSV( "0, 4294967295")); - gatts.add("testl", new LongArray(new long[]{Long.MIN_VALUE, Long.MAX_VALUE})); - gatts.add("testul", ULongArray.fromCSV("0, 9223372036854775807, 18446744073709551615")); - gatts.add("testi", new IntArray(new int[]{Integer.MIN_VALUE, Integer.MAX_VALUE})); - - table.addColumn(0, "aString", - new StringArray(new String[]{"a\u00fcb\nc\td\u20ace", "ab", "", "cd", ""}), - (new Attributes()).add("test", "a\u00fcb\nc\td\u20ace")); - - table.addColumn(1, "aChar", - new CharArray(new char[]{'\u00fc', (char)0, 'A', '\t', '\u20ac'}), - (new Attributes()).add("test", '\u00fc')); - - table.addColumn(2, "aByte", //min, med, fv, max-1, max - new ByteArray(new byte[]{Byte.MIN_VALUE, 0, 99, 126, Byte.MAX_VALUE}).setMaxIsMV(true), - (new Attributes()).add("_FillValue", ByteArray.fromCSV("99")) - .add("test", ByteArray.fromCSV("-128, 127"))); - table.addColumn(3, "aUByte", - new UByteArray(new short[]{0, 127, 99, 254, 255}).setMaxIsMV(true), - (new Attributes()).add("_FillValue", UByteArray.fromCSV("99")) - .add("test", UByteArray.fromCSV("0, 255"))); - table.addColumn(4, "aShort", - new ShortArray(new short[]{Short.MIN_VALUE, 0, 9999, 32766, Short.MAX_VALUE}).setMaxIsMV(true), - (new Attributes()).add("_FillValue", ShortArray.fromCSV("9999")) - .add("test", ShortArray.fromCSV("-32768, 32767"))); - table.addColumn(5, "aUShort", - UShortArray.fromCSV("0, 32767, 9999, 65534, 65535").setMaxIsMV(true), - (new Attributes()).add("_FillValue", UShortArray.fromCSV("9999")) - .add("test", UShortArray.fromCSV("0, 65535"))); - table.addColumn(6, "anInt", - new IntArray(new int[]{Integer.MIN_VALUE, 0, 999999999, Integer.MAX_VALUE-1, Integer.MAX_VALUE}).setMaxIsMV(true), - (new Attributes()).add("_FillValue", IntArray.fromCSV("999999999")) - .add("test", IntArray.fromCSV("-2147483648, 2147483647"))); - table.addColumn(7, "aUInt", - new UIntArray(new long[]{0, 7, Integer.MAX_VALUE, Math2.UINT_MAX_VALUE-1, Math2.UINT_MAX_VALUE}).setMaxIsMV(true), - (new Attributes()).add("_FillValue", UIntArray.fromCSV("999999999")) - .add("test", UIntArray.fromCSV("0, 4294967295"))); - table.addColumn(8, "aLong", - new LongArray(new long[]{Long.MIN_VALUE, 0, 8, Long.MAX_VALUE-1, Long.MAX_VALUE}).setMaxIsMV(true), - (new Attributes()).add("_FillValue", LongArray.fromCSV("999999999999")) - .add("test", LongArray.fromCSV("-9223372036854775808, 9223372036854775807"))); - table.addColumn(9, "aULong", - ULongArray.fromCSV("0, 1, 9223372036854775807, 18446744073709551614, 18446744073709551615").setMaxIsMV(true), - (new Attributes()).add("_FillValue", ULongArray.fromCSV("999999999999")) - .add("test", ULongArray.fromCSV("0, 18446744073709551615"))); - table.addColumn(10, "aFloat", - new FloatArray(new float[]{-Float.MAX_VALUE, 2.2f, Float.MIN_VALUE, Float.MAX_VALUE, Float.NaN}), - (new Attributes()).add("_FillValue", 1e36f) - .add("test", new FloatArray(new float[]{-Float.MAX_VALUE, Float.NaN}))); - table.addColumn(11, "aDouble", - new DoubleArray(new double[]{-Double.MAX_VALUE, 3.3, Double.MIN_VALUE, Double.MAX_VALUE, Double.NaN}), - (new Attributes()).add("_FillValue", 1e300) - .add("test", new DoubleArray(new double[]{-Double.MAX_VALUE, Double.NaN}))); - return table; - - } - - - /** - * This tests saveAsEnhancedFlatNcFile and readEnhancedFlatNcFile. - */ - public static void testEnhancedFlatNcFile() throws Exception { - - String2.log("\n*** Table.testEnhancedFlatNcFile()"); - String results, expected; - String fileName = File2.getSystemTempDirectory() + "enhancedFlatNcFile.nc"; - - Table table = makeToughTestTable(); - expected = String2.annotatedString(table.toString()); - String2.log("expected=\n" + expected); - - table.saveAsEnhancedFlatNc(fileName); - results = String2.annotatedString(table.toString()); - Test.ensureEqual(results, expected, "a"); //saveAsEnhancedFlatNc didn't change anything - table.clear(); - - table.readEnhancedFlatNc(fileName, null); - table.globalAttributes().remove("id"); - results = String2.annotatedString(table.toString()); - expected = -"{[10]\n" + -"dimensions:[10]\n" + -"[9]row = 5 ;[10]\n" + -"[9]aString_strlen = 9 ;[10]\n" + -"variables:[10]\n" + -"[9]char aString(row, aString_strlen) ;[10]\n" + -"[9][9]aString:test = \"a[252]b[10]\n" + -"c\\td[8364]e\" ;[10]\n" + -"[9]char aChar(row) ;[10]\n" + -"[9][9]aChar:test = \"[252]\" ;[10]\n" + -"[9]byte aByte(row) ;[10]\n" + -"[9][9]aByte:_FillValue = 99 ;[10]\n" + -"[9][9]aByte:test = -128, 127 ;[10]\n" + -"[9]ubyte aUByte(row) ;[10]\n" + -"[9][9]aUByte:_FillValue = 99 ;[10]\n" + -"[9][9]aUByte:test = 0, 255 ;[10]\n" + -"[9]short aShort(row) ;[10]\n" + -"[9][9]aShort:_FillValue = 9999 ;[10]\n" + -"[9][9]aShort:test = -32768, 32767 ;[10]\n" + -"[9]ushort aUShort(row) ;[10]\n" + -"[9][9]aUShort:_FillValue = 9999 ;[10]\n" + -"[9][9]aUShort:test = 0, 65535 ;[10]\n" + -"[9]int anInt(row) ;[10]\n" + -"[9][9]anInt:_FillValue = 999999999 ;[10]\n" + -"[9][9]anInt:test = -2147483648, 2147483647 ;[10]\n" + -"[9]uint aUInt(row) ;[10]\n" + -"[9][9]aUInt:_FillValue = 999999999 ;[10]\n" + -"[9][9]aUInt:test = 0, 4294967295 ;[10]\n" + -"[9]long aLong(row) ;[10]\n" + -"[9][9]aLong:_FillValue = 999999999999 ;[10]\n" + -"[9][9]aLong:test = -9223372036854775808, 9223372036854775807 ;[10]\n" + -"[9]ulong aULong(row) ;[10]\n" + -"[9][9]aULong:_FillValue = 999999999999 ;[10]\n" + -"[9][9]aULong:test = 0, 18446744073709551615 ;[10]\n" + -"[9]float aFloat(row) ;[10]\n" + -"[9][9]aFloat:_FillValue = 1.0E36f ;[10]\n" + -"[9][9]aFloat:test = -3.4028235E38f, NaNf ;[10]\n" + -"[9]double aDouble(row) ;[10]\n" + -"[9][9]aDouble:_FillValue = 1.0E300 ;[10]\n" + -"[9][9]aDouble:test = -1.7976931348623157E308, NaN ;[10]\n" + -"[10]\n" + -"// global attributes:[10]\n" + -"[9][9]:testc = \"[252]\" ;[10]\n" + -"[9][9]:testi = -2147483648, 2147483647 ;[10]\n" + -"[9][9]:testl = -9223372036854775808, 9223372036854775807 ;[10]\n" + -"[9][9]:tests = \"a[252]b[10]\n" + -"c\\td[8364]z\" ;[10]\n" + -"[9][9]:testub = 0, 255 ;[10]\n" + -"[9][9]:testui = 0, 4294967295 ;[10]\n" + -"[9][9]:testul = 0, 9223372036854775807, 18446744073709551615 ;[10]\n" + -"[9][9]:testus = 0, 65535 ;[10]\n" + -"}[10]\n" + -"aString,aChar,aByte,aUByte,aShort,aUShort,anInt,aUInt,aLong,aULong,aFloat,aDouble[10]\n" + -"a\\u00fcb\\nc\\td\\u20ace,\\u00fc,-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308[10]\n" + -"ab,\\u0000,0,127,0,32767,0,7,0,1,2.2,3.3[10]\n" + -",A,99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324[10]\n" + -"cd,\\t,126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308[10]\n" + -",\\u20ac,,,,,,,,,,[10]\n" + -"[end]"; - Test.ensureEqual(results, expected, "b"); - } - - - /** * This reads all rows of all of the specified columns in a flat .nc file * or an http: (several 1D variables (columns), all referencing the @@ -8060,104 +6884,6 @@ else if (treatDimensionsAs[d0].length < 2) } } - /** - * Test readMultidimNc with treatDimensionsAs specified. - */ - public static void testHardReadMultidimNc() throws Exception { - String fileName = String2.unitTestDataDir + "nc/GLsubdir/GL_201207_TS_DB_44761.nc"; - String2.log("\n*** Table.testHardReadMultidimNc(" + fileName + ")"); - Table.debugMode = true; - Table table = new Table(); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readMultidimNc(fileName, - StringArray.fromCSV("TIME,LATITUDE,LONGITUDE,DEPTH,TEMP,TEMP_DM"), //loadVarNames, - null, //loadDimNames, - new String[][]{{"LATITUDE","LONGITUDE","TIME"}}, //treatDimensionsAs - true, //getMetadata, - 0, //standardizeWhat, - true, //removeMVRows, - null, null, null); //conVars, conOps, conVals - String2.log(table.toString(5)); - String results = table.dataToString(5); - String expected = -"TIME,LATITUDE,LONGITUDE,DEPTH,TEMP,TEMP_DM\n" + -"22837.541666666668,48.309,-44.112,-99999.0,12.6,R\n" + -"22837.583333333332,48.313,-44.111,-99999.0,12.6,R\n" + -"22837.625,48.317,-44.107,-99999.0,12.7,R\n" + -"22837.666666666668,48.318,-44.103,-99999.0,13.0,R\n" + -"22837.708333333332,48.315,-44.097,-99999.0,13.1,R\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //time - Test.ensureEqual(table.getColumnName(0), "TIME", ""); - Test.ensureEqual(table.columnAttributes(0).getString("units"), - "days since 1950-01-01T00:00:00Z", "results=\n" + results); - Test.ensureEqual(table.columnAttributes(0).getDouble("valid_min"), - 0.0, "results=\n" + results); - Test.ensureEqual(table.columnAttributes(0).getDouble("valid_max"), - 90000.0, "results=\n" + results); - //depth - Test.ensureEqual(table.getColumnName(3), "DEPTH", ""); - Test.ensureEqual(table.columnAttributes(3).getFloat("_FillValue"), - -99999f, "results=\n" + results); - Test.ensureEqual(table.columnAttributes(3).getString("units"), - "meter", "results=\n" + results); - //temp - Test.ensureEqual(table.getColumnName(4), "TEMP", ""); - Test.ensureEqual(table.columnAttributes(4).getFloat("_FillValue"), - 9.96921E36f, "results=\n" + results); - Test.ensureEqual(table.columnAttributes(4).getString("units"), - "degree_Celsius", "results=\n" + results); - - - //standardizeWhat - table.clear(); - table.readMultidimNc(fileName, - StringArray.fromCSV("TIME,LATITUDE,LONGITUDE,DEPTH,TEMP,TEMP_DM"), //loadVarNames, - null, //loadDimNames, - new String[][]{{"LATITUDE","LONGITUDE","TIME"}}, //treatDimensionsAs - true, //getMetadata, - 1+2+4096, //standardizeWhat, - true, //removeMVRows, - null, null, null); //conVars, conOps, conVals - String2.log(table.toString(5)); - results = table.dataToString(5); - expected = -"TIME,LATITUDE,LONGITUDE,DEPTH,TEMP,TEMP_DM\n" + -"1.3420116E9,48.309,-44.112,,12.6,R\n" + -"1.3420152E9,48.313,-44.111,,12.6,R\n" + -"1.3420188E9,48.317,-44.107,,12.7,R\n" + -"1.3420224E9,48.318,-44.103,,13.0,R\n" + -"1.342026E9,48.315,-44.097,,13.1,R\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //time - Test.ensureEqual(table.getColumnName(0), "TIME", ""); - Test.ensureEqual(table.columnAttributes(0).getString("units"), - "seconds since 1970-01-01T00:00:00Z", "results=\n" + results); - Test.ensureEqual(table.columnAttributes(0).getDouble("valid_min"), - -6.31152E8, "results=\n" + results); - Test.ensureEqual(table.columnAttributes(0).getDouble("valid_max"), - 7.144848E9, "results=\n" + results); - //depth - Test.ensureEqual(table.getColumnName(3), "DEPTH", ""); - Test.ensureEqual(table.columnAttributes(3).getFloat("_FillValue"), - Float.NaN, "results=\n" + results); - Test.ensureEqual(table.columnAttributes(3).getString("units"), - "m", "results=\n" + results); - //temp - Test.ensureEqual(table.getColumnName(4), "TEMP", ""); - Test.ensureEqual(table.columnAttributes(4).getFloat("_FillValue"), - Float.NaN, "results=\n" + results); - Test.ensureEqual(table.columnAttributes(4).getString("units"), - "degree_C", "results=\n" + results); - - - Table.debugMode = false; - } - - - /** * This standardizes every column. See Attributes.unpackVariable for details. */ @@ -8179,8 +6905,6 @@ public void standardizeLastColumn(int standardizeWhat) throws Exception { standardizeColumn(standardizeWhat, nColumns() - 1); } - - /** * This inserts columns starting at column #0 with the indices for the * specified shape (0, 1, 2, ..., for each dimension in shape[]). @@ -8209,579 +6933,6 @@ public void addIndexColumns(int shape[]) { } } - public static void testAddIndexColumns() throws Exception { - Table table = new Table(); - table.addIndexColumns(new int[]{3,2,4}); - String results = table.dataToString(); - String expected = -"_index_0,_index_1,_index_2\n" + -"0,0,0\n" + -"0,0,1\n" + -"0,0,2\n" + -"0,0,3\n" + -"0,1,0\n" + -"0,1,1\n" + -"0,1,2\n" + -"0,1,3\n" + -"1,0,0\n" + -"1,0,1\n" + -"1,0,2\n" + -"1,0,3\n" + -"1,1,0\n" + -"1,1,1\n" + -"1,1,2\n" + -"1,1,3\n" + -"2,0,0\n" + -"2,0,1\n" + -"2,0,2\n" + -"2,0,3\n" + -"2,1,0\n" + -"2,1,1\n" + -"2,1,2\n" + -"2,1,3\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } - - - /** This tests readMultidimNc by reading an Argo Profile file. */ - public static void testReadMultidimNc() throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebugMode = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadMultidimNc"); - Table table = new Table(); - //ftp://ftp.ifremer.fr/ifremer/argo/dac/csio/2901175/2901175_prof.nc - String fiName = String2.unitTestDataDir + "nc/2901175_prof.nc"; - String2.log(NcHelper.ncdump(fiName, "-h")); - String results, expectedStart, expectedEnd; - /* */ - - //** don't specify varNames or dimNames -- it find vars with most dims - table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, - true, 0, false, //readMetadata, standardizeWhat=0, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -//static vars and vars like char SCIENTIFIC_CALIB_COEFFICIENT(N_PROF=254, N_CALIB=1, N_PARAM=3, STRING256=256); -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 762, "nRows"); //254*3 - - //* same but quick reject based on constraint - table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, - true, 0, false, //readMetadata, standardizeWhat=0, removeMVRows - StringArray.fromCSV("FORMAT_VERSION,FORMAT_VERSION"), //conVars - StringArray.fromCSV("=,="), //conOps - StringArray.fromCSV("3.1,3.2")); //conVals - Test.ensureEqual(table.nRows(), 0, "nRows"); - - - //* test don't removeMVRows - table.readMultidimNc(fiName, null, - StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), - null, - true, 0, false, //readMetadata, standardizeWhat=0, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.toString(3); - expectedStart = -"{\n" + -"dimensions:\n" + -"\trow = 18034 ;\n" + -"\tDATA_TYPE_strlen = 12 ;\n" + -"\tFORMAT_VERSION_strlen = 3 ;\n" + -"\tHANDBOOK_VERSION_strlen = 3 ;\n" + -"\tREFERENCE_DATE_TIME_strlen = 14 ;\n" + -"\tDATE_CREATION_strlen = 14 ;\n" + -"\tDATE_UPDATE_strlen = 14 ;\n" + -"\tPLATFORM_NUMBER_strlen = 7 ;\n" + -"\tPROJECT_NAME_strlen = 18 ;\n" + -"\tPI_NAME_strlen = 11 ;\n" + -"\tDATA_CENTRE_strlen = 2 ;\n" + -"\tDC_REFERENCE_strlen = 14 ;\n" + -"\tDATA_STATE_INDICATOR_strlen = 2 ;\n" + -"\tPLATFORM_TYPE_strlen = 4 ;\n" + -"\tFLOAT_SERIAL_NO_strlen = 13 ;\n" + -"\tFIRMWARE_VERSION_strlen = 6 ;\n" + -"\tWMO_INST_TYPE_strlen = 3 ;\n" + -"\tPOSITIONING_SYSTEM_strlen = 5 ;\n" + -"\tVERTICAL_SAMPLING_SCHEME_strlen = 26 ;\n" + -"variables:\n" + -"\tchar DATA_TYPE(row, DATA_TYPE_strlen) ;\n" + -"\t\tDATA_TYPE:conventions = \"Argo reference table 1\" ;\n" + -"\t\tDATA_TYPE:long_name = \"Data type\" ;\n" + -"\tchar FORMAT_VERSION(row, FORMAT_VERSION_strlen) ;\n" + -"\t\tFORMAT_VERSION:long_name = \"File format version\" ;\n" + -"\tchar HANDBOOK_VERSION(row, HANDBOOK_VERSION_strlen) ;\n" + -"\t\tHANDBOOK_VERSION:long_name = \"Data handbook version\" ;\n" + -"\tchar REFERENCE_DATE_TIME(row, REFERENCE_DATE_TIME_strlen) ;\n" + -"\t\tREFERENCE_DATE_TIME:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tREFERENCE_DATE_TIME:long_name = \"Date of reference for Julian days\" ;\n" + -"\tchar DATE_CREATION(row, DATE_CREATION_strlen) ;\n" + -"\t\tDATE_CREATION:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tDATE_CREATION:long_name = \"Date of file creation\" ;\n" + -"\tchar DATE_UPDATE(row, DATE_UPDATE_strlen) ;\n" + -"\t\tDATE_UPDATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tDATE_UPDATE:long_name = \"Date of update of this file\" ;\n" + -"\tchar PLATFORM_NUMBER(row, PLATFORM_NUMBER_strlen) ;\n" + -"\t\tPLATFORM_NUMBER:conventions = \"WMO float identifier : A9IIIII\" ;\n" + -"\t\tPLATFORM_NUMBER:long_name = \"Float unique identifier\" ;\n" + -"\tchar PROJECT_NAME(row, PROJECT_NAME_strlen) ;\n" + -"\t\tPROJECT_NAME:long_name = \"Name of the project\" ;\n" + -"\tchar PI_NAME(row, PI_NAME_strlen) ;\n" + -"\t\tPI_NAME:long_name = \"Name of the principal investigator\" ;\n" + -"\tint CYCLE_NUMBER(row) ;\n" + -"\t\tCYCLE_NUMBER:_FillValue = 99999 ;\n" + -"\t\tCYCLE_NUMBER:conventions = \"0...N, 0 : launch cycle (if exists), 1 : first complete cycle\" ;\n" + -"\t\tCYCLE_NUMBER:long_name = \"Float cycle number\" ;\n" + -"\tchar DIRECTION(row) ;\n" + -"\t\tDIRECTION:conventions = \"A: ascending profiles, D: descending profiles\" ;\n" + -"\t\tDIRECTION:long_name = \"Direction of the station profiles\" ;\n" + -"\tchar DATA_CENTRE(row, DATA_CENTRE_strlen) ;\n" + -"\t\tDATA_CENTRE:conventions = \"Argo reference table 4\" ;\n" + -"\t\tDATA_CENTRE:long_name = \"Data centre in charge of float data processing\" ;\n" + -"\tchar DC_REFERENCE(row, DC_REFERENCE_strlen) ;\n" + -"\t\tDC_REFERENCE:conventions = \"Data centre convention\" ;\n" + -"\t\tDC_REFERENCE:long_name = \"Station unique identifier in data centre\" ;\n" + -"\tchar DATA_STATE_INDICATOR(row, DATA_STATE_INDICATOR_strlen) ;\n" + -"\t\tDATA_STATE_INDICATOR:conventions = \"Argo reference table 6\" ;\n" + -"\t\tDATA_STATE_INDICATOR:long_name = \"Degree of processing the data have passed through\" ;\n" + -"\tchar DATA_MODE(row) ;\n" + -"\t\tDATA_MODE:conventions = \"R : real time; D : delayed mode; A : real time with adjustment\" ;\n" + -"\t\tDATA_MODE:long_name = \"Delayed mode or real time data\" ;\n" + -"\tchar PLATFORM_TYPE(row, PLATFORM_TYPE_strlen) ;\n" + -"\t\tPLATFORM_TYPE:conventions = \"Argo reference table 23\" ;\n" + -"\t\tPLATFORM_TYPE:long_name = \"Type of float\" ;\n" + -"\tchar FLOAT_SERIAL_NO(row, FLOAT_SERIAL_NO_strlen) ;\n" + -"\t\tFLOAT_SERIAL_NO:long_name = \"Serial number of the float\" ;\n" + -"\tchar FIRMWARE_VERSION(row, FIRMWARE_VERSION_strlen) ;\n" + -"\t\tFIRMWARE_VERSION:long_name = \"Instrument firmware version\" ;\n" + -"\tchar WMO_INST_TYPE(row, WMO_INST_TYPE_strlen) ;\n" + -"\t\tWMO_INST_TYPE:conventions = \"Argo reference table 8\" ;\n" + -"\t\tWMO_INST_TYPE:long_name = \"Coded instrument type\" ;\n" + -"\tdouble JULD(row) ;\n" + -"\t\tJULD:_FillValue = 999999.0 ;\n" + -"\t\tJULD:axis = \"T\" ;\n" + -"\t\tJULD:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + -"\t\tJULD:long_name = \"Julian day (UTC) of the station relative to REFERENCE_DATE_TIME\" ;\n" + -"\t\tJULD:resolution = 0.0 ;\n" + -"\t\tJULD:standard_name = \"time\" ;\n" + -"\t\tJULD:units = \"days since 1950-01-01 00:00:00 UTC\" ;\n" + -"\tchar JULD_QC(row) ;\n" + -"\t\tJULD_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tJULD_QC:long_name = \"Quality on date and time\" ;\n" + -"\tdouble JULD_LOCATION(row) ;\n" + -"\t\tJULD_LOCATION:_FillValue = 999999.0 ;\n" + -"\t\tJULD_LOCATION:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + -"\t\tJULD_LOCATION:long_name = \"Julian day (UTC) of the location relative to REFERENCE_DATE_TIME\" ;\n" + -"\t\tJULD_LOCATION:resolution = 0.0 ;\n" + -"\t\tJULD_LOCATION:units = \"days since 1950-01-01 00:00:00 UTC\" ;\n" + -"\tdouble LATITUDE(row) ;\n" + -"\t\tLATITUDE:_FillValue = 99999.0 ;\n" + -"\t\tLATITUDE:axis = \"Y\" ;\n" + -"\t\tLATITUDE:long_name = \"Latitude of the station, best estimate\" ;\n" + -"\t\tLATITUDE:standard_name = \"latitude\" ;\n" + -"\t\tLATITUDE:units = \"degree_north\" ;\n" + -"\t\tLATITUDE:valid_max = 90.0 ;\n" + -"\t\tLATITUDE:valid_min = -90.0 ;\n" + -"\tdouble LONGITUDE(row) ;\n" + -"\t\tLONGITUDE:_FillValue = 99999.0 ;\n" + -"\t\tLONGITUDE:axis = \"X\" ;\n" + -"\t\tLONGITUDE:long_name = \"Longitude of the station, best estimate\" ;\n" + -"\t\tLONGITUDE:standard_name = \"longitude\" ;\n" + -"\t\tLONGITUDE:units = \"degree_east\" ;\n" + -"\t\tLONGITUDE:valid_max = 180.0 ;\n" + -"\t\tLONGITUDE:valid_min = -180.0 ;\n" + -"\tchar POSITION_QC(row) ;\n" + -"\t\tPOSITION_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tPOSITION_QC:long_name = \"Quality on position (latitude and longitude)\" ;\n" + -"\tchar POSITIONING_SYSTEM(row, POSITIONING_SYSTEM_strlen) ;\n" + -"\t\tPOSITIONING_SYSTEM:long_name = \"Positioning system\" ;\n" + -"\tchar PROFILE_PRES_QC(row) ;\n" + -"\t\tPROFILE_PRES_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_PRES_QC:long_name = \"Global quality flag of PRES profile\" ;\n" + -"\tchar PROFILE_TEMP_QC(row) ;\n" + -"\t\tPROFILE_TEMP_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_TEMP_QC:long_name = \"Global quality flag of TEMP profile\" ;\n" + -"\tchar PROFILE_PSAL_QC(row) ;\n" + -"\t\tPROFILE_PSAL_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_PSAL_QC:long_name = \"Global quality flag of PSAL profile\" ;\n" + -"\tchar VERTICAL_SAMPLING_SCHEME(row, VERTICAL_SAMPLING_SCHEME_strlen) ;\n" + -"\t\tVERTICAL_SAMPLING_SCHEME:conventions = \"Argo reference table 16\" ;\n" + -"\t\tVERTICAL_SAMPLING_SCHEME:long_name = \"Vertical sampling scheme\" ;\n" + -"\tint CONFIG_MISSION_NUMBER(row) ;\n" + -"\t\tCONFIG_MISSION_NUMBER:_FillValue = 99999 ;\n" + -"\t\tCONFIG_MISSION_NUMBER:conventions = \"1...N, 1 : first complete mission\" ;\n" + -"\t\tCONFIG_MISSION_NUMBER:long_name = \"Unique number denoting the missions performed by the float\" ;\n" + -"\tfloat PRES(row) ;\n" + -"\t\tPRES:_FillValue = 99999.0f ;\n" + -"\t\tPRES:axis = \"Z\" ;\n" + -"\t\tPRES:C_format = \"%7.1f\" ;\n" + -"\t\tPRES:FORTRAN_format = \"F7.1\" ;\n" + -"\t\tPRES:long_name = \"Sea water pressure, equals 0 at sea-level\" ;\n" + -"\t\tPRES:resolution = 1.0f ;\n" + -"\t\tPRES:standard_name = \"sea_water_pressure\" ;\n" + -"\t\tPRES:units = \"decibar\" ;\n" + -"\t\tPRES:valid_max = 12000.0f ;\n" + -"\t\tPRES:valid_min = 0.0f ;\n" + -"\tchar PRES_QC(row) ;\n" + -"\t\tPRES_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tPRES_QC:long_name = \"quality flag\" ;\n" + -"\tfloat PRES_ADJUSTED(row) ;\n" + -"\t\tPRES_ADJUSTED:_FillValue = 99999.0f ;\n" + -"\t\tPRES_ADJUSTED:axis = \"Z\" ;\n" + -"\t\tPRES_ADJUSTED:C_format = \"%7.1f\" ;\n" + -"\t\tPRES_ADJUSTED:FORTRAN_format = \"F7.1\" ;\n" + -"\t\tPRES_ADJUSTED:long_name = \"Sea water pressure, equals 0 at sea-level\" ;\n" + -"\t\tPRES_ADJUSTED:resolution = 1.0f ;\n" + -"\t\tPRES_ADJUSTED:standard_name = \"sea_water_pressure\" ;\n" + -"\t\tPRES_ADJUSTED:units = \"decibar\" ;\n" + -"\t\tPRES_ADJUSTED:valid_max = 12000.0f ;\n" + -"\t\tPRES_ADJUSTED:valid_min = 0.0f ;\n" + -"\tchar PRES_ADJUSTED_QC(row) ;\n" + -"\t\tPRES_ADJUSTED_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tPRES_ADJUSTED_QC:long_name = \"quality flag\" ;\n" + -"\tfloat PRES_ADJUSTED_ERROR(row) ;\n" + -"\t\tPRES_ADJUSTED_ERROR:_FillValue = 99999.0f ;\n" + -"\t\tPRES_ADJUSTED_ERROR:C_format = \"%7.1f\" ;\n" + -"\t\tPRES_ADJUSTED_ERROR:FORTRAN_format = \"F7.1\" ;\n" + -"\t\tPRES_ADJUSTED_ERROR:long_name = \"Contains the error on the adjusted values as determined by the delayed mode QC process\" ;\n" + -"\t\tPRES_ADJUSTED_ERROR:resolution = 1.0f ;\n" + -"\t\tPRES_ADJUSTED_ERROR:units = \"decibar\" ;\n" + -"\tfloat TEMP(row) ;\n" + -"\t\tTEMP:_FillValue = 99999.0f ;\n" + -"\t\tTEMP:C_format = \"%9.3f\" ;\n" + -"\t\tTEMP:FORTRAN_format = \"F9.3\" ;\n" + -"\t\tTEMP:long_name = \"Sea temperature in-situ ITS-90 scale\" ;\n" + -"\t\tTEMP:resolution = 0.001f ;\n" + -"\t\tTEMP:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTEMP:units = \"degree_Celsius\" ;\n" + -"\t\tTEMP:valid_max = 40.0f ;\n" + -"\t\tTEMP:valid_min = -2.5f ;\n" + -"\tchar TEMP_QC(row) ;\n" + -"\t\tTEMP_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tTEMP_QC:long_name = \"quality flag\" ;\n" + -"\tfloat TEMP_ADJUSTED(row) ;\n" + -"\t\tTEMP_ADJUSTED:_FillValue = 99999.0f ;\n" + -"\t\tTEMP_ADJUSTED:C_format = \"%9.3f\" ;\n" + -"\t\tTEMP_ADJUSTED:FORTRAN_format = \"F9.3\" ;\n" + -"\t\tTEMP_ADJUSTED:long_name = \"Sea temperature in-situ ITS-90 scale\" ;\n" + -"\t\tTEMP_ADJUSTED:resolution = 0.001f ;\n" + -"\t\tTEMP_ADJUSTED:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTEMP_ADJUSTED:units = \"degree_Celsius\" ;\n" + -"\t\tTEMP_ADJUSTED:valid_max = 40.0f ;\n" + -"\t\tTEMP_ADJUSTED:valid_min = -2.5f ;\n" + -"\tchar TEMP_ADJUSTED_QC(row) ;\n" + -"\t\tTEMP_ADJUSTED_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tTEMP_ADJUSTED_QC:long_name = \"quality flag\" ;\n" + -"\tfloat TEMP_ADJUSTED_ERROR(row) ;\n" + -"\t\tTEMP_ADJUSTED_ERROR:_FillValue = 99999.0f ;\n" + -"\t\tTEMP_ADJUSTED_ERROR:C_format = \"%9.3f\" ;\n" + -"\t\tTEMP_ADJUSTED_ERROR:FORTRAN_format = \"F9.3\" ;\n" + -"\t\tTEMP_ADJUSTED_ERROR:long_name = \"Contains the error on the adjusted values as determined by the delayed mode QC process\" ;\n" + -"\t\tTEMP_ADJUSTED_ERROR:resolution = 0.001f ;\n" + -"\t\tTEMP_ADJUSTED_ERROR:units = \"degree_Celsius\" ;\n" + -"\tfloat PSAL(row) ;\n" + -"\t\tPSAL:_FillValue = 99999.0f ;\n" + -"\t\tPSAL:C_format = \"%9.3f\" ;\n" + -"\t\tPSAL:FORTRAN_format = \"F9.3\" ;\n" + -"\t\tPSAL:long_name = \"Practical salinity\" ;\n" + -"\t\tPSAL:resolution = 0.001f ;\n" + -"\t\tPSAL:standard_name = \"sea_water_salinity\" ;\n" + -"\t\tPSAL:units = \"psu\" ;\n" + -"\t\tPSAL:valid_max = 41.0f ;\n" + -"\t\tPSAL:valid_min = 2.0f ;\n" + -"\tchar PSAL_QC(row) ;\n" + -"\t\tPSAL_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tPSAL_QC:long_name = \"quality flag\" ;\n" + -"\tfloat PSAL_ADJUSTED(row) ;\n" + -"\t\tPSAL_ADJUSTED:_FillValue = 99999.0f ;\n" + -"\t\tPSAL_ADJUSTED:C_format = \"%9.3f\" ;\n" + -"\t\tPSAL_ADJUSTED:FORTRAN_format = \"F9.3\" ;\n" + -"\t\tPSAL_ADJUSTED:long_name = \"Practical salinity\" ;\n" + -"\t\tPSAL_ADJUSTED:resolution = 0.001f ;\n" + -"\t\tPSAL_ADJUSTED:standard_name = \"sea_water_salinity\" ;\n" + -"\t\tPSAL_ADJUSTED:units = \"psu\" ;\n" + -"\t\tPSAL_ADJUSTED:valid_max = 41.0f ;\n" + -"\t\tPSAL_ADJUSTED:valid_min = 2.0f ;\n" + -"\tchar PSAL_ADJUSTED_QC(row) ;\n" + -"\t\tPSAL_ADJUSTED_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tPSAL_ADJUSTED_QC:long_name = \"quality flag\" ;\n" + -"\tfloat PSAL_ADJUSTED_ERROR(row) ;\n" + -"\t\tPSAL_ADJUSTED_ERROR:_FillValue = 99999.0f ;\n" + -"\t\tPSAL_ADJUSTED_ERROR:C_format = \"%9.3f\" ;\n" + -"\t\tPSAL_ADJUSTED_ERROR:FORTRAN_format = \"F9.3\" ;\n" + -"\t\tPSAL_ADJUSTED_ERROR:long_name = \"Contains the error on the adjusted values as determined by the delayed mode QC process\" ;\n" + -"\t\tPSAL_ADJUSTED_ERROR:resolution = 0.001f ;\n" + -"\t\tPSAL_ADJUSTED_ERROR:units = \"psu\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:Conventions = \"Argo-3.1 CF-1.6\" ;\n" + -"\t\t:featureType = \"trajectoryProfile\" ;\n" + -"\t\t:history = \"2016-04-15T20:47:22Z creation\" ;\n" + -"\t\t:institution = \"Coriolis GDAC\" ;\n" + -"\t\t:references = \"http://www.argodatamgt.org/Documentation\" ;\n" + -"\t\t:source = \"Argo float\" ;\n" + -"\t\t:title = \"Argo float vertical profile\" ;\n" + -"\t\t:user_manual_version = \"3.1\" ;\n" + -"}\n"; - Test.ensureEqual(results.substring(0, expectedStart.length()), expectedStart, "results=\n" + results); - - results = table.dataToString(3); - expectedStart = -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,5.9,1,5.8,1,2.4,24.989,1,24.989,1,0.002,34.555,1,34.55511,1,0.01\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,10.0,1,9.9,1,2.4,24.99,1,24.99,1,0.002,34.554,1,34.55505,1,0.01\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,20.1,1,20.0,1,2.4,24.69,1,24.69,1,0.002,34.56,1,34.56191,1,0.01\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 18034, "nRows"); //254*71 - - //and the end of that table - table.removeRows(0, table.nRows() - 3); - results = table.dataToString(5); - expectedEnd = -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1899.9,1,1899.3,1,99999.0,2.055,1,2.055,1,99999.0,34.612,1,34.612,1,99999.0\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1950.0,1,1949.4,1,99999.0,2.014,1,2.014,1,99999.0,34.617,1,34.617,1,99999.0\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,99999.0,\" \",99999.0,\" \",99999.0,99999.0,\" \",99999.0,\" \",99999.0,99999.0,\" \",99999.0,\" \",99999.0\n"; - Test.ensureEqual(results, expectedEnd, "results=\n" + results); - - - //* test do removeMVRows - table.readMultidimNc(fiName, null, StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); - - //and test data at the end of that table - table.removeRows(0, table.nRows() - 3); - results = table.dataToString(5); - expectedEnd = -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1850.0,1,1849.4,1,99999.0,2.106,1,2.106,1,99999.0,34.604,1,34.604,1,99999.0\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1899.9,1,1899.3,1,99999.0,2.055,1,2.055,1,99999.0,34.612,1,34.612,1,99999.0\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1950.0,1,1949.4,1,99999.0,2.014,1,2.014,1,99999.0,34.617,1,34.617,1,99999.0\n"; - Test.ensureEqual(results, expectedEnd, "results=\n" + results); - - //* same but quick reject based on constraint LAT,LON 26.587,154.853 - //*** this takes 9ms while test above takes 99ms! - table.readMultidimNc(fiName, null, StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - StringArray.fromCSV("LATITUDE"), //conVars - StringArray.fromCSV("="), //conOps - StringArray.fromCSV("45")); //conVals - Test.ensureEqual(table.nRows(), 0, "nRows"); - - //* test different dim order (should be rearranged so the same) - table.readMultidimNc(fiName, null, StringArray.fromCSV("N_LEVELS, ZZTOP, N_PROF"), null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); - - //and test data at the end of that table - table.removeRows(0, table.nRows() - 3); - results = table.dataToString(5); - Test.ensureEqual(results, expectedEnd, "results=\n" + results); - - //* test read all and constrain PLATFORM_NUMBER - //Roland reported this problem 2016-06-21: returned 0 rows, saying: - //"Returning an empty table because var=PLATFORM_NUMBER failed its constraints, including =2901175. time=0" - - table.readMultidimNc(fiName, StringArray.fromCSV( - "DATA_TYPE, FORMAT_VERSION, HANDBOOK_VERSION, REFERENCE_DATE_TIME, DATE_CREATION, " + - "DATE_UPDATE, PLATFORM_NUMBER, PROJECT_NAME, PI_NAME, CYCLE_NUMBER, DIRECTION, " + - "DATA_CENTRE, DC_REFERENCE, DATA_STATE_INDICATOR, DATA_MODE, PLATFORM_TYPE, " + - "FLOAT_SERIAL_NO, FIRMWARE_VERSION, WMO_INST_TYPE, JULD, JULD_QC, JULD_LOCATION, " + - "LATITUDE, LONGITUDE, POSITION_QC, POSITIONING_SYSTEM, PROFILE_PRES_QC, " + - "PROFILE_TEMP_QC, PROFILE_PSAL_QC, VERTICAL_SAMPLING_SCHEME, " + - "CONFIG_MISSION_NUMBER, PRES, PRES_QC, PRES_ADJUSTED, PRES_ADJUSTED_QC, " + - "PRES_ADJUSTED_ERROR, TEMP, TEMP_QC, TEMP_ADJUSTED, TEMP_ADJUSTED_QC, " + - "TEMP_ADJUSTED_ERROR, PSAL, PSAL_QC, PSAL_ADJUSTED, PSAL_ADJUSTED_QC, " + - "PSAL_ADJUSTED_ERROR"), null, null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - StringArray.fromCSV("PLATFORM_NUMBER"), //conVars, conOps, conVals - StringArray.fromCSV("="), - StringArray.fromCSV("2901175")); - results = table.dataToString(3); - expectedStart = -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION," + -"DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE," + -"DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO," + -"FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE," + -"POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC," + -"VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED," + -"PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC," + -"TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + - -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175," + -"CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846," + -"21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1," + -"ARGOS,A,A,A,,1,5.9,1,5.8,1,2.4,24.989,1,24.989,1,0.002,34.555,1,34.55511," + -"1,0.01\n" + - -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175," + -"CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846," + -"21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1," + -"ARGOS,A,A,A,,1,10.0,1,9.9,1,2.4,24.99,1,24.99,1,0.002,34.554,1,34.55505," + -"1,0.01\n" + - -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175," + -"CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846," + -"21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1," + -"ARGOS,A,A,A,,1,20.1,1,20.0,1,2.4,24.69,1,24.69,1,0.002,34.56,1,34.56191," + -"1,0.01\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); //same as when all variables were explicitly loaded - - - - //* test different varNames - table.readMultidimNc(fiName, - StringArray.fromCSV("DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR"), - null, null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); - - //and test data at the end of that table - table.removeRows(0, table.nRows() - 3); - results = table.dataToString(5); - Test.ensureEqual(results, expectedEnd, "results=\n" + results); - - - //* test do removeMVRows when loadVariables is limited (to ensure all are loaded for the test) - table.readMultidimNc(fiName, StringArray.fromCSV("LONGITUDE,PRES,PSAL_ADJUSTED_ERROR"), - null, null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"LONGITUDE,PRES,PSAL_ADJUSTED_ERROR\n" + -"123.36499786376953,5.9,0.01\n" + -"123.36499786376953,10.0,0.01\n" + -"123.36499786376953,20.1,0.01\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); //same as when all variables were explicitly loaded - - //and test data at the end of that table - table.removeRows(0, table.nRows() - 3); - results = table.dataToString(5); - expectedEnd = -"LONGITUDE,PRES,PSAL_ADJUSTED_ERROR\n" + -"154.853,1850.0,99999.0\n" + //these rows were're removed because other full-dim vars had values -"154.853,1899.9,99999.0\n" + -"154.853,1950.0,99999.0\n"; - Test.ensureEqual(results, expectedEnd, "results=\n" + results); - - - //* test read JULD - table.readMultidimNc(fiName, StringArray.fromCSV("JULD"), null, null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"JULD\n" + -"21660.34238425926\n" + -"21670.351828703704\n" + -"21680.386898148146\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 254, "nRows"); //same as when all variables were explicitly loaded - - table.removeRows(0, 251); - results = table.dataToString(1000); - expectedStart = -"JULD\n" + -"24190.451828703703\n" + -"24200.381412037037\n" + -"24210.44662037037\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - - - //* test read JULD && PRES - table.readMultidimNc(fiName, StringArray.fromCSV("JULD,PRES"), null, null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"JULD,PRES\n" + -"21660.34238425926,5.9\n" + //JULD is correctly JOINed -"21660.34238425926,10.0\n" + -"21660.34238425926,20.1\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); //same as when all variables were explicitly loaded - - table.removeRows(0, 17263); - results = table.dataToString(1000); - expectedStart = -"JULD,PRES\n" + -"24210.44662037037,1850.0\n" + //JULD is correctly JOINed -"24210.44662037037,1899.9\n" + -"24210.44662037037,1950.0\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - - - //* test read just static vars, in a different order - table.readMultidimNc(fiName, - StringArray.fromCSV("HANDBOOK_VERSION,FORMAT_VERSION,DATA_TYPE"), - null, null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"HANDBOOK_VERSION,FORMAT_VERSION,DATA_TYPE\n" + -"1.2,3.1,Argo profile\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - - - //* test read 0 dim variable -> empty table - table.readMultidimNc(fiName, - StringArray.fromCSV("HISTORY_INSTITUTION"), - null, null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - //* test read non-existent dim -> just scalar vars - table.readMultidimNc(fiName, - null, StringArray.fromCSV("ZZTOP"), null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - - //* test read non-existent Var -> empty table - table.readMultidimNc(fiName, - StringArray.fromCSV("ZZTOP"), null, null, - true, 0, true, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - //done - /* */ - debugMode = oDebugMode; - } - /** * 2021: NOT FINISHED. This reads and flattens a group of variables in a sequence or nested sequence * in a .nc or .bufr file. @@ -9024,979 +7175,6 @@ public static void testReadMultidimNc() throws Exception { } */ - /** NOT FINISHED. This tests readNcSequence. */ -/* public static void testReadNcSequence() throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebugMode = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcSequence"); - Table table = new Table(); - String fiName = "/data/andy/pilot_20210818202736_IUPA50_EGRR_181930.bufr"; //String2.unitTestDataDir + ""; - String2.log(NcHelper.ncdump(fiName, "")); - String results, expectedStart, expectedEnd; - - //** don't specify varNames or dimNames -- it find vars with most dims - table.readNcSequence(fiName, new StringArray(), new StringArray(), - true, 0, //readMetadata, standardizeWhat=0 - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -//static vars and vars like char SCIENTIFIC_CALIB_COEFFICIENT(N_PROF=254, N_CALIB=1, N_PARAM=3, STRING256=256); -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 762, "nRows"); //254*3 - - //* same but quick reject based on constraint - table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, - true, 0, false, //readMetadata, standardizeWhat=0, removeMVRows - StringArray.fromCSV("FORMAT_VERSION,FORMAT_VERSION"), //conVars - StringArray.fromCSV("=,="), //conOps - StringArray.fromCSV("3.1,3.2")); //conVals - Test.ensureEqual(table.nRows(), 0, "nRows"); - - //done - debugMode = oDebugMode; - } */ - - /** This tests unpack by reading an Argo Profile file. */ - public static void testUnpack() throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebugMode = debugMode; - debugMode = true; - String2.log("\n*** Table.testUnpack"); - Table table = new Table(); - //ftp://ftp.ifremer.fr/ifremer/argo/dac/csio/2901175/2901175_prof.nc - String fiName = String2.unitTestDataDir + "nc/2901175_prof.nc"; - String results, expected; - - //** test the original packed format for comparison - table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, - true, 0, false, //readMetadata, unpack, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.toString(3); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 762 ;\n" + -"\tDATA_TYPE_strlen = 12 ;\n" + -"\tFORMAT_VERSION_strlen = 3 ;\n" + -"\tHANDBOOK_VERSION_strlen = 3 ;\n" + -"\tREFERENCE_DATE_TIME_strlen = 14 ;\n" + -"\tDATE_CREATION_strlen = 14 ;\n" + -"\tDATE_UPDATE_strlen = 14 ;\n" + -"\tPLATFORM_NUMBER_strlen = 7 ;\n" + -"\tPROJECT_NAME_strlen = 18 ;\n" + -"\tPI_NAME_strlen = 11 ;\n" + -"\tSTATION_PARAMETERS_strlen = 4 ;\n" + -"\tDATA_CENTRE_strlen = 2 ;\n" + -"\tDC_REFERENCE_strlen = 14 ;\n" + -"\tDATA_STATE_INDICATOR_strlen = 2 ;\n" + -"\tPLATFORM_TYPE_strlen = 4 ;\n" + -"\tFLOAT_SERIAL_NO_strlen = 13 ;\n" + -"\tFIRMWARE_VERSION_strlen = 6 ;\n" + -"\tWMO_INST_TYPE_strlen = 3 ;\n" + -"\tPOSITIONING_SYSTEM_strlen = 5 ;\n" + -"\tVERTICAL_SAMPLING_SCHEME_strlen = 26 ;\n" + -"\tPARAMETER_strlen = 4 ;\n" + -"\tSCIENTIFIC_CALIB_EQUATION_strlen = 153 ;\n" + -"\tSCIENTIFIC_CALIB_COEFFICIENT_strlen = 55 ;\n" + -"\tSCIENTIFIC_CALIB_COMMENT_strlen = 124 ;\n" + -"\tSCIENTIFIC_CALIB_DATE_strlen = 14 ;\n" + -"variables:\n" + -"\tchar DATA_TYPE(row, DATA_TYPE_strlen) ;\n" + -"\t\tDATA_TYPE:conventions = \"Argo reference table 1\" ;\n" + -"\t\tDATA_TYPE:long_name = \"Data type\" ;\n" + -"\tchar FORMAT_VERSION(row, FORMAT_VERSION_strlen) ;\n" + -"\t\tFORMAT_VERSION:long_name = \"File format version\" ;\n" + -"\tchar HANDBOOK_VERSION(row, HANDBOOK_VERSION_strlen) ;\n" + -"\t\tHANDBOOK_VERSION:long_name = \"Data handbook version\" ;\n" + -"\tchar REFERENCE_DATE_TIME(row, REFERENCE_DATE_TIME_strlen) ;\n" + -"\t\tREFERENCE_DATE_TIME:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tREFERENCE_DATE_TIME:long_name = \"Date of reference for Julian days\" ;\n" + -"\tchar DATE_CREATION(row, DATE_CREATION_strlen) ;\n" + -"\t\tDATE_CREATION:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tDATE_CREATION:long_name = \"Date of file creation\" ;\n" + -"\tchar DATE_UPDATE(row, DATE_UPDATE_strlen) ;\n" + -"\t\tDATE_UPDATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tDATE_UPDATE:long_name = \"Date of update of this file\" ;\n" + -"\tchar PLATFORM_NUMBER(row, PLATFORM_NUMBER_strlen) ;\n" + -"\t\tPLATFORM_NUMBER:conventions = \"WMO float identifier : A9IIIII\" ;\n" + -"\t\tPLATFORM_NUMBER:long_name = \"Float unique identifier\" ;\n" + -"\tchar PROJECT_NAME(row, PROJECT_NAME_strlen) ;\n" + -"\t\tPROJECT_NAME:long_name = \"Name of the project\" ;\n" + -"\tchar PI_NAME(row, PI_NAME_strlen) ;\n" + -"\t\tPI_NAME:long_name = \"Name of the principal investigator\" ;\n" + -"\tchar STATION_PARAMETERS(row, STATION_PARAMETERS_strlen) ;\n" + -"\t\tSTATION_PARAMETERS:conventions = \"Argo reference table 3\" ;\n" + -"\t\tSTATION_PARAMETERS:long_name = \"List of available parameters for the station\" ;\n" + -"\tint CYCLE_NUMBER(row) ;\n" + -"\t\tCYCLE_NUMBER:_FillValue = 99999 ;\n" + -"\t\tCYCLE_NUMBER:conventions = \"0...N, 0 : launch cycle (if exists), 1 : first complete cycle\" ;\n" + -"\t\tCYCLE_NUMBER:long_name = \"Float cycle number\" ;\n" + -"\tchar DIRECTION(row) ;\n" + -"\t\tDIRECTION:conventions = \"A: ascending profiles, D: descending profiles\" ;\n" + -"\t\tDIRECTION:long_name = \"Direction of the station profiles\" ;\n" + -"\tchar DATA_CENTRE(row, DATA_CENTRE_strlen) ;\n" + -"\t\tDATA_CENTRE:conventions = \"Argo reference table 4\" ;\n" + -"\t\tDATA_CENTRE:long_name = \"Data centre in charge of float data processing\" ;\n" + -"\tchar DC_REFERENCE(row, DC_REFERENCE_strlen) ;\n" + -"\t\tDC_REFERENCE:conventions = \"Data centre convention\" ;\n" + -"\t\tDC_REFERENCE:long_name = \"Station unique identifier in data centre\" ;\n" + -"\tchar DATA_STATE_INDICATOR(row, DATA_STATE_INDICATOR_strlen) ;\n" + -"\t\tDATA_STATE_INDICATOR:conventions = \"Argo reference table 6\" ;\n" + -"\t\tDATA_STATE_INDICATOR:long_name = \"Degree of processing the data have passed through\" ;\n" + -"\tchar DATA_MODE(row) ;\n" + -"\t\tDATA_MODE:conventions = \"R : real time; D : delayed mode; A : real time with adjustment\" ;\n" + -"\t\tDATA_MODE:long_name = \"Delayed mode or real time data\" ;\n" + -"\tchar PLATFORM_TYPE(row, PLATFORM_TYPE_strlen) ;\n" + -"\t\tPLATFORM_TYPE:conventions = \"Argo reference table 23\" ;\n" + -"\t\tPLATFORM_TYPE:long_name = \"Type of float\" ;\n" + -"\tchar FLOAT_SERIAL_NO(row, FLOAT_SERIAL_NO_strlen) ;\n" + -"\t\tFLOAT_SERIAL_NO:long_name = \"Serial number of the float\" ;\n" + -"\tchar FIRMWARE_VERSION(row, FIRMWARE_VERSION_strlen) ;\n" + -"\t\tFIRMWARE_VERSION:long_name = \"Instrument firmware version\" ;\n" + -"\tchar WMO_INST_TYPE(row, WMO_INST_TYPE_strlen) ;\n" + -"\t\tWMO_INST_TYPE:conventions = \"Argo reference table 8\" ;\n" + -"\t\tWMO_INST_TYPE:long_name = \"Coded instrument type\" ;\n" + -"\tdouble JULD(row) ;\n" + -"\t\tJULD:_FillValue = 999999.0 ;\n" + -"\t\tJULD:axis = \"T\" ;\n" + -"\t\tJULD:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + -"\t\tJULD:long_name = \"Julian day (UTC) of the station relative to REFERENCE_DATE_TIME\" ;\n" + -"\t\tJULD:resolution = 0.0 ;\n" + -"\t\tJULD:standard_name = \"time\" ;\n" + -"\t\tJULD:units = \"days since 1950-01-01 00:00:00 UTC\" ;\n" + -"\tchar JULD_QC(row) ;\n" + -"\t\tJULD_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tJULD_QC:long_name = \"Quality on date and time\" ;\n" + -"\tdouble JULD_LOCATION(row) ;\n" + -"\t\tJULD_LOCATION:_FillValue = 999999.0 ;\n" + -"\t\tJULD_LOCATION:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + -"\t\tJULD_LOCATION:long_name = \"Julian day (UTC) of the location relative to REFERENCE_DATE_TIME\" ;\n" + -"\t\tJULD_LOCATION:resolution = 0.0 ;\n" + -"\t\tJULD_LOCATION:units = \"days since 1950-01-01 00:00:00 UTC\" ;\n" + -"\tdouble LATITUDE(row) ;\n" + -"\t\tLATITUDE:_FillValue = 99999.0 ;\n" + -"\t\tLATITUDE:axis = \"Y\" ;\n" + -"\t\tLATITUDE:long_name = \"Latitude of the station, best estimate\" ;\n" + -"\t\tLATITUDE:standard_name = \"latitude\" ;\n" + -"\t\tLATITUDE:units = \"degree_north\" ;\n" + -"\t\tLATITUDE:valid_max = 90.0 ;\n" + -"\t\tLATITUDE:valid_min = -90.0 ;\n" + -"\tdouble LONGITUDE(row) ;\n" + -"\t\tLONGITUDE:_FillValue = 99999.0 ;\n" + -"\t\tLONGITUDE:axis = \"X\" ;\n" + -"\t\tLONGITUDE:long_name = \"Longitude of the station, best estimate\" ;\n" + -"\t\tLONGITUDE:standard_name = \"longitude\" ;\n" + -"\t\tLONGITUDE:units = \"degree_east\" ;\n" + -"\t\tLONGITUDE:valid_max = 180.0 ;\n" + -"\t\tLONGITUDE:valid_min = -180.0 ;\n" + -"\tchar POSITION_QC(row) ;\n" + -"\t\tPOSITION_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tPOSITION_QC:long_name = \"Quality on position (latitude and longitude)\" ;\n" + -"\tchar POSITIONING_SYSTEM(row, POSITIONING_SYSTEM_strlen) ;\n" + -"\t\tPOSITIONING_SYSTEM:long_name = \"Positioning system\" ;\n" + -"\tchar PROFILE_PRES_QC(row) ;\n" + -"\t\tPROFILE_PRES_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_PRES_QC:long_name = \"Global quality flag of PRES profile\" ;\n" + -"\tchar PROFILE_TEMP_QC(row) ;\n" + -"\t\tPROFILE_TEMP_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_TEMP_QC:long_name = \"Global quality flag of TEMP profile\" ;\n" + -"\tchar PROFILE_PSAL_QC(row) ;\n" + -"\t\tPROFILE_PSAL_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_PSAL_QC:long_name = \"Global quality flag of PSAL profile\" ;\n" + -"\tchar VERTICAL_SAMPLING_SCHEME(row, VERTICAL_SAMPLING_SCHEME_strlen) ;\n" + -"\t\tVERTICAL_SAMPLING_SCHEME:conventions = \"Argo reference table 16\" ;\n" + -"\t\tVERTICAL_SAMPLING_SCHEME:long_name = \"Vertical sampling scheme\" ;\n" + -"\tint CONFIG_MISSION_NUMBER(row) ;\n" + -"\t\tCONFIG_MISSION_NUMBER:_FillValue = 99999 ;\n" + -"\t\tCONFIG_MISSION_NUMBER:conventions = \"1...N, 1 : first complete mission\" ;\n" + -"\t\tCONFIG_MISSION_NUMBER:long_name = \"Unique number denoting the missions performed by the float\" ;\n" + -"\tchar PARAMETER(row, PARAMETER_strlen) ;\n" + -"\t\tPARAMETER:conventions = \"Argo reference table 3\" ;\n" + -"\t\tPARAMETER:long_name = \"List of parameters with calibration information\" ;\n" + -"\tchar SCIENTIFIC_CALIB_EQUATION(row, SCIENTIFIC_CALIB_EQUATION_strlen) ;\n" + -"\t\tSCIENTIFIC_CALIB_EQUATION:long_name = \"Calibration equation for this parameter\" ;\n" + -"\tchar SCIENTIFIC_CALIB_COEFFICIENT(row, SCIENTIFIC_CALIB_COEFFICIENT_strlen) ;\n" + -"\t\tSCIENTIFIC_CALIB_COEFFICIENT:long_name = \"Calibration coefficients for this equation\" ;\n" + -"\tchar SCIENTIFIC_CALIB_COMMENT(row, SCIENTIFIC_CALIB_COMMENT_strlen) ;\n" + -"\t\tSCIENTIFIC_CALIB_COMMENT:long_name = \"Comment applying to this parameter calibration\" ;\n" + -"\tchar SCIENTIFIC_CALIB_DATE(row, SCIENTIFIC_CALIB_DATE_strlen) ;\n" + -"\t\tSCIENTIFIC_CALIB_DATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tSCIENTIFIC_CALIB_DATE:long_name = \"Date of calibration\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:Conventions = \"Argo-3.1 CF-1.6\" ;\n" + -"\t\t:featureType = \"trajectoryProfile\" ;\n" + -"\t\t:history = \"2016-04-15T20:47:22Z creation\" ;\n" + -"\t\t:institution = \"Coriolis GDAC\" ;\n" + -"\t\t:references = \"http://www.argodatamgt.org/Documentation\" ;\n" + -"\t\t:source = \"Argo float\" ;\n" + -"\t\t:title = \"Argo float vertical profile\" ;\n" + -"\t\t:user_manual_version = \"3.1\" ;\n" + -"}\n" + -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - //** don't specify varNames or dimNames -- it find vars with most dims - table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, - true, 3, false, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.toString(3); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 762 ;\n" + -"\tDATA_TYPE_strlen = 12 ;\n" + -"\tFORMAT_VERSION_strlen = 3 ;\n" + -"\tHANDBOOK_VERSION_strlen = 3 ;\n" + -"\tREFERENCE_DATE_TIME_strlen = 14 ;\n" + -"\tDATE_CREATION_strlen = 14 ;\n" + -"\tDATE_UPDATE_strlen = 14 ;\n" + -"\tPLATFORM_NUMBER_strlen = 7 ;\n" + -"\tPROJECT_NAME_strlen = 18 ;\n" + -"\tPI_NAME_strlen = 11 ;\n" + -"\tSTATION_PARAMETERS_strlen = 4 ;\n" + -"\tDATA_CENTRE_strlen = 2 ;\n" + -"\tDC_REFERENCE_strlen = 14 ;\n" + -"\tDATA_STATE_INDICATOR_strlen = 2 ;\n" + -"\tPLATFORM_TYPE_strlen = 4 ;\n" + -"\tFLOAT_SERIAL_NO_strlen = 13 ;\n" + -"\tFIRMWARE_VERSION_strlen = 6 ;\n" + -"\tWMO_INST_TYPE_strlen = 3 ;\n" + -"\tPOSITIONING_SYSTEM_strlen = 5 ;\n" + -"\tVERTICAL_SAMPLING_SCHEME_strlen = 26 ;\n" + -"\tPARAMETER_strlen = 4 ;\n" + -"\tSCIENTIFIC_CALIB_EQUATION_strlen = 153 ;\n" + -"\tSCIENTIFIC_CALIB_COEFFICIENT_strlen = 55 ;\n" + -"\tSCIENTIFIC_CALIB_COMMENT_strlen = 124 ;\n" + -"\tSCIENTIFIC_CALIB_DATE_strlen = 14 ;\n" + -"variables:\n" + -"\tchar DATA_TYPE(row, DATA_TYPE_strlen) ;\n" + -"\t\tDATA_TYPE:conventions = \"Argo reference table 1\" ;\n" + -"\t\tDATA_TYPE:long_name = \"Data type\" ;\n" + -"\tchar FORMAT_VERSION(row, FORMAT_VERSION_strlen) ;\n" + -"\t\tFORMAT_VERSION:long_name = \"File format version\" ;\n" + -"\tchar HANDBOOK_VERSION(row, HANDBOOK_VERSION_strlen) ;\n" + -"\t\tHANDBOOK_VERSION:long_name = \"Data handbook version\" ;\n" + -"\tchar REFERENCE_DATE_TIME(row, REFERENCE_DATE_TIME_strlen) ;\n" + -"\t\tREFERENCE_DATE_TIME:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tREFERENCE_DATE_TIME:long_name = \"Date of reference for Julian days\" ;\n" + -"\tchar DATE_CREATION(row, DATE_CREATION_strlen) ;\n" + -"\t\tDATE_CREATION:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tDATE_CREATION:long_name = \"Date of file creation\" ;\n" + -"\tchar DATE_UPDATE(row, DATE_UPDATE_strlen) ;\n" + -"\t\tDATE_UPDATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tDATE_UPDATE:long_name = \"Date of update of this file\" ;\n" + -"\tchar PLATFORM_NUMBER(row, PLATFORM_NUMBER_strlen) ;\n" + -"\t\tPLATFORM_NUMBER:conventions = \"WMO float identifier : A9IIIII\" ;\n" + -"\t\tPLATFORM_NUMBER:long_name = \"Float unique identifier\" ;\n" + -"\tchar PROJECT_NAME(row, PROJECT_NAME_strlen) ;\n" + -"\t\tPROJECT_NAME:long_name = \"Name of the project\" ;\n" + -"\tchar PI_NAME(row, PI_NAME_strlen) ;\n" + -"\t\tPI_NAME:long_name = \"Name of the principal investigator\" ;\n" + -"\tchar STATION_PARAMETERS(row, STATION_PARAMETERS_strlen) ;\n" + -"\t\tSTATION_PARAMETERS:conventions = \"Argo reference table 3\" ;\n" + -"\t\tSTATION_PARAMETERS:long_name = \"List of available parameters for the station\" ;\n" + -"\tint CYCLE_NUMBER(row) ;\n" + -"\t\tCYCLE_NUMBER:_FillValue = 2147483647 ;\n" + -"\t\tCYCLE_NUMBER:conventions = \"0...N, 0 : launch cycle (if exists), 1 : first complete cycle\" ;\n" + -"\t\tCYCLE_NUMBER:long_name = \"Float cycle number\" ;\n" + -"\tchar DIRECTION(row) ;\n" + -"\t\tDIRECTION:conventions = \"A: ascending profiles, D: descending profiles\" ;\n" + -"\t\tDIRECTION:long_name = \"Direction of the station profiles\" ;\n" + -"\tchar DATA_CENTRE(row, DATA_CENTRE_strlen) ;\n" + -"\t\tDATA_CENTRE:conventions = \"Argo reference table 4\" ;\n" + -"\t\tDATA_CENTRE:long_name = \"Data centre in charge of float data processing\" ;\n" + -"\tchar DC_REFERENCE(row, DC_REFERENCE_strlen) ;\n" + -"\t\tDC_REFERENCE:conventions = \"Data centre convention\" ;\n" + -"\t\tDC_REFERENCE:long_name = \"Station unique identifier in data centre\" ;\n" + -"\tchar DATA_STATE_INDICATOR(row, DATA_STATE_INDICATOR_strlen) ;\n" + -"\t\tDATA_STATE_INDICATOR:conventions = \"Argo reference table 6\" ;\n" + -"\t\tDATA_STATE_INDICATOR:long_name = \"Degree of processing the data have passed through\" ;\n" + -"\tchar DATA_MODE(row) ;\n" + -"\t\tDATA_MODE:conventions = \"R : real time; D : delayed mode; A : real time with adjustment\" ;\n" + -"\t\tDATA_MODE:long_name = \"Delayed mode or real time data\" ;\n" + -"\tchar PLATFORM_TYPE(row, PLATFORM_TYPE_strlen) ;\n" + -"\t\tPLATFORM_TYPE:conventions = \"Argo reference table 23\" ;\n" + -"\t\tPLATFORM_TYPE:long_name = \"Type of float\" ;\n" + -"\tchar FLOAT_SERIAL_NO(row, FLOAT_SERIAL_NO_strlen) ;\n" + -"\t\tFLOAT_SERIAL_NO:long_name = \"Serial number of the float\" ;\n" + -"\tchar FIRMWARE_VERSION(row, FIRMWARE_VERSION_strlen) ;\n" + -"\t\tFIRMWARE_VERSION:long_name = \"Instrument firmware version\" ;\n" + -"\tchar WMO_INST_TYPE(row, WMO_INST_TYPE_strlen) ;\n" + -"\t\tWMO_INST_TYPE:conventions = \"Argo reference table 8\" ;\n" + -"\t\tWMO_INST_TYPE:long_name = \"Coded instrument type\" ;\n" + -"\tdouble JULD(row) ;\n" + -"\t\tJULD:_FillValue = NaN ;\n" + -"\t\tJULD:axis = \"T\" ;\n" + -"\t\tJULD:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + -"\t\tJULD:long_name = \"Julian day (UTC) of the station relative to REFERENCE_DATE_TIME\" ;\n" + -"\t\tJULD:resolution = 0.0 ;\n" + -"\t\tJULD:standard_name = \"time\" ;\n" + -"\t\tJULD:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + -"\tchar JULD_QC(row) ;\n" + -"\t\tJULD_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tJULD_QC:long_name = \"Quality on date and time\" ;\n" + -"\tdouble JULD_LOCATION(row) ;\n" + -"\t\tJULD_LOCATION:_FillValue = NaN ;\n" + -"\t\tJULD_LOCATION:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + -"\t\tJULD_LOCATION:long_name = \"Julian day (UTC) of the location relative to REFERENCE_DATE_TIME\" ;\n" + -"\t\tJULD_LOCATION:resolution = 0.0 ;\n" + -"\t\tJULD_LOCATION:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + -"\tdouble LATITUDE(row) ;\n" + -"\t\tLATITUDE:_FillValue = NaN ;\n" + -"\t\tLATITUDE:axis = \"Y\" ;\n" + -"\t\tLATITUDE:long_name = \"Latitude of the station, best estimate\" ;\n" + -"\t\tLATITUDE:standard_name = \"latitude\" ;\n" + -"\t\tLATITUDE:units = \"degree_north\" ;\n" + -"\t\tLATITUDE:valid_max = 90.0 ;\n" + -"\t\tLATITUDE:valid_min = -90.0 ;\n" + -"\tdouble LONGITUDE(row) ;\n" + -"\t\tLONGITUDE:_FillValue = NaN ;\n" + -"\t\tLONGITUDE:axis = \"X\" ;\n" + -"\t\tLONGITUDE:long_name = \"Longitude of the station, best estimate\" ;\n" + -"\t\tLONGITUDE:standard_name = \"longitude\" ;\n" + -"\t\tLONGITUDE:units = \"degree_east\" ;\n" + -"\t\tLONGITUDE:valid_max = 180.0 ;\n" + -"\t\tLONGITUDE:valid_min = -180.0 ;\n" + -"\tchar POSITION_QC(row) ;\n" + -"\t\tPOSITION_QC:conventions = \"Argo reference table 2\" ;\n" + -"\t\tPOSITION_QC:long_name = \"Quality on position (latitude and longitude)\" ;\n" + -"\tchar POSITIONING_SYSTEM(row, POSITIONING_SYSTEM_strlen) ;\n" + -"\t\tPOSITIONING_SYSTEM:long_name = \"Positioning system\" ;\n" + -"\tchar PROFILE_PRES_QC(row) ;\n" + -"\t\tPROFILE_PRES_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_PRES_QC:long_name = \"Global quality flag of PRES profile\" ;\n" + -"\tchar PROFILE_TEMP_QC(row) ;\n" + -"\t\tPROFILE_TEMP_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_TEMP_QC:long_name = \"Global quality flag of TEMP profile\" ;\n" + -"\tchar PROFILE_PSAL_QC(row) ;\n" + -"\t\tPROFILE_PSAL_QC:conventions = \"Argo reference table 2a\" ;\n" + -"\t\tPROFILE_PSAL_QC:long_name = \"Global quality flag of PSAL profile\" ;\n" + -"\tchar VERTICAL_SAMPLING_SCHEME(row, VERTICAL_SAMPLING_SCHEME_strlen) ;\n" + -"\t\tVERTICAL_SAMPLING_SCHEME:conventions = \"Argo reference table 16\" ;\n" + -"\t\tVERTICAL_SAMPLING_SCHEME:long_name = \"Vertical sampling scheme\" ;\n" + -"\tint CONFIG_MISSION_NUMBER(row) ;\n" + -"\t\tCONFIG_MISSION_NUMBER:_FillValue = 2147483647 ;\n" + -"\t\tCONFIG_MISSION_NUMBER:conventions = \"1...N, 1 : first complete mission\" ;\n" + -"\t\tCONFIG_MISSION_NUMBER:long_name = \"Unique number denoting the missions performed by the float\" ;\n" + -"\tchar PARAMETER(row, PARAMETER_strlen) ;\n" + -"\t\tPARAMETER:conventions = \"Argo reference table 3\" ;\n" + -"\t\tPARAMETER:long_name = \"List of parameters with calibration information\" ;\n" + -"\tchar SCIENTIFIC_CALIB_EQUATION(row, SCIENTIFIC_CALIB_EQUATION_strlen) ;\n" + -"\t\tSCIENTIFIC_CALIB_EQUATION:long_name = \"Calibration equation for this parameter\" ;\n" + -"\tchar SCIENTIFIC_CALIB_COEFFICIENT(row, SCIENTIFIC_CALIB_COEFFICIENT_strlen) ;\n" + -"\t\tSCIENTIFIC_CALIB_COEFFICIENT:long_name = \"Calibration coefficients for this equation\" ;\n" + -"\tchar SCIENTIFIC_CALIB_COMMENT(row, SCIENTIFIC_CALIB_COMMENT_strlen) ;\n" + -"\t\tSCIENTIFIC_CALIB_COMMENT:long_name = \"Comment applying to this parameter calibration\" ;\n" + -"\tchar SCIENTIFIC_CALIB_DATE(row, SCIENTIFIC_CALIB_DATE_strlen) ;\n" + -"\t\tSCIENTIFIC_CALIB_DATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + -"\t\tSCIENTIFIC_CALIB_DATE:long_name = \"Date of calibration\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:Conventions = \"Argo-3.1 CF-1.6\" ;\n" + -"\t\t:featureType = \"trajectoryProfile\" ;\n" + -"\t\t:history = \"2016-04-15T20:47:22Z creation\" ;\n" + -"\t\t:institution = \"Coriolis GDAC\" ;\n" + -"\t\t:references = \"http://www.argodatamgt.org/Documentation\" ;\n" + -"\t\t:source = \"Argo float\" ;\n" + -"\t\t:title = \"Argo float vertical profile\" ;\n" + -"\t\t:user_manual_version = \"3.1\" ;\n" + -"}\n" + -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + -//from raw file dif JULD_LOCATION dif JULD_LOCATION -//"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,1.240301582E9,1,1.240301812E9,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,1.240301582E9,1,1.240301812E9,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,1.240301582E9,1,1.240301812E9,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - - //done - /* */ - debugMode = oDebugMode; - } - - - /** This tests readVlenNc. */ - public static void testReadVlenNc() throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebugMode = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadVlenNc"); - Table table = new Table(); - String fiName = String2.unitTestBigDataDir + "nccf/vlen/rr2_vlen_test.nc"; - String2.log(NcHelper.ncdump(fiName, "-h")); - String results, expectedStart, expectedEnd; - /* */ - - //** don't specify varNames or dimNames -- it find vars with most dims - table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, - true, 0, false, //readMetadata, standardizeWhat, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -//static vars and vars like char SCIENTIFIC_CALIB_COEFFICIENT(N_PROF=254, N_CALIB=1, N_PARAM=3, STRING256=256); -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 762, "nRows"); //254*3 -/* - //* same but quick reject based on constraint - table.readVlenNc(fiName, new StringArray(), new StringArray(), - true, false, //readMetadata, removeMVRows - StringArray.fromCSV("FORMAT_VERSION,FORMAT_VERSION"), //conVars - StringArray.fromCSV("=,="), //conOps - StringArray.fromCSV("3.1,3.2")); //conVals - Test.ensureEqual(table.nRows(), 0, "nRows"); - - - - //* test do removeMVRows - table.readVlenNc(fiName, null, StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), - true, false, //readMetadata, removeMVRows - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3, true); - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); - - //and test data at the end of that table - table.removeRows(0, table.nRows() - 3); - results = table.dataToString(5); - expectedEnd = -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1850.0,1,1849.4,1,99999.0,2.106,1,2.106,1,99999.0,34.604,1,34.604,1,99999.0\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1899.9,1,1899.3,1,99999.0,2.055,1,2.055,1,99999.0,34.612,1,34.612,1,99999.0\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1950.0,1,1949.4,1,99999.0,2.014,1,2.014,1,99999.0,34.617,1,34.617,1,99999.0\n"; - Test.ensureEqual(results, expectedEnd, "results=\n" + results); - - //* same but quick reject based on constraint LAT,LON 26.587,154.853 - //*** this takes 9ms while test above takes 99ms! - table.readVlenNc(fiName, null, StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), - true, //readMetadata, - StringArray.fromCSV("LATITUDE"), //conVars - StringArray.fromCSV("="), //conOps - StringArray.fromCSV("45")); //conVals - Test.ensureEqual(table.nRows(), 0, "nRows"); - - //* test different dim order (should be rearranged so the same) - table.readVlenNc(fiName, null, StringArray.fromCSV("N_LEVELS, ZZTOP, N_PROF"), - true, //readMetadata, - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3, true); - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); - - //and test data at the end of that table - table.removeRows(0, table.nRows() - 3); - results = table.dataToString(5, true); - Test.ensureEqual(results, expectedEnd, "results=\n" + results); - - - //* test different varNames - table.readVlenNc(fiName, - StringArray.fromCSV("DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR"), - null, - true, //readMetadata, - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3, true); - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); - - //and test data at the end of that table - table.removeRows(0, table.nRows() - 3); - results = table.dataToString(5, true); - Test.ensureEqual(results, expectedEnd, "results=\n" + results); - - - //* test read JULD - table.readVlenNc(fiName, StringArray.fromCSV("JULD"), null, - true, //readMetadata, - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"JULD\n" + -"21660.34238425926\n" + -"21670.351828703704\n" + -"21680.386898148146\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 254, "nRows"); //same as when all variables were explicitly loaded - - table.removeRows(0, 251); - results = table.dataToString(1000); - expectedStart = -"JULD\n" + -"24190.451828703703\n" + -"24200.381412037037\n" + -"24210.44662037037\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - - - //* test read JULD && PRES - table.readVlenNc(fiName, StringArray.fromCSV("JULD,PRES"), null, - true, //readMetadata, - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"JULD,PRES\n" + -"21660.34238425926,5.9\n" + //JULD is correctly JOINed -"21660.34238425926,10.0\n" + -"21660.34238425926,20.1\n" + -"...\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - Test.ensureEqual(table.nRows(), 17266, "nRows"); //same as when all variables were explicitly loaded - - table.removeRows(0, 17263); - results = table.dataToString(1000); - expectedStart = -"JULD,PRES\n" + -"24210.44662037037,1850.0\n" + //JULD is correctly JOINed -"24210.44662037037,1899.9\n" + -"24210.44662037037,1950.0\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - - - //* test read just static vars, in a different order - table.readVlenNc(fiName, - StringArray.fromCSV("HANDBOOK_VERSION,FORMAT_VERSION,DATA_TYPE"), - null, - true, //readMetadata, - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"HANDBOOK_VERSION,FORMAT_VERSION,DATA_TYPE\n" + -"1.2,3.1,Argo profile\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - - - //* test read 0 dim variable -> empty table - table.readVlenNc(fiName, - StringArray.fromCSV("HISTORY_INSTITUTION"), - null, - true, //readMetadata, - null, null, null); //conVars, conOps, conVals - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - //* test read non-existent dim -> just scalar vars - table.readVlenNc(fiName, - null, - StringArray.fromCSV("ZZTOP"), - true, //readMetadata, - null, null, null); //conVars, conOps, conVals - results = table.dataToString(3); - expectedStart = -"DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE\n" + -"Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722\n"; - Test.ensureEqual(results, expectedStart, "results=\n" + results); - - //* test read non-existent Var -> empty table - table.readVlenNc(fiName, - StringArray.fromCSV("ZZTOP"), - null, - true, //readMetadata, - null, null, null); //conVars, conOps, conVals - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - //done - /* */ - debugMode = oDebugMode; - } - - /** This tests readNDNC. */ - public static void testReadNDNc() throws Exception { - verbose = true; - reallyVerbose = true; - String2.log("\n*** Table.testReadNDNc"); - Table table = new Table(); - String results, expected; - - //test no vars specified, 4D, only 2nd dim has >1 value, getMetadata - String fiName = "c:/u00/data/points/erdCalcofiSubsurface/1950/subsurface_19500106_69_144.nc"; - table.readNDNc(fiName, null, 0, //standardizeWhat=0 - null, 0, 0); - results = table.toString(); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 16 ;\n" + -"variables:\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:units = \"seconds since 1948-1-1\" ;\n" + -"\tfloat depth(row) ;\n" + -"\t\tdepth:long_name = \"depth index\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:_FillValue = -999.0f ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:missing_value = -999.0f ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:_FillValue = -999.0f ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:missing_value = -999.0f ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tint stationyear(row) ;\n" + -"\t\tstationyear:_FillValue = -9999 ;\n" + -"\t\tstationyear:long_name = \"Station Year\" ;\n" + -"\t\tstationyear:missing_value = -9999 ;\n" + -"\t\tstationyear:units = \"years\" ;\n" + -"\tint stationmonth(row) ;\n" + -"\t\tstationmonth:_FillValue = -9999 ;\n" + -"\t\tstationmonth:long_name = \"Station Month\" ;\n" + -"\t\tstationmonth:missing_value = -9999 ;\n" + -"\t\tstationmonth:units = \"months\" ;\n" + -"\tint stationday(row) ;\n" + -"\t\tstationday:_FillValue = -9999 ;\n" + -"\t\tstationday:long_name = \"Station Day\" ;\n" + -"\t\tstationday:missing_value = -9999 ;\n" + -"\t\tstationday:units = \"days\" ;\n" + -"\tint stime(row) ;\n" + -"\t\tstime:_FillValue = -9999 ;\n" + -"\t\tstime:long_name = \"Cast Time (GMT)\" ;\n" + -"\t\tstime:missing_value = -9999 ;\n" + -"\t\tstime:units = \"GMT\" ;\n" + -"\tfloat stationline(row) ;\n" + -"\t\tstationline:_FillValue = -999.0f ;\n" + -"\t\tstationline:long_name = \"CALCOFI Line Number\" ;\n" + -"\t\tstationline:missing_value = -999.0f ;\n" + -"\t\tstationline:units = \"number\" ;\n" + -"\tfloat stationnum(row) ;\n" + -"\t\tstationnum:_FillValue = -999.0f ;\n" + -"\t\tstationnum:long_name = \"CALCOFI Station Number\" ;\n" + -"\t\tstationnum:missing_value = -999.0f ;\n" + -"\t\tstationnum:units = \"number\" ;\n" + -"\tfloat temperature(row) ;\n" + -"\t\ttemperature:_FillValue = -999.0f ;\n" + -"\t\ttemperature:has_data = 1 ;\n" + -"\t\ttemperature:long_name = \"Temperature\" ;\n" + -"\t\ttemperature:missing_value = -999.0f ;\n" + -"\t\ttemperature:units = \"degC\" ;\n" + -"\tfloat salinity(row) ;\n" + -"\t\tsalinity:_FillValue = -999.0f ;\n" + -"\t\tsalinity:has_data = 1 ;\n" + -"\t\tsalinity:long_name = \"Salinity\" ;\n" + -"\t\tsalinity:missing_value = -999.0f ;\n" + -"\t\tsalinity:units = \"PSU\" ;\n" + -"\tfloat pressure(row) ;\n" + -"\t\tpressure:_FillValue = -999.0f ;\n" + -"\t\tpressure:has_data = 0 ;\n" + -"\t\tpressure:long_name = \"Pressure\" ;\n" + -"\t\tpressure:missing_value = -999.0f ;\n" + -"\t\tpressure:units = \"decibars\" ;\n" + -"\tfloat oxygen(row) ;\n" + -"\t\toxygen:_FillValue = -999.0f ;\n" + -"\t\toxygen:has_data = 1 ;\n" + -"\t\toxygen:long_name = \"Oxygen\" ;\n" + -"\t\toxygen:missing_value = -999.0f ;\n" + -"\t\toxygen:units = \"milliliters/liter\" ;\n" + -"\tfloat po4(row) ;\n" + -"\t\tpo4:_FillValue = -999.0f ;\n" + -"\t\tpo4:has_data = 1 ;\n" + -"\t\tpo4:long_name = \"Phosphate\" ;\n" + -"\t\tpo4:missing_value = -999.0f ;\n" + -"\t\tpo4:units = \"ugram-atoms/liter\" ;\n" + -"\tfloat silicate(row) ;\n" + -"\t\tsilicate:_FillValue = -999.0f ;\n" + -"\t\tsilicate:has_data = 0 ;\n" + -"\t\tsilicate:long_name = \"Silicate\" ;\n" + -"\t\tsilicate:missing_value = -999.0f ;\n" + -"\t\tsilicate:units = \"ugram-atoms/liter\" ;\n" + -"\tfloat no2(row) ;\n" + -"\t\tno2:_FillValue = -999.0f ;\n" + -"\t\tno2:has_data = 0 ;\n" + -"\t\tno2:long_name = \"Nitrite\" ;\n" + -"\t\tno2:missing_value = -999.0f ;\n" + -"\t\tno2:units = \"ugram-atoms/liter\" ;\n" + -"\tfloat no3(row) ;\n" + -"\t\tno3:_FillValue = -999.0f ;\n" + -"\t\tno3:has_data = 0 ;\n" + -"\t\tno3:long_name = \"Nitrate\" ;\n" + -"\t\tno3:missing_value = -999.0f ;\n" + -"\t\tno3:units = \"ugram-atoms/liter\" ;\n" + -"\tfloat nh3(row) ;\n" + -"\t\tnh3:_FillValue = -999.0f ;\n" + -"\t\tnh3:has_data = 0 ;\n" + -"\t\tnh3:long_name = \"Ammonia\" ;\n" + -"\t\tnh3:missing_value = -999.0f ;\n" + -"\t\tnh3:units = \"ugram-atoms/liter\" ;\n" + -"\tfloat chl(row) ;\n" + -"\t\tchl:_FillValue = -999.0f ;\n" + -"\t\tchl:has_data = 0 ;\n" + -"\t\tchl:long_name = \"Chlorophyll-a\" ;\n" + -"\t\tchl:missing_value = -999.0f ;\n" + -"\t\tchl:units = \"milligrams/meter**3\" ;\n" + -"\tfloat dark(row) ;\n" + -"\t\tdark:_FillValue = -999.0f ;\n" + -"\t\tdark:has_data = 0 ;\n" + -"\t\tdark:long_name = \"Dark Bottle C14 Assimilation\" ;\n" + -"\t\tdark:missing_value = -999.0f ;\n" + -"\t\tdark:units = \"milligrams/meter**3/experiment\" ;\n" + -"\tfloat primprod(row) ;\n" + -"\t\tprimprod:_FillValue = -999.0f ;\n" + -"\t\tprimprod:has_data = 0 ;\n" + -"\t\tprimprod:long_name = \"Mean Primary Production (C14 Assimilation)\" ;\n" + -"\t\tprimprod:missing_value = -999.0f ;\n" + -"\t\tprimprod:units = \"milligrams/meter**3/experiment\" ;\n" + -"\tfloat lightpercent(row) ;\n" + -"\t\tlightpercent:_FillValue = -999.0f ;\n" + -"\t\tlightpercent:has_data = 0 ;\n" + -"\t\tlightpercent:long_name = \"Percent Light (for incubations)\" ;\n" + -"\t\tlightpercent:missing_value = -999.0f ;\n" + -"\t\tlightpercent:units = \"milligrams/meter**3/experiment\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:history = \"created by ERD from Matlab database created by Andrew Leising from the CalCOFI Physical data\" ;\n" + -"\t\t:title = \"CalCOFI Physical Observations, 1949-2001\" ;\n" + -"}\n" + -"time,depth,lat,lon,stationyear,stationmonth,stationday,stime,stationline,stationnum,temperature,salinity,pressure,oxygen,po4,silicate,no2,no3,nh3,chl,dark,primprod,lightpercent\n" + -"6.3612E7,0.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,16.19,33.6,-999.0,5.3,0.42,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,22.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,16.18,33.6,-999.0,5.26,0.38,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,49.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,16.2,33.6,-999.0,5.3,0.36,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,72.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,14.95,33.58,-999.0,5.51,0.37,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,98.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,13.02,33.35,-999.0,5.35,0.45,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,147.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,11.45,33.36,-999.0,4.99,0.81,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,194.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,9.32,33.55,-999.0,4.47,1.19,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,241.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,8.51,33.85,-999.0,4.02,1.51,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,287.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,7.74,33.95,-999.0,3.48,1.76,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,384.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,6.42,33.97,-999.0,2.55,2.15,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,477.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,5.35,34.04,-999.0,1.29,2.48,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,576.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,4.83,34.14,-999.0,0.73,2.73,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,673.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,4.44,34.22,-999.0,0.48,2.9,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,768.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,4.15,34.31,-999.0,0.37,2.87,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,969.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,3.67,34.43,-999.0,0.49,2.8,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + -"6.3612E7,1167.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,3.3,34.49,-999.0,0.66,2.7,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test specify vars (including out-of-order axis var, and nonsense var), !getMetadata - table.readNDNc(fiName, new String[]{"temperature", "lat", "salinity", "junk"}, 0, //standardizeWhat=0 - "depth", 100, 200); - results = table.dataToString(); - expected = -"time,depth,lat,lon,temperature,salinity\n" + -"6.3612E7,147.0,33.31667,-128.53333,11.45,33.36\n" + -"6.3612E7,194.0,33.31667,-128.53333,9.32,33.55\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test String vars - fiName = "c:/erddapBPD/copy/cPostDet3/BARBARAx20BLOCK/LAMNAx20DITROPIS/Nx2fA/52038_A69-1303_1059305.nc"; - table.readNDNc(fiName, null, 0, //standardizeWhat=0 - null, 0, 0); - results = table.dataToString(4); - expected = -"row,unique_tag_id,PI,longitude,latitude,time,bottom_depth,common_name,date_public,line,position_on_subarray,project,riser_height,role,scientific_name,serial_number,stock,surgery_time,surgery_location,tagger\n" + -"0,52038_A69-1303_1059305,BARBARA BLOCK,-146.1137,60.7172,1.2192849E9,,SALMON SHARK,1.273271649385E9,,,HOPKINS MARINE STATION,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,1059305,N/A,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\n" + -"1,52038_A69-1303_1059305,BARBARA BLOCK,-146.32355,60.66713,1.233325298E9,127.743902439024,SALMON SHARK,1.273271649385E9,PORT GRAVINA,6,HOPKINS MARINE STATION,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,1059305,N/A,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\n" + -"2,52038_A69-1303_1059305,BARBARA BLOCK,-146.32355,60.66713,1.233325733E9,127.743902439024,SALMON SHARK,1.273271649385E9,PORT GRAVINA,6,HOPKINS MARINE STATION,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,1059305,N/A,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\n" + -"3,52038_A69-1303_1059305,BARBARA BLOCK,-146.32355,60.66713,1.233325998E9,127.743902439024,SALMON SHARK,1.273271649385E9,PORT GRAVINA,6,HOPKINS MARINE STATION,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,1059305,N/A,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test 4D but request axis vars only, with constraints - fiName = "/u00/data/points/ndbcMet2/historical/NDBC_51001_met.nc"; //implied c: - table.readNDNc(fiName, new String[]{"LON", "LAT", "TIME"}, 0, //standardizeWhat=0 - "TIME", 1.2051936e9, 1.20528e9); - results = table.dataToString(4); - expected = -"LON,LAT,TIME\n" + -"-162.279,23.445,1.2051894E9\n" + -"-162.279,23.445,1.205193E9\n" + -"-162.279,23.445,1.2051966E9\n" + -"-162.279,23.445,1.2052002E9\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - } - - - /** This tests readNDNC. */ - public static void testReadNDNc2() throws Exception { - verbose = true; - reallyVerbose = true; - String2.log("\n*** Table.testReadNDNc2"); - String fiName = "c:/data/wod/monthly/APB/199804-199804/wod_008015632O.nc"; - Table table = new Table(); - String results, expected; - - //test no vars specified - table.readNDNc(fiName, null, 0, //standardizeWhat=0 - null, 0, 0); - results = table.toString(); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 11 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\tProject_strlen = 49 ;\n" + -"\tdataset_strlen = 14 ;\n" + -"variables:\n" + -"\tfloat z(row) ;\n" + -"\t\tz:long_name = \"depth_below_sea_level\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"altitude\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:flag_definitions = \"WODfp\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:Instrument_(WOD_code) = \"UNDERWAY: MK3 data recording tag (Wildlife Computers) mounted on elephant seal\" ;\n" + -"\t\tTemperature:long_name = \"Temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\t\tTemperature:WODprofile_flag = 9 ;\n" + -"\tint Temperature_sigfigs(row) ;\n" + -"\tint Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_definitions = \"WODf\" ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:country = \"UNITED STATES\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:axis = \"Y\" ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:axis = \"X\" ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:axis = \"T\" ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units = \"NODC_code\" ;\n" + -"\tchar Project(row, Project_strlen) ;\n" + -"\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + -"\t\tProject:long_name = \"Project_name\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tfloat ARGOS_last_fix(row) ;\n" + -"\t\tARGOS_last_fix:units = \"hours\" ;\n" + -"\tfloat ARGOS_next_fix(row) ;\n" + -"\t\tARGOS_next_fix:units = \"hours\" ;\n" + -"\tint crs(row) ;\n" + -"\t\tcrs:epsg_code = \"EPSG:4326\" ;\n" + -"\t\tcrs:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\tcrs:inverse_flattening = 298.25723f ;\n" + -"\t\tcrs:longitude_of_prime_meridian = 0.0f ;\n" + -"\t\tcrs:semi_major_axis = 6378137.0f ;\n" + -"\tint profile(row) ;\n" + -"\tint WODf(row) ;\n" + -"\t\tWODf:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tWODf:flag_values = \"0 1 2 3 4 5 6 7 8 9\" ;\n" + -"\t\tWODf:long_name = \"WOD_observation_flag\" ;\n" + -"\tint WODfp(row) ;\n" + -"\t\tWODfp:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tWODfp:flag_values = \"0 1 2 3 4 5 6 7 8 9\" ;\n" + -"\t\tWODfp:long_name = \"WOD_profile_flag\" ;\n" + -"\tint WODfd(row) ;\n" + -"\t\tWODfd:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tWODfd:flag_values = \"0 1 2\" ;\n" + -"\t\tWODfd:long_name = \"WOD_depth_level_\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cf_role = \"profile_id\" ;\n" + -"\t\t:Conventions = \"CF-1.5\" ;\n" + -"\t\t:featureType = \"profile\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:Metadata_Conventions = \"Unidata Dataset Discovery v1.0\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF-1.5\" ;\n" + -"}\n" + -"z,Temperature,Temperature_sigfigs,Temperature_WODflag,WOD_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,dataset,ARGOS_last_fix,ARGOS_next_fix,crs,profile,WODf,WODfp,WODfd\n" + -"0.0,7.9,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"10.0,7.9,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"42.0,7.8,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"76.0,7.8,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"120.0,7.8,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"166.0,7.5,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"212.0,7.0,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"260.0,6.5,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"308.0,5.8,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"354.0,5.2,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + -"402.0,4.9,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test specify 0D and 1D data vars (out-of-order, implied axis var, and nonsense var), !getMetadata - table.readNDNc(fiName, new String[]{ - "lon", "lat", "time", "Temperature", "WOD_cruise_identifier", "junk"}, 0, //standardizeWhat=0 - "z", 100, 200); - results = table.dataToString(); - expected = -"z,Temperature,WOD_cruise_identifier,lat,lon,time\n" + -"120.0,7.8,US025547,45.28,-142.24,83369.90625\n" + -"166.0,7.5,US025547,45.28,-142.24,83369.90625\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //request axis vars only, with constraints - table.readNDNc(fiName, new String[]{"z"}, 0, //standardizeWhat=0 - "z", 100, 200); - results = table.dataToString(); - expected = -"z\n" + -"120.0\n" + -"166.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //request 0D vars only, with constraints (ignored) - table.readNDNc(fiName, new String[]{ - "WOD_cruise_identifier", "Project", "junk", "lon", "lat"}, 0, //standardizeWhat=0 - "z", 100, 200); - results = table.dataToString(); - expected = -"WOD_cruise_identifier,lat,lon,Project\n" + -"US025547,45.28,-142.24,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES)\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //request axis var and 0D vars only, with constraints - table.readNDNc(fiName, new String[]{ - "WOD_cruise_identifier", "Project", "z", "junk", "lon", "lat"}, 0, //standardizeWhat=0 - "z", 100, 200); - results = table.dataToString(); - expected = -"z,WOD_cruise_identifier,lat,lon,Project\n" + -"120.0,US025547,45.28,-142.24,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES)\n" + -"166.0,US025547,45.28,-142.24,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES)\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - } - /** Used by readNcCF */ private int checkConsistent(String errorInMethod, String varName, int oldValue, int newValue) { @@ -11828,1866 +9006,164 @@ else if (loadVariableNames.size() > 0) } } + public static void testInteractiveNcCFMA(boolean pauseAfterEach) throws Exception { + //*************** trajectory multiple multidimensional --- + try { - /** This tests reading an ncCF Contiguous Ragged Array file with 7(!) sample_dimension's. - */ - public static void testReadNcCF7SampleDims() throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCF7SampleDims"); - Table table = new Table(); - String results, expected; - //From Ajay Krishnan, NCEI/NODC, from - //https://data.nodc.noaa.gov/thredds/catalog/testdata/wod_ragged/05052016/catalog.html?dataset=testdata/wod_ragged/05052016/ind199105_ctd.nc - String fileName = String2.unitTestDataDir + - "nccf/ncei/ind199105_ctd.nc"; - Attributes gatts; - String scalarVars = ",crs,WODf,WODfd"; - - String2.log("\n\n** Testing " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - //String2.pressEnterToContinue(NcHelper.ncdump(fileName, "-v crs;WODf;WODfd")); - //String2.pressEnterToContinue(NcHelper.ncdump(fileName, - // "-v Temperature_row_size;Salinity_row_size;Oxygen_row_size;Pressure_row_size;Chlorophyll_row_size")); - - //test reading just specified legit "z_obs" outer and inner variables - table.readNcCF(fileName, StringArray.fromCSV( - "zztop,wod_unique_cast,lat,lon,time,z,z_WODflag" + scalarVars), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -//with netcdf-java 4.6.5 and before, the last 3 vars had 0's. -//with netcdf-java 4.6.6 and after, they are the default cf missing values -//Unidata says it is not a bug. 4.6.6 is correct. see email from Sean Arms June 15, 2016 -//I notified source of files: Ajay Krisnan, but he never replied. -//so I'm going with 4.6.6 and odd values -//was -//"wod_unique_cast,lat,lon,time,z,z_WODflag,crs,WODf,WODfd\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,2.9759612,0,0,0,0\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,3.967939,0,0,0,0\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,5.9518795,0,0,0,0\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,7.9358006,0,0,0,0\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,9.919703,0,0,0,0\n" + -//"...\n"; -"wod_unique_cast,lat,lon,time,z,z_WODflag,crs,WODf,WODfd\n" + -"3390296,-43.7802,67.3953,80838.31180554628,2.9759612,0,-2147483647,-32767,-32767\n" + -"3390296,-43.7802,67.3953,80838.31180554628,3.967939,0,-2147483647,-32767,-32767\n" + -"3390296,-43.7802,67.3953,80838.31180554628,5.9518795,0,-2147483647,-32767,-32767\n" + -"3390296,-43.7802,67.3953,80838.31180554628,7.9358006,0,-2147483647,-32767,-32767\n" + -"3390296,-43.7802,67.3953,80838.31180554628,9.919703,0,-2147483647,-32767,-32767\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + Table table = new Table(); + String results, expected; + String pauseMessage = "\nOK?"; + String fileName = String2.unitTestDataDir + "CFPointConventions/trajectory/" + + "trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/" + + "trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.nc"; + String2.log("\n\n** Testing multiple multidimensional file\n" + + " " + fileName); + String2.log(NcHelper.ncdump(fileName, "-h")); - //test reading just specified legit "Temperature_obs" outer and inner variables - table.readNcCF(fileName, StringArray.fromCSV( - "zztop,wod_unique_cast,lat,lon,time,Temperature,Temperature_WODflag" + scalarVars), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -//was -//"wod_unique_cast,lat,lon,time,Temperature,Temperature_WODflag,crs,WODf,WODfd\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,14.519,0,0,0,0\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,14.526,0,0,0,0\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,14.537,0,0,0,0\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,14.533,0,0,0,0\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,14.532,0,0,0,0\n" + -//"...\n"; -"wod_unique_cast,lat,lon,time,Temperature,Temperature_WODflag,crs,WODf,WODfd\n" + -"3390296,-43.7802,67.3953,80838.31180554628,14.519,0,-2147483647,-32767,-32767\n" + -"3390296,-43.7802,67.3953,80838.31180554628,14.526,0,-2147483647,-32767,-32767\n" + -"3390296,-43.7802,67.3953,80838.31180554628,14.537,0,-2147483647,-32767,-32767\n" + -"3390296,-43.7802,67.3953,80838.31180554628,14.533,0,-2147483647,-32767,-32767\n" + -"3390296,-43.7802,67.3953,80838.31180554628,14.532,0,-2147483647,-32767,-32767\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + // + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - //test reading just specified legit outer variables - table.readNcCF(fileName, StringArray.fromCSV( - "zztop,wod_unique_cast,lat,lon,time" + scalarVars), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -//was -//"wod_unique_cast,lat,lon,time,crs,WODf,WODfd\n" + -//"3390296,-43.7802,67.3953,80838.31180554628,0,0,0\n" + -//"3390301,-44.5177,67.9403,80838.68055558205,0,0,0\n" + -//"3390310,-45.2592,68.3755,80839.08888889104,0,0,0\n" + -//"3390318,-46.0113,68.7568,80839.39652776718,0,0,0\n" + -//"3390328,-47.0115,69.431,80839.87291669846,0,0,0\n" + -//"...\n"; -"wod_unique_cast,lat,lon,time,crs,WODf,WODfd\n" + -"3390296,-43.7802,67.3953,80838.31180554628,-2147483647,-32767,-32767\n" + -"3390301,-44.5177,67.9403,80838.68055558205,-2147483647,-32767,-32767\n" + -"3390310,-45.2592,68.3755,80839.08888889104,-2147483647,-32767,-32767\n" + -"3390318,-46.0113,68.7568,80839.39652776718,-2147483647,-32767,-32767\n" + -"3390328,-47.0115,69.431,80839.87291669846,-2147483647,-32767,-32767\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - //test reading just specified legit "Temperature_obs" inner variables - table.readNcCF(fileName, StringArray.fromCSV( - "zztop,Temperature,Temperature_WODflag" + scalarVars), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -//was -//"Temperature,Temperature_WODflag,crs,WODf,WODfd\n" + -//"14.519,0,0,0,0\n" + -//"14.526,0,0,0,0\n" + -//"14.537,0,0,0,0\n" + -//"14.533,0,0,0,0\n" + -//"14.532,0,0,0,0\n" + -//"...\n"; -"Temperature,Temperature_WODflag,crs,WODf,WODfd\n" + -"14.519,0,-2147483647,-32767,-32767\n" + -"14.526,0,-2147483647,-32767,-32767\n" + -"14.537,0,-2147483647,-32767,-32767\n" + -"14.533,0,-2147483647,-32767,-32767\n" + -"14.532,0,-2147483647,-32767,-32767\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - //test reading just specified legit scalar variables - table.readNcCF(fileName, StringArray.fromCSV( - "zztop,WODf,crs"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -//was -//"WODf,crs\n" + -//"0,0\n"; -"WODf,crs\n" + -"-32767,-2147483647\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - //test reading WHOLE file (should just catch z_obs dimension) - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(3); - expected = -//note it catches z_obs dimension (z, z_WODflag, z_sigfig), not others. -// Temperature_row_size, and Temperature_WODprofileflag are [casts], and don't use Temperature_obs. -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast," + -"lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Cast_Tow_number," + -"Orig_Stat_Num,Bottom_Depth,Cast_Duration,Cast_Direction,High_res_pair,dataset," + -"dbase_orig,origflagset,z,z_WODflag,z_sigfig,Temperature_row_size," + -"Temperature_WODprofileflag,Temperature_Scale,Temperature_Instrument," + -"Salinity_row_size,Salinity_WODprofileflag,Salinity_Scale,Salinity_Instrument," + -"Oxygen_row_size,Oxygen_WODprofileflag,Oxygen_Instrument,Oxygen_Original_units," + -"Pressure_row_size,Chlorophyll_row_size,Chlorophyll_WODprofileflag," + -"Chlorophyll_Instrument,Chlorophyll_uncalibrated,Conductivit_row_size,crs,WODf,WODfp,WODfd\n" + - -"FRANCE,FR008787,35MF68SUZIL,3390296,-43.7802,67.3953,80838.31180554628," + -"19910501,7.483333,841,WORLD OCEAN CIRCULATION EXPERIMENT (WOCE)," + -"MARION DUFRESNE (C.s.FNGB;built 1972;decomm-d 1995;renamed Fres;IMO7208388)," + -"NATIONAL MUSEUM OF NATURAL HISTORY (PARIS),1,37.0,4438.0,9.96921E36,,7498735," + -"CTD,WHO/CCHDO,WOCE,2.9759612,0,3,2204,0,,CTD: NEIL BROWN MARK IIIB,2204,0,," + -"CTD: NEIL BROWN MARK IIIB,2204,5,CTD: NEIL BROWN MARK IIIB,umol/kg,2204,0,0,," + -//was "-2147483647,0,0,0,0,0\n" + -"-2147483647,0,-2147483647,-32767,-32767,-32767\n" + - -"FRANCE,FR008787,35MF68SUZIL,3390296,-43.7802,67.3953,80838.31180554628," + -"19910501,7.483333,841,WORLD OCEAN CIRCULATION EXPERIMENT (WOCE)," + -"MARION DUFRESNE (C.s.FNGB;built 1972;decomm-d 1995;renamed Fres;IMO7208388)," + -"NATIONAL MUSEUM OF NATURAL HISTORY (PARIS),1,37.0,4438.0,9.96921E36,,7498735," + -"CTD,WHO/CCHDO,WOCE,3.967939,0,3,2204,0,,CTD: NEIL BROWN MARK IIIB,2204,0,," + -"CTD: NEIL BROWN MARK IIIB,2204,5,CTD: NEIL BROWN MARK IIIB,umol/kg,2204,0,0,," + -//was "-2147483647,0,0,0,0,0\n" + -"-2147483647,0,-2147483647,-32767,-32767,-32767\n" + - -"FRANCE,FR008787,35MF68SUZIL,3390296,-43.7802,67.3953,80838.31180554628," + -"19910501,7.483333,841,WORLD OCEAN CIRCULATION EXPERIMENT (WOCE)," + -"MARION DUFRESNE (C.s.FNGB;built 1972;decomm-d 1995;renamed Fres;IMO7208388)," + -"NATIONAL MUSEUM OF NATURAL HISTORY (PARIS),1,37.0,4438.0,9.96921E36,,7498735," + -"CTD,WHO/CCHDO,WOCE,5.9518795,0,3,2204,0,,CTD: NEIL BROWN MARK IIIB,2204,0,," + -"CTD: NEIL BROWN MARK IIIB,2204,5,CTD: NEIL BROWN MARK IIIB,umol/kg,2204,0,0,," + -//was "-2147483647,0,0,0,0,0\n" + -"-2147483647,0,-2147483647,-32767,-32767,-32767\n" + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - results = table.globalAttributes().getString("cdm_data_type"); - expected = "Profile"; - Test.ensureEqual(results, expected, "results=\n" + results); + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - results = table.globalAttributes().getString("subsetVariables"); - expected = -"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, " + -"lat, lon, time, date, GMT_time, Access_no, Project, Platform, Institute, " + -"Cast_Tow_number, Orig_Stat_Num, Bottom_Depth, Cast_Duration, Cast_Direction, " + -"High_res_pair, dataset, dbase_orig, origflagset, Temperature_row_size, " + -"Temperature_WODprofileflag, Temperature_Scale, Temperature_Instrument, " + -"Salinity_row_size, Salinity_WODprofileflag, Salinity_Scale, Salinity_Instrument, " + -"Oxygen_row_size, Oxygen_WODprofileflag, Oxygen_Instrument, Oxygen_Original_units, " + -"Pressure_row_size, " + -"Chlorophyll_row_size, Chlorophyll_WODprofileflag, Chlorophyll_Instrument, " + -"Chlorophyll_uncalibrated, Conductivit_row_size, crs, WODf, WODfp, WODfd"; - Test.ensureEqual(results, expected, "results=\n" + results); + // + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - results = table.globalAttributes().getString("cdm_profile_variables"); - //same expected - Test.ensureEqual(results, expected, "results=\n" + results); + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - //test reading row_size vars -- are they actually read? - table.readNcCF(fileName, StringArray.fromCSV( - "zztop,z_row_size,Temperature_row_size,Salinity_row_size,Oxygen_row_size," + - "Pressure_row_size,Chlorophyll_row_size,Conductivity_row_size"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(7); - expected = //verified with dumpString above -"Temperature_row_size,Salinity_row_size,Oxygen_row_size,Pressure_row_size,Chlorophyll_row_size\n" + -"2204,2204,2204,2204,0\n" + -"1844,1844,1844,1844,0\n" + -"1684,1684,1684,1684,0\n" + -"1587,1587,1587,1587,0\n" + -"357,357,357,357,0\n" + -"34,34,0,34,34\n" + -"34,34,0,34,34\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); - - //test request for vars with 2 different sample_dimensions - // second sample_dim throws error - results = "shouldn't happen"; - try { - table.readNcCF(fileName, StringArray.fromCSV( - "zztop,wod_unique_cast,lat,lon,time,z,z_WODflag,Temperature,Temperature_WODflag" + scalarVars), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - - } catch (Throwable t2) { - results = t2.toString(); - } - expected = "Invalid request: loadVariables includes variables that use two different sample_dimension's (z_obs and Temperature_obs)."; - int po = Math.max(0, results.indexOf(expected)); - Test.ensureEqual(results.substring(po), expected, "results=\n" + results); - debugMode = oDebug; - } - - - /** This tests readNcCF reading point files. */ - public static void testReadNcCFPoint(boolean pauseAfterEach) throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCFPoint"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected; - String fileName = String2.unitTestDataDir + "CFPointConventions/point/point-H.1/point-H.1.nc"; - Attributes gatts; - -/* */ - //*************** point - String2.log("\n\n** Testing " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - //String2.log(table.toCSVString()); - results = table.dataToString(5); - expected = -"obs,lat,lon,alt,time,temperature,humidity\n" + -"0,41.0,112.0,7.745540487338979,573,26.225288,11.245576\n" + -"1,179.0,68.0,3.0855444414144264,2248,12.695349,67.73824\n" + -"2,10.0,11.0,3.254759157455159,71,21.193731,48.589462\n" + -"3,106.0,22.0,4.549437636401848,1714,35.339344,39.594116\n" + -"4,75.0,16.0,6.061720687265453,1209,22.593496,28.170149\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#1a " + pauseMessage); - - - table.readNcCF(fileName, StringArray.fromCSV( - "row,obs,lat,lon,alt,time,temperature,humidity"), - 0, //standardizeWhat=0 - StringArray.fromCSV(""), - StringArray.fromCSV(""), - StringArray.fromCSV("")); - results = table.dataToString(5); - //expected is same - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#1b " + pauseMessage); - - - results = table.columnAttributes(6).toString(); - expected = -" coordinates=time lat lon alt\n" + -" long_name=Humidity\n" + -" missing_value=-999.9f\n" + -" standard_name=specific_humidity\n" + -" units=Percent\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - results = table.globalAttributes().toString(); - expected = -" Conventions=CF-1.6\n" + -" featureType=point\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - table.readNcCF(fileName, StringArray.fromCSV( - "obs,lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("obs"), - StringArray.fromCSV("="), - StringArray.fromCSV("2")); - results = table.dataToString(); - expected = -"obs,lat,time,temperature\n" + -"2,10.0,71,21.193731\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#1c " + pauseMessage); - - table.readNcCF(fileName, StringArray.fromCSV( - "obs,lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("71")); - results = table.dataToString(); - expected = -"obs,lat,time,temperature\n" + -"2,10.0,71,21.193731\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#1d " + pauseMessage); - - table.readNcCF(fileName, StringArray.fromCSV( - "obs,lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("21.193731")); - results = table.dataToString(); - expected = -"obs,lat,time,temperature\n" + -"2,10.0,71,21.193731\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#1e " + pauseMessage); - - //this is important test of just getting dimension values - //(when there is no corresponding variable) - table.readNcCF(fileName, StringArray.fromCSV( - "obs"), - 0, //standardizeWhat=0 - StringArray.fromCSV("obs"), - StringArray.fromCSV("="), - StringArray.fromCSV("2")); - results = table.dataToString(); - expected = -"obs\n" + -"2\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - //and test that it gets the global attributes from the file. - results = table.globalAttributes().toString(); - expected = -" Conventions=CF-1.6\n" + -" featureType=point\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#1f " + pauseMessage); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("21.193731")); - results = table.dataToString(); - expected = -"temperature\n" + -"21.193731\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#1g " + pauseMessage); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "obs,lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("obs"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "obs,lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "obs,lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("obs"), - 0, //standardizeWhat=0 - StringArray.fromCSV("obs"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - - String2.log("\n*** Table.testReadNcCFPoint finished successfully"); - debugMode = oDebug; - } - - - - /** This tests readNcCF nLevels=1. */ - public static void testReadNcCF1(boolean pauseAfterEach) throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCF1"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected; - String profileFileName = String2.unitTestDataDir + "nccf/Profile.nc"; - Attributes gatts; - -/* */ - //*************** contiguous profileFileName - String2.log("\n\n** Testing profile contiguousRagged\n" + - " " + profileFileName); - String2.log(NcHelper.ncdump(profileFileName, "-h")); - - - String2.log("\n\n** Test nLevels=1/contiguousRagged no loadVars, no constraints"); - table.readNcCF(profileFileName, null, 0, //standardizeWhat=0 - null, null, null); - //String2.log(table.toCSVString()); - results = table.dataToString(5); - expected = -"id,longitude,latitude,time,altitude,chlorophyll,chlorophyll_qc,oxygen,oxygen_qc,pressure,pressure_qc,salinity,salinity_qc,temperature,temperature_qc\n" + -"465958,163.08,39.0,1.107754559E9,-2.0,,,,,,,,,10.1,0.0\n" + -"465958,163.08,39.0,1.107754559E9,-58.0,,,,,,,,,9.9,0.0\n" + -"465958,163.08,39.0,1.107754559E9,-96.0,,,,,,,,,9.2,0.0\n" + -"465958,163.08,39.0,1.107754559E9,-138.0,,,,,,,,,8.8,0.0\n" + -"465958,163.08,39.0,1.107754559E9,-158.0,,,,,,,,,8.1,0.0\n" + -"...\n"; - Test.ensureEqual(results, expected, ""); - Test.ensureEqual(table.nRows(), 118, table.toString()); - results = table.columnAttributes(0).toString(); - expected = -" actual_range=465958i,848984i\n" + -" cf_role=profile_id\n" + -" colorBarMaximum=1000000.0d\n" + -" colorBarMinimum=0.0d\n" + -" ioos_category=Identifier\n" + -" long_name=Sequence ID\n" + -" missing_value=2147483647i\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "id, longitude, latitude, time", gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "id, longitude, latitude, time", gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue("#1a " + pauseMessage); - - // - String2.log("\n\n** Test 1 non-existent loadVar test:ncCFcc.set(27)"); - table.readNcCF(profileFileName, StringArray.fromCSV("zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV(""), - StringArray.fromCSV(""), - StringArray.fromCSV("")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#1aa " + pauseMessage); - - // - String2.log("\n\n** Test nLevels=1/contiguousRagged " + - "many loadVars, constraints, NO_DATA"); - table.readNcCF(profileFileName, StringArray.fromCSV( - "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("id"), - StringArray.fromCSV("="), - StringArray.fromCSV("zztop")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#1b " + pauseMessage); - - table.readNcCF(profileFileName, StringArray.fromCSV( - "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("id"), - StringArray.fromCSV("="), - StringArray.fromCSV("zztop")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(profileFileName, StringArray.fromCSV( - "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("longitude"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(profileFileName, StringArray.fromCSV( - "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(profileFileName, StringArray.fromCSV( - "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - String2.log("\n\n** Test nLevels=1/contiguousRagged " + - "just outerTable loadVars, no constraints"); - table.readNcCF(profileFileName, - StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"longitude,latitude,time,id\n" + -"163.08,39.0,1.107754559E9,465958\n" + -"225.84,16.05,1.1077371E9,580888\n" + -"225.4,15.11,1.107751391E9,580889\n" + -"225.0,14.25,1.107764388E9,580890\n" + -"224.49,13.23,1.10778048E9,580891\n" + -"214.66,54.8,1.107759959E9,848984\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "id, longitude, latitude, time", gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "id, longitude, latitude, time", gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue("#1d " + pauseMessage); - - table.readNcCF(profileFileName, - StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, //standardizeWhat=0 - StringArray.fromCSV("id"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(profileFileName, - StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, //standardizeWhat=0 - StringArray.fromCSV("latitude"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(profileFileName, - StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - String2.log("\n\n** Test nLevels=1/contiguousRagged " + - "just outerTable loadVars, constraints"); - table.readNcCF(profileFileName, - StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, //standardizeWhat=0 - - StringArray.fromCSV("id"), - StringArray.fromCSV("="), - StringArray.fromCSV("848984")); - results = table.dataToString(); - expected = -"longitude,latitude,time,id\n" + -"214.66,54.8,1.107759959E9,848984\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "id, longitude, latitude, time", gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "id, longitude, latitude, time", gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue("#1e " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/contiguousRagged " + - "just outerTable loadVars, constraints, NO_DATA"); - table.readNcCF(profileFileName, - StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, //standardizeWhat=0 - StringArray.fromCSV("id"), - StringArray.fromCSV("="), - StringArray.fromCSV("zztop")); - Test.ensureEqual(table.nColumns(), 0, ""); - Test.ensureEqual(table.nRows(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#1f " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/contiguousRagged, specific loadVars, constraints"); - table.readNcCF(profileFileName, StringArray.fromCSV( - "longitude,latitude,time,altitude,temperature,temperature_qc,zztop,id"), - 0, //standardizeWhat=0 - StringArray.fromCSV("id,temperature"), - StringArray.fromCSV("=,>="), - StringArray.fromCSV("848984,5")); - results = table.dataToString(); - expected = -"longitude,latitude,time,altitude,temperature,temperature_qc,id\n" + -"214.66,54.8,1.107759959E9,-2.0,5.8,0.0,848984\n" + -"214.66,54.8,1.107759959E9,-95.0,5.6,0.0,848984\n" + -"214.66,54.8,1.107759959E9,-101.0,5.4,0.0,848984\n" + -"214.66,54.8,1.107759959E9,-107.0,5.0,0.0,848984\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "id, longitude, latitude, time", gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "id, longitude, latitude, time", gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue("#1g " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/contiguousRagged just obs loadVars, no constraints"); - table.readNcCF(profileFileName, - StringArray.fromCSV("salinity,temperature,zztop"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"salinity,temperature\n" + -",10.1\n" + -",9.9\n" + -",9.2\n" + -",8.8\n" + -",8.1\n" + -",8.1\n" + -",7.4\n" + -",6.7\n" + -",6.0\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 118, table.dataToString()); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - null, gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - null, gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue("#1h " + pauseMessage); - - table.readNcCF(profileFileName, - StringArray.fromCSV("salinity"), 0, //standardizeWhat=0 - StringArray.fromCSV("salinity"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - String2.log("\n\n** Test nLevels=1/contiguousRagged just obs loadVars, constraints"); - table.readNcCF(profileFileName, - StringArray.fromCSV("temperature,zztop"), 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">"), - StringArray.fromCSV("24.5")); - results = table.dataToString(); - expected = -"temperature\n" + -"24.8\n" + -"24.7\n" + -"25.0\n" + -"24.9\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - null, gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - null, gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue("#1i " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/contiguousRagged " + - "just obs loadVars, constraints, NO_DATA"); - table.readNcCF(profileFileName, - StringArray.fromCSV("temperature,zztop"), 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-195")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#1j " + pauseMessage); - - //test quick reject - //if (constraintVar!=NaN or constraintVar=(finite)) and var not in file, - String2.log("\n\n** Test #1m quick reject var=(nonNumber) if var not in file: NO_DATA"); - table.readNcCF(profileFileName, - StringArray.fromCSV("temperature,zzStation"), 0, //standardizeWhat=0 - StringArray.fromCSV("zzStation"), - StringArray.fromCSV("="), - StringArray.fromCSV("WXURP")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#1m " + pauseMessage); - - String2.log("\n\n** Test #1n quick reject var!=\"\" if var not in file: NO_DATA"); - table.readNcCF(profileFileName, - StringArray.fromCSV("temperature,zzStation"), 0, //standardizeWhat=0 - StringArray.fromCSV("zzStation"), - StringArray.fromCSV("!="), - new StringArray(new String[]{""})); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#1n " + pauseMessage); - - //but this can't be quickly rejected - String2.log("\n\n** Test #1o can't quick reject var=99 if var not in file\n" + - "(since 99 might be defined as missing_value)"); - table.readNcCF(profileFileName, - StringArray.fromCSV("temperature,zzStation"), 0, //standardizeWhat=0 - StringArray.fromCSV("zzStation"), - StringArray.fromCSV("="), - new StringArray(new String[]{"99"})); - Test.ensureEqual(table.nRows(), 118, ""); - Test.ensureEqual(table.nColumns(), 1, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#1o " + pauseMessage); - - -/* */ - //*************** nLevels=1 TimeSeries - for (int type = 0; type < 2; type++) { - //ncCF1b and ncCFMA1b have same data, so tests are the same! - String fileType = type == 0? "contiguous" : "multidimensional"; - //from EDDTableFromNcFiles.testNcCF1b() and testNcCFMA1b(); - String fileName = String2.unitTestDataDir + "nccf/" + (type == 0? "ncCF1b.nc" : "ncCFMA1b.nc"); - - String2.log("\n\n** Testing nLevels=1/" + fileType + "\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - - - String2.log("\n\n** Test nLevels=1/" + fileType + " no loadVars, no constraints"); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); -String2.log(table.toString()); - results = table.dataToString(5); - expected = -"line_station,longitude,latitude,altitude,time,obsScientific,obsValue,obsUnits\n" + -"076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Argyropelecus sladeni,2,number of larvae\n" + -"076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Chauliodus macouni,3,number of larvae\n" + -"076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Danaphos oculatus,4,number of larvae\n" + -"076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Diogenichthys atlanticus,3,number of larvae\n" + -"076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Idiacanthus antrostomus,3,number of larvae\n" + -"...\n"; - Test.ensureEqual(results, expected, ""); - Test.ensureEqual(table.nRows(), 23, table.toString()); - results = table.columnAttributes(0).toString(); - expected = -" cf_role=timeseries_id\n" + -" ioos_category=Identifier\n" + -" long_name=CalCOFI Line + Station\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), - "line_station", gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "line_station", gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2a " + pauseMessage); - - table.readNcCF(fileName, StringArray.fromCSV(""), 0, //standardizeWhat=0 - StringArray.fromCSV("line_station"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV(""), 0, //standardizeWhat=0 - StringArray.fromCSV("longitude"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV(""), 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV(""), 0, //standardizeWhat=0 - StringArray.fromCSV("obsValue"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - String2.log("\n\n** Test nLevels=1/" + fileType + " " + - "just outerTable loadVars, no constraints"); - table.readNcCF(fileName, StringArray.fromCSV( - "line_station,zztop"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"line_station\n" + -"076.7_100\n" + -"080_100\n" + -"083.3_100\n"; //4 row with all mv was removed - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), - "line_station", gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "line_station", gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2b " + pauseMessage); - - table.readNcCF(fileName, StringArray.fromCSV("line_station"), - 0, //standardizeWhat=0 - StringArray.fromCSV("line_station"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - String2.log("\n\n** Test nLevels=1/" + fileType + " " + - "just outerTable loadVars, constraints"); - table.readNcCF(fileName, StringArray.fromCSV("line_station,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("line_station"), - StringArray.fromCSV("="), - StringArray.fromCSV("083.3_100")); - results = table.dataToString(); - expected = -"line_station\n" + -"083.3_100\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), - "line_station", gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "line_station", gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2c " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/" + fileType + " " + - "just outerTable loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, - StringArray.fromCSV("line_station,zztop"), 0, //standardizeWhat=0 - StringArray.fromCSV("line_station"), - StringArray.fromCSV("="), - StringArray.fromCSV("zztop")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2d " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/" + fileType + ", specific loadVars, constraints"); - table.readNcCF(fileName, StringArray.fromCSV( - "longitude,latitude,altitude,time,line_station,zztop,obsScientific,obsValue,obsUnits"), - 0, //standardizeWhat=0 - StringArray.fromCSV("line_station,obsValue"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("083.3_100,1")); - results = table.dataToString(); - expected = -"longitude,latitude,altitude,time,line_station,obsScientific,obsValue,obsUnits\n" + -"-123.49333,32.245,-211.5,1.10027676E9,083.3_100,Argyropelecus sladeni,1,number of larvae\n" + -"-123.49333,32.245,-211.5,1.10027676E9,083.3_100,Diogenichthys atlanticus,1,number of larvae\n" + -"-123.49333,32.245,-211.5,1.10027676E9,083.3_100,Idiacanthus antrostomus,1,number of larvae\n" + -"-123.49333,32.245,-211.5,1.10027676E9,083.3_100,Tetragonurus cuvieri,1,number of larvae\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), - "line_station", gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "line_station", gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2e " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/" + fileType + - ", specific loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, StringArray.fromCSV( - "longitude,latitude,altitude,time,line_station,zztop,obsScientific,obsValue,obsUnits"), - 0, //standardizeWhat=0 - StringArray.fromCSV("line_station,obsValue"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("083.3_100,-9")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2f " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/" + fileType + " just obs loadVars, no constraints"); - table.readNcCF(fileName, StringArray.fromCSV( - "obsScientific,obsValue,obsUnits,zztop"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"obsScientific,obsValue,obsUnits\n" + -"Argyropelecus sladeni,2,number of larvae\n" + -"Chauliodus macouni,3,number of larvae\n" + -"Danaphos oculatus,4,number of larvae\n" + -"Diogenichthys atlanticus,3,number of larvae\n" + -"Idiacanthus antrostomus,3,number of larvae\n" + -"Lestidiops ringens,1,number of larvae\n" + -"Melamphaes lugubris,1,number of larvae\n" + -"Protomyctophum crockeri,4,number of larvae\n" + -"Stenobrachius leucopsarus,1,number of larvae\n" + -"Total Fish Larvae,22,number of larvae\n" + -"Argyropelecus affinis,1,number of larvae\n" + -"Argyropelecus sladeni,2,number of larvae\n" + -"Danaphos oculatus,1,number of larvae\n" + -"Idiacanthus antrostomus,2,number of larvae\n" + -"Melamphaes parvus,1,number of larvae\n" + -"Nannobrachium spp,2,number of larvae\n" + -"Protomyctophum crockeri,1,number of larvae\n" + -"Total Fish Larvae,10,number of larvae\n" + -"Argyropelecus sladeni,1,number of larvae\n" + -"Diogenichthys atlanticus,1,number of larvae\n" + -"Idiacanthus antrostomus,1,number of larvae\n" + -"Tetragonurus cuvieri,1,number of larvae\n" + -"Total Fish Larvae,4,number of larvae\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), - null, gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - null, gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2g " + pauseMessage); - - table.readNcCF(fileName, StringArray.fromCSV("obsScientific"), - 0, //standardizeWhat=0 - StringArray.fromCSV("obsScientific"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - String2.log("\n\n** Test nLevels=1/" + fileType + " just obs loadVars, constraints"); - table.readNcCF(fileName, - StringArray.fromCSV("obsScientific,obsValue,obsUnits,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("obsValue"), - StringArray.fromCSV("="), - StringArray.fromCSV("4")); - results = table.dataToString(); - expected = -"obsScientific,obsValue,obsUnits\n" + -"Danaphos oculatus,4,number of larvae\n" + -"Protomyctophum crockeri,4,number of larvae\n" + -"Total Fish Larvae,4,number of larvae\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), - null, gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - null, gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2h " + pauseMessage); - - - String2.log("\n\n** Test nLevels=1/" + fileType + - " just obs loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, - StringArray.fromCSV("obsScientific,obsValue,obsUnits,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("obsValue"), - StringArray.fromCSV("="), - StringArray.fromCSV("-99")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #2i " + pauseMessage); - - } //end nLevels=1 type loop - -/* */ - //********* expected errors - String2.log("\n** Expected errors"); - try { - table.readNcCF(String2.unitTestDataDir + "nccf/badIndexed1To6.nc", null, - 0, //standardizeWhat=0 - null, null, null); - throw new SimpleException("Shouldn't get here."); - - } catch (Exception e) { - if (e.toString().indexOf( - "Invalid file: The index values must be 0 - 5, but parentIndex[88]=6.") < 0) - throw e; - } - - - //******* another test file, from Kevin O'Brien - try { - table.readNcCF("c:/data/kevin/interpolated_gld.20120620_045152_meta_2.nc", - null, 0, //standardizeWhat=0 - null, null, null); - throw new SimpleException("Shouldn't get here."); - - } catch (Exception e) { - if (e.toString().indexOf( - "Invalid contiguous ragged file: The sum of the values in the rowSizes " + - "variable (rowSize sum=1024368) is greater than the size of the " + - "observationDimension (obs size=1022528).") < 0) - throw e; - } - - /* */ - debugMode = oDebug; - } - - /** This tests readNcCF nLevels=1. */ - public static void testReadNcCF1Kevin() throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCF1Kevin"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected; - String fileName = "c:/data/kevin/interpolated_gld.20120620_045152_meta_2.nc"; //from Kevin O'Brien - Attributes gatts; - - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - String2.log(table.toString()); - debugMode = oDebug; - } - - /** This tests reading the gocd nccf files. */ - public static void testReadGocdNcCF() throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadGocdNcCF"); - Table table = new Table(); - String results, expected; - String fileName; - int po; - ByteArrayOutputStream os = new ByteArrayOutputStream(); - -/* - //*************** non-standard timeSeries file -- TOO WEIRD, don't support it - //some var var[time=7022][z=1], depth[z=1] - //and other station vars (latitude, longitude) with no dimensions - fileName = "/data/gocd/gocdNcCF/gocd_v3_cmetr.nc"; - String2.log("\n\n** Testing " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); -// dimensions: -// z = 1; -// time = 7022; -// float sampling_interval; // :_FillValue = 9999.9f; // float -// float seafloor_depth; -// float latitude; -// float longitude; -// int latitude_quality_flag; -// int longitude_quality_flag; -// int crs; - -// float depth(z=1); -// int depth_quality_flag(z=1); - -// double time(time=7022); -// int time_quality_flag(time=7022); - -// float u(time=7022, z=1); -// int u_quality_flag(time=7022, z=1); -// float v(time=7022, z=1); -// int v_quality_flag(time=7022, z=1); -// float current_speed(time=7022, z=1); -// int current_speed_quality_flag(time=7022, z=1); -// float current_direction(time=7022, z=1); -// int current_direction_quality_flag(time=7022, z=1); - -// global attributes: -// :gocd_id = "gocd_a0084999_tr1162.nc"; -// :id = "0093183"; -// :featureType = "timeSeries"; -// :cdm_data_type = "Station"; -// :instrument_type = ""; - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - //String2.log(table.toCSVString()); - results = table.dataToString(5); - expected = -"zztop\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - /* */ - - - //*************** trajectory profile - //This is important test of Table.readNcCF - // if multidimensional file, 2 levels, and outerDim=ScalarDim - // this tests if var[scalarDim][obs] was read (e.g., depth[obs] - //File dims are outerDim=[scalarDim], inner=[time], obs=[obs] - table = new Table(); - fileName = String2.unitTestDataDir + "gocdNcCF/gocd_v3_sadcp.nc"; - String2.log("\n\n** Testing " + fileName); - results = NcHelper.ncdump(fileName, "-h"); - String2.log(results); -//just the structure, rearranged into groups -// dimensions: -// time = 501; -// z = 70; - -// float sampling_interval; -// int crs; -// -// float seafloor_depth(time=501); -// float latitude(time=501); -// float longitude(time=501); -// double time(time=501); -// int latitude_quality_flag(time=501); -// int longitude_quality_flag(time=501); -// int time_quality_flag(time=501); -// -// float depth(z=70); -// int depth_quality_flag(z=70); -// -// float u(time=501, z=70); -// int u_quality_flag(time=501, z=70); -// float v(time=501, z=70); -// int v_quality_flag(time=501, z=70); -// float current_speed(time=501, z=70); -// int current_speed_quality_flag(time=501, z=70); -// float current_direction(time=501, z=70); -// int current_direction_quality_flag(time=501, z=70); - - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - os.reset(); - table.saveAsDAS(os, SEQUENCE_NAME); - results = os.toString(); - expected = -"Attributes {\n" + -" s {\n" + -" sampling_interval {\n" + -" Float32 _FillValue 9999.9;\n" + -" String long_name \"Sampling Interval\";\n" + -" String units \"minutes\";\n" + -" }\n" + -" seafloor_depth {\n" + -" Float32 _FillValue 9999.9;\n" + -" String long_name \"Seafloor Depth\";\n" + -" String postive \"down\";\n" + -" String units \"meters\";\n" + -" }\n" + -" latitude {\n" + -" Float32 _FillValue 9999.9;\n" + -" String ancillary_variables \"latitude_quality_flag\";\n" + -" String axis \"Y\";\n" + -" Float64 data_max 21.0958;\n" + -" Float64 data_min -14.3883;\n" + -" String grid_mapping \"crs\";\n" + -" String long_name \"latitude\";\n" + -" String standard_name \"latitude\";\n" + -" String units \"degrees_north\";\n" + -" Float32 valid_max 90.0;\n" + -" Float32 valid_min -90.0;\n" + -" }\n" + -" longitude {\n" + -" Float32 _FillValue 9999.9;\n" + -" String ancillary_variables \"longitude_quality_flag\";\n" + -" String axis \"X\";\n" + -" Float64 data_max -158.3554;\n" + -" Float64 data_min -176.8126;\n" + -" String grid_mapping \"crs\";\n" + -" String long_name \"longitude\";\n" + -" String standard_name \"longitude\";\n" + -" String units \"degrees_east\";\n" + -" Float32 valid_max 180.0;\n" + -" Float32 valid_min -180.0;\n" + -" }\n" + -" latitude_quality_flag {\n" + -" Int32 _FillValue -9;\n" + -" String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + -" Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + -" String long_name \"Latitude Quality Flag\";\n" + -" }\n" + -" longitude_quality_flag {\n" + -" Int32 _FillValue -9;\n" + -" String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + -" Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + -" String long_name \"Longitude Quality Flag\";\n" + -" }\n" + -" depth {\n" + -" String C_format \"%7.2f\";\n" + -" Float64 data_max 720.0;\n" + -" Float64 data_min 30.0;\n" + -" String FORTRAN_format \"F7.2\";\n" + -" String long_name \"Depth\";\n" + -" String postive \"down\";\n" + -" String units \"meters\";\n" + -" Float32 valid_max 15000.0;\n" + -" Float32 valid_min 0.0;\n" + -" }\n" + -" depth_quality_flag {\n" + -" Int32 _FillValue -9;\n" + -" String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + -" Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + -" String long_name \"Depth QC Flags\";\n" + -" }\n" + -" time {\n" + -" String ancillary_variables \"time_quality_flag\";\n" + -" String axis \"T\";\n" + -" String C_format \"%9.4f\";\n" + -" Float64 data_max 38751.8319444442;\n" + -" Float64 data_min 38730.9986111112;\n" + -" String FORTRAN_format \"F9.4\";\n" + -" String long_name \"time\";\n" + -" String standard_name \"time\";\n" + -" String units \"days since 1900-01-01 00:00:00Z\";\n" + -" }\n" + -" time_quality_flag {\n" + -" Int32 _FillValue -9;\n" + -" String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + -" Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + -" String long_name \"Time Quality Flag\";\n" + -" }\n" + -" u {\n" + -" Float32 _FillValue 9999.9;\n" + -" String ancillary_variables \"u_quality_flag\";\n" + -" String C_format \"%7.4f\";\n" + -" String cell_methods \"time:point z:point\";\n" + -" String coordinates \"time z\";\n" + -" Float64 data_max 0.883000030517578;\n" + -" Float64 data_min -1.25;\n" + -" String FORTRAN_format \"F7.4\";\n" + -" String grid_mapping \"crs\";\n" + -" String long_name \"Eastward Velocity Component\";\n" + -" String standard_name \"eastward_sea_water_velocity\";\n" + -" String units \"m s-1\";\n" + -" Float64 valid_max 5.0;\n" + -" Float64 valid_min -5.0;\n" + -" }\n" + -" u_quality_flag {\n" + -" Int32 _FillValue -9;\n" + -" String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + -" Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + -" String long_name \"Eastward Velocity component QC Flags\";\n" + -" }\n" + -" v {\n" + -" Float32 _FillValue 9999.9;\n" + -" String ancillary_variables \"v_quality_flag\";\n" + -" String C_format \"%7.4f\";\n" + -" String cell_methods \"time:point z:point\";\n" + -" String coordinates \"time z\";\n" + -" Float64 data_max 0.733;\n" + -" Float64 data_min -0.695;\n" + -" String FORTRAN_format \"F7.4\";\n" + -" String grid_mapping \"crs\";\n" + -" String long_name \"Northward Velocity Component\";\n" + -" String standard_name \"northward_sea_water_velocity\";\n" + -" String units \"m s-1\";\n" + -" Float64 valid_max 5.0;\n" + -" Float64 valid_min -5.0;\n" + -" }\n" + -" v_quality_flag {\n" + -" Int32 _FillValue -9;\n" + -" String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + -" Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + -" String long_name \"Northward Velocity component QC Flags\";\n" + -" }\n" + -" current_speed {\n" + -" Float32 _FillValue 9999.9;\n" + -" String ancillary_variables \"current_direction_quality_flag\";\n" + -" String C_format \"%7.4f\";\n" + -" String cell_methods \"time:point z:point\";\n" + -" String coordinates \"time z\";\n" + -" Float64 data_max 141.42;\n" + -" Float64 data_min 0.0;\n" + -" String FORTRAN_format \"F7.4\";\n" + -" String grid_mapping \"crs\";\n" + -" String long_name \"Current_Speed\";\n" + -" String units \"m s-1\";\n" + -" Float64 valid_max 7.0711;\n" + -" Float64 valid_min 0.0;\n" + -" }\n" + -" current_speed_quality_flag {\n" + -" String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + -" Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + -" String long_name \"Current Speed QC Flags\";\n" + -" }\n" + -" current_direction {\n" + -" Float32 _FillValue 9999.9;\n" + -" String ancillary_variables \"current_direction_quality_flag\";\n" + -" String C_format \"%5.1f\";\n" + -" String cell_methods \"time:point z:point\";\n" + -" String comment \"True Direction toward which current is flowing\";\n" + -" String coordinates \"time z\";\n" + -" Float64 data_max 360.0;\n" + -" Float64 data_min 0.3;\n" + -" String FORTRAN_format \"F5.1\";\n" + -" String grid_mapping \"crs\";\n" + -" String long_name \"Current Direction\";\n" + -" String units \"degrees\";\n" + -" Float64 valid_max 360.0;\n" + -" Float64 valid_min 0.0;\n" + -" }\n" + -" current_direction_quality_flag {\n" + -" String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + -" Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + -" String long_name \"Current Direction QC Flags\";\n" + -" }\n" + -" crs {\n" + -" String epsg_code \"EPSG:4326\";\n" + -" String grid_mapping_name \"latitude_longitude\";\n" + -" String inverse_flattening \"298.257223563\";\n" + -" String long_name \"Coordinate Reference System\";\n" + -" String longitude_of_prime_meridian \"0.0f\";\n" + -" String semi_major_axis \"6378137.0\";\n" + -" }\n" + -" }\n" + -" NC_GLOBAL {\n" + -" String acknowledgment \"These data were acquired from the US NOAA National Centers for Environmental Information (NCEI) on [DATE] from http://www.nodc.noaa.gov/gocd/.\";\n" + -" String cdm_data_type \"TrajectoryProfile\";\n" + -" String cdm_profile_variables \"seafloor_depth, latitude, longitude, latitude_quality_flag, longitude_quality_flag, time, time_quality_flag\";\n" + -" String cdm_trajectory_variables \"sampling_interval, crs\";\n" + -" String contributor \"University of Hawaii and NOAA/NMFS\";\n" + -" String Conventions \"CF-1.6\";\n" + -" String creator_email \"Charles.Sun@noaa.gov\";\n" + -" String creator_name \"Charles Sun\";\n" + -" String creator_url \"http://www.nodc.noaa.gov\";\n" + -" String date_created \"2014-12-15T20:20:04Z\";\n" + -" String date_issued \"2016-01-18T04:39:10Z\";\n" + -" String date_modified \"2016-01-18T04:39:10Z\";\n" + -" String featureType \"trajectoryProfile\";\n" + -" Float32 geospatial_lat_max 21.0958;\n" + -" Float32 geospatial_lat_min -14.3883;\n" + -" String geospatial_lat_resolution \"point\";\n" + -" String geospatial_lat_units \"degrees_north\";\n" + -" Float32 geospatial_lon_max -158.3554;\n" + -" Float32 geospatial_lon_min -176.8126;\n" + -" String geospatial_lon_resolution \"point\";\n" + -" String geospatial_lon_units \"degrees_east\";\n" + -" Float32 geospatial_vertical_max 720.0;\n" + -" Float32 geospatial_vertical_min 30.0;\n" + -" String geospatial_vertical_positive \"down\";\n" + -" String geospatial_vertical_resolution \"point\";\n" + -" String geospatial_vertical_units \"meters\";\n" + -" String gocd_format_version \"GOCD-3.0\";\n" + -" String gocd_id \"gocd_a0067774_01192v3.nc\";\n" + -" String grid_mapping_epsg_code \"EPSG:4326\";\n" + -" String grid_mapping_inverse_flattening \"298.257223563\";\n" + -" String grid_mapping_long_name \"Coordinate Reference System\";\n" + -" String grid_mapping_longitude_of_prime_meridian \"0.0f\";\n" + -" String grid_mapping_name \"latitude_longitude\";\n" + -" String grid_mapping_semi_major_axis \"6378137.0\";\n" + -" String history \"Wed Feb 10 18:31:43 2016: ncrename -d depth,z test.nc\n" + -"2016-01-18T04:39:10Z csun updateOCD.R Version 2.0\n" + -"Thu Jan 7 15:59:35 2016: ncatted -a valid_max,seafloor_depth,d,, ../V3/a0067774/gocd_a0067774_01192v3.nc\n" + -"Thu Jan 7 15:59:35 2016: ncatted -a valid_min,seafloor_depth,d,, ../V3/a0067774/gocd_a0067774_01192v3.nc\n" + -"Thu Jan 7 15:59:35 2016: ncatted -a missing_value,seafloor_depth,d,, ../V3/a0067774/gocd_a0067774_01192v3.nc\n" + -"Thu Jan 7 15:59:35 2016: ncatted -a missing_value,sampling_interval,d,, ../V3/a0067774/gocd_a0067774_01192v3.nc\n" + -"2016-01-07T14:01:54Z csun updateGOCD.R Version 1.0\n" + -"2014-12-15T20:20:04Z csun convJASADCP.f90 Version 1.0\";\n" + -" String id \"0093183\";\n" + -" String institution \"NOAA National Centers for Environmental Information\";\n" + -" String instrument_type \"Ocean Surveyor OS75\";\n" + -" String keywords \"EARTH SCIENCE,OCEANS,OCEAN CIRCULATION,OCEAN CURRENTS\";\n" + -" String keywords_vocabulary \"GCMD Science Keywords\";\n" + -" String license \"These data are openly available to the public Please acknowledge the use of these data with the text given in the acknowledgment attribute.\";\n" + -" String Metadata_Conventions \"Unidata Dataset Discovery v1.0\";\n" + -" String naming_authority \"gov.noaa.nodc\";\n" + -" String principal_invesigator \"E.Firing,J.Hummon,R.Brainard\";\n" + -" String project_name \"Coral Reef Ecosystem Investigations\";\n" + -" String publisher_email \"NODC.Services@noaa.gov\";\n" + -" String publisher_name \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION - IN295\";\n" + -" String publisher_url \"http://www.nodc.noaa.gov/\";\n" + -" String QC_indicator \"Contact Principle Investigaror(s)\";\n" + //sic -" String QC_Manual \"Contact Principle Investigaror(s)\";\n" + -" String QC_Software \"Contact Principle Investigaror(s)\";\n" + -" String QC_test_codes \"Contact Principle Investigaror(s)\";\n" + -" String QC_test_names \"Contact Principle Investigaror(s)\";\n" + -" String QC_test_results \"Contact Principle Investigaror(s)\";\n" + -" String references \"http://www.nodc.noaa.gov/\";\n" + -" String source \"global ocean currents in the NCEI archive holdings\";\n" + -" String standard_name_vocabulary \"CF-1.6\";\n" + -" String subsetVariables \"sampling_interval, crs, seafloor_depth, latitude, longitude, latitude_quality_flag, longitude_quality_flag, time, time_quality_flag\";\n" + -" String summary \"global ocean currents in the NCEI archive holdings\";\n" + -" String time_coverage_duration \"P0Y020DT20H00M00S\";\n" + -" String time_coverage_end \"2006-02-05T19:58:00Z\";\n" + -" String time_coverage_resolution \"R000501/2006-01-15T23:58:00Z/P0Y020DT20H00M00\";\n" + -" String time_coverage_start \"2006-01-15T23:58:00Z\";\n" + -" String title \"Global Ocean Currents Database - gocd_a0067774_01192v3.nc\";\n" + -" String uuid \"26f4a163-4c81-437b-9ad7-796822d1ce49\";\n" + -" }\n" + -"}\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - os.reset(); - table.saveAsDDS(os, SEQUENCE_NAME); - results = os.toString(); - expected = -"Dataset {\n" + -" Sequence {\n" + -" Float32 sampling_interval;\n" + -" Float32 seafloor_depth;\n" + -" Float32 latitude;\n" + -" Float32 longitude;\n" + -" Int32 latitude_quality_flag;\n" + -" Int32 longitude_quality_flag;\n" + -" Float32 depth;\n" + -" Int32 depth_quality_flag;\n" + -" Float64 time;\n" + -" Int32 time_quality_flag;\n" + -" Float32 u;\n" + -" Int32 u_quality_flag;\n" + -" Float32 v;\n" + -" Int32 v_quality_flag;\n" + -" Float32 current_speed;\n" + -" Int32 current_speed_quality_flag;\n" + -" Float32 current_direction;\n" + -" Int32 current_direction_quality_flag;\n" + -" Int32 crs;\n" + -" } s;\n" + -"} s;\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //String2.log(table.toCSVString()); - results = table.dataToString(5); - expected = -"sampling_interval,seafloor_depth,latitude,longitude,latitude_quality_flag,longitude_quality_flag," + - "depth,depth_quality_flag,time,time_quality_flag,u,u_quality_flag,v,v_quality_flag," + - "current_speed,current_speed_quality_flag,current_direction," + - "current_direction_quality_flag,crs\n" + -// sapmInt,sfDpth lat lon depth time u v cspeed cdir crs -"9999.9,9999.9,21.0958,-158.3554,1,1,30.0,1,38730.9986,1,-0.004,1,0.174,1,0.174,1,358.7,1,0\n" + -"9999.9,9999.9,21.0958,-158.3554,1,1,40.0,1,38730.9986,1,-0.008,1,0.169,1,0.1692,1,357.3,1,0\n" + -"9999.9,9999.9,21.0958,-158.3554,1,1,50.0,1,38730.9986,1,-0.01,1,0.165,1,0.1653,1,356.5,1,0\n" + -"9999.9,9999.9,21.0958,-158.3554,1,1,60.0,1,38730.9986,1,-0.009,1,0.163,1,0.1632,1,356.8,1,0\n" + -"9999.9,9999.9,21.0958,-158.3554,1,1,70.0,1,38730.9986,1,-0.012,1,0.173,1,0.1734,1,356.0,1,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - results = table.dataToString(); //no row numbers - expected = //why are cspeed and cdir known, but u,v not? -//sampInt sfDpth lat lon depth time u v cspeed cdir crs -"9999.9,9999.9,-14.2758,-170.6805,1,1,680.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n" + -"9999.9,9999.9,-14.2758,-170.6805,1,1,690.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n" + -"9999.9,9999.9,-14.2758,-170.6805,1,1,700.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n" + -"9999.9,9999.9,-14.2758,-170.6805,1,1,710.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n" + -"9999.9,9999.9,-14.2758,-170.6805,1,1,720.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n"; - po = results.indexOf(expected.substring(0, 40)); - Test.ensureEqual(results.substring(po), expected, - "results=\n" + results.substring(po)); - /* */ - - - //*************** a similar test - // 2 levels, and outerDim=ScalarDim - // this tests if var[scalarDim][obs] was read (e.g., depth[obs] - //File dims are outerDim=[scalarDim], inner=[time], obs=[obs] - table = new Table(); - fileName = "/data/gocd/gocd_v3_madcp.nc"; - String2.log("\n\n** Testing " + fileName); - results = NcHelper.ncdump(fileName, "-h"); - String2.log(results); -//just the structure, rearranged into groups -// z = 14; -// time = 3188; -// int crs; -// float sampling_interval; -// float seafloor_depth; -// float latitude; -// float longitude; -// int latitude_quality_flag; -// int longitude_quality_flag; - -// float depth(z=14); -// int depth_quality_flag(z=14); - -// double time(time=3188); -// int time_quality_flag(time=3188); - -// float u(time=3188, z=14); -// int u_quality_flag(time=3188, z=14); -// float v(time=3188, z=14); -// int v_quality_flag(time=3188, z=14); -// float current_speed(time=3188, z=14); -// int current_speed_quality_flag(time=3188, z=14); -// float current_direction(time=3188, z=14); -// int current_direction_quality_flag(time=3188, z=14); - - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - os.reset(); - table.saveAsDDS(os, SEQUENCE_NAME); - results = os.toString(); - expected = -"Dataset {\n" + -" Sequence {\n" + -" Float32 sampling_interval;\n" + -" Float32 seafloor_depth;\n" + -" Float32 latitude;\n" + -" Float32 longitude;\n" + -" Int32 latitude_quality_flag;\n" + -" Int32 longitude_quality_flag;\n" + -" Float32 depth;\n" + -" Int32 depth_quality_flag;\n" + -" Float64 time;\n" + -" Int32 time_quality_flag;\n" + -" Float32 u;\n" + -" Int32 u_quality_flag;\n" + -" Float32 v;\n" + -" Int32 v_quality_flag;\n" + -" Float32 current_speed;\n" + -" Int32 current_speed_quality_flag;\n" + -" Float32 current_direction;\n" + -" Int32 current_direction_quality_flag;\n" + -" Int32 crs;\n" + -" } s;\n" + -"} s;\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //String2.log(table.toCSVString()); - results = table.dataToString(5); - expected = -"sampling_interval,seafloor_depth,latitude,longitude," + -"latitude_quality_flag,longitude_quality_flag,depth,depth_quality_flag,time,time_quality_flag,u,u_quality_flag,v,v_quality_flag," + -"current_speed,current_speed_quality_flag,current_direction," + -"current_direction_quality_flag,crs\n" + -// si sDepth lat lon q q depth q time q u q v q cspeed q cDir q crs -"60.0,32.6386,42.37859,-70.78094,1,1,26.34,1,38621.7448,1,0.0066,1,0.0072,1,0.0111,1,42.8,1,0\n" + -"60.0,32.6386,42.37859,-70.78094,1,1,24.34,1,38621.7448,1,0.0279,1,-0.008,1,0.0292,1,106.0,1,0\n" + -"60.0,32.6386,42.37859,-70.78094,1,1,22.34,1,38621.7448,1,0.0325,1,2.0E-4,1,0.033,1,89.7,1,0\n" + -"60.0,32.6386,42.37859,-70.78094,1,1,20.34,1,38621.7448,1,-0.0094,1,0.0011,1,0.0121,1,277.0,1,0\n" + -"60.0,32.6386,42.37859,-70.78094,1,1,18.34,1,38621.7448,1,-0.0383,1,-0.0367,1,0.0532,1,226.2,1,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - results = table.dataToString(); //no row numbers - //String2.log(results); - expected = //why are cspeed and cdir known, but u,v not? -//si sDepth lat lon q q depth q time q u q v q cspeed q cDir q crs -"60.0,32.6386,42.37859,-70.78094,1,1,8.34,1,38754.5365,1,-0.0177,1,-0.0152,1,0.0257,1,229.2,1,0\n" + -"60.0,32.6386,42.37859,-70.78094,1,1,6.34,1,38754.5365,1,-0.0186,1,-0.0145,1,0.0251,1,232.0,1,0\n" + -"60.0,32.6386,42.37859,-70.78094,1,1,4.34,1,38754.5365,1,-0.0149,1,-0.0181,1,0.03,1,219.4,1,0\n" + -"60.0,32.6386,42.37859,-70.78094,1,1,2.34,1,38754.5365,1,-0.0026,2,-0.0202,2,0.0293,1,187.4,2,0\n" + -"60.0,32.6386,42.37859,-70.78094,1,1,0.34,1,38754.5365,1,9999.9,9,9999.9,9,9999.9,9,45.0,9,0\n"; - po = results.indexOf(expected.substring(0, 80)); - Test.ensureEqual(results.substring(po), expected, - "results=\n" + results.substring(po)); - /* */ - - - // ************* v4 file #1 timeSeries has - // featureType=timeSeriesProfile cdm_data_type=profile - // outerdim=scalar var[time=6952][z=1] time[time=6952] depth[z=1] - table = new Table(); - fileName = "/data/gocd/gocd_a0000841_rcm00566_v4.nc"; - String2.log("\n\n** Testing " + fileName); - results = NcHelper.ncdump(fileName, "-h"); - String2.log(results); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - String2.log(table.dataToString()); - results = table.dataToString(5); - expected = -"sampling_interval,seafloor_depth,latitude,longitude,latitude_quality_flag," + -"longitude_quality_flag,depth,depth_quality_flag,time,time_quality_flag," + -"u,u_quality_flag,v,v_quality_flag,current_speed,current_speed_quality_flag," + -"current_direction,current_direction_quality_flag,crs\n" + -//si sd lat lon q q depth q time q u q v q cSpeed p dir q crs -"60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.424999999814,1,0.015,1,0.0865,1,0.0878,1,9.8,1,0\n" + -"60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.46666666679,1,-0.0045,1,0.0933,1,0.0934,1,357.2,1,0\n" + -"60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.508333333302,1,-0.0072,1,0.0856,1,0.0859,1,355.2,1,0\n" + -"60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.549999999814,1,-0.0065999995,1,0.1025,1,0.1027,1,356.3,1,0\n" + -"60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.59166666679,1,-0.0036,1,0.11200001,1,0.1121,1,358.2,1,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - /* */ - - //********************* v4 file #2 has -/* // featureType=timeSeriesProfile cdm_data_type=profile - // latitude=scalar var[time=126][z=12] time[time=126] depth[z=12] - table = new Table(); - fileName = "/data/gocd/gocd_a0060062_4381adc-a_v4.nc"; - String2.log("\n\n** Testing " + fileName); - results = NcHelper.ncdump(fileName, "-h"); - String2.log(results); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - String2.log(table.dataToString()); - results = table.dataToString(5); - expected = -"zz\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - /* */ - - String2.log("\n*** Table.testReadGocdNcCF finished successfully"); - debugMode = oDebug; - - } - - /** This tests readNcCF nLevels=2. */ - public static void testReadNcCF2(boolean pauseAfterEach) throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCF2"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected; - Attributes gatts; - - - //*************** nLevels=2 multidimensional - for (int type = 0; type < 2; type++) { - //ncCF2b and ncCFMA2b have same data, so tests are the same! - String fileType = type == 0? "ragged" : "multidimensional"; - //from EDDTableFromNcFiles.testNcCF2b() and testNcCFMA2b(); - String fileName = String2.unitTestDataDir + "nccf/" + - (type == 0? "ncCF2b.nc" : "ncCFMA2b.nc"); - String msg = "ERROR when type=" + type + ": "; - - String2.log("\n\n** Testing type=" + type + " nLevels=2/" + fileType + "\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); -/* */ - String2.log("\n\n** Test nLevels=2/" + fileType + " no loadVars, no constraints"); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); -String2.log(table.toString()); - results = table.dataToString(5); - expected = -"platform,cruise,org,type,station_id,longitude,latitude,time,depth,temperature,salinity\n" + -"33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,4.0,-1.84,35.64\n" + -"33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,10.0,-1.84,35.64\n" + -"33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,20.0,-1.83,35.64\n" + -"33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,30.0,-1.83,35.64\n" + -"33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,49.0,-1.83,35.64\n" + -"...\n"; - Test.ensureEqual(results, expected, msg); - Test.ensureEqual(table.nRows(), 53, msg + table.toString()); - results = table.columnAttributes(0).toString(); - expected = -" comment=See the list of platform codes (sorted in various ways) at http://www.nodc.noaa.gov/GTSPP/document/codetbls/calllist.html\n" + -" ioos_category=Identifier\n" + -" long_name=GTSPP Platform Code\n" + -" references=http://www.nodc.noaa.gov/gtspp/document/codetbls/callist.html\n"; - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "org, type, station_id, longitude, latitude, time", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "platform, cruise, org, type, station_id, longitude, latitude, time", - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue("type=" + type + ": " + fileType + " #3a " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("cruise,latitude,depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("cruise"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, msg); - Test.ensureEqual(table.nColumns(), 0, msg); - - table.readNcCF(fileName, - StringArray.fromCSV("cruise,latitude,depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("latitude"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, msg); - Test.ensureEqual(table.nColumns(), 0, msg); - - table.readNcCF(fileName, - StringArray.fromCSV("cruise,latitude,depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("depth"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, msg); - Test.ensureEqual(table.nColumns(), 0, msg); - - table.readNcCF(fileName, - StringArray.fromCSV("cruise,latitude,depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, msg); - Test.ensureEqual(table.nColumns(), 0, msg); + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, //standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); // table.readNcCF(fileName, - StringArray.fromCSV("latitude,depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("latitude"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, msg); - Test.ensureEqual(table.nColumns(), 0, msg); - - table.readNcCF(fileName, - StringArray.fromCSV("latitude,depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("depth"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, msg); - Test.ensureEqual(table.nColumns(), 0, msg); - - table.readNcCF(fileName, - StringArray.fromCSV("latitude,depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, msg); - Test.ensureEqual(table.nColumns(), 0, msg); - - // - table.readNcCF(fileName, StringArray.fromCSV("depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("depth"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, msg); - Test.ensureEqual(table.nColumns(), 0, msg); - - table.readNcCF(fileName, StringArray.fromCSV("depth,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV("latitude,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("latitude"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("latitude,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV("latitude,cruise"), + StringArray.fromCSV("lat,trajectory_name"), 0, //standardizeWhat=0 - StringArray.fromCSV("latitude"), + StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("-12345")); Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); - table.readNcCF(fileName, StringArray.fromCSV("latitude,cruise"), + table.readNcCF(fileName, + StringArray.fromCSV("lat,trajectory_name"), 0, //standardizeWhat=0 - StringArray.fromCSV("cruise"), + StringArray.fromCSV("trajectory_name"), StringArray.fromCSV("="), StringArray.fromCSV("-12345")); Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); // - table.readNcCF(fileName, StringArray.fromCSV("depth,cruise"), + table.readNcCF(fileName, + StringArray.fromCSV("z,trajectory_name"), 0, //standardizeWhat=0 - StringArray.fromCSV("depth"), + StringArray.fromCSV("z"), StringArray.fromCSV("="), StringArray.fromCSV("-12345")); Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); - table.readNcCF(fileName, StringArray.fromCSV("depth,cruise"), + table.readNcCF(fileName, + StringArray.fromCSV("z,trajectory_name"), 0, //standardizeWhat=0 - StringArray.fromCSV("cruise"), + StringArray.fromCSV("trajectory_name"), StringArray.fromCSV("="), StringArray.fromCSV("-12345")); Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); // - table.readNcCF(fileName, StringArray.fromCSV("temperature,cruise"), + table.readNcCF(fileName, + StringArray.fromCSV("temperature,trajectory_name"), 0, //standardizeWhat=0 StringArray.fromCSV("temperature"), StringArray.fromCSV("="), @@ -13695,32 +9171,36 @@ public static void testReadNcCF2(boolean pauseAfterEach) throws Exception { Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); - table.readNcCF(fileName, StringArray.fromCSV("temperature,cruise"), + table.readNcCF(fileName, + StringArray.fromCSV("temperature,trajectory_name"), 0, //standardizeWhat=0 - StringArray.fromCSV("cruise"), + StringArray.fromCSV("trajectory_name"), StringArray.fromCSV("="), StringArray.fromCSV("-12345")); Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); // - table.readNcCF(fileName, StringArray.fromCSV("cruise"), + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name"), 0, //standardizeWhat=0 - StringArray.fromCSV("cruise"), + StringArray.fromCSV("trajectory_name"), StringArray.fromCSV("="), StringArray.fromCSV("-12345")); Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); - table.readNcCF(fileName, StringArray.fromCSV("latitude"), + table.readNcCF(fileName, + StringArray.fromCSV("lat"), 0, //standardizeWhat=0 - StringArray.fromCSV("latitude"), + StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("-12345")); Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); - table.readNcCF(fileName, StringArray.fromCSV("temperature"), + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), 0, //standardizeWhat=0 StringArray.fromCSV("temperature"), StringArray.fromCSV("="), @@ -13728,9729 +9208,550 @@ public static void testReadNcCF2(boolean pauseAfterEach) throws Exception { Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); - table.readNcCF(fileName, StringArray.fromCSV("depth"), + table.readNcCF(fileName, + StringArray.fromCSV("z"), 0, //standardizeWhat=0 - StringArray.fromCSV("depth"), + StringArray.fromCSV("z"), StringArray.fromCSV("="), StringArray.fromCSV("-12345")); Test.ensureEqual(table.nRows(), 0, ""); Test.ensureEqual(table.nColumns(), 0, ""); - // - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just outerTable loadVars, constraints"); - table.readNcCF(fileName, StringArray.fromCSV("platform,cruise,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("platform"), - StringArray.fromCSV("="), - StringArray.fromCSV("33P2")); - results = table.dataToString(); + table.readNcCF(fileName, null, 0, //standardizeWhat=0 + null, null, null); + results = table.dataToString(55); expected = -"platform,cruise\n" + -"33P2,Q990046312\n"; - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), null, - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), "platform, cruise", - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue("type=" + type + ": " + fileType + " #3b " + pauseMessage); - - // - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just outerTable loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, StringArray.fromCSV("platform,cruise,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("platform"), - StringArray.fromCSV("="), - StringArray.fromCSV("zztop")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3c " + pauseMessage); - - - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just innerTable loadVars, no constraints"); - String2.log("ncdump of " + fileName + "\n" + NcHelper.ncdump(fileName, "-v station_id;type")); - table.readNcCF(fileName, - StringArray.fromCSV("station_id,zztop,type"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -//before: 4th row with mv's is removed -//2020-08-03 now it isn't removed for type=1 because station_id is int with no defined _FillValue or missing_value and [3]=2147483647! -// In other words: this is a flaw in the data file. -// note type0=ragged, type1=multidimensional -"station_id,type\n" + -"13968849,TE\n" + -"13968850,TE\n" + -"13933177,BA\n" + -(type == 0? "" : "2147483647,\n"); - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), "type, station_id", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), "type, station_id", - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3d " + pauseMessage); - - - // - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just innerTable loadVars, constraints"); - table.readNcCF(fileName, StringArray.fromCSV("station_id,zztop,type"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_id"), - StringArray.fromCSV("="), - StringArray.fromCSV("13933177")); - results = table.dataToString(); - expected = -"station_id,type\n" + -"13933177,BA\n"; - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), "type, station_id", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), "type, station_id", - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3e " + pauseMessage); - - - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just innerTable loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, StringArray.fromCSV("station_id,zztop,type"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_id"), - StringArray.fromCSV("="), - StringArray.fromCSV("zztop")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3f " + pauseMessage); - - - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just outerTable and innerTable loadVars, no constraints"); - table.readNcCF(fileName, StringArray.fromCSV( - "cruise,org,type,station_id,longitude,latitude,time,zztop,platform"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"cruise,org,type,station_id,longitude,latitude,time,platform\n" + -"Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,33P2\n" + -"Q990046312,ME,TE,13968850,176.64,-75.43,1.335216E9,33P2\n" + -"SHIP 12,ME,BA,13933177,173.54,-34.58,1.33514142E9,9999\n" + -(type == 0? "" : "SHIP 12,,,2147483647,,,,9999\n"); //2020-08-03 this also appeared. See 2020-08-03 comments above - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "org, type, station_id, longitude, latitude, time", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "platform, cruise, org, type, station_id, longitude, latitude, time", - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3g " + pauseMessage); - - - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just outerTable and innerTable loadVars, constraints"); - table.readNcCF(fileName, StringArray.fromCSV( - "row,cruise,org,type,station_id,longitude,latitude,time,zztop,platform"), - 0, //standardizeWhat=0 - StringArray.fromCSV("platform,station_id"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("33P2,13968850")); - results = table.dataToString(); - expected = -"cruise,org,type,station_id,longitude,latitude,time,platform\n" + -"Q990046312,ME,TE,13968850,176.64,-75.43,1.335216E9,33P2\n"; - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "org, type, station_id, longitude, latitude, time", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "platform, cruise, org, type, station_id, longitude, latitude, time", - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3h " + pauseMessage); - - // - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just outerTable and innerTable loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, StringArray.fromCSV( - "row,cruise,org,type,station_id,longitude,latitude,time,zztop,platform"), - 0, //standardizeWhat=0 - StringArray.fromCSV("platform,station_id"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("33P2,zztop")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3i " + pauseMessage); - - - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just outerTable and obs loadVars, constraints"); - table.readNcCF(fileName, - StringArray.fromCSV("salinity,platform,zztop,cruise"), - 0, //standardizeWhat=0 - StringArray.fromCSV("platform,salinity"), - StringArray.fromCSV("=,>="), - StringArray.fromCSV("33P2,35.98")); - results = table.dataToString(); - expected = -"salinity,platform,cruise\n" + -"35.99,33P2,Q990046312\n" + -"36.0,33P2,Q990046312\n" + -"35.98,33P2,Q990046312\n"; - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), null, - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), "platform, cruise", - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3j " + pauseMessage); - - - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just outerTable and obs loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, - StringArray.fromCSV("salinity,platform,zztop,cruise"), - 0, //standardizeWhat=0 - StringArray.fromCSV("platform,salinity"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("33P2,-100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3k " + pauseMessage); - - - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just innerTable and obs loadVars, no constraints"); - table.readNcCF(fileName, StringArray.fromCSV( - "latitude,longitude,time,zztop,salinity"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"latitude,longitude,time,salinity\n" + -"-75.45,176.64,1.3351446E9,35.64\n" + -"-75.45,176.64,1.3351446E9,35.64\n" + -"-75.45,176.64,1.3351446E9,35.64\n" + -"-75.45,176.64,1.3351446E9,35.64\n" + -"-75.45,176.64,1.3351446E9,35.64\n" + -"-75.45,176.64,1.3351446E9,35.63\n" + -"-75.45,176.64,1.3351446E9,35.59\n" + -"-75.45,176.64,1.3351446E9,35.52\n" + -"-75.45,176.64,1.3351446E9,35.56\n" + -"-75.45,176.64,1.3351446E9,35.77\n" + -"-75.45,176.64,1.3351446E9,35.81\n" + -"-75.45,176.64,1.3351446E9,35.82\n" + -"-75.45,176.64,1.3351446E9,35.88\n" + -"-75.45,176.64,1.3351446E9,35.94\n" + -"-75.45,176.64,1.3351446E9,35.99\n" + -"-75.45,176.64,1.3351446E9,36.0\n" + -"-75.43,176.64,1.335216E9,35.64\n" + -"-75.43,176.64,1.335216E9,35.64\n" + -"-75.43,176.64,1.335216E9,35.64\n" + -"-75.43,176.64,1.335216E9,35.64\n" + -"-75.43,176.64,1.335216E9,35.63\n" + -"-75.43,176.64,1.335216E9,35.63\n" + -"-75.43,176.64,1.335216E9,35.61\n" + -"-75.43,176.64,1.335216E9,35.58\n" + -"-75.43,176.64,1.335216E9,35.5\n" + -"-75.43,176.64,1.335216E9,35.77\n" + -"-75.43,176.64,1.335216E9,35.81\n" + -"-75.43,176.64,1.335216E9,35.86\n" + -"-75.43,176.64,1.335216E9,35.9\n" + -"-75.43,176.64,1.335216E9,35.93\n" + -"-75.43,176.64,1.335216E9,35.96\n" + -"-75.43,176.64,1.335216E9,35.98\n"; - -//multidimensional deletes these rows because all read obs columns have mv's -//This is not ideal, but I don't want to read all obs columns in file to determine which rows to delete. -if (fileType.equals("ragged")) - expected += -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n" + -"-34.58,173.54,1.33514142E9,\n"; - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "longitude, latitude, time", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "longitude, latitude, time", - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3l " + pauseMessage); - - - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just innerTable and obs loadVars, constraints"); - table.readNcCF(fileName, - StringArray.fromCSV("latitude,longitude,time,zztop,salinity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,salinity"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("1.335216E9,35.77")); - results = table.dataToString(); - expected = -"latitude,longitude,time,salinity\n" + -"-75.43,176.64,1.335216E9,35.77\n"; - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), - "longitude, latitude, time", msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), - "longitude, latitude, time", msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3m " + pauseMessage); - - - // - String2.log("\n\n** Test nLevels=2/" + fileType + " " + - "just innerTable and obs loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, - StringArray.fromCSV("latitude,longitude,time,zztop,salinity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,salinity"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("1.335216E9,-1000")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3n " + pauseMessage); - + //rows that a human thinks should be rejected are kept + //probably because trajectory_info and trajectory_name aren't missing values + // AND because lat,lon have missing values but there is no missing_value attribute. + "lat,lon,trajectory_info,trajectory_name,time,z,temperature,humidity\n" + + "2.152863,-35.078842,0,Trajectory0,0,0.0,13.466983,65.38418\n" + + "33.60481,-44.12696,0,Trajectory0,3600,1.0,23.050304,7.0401154\n" + + "22.562508,-18.115444,0,Trajectory0,7200,2.0,15.112072,45.15019\n" + + "13.432817,-21.772585,0,Trajectory0,10800,3.0,22.97767,12.618799\n" + + "43.011986,-28.655304,0,Trajectory0,14400,4.0,21.318092,4.788235\n" + + "18.84832,-25.418892,0,Trajectory0,18000,5.0,27.496708,66.337166\n" + + "18.040411,-30.469133,0,Trajectory0,21600,6.0,30.678926,31.57974\n" + + "32.34516,-75.79432,0,Trajectory0,25200,7.0,12.096431,11.228316\n" + + "8.652234,-69.01581,0,Trajectory0,28800,8.0,12.523737,47.003998\n" + + "18.905367,-18.362652,0,Trajectory0,32400,9.0,22.805552,8.789174\n" + + "12.184539,-42.194824,0,Trajectory0,36000,10.0,17.411797,40.25377\n" + + "16.498188,-74.44906,0,Trajectory0,39600,11.0,27.783548,20.712833\n" + + "1.5479256,-53.522717,0,Trajectory0,43200,12.0,11.809888,5.6157913\n" + + "22.033587,-28.557417,0,Trajectory0,46800,13.0,13.730549,2.8293543\n" + + "5.997217,-35.043163,0,Trajectory0,50400,14.0,6.549969,30.482803\n" + + "8.580469,-45.364418,0,Trajectory0,54000,15.0,11.789269,2.303839\n" + + "6.253441,-9.302229,0,Trajectory0,57600,16.0,24.03656,56.802467\n" + + "12.948677,-20.07699,0,Trajectory0,61200,17.0,17.980707,66.24162\n" + + "41.49208,-19.628315,0,Trajectory0,64800,18.0,0.44739303,25.76894\n" + + "25.784758,-65.65333,0,Trajectory0,68400,19.0,13.147206,1.4286463\n" + + "25.884523,-64.92309,0,Trajectory0,72000,20.0,21.278152,72.43937\n" + + "7.5993505,-33.58001,0,Trajectory0,75600,21.0,14.465093,74.04942\n" + + "23.801714,-8.210893,0,Trajectory0,79200,22.0,17.250273,43.468597\n" + + "24.086273,-16.376455,0,Trajectory0,82800,23.0,36.73325,56.15435\n" + + "8.838917,-65.32871,0,Trajectory0,86400,24.0,21.714993,32.324383\n" + + "3.049409,-50.187355,0,Trajectory0,90000,25.0,17.755543,7.7604437\n" + + "32.699135,-13.603052,0,Trajectory0,93600,26.0,21.764454,68.36558\n" + + "28.82149,-4.238066,0,Trajectory0,97200,27.0,4.18221,75.262665\n" + + "4.573595,-15.691054,0,Trajectory0,100800,28.0,36.230297,74.156654\n" + + "30.231867,-29.110548,0,Trajectory0,104400,29.0,10.372004,8.0368805\n" + + "26.295082,-24.224209,0,Trajectory0,108000,30.0,7.0729938,31.468176\n" + + "26.146648,-35.461746,0,Trajectory0,111600,31.0,12.3075285,71.35397\n" + + "18.875525,-11.409157,0,Trajectory0,115200,32.0,30.241188,45.14291\n" + + "44.57873,-29.37942,0,Trajectory0,118800,33.0,21.847982,61.776512\n" + + "40.911667,-31.65526,0,Trajectory0,122400,34.0,30.369759,29.810774\n" + + "9.5415745,-57.1067,0,Trajectory0,126000,35.0,15.864324,33.90924\n" + + //these aren't rejected because + //* trajectory_info has the attribute missing_value=-999, + // but the data above has trajectory_info=0, which isn't a missing value. + //* trajectory_name is a string, so my reader doesn't expect a + // missing_value attribute, but my reader does treat a data + // value of "" (nothing) as a missing value. Unfortunately, this + // file has other values (e.g., "Trajectory0"), so my reader + // treats those as not missing values. + //* lat and lon have data values of -999.9 which is probably + // intended to be a missing value marker, but those variables + // have no missing_value attributes, so my program treats them as + // valid values. + //I reported to Kyle 2012-10-03 and hope he'll make changes - String2.log("\n\n** Test nLevels=2/" + fileType + " just obs loadVars, constraints"); - table.readNcCF(fileName, StringArray.fromCSV("temperature,salinity,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("salinity"), - StringArray.fromCSV("="), - StringArray.fromCSV("35.77")); - results = table.dataToString(); + //"36,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"37,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"38,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"39,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"40,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"41,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"42,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"43,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"44,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"45,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"46,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"47,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"48,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + //"49,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + + "36,13.633951,-61.779095,1,Trajectory1,0,0.0,31.081379,7.8967414\n" + + "37,41.583824,-52.047775,1,Trajectory1,3600,1.0,23.026224,25.034555\n" + + "38,14.176689,-15.26571,1,Trajectory1,7200,2.0,21.750353,61.35738\n" + + "39,23.482225,-69.246284,1,Trajectory1,10800,3.0,25.214777,70.63098\n" + + "40,8.910114,-12.47847,1,Trajectory1,14400,4.0,29.234118,53.387733\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 200, ""); + results = table.columnAttributes(5).toString(); //temperature expected = -"temperature,salinity\n" + -"-1.1,35.77\n" + -"-1.12,35.77\n"; - Test.ensureEqual(results, expected, msg + "results=\n" + results); - gatts = table.globalAttributes(); - Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("cdm_profile_variables"), null, - msg + gatts.toString()); - Test.ensureEqual(gatts.getString("subsetVariables"), null, - msg + gatts.toString()); - if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3o " + pauseMessage); - - - // - String2.log("\n\n** Test nLevels=2/" + fileType + - " just obs loadVars, constraints, NO_DATA"); - table.readNcCF(fileName, StringArray.fromCSV("temperature,salinity,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("salinity"), - StringArray.fromCSV("="), - StringArray.fromCSV("-1000")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); + " axis=Z\n" + + " long_name=height above mean sea level\n" + + " missing_value=-999.9f\n" + + " positive=up\n" + + " standard_name=altitude\n" + + " units=m\n"; + Test.ensureEqual(results, expected, "results=\n" + results); if (pauseAfterEach) - String2.pressEnterToContinue(fileType + " #3p " + pauseMessage); + String2.pressEnterToContinue("#8b " + pauseMessage); - } //end nLevels=2 type loop - debugMode = oDebug; + + } catch (Exception e) { + //String2.pressEnterToContinue( + Test.knownProblem( + "KYLE WILCOX'S DSG TEST FILE.", + MustBe.throwableToString(e) + + "\nI reported this problem to Kyle 2012-10-03" + + "\n2013-10-30 Since Kyle changed jobs, it is unlikely he will ever fix this."); + } } - - /** This tests readNcCF profile files from ASA - * via https://github.com/asascience-open/CFPointConventions - * stored in unitTestDataDir/CFPointConventions. + /** + * This reads an NCEI-style invalid CF DSG Contiguous Ragged Array .nc file. + * Suitable sample files are from https://data.nodc.noaa.gov/thredds/catalog/ncei/wod/ + * See local copies in /erddapTestBig/nccf/wod/ + * + * @param colNames If empty, this reads all columns. + * If conNames... specified and this is specified, this includes all of the conNames. + * @param standardizeWhat see Attributes.unpackVariable's standardizeWhat + * @param conNames may be null or size=0; + * @throws Exception if trouble. + * No matching data is not an error and returns an empty table (0 rows and 0 columns). */ - public static void testReadNcCFASAProfile(boolean pauseAfterEach) throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCFASAProfile"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected, fileName; - -/* */ - //*************** profile contiguous - fileName = String2.unitTestDataDir + "CFPointConventions/profile/" + - "profile-Contiguous-Ragged-MultipleProfiles-H.3.4/" + - "profile-Contiguous-Ragged-MultipleProfiles-H.3.4.nc"; - String2.log("\n\n** Testing contiguous file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(18); - expected = -/* pre 2012-10-02 was -"lat,lon,profile,time,z,temperature,humidity\n" + -"137.0,30.0,0,0,8.055641,32.962334,14.262256\n" + -"137.0,30.0,0,0,8.9350815,25.433783,41.722572\n" + -"137.0,30.0,0,0,5.1047354,4.0391192,44.34395\n" + -"137.0,30.0,0,0,4.2890472,6.0850625,13.220096\n" + -"137.0,30.0,0,0,1.9311341,32.794086,32.313293\n"; */ -//z seems to be made up numbers. not in order (for a given profile) as one would expect. -"lat,lon,profile,time,z,temperature,humidity\n" + -"34.0,115.0,0,0,9.913809,30.592709,32.71529\n" + -"34.0,115.0,0,0,5.699307,17.442251,76.26051\n" + -"34.0,115.0,0,0,0.617254,14.230382,13.789284\n" + -"34.0,115.0,0,0,2.6114788,38.859676,21.792738\n" + -"34.0,115.0,0,0,6.519849,28.003593,33.264217\n" + -"34.0,115.0,0,0,8.975919,10.699942,61.52172\n" + -"34.0,115.0,0,0,9.912431,32.747574,85.96188\n" + -"34.0,115.0,0,0,7.5545244,18.109398,41.733406\n" + -"34.0,115.0,0,0,7.568512,10.165248,84.50128\n" + -"34.0,115.0,0,0,3.376015,0.48572874,5.2108083\n" + -"11.0,95.0,1,3600,0.16332848,1.193263,87.431725\n" + -"11.0,95.0,1,3600,4.9485574,31.53037,65.04175\n" + -"11.0,95.0,1,3600,6.424919,11.956788,54.758873\n" + -"11.0,95.0,1,3600,4.7111635,36.69692,50.6536\n" + -"11.0,95.0,1,3600,6.854408,21.065716,83.941765\n" + -"11.0,95.0,1,3600,9.321201,31.395382,17.139112\n" + -"176.0,17.0,2,7200,7.2918577,17.65049,66.33111\n" + -"176.0,17.0,2,7200,3.270435,35.854877,17.296724\n" + -"...\n"; - - - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 58, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#4a " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); + public void readInvalidCRA(String fullName, StringArray colNames, + int standardizeWhat, + StringArray conNames, StringArray conOps, StringArray conVals) throws Exception { - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); + String msg = " Table.readInvalidCRA " + fullName; + long time = System.currentTimeMillis(); + clear(); + if (colNames == null) + colNames = new StringArray(1, false); + //String2.log(NcHelper.ncdump(fullName, "-h")); + Attributes gridMappingAtts = null; + NetcdfFile ncFile = NcHelper.openFile(fullName); + try { - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); + NcHelper.getGroupAttributes(ncFile.getRootGroup(), globalAttributes()); + Attributes gatts = globalAttributes(); - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); + //ensure featureType=Profile (other single level types could be supported -- need examples) + String featureType = gatts.getString("featureType"); + featureType = featureType == null? "" : String2.toTitleCase(featureType); + Test.ensureEqual(featureType, "Profile", "Unexpected featureType."); - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); + //find vars with sample_dimension, find outerDimName, largestInnerDim + String profileIDVarName = null; + int profileIDVarNumber = -1; + String outerDimName = null; //e.g., cast + Dimension outerDim = null; + String largestInnerDimName = null; //e.g., z_obs + int largestInnerDimSize = -1; + List varList = ncFile.getVariables(); + int nVars = varList.size(); + String vNames[] = new String[nVars]; + Attributes vatts[] = new Attributes[nVars]; + PAType varPATypes[] = new PAType[nVars]; + boolean isCharArray[] = new boolean[nVars]; + int nDims[] = new int[nVars]; + int realNDims[] = new int[nVars]; + String varMissingValues[] = new String[nVars]; + boolean varHasSampleDimensionAtt[] = new boolean[nVars]; + HashMap rowSizesHM = new HashMap(); //e.g., sample_dimension="z_obs" -> z_row_size PA + for (int v = 0; v < nVars; v++) { + Variable var = varList.get(v); + vNames[v] = var.getFullName(); + vatts[v] = new Attributes(); + NcHelper.getVariableAttributes(var, vatts[v]); - // - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); + //does this var point to the pseudo-data var with CF grid_mapping (projection) information? + if (gridMappingAtts == null) { + gridMappingAtts = NcHelper.getGridMappingAtts(ncFile, + vatts[v].getString("grid_mapping")); + if (gridMappingAtts != null) + globalAttributes.add(gridMappingAtts); + } - table.readNcCF(fileName, StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV("lat,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("lat,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - table.readNcCF(fileName, StringArray.fromCSV("z,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("z,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV("temperature,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("temperature,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV("profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV("z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - //test get outer+obs variables with outer constraint - table.readNcCF(fileName, StringArray.fromCSV("profile,lat,lon,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("11")); - results = table.dataToString(); - expected = -"profile,lat,lon,temperature\n" + -"1,11.0,95.0,1.193263\n" + -"1,11.0,95.0,31.53037\n" + -"1,11.0,95.0,11.956788\n" + -"1,11.0,95.0,36.69692\n" + -"1,11.0,95.0,21.065716\n" + -"1,11.0,95.0,31.395382\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test get outer+obs variables with obs constraint - table.readNcCF(fileName, StringArray.fromCSV("profile,lat,lon,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), StringArray.fromCSV("="), StringArray.fromCSV("11.956788")); - results = table.dataToString(); - expected = -"profile,lat,lon,temperature\n" + -"1,11.0,95.0,11.956788\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test get obs variables with outer constraint - table.readNcCF(fileName, StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("11")); - results = table.dataToString(); - expected = -"lat,temperature\n" + -"11.0,1.193263\n" + -"11.0,31.53037\n" + -"11.0,11.956788\n" + -"11.0,36.69692\n" + -"11.0,21.065716\n" + -"11.0,31.395382\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - - - //*************** profile incomplete multidimensional --- - fileName = String2.unitTestDataDir + "CFPointConventions/profile/" + - "profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/" + - "profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.nc"; - String2.log("\n\n** Testing incomplete\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(45); - expected = -"lat,lon,profile,time,alt,temperature,humidity,wind_speed\n" + -"171.0,119.0,0,0,3.6755686,17.65279,-999.9,51.078896\n" + -"171.0,119.0,0,0,0.26343155,6.2052555,-999.9,64.199974\n" + -"171.0,119.0,0,0,3.175112,12.011641,-999.9,6.9850345\n" + -"171.0,119.0,0,0,4.208357,21.89748,-999.9,58.273148\n" + -"171.0,119.0,0,0,2.6554945,21.416033,-999.9,71.660774\n" + -"171.0,119.0,0,0,4.9972143,1.4952343,-999.9,31.470207\n" + -"171.0,119.0,0,0,1.9827757,21.466,-999.9,11.440447\n" + -"171.0,119.0,0,0,4.1058283,14.191161,-999.9,21.072964\n" + -"171.0,119.0,0,0,5.648934,7.727216,-999.9,20.63561\n" + -"171.0,119.0,0,0,1.2512851,21.434706,-999.9,60.469204\n" + -"171.0,119.0,0,0,9.600934,2.1928697,-999.9,71.77351\n" + -"171.0,119.0,0,0,1.9799258,16.0188,-999.9,55.211063\n" + -"171.0,119.0,0,0,1.2364764,3.242274,-999.9,11.2599\n" + -"171.0,119.0,0,0,2.834809,39.97538,-999.9,84.81159\n" + -"171.0,119.0,0,0,3.950956,19.135057,-999.9,29.651375\n" + -"171.0,119.0,0,0,8.663035,36.685486,-999.9,16.686064\n" + -"171.0,119.0,0,0,1.8081368,31.313751,-999.9,55.862072\n" + -"171.0,119.0,0,0,7.7147174,22.89713,-999.9,55.927597\n" + -"171.0,119.0,0,0,9.629576,18.616583,-999.9,68.66041\n" + -"171.0,119.0,0,0,6.9754705,7.9321976,-999.9,60.648094\n" + -"171.0,119.0,0,0,2.7991323,11.907311,-999.9,67.411575\n" + -"171.0,119.0,0,0,1.5943866,29.448673,-999.9,79.15605\n" + -"171.0,119.0,0,0,0.9762172,3.3020692,-999.9,85.00339\n" + -"171.0,119.0,0,0,5.5088353,12.813819,-999.9,77.104706\n" + -"171.0,119.0,0,0,7.2601357,38.730194,-999.9,18.446539\n" + -"171.0,119.0,0,0,8.384121,19.790619,-999.9,74.80566\n" + -"171.0,119.0,0,0,6.4686337,23.498947,-999.9,76.68345\n" + -"171.0,119.0,0,0,2.0993211,21.344112,-999.9,28.282118\n" + -"171.0,119.0,0,0,0.8403456,17.045395,-999.9,88.80201\n" + -"171.0,119.0,0,0,9.251101,15.639243,-999.9,70.71877\n" + -"171.0,119.0,0,0,1.3482393,9.54115,-999.9,59.91356\n" + -"171.0,119.0,0,0,3.6940877,30.967232,-999.9,35.620453\n" + -"171.0,119.0,0,0,6.3351345,6.0343504,-999.9,44.98056\n" + -"171.0,119.0,0,0,6.3332343,20.940767,-999.9,76.89658\n" + -"171.0,119.0,0,0,0.053762503,20.765089,-999.9,12.856414\n" + -"171.0,119.0,0,0,1.0131614,12.508157,-999.9,69.99224\n" + -"171.0,119.0,0,0,4.424666,37.28969,-999.9,24.69326\n" + -"171.0,119.0,0,0,1.5825375,17.199543,-999.9,63.037647\n" + -"171.0,119.0,0,0,3.072151,13.194056,-999.9,33.561863\n" + -"171.0,119.0,0,0,5.897976,6.350154,-999.9,9.787908\n" + -"171.0,119.0,0,0,1.6135278,22.95996,-999.9,85.10665\n" + -"171.0,119.0,0,0,6.9384937,7.619196,-999.9,33.569344\n" + -"155.0,158.0,1,3600,2.1733663,4.981018,-999.9,41.24567\n" + -"155.0,158.0,1,3600,2.189715,16.313164,-999.9,8.15441\n" + -"155.0,158.0,1,3600,9.445334,18.173727,-999.9,52.259445\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - // 42 * 142 = 5964 obs spaces, so it is incomplete - Test.ensureEqual(table.nRows(), 5754, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#4b " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - table.readNcCF(fileName, - StringArray.fromCSV("alt,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("alt,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("temperature,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - - //*************** profile indexed IMPORTANT - I didn't have sample of indexed - try { - fileName = String2.unitTestDataDir + "CFPointConventions/profile/" + - "profile-Indexed-Ragged-MultipleProfiles-H.3.5/" + - "profile-Indexed-Ragged-MultipleProfiles-H.3.5.nc"; - String2.log("\n\n** Testing indexed file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); -String2.log(table.dataToString()); - results = table.dataToString(20); - expected = -"lat,lon,profile,time,z,temperature,humidity\n" + -"93.0,71.0,0,0,0.38200212,23.69535,52.60904\n" + -"93.0,71.0,0,0,1.200709,29.121883,12.060117\n" + -"93.0,71.0,0,0,2.6969194,23.355228,9.943134\n" + -"93.0,71.0,0,0,3.4035592,21.57062,75.10006\n" + -"93.0,71.0,0,0,5.829337,2.9969826,17.760695\n" + -"93.0,71.0,0,0,5.8626857,37.635395,86.32262\n" + -"93.0,71.0,0,0,6.5773344,2.3481517,85.33706\n" + -"93.0,71.0,0,0,7.7204447,5.337912,54.993973\n" + -"93.0,71.0,0,0,8.301987,32.431896,88.71708\n" + -"93.0,71.0,0,0,9.088309,30.518106,44.74581\n" + -"45.0,151.0,1,3600,0.47979552,28.567852,65.933014\n" + -"45.0,151.0,1,3600,0.594338,7.940218,79.38502\n" + -"45.0,151.0,1,3600,4.0314445,20.808128,13.365513\n" + -"45.0,151.0,1,3600,6.101271,4.62561,8.945877\n" + -"45.0,151.0,1,3600,6.1228404,13.251722,50.431633\n" + -"45.0,151.0,1,3600,8.454789,17.803867,4.852586\n" + -"169.0,145.0,2,7200,1.9213479,7.1473145,11.227387\n" + -"169.0,145.0,2,7200,3.328237,27.21546,29.352453\n" + -"112.0,9.0,3,10800,0.009190708,6.3910594,56.909916\n" + -"112.0,9.0,3,10800,0.013856917,13.634793,63.741573\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 100, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#4c " + pauseMessage); - -//"19,112.0,9.0,3,10800,0.013856917,13.634793,63.741573\n"; - table.readNcCF(fileName, - StringArray.fromCSV("profile,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile,temperature"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("3,13.634793")); - results = table.dataToString(); - expected = -"profile,temperature\n" + -"3,13.634793\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - // - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("temperature,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - - //"19,112.0,9.0,3,10800,0.013856917,13.634793,63.741573\n"; - table.readNcCF(fileName, - StringArray.fromCSV("profile,z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile,z"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("3,0.013856917")); - results = table.dataToString(); - expected = -"profile,z\n" + -"3,0.013856917\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - String2.log("\n\n** Testing indexed file NO_DATA - inner"); - table.readNcCF(fileName, - StringArray.fromCSV("lat,lon,profile,time,z,temperature,humidity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-10000")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#4d " + pauseMessage); - - - String2.log("\n\n** Testing indexed file NO_DATA - odd combo"); - table.readNcCF(fileName, - StringArray.fromCSV("lat,lon,profile,time,z,temperature,humidity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat,z"), - StringArray.fromCSV("=,="), - StringArray.fromCSV("93,0.594338")); //actual values, but never in this combination - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#4e " + pauseMessage); - - - String2.log("\n\n** Testing indexed file NO_DATA - outer"); - table.readNcCF(fileName, - StringArray.fromCSV("lat,lon,profile,time,z,temperature,humidity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("humidity"), - StringArray.fromCSV("="), - StringArray.fromCSV("-10000")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#4f " + pauseMessage); - - } catch (Exception e) { - String2.pressEnterToContinue(MustBe.throwableToString(e)); - } - - - //*************** profile orthogonal - fileName = String2.unitTestDataDir + "CFPointConventions/profile/" + - "profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/" + - "profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.nc"; - String2.log("\n\n** Testing orthogonal file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(55); - expected = //z[obs] is in the innerTable -"lat,lon,profile,time,z,temperature,humidity\n" + -"19.0,116.0,0,0,1.6315197,15.477672,45.439682\n" + -"19.0,116.0,0,0,7.0598154,31.758614,35.987625\n" + -"19.0,116.0,0,0,0.36953768,2.4893014,65.79051\n" + -"19.0,116.0,0,0,7.5342026,26.857018,48.042828\n" + -"19.0,116.0,0,0,7.404938,19.151163,35.629215\n" + -"19.0,116.0,0,0,1.4442251,24.565704,37.29833\n" + -"19.0,116.0,0,0,9.80883,15.455084,23.763685\n" + -"19.0,116.0,0,0,8.060886,26.090511,14.579169\n" + -"19.0,116.0,0,0,1.965906,8.010671,69.79476\n" + -"19.0,116.0,0,0,9.60608,26.692741,78.83376\n" + -"19.0,116.0,0,0,9.839138,39.378746,37.22304\n" + -"19.0,116.0,0,0,6.2004266,14.685706,39.81143\n" + -"19.0,116.0,0,0,6.9113455,7.344667,18.64804\n" + -"19.0,116.0,0,0,8.798231,7.1495833,25.831097\n" + -"19.0,116.0,0,0,2.3565977,0.25708458,32.442547\n" + -"19.0,116.0,0,0,8.742956,34.86492,49.41099\n" + -"19.0,116.0,0,0,8.557564,35.413876,66.573906\n" + -"19.0,116.0,0,0,9.6161375,37.28068,4.6605506\n" + -"19.0,116.0,0,0,6.610992,5.4654717,60.635574\n" + -"19.0,116.0,0,0,1.936887,33.513893,82.823166\n" + -"19.0,116.0,0,0,3.0184858,31.41321,75.51568\n" + -"19.0,116.0,0,0,2.5581324,15.092895,79.2067\n" + -"19.0,116.0,0,0,7.1288857,20.573462,27.601343\n" + -"19.0,116.0,0,0,1.5220404,0.5649648,3.6447735\n" + -"19.0,116.0,0,0,3.276416,27.345316,62.10269\n" + -"19.0,116.0,0,0,0.40930283,27.671362,79.762955\n" + -"19.0,116.0,0,0,2.4845016,31.252121,61.57929\n" + -"19.0,116.0,0,0,9.366717,9.342631,78.63049\n" + -"19.0,116.0,0,0,0.3365049,20.81806,29.236477\n" + -"19.0,116.0,0,0,7.646478,3.1961684,7.8138685\n" + -"19.0,116.0,0,0,5.075439,36.427265,20.879707\n" + -"19.0,116.0,0,0,5.1594234,18.314194,6.4109855\n" + -"19.0,116.0,0,0,2.1663764,10.056105,5.798549\n" + -"19.0,116.0,0,0,9.028424,5.7192965,56.243206\n" + -"19.0,116.0,0,0,9.031402,13.884695,36.763905\n" + -"19.0,116.0,0,0,5.26929,3.5693107,84.04594\n" + -"19.0,116.0,0,0,2.6247969,8.933488,28.76576\n" + -"19.0,116.0,0,0,9.745737,24.357897,76.431816\n" + -"19.0,116.0,0,0,3.722143,17.96677,18.759092\n" + -"19.0,116.0,0,0,1.9264901,28.71267,52.148735\n" + -"19.0,116.0,0,0,3.9815784,35.91171,33.082714\n" + -"19.0,116.0,0,0,4.657818,31.10753,65.25383\n" + -"109.0,178.0,1,3600,1.6315197,26.582031,10.312429\n" + -"109.0,178.0,1,3600,7.0598154,4.909754,50.415916\n" + -"109.0,178.0,1,3600,0.36953768,30.069138,36.845417\n" + -"109.0,178.0,1,3600,7.5342026,3.341837,52.53064\n" + -"109.0,178.0,1,3600,7.404938,36.832874,81.62572\n" + -"109.0,178.0,1,3600,1.4442251,21.88992,78.833565\n" + -"109.0,178.0,1,3600,9.80883,25.902088,50.43351\n" + -"109.0,178.0,1,3600,8.060886,30.653927,81.53324\n" + -"109.0,178.0,1,3600,1.965906,0.8834069,86.67266\n" + -"109.0,178.0,1,3600,9.60608,27.2307,74.25348\n" + -"109.0,178.0,1,3600,9.839138,15.706074,86.22133\n" + -"109.0,178.0,1,3600,6.2004266,34.751484,79.71265\n" + -"109.0,178.0,1,3600,6.9113455,16.43026,30.387852\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 5964, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#4g " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("profile,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("profile,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("profile,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - /* */ - debugMode = oDebug; - } - - /** This tests readNcCF timeseries files from ASA - * via https://github.com/asascience-open/CFPointConventions - * stored in unitTestDataDir/CFPointConventions. - */ - public static void testReadNcCFASATimeSeries(boolean pauseAfterEach) throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCFASATimeseries"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected, fileName; - - - //*************** timeseries orthogonal - fileName = String2.unitTestDataDir + "CFPointConventions/timeseries/" + - "timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/" + - "timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.nc"; - String2.log("\n\n** Testing orthogonal file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); -//!!! obs vars are temperature[time=100][station=10] -//so outer=time and inner is station! - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(12); - expected = -"lat,lon,station_name,alt,time,temperature,humidity\n" + -"8.0,146.0,Station-0,0.8488673,0,18.618036,27.177536\n" + -"4.0,53.0,Station-1,1.8478156,0,13.216496,83.71079\n" + -"90.0,159.0,Station-2,3.4614673,0,39.300182,44.69293\n" + -"55.0,25.0,Station-3,4.8902116,0,17.008652,2.3659434\n" + -"115.0,30.0,Station-4,9.45969,0,24.951536,7.1026664\n" + -"165.0,125.0,Station-5,0.17808062,0,35.995247,41.411594\n" + -"143.0,175.0,Station-6,8.85507,0,24.334364,39.776123\n" + -"157.0,175.0,Station-7,0.47320434,0,33.077255,1.1665242\n" + -"101.0,80.0,Station-8,7.470208,0,6.9397545,72.75068\n" + -"167.0,57.0,Station-9,0.6709764,0,28.991974,71.65753\n" + -"8.0,146.0,Station-0,0.8488673,3600,3.0675685,53.43748\n" + -"4.0,53.0,Station-1,1.8478156,3600,37.31892,46.79294\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 1000, ""); - results = table.columnAttributes(5).toString(); //temperature - expected = -" coordinates=lat lon alt\n" + //this is what source has. But it should include time. -" long_name=Air Temperature\n" + -" missing_value=-999.9f\n" + -" standard_name=air_temperature\n" + -" units=Celsius\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#5a " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("alt,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("alt,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - // - table.readNcCF(fileName, - StringArray.fromCSV("alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - //read just inner [station] vars - table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"station_name,lat,lon\n" + -"Station-0,8.0,146.0\n" + -"Station-1,4.0,53.0\n" + -"Station-2,90.0,159.0\n" + -"Station-3,55.0,25.0\n" + -"Station-4,115.0,30.0\n" + -"Station-5,165.0,125.0\n" + -"Station-6,143.0,175.0\n" + -"Station-7,157.0,175.0\n" + -"Station-8,101.0,80.0\n" + -"Station-9,167.0,57.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just inner [station] vars, with constraint - table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), StringArray.fromCSV(">"), StringArray.fromCSV("150")); - results = table.dataToString(); - expected = -"station_name,lat,lon\n" + -"Station-5,165.0,125.0\n" + -"Station-7,157.0,175.0\n" + -"Station-9,167.0,57.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just outer [time] vars - table.readNcCF(fileName, StringArray.fromCSV("time"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -"time\n" + -"0\n" + -"3600\n" + -"7200\n" + -"10800\n" + -"14400\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 100, ""); - - //read just outer [time] vars, with constraint - table.readNcCF(fileName, StringArray.fromCSV("time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,time"), StringArray.fromCSV(">,<"), StringArray.fromCSV("7000,11000")); - results = table.dataToString(); - expected = -"time\n" + -"7200\n" + -"10800\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just outer+inner [time][station] vars - table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon,time"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"station_name,lat,lon,time\n" + -"Station-0,8.0,146.0,0\n" + -"Station-1,4.0,53.0,0\n" + -"Station-2,90.0,159.0,0\n" + -"Station-3,55.0,25.0,0\n" + -"Station-4,115.0,30.0,0\n" + -"Station-5,165.0,125.0,0\n" + -"Station-6,143.0,175.0,0\n" + -"Station-7,157.0,175.0,0\n" + -"Station-8,101.0,80.0,0\n" + -"Station-9,167.0,57.0,0\n" + -"Station-0,8.0,146.0,3600\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 10*100, ""); - - expected = -"Station-0,8.0,146.0,345600\n" + -"Station-1,4.0,53.0,345600\n" + -"Station-2,90.0,159.0,345600\n" + -"Station-3,55.0,25.0,345600\n" + -"Station-4,115.0,30.0,345600\n" + -"Station-5,165.0,125.0,345600\n" + -"Station-6,143.0,175.0,345600\n" + -"Station-7,157.0,175.0,345600\n" + -"Station-8,101.0,80.0,345600\n" + -"Station-9,167.0,57.0,345600\n"; - int po = results.indexOf(expected); - Test.ensureTrue(po > 0, "po=" + po); - Test.ensureEqual(results.substring(po, po + expected.length()), expected, "results=\n" + results); - - //read just outer+inner [time][station] vars, with outer [time] constraint - table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), StringArray.fromCSV("="), StringArray.fromCSV("345600")); - results = table.dataToString(); - expected = -"station_name,lat,lon,time\n" + -"Station-0,8.0,146.0,345600\n" + -"Station-1,4.0,53.0,345600\n" + -"Station-2,90.0,159.0,345600\n" + -"Station-3,55.0,25.0,345600\n" + -"Station-4,115.0,30.0,345600\n" + -"Station-5,165.0,125.0,345600\n" + -"Station-6,143.0,175.0,345600\n" + -"Station-7,157.0,175.0,345600\n" + -"Station-8,101.0,80.0,345600\n" + -"Station-9,167.0,57.0,345600\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just outer+inner [time][station] vars, with inner [station] constraint - table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("165")); - results = table.dataToString(); - expected = -"station_name,lat,lon,time\n" + -"Station-5,165.0,125.0,0\n" + -"Station-5,165.0,125.0,3600\n" + -"Station-5,165.0,125.0,7200\n" + -"Station-5,165.0,125.0,10800\n" + -"Station-5,165.0,125.0,14400\n" + -"Station-5,165.0,125.0,18000\n" + -"Station-5,165.0,125.0,21600\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 100, ""); - - //read just outer+inner [time][station] vars, with outer and inner constraint - table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); - results = table.dataToString(); - expected = -"station_name,lat,lon,time\n" + -"Station-5,165.0,125.0,345600\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just outer+inner+obs vars, with outer and inner constraint - table.readNcCF(fileName, StringArray.fromCSV(""), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); - results = table.dataToString(); - expected = -"lat,lon,station_name,alt,time,temperature,humidity\n" + -"165.0,125.0,Station-5,0.17808062,345600,38.457962,28.075706\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just outer+obs vars, with outer and inner constraint - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, StringArray.fromCSV("lat,time,temperature,humidity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); - results = table.dataToString(); - expected = -"lat,time,temperature,humidity\n" + -"165.0,345600,38.457962,28.075706\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just inner+obs vars, with outer and inner constraint - table.readNcCF(fileName, StringArray.fromCSV("lat,lon,station_name,time,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); - results = table.dataToString(); - expected = -"lat,lon,station_name,time,temperature\n" + -"165.0,125.0,Station-5,345600,38.457962\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just obs vars, with outer and inner constraint - table.readNcCF(fileName, StringArray.fromCSV("time,lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); - results = table.dataToString(); - expected = -"time,lat,temperature\n" + -"345600,165.0,38.457962\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - //*************** timeseries incomplete multidimensional --- - fileName = String2.unitTestDataDir + "CFPointConventions/timeseries/" + - "timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/" + - "timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.nc"; - String2.log("\n\n** Testing incomplete file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(24); - expected = -"lat,lon,station_elevation,station_info,station_name,alt,time,temperature,humidity\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,0,17.0,56.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,3600,7.0,49.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,7200,19.0,86.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,10800,5.0,81.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,14400,0.0,55.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,18000,10.0,9.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,21600,32.0,57.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,25200,39.0,39.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,28800,39.0,68.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,32400,29.0,6.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,36000,26.0,12.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,39600,24.0,72.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,43200,14.0,80.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,46800,38.0,52.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,50400,35.0,46.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,54000,33.0,48.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,57600,34.0,85.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,61200,27.0,3.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,64800,37.0,61.0\n" + -"121.0,81.0,4.859895,0,Station-0,1.9358816,68400,0.0,0.0\n" + -"150.0,73.0,2.6002314,1,Station-1,4.052759,0,25.0,73.0\n" + -"150.0,73.0,2.6002314,1,Station-1,4.052759,3600,29.0,74.0\n" + -"150.0,73.0,2.6002314,1,Station-1,4.052759,7200,33.0,88.0\n" + -"150.0,73.0,2.6002314,1,Station-1,4.052759,10800,25.0,3.0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 200, ""); - results = table.columnAttributes(7).toString(); //temperature - expected = -" coordinates=time lat lon alt\n" + -" long_name=Air Temperature\n" + -" missing_value=-999.9f\n" + -" standard_name=air_temperature\n" + -" units=Celsius\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#5b " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - //read just outer [station] vars - table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon"), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"station_name,lat,lon\n" + -"Station-0,121.0,81.0\n" + -"Station-1,150.0,73.0\n" + -"Station-2,107.0,152.0\n" + -"Station-3,117.0,143.0\n" + -"Station-4,107.0,11.0\n" + -"Station-5,161.0,100.0\n" + -"Station-6,150.0,169.0\n" + -"Station-7,176.0,85.0\n" + -"Station-8,83.0,126.0\n" + -"Station-9,84.0,170.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just outer [station] vars, with constraint - table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), StringArray.fromCSV(">"), StringArray.fromCSV("155")); - results = table.dataToString(); - expected = -"station_name,lat,lon\n" + -"Station-5,161.0,100.0\n" + -"Station-7,176.0,85.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //There are no just inner[obs] variables - - //read just outer+obs vars, with outer constraint - table.readNcCF(fileName, StringArray.fromCSV("lat,time,temperature,humidity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("150")); - results = table.dataToString(); - expected = -//metadata mv=-999.9 for temp and humidity, so 9e36 below are "valid" values -"lat,time,temperature,humidity\n" + -"150.0,0,25.0,73.0\n" + -"150.0,3600,29.0,74.0\n" + -"150.0,7200,33.0,88.0\n" + -"150.0,10800,25.0,3.0\n" + -"150.0,14400,2.0,70.0\n" + -"150.0,18000,9.0,37.0\n" + -"150.0,21600,10.0,45.0\n" + -"150.0,25200,33.0,24.0\n" + -"150.0,28800,1.0,43.0\n" + -"150.0,32400,26.0,0.0\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,-2147483647,9.96921E36,9.96921E36\n" + -"150.0,0,18.0,4.0\n" + -"150.0,3600,18.0,83.0\n" + -"150.0,7200,27.0,10.0\n" + -"150.0,10800,33.0,43.0\n" + -"150.0,14400,34.0,31.0\n" + -"150.0,18000,0.0,69.0\n" + -"150.0,21600,27.0,34.0\n" + -"150.0,25200,3.0,41.0\n" + -"150.0,28800,38.0,14.0\n" + -"150.0,32400,20.0,5.0\n" + -"150.0,36000,26.0,48.0\n" + -"150.0,39600,11.0,29.0\n" + -"150.0,43200,22.0,60.0\n" + -"150.0,46800,39.0,63.0\n" + -"150.0,50400,27.0,18.0\n" + -"150.0,54000,26.0,84.0\n" + -"150.0,57600,26.0,71.0\n" + -"150.0,61200,33.0,25.0\n" + -"150.0,64800,27.0,17.0\n" + -"150.0,68400,17.0,79.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just outer+obs vars, with outer + obs constraint - table.readNcCF(fileName, StringArray.fromCSV("lat,time,temperature,humidity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat,humidity"), StringArray.fromCSV("=,="), StringArray.fromCSV("150,43")); - results = table.dataToString(); - expected = -"lat,time,temperature,humidity\n" + -"150.0,28800,1.0,43.0\n" + -"150.0,10800,33.0,43.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just outer+obs vars, - table.readNcCF(fileName, StringArray.fromCSV("time,temperature,humidity"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,temperature"), StringArray.fromCSV("=,="), StringArray.fromCSV("7200,33")); - results = table.dataToString(); - expected = -//"22,150.0,73.0,2.6002314,1,Station-1,4.052759,7200,33.0,88.0\n" + from above -"time,temperature,humidity\n" + -"7200,33.0,88.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just obs vars, with outer and obs constraint - table.readNcCF(fileName, StringArray.fromCSV("time,lon,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,lon"), StringArray.fromCSV("=,="), StringArray.fromCSV("7200,73")); - results = table.dataToString(); - expected = -"time,lon,alt,temperature\n" + -"7200,73.0,4.052759,33.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - /* */ - //read just obs vars, with outer and obs constraint - table.readNcCF(fileName, StringArray.fromCSV("time,lon,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lon,temperature"), StringArray.fromCSV("=,="), StringArray.fromCSV("73,33")); - results = table.dataToString(); - expected = -"time,lon,alt,temperature\n" + -"7200,73.0,4.052759,33.0\n" + -"25200,73.0,4.052759,33.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //read just obs vars, with outer and obs constraint - table.readNcCF(fileName, StringArray.fromCSV("time,lon,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time,temperature"), StringArray.fromCSV("=,="), StringArray.fromCSV("7200,33")); - results = table.dataToString(); - expected = -"time,lon,alt,temperature\n" + -"7200,73.0,4.052759,33.0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - debugMode = oDebug; - } - - /** This tests readNcCF trajectory files from ASA - * via https://github.com/asascience-open/CFPointConventions - * stored in unitTestDataDir/CFPointConventions. - */ - public static void testReadNcCFASATrajectory(boolean pauseAfterEach) throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCFASATrajectory"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected, fileName; - -/* */ - //*************** trajectory contiguous - fileName = String2.unitTestDataDir + "CFPointConventions/trajectory/" + - "trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/" + - "trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.nc"; - String2.log("\n\n** Testing contiguous file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(20); - expected = -"lat,lon,trajectory_info,trajectory_name,time,z,temperature,humidity\n" + -"16.937433,-35.901237,0,Trajectory0,0,0.0,18.559397,46.487503\n" + -"32.011345,-8.81588,0,Trajectory0,3600,1.0,34.649773,16.22458\n" + -"3.137092,-64.15942,0,Trajectory0,7200,2.0,35.318504,77.41457\n" + -"10.783036,-11.503419,0,Trajectory0,10800,3.0,19.39111,56.601\n" + -"4.6016994,-6.416601,0,Trajectory0,14400,4.0,5.4162874,62.606712\n" + -"25.337688,-69.37197,0,Trajectory0,18000,5.0,2.604784,16.390015\n" + -"30.219189,-71.78619,0,Trajectory0,21600,6.0,22.968603,62.276855\n" + -"5.3421707,-29.245968,0,Trajectory0,25200,7.0,8.609019,14.976101\n" + -"25.687958,-57.089973,0,Trajectory0,28800,8.0,9.202528,79.17113\n" + -"31.82367,-58.56237,0,Trajectory0,32400,9.0,1.5670301,26.49425\n" + -"23.310976,-3.997997,0,Trajectory0,36000,10.0,23.187065,64.34719\n" + -"43.486816,-62.39688,0,Trajectory0,39600,11.0,37.44155,29.570276\n" + -"44.56024,-54.139122,0,Trajectory0,43200,12.0,11.75348,72.36402\n" + -"42.48622,-42.518707,1,Trajectory1,0,0.0,20.665886,67.27393\n" + -"32.187572,-73.20317,1,Trajectory1,3600,1.0,26.498121,79.754486\n" + -"6.4802227,-72.74957,1,Trajectory1,7200,2.0,17.64227,70.126625\n" + -"38.596996,-67.64374,1,Trajectory1,10800,3.0,23.615097,59.626125\n" + -"24.085066,-63.833694,1,Trajectory1,14400,4.0,30.743101,35.862038\n" + -"24.221394,-57.373817,1,Trajectory1,18000,5.0,39.391495,28.661589\n" + -"22.637892,-47.858807,1,Trajectory1,21600,6.0,1.2310536,55.708595\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 163, ""); - results = table.columnAttributes(5).toString(); //temperature - expected = -" axis=Z\n" + -" long_name=height above mean sea level\n" + -" missing_value=-999.0f\n" + -" positive=up\n" + -" standard_name=altitude\n" + -" units=m\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#8a " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("temperature,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - - - //*************** trajectory single multidimensional --- - fileName = String2.unitTestDataDir + "CFPointConventions/trajectory/" + - "trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/" + - "trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.nc"; - String2.log("\n\n** Testing single multidimensional file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -"lat,lon,trajectory_info,trajectory_name,time,z,temperature,humidity\n" + -"42.003387,-7.9335957,0,Trajectory1,0,0.0,12.522581,35.668747\n" + -"8.972063,-46.335754,0,Trajectory1,3600,1.0,25.658121,1.0647067\n" + -"25.841967,-49.1959,0,Trajectory1,7200,2.0,35.43442,13.059927\n" + -"35.699753,-40.790943,0,Trajectory1,10800,3.0,35.752117,48.576355\n" + -"11.132234,-25.553247,0,Trajectory1,14400,4.0,6.082586,64.91749\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 100, ""); - results = table.columnAttributes(table.findColumnNumber("temperature")).toString(); - expected = -" coordinates=time lat lon z\n" + -" long_name=Air Temperature\n" + -" missing_value=-999.9f\n" + -" standard_name=air_temperature\n" + -" units=Celsius\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#8c " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("temperature,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - //*************** trajectory indexed --- - fileName = String2.unitTestDataDir + "CFPointConventions/trajectory/" + - "trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/" + - "trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.nc"; - String2.log("\n\n** Testing indexed file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -"lat,lon,trajectory_info,trajectory_name,time,z,temperature,humidity\n" + -"11.256147,-5.989336,8,Trajectory8,72000,12.518082,14.902713,37.237553\n" + -"26.104128,-2.6626983,3,Trajectory3,111600,7.372036,24.243849,12.862466\n" + -"22.414213,-23.53803,4,Trajectory4,68400,5.7999315,1.4940661,20.668322\n" + -"22.181162,-34.355854,4,Trajectory4,122400,20.127024,6.8310843,55.93755\n" + -"2.177301,-58.388607,5,Trajectory5,162000,1.764841,27.893003,28.2276\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 213, ""); - results = table.columnAttributes(6).toString(); //temperature - expected = -" coordinates=time lat lon z\n" + -" long_name=Air Temperature\n" + -" missing_value=-999.9f\n" + -" standard_name=air_temperature\n" + -" units=Celsius\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#8d " + pauseMessage); - - // - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("temperature,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - /* */ - debugMode = oDebug; - } - - - public static void testInteractiveNcCFMA(boolean pauseAfterEach) throws Exception { - //*************** trajectory multiple multidimensional --- - try { - - Table table = new Table(); - String results, expected; - String pauseMessage = "\nOK?"; - String fileName = String2.unitTestDataDir + "CFPointConventions/trajectory/" + - "trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/" + - "trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.nc"; - String2.log("\n\n** Testing multiple multidimensional file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - - // - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("lat,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("z,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("temperature,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature,trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, - StringArray.fromCSV("trajectory_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, - StringArray.fromCSV("z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(55); - expected = - //rows that a human thinks should be rejected are kept - //probably because trajectory_info and trajectory_name aren't missing values - // AND because lat,lon have missing values but there is no missing_value attribute. - "lat,lon,trajectory_info,trajectory_name,time,z,temperature,humidity\n" + - "2.152863,-35.078842,0,Trajectory0,0,0.0,13.466983,65.38418\n" + - "33.60481,-44.12696,0,Trajectory0,3600,1.0,23.050304,7.0401154\n" + - "22.562508,-18.115444,0,Trajectory0,7200,2.0,15.112072,45.15019\n" + - "13.432817,-21.772585,0,Trajectory0,10800,3.0,22.97767,12.618799\n" + - "43.011986,-28.655304,0,Trajectory0,14400,4.0,21.318092,4.788235\n" + - "18.84832,-25.418892,0,Trajectory0,18000,5.0,27.496708,66.337166\n" + - "18.040411,-30.469133,0,Trajectory0,21600,6.0,30.678926,31.57974\n" + - "32.34516,-75.79432,0,Trajectory0,25200,7.0,12.096431,11.228316\n" + - "8.652234,-69.01581,0,Trajectory0,28800,8.0,12.523737,47.003998\n" + - "18.905367,-18.362652,0,Trajectory0,32400,9.0,22.805552,8.789174\n" + - "12.184539,-42.194824,0,Trajectory0,36000,10.0,17.411797,40.25377\n" + - "16.498188,-74.44906,0,Trajectory0,39600,11.0,27.783548,20.712833\n" + - "1.5479256,-53.522717,0,Trajectory0,43200,12.0,11.809888,5.6157913\n" + - "22.033587,-28.557417,0,Trajectory0,46800,13.0,13.730549,2.8293543\n" + - "5.997217,-35.043163,0,Trajectory0,50400,14.0,6.549969,30.482803\n" + - "8.580469,-45.364418,0,Trajectory0,54000,15.0,11.789269,2.303839\n" + - "6.253441,-9.302229,0,Trajectory0,57600,16.0,24.03656,56.802467\n" + - "12.948677,-20.07699,0,Trajectory0,61200,17.0,17.980707,66.24162\n" + - "41.49208,-19.628315,0,Trajectory0,64800,18.0,0.44739303,25.76894\n" + - "25.784758,-65.65333,0,Trajectory0,68400,19.0,13.147206,1.4286463\n" + - "25.884523,-64.92309,0,Trajectory0,72000,20.0,21.278152,72.43937\n" + - "7.5993505,-33.58001,0,Trajectory0,75600,21.0,14.465093,74.04942\n" + - "23.801714,-8.210893,0,Trajectory0,79200,22.0,17.250273,43.468597\n" + - "24.086273,-16.376455,0,Trajectory0,82800,23.0,36.73325,56.15435\n" + - "8.838917,-65.32871,0,Trajectory0,86400,24.0,21.714993,32.324383\n" + - "3.049409,-50.187355,0,Trajectory0,90000,25.0,17.755543,7.7604437\n" + - "32.699135,-13.603052,0,Trajectory0,93600,26.0,21.764454,68.36558\n" + - "28.82149,-4.238066,0,Trajectory0,97200,27.0,4.18221,75.262665\n" + - "4.573595,-15.691054,0,Trajectory0,100800,28.0,36.230297,74.156654\n" + - "30.231867,-29.110548,0,Trajectory0,104400,29.0,10.372004,8.0368805\n" + - "26.295082,-24.224209,0,Trajectory0,108000,30.0,7.0729938,31.468176\n" + - "26.146648,-35.461746,0,Trajectory0,111600,31.0,12.3075285,71.35397\n" + - "18.875525,-11.409157,0,Trajectory0,115200,32.0,30.241188,45.14291\n" + - "44.57873,-29.37942,0,Trajectory0,118800,33.0,21.847982,61.776512\n" + - "40.911667,-31.65526,0,Trajectory0,122400,34.0,30.369759,29.810774\n" + - "9.5415745,-57.1067,0,Trajectory0,126000,35.0,15.864324,33.90924\n" + - //these aren't rejected because - //* trajectory_info has the attribute missing_value=-999, - // but the data above has trajectory_info=0, which isn't a missing value. - //* trajectory_name is a string, so my reader doesn't expect a - // missing_value attribute, but my reader does treat a data - // value of "" (nothing) as a missing value. Unfortunately, this - // file has other values (e.g., "Trajectory0"), so my reader - // treats those as not missing values. - //* lat and lon have data values of -999.9 which is probably - // intended to be a missing value marker, but those variables - // have no missing_value attributes, so my program treats them as - // valid values. - //I reported to Kyle 2012-10-03 and hope he'll make changes - - //"36,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"37,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"38,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"39,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"40,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"41,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"42,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"43,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"44,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"45,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"46,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"47,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"48,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - //"49,-999.9,-999.9,0,Trajectory0,-999,-999.9,-999.9,-999.9\n" + - "36,13.633951,-61.779095,1,Trajectory1,0,0.0,31.081379,7.8967414\n" + - "37,41.583824,-52.047775,1,Trajectory1,3600,1.0,23.026224,25.034555\n" + - "38,14.176689,-15.26571,1,Trajectory1,7200,2.0,21.750353,61.35738\n" + - "39,23.482225,-69.246284,1,Trajectory1,10800,3.0,25.214777,70.63098\n" + - "40,8.910114,-12.47847,1,Trajectory1,14400,4.0,29.234118,53.387733\n" + - "...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 200, ""); - results = table.columnAttributes(5).toString(); //temperature - expected = - " axis=Z\n" + - " long_name=height above mean sea level\n" + - " missing_value=-999.9f\n" + - " positive=up\n" + - " standard_name=altitude\n" + - " units=m\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#8b " + pauseMessage); - - - - } catch (Exception e) { - //String2.pressEnterToContinue( - Test.knownProblem( - "KYLE WILCOX'S DSG TEST FILE.", - MustBe.throwableToString(e) + - "\nI reported this problem to Kyle 2012-10-03" + - "\n2013-10-30 Since Kyle changed jobs, it is unlikely he will ever fix this."); - } - } - - /** This tests readNcCF timeSeriesProfile files from ASA - * via https://github.com/asascience-open/CFPointConventions - * stored in unitTestDataDir/CFPointConventions. - */ - public static void testReadNcCFASATimeSeriesProfile(boolean pauseAfterEach) throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCFASATimeSeriesProfile"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected, fileName; - String orthoMultiDimH51FileName = String2.unitTestDataDir + - "CFPointConventions/timeSeriesProfile/" + - "timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/" + - "timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.nc"; - String raggedSingleStationFileName = String2.unitTestDataDir + - "CFPointConventions/timeSeriesProfile/" + - "timeSeriesProfile-Ragged-SingleStation-H.5.3/" + - "timeSeriesProfile-Ragged-SingleStation-H.5.3.nc"; - - - //*************** timeSeriesProfile multidimensional --- - fileName = String2.unitTestDataDir + "CFPointConventions/timeSeriesProfile/" + - "timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/" + - "timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.nc"; - String2.log("\n\n** Testing incomplete file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -"lat,lon,station_info,station_name,alt,time,temperature\n" + -"37.5,-76.5,0,Station1,0.0,0,0.0\n" + -"37.5,-76.5,0,Station1,2.5,0,0.1\n" + -"37.5,-76.5,0,Station1,5.0,0,0.2\n" + -"37.5,-76.5,0,Station1,7.5,0,0.3\n" + -"37.5,-76.5,0,Station1,10.0,0,0.4\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 240, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6a " + pauseMessage); - - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - //*************** timeSeriesProfile multidimensional single station - fileName = String2.unitTestDataDir + "CFPointConventions/timeSeriesProfile/" + - "timeSeriesProfile-Multidimensional-SingleStation-H.5.2/" + - "timeSeriesProfile-Multidimensional-SingleStation-H.5.2.nc"; - String2.log("\n\n** Testing contiguous file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"lat,lon,station_info,station_name,alt,time,temperature\n" + -"37.5,-76.5,0,Station1,0.0,0,0.0\n" + -"37.5,-76.5,0,Station1,2.5,0,0.1\n" + -"37.5,-76.5,0,Station1,5.0,0,0.2\n" + -"37.5,-76.5,0,Station1,7.5,0,0.3\n" + -"37.5,-76.5,0,Station1,10.0,0,0.4\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - expected = -"37.5,-76.5,0,Station1,287.5,10800,11.5\n" + -"37.5,-76.5,0,Station1,290.0,10800,11.6\n" + -"37.5,-76.5,0,Station1,292.5,10800,11.7\n" + -"37.5,-76.5,0,Station1,295.0,10800,11.8\n" + -"37.5,-76.5,0,Station1,297.5,10800,11.9\n"; - Test.ensureEqual(results.substring(results.length() - expected.length()), - expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 120, ""); - results = table.columnAttributes(table.findColumnNumber("alt")).toString(); - expected = -" axis=Z\n" + -" positive=up\n" + -" units=m\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - results = table.columnAttributes(table.findColumnNumber("temperature")).toString(); - expected = -" coordinates=time lat lon alt\n" + -" long_name=Water Temperature\n" + -" missing_value=-999.9f\n" + -" units=Celsius\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6b " + pauseMessage); - - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - //*************** timeSeriesProfile orthogonal multidimensional --- - //!!! IMPORTANT/ONLY test of file with variable[innerDim] for innerTable - // and variable[time][z][station] which is allowed, ordering - fileName = orthoMultiDimH51FileName; - String2.log("\n\n** Testing incomplete file\n" + " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(12); - expected = -"lat,lon,alt,station_info,station_name,time,temperature,humidity\n" + -"37.5,-76.5,0.0,0,Station1,0,15.698009,89.70879\n" + -"32.5,-78.3,0.0,1,Station2,0,8.11997,33.637585\n" + -"37.5,-76.5,10.0,0,Station1,0,10.9166565,55.78947\n" + -"32.5,-78.3,10.0,1,Station2,0,39.356647,65.43795\n" + -"37.5,-76.5,20.0,0,Station1,0,15.666663,50.176994\n" + -"32.5,-78.3,20.0,1,Station2,0,33.733116,58.14976\n" + -"37.5,-76.5,30.0,0,Station1,0,1.1587523,36.855045\n" + -"32.5,-78.3,30.0,1,Station2,0,4.65479,63.862186\n" + -"37.5,-76.5,0.0,0,Station1,3600,31.059647,65.01694\n" + -"32.5,-78.3,0.0,1,Station2,3600,33.374344,22.771135\n" + -"37.5,-76.5,10.0,0,Station1,3600,5.680936,35.675472\n" + -"32.5,-78.3,10.0,1,Station2,3600,17.763374,38.54674\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 800, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6c " + pauseMessage); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - fileName = orthoMultiDimH51FileName; - String2.log("\n\n** Testing incomplete file with constraints\n" + - " " + fileName); - //String2.log(NcHelper.ncdump(orthoMultiDimH51FileName, "-h")); - table.readNcCF(fileName, null, - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("Station1")); - results = table.dataToString(12); - expected = -"lat,lon,alt,station_info,station_name,time,temperature,humidity\n" + -"37.5,-76.5,0.0,0,Station1,0,15.698009,89.70879\n" + -"37.5,-76.5,10.0,0,Station1,0,10.9166565,55.78947\n" + -"37.5,-76.5,20.0,0,Station1,0,15.666663,50.176994\n" + -"37.5,-76.5,30.0,0,Station1,0,1.1587523,36.855045\n" + -"37.5,-76.5,0.0,0,Station1,3600,31.059647,65.01694\n" + -"37.5,-76.5,10.0,0,Station1,3600,5.680936,35.675472\n" + -"37.5,-76.5,20.0,0,Station1,3600,24.156359,45.77856\n" + -"37.5,-76.5,30.0,0,Station1,3600,25.934822,35.178967\n" + -"37.5,-76.5,0.0,0,Station1,7200,6.518481,12.735875\n" + -"37.5,-76.5,10.0,0,Station1,7200,4.463567,47.44697\n" + -"37.5,-76.5,20.0,0,Station1,7200,29.448772,20.438272\n" + -"37.5,-76.5,30.0,0,Station1,7200,37.245636,62.655357\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 400, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6d " + pauseMessage); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - //test just variable[obs] (interiorTable) - String2.log("\n\n** Testing incomplete file\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, StringArray.fromCSV("lat,lon,station_name,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("Station1")); - results = table.dataToString(); - expected = -"lat,lon,station_name\n" + -"37.5,-76.5,Station1\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 1, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6e " + pauseMessage); - - - //********** NO_DATA - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, outer/inner/obsVar - String2.log("\n\n** Testing orthoMultiDimH51FileName just outer/inner/obsVar, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("time,zztop,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDa " + pauseMessage); - - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just outerVar - String2.log("\n\n** Testing orthoMultiDimH51FileName just outerVar, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("zztop,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDb " + pauseMessage); - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just innerVar - String2.log("\n\n** Testing orthoMultiDimH51FileName just innerVar, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("alt,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("10000")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDc " + pauseMessage); - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just obsVar - String2.log("\n\n** Testing orthoMultiDimH51File just obsVar, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("zztop,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDd " + pauseMessage); - - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just outerVar* and innerVar - String2.log("\n\n** Testing orthoMultiDimH51File just outer*/innerVar, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("zztop,time,alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDe1 " + pauseMessage); - - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just outerVar and innerVar* - String2.log("\n\n** Testing orthoMultiDimH51File just outer/innerVar*, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("zztop,time,alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("10000")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDe2 " + pauseMessage); - - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just outerVar* and obsVar - String2.log("\n\n** Testing orthoMultiDimH51File just outer*/obsVar, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("time,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDf1 " + pauseMessage); - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just outerVar and obsVar* - String2.log("\n\n** Testing orthoMultiDimH51File just outer/obsVar*, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("time,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDf2 " + pauseMessage); - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just innerVar* and obsVar - String2.log("\n\n** Testing orthoMultiDimH51File just inner*/obsVar, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("alt,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("10000")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDg1 " + pauseMessage); - - //********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just innerVar and obsVar* - String2.log("\n\n** Testing orthoMultiDimH51File just inner/obsVar*, NO_DATA\n" + - " " + orthoMultiDimH51FileName); - table.readNcCF(orthoMultiDimH51FileName, - StringArray.fromCSV("alt,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#6NDg2 " + pauseMessage); - - - //******* - //*************** timeSeriesProfile ragged --- - fileName = String2.unitTestDataDir + "CFPointConventions/timeSeriesProfile/" + - "timeSeriesProfile-Ragged-MultipeStations-H.5.3/" + - "timeSeriesProfile-Ragged-MultipeStations-H.5.3.nc"; - String2.log("\n\n** Testing timeSeriesProfile ragged file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -//file has: -//lat, lon, station_info, station_name, profile, time, station_index, row_size, height, temperature -"lat,lon,station_info,station_name,profile,time,height,temperature\n" + -"37.5,-76.5,0,Station1,0,0,0.5,6.7\n" + -"37.5,-76.5,0,Station1,0,0,1.5,6.9\n" + -"32.5,-78.3,1,Station2,1,3600,0.8,7.6\n" + -"32.5,-78.3,1,Station2,1,3600,1.8,7.7\n" + -"32.5,-78.3,1,Station2,1,3600,2.8,7.9\n" + -"32.5,-78.3,1,Station2,1,3600,3.8,8.0\n" + -"37.5,-76.5,0,Station1,2,7200,0.5,6.7\n" + -"37.5,-76.5,0,Station1,2,7200,1.5,7.0\n" + -"32.5,-78.3,1,Station2,3,10800,0.8,8.2\n" + -"32.5,-78.3,1,Station2,3,10800,1.8,7.7\n" + -"32.5,-78.3,1,Station2,3,10800,2.8,7.8\n" + -"32.5,-78.3,1,Station2,3,10800,3.8,9.1\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 12, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6j " + pauseMessage); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "height,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "height,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "height,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "height,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "height"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - //*************** timeSeriesProfile ragged single station --- - //This is ONLY TEST FILE of nLevels=2 single station (outerTable are scalar vars)!!!!!!!! - //Note also the lack of a stationIndex var with instance_dimension="someDimension" - // since there is no instance_dimension - fileName = raggedSingleStationFileName; - String2.log("\n\n** Testing raggedSingleStationFile\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"lat,lon,station_info,station_name,profile,time,height,temperature\n" + -"37.5,-76.5,0,Station1,0,0,0.5,6.7\n" + -"37.5,-76.5,0,Station1,0,0,1.5,6.9\n" + -"37.5,-76.5,0,Station1,1,3600,0.5,6.8\n" + -"37.5,-76.5,0,Station1,1,3600,1.5,7.9\n" + -"37.5,-76.5,0,Station1,2,7200,0.5,6.8\n" + -"37.5,-76.5,0,Station1,2,7200,1.5,7.9\n" + -"37.5,-76.5,0,Station1,2,7200,2.5,8.4\n" + -"37.5,-76.5,0,Station1,3,10800,0.5,5.7\n" + -"37.5,-76.5,0,Station1,3,10800,1.5,9.2\n" + -"37.5,-76.5,0,Station1,3,10800,2.5,8.3\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 10, ""); - results = table.columnAttributes(table.findColumnNumber("profile")).toString(); - expected = -" cf_role=profile_id\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6m " + pauseMessage); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "station_name,lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "height,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "height,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "height,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "height,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "height,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "station_name"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_name"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "height"), - 0, //standardizeWhat=0 - StringArray.fromCSV("height"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - //*************** timeSeriesProfile ragged single station --- just outerVar - String2.log("\n\n** Testing raggedSingleStationFile just outerVar\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("zztop,lat,lon,station_info,station_name"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"lat,lon,station_info,station_name\n" + -"37.5,-76.5,0,Station1\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 1, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station latitude\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6n " + pauseMessage); - - //*************** timeSeriesProfile ragged single station --- just innerVar - String2.log("\n\n** Testing raggedSingleStationFile just innerVar\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("time,zztop,profile"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"time,profile\n" + -"0,0\n" + -"3600,1\n" + -"7200,2\n" + -"10800,3\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 4, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=time\n" + -" missing_value=-999i\n" + -" standard_name=time\n" + -" units=seconds since 1990-01-01 00:00:00\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6o " + pauseMessage); - - //*************** timeSeriesProfile ragged single station --- just outerVar and innerVar - String2.log("\n\n** Testing raggedSingleStationFile just outerVar and innerVar\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("station_info,station_name,lon,lat,time,profile,"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"station_info,station_name,lon,lat,time,profile\n" + -"0,Station1,-76.5,37.5,0,0\n" + -"0,Station1,-76.5,37.5,3600,1\n" + -"0,Station1,-76.5,37.5,7200,2\n" + -"0,Station1,-76.5,37.5,10800,3\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 4, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station info\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6p " + pauseMessage); - - //*************** timeSeriesProfile ragged single station --- just outerVar and obsVar - String2.log("\n\n** Testing raggedSingleStationFile just outerVar and obsVar\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("station_info,temperature,zztop,station_name,"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("8")); - results = table.dataToString(); - expected = -"station_info,temperature,station_name\n" + -"0,8.4,Station1\n" + -"0,9.2,Station1\n" + -"0,8.3,Station1\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 3, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station info\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6q " + pauseMessage); - - //*************** timeSeriesProfile ragged single station --- just innerVar and obsVar - String2.log("\n\n** Testing raggedSingleStationFile just innerVar and obsVar\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("temperature,zztop,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("8")); - results = table.dataToString(); - expected = -"temperature,time\n" + -"8.4,7200\n" + -"9.2,10800\n" + -"8.3,10800\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 3, ""); - results = table.columnAttributes(0).toString(); - expected = -" coordinates=time lat lon height\n" + -" long_name=Water Temperature\n" + -" missing_value=-999.9f\n" + -" standard_name=sea_water_temperature\n" + -" units=Celsius\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#6r " + pauseMessage); - - - //********** NO_DATA - //********** timeSeriesProfile ragged single station --- NO_DATA, outer/inner/obsVar - String2.log("\n\n** Testing raggedSingleStationFile just outer/inner/obsVar, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("station_info,zztop,profile,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7a " + pauseMessage); - - - //********** timeSeriesProfile ragged single station --- NO_DATA, just outerVar - String2.log("\n\n** Testing raggedSingleStationFile just outerVar, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("zztop,station_info"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_info"), - StringArray.fromCSV("="), - StringArray.fromCSV("10")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7b " + pauseMessage); - - //********** timeSeriesProfile ragged single station --- NO_DATA, just innerVar - String2.log("\n\n** Testing raggedSingleStationFile just innerVar, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("profile,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7c " + pauseMessage); - - //********** timeSeriesProfile ragged single station --- NO_DATA, just obsVar - String2.log("\n\n** Testing raggedSingleStationFile just obsVar, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("zztop,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7d " + pauseMessage); - - - //********** timeSeriesProfile ragged single station --- NO_DATA, just outerVar* and innerVar - String2.log("\n\n** Testing raggedSingleStationFile just outer*/innerVar, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("zztop,station_info,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_info"), - StringArray.fromCSV("="), - StringArray.fromCSV("10")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7e1 " + pauseMessage); - - - //********** timeSeriesProfile ragged single station --- NO_DATA, just outerVar and innerVar* - String2.log("\n\n** Testing raggedSingleStationFile just outer/innerVar*, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("zztop,station_info,profile"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7e2 " + pauseMessage); - - - //********** timeSeriesProfile ragged single station --- NO_DATA, just outerVar* and obsVar - String2.log("\n\n** Testing raggedSingleStationFile just outer*/obsVar, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("temperature,station_info,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station_info"), - StringArray.fromCSV("="), - StringArray.fromCSV("10")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7f1 " + pauseMessage); - - //********** timeSeriesProfile ragged single station --- NO_DATA, just outerVar and obsVar* - String2.log("\n\n** Testing raggedSingleStationFile just outer/obsVar*, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("temperature,station_info,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7f2 " + pauseMessage); - - //********** timeSeriesProfile ragged single station --- NO_DATA, just innerVar* and obsVar - String2.log("\n\n** Testing raggedSingleStationFile just inner*/obsVar, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("temperature,profile,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("profile"), - StringArray.fromCSV("="), - StringArray.fromCSV("-1")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7g1 " + pauseMessage); - - //********** timeSeriesProfile ragged single station --- NO_DATA, just innerVar and obsVar* - String2.log("\n\n** Testing raggedSingleStationFile just inner/obsVar*, NO_DATA\n" + - " " + raggedSingleStationFileName); - table.readNcCF(raggedSingleStationFileName, - StringArray.fromCSV("temperature,profile,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#7g2 " + pauseMessage); - - - /* */ - debugMode = oDebug; - } - - /** This tests readNcCF trajectoryProfile files from ASA - * via https://github.com/asascience-open/CFPointConventions - * stored in unitTestDataDir/CFPointConventions. - */ - public static void testReadNcCFASATrajectoryProfile(boolean pauseAfterEach) throws Exception { - verbose = true; - reallyVerbose = true; - boolean oDebug = debugMode; - debugMode = true; - String2.log("\n*** Table.testReadNcCFASATrajectoryProfile"); - String pauseMessage = "\nOK?"; - Table table = new Table(); - String results, expected, fileName; - String orthoMultiDimH61FileName = String2.unitTestDataDir + - "CFPointConventions/trajectoryProfile/" + - "trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/" + - "trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.nc"; - String raggedMultipleStationFileName = String2.unitTestDataDir + - "CFPointConventions/trajectoryProfile/" + - "trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/" + - "trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.nc"; - -/* */ - //*************** trajectoryProfile multidimensional single station - try { - fileName = String2.unitTestDataDir + - "CFPointConventions/trajectoryProfile/" + - "trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/" + - "trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.nc"; - String2.log("\n\n** Testing contiguous file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "-h")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"lat,lon,trajectory,alt,time,temperature,salinity\n" + -"4.9986253,-35.718536,0,0.0,0,3.2502668,79.006065\n" + -"4.9986253,-35.718536,0,1.0,0,30.566391,37.089394\n" + -"4.9986253,-35.718536,0,2.0,0,0.8428718,20.478456\n" + -"1.4658529,-25.19569,0,0.0,3600,27.982288,17.57356\n" + -"1.4658529,-25.19569,0,1.0,3600,15.750698,11.152985\n" + -"1.4658529,-25.19569,0,2.0,3600,39.36954,31.84863\n" + -"1.4658529,-25.19569,0,3.0,3600,8.506618,77.88138\n" + -"1.4658529,-25.19569,0,4.0,3600,39.580475,77.575645\n" + -"38.299484,-55.72639,0,0.0,7200,36.646107,77.1104\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 20, ""); - results = table.columnAttributes(table.findColumnNumber("lat")).toString(); - expected = -" long_name=Latitude\n" + -" missing_value=-999.9f\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - results = table.columnAttributes(table.findColumnNumber("alt")).toString(); - expected = -" axis=Z\n" + -" long_name=height below mean sea level\n" + -" missing_value=-999.9f\n" + -" positive=down\n" + -" standard_name=altitude\n" + -" units=m\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10a " + pauseMessage); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - } catch (Exception e) { - String2.pressEnterToContinue(MustBe.throwableToString(e)); - } - - - - //*************** trajectoryProfile orthogonal multidimensional --- - try { - fileName = orthoMultiDimH61FileName; - String2.log("\n\n** Testing orthogonal multidim file\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(14); - expected = -"lat,lon,trajectory,alt,time,temperature,salinity\n" + -"18.736742,-28.520071,0,0.0,0,8.067447,62.835354\n" + -"18.736742,-28.520071,0,1.0,0,15.871663,27.454027\n" + -"18.736742,-28.520071,0,2.0,0,32.306496,61.80094\n" + -"18.736742,-28.520071,0,3.0,0,27.631369,74.84051\n" + -"18.736742,-28.520071,0,4.0,0,22.757963,73.378914\n" + -"39.43245,-57.711514,1,0.0,0,36.39878,77.23479\n" + -"39.43245,-57.711514,1,1.0,0,14.957566,7.621207\n" + -"39.43245,-57.711514,1,2.0,0,5.405648,56.557266\n" + -"39.43245,-57.711514,1,3.0,0,4.9267964,75.427795\n" + -"39.43245,-57.711514,1,4.0,0,7.806849,42.65483\n" + -"39.43245,-57.711514,1,5.0,0,28.784224,13.940006\n" + -"39.43245,-57.711514,1,6.0,0,19.139135,53.46242\n" + -"25.034857,-62.39183,1,0.0,3600,24.302265,62.551056\n" + -"25.034857,-62.39183,1,1.0,3600,11.195762,4.3670874\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 65, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=Latitude\n" + -" missing_value=-999.9f\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10c " + pauseMessage); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "alt,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "alt"), - 0, //standardizeWhat=0 - StringArray.fromCSV("alt"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - - String2.log("\n\n** Testing incomplete file with constraints\n" + - " " + orthoMultiDimH61FileName); - //String2.log(NcHelper.ncdump(orthoMultiDimH61FileName, "-h")); - table.readNcCF(orthoMultiDimH61FileName, null, - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("1")); - results = table.dataToString(); - expected = -"lat,lon,trajectory,alt,time,temperature,salinity\n" + -"39.43245,-57.711514,1,0.0,0,36.39878,77.23479\n" + -"39.43245,-57.711514,1,1.0,0,14.957566,7.621207\n" + -"39.43245,-57.711514,1,2.0,0,5.405648,56.557266\n" + -"39.43245,-57.711514,1,3.0,0,4.9267964,75.427795\n" + -"39.43245,-57.711514,1,4.0,0,7.806849,42.65483\n" + -"39.43245,-57.711514,1,5.0,0,28.784224,13.940006\n" + -"39.43245,-57.711514,1,6.0,0,19.139135,53.46242\n" + -"25.034857,-62.39183,1,0.0,3600,24.302265,62.551056\n" + -"25.034857,-62.39183,1,1.0,3600,11.195762,4.3670874\n" + -"25.034857,-62.39183,1,2.0,3600,20.055767,62.966892\n" + -"25.034857,-62.39183,1,3.0,3600,38.838474,49.101334\n" + -"25.034857,-62.39183,1,4.0,3600,16.995031,19.580278\n" + -"25.034857,-62.39183,1,5.0,3600,5.6433516,62.23398\n" + -"25.034857,-62.39183,1,6.0,3600,3.8319156,3.1172054\n" + -"27.619982,-46.87254,1,0.0,7200,26.57189,22.247057\n" + -"27.619982,-46.87254,1,1.0,7200,6.7928324,61.507736\n" + -"27.619982,-46.87254,1,2.0,7200,37.85058,49.765\n" + -"27.619982,-46.87254,1,3.0,7200,31.926285,65.68376\n" + -"27.619982,-46.87254,1,4.0,7200,36.00912,39.43354\n" + -"27.619982,-46.87254,1,5.0,7200,1.9108725,22.057114\n" + -"27.619982,-46.87254,1,6.0,7200,23.234598,62.765938\n" + -"16.401363,-38.747154,1,0.0,10800,39.38336,41.227074\n" + -"16.401363,-38.747154,1,1.0,10800,22.487091,60.7646\n" + -"16.401363,-38.747154,1,2.0,10800,16.574474,5.8886514\n" + -"16.401363,-38.747154,1,3.0,10800,3.2033331,48.783085\n" + -"16.401363,-38.747154,1,4.0,10800,32.13747,12.481885\n" + -"16.401363,-38.747154,1,5.0,10800,5.927774,46.63955\n" + -"16.401363,-38.747154,1,6.0,10800,9.936579,44.746056\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 28, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=Latitude\n" + -" missing_value=-999.9f\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10d " + pauseMessage); - - //test just variable[obs] (interiorTable) - String2.log("\n\n** Testing incomplete file\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, StringArray.fromCSV("lat,lon,trajectory,time,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("2")); - results = table.dataToString(); - expected = -"lat,lon,trajectory,time\n" + -"22.20038,-74.5625,2,0\n" + -"39.905518,-15.35749,2,3600\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - results = table.columnAttributes(0).toString(); - expected = -" long_name=Latitude\n" + -" missing_value=-999.9f\n" + -" standard_name=latitude\n" + -" units=degrees_north\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10e " + pauseMessage); - } catch (Exception e) { - String2.pressEnterToContinue(MustBe.throwableToString(e)); - } - - - //********** NO_DATA - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, outer/inner/obsVar - String2.log("\n\n** Testing orthoMultiDimH61FileName just outer/inner/obsVar, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("trajectory,lat,zztop,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDa " + pauseMessage); - - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just outerVar - String2.log("\n\n** Testing orthoMultiDimH61FileName just outerVar, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("zztop,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDb " + pauseMessage); - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just innerVar - String2.log("\n\n** Testing orthoMultiDimH61FileName just innerVar, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("lat,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDc " + pauseMessage); - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just obsVar - String2.log("\n\n** Testing orthoMultiDimH51File just obsVar, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("zztop,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDd " + pauseMessage); - - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just outerVar* and innerVar - String2.log("\n\n** Testing orthoMultiDimH51File just outer* /innerVar, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("zztop,trajectory,lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDe1 " + pauseMessage); - - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just outerVar and innerVar* - String2.log("\n\n** Testing orthoMultiDimH51File just outer/innerVar*, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("zztop,trajectory,lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDe2 " + pauseMessage); - - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just outerVar* and obsVar - String2.log("\n\n** Testing orthoMultiDimH51File just outer* /obsVar, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("trajectory,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDf1 " + pauseMessage); - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just outerVar and obsVar* - String2.log("\n\n** Testing orthoMultiDimH51File just outer/obsVar*, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("trajectory,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDf2 " + pauseMessage); - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just innerVar* and obsVar - String2.log("\n\n** Testing orthoMultiDimH51File just inner* /obsVar, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("lat,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDg1 " + pauseMessage); - - //********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just innerVar and obsVar* - String2.log("\n\n** Testing orthoMultiDimH51File just inner/obsVar*, NO_DATA\n" + - " " + orthoMultiDimH61FileName); - table.readNcCF(orthoMultiDimH61FileName, - StringArray.fromCSV("lat,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#10NDg2 " + pauseMessage); - - - //******* - //*************** trajectoryProfile ragged multiple station --- - try { - fileName = raggedMultipleStationFileName; - String2.log("\n\n** Testing raggedMultipleStationFile\n" + - " " + fileName); - String2.log(NcHelper.ncdump(fileName, "")); - table.readNcCF(fileName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"trajectory,lat,lon,time,z,temperature,humidity\n" + -"0,49.0,-60.0,176400,0.0,39.174652,78.30777\n" + -"0,49.0,-60.0,176400,1.0,30.924078,58.185684\n" + -"0,49.0,-60.0,176400,2.0,19.258087,47.014008\n" + -"0,49.0,-60.0,176400,3.0,33.512325,77.832664\n" + -"0,49.0,-60.0,176400,4.0,35.435345,55.649605\n" + -"0,49.0,-60.0,176400,5.0,17.33441,60.725643\n" + -"0,49.0,-60.0,176400,6.0,6.3611813,40.747665\n" + -"0,49.0,-60.0,176400,7.0,37.18272,32.312344\n" + -"0,49.0,-60.0,176400,8.0,31.59126,30.934\n" + -"0,49.0,-60.0,176400,9.0,36.08196,48.639427\n" + -"0,49.0,-60.0,176400,10.0,22.3596,16.427603\n" + -"0,49.0,-60.0,176400,11.0,6.2299767,16.590557\n" + -"0,53.0,-60.0,104400,0.0,13.244916,28.135975\n" + -"0,53.0,-60.0,104400,1.0,17.160164,41.951385\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, - "results=\n" + results); - expected = -"4,47.0,-44.0,136800,33.0,8.7725,74.930565\n" + -"4,47.0,-44.0,136800,34.0,29.10568,31.136621\n" + -"4,47.0,-44.0,136800,35.0,4.7999196,18.904522\n" + -"4,47.0,-44.0,136800,36.0,1.4633778,47.546745\n" + -"4,47.0,-44.0,136800,37.0,24.846626,77.9313\n" + -"4,47.0,-44.0,136800,38.0,16.368006,8.343946\n"; - Test.ensureEqual( - results.substring(results.length() - expected.length(), results.length()), - expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 594, ""); - results = table.columnAttributes(0).toString(); - expected = -" cf_role=trajectory_id\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10m " + pauseMessage); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory,lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "z,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "lat,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "z,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "z,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "z,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "z,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - // - table.readNcCF(fileName, StringArray.fromCSV( - "trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "lat"), - 0, //standardizeWhat=0 - StringArray.fromCSV("lat"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - table.readNcCF(fileName, StringArray.fromCSV( - "z"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-12345")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - - //*************** trajectoryProfile ragged multiple station --- just outerVar - String2.log("\n\n** Testing raggedMultipleStationFile just outerVar\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("zztop,trajectory"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(20); - expected = -"trajectory\n" + -"0\n" + -"1\n" + -"2\n" + -"3\n" + -"4\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 5, ""); - results = table.columnAttributes(0).toString(); - expected = -" cf_role=trajectory_id\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10n " + pauseMessage); - - //*************** trajectoryProfile ragged multiple station --- just innerVar - String2.log("\n\n** Testing raggedMultipleStationFile just innerVar\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("time,zztop,trajectory"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"time,trajectory\n" + -"176400,0\n" + -"104400,0\n" + -"140400,0\n" + -"151200,0\n" + -"111600,1\n" + -"36000,1\n" + -"64800,1\n" + -"46800,1\n" + -"0,2\n" + -"162000,2\n" + -"180000,2\n" + -"129600,2\n" + -"154800,3\n" + -"3600,3\n" + -"122400,3\n" + -"32400,3\n" + -"136800,4\n" + -"140400,4\n" + -"140400,4\n" + -"136800,4\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 20, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=time of measurement\n" + -" missing_value=-999i\n" + -" standard_name=time\n" + -" units=seconds since 1990-01-01 00:00:00\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10o " + pauseMessage); - - //*************** trajectoryProfile ragged multiple station --- just outerVar and innerVar - String2.log("\n\n** Testing raggedMultipleStationFile just outerVar and innerVar\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("lon,lat,time,trajectory,"), - 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(); - expected = -"lon,lat,time,trajectory\n" + -"-60.0,49.0,176400,0\n" + -"-60.0,53.0,104400,0\n" + -"-63.0,45.0,140400,0\n" + -"-62.0,45.0,151200,0\n" + -"-56.0,54.0,111600,1\n" + -"-68.0,53.0,36000,1\n" + -"-66.0,43.0,64800,1\n" + -"-47.0,58.0,46800,1\n" + -"-52.0,47.0,0,2\n" + -"-50.0,48.0,162000,2\n" + -"-60.0,59.0,180000,2\n" + -"-71.0,42.0,129600,2\n" + -"-66.0,53.0,154800,3\n" + -"-53.0,50.0,3600,3\n" + -"-67.0,56.0,122400,3\n" + -"-73.0,48.0,32400,3\n" + -"-67.0,47.0,136800,4\n" + -"-45.0,43.0,140400,4\n" + -"-40.0,54.0,140400,4\n" + -"-44.0,47.0,136800,4\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 20, ""); - results = table.columnAttributes(0).toString(); - expected = -" long_name=station longitude\n" + -" standard_name=longitude\n" + -" units=degrees_east\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10p " + pauseMessage); - - //*************** trajectoryProfile ragged multiple station --- just outerVar and obsVar - String2.log("\n\n** Testing raggedMultipleStationFile just outerVar and obsVar\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("trajectory,temperature,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("39")); - results = table.dataToString(); - expected = -"trajectory,temperature\n" + -"0,39.174652\n" + -"0,39.157566\n" + -"0,39.915646\n" + -"0,39.041203\n" + -"1,39.104313\n" + -"1,39.74818\n" + -"1,39.077923\n" + -"1,39.406986\n" + -"2,39.85588\n" + -"2,39.213017\n" + -"2,39.89851\n" + -"2,39.404697\n" + -"2,39.012913\n" + -"3,39.276768\n" + -"3,39.832867\n" + -"3,39.119217\n" + -"3,39.335064\n" + -"3,39.261826\n" + -"3,39.501484\n" + -"4,39.015987\n" + -"4,39.5769\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 21, ""); - results = table.columnAttributes(0).toString(); - expected = -" cf_role=trajectory_id\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10q " + pauseMessage); - - //*************** trajectoryProfile ragged multiple station --- just innerVar and obsVar - String2.log("\n\n** Testing raggedMultipleStationFile just innerVar and obsVar\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("temperature,zztop,time"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("39")); - results = table.dataToString(); - expected = -"temperature,time\n" + -"39.174652,176400\n" + -"39.157566,104400\n" + -"39.915646,104400\n" + -"39.041203,104400\n" + -"39.104313,111600\n" + -"39.74818,36000\n" + -"39.077923,64800\n" + -"39.406986,64800\n" + -"39.85588,0\n" + -"39.213017,180000\n" + -"39.89851,180000\n" + -"39.404697,180000\n" + -"39.012913,180000\n" + -"39.276768,154800\n" + -"39.832867,3600\n" + -"39.119217,122400\n" + -"39.335064,122400\n" + -"39.261826,122400\n" + -"39.501484,122400\n" + -"39.015987,140400\n" + -"39.5769,136800\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 21, ""); - results = table.columnAttributes(0).toString(); - expected = -" coordinates=time lat lon z\n" + -" long_name=Air Temperature\n" + -" missing_value=-999.9f\n" + -" standard_name=air_temperature\n" + -" units=Celsius\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - if (pauseAfterEach) - String2.pressEnterToContinue("#10r " + pauseMessage); - - - //********** NO_DATA - //********** trajectoryProfile ragged multiple station --- NO_DATA, outer/inner/obsVar - String2.log("\n\n** Testing raggedMultipleStationFile just outer/inner/obsVar, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("trajectory,zztop,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11a " + pauseMessage); - - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just outerVar - String2.log("\n\n** Testing raggedMultipleStationFile just outerVar, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("zztop,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("10")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11b " + pauseMessage); - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just innerVar - String2.log("\n\n** Testing raggedMultipleStationFile just innerVar, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("time,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11c " + pauseMessage); - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just obsVar - String2.log("\n\n** Testing raggedMultipleStationFile just obsVar, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("zztop,temperature"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11d " + pauseMessage); - - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just outerVar* and innerVar - String2.log("\n\n** Testing raggedMultipleStationFile just outer*/innerVar, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("zztop,z,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11e1 " + pauseMessage); - - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just outerVar and innerVar* - String2.log("\n\n** Testing raggedMultipleStationFile just outer/innerVar*, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("zztop,z,trajectory"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-5")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11e2 " + pauseMessage); - - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just outerVar* and obsVar - String2.log("\n\n** Testing raggedMultipleStationFile just outer*/obsVar, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("temperature,trajectory,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("trajectory"), - StringArray.fromCSV("="), - StringArray.fromCSV("-10")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11f1 " + pauseMessage); - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just outerVar and obsVar* - String2.log("\n\n** Testing raggedMultipleStationFile just outer/obsVar*, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("temperature,trajectory,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11f2 " + pauseMessage); - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just innerVar* and obsVar - String2.log("\n\n** Testing raggedMultipleStationFile just inner*/obsVar, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("temperature,z,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("z"), - StringArray.fromCSV("="), - StringArray.fromCSV("-1")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11g1 " + pauseMessage); - - //********** trajectoryProfile ragged multiple station --- NO_DATA, just innerVar and obsVar* - String2.log("\n\n** Testing raggedMultipleStationFile just inner/obsVar*, NO_DATA\n" + - " " + raggedMultipleStationFileName); - table.readNcCF(raggedMultipleStationFileName, - StringArray.fromCSV("temperature,z,zztop"), - 0, //standardizeWhat=0 - StringArray.fromCSV("temperature"), - StringArray.fromCSV(">="), - StringArray.fromCSV("100")); - Test.ensureEqual(table.nRows(), 0, ""); - Test.ensureEqual(table.nColumns(), 0, ""); - if (pauseAfterEach) - String2.pressEnterToContinue("#11g2 " + pauseMessage); - - } catch (Exception e) { - String2.pressEnterToContinue(MustBe.throwableToString(e)); - } - /* */ - debugMode = oDebug; - } - - /** - * This reads an NCEI-style invalid CF DSG Contiguous Ragged Array .nc file. - * Suitable sample files are from https://data.nodc.noaa.gov/thredds/catalog/ncei/wod/ - * See local copies in /erddapTestBig/nccf/wod/ - * - * @param colNames If empty, this reads all columns. - * If conNames... specified and this is specified, this includes all of the conNames. - * @param standardizeWhat see Attributes.unpackVariable's standardizeWhat - * @param conNames may be null or size=0; - * @throws Exception if trouble. - * No matching data is not an error and returns an empty table (0 rows and 0 columns). - */ - public void readInvalidCRA(String fullName, StringArray colNames, - int standardizeWhat, - StringArray conNames, StringArray conOps, StringArray conVals) throws Exception { - - String msg = " Table.readInvalidCRA " + fullName; - long time = System.currentTimeMillis(); - clear(); - if (colNames == null) - colNames = new StringArray(1, false); - //String2.log(NcHelper.ncdump(fullName, "-h")); - Attributes gridMappingAtts = null; - NetcdfFile ncFile = NcHelper.openFile(fullName); - try { - - NcHelper.getGroupAttributes(ncFile.getRootGroup(), globalAttributes()); - Attributes gatts = globalAttributes(); - - //ensure featureType=Profile (other single level types could be supported -- need examples) - String featureType = gatts.getString("featureType"); - featureType = featureType == null? "" : String2.toTitleCase(featureType); - Test.ensureEqual(featureType, "Profile", "Unexpected featureType."); - - //find vars with sample_dimension, find outerDimName, largestInnerDim - String profileIDVarName = null; - int profileIDVarNumber = -1; - String outerDimName = null; //e.g., cast - Dimension outerDim = null; - String largestInnerDimName = null; //e.g., z_obs - int largestInnerDimSize = -1; - List varList = ncFile.getVariables(); - int nVars = varList.size(); - String vNames[] = new String[nVars]; - Attributes vatts[] = new Attributes[nVars]; - PAType varPATypes[] = new PAType[nVars]; - boolean isCharArray[] = new boolean[nVars]; - int nDims[] = new int[nVars]; - int realNDims[] = new int[nVars]; - String varMissingValues[] = new String[nVars]; - boolean varHasSampleDimensionAtt[] = new boolean[nVars]; - HashMap rowSizesHM = new HashMap(); //e.g., sample_dimension="z_obs" -> z_row_size PA - for (int v = 0; v < nVars; v++) { - Variable var = varList.get(v); - vNames[v] = var.getFullName(); - vatts[v] = new Attributes(); - NcHelper.getVariableAttributes(var, vatts[v]); - - //does this var point to the pseudo-data var with CF grid_mapping (projection) information? - if (gridMappingAtts == null) { - gridMappingAtts = NcHelper.getGridMappingAtts(ncFile, - vatts[v].getString("grid_mapping")); - if (gridMappingAtts != null) - globalAttributes.add(gridMappingAtts); - } - - varPATypes[v] = NcHelper.getElementPAType(var); //exception if trouble - nDims[v] = var.getRank(); - isCharArray[v] = nDims[v] > 0 && varPATypes[v] == PAType.CHAR; - if (varPATypes[v] == PAType.CHAR) - varPATypes[v] = PAType.STRING; //assume all char -> string - realNDims[v] = nDims[v] - (isCharArray[v]? 1 : 0); - varMissingValues[v] = vatts[v].getString("_FillValue"); - if (varMissingValues[v] == null) - varMissingValues[v] = vatts[v].getString("missing_value"); - if (varMissingValues[v] == null) - varMissingValues[v] = ""; - - //profile_id? - String cfRole = vatts[v].getString("cf_role"); - if (cfRole != null) - cfRole = cfRole.toLowerCase(); - if ("profile_id".equals(cfRole)) { - if (debugMode) msg += - "\n>> found cf_role=profile_id for var=" + vNames[v]; - if (profileIDVarName != null) - throw new RuntimeException( - "Two variables have the attribute cf_role=profile_id: " + - profileIDVarName + " and " + vNames[v] + "."); - profileIDVarName = vNames[v]; - profileIDVarNumber = v; - - Test.ensureEqual(realNDims[v], 1, - "Unexpected number of dimensions for var=" + vNames[v]); - Dimension tOuterDim = var.getDimension(0); - String tOuterDimName = tOuterDim.getName(); - Test.ensureNotNull(tOuterDimName, - "Unexpected dimensionName=null for var=" + vNames[v]); - if (outerDimName == null) { - outerDimName = tOuterDimName; - outerDim = tOuterDim; - } else { - Test.ensureEqual(tOuterDimName, outerDimName, - "Unexpected dimension for var=" + vNames[v]); - } - } - - //gather sample_dimension atts and row_size PAs - //INVALID FILES: Primary_Investigator_rowsize doesn't have sample_dimension: so fix it - // See "numberofpis" below for additional, related fixes. - String sampleDimension = vNames[v].equals("Primary_Investigator_rowsize")? - "numberofpis" : - vatts[v].getString("sample_dimension"); - if (sampleDimension != null) { - if (debugMode) msg += - "\n>> found sample_dimension=" + sampleDimension + " for var=" + vNames[v]; - varHasSampleDimensionAtt[v] = true; - - //get/verify outerDimName, e.g., casts - Test.ensureEqual(realNDims[v], 1, - "Unexpected number of dimensions for var=" + vNames[v]); - Dimension tOuterDim = var.getDimension(0); - String tOuterDimName = tOuterDim.getName(); - Test.ensureNotNull(tOuterDimName, - "Unexpected dimensionName=null for var=" + vNames[v]); - if (outerDimName == null) { - outerDimName = tOuterDimName; - outerDim = tOuterDim; - } else { - Test.ensureEqual(tOuterDimName, outerDimName, - "Unexpected dimension for var=" + vNames[v]); - } - - //get rowSizes - rowSizesHM.put(sampleDimension, NcHelper.getPrimitiveArray(var)); - //no need to unpack rowSizes - - //is it the largest sample_dimension (e.g., z_obs)? - Dimension dim = ncFile.findDimension(sampleDimension); - int tSize = dim.getLength(); - if (tSize > largestInnerDimSize) { - largestInnerDimSize = tSize; - largestInnerDimName = sampleDimension; - } - } - } - Test.ensureNotNull(profileIDVarName, - "No variable was found with a cf_role=profile_id attribute."); - Test.ensureTrue(outerDimName != null, - "No outer dimension (e.g., casts) found!"); - Test.ensureTrue(largestInnerDimSize > 0, - "No row_size variables with a sample_dimension attribute (e.g., z_obs) were found!"); - int outerDimSize = outerDim.getLength(); - - //read the outerDim vars (including scalars and primary_investigator) - if (debugMode) msg += "\n>> read the outerDim"; - Table outerTable = new Table(); - StringArray cdm_profile_variables = new StringArray(); - for (int v = 0; v < nVars; v++) { - Variable var = varList.get(v); - Attributes vatt = vatts[v]; - - //if varName isn't in colNames, skip it - if (colNames.size() > 0 && colNames.indexOf(vNames[v]) < 0) - continue; - - //scalar? e.g., crs - if (realNDims[v] == 0) { - if (debugMode) msg += "\n>> found scalar var=" + vNames[v]; - - if ("crs".equals(vNames[v])) { - //if crs, ignore value and promote to vatts to gatt - String[] vattNames = vatt.getNames(); - int vattSize = vattNames.length; - for (int va = 0; va < vattSize; va++) - gatts.add(vNames[v] + "_" + vattNames[va], vatt.get(vattNames[va])); - } else { - //add to outerTable - outerTable.addColumn(outerTable.nColumns(), vNames[v], - NcHelper.getPrimitiveArray(var), vatt); - outerTable.standardizeLastColumn(standardizeWhat); - } - continue; - - } else if (realNDims[v] == 1) { - Dimension dim = var.getDimension(0); - String dimName = dim.getName(); - - //FIX flaws related to Primary_Investigator / numberofpis. - //Treat numberofpis differently than other dimNames: - // convert PI's for each cast into /-separated string since some have internal ';'. - if (dimName.equals("numberofpis")) { - PrimitiveArray rowSizesPA = rowSizesHM.get(dimName); - Test.ensureNotNull(rowSizesPA, - "No row_size info for dim=" + dimName + " for var=" + vNames[v]); - PrimitiveArray varPA = NcHelper.getPrimitiveArray(var); - StringArray newPA = new StringArray(outerDimSize, false); - PrimitiveArray tSubset = null; - int thisPo = 0; - for (int outer = 0; outer < outerDimSize; outer++) { - int thisChunkSize = rowSizesPA.getInt(outer); - tSubset = varPA.subset(tSubset, thisPo, 1, thisPo + thisChunkSize - 1); - //usually just 0 or 1 pi's, gld has more - String tts = String2.toSVString(tSubset.toStringArray(), "/", false); - newPA.add(tts); - thisPo += thisChunkSize; - } - //add to outerTable - outerTable.addColumn(outerTable.nColumns(), vNames[v], - newPA, vatt); - outerTable.standardizeLastColumn(standardizeWhat); - continue; - } - - if (!outerDimName.equals(dimName)) - continue; - if (varHasSampleDimensionAtt[v]) - //it's a row_size var with a sample_dimension att - continue; - - //add to outerTable - outerTable.addColumn(outerTable.nColumns(), vNames[v], - NcHelper.getPrimitiveArray(var), vatt); //char -> String - outerTable.standardizeLastColumn(standardizeWhat); - } - } - - //expand scalars to same number of rows as outerDim - ensureColumnsAreSameSize_LastValue(); - - //set cdm_profile_variables - String cpv = outerTable.getColumnNamesCSSVString(); - cpv = String2.replaceAll(cpv, ", lat,", ", latitude,"); - cpv = String2.replaceAll(cpv, ", lon,", ", longitude,"); - cpv = String2.replaceAll(cpv, ", z,", ", depth,"); - //the numeric time variable is called time - if (cpv.length() > 0) - gatts.set("cdm_profile_variables", cpv); - - //apply constraints, but keep all rows - if (debugMode) String2.log(">> apply constraints"); - BitSet keepOuter = new BitSet(); - keepOuter.set(0, outerDimSize); - if (outerTable.nRows() > 0 && - outerTable.tryToApplyConstraints(profileIDVarNumber, - conNames, conOps, conVals, keepOuter) == 0) { - //No matching data is not an error and returns an empty table (0 rows and 0 columns). - if (reallyVerbose) msg += " finished. " + - MustBe.THERE_IS_NO_DATA + - " Just outer table. time" + (System.currentTimeMillis() - time) + "ms"; - return; - } - boolean keepAllOuter = keepOuter.nextClearBit(0) == -1; - - //are we done? - if (debugMode) msg += "\n>> are we done because just outer columns?"; - if (colNames.size() > 0) { - //are all colNames in outerTable? - boolean done = true; - for (int col = 0; col < colNames.size(); col++) { - if (outerTable.findColumnNumber(colNames.get(col)) < 0) { - done = false; - break; - } - } - - if (done) { - ncFile.close(); - outerTable.justKeep(keepOuter); - outerTable.reorderColumns(colNames, true); - outerTable.decodeCharsAndStrings(); - outerTable.convertToUnsignedPAs(); - - //copy outerTable to this table - for (int col = 0; col < outerTable.nColumns(); col++) - addColumn(col, outerTable.getColumnName(col), - outerTable.getColumn(col), outerTable.columnAttributes(col)); - - if (reallyVerbose) msg += - " finished. Just outer table. nRows=" + - nRows() + " nCols=" + nColumns() + - " time=" + (System.currentTimeMillis() - time) + "ms"; - return; - } - } - - //find nActiveInnerRows and largestLargestChunkSize - PrimitiveArray largestRowSizes = rowSizesHM.get(largestInnerDimName); - int checkNTotalInnerRows = 0; - int nActiveInnerRows = 0; - int largestLargestChunkSize = 0; - for (int outer = 0; outer < outerDimSize; outer++) { - int tChunkSize = largestRowSizes.getInt(outer); - checkNTotalInnerRows += tChunkSize; - if (!keepOuter.get(outer)) //skip this outer - continue; - nActiveInnerRows += tChunkSize; - largestLargestChunkSize = Math.max(largestLargestChunkSize, tChunkSize); - } - if (checkNTotalInnerRows != largestInnerDimSize) - throw new RuntimeException("Invalid file: The sum of the row sizes for " + - largestInnerDimName + " (" + checkNTotalInnerRows + ") doesn't equal the size of dimension=" + - largestInnerDimName + " (" + largestInnerDimSize + ")."); - - //expand the kept outerTable rows in this table - for (int col = 0; col < outerTable.nColumns(); col++) { - String tName = outerTable.getColumnName(col); - - //if varName isn't in colNames, skip it - if (colNames.size() > 0 && colNames.indexOf(tName) < 0) - continue; - if (debugMode) msg += "\n>> expand outerTable into this table, var=" + tName; - - PrimitiveArray otpa = outerTable.getColumn(col); - PrimitiveArray newPA = PrimitiveArray.factory(otpa.elementType(), - nActiveInnerRows, false); - addColumn(nColumns(), tName, newPA, outerTable.columnAttributes(col)); - - for (int outer = 0; outer < outerDimSize; outer++) { - - if (!keepOuter.get(outer)) { - //skip this outer, e.g., this cast - continue; - } - - //addN of that value - newPA.addNStrings(largestRowSizes.getInt(outer), otpa.getString(outer)); - } - } - outerTable = null; //encourage gc - - //make the innerTable in this table - for (int v = 0; v < nVars; v++) { - Variable var = varList.get(v); - Attributes vatt = vatts[v]; - - //if varName isn't in colNames, skip it - if (colNames.size() > 0 && colNames.indexOf(vNames[v]) < 0) - continue; - - //find 1D vars where dim isn't outerDimName, e.g., Temperature - if (realNDims[v] != 1) - continue; - Dimension dim = var.getDimension(0); - String dimName = dim.getName(); - if (outerDimName.equals(dimName) || //already in outer table? - dimName.equals("numberofpis")) - continue; - - //Let's do this! - if (debugMode) msg += - "\n>> make the innerTable in this table, v[" + v + "]=" + vNames[v]; - - //get the row_size info - PrimitiveArray rowSizesPA = rowSizesHM.get(dimName); - Test.ensureNotNull(rowSizesPA, - "No row_size info for dim=" + dimName + " for var=" + vNames[v]); - - //get the var's data - PrimitiveArray varPA = NcHelper.getPrimitiveArray(var); - varPA = vatts[v].standardizeVariable(standardizeWhat, vNames[v], varPA); - - //can we use varPA as is? - if (keepAllOuter && varPA.size() == largestInnerDimSize) { - addColumn(nColumns(), vNames[v], varPA, vatts[v]); - continue; - } - - //build newPA, with correct size for each cast, and just keep the keepOuter chunks - PrimitiveArray newPA = PrimitiveArray.factory(varPATypes[v], - nActiveInnerRows, false); - - int thisPo = 0; - PrimitiveArray tSubset = null; - for (int outer = 0; outer < outerDimSize; outer++) { - int largestChunkSize = largestRowSizes.getInt(outer); - int thisChunkSize = rowSizesPA.getInt(outer); - - if (!keepOuter.get(outer)) { - //skip this outer - thisPo += thisChunkSize; - continue; - } - - if (thisChunkSize == 0) { - //This deals with the main invalid part of these files. - //add missing values to newPA - newPA.addNStrings(largestChunkSize, varMissingValues[v]); - - } else if (thisChunkSize == largestChunkSize) { - //copy values into newPA - tSubset = varPA.subset(tSubset, thisPo, 1, thisPo + thisChunkSize - 1); - newPA.append(tSubset); - - //only need to do once, but not extant till here - tSubset.clear(); //speeds up ensureCapacity - tSubset.ensureCapacity(largestLargestChunkSize); - - } else { - throw new RuntimeException("For " + outerDimName + "[" + outer + - "], the number of " + dimName + " values (" + thisChunkSize + - ") doesn't equal the number of " + largestInnerDimName + - " values (" + largestChunkSize + ")."); - } - thisPo += thisChunkSize; - } - if (thisPo != varPA.size()) - throw new RuntimeException("Invalid file: The sum of the row sizes for " + - dimName + " (" + thisPo + ") doesn't equal the size of dimension=" + - dimName + " (" + varPA.size() + ")."); - - addColumn(nColumns(), vNames[v], newPA, vatts[v]); - } - - //finish up - //apply all constraints - tryToApplyConstraintsAndKeep(findColumnNumber(profileIDVarName), //may be -1 - conNames, conOps, conVals); //may be 0 rows left - - //put in colNames order - if (colNames.size() > 0) - reorderColumns(colNames, true); - - //we're done - if (reallyVerbose) String2.log(msg + - " finished. nRows=" + nRows() + " nCols=" + nColumns() + - " time=" + (System.currentTimeMillis() - time) + "ms"); - } finally { - try {if (ncFile != null) ncFile.close(); } catch (Exception e9) {} - } - } - - - public static void testReadInvalidCRA() throws Exception { - String2.log("\n*** Table.testReadInvalidCRA()"); - StringArray colNames, conNames, conOps, conVals; - Table table = new Table(); - table.debugMode = true; - String dir = String2.unitTestBigDataDir + "nccf/wod/"; - String fullName, results, expected; - //String doAllString = String2.getStringFromSystemIn( - // "Do all the tests, including ones that are slow and take lots of memory (y/n)?"); - boolean doAll = true; //doAllString.startsWith("y"); -/* */ - //read all - fullName = dir + "wod_apb_2005.nc"; - if (doAll) { - table.readInvalidCRA(fullName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.toString(5); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 19223385 ;\n" + -"\tcountry_strlen = 13 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\toriginators_cruise_identifier_strlen = 15 ;\n" + -"\tProject_strlen = 60 ;\n" + -"\tPlatform_strlen = 19 ;\n" + -"\tdataset_strlen = 14 ;\n" + -"\tOcean_Vehicle_strlen = 13 ;\n" + -"\tTemperature_Instrument_strlen = 73 ;\n" + -"\tSalinity_Instrument_strlen = 73 ;\n" + -"\tPrimary_Investigator_strlen = 20 ;\n" + -"\tPrimary_Investigator_VAR_strlen = 13 ;\n" + -"variables:\n" + -"\tchar country(row, country_strlen) ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\t\tGMT_time:units = \"hours\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:_FillValue = -99999 ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + -"\tchar Project(row, Project_strlen) ;\n" + -"\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + -"\t\tProject:long_name = \"Project_name\" ;\n" + -"\tchar Platform(row, Platform_strlen) ;\n" + -"\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + -"\t\tPlatform:long_name = \"Platform_name\" ;\n" + -"\tint Orig_Stat_Num(row) ;\n" + -"\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + -"\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + -"\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tchar Ocean_Vehicle(row, Ocean_Vehicle_strlen) ;\n" + -"\t\tOcean_Vehicle:comment = \"Ocean_vehicle\" ;\n" + -"\tbyte Temperature_WODprofileflag(row) ;\n" + -"\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + -"\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + -"\tint Temperature_uncalibrated(row) ;\n" + -"\t\tTemperature_uncalibrated:_FillValue = -99999 ;\n" + -"\t\tTemperature_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + -"\tbyte Salinity_WODprofileflag(row) ;\n" + -"\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + -"\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + -"\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + -"\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + -"\tfloat z(row) ;\n" + -"\t\tz:ancillary_variables = \"z_sigfigs z_WODflag\" ;\n" + -"\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"depth\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tbyte z_WODflag(row) ;\n" + -"\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + -"\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + -"\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_sigfigs(row) ;\n" + -"\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag\" ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\tbyte Temperature_sigfigs(row) ;\n" + -"\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + -"\tbyte Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tfloat Pressure(row) ;\n" + -"\t\tPressure:_FillValue = -1.0E10f ;\n" + -"\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag\" ;\n" + -"\t\tPressure:coordinates = \"time lat lon z\" ;\n" + -"\t\tPressure:grid_mapping = \"crs\" ;\n" + -"\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:units = \"dbar\" ;\n" + -"\tbyte Pressure_sigfigs(row) ;\n" + -"\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + -"\tfloat Salinity(row) ;\n" + -"\t\tSalinity:_FillValue = -1.0E10f ;\n" + -"\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag\" ;\n" + -"\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + -"\t\tSalinity:grid_mapping = \"crs\" ;\n" + -"\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + -"\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + -"\tbyte Salinity_sigfigs(row) ;\n" + -"\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + -"\tbyte Salinity_WODflag(row) ;\n" + -"\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Orig_Stat_Num, dataset, Ocean_Vehicle, Temperature_WODprofileflag, Temperature_Instrument, Temperature_uncalibrated, Salinity_WODprofileflag, Salinity_Instrument, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + -"\t\t:Conventions = \"CF-1.6\" ;\n" + -"\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + -"\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:crs_inverse_flattening = 298.25723f ;\n" + -"\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:crs_semi_major_axis = 6378137.0f ;\n" + -"\t\t:date_created = \"2018-03-24\" ;\n" + -"\t\t:date_modified = \"2018-03-24\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 66.6276f ;\n" + -"\t\t:geospatial_lat_min = -71.2137f ;\n" + -"\t\t:geospatial_lat_resolution = \"point\" ;\n" + -"\t\t:geospatial_lon_max = 8.102386f ;\n" + -"\t\t:geospatial_lon_min = 55.2659f ;\n" + -"\t\t:geospatial_lon_resolution = \"point\" ;\n" + -"\t\t:geospatial_vertical_max = 1975.4133f ;\n" + -"\t\t:geospatial_vertical_min = 0.0f ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"meters\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_apb_2005.nc\" ;\n" + -"\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + -"\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + -"\t\t:project = \"World Ocean Database\" ;\n" + -"\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + -"\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + -"\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + -"\t\t:source = \"World Ocean Database\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + -"\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + -"\t\t:time_coverage_end = \"2005-12-31\" ;\n" + -"\t\t:time_coverage_start = \"2005-01-01\" ;\n" + -"\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + -"}\n" + -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + -"UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,0.0,0,1,12.3,3,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,1.0,0,2,12.35,4,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,8.5,0,2,12.35,4,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,22.5,0,3,12.35,4,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,36.5,0,3,12.35,4,0,-1.0E10,,-1.0E10,,\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - table.removeRows(0, 10000000); - results = table.dataToString(5); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + -"UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,55.0,0,3,8.2,2,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,66.0,0,3,8.1,2,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,77.5,0,3,7.75,3,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,89.5,0,3,7.6,2,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,101.0,0,4,7.35,3,0,-1.0E10,,-1.0E10,,\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - table.removeRows(0, 9223380); - results = table.dataToString(); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + -"UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,550.0,0,4,5.95,3,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,557.5,0,4,5.85,3,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,564.0,0,4,5.85,3,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,570.5,0,4,5.8,2,0,-1.0E10,,-1.0E10,,\n" + -"UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,579.0,0,4,5.8,2,0,-1.0E10,,-1.0E10,,\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } - - //*** just read outer col - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast","time"}), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); - expected = -"wod_unique_cast,time\n" + -"14009590,85832.01060199086\n" + -"14009591,85832.03254599497\n" + -"14009592,85832.01828699\n" + -"14009593,85832.0382870026\n" + -"14009594,85832.01134299766\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 346231, ""); - - table.removeRows(0, 346226); - results = table.dataToString(); - expected = -"wod_unique_cast,time\n" + -"14331030,86196.96106499434\n" + -"14331031,86196.97773098946\n" + -"14331032,86196.99402803183\n" + -"14331033,86196.97189801931\n" + -"14331034,86196.99254602194\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - //just read outer col with constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast","time"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"14148754"})); - results = table.dataToString(5); -//from above -//"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + -//"UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,55.0,0,3,8.2,2,0,-1.0E10,,-1.0E10,,\n" + - expected = -"wod_unique_cast,time\n" + -"14148754,86025.06550899148\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - //*** just read inner col - table.readInvalidCRA(fullName, - new StringArray(new String[]{"z", "Temperature","Temperature_sigfigs"}), 0, //standardizeWhat=0 - null, null, null); - results = table.dataToString(5); -//from above -//...z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + -//...0.0,0,1,12.3,3,0,-1.0E10,,-1.0E10,,\n" + -//...1.0,0,2,12.35,4,0,-1.0E10,,-1.0E10,,\n" + -//...8.5,0,2,12.35,4,0,-1.0E10,,-1.0E10,,\n" + -//...22.5,0,3,12.35,4,0,-1.0E10,,-1.0E10,,\n" + -//...36.5,0,3,12.35,4,0,-1.0E10,,-1.0E10,,\n" + - expected = -"z,Temperature,Temperature_sigfigs\n" + -"0.0,12.3,3\n" + -"1.0,12.35,4\n" + -"8.5,12.35,4\n" + -"22.5,12.35,4\n" + -"36.5,12.35,4\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 19223385, ""); - - table.removeRows(0, 19223380); - results = table.dataToString(); -//from above -//...z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + -//...550.0,0,4,5.95,3,0,-1.0E10,,-1.0E10,,\n" + -//...557.5,0,4,5.85,3,0,-1.0E10,,-1.0E10,,\n" + -//...564.0,0,4,5.85,3,0,-1.0E10,,-1.0E10,,\n" + -//...570.5,0,4,5.8,2,0,-1.0E10,,-1.0E10,,\n" + -//...579.0,0,4,5.8,2,0,-1.0E10,,-1.0E10,,\n"; - expected = -"z,Temperature,Temperature_sigfigs\n" + -"550.0,5.95,3\n" + -"557.5,5.85,3\n" + -"564.0,5.85,3\n" + -"570.5,5.8,2\n" + -"579.0,5.8,2\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - //just read inner col with constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"z", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"570.5", "5.8"})); - results = table.dataToString(5); - expected = -"z,Temperature,Temperature_WODflag\n" + -"570.5,5.8,0\n" + -"570.5,5.8,0\n" + -"570.5,5.8,0\n" + -"570.5,5.8,0\n" + -"570.5,5.8,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 22, ""); - - - //read outer and inner col with outer constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"14148754"})); - results = table.dataToString(10); -//from above -//...wod_unique_cast,...z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + -//...14148754,... 55.0,0,3,8.2,2,0,-1.0E10,,-1.0E10,,\n" + -//...14148754,... 66.0,0,3,8.1,2,0,-1.0E10,,-1.0E10,,\n" + -//...14148754,... 77.5,0,3,7.75,3,0,-1.0E10,,-1.0E10,,\n" + -//...14148754,... 89.5,0,3,7.6,2,0,-1.0E10,,-1.0E10,,\n" + - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"14148754,86025.06550899148,0.0,13.85,0\n" + -"14148754,86025.06550899148,0.5,13.85,0\n" + -"14148754,86025.06550899148,3.0,13.85,0\n" + -"14148754,86025.06550899148,15.0,13.55,0\n" + -"14148754,86025.06550899148,30.0,10.05,0\n" + -"14148754,86025.06550899148,43.5,8.4,0\n" + -"14148754,86025.06550899148,55.0,8.2,0\n" + -"14148754,86025.06550899148,66.0,8.1,0\n" + -"14148754,86025.06550899148,77.5,7.75,0\n" + -"14148754,86025.06550899148,89.5,7.6,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 90, ""); - - //read outer and inner col with outer and inner constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"14148754", "13.55"})); - results = table.dataToString(5); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"14148754,86025.06550899148,15.0,13.55,0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - //*** list the non-"" PI's - table.readInvalidCRA(fullName, - new StringArray(new String[]{"Primary_Investigator"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"Primary_Investigator"}), - new StringArray(new String[]{"!="}), - new StringArray(new String[]{""})); - results = table.dataToString(5); - expected = -"Primary_Investigator\n" + -"COSTA; DR. DANIEL P.\n" + -"COSTA; DR. DANIEL P.\n" + -"COSTA; DR. DANIEL P.\n" + -"COSTA; DR. DANIEL P.\n" + -"COSTA; DR. DANIEL P.\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), 323499, ""); - - - //*** read all ctd !!! This fails with -Xmx6000m of memory. Succeeds with -Xmx8000m - fullName = dir + "wod_ctd_2005.nc"; - if (doAll) { - table.readInvalidCRA(fullName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.toString(5); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 14843110 ;\n" + -"\tcountry_strlen = 18 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\toriginators_cruise_identifier_strlen = 15 ;\n" + -"\toriginators_station_identifier_strlen = 9 ;\n" + -"\tProject_strlen = 71 ;\n" + -"\tPlatform_strlen = 80 ;\n" + -"\tInstitute_strlen = 80 ;\n" + -"\tCast_Direction_strlen = 4 ;\n" + -"\tWater_Color_strlen = 54 ;\n" + -"\tWave_Direction_strlen = 25 ;\n" + -"\tWave_Height_strlen = 9 ;\n" + -"\tSea_State_strlen = 42 ;\n" + -"\tWave_Period_strlen = 17 ;\n" + -"\tWind_Direction_strlen = 25 ;\n" + -"\tWeather_Condition_strlen = 169 ;\n" + -"\tCloud_Type_strlen = 18 ;\n" + -"\tCloud_Cover_strlen = 65 ;\n" + -"\tdataset_strlen = 4 ;\n" + -"\tRecorder_strlen = 47 ;\n" + -"\tdepth_eq_strlen = 8 ;\n" + -"\tVisibility_strlen = 24 ;\n" + -"\tneeds_z_fix_strlen = 16 ;\n" + -"\treal_time_strlen = 14 ;\n" + -"\tdbase_orig_strlen = 59 ;\n" + -"\torigflagset_strlen = 5 ;\n" + -"\tTemperature_Scale_strlen = 19 ;\n" + -"\tTemperature_Instrument_strlen = 74 ;\n" + -"\tSalinity_Scale_strlen = 15 ;\n" + -"\tSalinity_Instrument_strlen = 74 ;\n" + -"\tOxygen_Instrument_strlen = 103 ;\n" + -"\tOxygen_Method_strlen = 0 ;\n" + -"\tOxygen_Original_units_strlen = 60 ;\n" + -"\tPressure_Instrument_strlen = 65 ;\n" + -"\tChlorophyll_Instrument_strlen = 59 ;\n" + -"\tChlorophyll_Original_units_strlen = 32 ;\n" + -"\tPrimary_Investigator_strlen = 26 ;\n" + -"\tPrimary_Investigator_VAR_strlen = 13 ;\n" + -"variables:\n" + -"\tchar country(row, country_strlen) ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + -"\tchar originators_station_identifier(row, originators_station_identifier_strlen) ;\n" + -"\t\toriginators_station_identifier:long_name = \"originators_station_identifier\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\t\tGMT_time:units = \"hours\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:_FillValue = -99999 ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + -"\tchar Project(row, Project_strlen) ;\n" + -"\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + -"\t\tProject:long_name = \"Project_name\" ;\n" + -"\tchar Platform(row, Platform_strlen) ;\n" + -"\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + -"\t\tPlatform:long_name = \"Platform_name\" ;\n" + -"\tchar Institute(row, Institute_strlen) ;\n" + -"\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + -"\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + -"\tint Cast_Tow_number(row) ;\n" + -"\t\tCast_Tow_number:_FillValue = -99999 ;\n" + -"\t\tCast_Tow_number:comment = \"originator assigned sequential cast or tow_no\" ;\n" + -"\t\tCast_Tow_number:long_name = \"Cast_or_Tow_number\" ;\n" + -"\tint Orig_Stat_Num(row) ;\n" + -"\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + -"\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + -"\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + -"\tfloat Bottom_Depth(row) ;\n" + -"\t\tBottom_Depth:_FillValue = -1.0E10f ;\n" + -"\t\tBottom_Depth:standard_name = \"sea_floor_depth_below_sea_surface\" ;\n" + -"\t\tBottom_Depth:units = \"meters\" ;\n" + -"\tfloat Cast_Duration(row) ;\n" + -"\t\tCast_Duration:_FillValue = -1.0E10f ;\n" + -"\t\tCast_Duration:long_name = \"Cast_Duration\" ;\n" + -"\t\tCast_Duration:units = \"hours\" ;\n" + -"\tchar Cast_Direction(row, Cast_Direction_strlen) ;\n" + -"\t\tCast_Direction:long_name = \"Cast_Direction\" ;\n" + -"\tint High_res_pair(row) ;\n" + -"\t\tHigh_res_pair:_FillValue = -99999 ;\n" + -"\t\tHigh_res_pair:comment = \"WOD unique cast number for bottle/CTD from same rosette\" ;\n" + -"\t\tHigh_res_pair:long_name = \"WOD_high_resolution_pair_number\" ;\n" + -"\tchar Water_Color(row, Water_Color_strlen) ;\n" + -"\t\tWater_Color:long_name = \"Water_Color\" ;\n" + -"\t\tWater_Color:units_wod = \"Forel-Ule scale (00 to 21)\" ;\n" + -"\tfloat Water_Transpar(row) ;\n" + -"\t\tWater_Transpar:_FillValue = -1.0E10f ;\n" + -"\t\tWater_Transpar:comment = \"Secchi disk depth\" ;\n" + -"\t\tWater_Transpar:long_name = \"Water_Transparency\" ;\n" + -"\t\tWater_Transpar:units = \"meters\" ;\n" + -"\tchar Wave_Direction(row, Wave_Direction_strlen) ;\n" + -"\t\tWave_Direction:long_name = \"Wave_Direction\" ;\n" + -"\t\tWave_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + -"\tchar Wave_Height(row, Wave_Height_strlen) ;\n" + -"\t\tWave_Height:long_name = \"Wave_Height\" ;\n" + -"\t\tWave_Height:units_wod = \"WMO 1555 or NODC 0104\" ;\n" + -"\tchar Sea_State(row, Sea_State_strlen) ;\n" + -"\t\tSea_State:long_name = \"Sea_State\" ;\n" + -"\t\tSea_State:units_wod = \"WMO 3700 or NODC 0109\" ;\n" + -"\tchar Wave_Period(row, Wave_Period_strlen) ;\n" + -"\t\tWave_Period:long_name = \"Wave_Period\" ;\n" + -"\t\tWave_Period:units_wod = \"WMO 3155 or NODC 0378\" ;\n" + -"\tchar Wind_Direction(row, Wind_Direction_strlen) ;\n" + -"\t\tWind_Direction:long_name = \"Wind_Direction\" ;\n" + -"\t\tWind_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + -"\tfloat Wind_Speed(row) ;\n" + -"\t\tWind_Speed:_FillValue = -1.0E10f ;\n" + -"\t\tWind_Speed:standard_name = \"wind_speed\" ;\n" + -"\t\tWind_Speed:units = \"knots\" ;\n" + -"\tfloat Barometric_Pres(row) ;\n" + -"\t\tBarometric_Pres:_FillValue = -1.0E10f ;\n" + -"\t\tBarometric_Pres:long_name = \"Barometric_Pressure\" ;\n" + -"\t\tBarometric_Pres:units = \"millibars\" ;\n" + -"\tfloat Dry_Bulb_Temp(row) ;\n" + -"\t\tDry_Bulb_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tDry_Bulb_Temp:long_name = \"Dry_Bulb_Air_Temperature\" ;\n" + -"\t\tDry_Bulb_Temp:units = \"degree_C\" ;\n" + -"\tfloat Wet_Bulb_Temp(row) ;\n" + -"\t\tWet_Bulb_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tWet_Bulb_Temp:long_name = \"Wet_Bulb_Air_Temperature\" ;\n" + -"\t\tWet_Bulb_Temp:units = \"degree_C\" ;\n" + -"\tchar Weather_Condition(row, Weather_Condition_strlen) ;\n" + -"\t\tWeather_Condition:comment = \"Weather conditions at time of measurements\" ;\n" + -"\t\tWeather_Condition:long_name = \"Weather_Condition\" ;\n" + -"\tchar Cloud_Type(row, Cloud_Type_strlen) ;\n" + -"\t\tCloud_Type:long_name = \"Cloud_Type\" ;\n" + -"\t\tCloud_Type:units_wod = \"WMO 0500 or NODC 0053\" ;\n" + -"\tchar Cloud_Cover(row, Cloud_Cover_strlen) ;\n" + -"\t\tCloud_Cover:long_name = \"Cloud_Cover\" ;\n" + -"\t\tCloud_Cover:units_wod = \"WMO 2700 or NODC 0105\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tchar Recorder(row, Recorder_strlen) ;\n" + -"\t\tRecorder:comment = \"Device which recorded measurements\" ;\n" + -"\t\tRecorder:long_name = \"Recorder\" ;\n" + -"\t\tRecorder:units_wod = \"WMO code 4770\" ;\n" + -"\tchar depth_eq(row, depth_eq_strlen) ;\n" + -"\t\tdepth_eq:comment = \"which drop rate equation was used\" ;\n" + -"\t\tdepth_eq:long_name = \"depth_equation_used\" ;\n" + -"\tbyte Bottom_Hit(row) ;\n" + -"\t\tBottom_Hit:_FillValue = -9 ;\n" + -"\t\tBottom_Hit:comment = \"set to one if instrument hit bottom\" ;\n" + -"\t\tBottom_Hit:long_name = \"Bottom_Hit\" ;\n" + -"\tchar Visibility(row, Visibility_strlen) ;\n" + -"\t\tVisibility:long_name = \"Horizontal_visibility\" ;\n" + -"\t\tVisibility:units_wod = \"WMO Code 4300\" ;\n" + -"\tfloat Ref_Surf_Temp(row) ;\n" + -"\t\tRef_Surf_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tRef_Surf_Temp:comment = \"Reference_or_Sea_Surface_Temperature\" ;\n" + -"\t\tRef_Surf_Temp:units = \"degree_C\" ;\n" + -"\tchar needs_z_fix(row, needs_z_fix_strlen) ;\n" + -"\t\tneeds_z_fix:comment = \"instruction for fixing depths\" ;\n" + -"\t\tneeds_z_fix:long_name = \"z_fix_instructions\" ;\n" + -"\t\tneeds_z_fix:units_wod = \"WOD_code\" ;\n" + -"\tchar real_time(row, real_time_strlen) ;\n" + -"\t\treal_time:comment = \"timeliness and quality status\" ;\n" + -"\t\treal_time:long_name = \"real_time_data\" ;\n" + -"\tchar dbase_orig(row, dbase_orig_strlen) ;\n" + -"\t\tdbase_orig:comment = \"Database from which data were extracted\" ;\n" + -"\t\tdbase_orig:long_name = \"database_origin\" ;\n" + -"\tchar origflagset(row, origflagset_strlen) ;\n" + -"\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + -"\tbyte Temperature_WODprofileflag(row) ;\n" + -"\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Temperature_Scale(row, Temperature_Scale_strlen) ;\n" + -"\t\tTemperature_Scale:long_name = \"Scale upon which values were measured\" ;\n" + -"\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + -"\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + -"\tint Temperature_uncalibrated(row) ;\n" + -"\t\tTemperature_uncalibrated:_FillValue = -99999 ;\n" + -"\t\tTemperature_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + -"\tbyte Salinity_WODprofileflag(row) ;\n" + -"\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Salinity_Scale(row, Salinity_Scale_strlen) ;\n" + -"\t\tSalinity_Scale:long_name = \"Scale upon which values were measured\" ;\n" + -"\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + -"\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + -"\tint Salinity_uncalibrated(row) ;\n" + -"\t\tSalinity_uncalibrated:_FillValue = -99999 ;\n" + -"\t\tSalinity_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + -"\tbyte Oxygen_WODprofileflag(row) ;\n" + -"\t\tOxygen_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tOxygen_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tOxygen_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Oxygen_Instrument(row, Oxygen_Instrument_strlen) ;\n" + -"\t\tOxygen_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tOxygen_Instrument:long_name = \"Instrument\" ;\n" + -"\tchar Oxygen_Method(row, Oxygen_Method_strlen) ;\n" + -"\t\tOxygen_Method:comment = \"Method\" ;\n" + -"\tchar Oxygen_Original_units(row, Oxygen_Original_units_strlen) ;\n" + -"\t\tOxygen_Original_units:comment = \"Units originally used: coverted to standard units\" ;\n" + -"\tint Oxygen_uncalibrated(row) ;\n" + -"\t\tOxygen_uncalibrated:_FillValue = -99999 ;\n" + -"\t\tOxygen_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + -"\tchar Pressure_Instrument(row, Pressure_Instrument_strlen) ;\n" + -"\t\tPressure_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tPressure_Instrument:long_name = \"Instrument\" ;\n" + -"\tbyte Chlorophyll_WODprofileflag(row) ;\n" + -"\t\tChlorophyll_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tChlorophyll_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tChlorophyll_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Chlorophyll_Instrument(row, Chlorophyll_Instrument_strlen) ;\n" + -"\t\tChlorophyll_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tChlorophyll_Instrument:long_name = \"Instrument\" ;\n" + -"\tchar Chlorophyll_Original_units(row, Chlorophyll_Original_units_strlen) ;\n" + -"\t\tChlorophyll_Original_units:comment = \"Units originally used: coverted to standard units\" ;\n" + -"\tint Chlorophyll_uncalibrated(row) ;\n" + -"\t\tChlorophyll_uncalibrated:_FillValue = -99999 ;\n" + -"\t\tChlorophyll_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + -"\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + -"\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + -"\tfloat z(row) ;\n" + -"\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + -"\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"depth\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tbyte z_WODflag(row) ;\n" + -"\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + -"\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + -"\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_origflag(row) ;\n" + -"\t\tz_origflag:_FillValue = -9 ;\n" + -"\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + -"\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_sigfigs(row) ;\n" + -"\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\tbyte Temperature_sigfigs(row) ;\n" + -"\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + -"\tbyte Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tbyte Temperature_origflag(row) ;\n" + -"\t\tTemperature_origflag:_FillValue = -9 ;\n" + -"\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tfloat Salinity(row) ;\n" + -"\t\tSalinity:_FillValue = -1.0E10f ;\n" + -"\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag Salinity_origflag\" ;\n" + -"\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + -"\t\tSalinity:grid_mapping = \"crs\" ;\n" + -"\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + -"\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + -"\tbyte Salinity_sigfigs(row) ;\n" + -"\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + -"\tbyte Salinity_WODflag(row) ;\n" + -"\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tbyte Salinity_origflag(row) ;\n" + -"\t\tSalinity_origflag:_FillValue = -9 ;\n" + -"\t\tSalinity_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tSalinity_origflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tfloat Oxygen(row) ;\n" + -"\t\tOxygen:_FillValue = -1.0E10f ;\n" + -"\t\tOxygen:ancillary_variables = \"Oxygen_sigfigs Oxygen_WODflag Oxygen_WODprofileflag Oxygen_origflag\" ;\n" + -"\t\tOxygen:coordinates = \"time lat lon z\" ;\n" + -"\t\tOxygen:grid_mapping = \"crs\" ;\n" + -"\t\tOxygen:long_name = \"volume_fraction_of_oxygen_in_sea_water\" ;\n" + -"\t\tOxygen:standard_name = \"volume_fraction_of_oxygen_in_sea_water\" ;\n" + -"\t\tOxygen:units = \"ml/l\" ;\n" + -"\tbyte Oxygen_sigfigs(row) ;\n" + -"\t\tOxygen_sigfigs:long_name = \"volume_fraction_of_oxygen_in_sea_water significant_figures\" ;\n" + -"\tbyte Oxygen_WODflag(row) ;\n" + -"\t\tOxygen_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tOxygen_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tOxygen_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tOxygen_WODflag:standard_name = \"volume_fraction_of_oxygen_in_sea_water status_flag\" ;\n" + -"\tbyte Oxygen_origflag(row) ;\n" + -"\t\tOxygen_origflag:_FillValue = -9 ;\n" + -"\t\tOxygen_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tOxygen_origflag:standard_name = \"volume_fraction_of_oxygen_in_sea_water status_flag\" ;\n" + -"\tfloat Pressure(row) ;\n" + -"\t\tPressure:_FillValue = -1.0E10f ;\n" + -"\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag Pressure_origflag\" ;\n" + -"\t\tPressure:coordinates = \"time lat lon z\" ;\n" + -"\t\tPressure:grid_mapping = \"crs\" ;\n" + -"\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:units = \"dbar\" ;\n" + -"\tbyte Pressure_sigfigs(row) ;\n" + -"\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + -"\tbyte Pressure_origflag(row) ;\n" + -"\t\tPressure_origflag:_FillValue = -9 ;\n" + -"\t\tPressure_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tPressure_origflag:standard_name = \"sea_water_pressure status_flag\" ;\n" + -"\tfloat Chlorophyll(row) ;\n" + -"\t\tChlorophyll:_FillValue = -1.0E10f ;\n" + -"\t\tChlorophyll:ancillary_variables = \"Chlorophyll_sigfigs Chlorophyll_WODflag Chlorophyll_WODprofileflag Chlorophyll_origflag\" ;\n" + -"\t\tChlorophyll:coordinates = \"time lat lon z\" ;\n" + -"\t\tChlorophyll:grid_mapping = \"crs\" ;\n" + -"\t\tChlorophyll:long_name = \"mass_concentration_of_chlorophyll_in_sea_water\" ;\n" + -"\t\tChlorophyll:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water\" ;\n" + -"\t\tChlorophyll:units = \"ugram/l\" ;\n" + -"\tbyte Chlorophyll_sigfigs(row) ;\n" + -"\t\tChlorophyll_sigfigs:long_name = \"mass_concentration_of_chlorophyll_in_sea_water significant_figures\" ;\n" + -"\tbyte Chlorophyll_WODflag(row) ;\n" + -"\t\tChlorophyll_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tChlorophyll_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tChlorophyll_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tChlorophyll_WODflag:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water status_flag\" ;\n" + -"\tbyte Chlorophyll_origflag(row) ;\n" + -"\t\tChlorophyll_origflag:_FillValue = -9 ;\n" + -"\t\tChlorophyll_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tChlorophyll_origflag:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water status_flag\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, originators_station_identifier, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Institute, Cast_Tow_number, Orig_Stat_Num, Bottom_Depth, Cast_Duration, Cast_Direction, High_res_pair, Water_Color, Water_Transpar, Wave_Direction, Wave_Height, Sea_State, Wave_Period, Wind_Direction, Wind_Speed, Barometric_Pres, Dry_Bulb_Temp, Wet_Bulb_Temp, Weather_Condition, Cloud_Type, Cloud_Cover, dataset, Recorder, depth_eq, Bottom_Hit, Visibility, Ref_Surf_Temp, needs_z_fix, real_time, dbase_orig, origflagset, Temperature_WODprofileflag, Temperature_Scale, Temperature_Instrument, Temperature_uncalibrated, Salinity_WODprofileflag, Salinity_Scale, Salinity_Instrument, Salinity_uncalibrated, Oxygen_WODprofileflag, Oxygen_Instrument, Oxygen_Method, Oxygen_Original_units, Oxygen_uncalibrated, Pressure_Instrument, Chlorophyll_WODprofileflag, Chlorophyll_Instrument, Chlorophyll_Original_units, Chlorophyll_uncalibrated, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + -"\t\t:Conventions = \"CF-1.6\" ;\n" + -"\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + -"\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:crs_inverse_flattening = 298.25723f ;\n" + -"\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:crs_semi_major_axis = 6378137.0f ;\n" + -"\t\t:date_created = \"2018-03-24\" ;\n" + -"\t\t:date_modified = \"2018-03-24\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 89.986336f ;\n" + -"\t\t:geospatial_lat_min = -78.579f ;\n" + -"\t\t:geospatial_lat_resolution = \"point\" ;\n" + -"\t\t:geospatial_lon_max = 180.0f ;\n" + -"\t\t:geospatial_lon_min = -180.0f ;\n" + -"\t\t:geospatial_lon_resolution = \"point\" ;\n" + -"\t\t:geospatial_vertical_max = 6473.251f ;\n" + -"\t\t:geospatial_vertical_min = 0.0f ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"meters\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_ctd_2005.nc\" ;\n" + -"\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + -"\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + -"\t\t:project = \"World Ocean Database\" ;\n" + -"\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + -"\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + -"\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + -"\t\t:source = \"World Ocean Database\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + -"\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + -"\t\t:time_coverage_end = \"2005-12-31\" ;\n" + -"\t\t:time_coverage_start = \"2005-01-01\" ;\n" + -"\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + -"}\n" + -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Cast_Tow_number,Orig_Stat_Num,Bottom_Depth,Cast_Duration,Cast_Direction,High_res_pair,Water_Color,Water_Transpar,Wave_Direction,Wave_Height,Sea_State,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Scale,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Scale,Salinity_Instrument,Salinity_uncalibrated,Oxygen_WODprofileflag,Oxygen_Instrument,Oxygen_Method,Oxygen_Original_units,Oxygen_uncalibrated,Pressure_Instrument,Chlorophyll_WODprofileflag,Chlorophyll_Instrument,Chlorophyll_Original_units,Chlorophyll_uncalibrated,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + -"NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,0.0,0,-9,1,12.792,5,0,-9,34.702,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,1.0,0,-9,1,13.085,5,0,-9,34.573,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,2.0,0,-9,1,12.729,5,0,-9,34.562,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,3.0,0,-9,1,12.778,5,0,-9,34.585,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,7.0,0,-9,1,12.538,5,0,-9,34.629,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + varPATypes[v] = NcHelper.getElementPAType(var); //exception if trouble + nDims[v] = var.getRank(); + isCharArray[v] = nDims[v] > 0 && varPATypes[v] == PAType.CHAR; + if (varPATypes[v] == PAType.CHAR) + varPATypes[v] = PAType.STRING; //assume all char -> string + realNDims[v] = nDims[v] - (isCharArray[v]? 1 : 0); + varMissingValues[v] = vatts[v].getString("_FillValue"); + if (varMissingValues[v] == null) + varMissingValues[v] = vatts[v].getString("missing_value"); + if (varMissingValues[v] == null) + varMissingValues[v] = ""; - table.removeRows(0, 14843110 - 5); - results = table.dataToString(); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Cast_Tow_number,Orig_Stat_Num,Bottom_Depth,Cast_Duration,Cast_Direction,High_res_pair,Water_Color,Water_Transpar,Wave_Direction,Wave_Height,Sea_State,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Scale,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Scale,Salinity_Instrument,Salinity_uncalibrated,Oxygen_WODprofileflag,Oxygen_Instrument,Oxygen_Method,Oxygen_Original_units,Oxygen_uncalibrated,Pressure_Instrument,Chlorophyll_WODprofileflag,Chlorophyll_Instrument,Chlorophyll_Original_units,Chlorophyll_uncalibrated,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + -"NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,374.0,0,-9,3,8.695,4,0,-9,34.571,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,375.0,0,-9,3,8.692,4,0,-9,34.571,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,376.0,0,-9,3,8.686,4,0,-9,34.571,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,377.0,0,-9,3,8.682,4,0,-9,34.57,4,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + -"NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,378.0,0,-9,3,8.675,4,0,-9,34.57,4,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } + //profile_id? + String cfRole = vatts[v].getString("cf_role"); + if (cfRole != null) + cfRole = cfRole.toLowerCase(); + if ("profile_id".equals(cfRole)) { + if (debugMode) msg += + "\n>> found cf_role=profile_id for var=" + vNames[v]; + if (profileIDVarName != null) + throw new RuntimeException( + "Two variables have the attribute cf_role=profile_id: " + + profileIDVarName + " and " + vNames[v] + "."); + profileIDVarName = vNames[v]; + profileIDVarNumber = v; - //read outer and inner col with outer constraint -//from above -//"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Cast_Tow_number,Orig_Stat_Num,Bottom_Depth,Cast_Duration,Cast_Direction,High_res_pair,Water_Color,Water_Transpar,Wave_Direction,Wave_Height,Sea_State,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Scale,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Scale,Salinity_Instrument,Salinity_uncalibrated,Oxygen_WODprofileflag,Oxygen_Instrument,Oxygen_Method,Oxygen_Original_units,Oxygen_uncalibrated,Pressure_Instrument,Chlorophyll_WODprofileflag,Chlorophyll_Instrument,Chlorophyll_Original_units,Chlorophyll_uncalibrated,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + -//"NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,374.0,0,-9,3,8.695,4,0,-9,34.571,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + - fullName = dir + "wod_ctd_2005.nc"; - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"15077333"})); - results = table.dataToString(5); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"15077333,86196.95902776718,0.0,15.537,0\n" + -"15077333,86196.95902776718,1.0,15.544,0\n" + -"15077333,86196.95902776718,2.0,15.533,0\n" + -"15077333,86196.95902776718,3.0,15.516,0\n" + -"15077333,86196.95902776718,5.0,15.501,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(realNDims[v], 1, + "Unexpected number of dimensions for var=" + vNames[v]); + Dimension tOuterDim = var.getDimension(0); + String tOuterDimName = tOuterDim.getName(); + Test.ensureNotNull(tOuterDimName, + "Unexpected dimensionName=null for var=" + vNames[v]); + if (outerDimName == null) { + outerDimName = tOuterDimName; + outerDim = tOuterDim; + } else { + Test.ensureEqual(tOuterDimName, outerDimName, + "Unexpected dimension for var=" + vNames[v]); + } + } - //outer and inner constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"15077333", "15.533"})); - results = table.dataToString(); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"15077333,86196.95902776718,2.0,15.533,0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //gather sample_dimension atts and row_size PAs + //INVALID FILES: Primary_Investigator_rowsize doesn't have sample_dimension: so fix it + // See "numberofpis" below for additional, related fixes. + String sampleDimension = vNames[v].equals("Primary_Investigator_rowsize")? + "numberofpis" : + vatts[v].getString("sample_dimension"); + if (sampleDimension != null) { + if (debugMode) msg += + "\n>> found sample_dimension=" + sampleDimension + " for var=" + vNames[v]; + varHasSampleDimensionAtt[v] = true; + //get/verify outerDimName, e.g., casts + Test.ensureEqual(realNDims[v], 1, + "Unexpected number of dimensions for var=" + vNames[v]); + Dimension tOuterDim = var.getDimension(0); + String tOuterDimName = tOuterDim.getName(); + Test.ensureNotNull(tOuterDimName, + "Unexpected dimensionName=null for var=" + vNames[v]); + if (outerDimName == null) { + outerDimName = tOuterDimName; + outerDim = tOuterDim; + } else { + Test.ensureEqual(tOuterDimName, outerDimName, + "Unexpected dimension for var=" + vNames[v]); + } - //*** read all drb - fullName = dir + "wod_drb_2005.nc"; - if (doAll) { - table.readInvalidCRA(fullName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.toString(5); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 846878 ;\n" + -"\tcountry_strlen = 13 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\toriginators_cruise_identifier_strlen = 5 ;\n" + -"\tPlatform_strlen = 17 ;\n" + -"\tInstitute_strlen = 62 ;\n" + -"\tdataset_strlen = 13 ;\n" + -"\tOcean_Vehicle_strlen = 38 ;\n" + -"\tTemperature_Instrument_strlen = 50 ;\n" + -"\tSalinity_Instrument_strlen = 50 ;\n" + -"\tPrimary_Investigator_strlen = 14 ;\n" + -"\tPrimary_Investigator_VAR_strlen = 13 ;\n" + -"variables:\n" + -"\tchar country(row, country_strlen) ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\t\tGMT_time:units = \"hours\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:_FillValue = -99999 ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + -"\tchar Platform(row, Platform_strlen) ;\n" + -"\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + -"\t\tPlatform:long_name = \"Platform_name\" ;\n" + -"\tchar Institute(row, Institute_strlen) ;\n" + -"\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + -"\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + -"\tint Orig_Stat_Num(row) ;\n" + -"\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + -"\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + -"\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tchar Ocean_Vehicle(row, Ocean_Vehicle_strlen) ;\n" + -"\t\tOcean_Vehicle:comment = \"Ocean_vehicle\" ;\n" + -"\tbyte Temperature_WODprofileflag(row) ;\n" + -"\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + -"\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + -"\tbyte Salinity_WODprofileflag(row) ;\n" + -"\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + -"\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + -"\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + -"\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + -"\tfloat z(row) ;\n" + -"\t\tz:ancillary_variables = \"z_sigfigs z_WODflag\" ;\n" + -"\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"depth\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tbyte z_WODflag(row) ;\n" + -"\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + -"\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + -"\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_sigfigs(row) ;\n" + -"\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag\" ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\tbyte Temperature_sigfigs(row) ;\n" + -"\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + -"\tbyte Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tfloat Salinity(row) ;\n" + -"\t\tSalinity:_FillValue = -1.0E10f ;\n" + -"\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag\" ;\n" + -"\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + -"\t\tSalinity:grid_mapping = \"crs\" ;\n" + -"\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + -"\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + -"\tbyte Salinity_sigfigs(row) ;\n" + -"\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + -"\tbyte Salinity_WODflag(row) ;\n" + -"\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tfloat Pressure(row) ;\n" + -"\t\tPressure:_FillValue = -1.0E10f ;\n" + -"\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag\" ;\n" + -"\t\tPressure:coordinates = \"time lat lon z\" ;\n" + -"\t\tPressure:grid_mapping = \"crs\" ;\n" + -"\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:units = \"dbar\" ;\n" + -"\tbyte Pressure_sigfigs(row) ;\n" + -"\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Platform, Institute, Orig_Stat_Num, dataset, Ocean_Vehicle, Temperature_WODprofileflag, Temperature_Instrument, Salinity_WODprofileflag, Salinity_Instrument, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + -"\t\t:Conventions = \"CF-1.6\" ;\n" + -"\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + -"\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:crs_inverse_flattening = 298.25723f ;\n" + -"\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:crs_semi_major_axis = 6378137.0f ;\n" + -"\t\t:date_created = \"2018-03-25\" ;\n" + -"\t\t:date_modified = \"2018-03-25\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 89.625f ;\n" + -"\t\t:geospatial_lat_min = 76.025f ;\n" + -"\t\t:geospatial_lat_resolution = \"point\" ;\n" + -"\t\t:geospatial_lon_max = 180.0f ;\n" + -"\t\t:geospatial_lon_min = -180.0f ;\n" + -"\t\t:geospatial_lon_resolution = \"point\" ;\n" + -"\t\t:geospatial_vertical_max = 780.2189f ;\n" + -"\t\t:geospatial_vertical_min = 8.113341f ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"meters\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_drb_2005.nc\" ;\n" + -"\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + -"\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + -"\t\t:project = \"World Ocean Database\" ;\n" + -"\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + -"\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + -"\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + -"\t\t:source = \"World Ocean Database\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + -"\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + -"\t\t:time_coverage_end = \"2005-12-31\" ;\n" + -"\t\t:time_coverage_start = \"2005-01-01\" ;\n" + -"\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + -"}\n" + -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Institute,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Pressure,Pressure_sigfigs\n" + -"JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,25.348,0,6,-1.738,5,0,31.7095,6,0,-1.0E10,\n" + -"JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,50.694,0,6,-1.738,5,0,31.7078,6,0,-1.0E10,\n" + -"JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,81.104,0,6,-1.68,5,0,33.4528,6,0,-1.0E10,\n" + -"JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,121.808,0,7,-1.286,5,0,34.1678,6,0,-1.0E10,\n" + -"JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,203.193,0,7,0.432,4,0,34.7061,6,0,-1.0E10,\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //get rowSizes + rowSizesHM.put(sampleDimension, NcHelper.getPrimitiveArray(var)); + //no need to unpack rowSizes - table.removeRows(0, 846878 - 5); - results = table.dataToString(); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Institute,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Pressure,Pressure_sigfigs\n" + -"JAPAN,JP033440,,10909132,76.025,-11.6514,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504843054,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,106.845,0,7,-1.474,5,0,33.5642,6,0,-1.0E10,\n" + -"JAPAN,JP033440,,10909132,76.025,-11.6514,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504843054,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,148.032,0,7,-0.74,4,0,34.2258,6,0,-1.0E10,\n" + -"JAPAN,JP033440,,10909132,76.025,-11.6514,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504843054,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,194.357,0,7,-0.436,4,0,31.0866,6,0,-1.0E10,\n" + -"JAPAN,JP033441,,10909133,87.4024,-112.5225,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504846154,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,50.447,0,6,-1.6169,5,0,30.988,6,0,-1.0E10,\n" + -"JAPAN,JP033441,,10909133,87.4024,-112.5225,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504846154,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,121.051,0,7,-1.5004,5,0,34.0442,6,0,-1.0E10,\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } + //is it the largest sample_dimension (e.g., z_obs)? + Dimension dim = ncFile.findDimension(sampleDimension); + int tSize = dim.getLength(); + if (tSize > largestInnerDimSize) { + largestInnerDimSize = tSize; + largestInnerDimName = sampleDimension; + } + } + } + Test.ensureNotNull(profileIDVarName, + "No variable was found with a cf_role=profile_id attribute."); + Test.ensureTrue(outerDimName != null, + "No outer dimension (e.g., casts) found!"); + Test.ensureTrue(largestInnerDimSize > 0, + "No row_size variables with a sample_dimension attribute (e.g., z_obs) were found!"); + int outerDimSize = outerDim.getLength(); + //read the outerDim vars (including scalars and primary_investigator) + if (debugMode) msg += "\n>> read the outerDim"; + Table outerTable = new Table(); + StringArray cdm_profile_variables = new StringArray(); + for (int v = 0; v < nVars; v++) { + Variable var = varList.get(v); + Attributes vatt = vatts[v]; - //read outer and inner col with outer constraint - fullName = dir + "wod_drb_2005.nc"; - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"10909132"})); - results = table.dataToString(5); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"10909132,86196.95833331347,22.264,-1.818,0\n" + -"10909132,86196.95833331347,44.526,-1.816,0\n" + -"10909132,86196.95833331347,71.236,-1.798,0\n" + -"10909132,86196.95833331347,106.845,-1.474,0\n" + -"10909132,86196.95833331347,148.032,-0.74,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //if varName isn't in colNames, skip it + if (colNames.size() > 0 && colNames.indexOf(vNames[v]) < 0) + continue; - //outer and inner constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"10909132", "-1.798"})); - results = table.dataToString(); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"10909132,86196.95833331347,71.236,-1.798,0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //scalar? e.g., crs + if (realNDims[v] == 0) { + if (debugMode) msg += "\n>> found scalar var=" + vNames[v]; + if ("crs".equals(vNames[v])) { + //if crs, ignore value and promote to vatts to gatt + String[] vattNames = vatt.getNames(); + int vattSize = vattNames.length; + for (int va = 0; va < vattSize; va++) + gatts.add(vNames[v] + "_" + vattNames[va], vatt.get(vattNames[va])); + } else { + //add to outerTable + outerTable.addColumn(outerTable.nColumns(), vNames[v], + NcHelper.getPrimitiveArray(var), vatt); + outerTable.standardizeLastColumn(standardizeWhat); + } + continue; + } else if (realNDims[v] == 1) { + Dimension dim = var.getDimension(0); + String dimName = dim.getName(); - //*** read all gld - fullName = dir + "wod_gld_2005.nc"; - if (doAll) { - table.readInvalidCRA(fullName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.toString(5); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 3398337 ;\n" + -"\tcountry_strlen = 13 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\toriginators_cruise_identifier_strlen = 15 ;\n" + -"\tPlatform_strlen = 80 ;\n" + -"\tInstitute_strlen = 79 ;\n" + -"\tCast_Direction_strlen = 2 ;\n" + -"\tdataset_strlen = 6 ;\n" + -"\tOcean_Vehicle_strlen = 9 ;\n" + -"\torigflagset_strlen = 5 ;\n" + -"\tTemperature_Instrument_strlen = 70 ;\n" + -"\tSalinity_Instrument_strlen = 70 ;\n" + -"\tPrimary_Investigator_strlen = 33 ;\n" + -"\tPrimary_Investigator_VAR_strlen = 27 ;\n" + -"variables:\n" + -"\tchar country(row, country_strlen) ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\t\tGMT_time:units = \"hours\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:_FillValue = -99999 ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + -"\tchar Platform(row, Platform_strlen) ;\n" + -"\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + -"\t\tPlatform:long_name = \"Platform_name\" ;\n" + -"\tchar Institute(row, Institute_strlen) ;\n" + -"\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + -"\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + -"\tint Orig_Stat_Num(row) ;\n" + -"\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + -"\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + -"\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + -"\tchar Cast_Direction(row, Cast_Direction_strlen) ;\n" + -"\t\tCast_Direction:long_name = \"Cast_Direction\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tchar Ocean_Vehicle(row, Ocean_Vehicle_strlen) ;\n" + -"\t\tOcean_Vehicle:comment = \"Ocean_vehicle\" ;\n" + -"\tint WMO_ID(row) ;\n" + -"\t\tWMO_ID:_FillValue = -99999 ;\n" + -"\t\tWMO_ID:long_name = \"WMO_identification_code\" ;\n" + -"\tchar origflagset(row, origflagset_strlen) ;\n" + -"\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + -"\tbyte Temperature_WODprofileflag(row) ;\n" + -"\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + -"\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + -"\tbyte Salinity_WODprofileflag(row) ;\n" + -"\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + -"\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + -"\tbyte Chlorophyll_WODprofileflag(row) ;\n" + -"\t\tChlorophyll_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tChlorophyll_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tChlorophyll_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + -"\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + -"\tfloat z(row) ;\n" + -"\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + -"\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"depth\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tbyte z_WODflag(row) ;\n" + -"\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + -"\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + -"\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_origflag(row) ;\n" + -"\t\tz_origflag:_FillValue = -9 ;\n" + -"\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + -"\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_sigfigs(row) ;\n" + -"\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\tbyte Temperature_sigfigs(row) ;\n" + -"\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + -"\tbyte Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tbyte Temperature_origflag(row) ;\n" + -"\t\tTemperature_origflag:_FillValue = -9 ;\n" + -"\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tfloat Salinity(row) ;\n" + -"\t\tSalinity:_FillValue = -1.0E10f ;\n" + -"\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag Salinity_origflag\" ;\n" + -"\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + -"\t\tSalinity:grid_mapping = \"crs\" ;\n" + -"\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + -"\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + -"\tbyte Salinity_sigfigs(row) ;\n" + -"\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + -"\tbyte Salinity_WODflag(row) ;\n" + -"\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tbyte Salinity_origflag(row) ;\n" + -"\t\tSalinity_origflag:_FillValue = -9 ;\n" + -"\t\tSalinity_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tSalinity_origflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tfloat Pressure(row) ;\n" + -"\t\tPressure:_FillValue = -1.0E10f ;\n" + -"\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag Pressure_origflag\" ;\n" + -"\t\tPressure:coordinates = \"time lat lon z\" ;\n" + -"\t\tPressure:grid_mapping = \"crs\" ;\n" + -"\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:units = \"dbar\" ;\n" + -"\tbyte Pressure_sigfigs(row) ;\n" + -"\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + -"\tbyte Pressure_origflag(row) ;\n" + -"\t\tPressure_origflag:_FillValue = -9 ;\n" + -"\t\tPressure_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tPressure_origflag:standard_name = \"sea_water_pressure status_flag\" ;\n" + -"\tfloat Latitude(row) ;\n" + -"\t\tLatitude:_FillValue = -1.0E10f ;\n" + -"\t\tLatitude:ancillary_variables = \"Latitude_sigfigs Latitude_WODflag Latitude_WODprofileflag Latitude_origflag\" ;\n" + -"\t\tLatitude:coordinates = \"time lat lon z\" ;\n" + -"\t\tLatitude:grid_mapping = \"crs\" ;\n" + -"\t\tLatitude:long_name = \"latitude\" ;\n" + -"\t\tLatitude:standard_name = \"latitude\" ;\n" + -"\t\tLatitude:units = \"degrees_north\" ;\n" + -"\tbyte Latitude_sigfigs(row) ;\n" + -"\t\tLatitude_sigfigs:long_name = \"latitude significant_figures\" ;\n" + -"\tbyte Latitude_WODflag(row) ;\n" + -"\t\tLatitude_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tLatitude_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tLatitude_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tLatitude_WODflag:standard_name = \"latitude status_flag\" ;\n" + -"\tbyte Latitude_origflag(row) ;\n" + -"\t\tLatitude_origflag:_FillValue = -9 ;\n" + -"\t\tLatitude_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tLatitude_origflag:standard_name = \"latitude status_flag\" ;\n" + -"\tfloat Longitude(row) ;\n" + -"\t\tLongitude:_FillValue = -1.0E10f ;\n" + -"\t\tLongitude:ancillary_variables = \"Longitude_sigfigs Longitude_WODflag Longitude_WODprofileflag Longitude_origflag\" ;\n" + -"\t\tLongitude:coordinates = \"time lat lon z\" ;\n" + -"\t\tLongitude:grid_mapping = \"crs\" ;\n" + -"\t\tLongitude:long_name = \"longitude\" ;\n" + -"\t\tLongitude:standard_name = \"longitude\" ;\n" + -"\t\tLongitude:units = \"degrees_east\" ;\n" + -"\tbyte Longitude_sigfigs(row) ;\n" + -"\t\tLongitude_sigfigs:long_name = \"longitude significant_figures\" ;\n" + -"\tbyte Longitude_WODflag(row) ;\n" + -"\t\tLongitude_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tLongitude_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tLongitude_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tLongitude_WODflag:standard_name = \"longitude status_flag\" ;\n" + -"\tbyte Longitude_origflag(row) ;\n" + -"\t\tLongitude_origflag:_FillValue = -9 ;\n" + -"\t\tLongitude_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tLongitude_origflag:standard_name = \"longitude status_flag\" ;\n" + -"\tfloat JulianDay(row) ;\n" + -"\t\tJulianDay:_FillValue = -1.0E10f ;\n" + -"\t\tJulianDay:ancillary_variables = \"JulianDay_sigfigs JulianDay_WODflag JulianDay_WODprofileflag JulianDay_origflag\" ;\n" + -"\t\tJulianDay:coordinates = \"time lat lon z\" ;\n" + -"\t\tJulianDay:grid_mapping = \"crs\" ;\n" + -"\t\tJulianDay:long_name = \"JulianDay\" ;\n" + -"\tbyte JulianDay_sigfigs(row) ;\n" + -"\t\tJulianDay_sigfigs:long_name = \"JulianDay significant_figures\" ;\n" + -"\tbyte JulianDay_WODflag(row) ;\n" + -"\t\tJulianDay_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tJulianDay_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tJulianDay_WODflag:long_name = \"JulianDay st\" ;\n" + -"\tbyte JulianDay_origflag(row) ;\n" + -"\t\tJulianDay_origflag:_FillValue = -9 ;\n" + -"\t\tJulianDay_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tJulianDay_origflag:long_name = \"JulianDay st\" ;\n" + -"\tfloat Chlorophyll(row) ;\n" + -"\t\tChlorophyll:_FillValue = -1.0E10f ;\n" + -"\t\tChlorophyll:ancillary_variables = \"Chlorophyll_sigfigs Chlorophyll_WODflag Chlorophyll_WODprofileflag Chlorophyll_origflag\" ;\n" + -"\t\tChlorophyll:coordinates = \"time lat lon z\" ;\n" + -"\t\tChlorophyll:grid_mapping = \"crs\" ;\n" + -"\t\tChlorophyll:long_name = \"mass_concentration_of_chlorophyll_in_sea_water\" ;\n" + -"\t\tChlorophyll:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water\" ;\n" + -"\t\tChlorophyll:units = \"ugram/l\" ;\n" + -"\tbyte Chlorophyll_sigfigs(row) ;\n" + -"\t\tChlorophyll_sigfigs:long_name = \"mass_concentration_of_chlorophyll_in_sea_water significant_figures\" ;\n" + -"\tbyte Chlorophyll_WODflag(row) ;\n" + -"\t\tChlorophyll_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tChlorophyll_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tChlorophyll_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tChlorophyll_WODflag:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water status_flag\" ;\n" + -"\tbyte Chlorophyll_origflag(row) ;\n" + -"\t\tChlorophyll_origflag:_FillValue = -9 ;\n" + -"\t\tChlorophyll_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tChlorophyll_origflag:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water status_flag\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Platform, Institute, Orig_Stat_Num, Cast_Direction, dataset, Ocean_Vehicle, WMO_ID, origflagset, Temperature_WODprofileflag, Temperature_Instrument, Salinity_WODprofileflag, Salinity_Instrument, Chlorophyll_WODprofileflag, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + -"\t\t:Conventions = \"CF-1.6\" ;\n" + -"\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + -"\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:crs_inverse_flattening = 298.25723f ;\n" + -"\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:crs_semi_major_axis = 6378137.0f ;\n" + -"\t\t:date_created = \"2018-03-25\" ;\n" + -"\t\t:date_modified = \"2018-03-25\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 63.9972f ;\n" + -"\t\t:geospatial_lat_min = 22.481083f ;\n" + -"\t\t:geospatial_lat_resolution = \"point\" ;\n" + -"\t\t:geospatial_lon_max = 16.887665f ;\n" + -"\t\t:geospatial_lon_min = -158.30486f ;\n" + -"\t\t:geospatial_lon_resolution = \"point\" ;\n" + -"\t\t:geospatial_vertical_max = 1026.7106f ;\n" + -"\t\t:geospatial_vertical_min = -0.29778513f ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"meters\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_gld_2005.nc\" ;\n" + -"\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + -"\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + -"\t\t:project = \"World Ocean Database\" ;\n" + -"\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + -"\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + -"\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + -"\t\t:source = \"World Ocean Database\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + -"\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + -"\t\t:time_coverage_end = \"2005-12-31\" ;\n" + -"\t\t:time_coverage_start = \"2005-01-01\" ;\n" + -"\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + -"}\n" + -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Institute,Orig_Stat_Num,Cast_Direction,dataset,Ocean_Vehicle,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,Chlorophyll_WODprofileflag,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Latitude,Latitude_sigfigs,Latitude_WODflag,Latitude_origflag,Longitude,Longitude_sigfigs,Longitude_WODflag,Longitude_origflag,JulianDay,JulianDay_sigfigs,JulianDay_WODflag,JulianDay_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + -"UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,0.89629334,0,1,2,3.2594981,4,0,1,-1.0E10,-127,-127,-9,0.9058805,3,1,56.54242,7,0,1,-55.34162,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + -"UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,0.8763757,0,1,2,3.5394983,4,0,1,-1.0E10,-127,-127,-9,0.8857498,3,1,56.542416,7,0,1,-55.34162,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + -"UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,1.1153866,0,1,3,3.6717756,4,0,1,-1.0E10,-127,-127,-9,1.1273179,4,1,56.542416,7,0,1,-55.34162,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + -"UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,1.4639436,0,1,3,3.678846,4,0,1,34.7831,5,0,1,1.4796048,4,1,56.542416,7,0,1,-55.34162,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + -"UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,1.7925826,0,1,3,3.6769755,4,0,1,34.789787,5,0,1,1.811761,4,1,56.542416,7,0,1,-55.341618,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //FIX flaws related to Primary_Investigator / numberofpis. + //Treat numberofpis differently than other dimNames: + // convert PI's for each cast into /-separated string since some have internal ';'. + if (dimName.equals("numberofpis")) { + PrimitiveArray rowSizesPA = rowSizesHM.get(dimName); + Test.ensureNotNull(rowSizesPA, + "No row_size info for dim=" + dimName + " for var=" + vNames[v]); + PrimitiveArray varPA = NcHelper.getPrimitiveArray(var); + StringArray newPA = new StringArray(outerDimSize, false); + PrimitiveArray tSubset = null; + int thisPo = 0; + for (int outer = 0; outer < outerDimSize; outer++) { + int thisChunkSize = rowSizesPA.getInt(outer); + tSubset = varPA.subset(tSubset, thisPo, 1, thisPo + thisChunkSize - 1); + //usually just 0 or 1 pi's, gld has more + String tts = String2.toSVString(tSubset.toStringArray(), "/", false); + newPA.add(tts); + thisPo += thisChunkSize; + } + //add to outerTable + outerTable.addColumn(outerTable.nColumns(), vNames[v], + newPA, vatt); + outerTable.standardizeLastColumn(standardizeWhat); + continue; + } - table.removeRows(0, 3398337 - 5); - results = table.dataToString(); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Institute,Orig_Stat_Num,Cast_Direction,dataset,Ocean_Vehicle,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,Chlorophyll_WODprofileflag,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Latitude,Latitude_sigfigs,Latitude_WODflag,Latitude_origflag,Longitude,Longitude_sigfigs,Longitude_WODflag,Longitude_origflag,JulianDay,JulianDay_sigfigs,JulianDay_WODflag,JulianDay_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + -"UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,976.9241,0,1,5,3.5159547,4,0,1,34.39147,5,0,1,989.7248,6,1,47.007023,7,0,1,-127.15596,8,0,1,365.91602,8,0,1,-1.0E10,,,-9\n" + -"UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,980.71027,0,1,5,3.512552,4,0,1,34.39222,5,0,1,993.56976,6,1,47.007023,7,0,1,-127.15583,8,0,1,365.91406,8,0,1,-1.0E10,,,-9\n" + -"UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,984.67487,0,1,5,3.5072713,4,0,1,-1.0E10,-127,-127,-9,997.5959,6,1,47.00701,7,0,1,-127.15576,8,0,1,365.91406,8,0,1,-1.0E10,,,-9\n" + -"UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,987.4005,0,1,5,3.5013642,4,0,1,-1.0E10,-127,-127,-9,1000.36383,7,1,47.006985,7,0,1,-127.15577,8,0,1,365.9121,8,0,1,-1.0E10,,,-9\n" + -"UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,987.97534,0,1,5,3.5010133,4,0,1,-1.0E10,-127,-127,-9,1000.94763,7,1,47.00696,7,0,1,-127.15578,8,0,1,365.9121,8,0,1,-1.0E10,,,-9\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } + if (!outerDimName.equals(dimName)) + continue; + if (varHasSampleDimensionAtt[v]) + //it's a row_size var with a sample_dimension att + continue; + //add to outerTable + outerTable.addColumn(outerTable.nColumns(), vNames[v], + NcHelper.getPrimitiveArray(var), vatt); //char -> String + outerTable.standardizeLastColumn(standardizeWhat); + } + } + //expand scalars to same number of rows as outerDim + ensureColumnsAreSameSize_LastValue(); - //read outer and inner col with outer constraint - fullName = dir + "wod_gld_2005.nc"; - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"17842328"})); - results = table.dataToString(5); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"17842328,86196.91210919619,0.8763757,10.643924,0\n" + -"17842328,86196.91210919619,1.1950568,10.658873,0\n" + -"17842328,86196.91210919619,2.0614686,10.660649,0\n" + -"17842328,86196.91210919619,2.8780832,10.663277,0\n" + -"17842328,86196.91210919619,3.6449013,10.660924,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //set cdm_profile_variables + String cpv = outerTable.getColumnNamesCSSVString(); + cpv = String2.replaceAll(cpv, ", lat,", ", latitude,"); + cpv = String2.replaceAll(cpv, ", lon,", ", longitude,"); + cpv = String2.replaceAll(cpv, ", z,", ", depth,"); + //the numeric time variable is called time + if (cpv.length() > 0) + gatts.set("cdm_profile_variables", cpv); - //outer and inner constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"17842328", "10.660649"})); - results = table.dataToString(); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"17842328,86196.91210919619,2.0614686,10.660649,0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //apply constraints, but keep all rows + if (debugMode) String2.log(">> apply constraints"); + BitSet keepOuter = new BitSet(); + keepOuter.set(0, outerDimSize); + if (outerTable.nRows() > 0 && + outerTable.tryToApplyConstraints(profileIDVarNumber, + conNames, conOps, conVals, keepOuter) == 0) { + //No matching data is not an error and returns an empty table (0 rows and 0 columns). + if (reallyVerbose) msg += " finished. " + + MustBe.THERE_IS_NO_DATA + + " Just outer table. time" + (System.currentTimeMillis() - time) + "ms"; + return; + } + boolean keepAllOuter = keepOuter.nextClearBit(0) == -1; + //are we done? + if (debugMode) msg += "\n>> are we done because just outer columns?"; + if (colNames.size() > 0) { + //are all colNames in outerTable? + boolean done = true; + for (int col = 0; col < colNames.size(); col++) { + if (outerTable.findColumnNumber(colNames.get(col)) < 0) { + done = false; + break; + } + } + if (done) { + ncFile.close(); + outerTable.justKeep(keepOuter); + outerTable.reorderColumns(colNames, true); + outerTable.decodeCharsAndStrings(); + outerTable.convertToUnsignedPAs(); - //*** read all mrb - fullName = dir + "wod_mrb_2005.nc"; - if (doAll) { - table.readInvalidCRA(fullName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.toString(5); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 1184438 ;\n" + -"\tcountry_strlen = 13 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\toriginators_cruise_identifier_strlen = 5 ;\n" + -"\tProject_strlen = 80 ;\n" + -"\tPlatform_strlen = 14 ;\n" + -"\tInstitute_strlen = 62 ;\n" + -"\tWind_Direction_strlen = 25 ;\n" + -"\tdataset_strlen = 11 ;\n" + -"\treal_time_strlen = 14 ;\n" + -"\tdbase_orig_strlen = 24 ;\n" + -"\torigflagset_strlen = 24 ;\n" + -"\tTemperature_Instrument_strlen = 52 ;\n" + -"\tSalinity_Instrument_strlen = 52 ;\n" + -"variables:\n" + -"\tchar country(row, country_strlen) ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\t\tGMT_time:units = \"hours\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:_FillValue = -99999 ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + -"\tchar Project(row, Project_strlen) ;\n" + -"\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + -"\t\tProject:long_name = \"Project_name\" ;\n" + -"\tchar Platform(row, Platform_strlen) ;\n" + -"\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + -"\t\tPlatform:long_name = \"Platform_name\" ;\n" + -"\tchar Institute(row, Institute_strlen) ;\n" + -"\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + -"\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + -"\tint Orig_Stat_Num(row) ;\n" + -"\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + -"\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + -"\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + -"\tchar Wind_Direction(row, Wind_Direction_strlen) ;\n" + -"\t\tWind_Direction:long_name = \"Wind_Direction\" ;\n" + -"\t\tWind_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + -"\tfloat Wind_Speed(row) ;\n" + -"\t\tWind_Speed:_FillValue = -1.0E10f ;\n" + -"\t\tWind_Speed:standard_name = \"wind_speed\" ;\n" + -"\t\tWind_Speed:units = \"knots\" ;\n" + -"\tfloat Dry_Bulb_Temp(row) ;\n" + -"\t\tDry_Bulb_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tDry_Bulb_Temp:long_name = \"Dry_Bulb_Air_Temperature\" ;\n" + -"\t\tDry_Bulb_Temp:units = \"degree_C\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tchar real_time(row, real_time_strlen) ;\n" + -"\t\treal_time:comment = \"timeliness and quality status\" ;\n" + -"\t\treal_time:long_name = \"real_time_data\" ;\n" + -"\tchar dbase_orig(row, dbase_orig_strlen) ;\n" + -"\t\tdbase_orig:comment = \"Database from which data were extracted\" ;\n" + -"\t\tdbase_orig:long_name = \"database_origin\" ;\n" + -"\tint WMO_ID(row) ;\n" + -"\t\tWMO_ID:_FillValue = -99999 ;\n" + -"\t\tWMO_ID:long_name = \"WMO_identification_code\" ;\n" + -"\tchar origflagset(row, origflagset_strlen) ;\n" + -"\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + -"\tbyte Temperature_WODprofileflag(row) ;\n" + -"\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + -"\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + -"\tbyte Salinity_WODprofileflag(row) ;\n" + -"\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + -"\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + -"\tfloat z(row) ;\n" + -"\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + -"\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"depth\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tbyte z_WODflag(row) ;\n" + -"\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + -"\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + -"\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_origflag(row) ;\n" + -"\t\tz_origflag:_FillValue = -9 ;\n" + -"\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + -"\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_sigfigs(row) ;\n" + -"\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\tbyte Temperature_sigfigs(row) ;\n" + -"\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + -"\tbyte Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tbyte Temperature_origflag(row) ;\n" + -"\t\tTemperature_origflag:_FillValue = -9 ;\n" + -"\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tfloat Salinity(row) ;\n" + -"\t\tSalinity:_FillValue = -1.0E10f ;\n" + -"\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag Salinity_origflag\" ;\n" + -"\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + -"\t\tSalinity:grid_mapping = \"crs\" ;\n" + -"\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + -"\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + -"\tbyte Salinity_sigfigs(row) ;\n" + -"\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + -"\tbyte Salinity_WODflag(row) ;\n" + -"\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tbyte Salinity_origflag(row) ;\n" + -"\t\tSalinity_origflag:_FillValue = -9 ;\n" + -"\t\tSalinity_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tSalinity_origflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Institute, Orig_Stat_Num, Wind_Direction, Wind_Speed, Dry_Bulb_Temp, dataset, real_time, dbase_orig, WMO_ID, origflagset, Temperature_WODprofileflag, Temperature_Instrument, Salinity_WODprofileflag, Salinity_Instrument\" ;\n" + -"\t\t:Conventions = \"CF-1.6\" ;\n" + -"\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + -"\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:crs_inverse_flattening = 298.25723f ;\n" + -"\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:crs_semi_major_axis = 6378137.0f ;\n" + -"\t\t:date_created = \"2018-03-24\" ;\n" + -"\t\t:date_modified = \"2018-03-24\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 80.5578f ;\n" + -"\t\t:geospatial_lat_min = -18.89f ;\n" + -"\t\t:geospatial_lat_resolution = \"point\" ;\n" + -"\t\t:geospatial_lon_max = -0.02999878f ;\n" + -"\t\t:geospatial_lon_min = 80.48f ;\n" + -"\t\t:geospatial_lon_resolution = \"point\" ;\n" + -"\t\t:geospatial_vertical_max = 4309.0f ;\n" + -"\t\t:geospatial_vertical_min = 1.0f ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"meters\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_mrb_2005.nc\" ;\n" + -"\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + -"\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + -"\t\t:project = \"World Ocean Database\" ;\n" + -"\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + -"\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + -"\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + -"\t\t:source = \"World Ocean Database\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + -"\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + -"\t\t:time_coverage_end = \"2005-12-31\" ;\n" + -"\t\t:time_coverage_start = \"2005-01-01\" ;\n" + -"\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + -"}\n" + -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Wind_Direction,Wind_Speed,Dry_Bulb_Temp,dataset,real_time,dbase_orig,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag\n" + -"UNITED STATES,US029953,,12631835,80.5578,-68.9076,85832.0,20050101,0.0,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",28.294939,0,-9,5,-1.782,4,0,-9,32.662,5,0,-9\n" + -"UNITED STATES,US029953,,12631835,80.5578,-68.9076,85832.0,20050101,0.0,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",77.65329,0,-9,5,-1.755,4,0,-9,32.706,5,0,-9\n" + -"UNITED STATES,US029953,,12631835,80.5578,-68.9076,85832.0,20050101,0.0,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",126.99971,0,-9,6,-1.235,4,0,-9,33.404,5,0,-9\n" + -"UNITED STATES,US029953,,12631835,80.5578,-68.9076,85832.0,20050101,0.0,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",196.10425,0,-9,6,-0.396,3,0,-9,34.347,5,0,-9\n" + -"UNITED STATES,US029953,,12631836,80.5578,-68.9076,85832.01000976562,20050101,0.24023438,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",27.602451,0,-9,5,-1.782,4,0,-9,32.66,5,0,-9\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //copy outerTable to this table + for (int col = 0; col < outerTable.nColumns(); col++) + addColumn(col, outerTable.getColumnName(col), + outerTable.getColumn(col), outerTable.columnAttributes(col)); - table.removeRows(0, 1184438 - 5); - results = table.dataToString(); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Wind_Direction,Wind_Speed,Dry_Bulb_Temp,dataset,real_time,dbase_orig,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag\n" + -"BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,100.0,0,2,3,26.48,5,0,1,-1.0E10,-127,-127,-9\n" + -"BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,140.0,0,2,3,15.74,5,0,2,-1.0E10,-127,-127,-9\n" + -"BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,180.0,0,2,3,13.85,5,0,1,-1.0E10,-127,-127,-9\n" + -"BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,300.0,0,2,3,11.67,5,0,1,-1.0E10,-127,-127,-9\n" + -"BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,500.0,0,2,3,8.16,4,0,1,-1.0E10,-127,-127,-9\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } + if (reallyVerbose) msg += + " finished. Just outer table. nRows=" + + nRows() + " nCols=" + nColumns() + + " time=" + (System.currentTimeMillis() - time) + "ms"; + return; + } + } + + //find nActiveInnerRows and largestLargestChunkSize + PrimitiveArray largestRowSizes = rowSizesHM.get(largestInnerDimName); + int checkNTotalInnerRows = 0; + int nActiveInnerRows = 0; + int largestLargestChunkSize = 0; + for (int outer = 0; outer < outerDimSize; outer++) { + int tChunkSize = largestRowSizes.getInt(outer); + checkNTotalInnerRows += tChunkSize; + if (!keepOuter.get(outer)) //skip this outer + continue; + nActiveInnerRows += tChunkSize; + largestLargestChunkSize = Math.max(largestLargestChunkSize, tChunkSize); + } + if (checkNTotalInnerRows != largestInnerDimSize) + throw new RuntimeException("Invalid file: The sum of the row sizes for " + + largestInnerDimName + " (" + checkNTotalInnerRows + ") doesn't equal the size of dimension=" + + largestInnerDimName + " (" + largestInnerDimSize + ")."); + //expand the kept outerTable rows in this table + for (int col = 0; col < outerTable.nColumns(); col++) { + String tName = outerTable.getColumnName(col); - //read outer and inner col with outer constraint - fullName = dir + "wod_mrb_2005.nc"; - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"10688847"})); - results = table.dataToString(5); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"10688847,86196.0,1.0,27.98,0\n" + -"10688847,86196.0,20.0,27.98,0\n" + -"10688847,86196.0,40.0,27.99,0\n" + -"10688847,86196.0,60.0,28.0,0\n" + -"10688847,86196.0,80.0,27.97,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //if varName isn't in colNames, skip it + if (colNames.size() > 0 && colNames.indexOf(tName) < 0) + continue; + if (debugMode) msg += "\n>> expand outerTable into this table, var=" + tName; - //outer and inner constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"10688847", "27.99"})); - results = table.dataToString(); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"10688847,86196.0,40.0,27.99,0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + PrimitiveArray otpa = outerTable.getColumn(col); + PrimitiveArray newPA = PrimitiveArray.factory(otpa.elementType(), + nActiveInnerRows, false); + addColumn(nColumns(), tName, newPA, outerTable.columnAttributes(col)); + for (int outer = 0; outer < outerDimSize; outer++) { + if (!keepOuter.get(outer)) { + //skip this outer, e.g., this cast + continue; + } - //*** read all osd -- THIS FILE FAILS BECAUSE IT HAS DataType=Structure! - //fullName = dir + "wod_osd_2005.nc"; - //table.readInvalidCRA(fullName, null, null, null, null); - //results = table.toString(5); - //expected = "zztop\n"; - //Test.ensureEqual(results, expected, "results=\n" + results); + //addN of that value + newPA.addNStrings(largestRowSizes.getInt(outer), otpa.getString(outer)); + } + } + outerTable = null; //encourage gc - //table.removeRows(0, 146042 - 5); - //results = table.dataToString(); - //expected = "zztop\n"; - //Test.ensureEqual(results, expected, "results=\n" + results); + //make the innerTable in this table + for (int v = 0; v < nVars; v++) { + Variable var = varList.get(v); + Attributes vatt = vatts[v]; + //if varName isn't in colNames, skip it + if (colNames.size() > 0 && colNames.indexOf(vNames[v]) < 0) + continue; - //*** read all - fullName = dir + "wod_pfl_2005.nc"; - if (doAll) { - table.readInvalidCRA(fullName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.toString(5); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 4420114 ;\n" + -"\tcountry_strlen = 18 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\toriginators_cruise_identifier_strlen = 8 ;\n" + -"\tProject_strlen = 74 ;\n" + -"\tPlatform_strlen = 15 ;\n" + -"\tInstitute_strlen = 79 ;\n" + -"\tCast_Direction_strlen = 22 ;\n" + -"\tdataset_strlen = 15 ;\n" + -"\tRecorder_strlen = 44 ;\n" + -"\treal_time_strlen = 36 ;\n" + -"\tOcean_Vehicle_strlen = 68 ;\n" + -"\tdbase_orig_strlen = 22 ;\n" + -"\torigflagset_strlen = 21 ;\n" + -"\tTemperature_Instrument_strlen = 40 ;\n" + -"\tSalinity_Instrument_strlen = 40 ;\n" + -"\tSalinity_Method_strlen = 0 ;\n" + -"\tOxygen_Original_units_strlen = 7 ;\n" + -"\tPrimary_Investigator_strlen = 120 ;\n" + -"\tPrimary_Investigator_VAR_strlen = 97 ;\n" + -"variables:\n" + -"\tchar country(row, country_strlen) ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\t\tGMT_time:units = \"hours\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:_FillValue = -99999 ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + -"\tchar Project(row, Project_strlen) ;\n" + -"\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + -"\t\tProject:long_name = \"Project_name\" ;\n" + -"\tchar Platform(row, Platform_strlen) ;\n" + -"\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + -"\t\tPlatform:long_name = \"Platform_name\" ;\n" + -"\tchar Institute(row, Institute_strlen) ;\n" + -"\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + -"\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + -"\tint Orig_Stat_Num(row) ;\n" + -"\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + -"\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + -"\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + -"\tchar Cast_Direction(row, Cast_Direction_strlen) ;\n" + -"\t\tCast_Direction:long_name = \"Cast_Direction\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tchar Recorder(row, Recorder_strlen) ;\n" + -"\t\tRecorder:comment = \"Device which recorded measurements\" ;\n" + -"\t\tRecorder:long_name = \"Recorder\" ;\n" + -"\t\tRecorder:units_wod = \"WMO code 4770\" ;\n" + -"\tchar real_time(row, real_time_strlen) ;\n" + -"\t\treal_time:comment = \"timeliness and quality status\" ;\n" + -"\t\treal_time:long_name = \"real_time_data\" ;\n" + -"\tchar Ocean_Vehicle(row, Ocean_Vehicle_strlen) ;\n" + -"\t\tOcean_Vehicle:comment = \"Ocean_vehicle\" ;\n" + -"\tchar dbase_orig(row, dbase_orig_strlen) ;\n" + -"\t\tdbase_orig:comment = \"Database from which data were extracted\" ;\n" + -"\t\tdbase_orig:long_name = \"database_origin\" ;\n" + -"\tint WMO_ID(row) ;\n" + -"\t\tWMO_ID:_FillValue = -99999 ;\n" + -"\t\tWMO_ID:long_name = \"WMO_identification_code\" ;\n" + -"\tchar origflagset(row, origflagset_strlen) ;\n" + -"\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + -"\tbyte Temperature_WODprofileflag(row) ;\n" + -"\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + -"\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + -"\tfloat Temperature_Adjustment(row) ;\n" + -"\t\tTemperature_Adjustment:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature_Adjustment:comment = \"Adjustment made to original measurement values and measurement units\" ;\n" + -"\tbyte Salinity_WODprofileflag(row) ;\n" + -"\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + -"\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + -"\tchar Salinity_Method(row, Salinity_Method_strlen) ;\n" + -"\t\tSalinity_Method:comment = \"Method\" ;\n" + -"\tfloat Salinity_Adjustment(row) ;\n" + -"\t\tSalinity_Adjustment:_FillValue = -1.0E10f ;\n" + -"\t\tSalinity_Adjustment:comment = \"Adjustment made to original measurement values and measurement units\" ;\n" + -"\tint Salinity_(row) ;\n" + -"\t\tSalinity_:_FillValue = -99999 ;\n" + -"\tfloat Pressure_Adjustment(row) ;\n" + -"\t\tPressure_Adjustment:_FillValue = -1.0E10f ;\n" + -"\t\tPressure_Adjustment:comment = \"Adjustment made to original measurement values and measurement units\" ;\n" + -"\tbyte Oxygen_WODprofileflag(row) ;\n" + -"\t\tOxygen_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tOxygen_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tOxygen_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Oxygen_Original_units(row, Oxygen_Original_units_strlen) ;\n" + -"\t\tOxygen_Original_units:comment = \"Units originally used: coverted to standard units\" ;\n" + -"\tfloat Oxygen_Adjustment(row) ;\n" + -"\t\tOxygen_Adjustment:_FillValue = -1.0E10f ;\n" + -"\t\tOxygen_Adjustment:comment = \"Adjustment made to original measurement values and measurement units\" ;\n" + -"\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + -"\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + -"\tfloat z(row) ;\n" + -"\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + -"\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"depth\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tbyte z_WODflag(row) ;\n" + -"\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + -"\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + -"\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_origflag(row) ;\n" + -"\t\tz_origflag:_FillValue = -9 ;\n" + -"\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + -"\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_sigfigs(row) ;\n" + -"\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\tbyte Temperature_sigfigs(row) ;\n" + -"\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + -"\tbyte Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tbyte Temperature_origflag(row) ;\n" + -"\t\tTemperature_origflag:_FillValue = -9 ;\n" + -"\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tfloat Salinity(row) ;\n" + -"\t\tSalinity:_FillValue = -1.0E10f ;\n" + -"\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag Salinity_origflag\" ;\n" + -"\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + -"\t\tSalinity:grid_mapping = \"crs\" ;\n" + -"\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + -"\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + -"\tbyte Salinity_sigfigs(row) ;\n" + -"\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + -"\tbyte Salinity_WODflag(row) ;\n" + -"\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tbyte Salinity_origflag(row) ;\n" + -"\t\tSalinity_origflag:_FillValue = -9 ;\n" + -"\t\tSalinity_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tSalinity_origflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tfloat Pressure(row) ;\n" + -"\t\tPressure:_FillValue = -1.0E10f ;\n" + -"\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag Pressure_origflag\" ;\n" + -"\t\tPressure:coordinates = \"time lat lon z\" ;\n" + -"\t\tPressure:grid_mapping = \"crs\" ;\n" + -"\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:units = \"dbar\" ;\n" + -"\tbyte Pressure_sigfigs(row) ;\n" + -"\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + -"\tbyte Pressure_origflag(row) ;\n" + -"\t\tPressure_origflag:_FillValue = -9 ;\n" + -"\t\tPressure_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tPressure_origflag:standard_name = \"sea_water_pressure status_flag\" ;\n" + -"\tfloat Oxygen(row) ;\n" + -"\t\tOxygen:_FillValue = -1.0E10f ;\n" + -"\t\tOxygen:ancillary_variables = \"Oxygen_sigfigs Oxygen_WODflag Oxygen_WODprofileflag Oxygen_origflag\" ;\n" + -"\t\tOxygen:coordinates = \"time lat lon z\" ;\n" + -"\t\tOxygen:grid_mapping = \"crs\" ;\n" + -"\t\tOxygen:long_name = \"volume_fraction_of_oxygen_in_sea_water\" ;\n" + -"\t\tOxygen:standard_name = \"volume_fraction_of_oxygen_in_sea_water\" ;\n" + -"\t\tOxygen:units = \"ml/l\" ;\n" + -"\tbyte Oxygen_sigfigs(row) ;\n" + -"\t\tOxygen_sigfigs:long_name = \"volume_fraction_of_oxygen_in_sea_water significant_figures\" ;\n" + -"\tbyte Oxygen_WODflag(row) ;\n" + -"\t\tOxygen_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tOxygen_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tOxygen_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tOxygen_WODflag:standard_name = \"volume_fraction_of_oxygen_in_sea_water status_flag\" ;\n" + -"\tbyte Oxygen_origflag(row) ;\n" + -"\t\tOxygen_origflag:_FillValue = -9 ;\n" + -"\t\tOxygen_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tOxygen_origflag:standard_name = \"volume_fraction_of_oxygen_in_sea_water status_flag\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Institute, Orig_Stat_Num, Cast_Direction, dataset, Recorder, real_time, Ocean_Vehicle, dbase_orig, WMO_ID, origflagset, Temperature_WODprofileflag, Temperature_Instrument, Temperature_Adjustment, Salinity_WODprofileflag, Salinity_Instrument, Salinity_Method, Salinity_Adjustment, Salinity_, Pressure_Adjustment, Oxygen_WODprofileflag, Oxygen_Original_units, Oxygen_Adjustment, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + -"\t\t:Conventions = \"CF-1.6\" ;\n" + -"\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + -"\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:crs_inverse_flattening = 298.25723f ;\n" + -"\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:crs_semi_major_axis = 6378137.0f ;\n" + -"\t\t:date_created = \"2018-03-24\" ;\n" + -"\t\t:date_modified = \"2018-03-24\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 77.427f ;\n" + -"\t\t:geospatial_lat_min = -72.811f ;\n" + -"\t\t:geospatial_lat_resolution = \"point\" ;\n" + -"\t\t:geospatial_lon_max = 180.0f ;\n" + -"\t\t:geospatial_lon_min = -180.0f ;\n" + -"\t\t:geospatial_lon_resolution = \"point\" ;\n" + -"\t\t:geospatial_vertical_max = 6420.1216f ;\n" + -"\t\t:geospatial_vertical_min = -1.0f ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"meters\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_pfl_2005.nc\" ;\n" + -"\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + -"\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + -"\t\t:project = \"World Ocean Database\" ;\n" + -"\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + -"\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + -"\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + -"\t\t:source = \"World Ocean Database\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + -"\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + -"\t\t:time_coverage_end = \"2005-12-31\" ;\n" + -"\t\t:time_coverage_start = \"2005-01-01\" ;\n" + -"\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + -"}\n" + -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Cast_Direction,dataset,Recorder,real_time,Ocean_Vehicle,dbase_orig,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Temperature_Adjustment,Salinity_WODprofileflag,Salinity_Instrument,Salinity_Method,Salinity_Adjustment,Salinity_,Pressure_Adjustment,Oxygen_WODprofileflag,Oxygen_Original_units,Oxygen_Adjustment,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag\n" + -"JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,4.4739165,0,1,3,27.817,5,0,1,34.939,5,0,1,4.5,2,1,-1.0E10,,,-9\n" + -"JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,9.44482,0,1,3,27.745,5,0,1,34.942,5,0,1,9.5,2,1,-1.0E10,,,-9\n" + -"JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,13.91853,0,1,4,27.408,5,0,1,34.98,5,0,1,14.0,3,1,-1.0E10,,,-9\n" + -"JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,18.889206,0,1,4,27.286,5,0,1,34.997,5,0,1,19.0,3,1,-1.0E10,,,-9\n" + -"JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,24.257399,0,1,4,27.233,5,0,1,35.001,5,0,1,24.4,3,1,-1.0E10,,,-9\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //find 1D vars where dim isn't outerDimName, e.g., Temperature + if (realNDims[v] != 1) + continue; + Dimension dim = var.getDimension(0); + String dimName = dim.getName(); + if (outerDimName.equals(dimName) || //already in outer table? + dimName.equals("numberofpis")) + continue; - table.removeRows(0, 4420114 - 5); - results = table.dataToString(); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Cast_Direction,dataset,Recorder,real_time,Ocean_Vehicle,dbase_orig,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Temperature_Adjustment,Salinity_WODprofileflag,Salinity_Instrument,Salinity_Method,Salinity_Adjustment,Salinity_,Pressure_Adjustment,Oxygen_WODprofileflag,Oxygen_Original_units,Oxygen_Adjustment,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag\n" + -"UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,613.0759,0,1,5,0.474,3,0,1,34.071,5,0,2,618.7,6,1,-1.0E10,,,-9\n" + -"UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,632.8637,0,1,5,0.463,3,0,1,34.071,5,0,2,638.7,6,1,-1.0E10,,,-9\n" + -"UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,652.84753,0,1,5,0.448,3,0,1,34.07,5,0,2,658.9,6,1,-1.0E10,,,-9\n" + -"UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,672.5326,0,1,5,0.438,3,0,1,34.07,5,0,2,678.8,6,1,-1.0E10,,,-9\n" + -"UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,693.007,0,1,5,0.428,3,0,1,34.07,5,0,2,699.5,6,1,-1.0E10,,,-9\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } + //Let's do this! + if (debugMode) msg += + "\n>> make the innerTable in this table, v[" + v + "]=" + vNames[v]; + + //get the row_size info + PrimitiveArray rowSizesPA = rowSizesHM.get(dimName); + Test.ensureNotNull(rowSizesPA, + "No row_size info for dim=" + dimName + " for var=" + vNames[v]); - //read outer and inner col with outer constraint - fullName = dir + "wod_pfl_2005.nc"; - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"11898775"})); - results = table.dataToString(5); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"11898775,86196.9589958787,4.5649443,7.71,0\n" + -"11898775,86196.9589958787,13.892994,7.696,0\n" + -"11898775,86196.9589958787,24.014437,7.491,0\n" + -"11898775,86196.9589958787,33.83771,7.302,0\n" + -"11898775,86196.9589958787,43.958168,7.241,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //get the var's data + PrimitiveArray varPA = NcHelper.getPrimitiveArray(var); + varPA = vatts[v].standardizeVariable(standardizeWhat, vNames[v], varPA); - //outer and inner constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"11898775", "7.491"})); - results = table.dataToString(); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"11898775,86196.9589958787,24.014437,7.491,0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //can we use varPA as is? + if (keepAllOuter && varPA.size() == largestInnerDimSize) { + addColumn(nColumns(), vNames[v], varPA, vatts[v]); + continue; + } + //build newPA, with correct size for each cast, and just keep the keepOuter chunks + PrimitiveArray newPA = PrimitiveArray.factory(varPATypes[v], + nActiveInnerRows, false); + int thisPo = 0; + PrimitiveArray tSubset = null; + for (int outer = 0; outer < outerDimSize; outer++) { + int largestChunkSize = largestRowSizes.getInt(outer); + int thisChunkSize = rowSizesPA.getInt(outer); - //*** read all uor - fullName = dir + "wod_uor_2005.nc"; - if (doAll) { - table.readInvalidCRA(fullName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.toString(5); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 1169159 ;\n" + -"\tcountry_strlen = 6 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\toriginators_cruise_identifier_strlen = 9 ;\n" + -"\tPlatform_strlen = 73 ;\n" + -"\tWave_Height_strlen = 10 ;\n" + -"\tWave_Period_strlen = 17 ;\n" + -"\tWind_Direction_strlen = 25 ;\n" + -"\tWeather_Condition_strlen = 169 ;\n" + -"\tCloud_Cover_strlen = 65 ;\n" + -"\tdataset_strlen = 9 ;\n" + -"variables:\n" + -"\tchar country(row, country_strlen) ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\t\tGMT_time:units = \"hours\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:_FillValue = -99999 ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + -"\tchar Platform(row, Platform_strlen) ;\n" + -"\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + -"\t\tPlatform:long_name = \"Platform_name\" ;\n" + -"\tfloat Bottom_Depth(row) ;\n" + -"\t\tBottom_Depth:_FillValue = -1.0E10f ;\n" + -"\t\tBottom_Depth:standard_name = \"sea_floor_depth_below_sea_surface\" ;\n" + -"\t\tBottom_Depth:units = \"meters\" ;\n" + -"\tchar Wave_Height(row, Wave_Height_strlen) ;\n" + -"\t\tWave_Height:long_name = \"Wave_Height\" ;\n" + -"\t\tWave_Height:units_wod = \"WMO 1555 or NODC 0104\" ;\n" + -"\tchar Wave_Period(row, Wave_Period_strlen) ;\n" + -"\t\tWave_Period:long_name = \"Wave_Period\" ;\n" + -"\t\tWave_Period:units_wod = \"WMO 3155 or NODC 0378\" ;\n" + -"\tchar Wind_Direction(row, Wind_Direction_strlen) ;\n" + -"\t\tWind_Direction:long_name = \"Wind_Direction\" ;\n" + -"\t\tWind_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + -"\tfloat Wind_Speed(row) ;\n" + -"\t\tWind_Speed:_FillValue = -1.0E10f ;\n" + -"\t\tWind_Speed:standard_name = \"wind_speed\" ;\n" + -"\t\tWind_Speed:units = \"knots\" ;\n" + -"\tfloat Barometric_Pres(row) ;\n" + -"\t\tBarometric_Pres:_FillValue = -1.0E10f ;\n" + -"\t\tBarometric_Pres:long_name = \"Barometric_Pressure\" ;\n" + -"\t\tBarometric_Pres:units = \"millibars\" ;\n" + -"\tfloat Dry_Bulb_Temp(row) ;\n" + -"\t\tDry_Bulb_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tDry_Bulb_Temp:long_name = \"Dry_Bulb_Air_Temperature\" ;\n" + -"\t\tDry_Bulb_Temp:units = \"degree_C\" ;\n" + -"\tfloat Wet_Bulb_Temp(row) ;\n" + -"\t\tWet_Bulb_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tWet_Bulb_Temp:long_name = \"Wet_Bulb_Air_Temperature\" ;\n" + -"\t\tWet_Bulb_Temp:units = \"degree_C\" ;\n" + -"\tchar Weather_Condition(row, Weather_Condition_strlen) ;\n" + -"\t\tWeather_Condition:comment = \"Weather conditions at time of measurements\" ;\n" + -"\t\tWeather_Condition:long_name = \"Weather_Condition\" ;\n" + -"\tchar Cloud_Cover(row, Cloud_Cover_strlen) ;\n" + -"\t\tCloud_Cover:long_name = \"Cloud_Cover\" ;\n" + -"\t\tCloud_Cover:units_wod = \"WMO 2700 or NODC 0105\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tbyte Temperature_WODprofileflag(row) ;\n" + -"\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tbyte Salinity_WODprofileflag(row) ;\n" + -"\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tfloat z(row) ;\n" + -"\t\tz:ancillary_variables = \"z_sigfigs z_WODflag\" ;\n" + -"\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"depth\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tbyte z_WODflag(row) ;\n" + -"\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + -"\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + -"\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_sigfigs(row) ;\n" + -"\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag\" ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\tbyte Temperature_sigfigs(row) ;\n" + -"\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + -"\tbyte Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tfloat Salinity(row) ;\n" + -"\t\tSalinity:_FillValue = -1.0E10f ;\n" + -"\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag\" ;\n" + -"\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + -"\t\tSalinity:grid_mapping = \"crs\" ;\n" + -"\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + -"\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + -"\tbyte Salinity_sigfigs(row) ;\n" + -"\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + -"\tbyte Salinity_WODflag(row) ;\n" + -"\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + -"\tfloat Pressure(row) ;\n" + -"\t\tPressure:_FillValue = -1.0E10f ;\n" + -"\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag\" ;\n" + -"\t\tPressure:coordinates = \"time lat lon z\" ;\n" + -"\t\tPressure:grid_mapping = \"crs\" ;\n" + -"\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + -"\t\tPressure:units = \"dbar\" ;\n" + -"\tbyte Pressure_sigfigs(row) ;\n" + -"\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Platform, Bottom_Depth, Wave_Height, Wave_Period, Wind_Direction, Wind_Speed, Barometric_Pres, Dry_Bulb_Temp, Wet_Bulb_Temp, Weather_Condition, Cloud_Cover, dataset, Temperature_WODprofileflag, Salinity_WODprofileflag\" ;\n" + -"\t\t:Conventions = \"CF-1.6\" ;\n" + -"\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + -"\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:crs_inverse_flattening = 298.25723f ;\n" + -"\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:crs_semi_major_axis = 6378137.0f ;\n" + -"\t\t:date_created = \"2018-03-25\" ;\n" + -"\t\t:date_modified = \"2018-03-25\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 62.485f ;\n" + -"\t\t:geospatial_lat_min = 42.67f ;\n" + -"\t\t:geospatial_lat_resolution = \"point\" ;\n" + -"\t\t:geospatial_lon_max = -46.9317f ;\n" + -"\t\t:geospatial_lon_min = -65.84f ;\n" + -"\t\t:geospatial_lon_resolution = \"point\" ;\n" + -"\t\t:geospatial_vertical_max = 1443.402f ;\n" + -"\t\t:geospatial_vertical_min = 0.0f ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"meters\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_uor_2005.nc\" ;\n" + -"\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + -"\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + -"\t\t:project = \"World Ocean Database\" ;\n" + -"\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + -"\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + -"\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + -"\t\t:source = \"World Ocean Database\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + -"\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + -"\t\t:time_coverage_end = \"2005-12-17\" ;\n" + -"\t\t:time_coverage_start = \"2005-01-08\" ;\n" + -"\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + -"}\n" + -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Bottom_Depth,Wave_Height,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Cover,dataset,Temperature_WODprofileflag,Salinity_WODprofileflag,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Pressure,Pressure_sigfigs\n" + -"CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,0.0,0,1,1.321,4,0,33.597,5,0,0.0,1\n" + -"CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,0.099147804,0,1,1.321,4,0,33.598,5,0,0.1,1\n" + -"CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,0.19829556,0,1,1.321,4,0,33.601,5,0,0.2,1\n" + -"CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,0.79318106,0,1,1.321,4,0,33.603,5,0,0.8,1\n" + -"CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,1.487212,0,2,1.321,4,0,33.604,5,0,1.5,2\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + if (!keepOuter.get(outer)) { + //skip this outer + thisPo += thisChunkSize; + continue; + } - table.removeRows(0, 1169159 - 5); - results = table.dataToString(); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Bottom_Depth,Wave_Height,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Cover,dataset,Temperature_WODprofileflag,Salinity_WODprofileflag,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Pressure,Pressure_sigfigs\n" + -"CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.47443,0,4,2.176,4,0,34.101,5,0,199.3,4\n" + -"CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.57347,0,4,2.176,4,0,34.101,5,0,199.4,4\n" + -"CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.6725,0,4,2.174,4,0,34.102,5,0,199.5,4\n" + -"CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.77153,0,4,2.175,4,0,34.102,5,0,199.6,4\n" + -"CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.87054,0,4,2.178,4,0,34.102,5,0,199.7,4\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } + if (thisChunkSize == 0) { + //This deals with the main invalid part of these files. + //add missing values to newPA + newPA.addNStrings(largestChunkSize, varMissingValues[v]); + } else if (thisChunkSize == largestChunkSize) { + //copy values into newPA + tSubset = varPA.subset(tSubset, thisPo, 1, thisPo + thisChunkSize - 1); + newPA.append(tSubset); - //read outer and inner col with outer constraint - fullName = dir + "wod_uor_2005.nc"; - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"10749307"})); - results = table.dataToString(5); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"10749307,86182.78125,0.0,0.751,0\n" + -"10749307,86182.78125,0.099131815,0.776,0\n" + -"10749307,86182.78125,0.19826359,0.751,0\n" + -"10749307,86182.78125,0.29739532,0.777,0\n" + -"10749307,86182.78125,0.49565855,0.775,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //only need to do once, but not extant till here + tSubset.clear(); //speeds up ensureCapacity + tSubset.ensureCapacity(largestLargestChunkSize); - //outer and inner constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"10749307", "0.751"})); - results = table.dataToString(); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"10749307,86182.78125,0.0,0.751,0\n" + -"10749307,86182.78125,0.19826359,0.751,0\n" + -"10749307,86182.78125,2.4782808,0.751,0\n" + -"10749307,86182.78125,4.0643644,0.751,0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + } else { + throw new RuntimeException("For " + outerDimName + "[" + outer + + "], the number of " + dimName + " values (" + thisChunkSize + + ") doesn't equal the number of " + largestInnerDimName + + " values (" + largestChunkSize + ")."); + } + thisPo += thisChunkSize; + } + if (thisPo != varPA.size()) + throw new RuntimeException("Invalid file: The sum of the row sizes for " + + dimName + " (" + thisPo + ") doesn't equal the size of dimension=" + + dimName + " (" + varPA.size() + ")."); + addColumn(nColumns(), vNames[v], newPA, vatts[v]); + } + //finish up + //apply all constraints + tryToApplyConstraintsAndKeep(findColumnNumber(profileIDVarName), //may be -1 + conNames, conOps, conVals); //may be 0 rows left - //*** read all xbt - fullName = dir + "wod_xbt_2005.nc"; - if (doAll) { - table.readInvalidCRA(fullName, null, 0, //standardizeWhat=0 - null, null, null); - results = table.toString(5); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 25164853 ;\n" + -"\tcountry_strlen = 14 ;\n" + -"\tWOD_cruise_identifier_strlen = 8 ;\n" + -"\toriginators_cruise_identifier_strlen = 15 ;\n" + -"\toriginators_station_identifier_strlen = 10 ;\n" + -"\tProject_strlen = 59 ;\n" + -"\tPlatform_strlen = 80 ;\n" + -"\tInstitute_strlen = 79 ;\n" + -"\tWater_Color_strlen = 37 ;\n" + -"\tWave_Height_strlen = 9 ;\n" + -"\tWave_Period_strlen = 17 ;\n" + -"\tWind_Direction_strlen = 25 ;\n" + -"\tWeather_Condition_strlen = 169 ;\n" + -"\tCloud_Type_strlen = 17 ;\n" + -"\tCloud_Cover_strlen = 65 ;\n" + -"\tdataset_strlen = 3 ;\n" + -"\tRecorder_strlen = 47 ;\n" + -"\tdepth_eq_strlen = 9 ;\n" + -"\tRef_Type_strlen = 6 ;\n" + -"\tVisibility_strlen = 24 ;\n" + -"\tneeds_z_fix_strlen = 39 ;\n" + -"\treal_time_strlen = 14 ;\n" + -"\tdbase_orig_strlen = 13 ;\n" + -"\torigflagset_strlen = 4 ;\n" + -"\tTemperature_Instrument_strlen = 34 ;\n" + -"\tPrimary_Investigator_strlen = 28 ;\n" + -"\tPrimary_Investigator_VAR_strlen = 13 ;\n" + -"variables:\n" + -"\tchar country(row, country_strlen) ;\n" + -"\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + -"\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + -"\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + -"\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + -"\tint wod_unique_cast(row) ;\n" + -"\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + -"\tchar originators_station_identifier(row, originators_station_identifier_strlen) ;\n" + -"\t\toriginators_station_identifier:long_name = \"originators_station_identifier\" ;\n" + -"\tfloat lat(row) ;\n" + -"\t\tlat:long_name = \"latitude\" ;\n" + -"\t\tlat:standard_name = \"latitude\" ;\n" + -"\t\tlat:units = \"degrees_north\" ;\n" + -"\tfloat lon(row) ;\n" + -"\t\tlon:long_name = \"longitude\" ;\n" + -"\t\tlon:standard_name = \"longitude\" ;\n" + -"\t\tlon:units = \"degrees_east\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:long_name = \"time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + -"\tint date(row) ;\n" + -"\t\tdate:comment = \"YYYYMMDD\" ;\n" + -"\t\tdate:long_name = \"date\" ;\n" + -"\tfloat GMT_time(row) ;\n" + -"\t\tGMT_time:long_name = \"GMT_time\" ;\n" + -"\t\tGMT_time:units = \"hours\" ;\n" + -"\tint Access_no(row) ;\n" + -"\t\tAccess_no:_FillValue = -99999 ;\n" + -"\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + -"\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + -"\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + -"\tchar Project(row, Project_strlen) ;\n" + -"\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + -"\t\tProject:long_name = \"Project_name\" ;\n" + -"\tchar Platform(row, Platform_strlen) ;\n" + -"\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + -"\t\tPlatform:long_name = \"Platform_name\" ;\n" + -"\tchar Institute(row, Institute_strlen) ;\n" + -"\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + -"\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + -"\tint Orig_Stat_Num(row) ;\n" + -"\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + -"\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + -"\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + -"\tfloat Bottom_Depth(row) ;\n" + -"\t\tBottom_Depth:_FillValue = -1.0E10f ;\n" + -"\t\tBottom_Depth:standard_name = \"sea_floor_depth_below_sea_surface\" ;\n" + -"\t\tBottom_Depth:units = \"meters\" ;\n" + -"\tchar Water_Color(row, Water_Color_strlen) ;\n" + -"\t\tWater_Color:long_name = \"Water_Color\" ;\n" + -"\t\tWater_Color:units_wod = \"Forel-Ule scale (00 to 21)\" ;\n" + -"\tfloat Water_Transpar(row) ;\n" + -"\t\tWater_Transpar:_FillValue = -1.0E10f ;\n" + -"\t\tWater_Transpar:comment = \"Secchi disk depth\" ;\n" + -"\t\tWater_Transpar:long_name = \"Water_Transparency\" ;\n" + -"\t\tWater_Transpar:units = \"meters\" ;\n" + -"\tchar Wave_Height(row, Wave_Height_strlen) ;\n" + -"\t\tWave_Height:long_name = \"Wave_Height\" ;\n" + -"\t\tWave_Height:units_wod = \"WMO 1555 or NODC 0104\" ;\n" + -"\tchar Wave_Period(row, Wave_Period_strlen) ;\n" + -"\t\tWave_Period:long_name = \"Wave_Period\" ;\n" + -"\t\tWave_Period:units_wod = \"WMO 3155 or NODC 0378\" ;\n" + -"\tchar Wind_Direction(row, Wind_Direction_strlen) ;\n" + -"\t\tWind_Direction:long_name = \"Wind_Direction\" ;\n" + -"\t\tWind_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + -"\tfloat Wind_Speed(row) ;\n" + -"\t\tWind_Speed:_FillValue = -1.0E10f ;\n" + -"\t\tWind_Speed:standard_name = \"wind_speed\" ;\n" + -"\t\tWind_Speed:units = \"knots\" ;\n" + -"\tfloat Barometric_Pres(row) ;\n" + -"\t\tBarometric_Pres:_FillValue = -1.0E10f ;\n" + -"\t\tBarometric_Pres:long_name = \"Barometric_Pressure\" ;\n" + -"\t\tBarometric_Pres:units = \"millibars\" ;\n" + -"\tfloat Dry_Bulb_Temp(row) ;\n" + -"\t\tDry_Bulb_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tDry_Bulb_Temp:long_name = \"Dry_Bulb_Air_Temperature\" ;\n" + -"\t\tDry_Bulb_Temp:units = \"degree_C\" ;\n" + -"\tfloat Wet_Bulb_Temp(row) ;\n" + -"\t\tWet_Bulb_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tWet_Bulb_Temp:long_name = \"Wet_Bulb_Air_Temperature\" ;\n" + -"\t\tWet_Bulb_Temp:units = \"degree_C\" ;\n" + -"\tchar Weather_Condition(row, Weather_Condition_strlen) ;\n" + -"\t\tWeather_Condition:comment = \"Weather conditions at time of measurements\" ;\n" + -"\t\tWeather_Condition:long_name = \"Weather_Condition\" ;\n" + -"\tchar Cloud_Type(row, Cloud_Type_strlen) ;\n" + -"\t\tCloud_Type:long_name = \"Cloud_Type\" ;\n" + -"\t\tCloud_Type:units_wod = \"WMO 0500 or NODC 0053\" ;\n" + -"\tchar Cloud_Cover(row, Cloud_Cover_strlen) ;\n" + -"\t\tCloud_Cover:long_name = \"Cloud_Cover\" ;\n" + -"\t\tCloud_Cover:units_wod = \"WMO 2700 or NODC 0105\" ;\n" + -"\tchar dataset(row, dataset_strlen) ;\n" + -"\t\tdataset:long_name = \"WOD_dataset\" ;\n" + -"\tchar Recorder(row, Recorder_strlen) ;\n" + -"\t\tRecorder:comment = \"Device which recorded measurements\" ;\n" + -"\t\tRecorder:long_name = \"Recorder\" ;\n" + -"\t\tRecorder:units_wod = \"WMO code 4770\" ;\n" + -"\tchar depth_eq(row, depth_eq_strlen) ;\n" + -"\t\tdepth_eq:comment = \"which drop rate equation was used\" ;\n" + -"\t\tdepth_eq:long_name = \"depth_equation_used\" ;\n" + -"\tbyte Bottom_Hit(row) ;\n" + -"\t\tBottom_Hit:_FillValue = -9 ;\n" + -"\t\tBottom_Hit:comment = \"set to one if instrument hit bottom\" ;\n" + -"\t\tBottom_Hit:long_name = \"Bottom_Hit\" ;\n" + -"\tchar Ref_Type(row, Ref_Type_strlen) ;\n" + -"\t\tRef_Type:comment = \"Instrument for reference temperature\" ;\n" + -"\t\tRef_Type:long_name = \"Reference_Instrument\" ;\n" + -"\tchar Visibility(row, Visibility_strlen) ;\n" + -"\t\tVisibility:long_name = \"Horizontal_visibility\" ;\n" + -"\t\tVisibility:units_wod = \"WMO Code 4300\" ;\n" + -"\tfloat Ref_Surf_Temp(row) ;\n" + -"\t\tRef_Surf_Temp:_FillValue = -1.0E10f ;\n" + -"\t\tRef_Surf_Temp:comment = \"Reference_or_Sea_Surface_Temperature\" ;\n" + -"\t\tRef_Surf_Temp:units = \"degree_C\" ;\n" + -"\tchar needs_z_fix(row, needs_z_fix_strlen) ;\n" + -"\t\tneeds_z_fix:comment = \"instruction for fixing depths\" ;\n" + -"\t\tneeds_z_fix:long_name = \"z_fix_instructions\" ;\n" + -"\t\tneeds_z_fix:units_wod = \"WOD_code\" ;\n" + -"\tchar real_time(row, real_time_strlen) ;\n" + -"\t\treal_time:comment = \"timeliness and quality status\" ;\n" + -"\t\treal_time:long_name = \"real_time_data\" ;\n" + -"\tfloat Launch_height(row) ;\n" + -"\t\tLaunch_height:_FillValue = -1.0E10f ;\n" + -"\t\tLaunch_height:long_name = \"Height_of_instrument_launch\" ;\n" + -"\t\tLaunch_height:units = \"meters\" ;\n" + -"\tfloat sensor_depth(row) ;\n" + -"\t\tsensor_depth:_FillValue = -1.0E10f ;\n" + -"\t\tsensor_depth:long_name = \"Depth_of_sea_surface_sensor\" ;\n" + -"\t\tsensor_depth:units = \"meters\" ;\n" + -"\tchar dbase_orig(row, dbase_orig_strlen) ;\n" + -"\t\tdbase_orig:comment = \"Database from which data were extracted\" ;\n" + -"\t\tdbase_orig:long_name = \"database_origin\" ;\n" + -"\tchar origflagset(row, origflagset_strlen) ;\n" + -"\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + -"\tbyte Temperature_WODprofileflag(row) ;\n" + -"\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + -"\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + -"\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + -"\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + -"\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + -"\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + -"\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + -"\tfloat z(row) ;\n" + -"\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + -"\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + -"\t\tz:positive = \"down\" ;\n" + -"\t\tz:standard_name = \"depth\" ;\n" + -"\t\tz:units = \"m\" ;\n" + -"\tbyte z_WODflag(row) ;\n" + -"\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + -"\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + -"\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + -"\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_origflag(row) ;\n" + -"\t\tz_origflag:_FillValue = -9 ;\n" + -"\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + -"\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + -"\tbyte z_sigfigs(row) ;\n" + -"\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + -"\tfloat Temperature(row) ;\n" + -"\t\tTemperature:_FillValue = -1.0E10f ;\n" + -"\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + -"\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + -"\t\tTemperature:grid_mapping = \"crs\" ;\n" + -"\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + -"\t\tTemperature:units = \"degree_C\" ;\n" + -"\tbyte Temperature_sigfigs(row) ;\n" + -"\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + -"\tbyte Temperature_WODflag(row) ;\n" + -"\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + -"\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + -"\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + -"\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\tbyte Temperature_origflag(row) ;\n" + -"\t\tTemperature_origflag:_FillValue = -9 ;\n" + -"\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + -"\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, originators_station_identifier, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Institute, Orig_Stat_Num, Bottom_Depth, Water_Color, Water_Transpar, Wave_Height, Wave_Period, Wind_Direction, Wind_Speed, Barometric_Pres, Dry_Bulb_Temp, Wet_Bulb_Temp, Weather_Condition, Cloud_Type, Cloud_Cover, dataset, Recorder, depth_eq, Bottom_Hit, Ref_Type, Visibility, Ref_Surf_Temp, needs_z_fix, real_time, Launch_height, sensor_depth, dbase_orig, origflagset, Temperature_WODprofileflag, Temperature_Instrument, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + -"\t\t:Conventions = \"CF-1.6\" ;\n" + -"\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + -"\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:crs_inverse_flattening = 298.25723f ;\n" + -"\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:crs_semi_major_axis = 6378137.0f ;\n" + -"\t\t:date_created = \"2018-03-24\" ;\n" + -"\t\t:date_modified = \"2018-03-24\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 79.0612f ;\n" + -"\t\t:geospatial_lat_min = -77.556f ;\n" + -"\t\t:geospatial_lat_resolution = \"point\" ;\n" + -"\t\t:geospatial_lon_max = -0.011505127f ;\n" + -"\t\t:geospatial_lon_min = 180.0f ;\n" + -"\t\t:geospatial_lon_resolution = \"point\" ;\n" + -"\t\t:geospatial_vertical_max = 3124.0f ;\n" + -"\t\t:geospatial_vertical_min = 0.0f ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"meters\" ;\n" + -"\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + -"\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + -"\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + -"\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + -"\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + -"\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_xbt_2005.nc\" ;\n" + -"\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + -"\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + -"\t\t:project = \"World Ocean Database\" ;\n" + -"\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + -"\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + -"\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + -"\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + -"\t\t:source = \"World Ocean Database\" ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + -"\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + -"\t\t:time_coverage_end = \"2005-12-31\" ;\n" + -"\t\t:time_coverage_start = \"2005-01-01\" ;\n" + -"\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + -"}\n" + -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Bottom_Depth,Water_Color,Water_Transpar,Wave_Height,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Ref_Type,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,Launch_height,sensor_depth,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag\n" + -"UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,1.0,0,-9,2,5.0,4,0,-9\n" + -"UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,5.0,0,-9,2,5.0,4,0,-9\n" + -"UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,73.0,0,-9,3,5.1,4,0,-9\n" + -"UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,77.0,0,-9,3,4.9,4,0,-9\n" + -"UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,89.0,0,-9,3,5.0,4,0,-9\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //put in colNames order + if (colNames.size() > 0) + reorderColumns(colNames, true); - table.removeRows(0, 25164853 - 5); - results = table.dataToString(); - expected = -"country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Bottom_Depth,Water_Color,Water_Transpar,Wave_Height,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Ref_Type,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,Launch_height,sensor_depth,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag\n" + -"UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,88.0,0,-9,3,15.3,5,0,-9\n" + -"UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,98.0,0,-9,3,15.1,5,0,-9\n" + -"UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,102.0,0,-9,4,14.7,5,0,-9\n" + -"UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,167.0,0,-9,4,14.7,5,0,-9\n" + -"UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,200.0,0,-9,4,14.5,5,0,-9\n"; - Test.ensureEqual(results, expected, "results=\n" + results); + //we're done + if (reallyVerbose) String2.log(msg + + " finished. nRows=" + nRows() + " nCols=" + nColumns() + + " time=" + (System.currentTimeMillis() - time) + "ms"); + } finally { + try {if (ncFile != null) ncFile.close(); } catch (Exception e9) {} } - - - //read outer and inner col with outer constraint - fullName = dir + "wod_xbt_2005.nc"; - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast"}), - new StringArray(new String[]{"="}), - new StringArray(new String[]{"10731585"})); - results = table.dataToString(5); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"10731585,86196.0,0.0,15.8,0\n" + -"10731585,86196.0,23.0,15.7,0\n" + -"10731585,86196.0,47.0,15.3,0\n" + -"10731585,86196.0,50.0,15.4,0\n" + -"10731585,86196.0,65.0,15.2,0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //outer and inner constraint - table.readInvalidCRA(fullName, - new StringArray(new String[]{"wod_unique_cast", "time", "z", "Temperature","Temperature_WODflag"}), - 0, //standardizeWhat=0 - new StringArray(new String[]{"wod_unique_cast", "Temperature"}), - new StringArray(new String[]{"=", "="}), - new StringArray(new String[]{"10731585", "15.3"})); - results = table.dataToString(); - expected = -"wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + -"10731585,86196.0,47.0,15.3,0\n" + -"10731585,86196.0,88.0,15.3,0\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - /* */ - - table.debugMode = false; } /** @@ -25657,39 +11958,6 @@ public static String[] getDapQueryParts(String dapQuery) throws Exception { return parts.toArray(); } - /** This tests getDapQueryParts. */ - public static void testGetDapQueryParts() throws Exception { - String2.log("\n*** Table.testGetDapQueryParts"); - - //test Table.getDapQueryParts - Test.ensureEqual(getDapQueryParts(null), new String[]{""}, ""); - Test.ensureEqual(getDapQueryParts(""), new String[]{""}, ""); - Test.ensureEqual(getDapQueryParts(" "), new String[]{" "}, ""); - Test.ensureEqual(getDapQueryParts("ab%3dc"), new String[]{"ab=c"}, ""); - Test.ensureEqual(getDapQueryParts("a&b&c"), new String[]{"a", "b", "c"}, ""); - Test.ensureEqual(getDapQueryParts("&&"), new String[]{"", "", ""}, ""); - Test.ensureEqual(getDapQueryParts("a&b=R%26D"), new String[]{"a", "b=R&D"}, ""); //& visible - Test.ensureEqual(getDapQueryParts("a%26b=\"R%26D\""), new String[]{"a", "b=\"R&D\""}, ""); //& encoded - Test.ensureEqual(getDapQueryParts("a%26b=\"R%26D\"%26c"), new String[]{"a", "b=\"R&D\"", "c"}, ""); //& encoded - Test.ensureEqual(getDapQueryParts("a%26b%3dR-D"), new String[]{"a", "b=R-D"}, ""); - - //*** test getDapQueryParts (decoded) with invalid queries - String error = ""; - try { - getDapQueryParts("a%26b=\"R%26D"); //decoded. unclosed " - - } catch (Throwable t) { - error = MustBe.throwableToString(t); - } - - Test.ensureEqual(String2.split(error, '\n')[0], - "SimpleException: Query error: A closing doublequote is missing.", - "error=" + error); - - String2.log("\n*** Table.testGetDapQueryParts succeeded"); - } - - /** * This parses a PERCENT ENCODED OPeNDAP DAP-style query intended to subset this table. * This checks the validity of the resultsVariable and constraintVariable names. @@ -26038,288 +12306,6 @@ else throw new SimpleException(QUERY_ERROR + } } - - /** - * This tests parseDapQuery. - */ - public static void testParseDapQuery() throws Exception { - String2.log("\n*** Table.testParseDapQuery"); - - Table table = makeEmptyTable( - new String[]{"myDouble","myString","time","myInt"}, - new String[]{"double","String","double","int"}); - table.columnAttributes("time").add("units", Calendar2.SECONDS_SINCE_1970); - StringArray rVar = new StringArray(); - StringArray cVar = new StringArray(); - StringArray cOp = new StringArray(); - StringArray cVal = new StringArray(); - String results; - - //*** test valid queries - table.parseDapQuery("", rVar, cVar, cOp, cVal, false); //fix - Test.ensureEqual(rVar.toString(), "myDouble, myString, time, myInt", ""); - Test.ensureEqual(cVar.toString(), "", ""); - Test.ensureEqual(cOp.toString(), "", ""); - Test.ensureEqual(cVal.toString(), "", ""); - - table.parseDapQuery("myString,myDouble", rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myString, myDouble", ""); - Test.ensureEqual(cVar.toString(), "", ""); - Test.ensureEqual(cOp.toString(), "", ""); - Test.ensureEqual(cVal.toString(), "", ""); - - table.parseDapQuery("myDouble&myString=\"something\"", rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myDouble", ""); - Test.ensureEqual(cVar.toString(), "myString", ""); - Test.ensureEqual(cOp.toString(), "=", ""); - Test.ensureEqual(cVal.toString(), "something", ""); - - table.parseDapQuery("myDouble&myInt=~\"regex\"", rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myDouble", ""); - Test.ensureEqual(cVar.toString(), "myInt", ""); - Test.ensureEqual(cOp.toString(), "=~", ""); - Test.ensureEqual(cVal.toString(), "regex", ""); - - table.parseDapQuery("myDouble&time>=1.4229216E9", rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myDouble", ""); - Test.ensureEqual(cVar.toString(), "time", ""); - Test.ensureEqual(cOp.toString(), ">=", ""); - Test.ensureEqual(cVal.toString(), "1.4229216E9", ""); - - table.parseDapQuery("myDouble&time>=2015-02-03", rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myDouble", ""); - Test.ensureEqual(cVar.toString(), "time", ""); - Test.ensureEqual(cOp.toString(), ">=", ""); - Test.ensureEqual(cVal.toString(), "1.4229216E9", ""); - - table.parseDapQuery("myDouble&myInt=NaN", rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myDouble", ""); - Test.ensureEqual(cVar.toString(), "myInt", ""); - Test.ensureEqual(cOp.toString(), "=", ""); - Test.ensureEqual(cVal.toString(), "NaN", ""); - - table.parseDapQuery( - "&time!=2015-02-03&myInt<5.1&myString=\"Nate\"&orderBy(\"myString,myInt\")&distinct()", - rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myDouble, myString, time, myInt", ""); - Test.ensureEqual(cVar.toString(), "time, myInt, myString", ""); - Test.ensureEqual(cOp.toString(), "!=, <, =", ""); - Test.ensureEqual(cVal.toString(), "1.4229216E9, 5.1, Nate", ""); - - //s - table.parseDapQuery("s", rVar, cVar, cOp, cVal, false); //fix - Test.ensureEqual(rVar.toString(), "myDouble, myString, time, myInt", ""); - Test.ensureEqual(cVar.toString(), "", ""); - Test.ensureEqual(cOp.toString(), "", ""); - Test.ensureEqual(cVal.toString(), "", ""); - - table.parseDapQuery("s.myDouble&s.time>=2015-02-03", rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myDouble", ""); - Test.ensureEqual(cVar.toString(), "time", ""); - Test.ensureEqual(cOp.toString(), ">=", ""); - Test.ensureEqual(cVal.toString(), "1.4229216E9", ""); - - table.parseDapQuery( - "&s.time!=2015-02-03&s.myInt<5.1&s.myString=\"Nate\"&orderBy(\"s.myString,s.myInt\")&distinct()", - rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "myDouble, myString, time, myInt", ""); - Test.ensureEqual(cVar.toString(), "time, myInt, myString", ""); - Test.ensureEqual(cOp.toString(), "!=, <, =", ""); - Test.ensureEqual(cVal.toString(), "1.4229216E9, 5.1, Nate", ""); - - //Tests of time related to "now" - double now = System.currentTimeMillis() / 1000.0; - String2.log("epochSecondsNow=" + now); - table.parseDapQuery("time&time>now&time>now%2Bsecond&time>now-minute&time>now-44days", - rVar, cVar, cOp, cVal, false); - Test.ensureEqual(rVar.toString(), "time", ""); - Test.ensureEqual(cVar.toString(), "time, time, time, time", ""); - Test.ensureEqual(cOp.toString(), ">, >, >, >", ""); - Test.ensureTrue(Math.abs(cVal.getDouble(0) - (now) ) < 20, cVal.get(0)); - Test.ensureTrue(Math.abs(cVal.getDouble(1) - (now+1 ) ) < 20, cVal.get(1)); - Test.ensureTrue(Math.abs(cVal.getDouble(2) - (now-60) ) < 20, cVal.get(2)); - Test.ensureTrue(Math.abs(cVal.getDouble(3) - (now-44*86400)) < 20, cVal.get(3)); - - - //********* tests that fail - results = "invalid request var"; - try { - table.parseDapQuery("time,MyInt", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Unrecognized variable=\"MyInt\".", ""); - - results = "listed twice"; - try { - table.parseDapQuery("time,myInt,time", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: variable=time is listed twice in the results variables list.", ""); - - results = "invalid constraint var"; - try { - table.parseDapQuery("time&MyDouble>5", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Unrecognized constraint variable=\"MyDouble\".", ""); - - results = "missing &"; - try { - table.parseDapQuery("myInt>5", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: All constraints (including \"myInt>...\") must be preceded by '&'.", ""); - - results = "missing & with date with double col"; - try { - table.parseDapQuery("myDouble>2014-01-01T00:00:00Z", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: All constraints (including \"myDouble>...\") must be preceded by '&'.", ""); - - results = "invalid op"; - try { - table.parseDapQuery("&myInt==5", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Use '=' instead of '==' in constraints.", ""); - - results = "invalid NAN value"; - try { - table.parseDapQuery("&myInt=NAN", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Numeric tests of NaN must use \"NaN\", not value=\"NAN\".", ""); - - results = "invalid NaN value, something"; - try { - table.parseDapQuery("&myInt=something", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Numeric tests of NaN must use \"NaN\", not value=\"something\".", ""); - - results = "invalid NaN value"; - try { - table.parseDapQuery("&myInt=1e1000", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Numeric tests of NaN must use \"NaN\", not value=\"1e1000\".", ""); - - results = "invalid regex op"; - try { - table.parseDapQuery("&myInt~=\"regex\"", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Use '=~' instead of '~=' in constraints.", ""); - - results = "missing \"\" for string"; - try { - table.parseDapQuery("&myString=something", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: For constraints of String variables, the right-hand-side value must be surrounded by double quotes.\n" + - "Bad constraint: myString=something", - "results=" + results); - - results = "missing \"\" for regex"; - try { - table.parseDapQuery("&myInt=~something", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: For =~ constraints of numeric variables, the right-hand-side value must be surrounded by double quotes.\n" + - "Bad constraint: myInt=~something", - "results=" + results); - - results = "invalid now units"; - try { - table.parseDapQuery("&time>now-2dayss", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Invalid \"now\" constraint: \"now-2dayss\". " + - "Timestamp constraints with \"now\" must be in the form \"now[+|-positiveInteger[millis|seconds|minutes|hours|days|months|years]]\" (or singular units).", - "results=" + results); - - results = "invalid now option -"; - try { - table.parseDapQuery("&time>now-", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Invalid \"now\" constraint: \"now-\". " + - "Timestamp constraints with \"now\" must be in the form \"now[+|-positiveInteger[millis|seconds|minutes|hours|days|months|years]]\" (or singular units).", - "results=" + results); - - results = "invalid now option -+"; - try { - table.parseDapQuery("&time>now-%2B4seconds", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Invalid \"now\" constraint: \"now-+4seconds\". " + - "Timestamp constraints with \"now\" must be in the form \"now[+|-positiveInteger[millis|seconds|minutes|hours|days|months|years]]\" (or singular units).", - "results=" + results); - - results = "invalid now option +-"; - try { - table.parseDapQuery("&time>now%2B-4seconds", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Invalid \"now\" constraint: \"now+-4seconds\". " + - "Timestamp constraints with \"now\" must be in the form \"now[+|-positiveInteger[millis|seconds|minutes|hours|days|months|years]]\" (or singular units).", - "results=" + results); - - results = "invalid now option"; - try { - table.parseDapQuery("&time>now=2days", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: Unrecognized constraint variable=\"time>now\".", - "results=" + results); - - results = "unknown filter"; - try { - table.parseDapQuery("&Distinct()", rVar, cVar, cOp, cVal, false); - } catch (Throwable t) { - results = t.toString(); - } - Test.ensureEqual(results, - "com.cohort.util.SimpleException: Query error: No operator found in constraint=\"Distinct()\".", ""); - - String2.log("\n*** Table.testParseDapQuery finished successfully."); - } - /** * This converts the missing values to standard (e.g., NaN) missing values, * but doesn't erase the missing_value and _FillValue metadata so the table can be reused. @@ -26519,106 +12505,6 @@ public int subsetViaDapQuery(String dapQuery) throws Exception { return nRows(); } - /** - * This tests subsetViaDapQuery. - */ - public static void testSubsetViaDapQuery() throws Exception { - String2.log("\n*** Table.testSubsetViaDapQuery"); - String results, expected; - Table table; - - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery(""); - results = table.dataToString(); - expected = -"Time,Longitude,Latitude,Double Data,Int Data,Short Data,Byte Data,Char Data,String Data\n" + -"0.0,-3,1.0,-1.0E300,-2000000000,-32000,-120,\",\",a\n" + -"1.125504062E9,-2,1.5,3.123,2,7,8,\"\"\"\",bb\n" + -"1.130954649E9,-1,2.0,1.0E300,2000000000,32000,120,\\u20ac,ccc\n" + -",,,,,,,,\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - // !=NaN - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery("&Latitude!=NaN"); - results = table.dataToString(); - expected = -"Time,Longitude,Latitude,Double Data,Int Data,Short Data,Byte Data,Char Data,String Data\n" + -"0.0,-3,1.0,-1.0E300,-2000000000,-32000,-120,\",\",a\n" + -"1.125504062E9,-2,1.5,3.123,2,7,8,\"\"\"\",bb\n" + -"1.130954649E9,-1,2.0,1.0E300,2000000000,32000,120,\\u20ac,ccc\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - // =NaN - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery("&Latitude=NaN"); - results = table.dataToString(); - expected = -"Time,Longitude,Latitude,Double Data,Int Data,Short Data,Byte Data,Char Data,String Data\n" + -",,,,,,,,\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //1125504062 seconds since 1970-01-01T00:00:00Z = 2005-08-31T16:01:02Z - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery("&Time>2005-08-31T16:01:02Z"); - results = table.dataToString(); - expected = -"Time,Longitude,Latitude,Double Data,Int Data,Short Data,Byte Data,Char Data,String Data\n" + -"1.130954649E9,-1,2.0,1.0E300,2000000000,32000,120,\\u20ac,ccc\n"; -//mv row removed because tests related to NaN (except NaN=NaN) return false. - Test.ensureEqual(results, expected, "results=\n" + results); - - //1125504062 seconds since 1970-01-01T00:00:00Z = 2005-08-31T16:01:02Z - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery("String Data,Time&Time>=2005-08-31T16:01:02Z"); - results = table.dataToString(); - expected = -"String Data,Time\n" + -"bb,1.125504062E9\n" + -"ccc,1.130954649E9\n"; -//mv row removed because tests related to NaN (except NaN=NaN) return false. - Test.ensureEqual(results, expected, "results=\n" + results); - - //constraint var needn't be in resultsVars - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery("String Data&Time>=2005-08-31T16:01:02Z"); - results = table.dataToString(); - expected = -"String Data\n" + -"bb\n" + -"ccc\n"; -//mv row removed because tests related to NaN (except NaN=NaN) return false. - Test.ensureEqual(results, expected, "results=\n" + results); - - //return 0 rows - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery("Longitude,Time&Time=2005-08-31"); - results = table.dataToString(); - expected = -"Longitude,Time\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //string - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery("String Data,Time&Time>1970-01-01&String Data=\"bb\""); - results = table.dataToString(); - expected = -"String Data,Time\n" + -"bb,1.125504062E9\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //regex - table = getTestTable(false, true); //includeLongs, Strings - table.subsetViaDapQuery("String Data,Time&String Data=~\"b{1,5}\""); - results = table.dataToString(); - expected = -"String Data,Time\n" + -"bb,1.125504062E9\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - String2.log("\n*** Table.testSubsetViaDapQuery finished successfully"); - } - /** * If two or more adjacent rows are duplicates, this removes * the duplicates (leaving the original row). @@ -27438,139 +13324,6 @@ private void withRounding(final String responsible, String[] keyColumnNames, } } - /** This tests orderByMax, orderByMin, orderByMinMax */ - public static void testOrderByMinMax() throws Exception { - - for (int proc = 0; proc < 3; proc++) { - String2.log("Table.testOrderBy" + - (proc == 1? "" : "Max") + - (proc == 0? "" : "Min")); - - //*** test #1 - PrimitiveArray substation = PrimitiveArray.csvFactory(PAType.INT, - "10, 20, 20, 30, 10, 10, 10"); - PrimitiveArray station = PrimitiveArray.csvFactory(PAType.STRING, - " a, a, a, b, c, c, c"); - PrimitiveArray time = PrimitiveArray.csvFactory(PAType.INT, - " 1, 1, 2, 1, 1, 2, 3"); - PrimitiveArray other = PrimitiveArray.csvFactory(PAType.INT, - "99, 95, 92, 91, 93, 98, 90"); - Table table = new Table(); - table.addColumn("substation", substation); - table.addColumn("station", station); - table.addColumn("time", time); - table.addColumn("other", other); - - //unsort by sorting on 'other' - table.ascendingSort(new int[]{3}); - - //orderBy... - String vars[] = new String[]{"station", "substation", "time"}; - if (proc == 0) table.orderByMax(vars); - if (proc == 1) table.orderByMin(vars); - if (proc == 2) table.orderByMinMax(vars); - String results = table.dataToString(); - String expected[] = new String[]{ -"substation,station,time,other\n" + -"10,a,1,99\n" + -"20,a,2,92\n" + -"30,b,1,91\n" + -"10,c,3,90\n", -"substation,station,time,other\n" + -"10,a,1,99\n" + -"20,a,1,95\n" + -"30,b,1,91\n" + -"10,c,1,93\n", -"substation,station,time,other\n" + -"10,a,1,99\n" + //note duplicate of 1 row of data -"10,a,1,99\n" + -"20,a,1,95\n" + -"20,a,2,92\n" + -"30,b,1,91\n" + //note duplicate -"30,b,1,91\n" + -"10,c,1,93\n" + -"10,c,3,90\n"}; - Test.ensureEqual(results, expected[proc], "proc=" + proc + " results=\n" + results); - - - //*** test #2 - PrimitiveArray time2 = PrimitiveArray.csvFactory(PAType.INT, - " 1, 1, 2, 1, 1, 2, 3"); - PrimitiveArray other2 = PrimitiveArray.csvFactory(PAType.INT, - "99, 95, 92, 91, 93, 98, 90"); - table = new Table(); - table.addColumn("time", time2); - table.addColumn("other", other2); - - //unsort by sorting on 'other' - table.ascendingSort(new int[]{1}); - - //orderBy... - vars = new String[]{"time"}; - if (proc == 0) table.orderByMax(vars); - if (proc == 1) table.orderByMin(vars); - if (proc == 2) table.orderByMinMax(vars); - results = table.dataToString(); - expected = new String[]{ -"time,other\n" + -"3,90\n", -"time,other\n" + -"1,91\n", //for ties, the one that is picked isn't specified. unsort above causes 91 to be first. -"time,other\n" + -"1,91\n" + //for ties, the one that is picked isn't specified. unsort above causes 91 to be first. -"3,90\n"}; - - Test.ensureEqual(results, expected[proc], "proc=" + proc + " results=\n" + results); - - - //*** test #3 - PrimitiveArray time3 = PrimitiveArray.csvFactory(PAType.INT, - " 1"); - PrimitiveArray other3 = PrimitiveArray.csvFactory(PAType.INT, - "99"); - table = new Table(); - table.addColumn("time", time3); - table.addColumn("other", other3); - - //unsort by sorting on 'other' - table.ascendingSort(new int[]{1}); - - //orderBy... - vars = new String[]{"time"}; - if (proc == 0) table.orderByMax(vars); - if (proc == 1) table.orderByMin(vars); - if (proc == 2) table.orderByMinMax(vars); - results = table.dataToString(); - expected = new String[]{ -"time,other\n" + -"1,99\n", -"time,other\n" + -"1,99\n", -"time,other\n" + -"1,99\n" + -"1,99\n"}; - Test.ensureEqual(results, expected[proc], "proc=" + proc + " results=\n" + results); - - - //*** test #4 - PrimitiveArray time4 = new IntArray(); - PrimitiveArray other4 = new IntArray(); - table = new Table(); - table.addColumn("time", time4); - table.addColumn("other", other4); - - //orderBy... - vars = new String[]{"time"}; - if (proc == 0) table.orderByMax(vars); - if (proc == 1) table.orderByMin(vars); - if (proc == 2) table.orderByMinMax(vars); - results = table.dataToString(); - String expected4 = "time,other\n"; - Test.ensureEqual(results, expected4, "proc=" + proc + " results=\n" + results); - } - - } - /** * This is a higher level orderByClosest that takes the csv string * with the names of the orderBy columns plus the interval @@ -27792,120 +13545,6 @@ public void orderByClosest(int keyColumns[], double numberTimeUnits[]) throws Ex temporarilySwitchNaNToFakeMissingValues(keyColumns); } - /** - * This tests orderByClosest. - */ - public static void testOrderByClosest() throws Exception { - String2.log("\n*** Table.testOrderByClosest()"); - - //regular: 2 minutes - String2.log("\nTest 2 minutes"); - StringArray sar = new StringArray(new String[]{ - "b", "b", "b", "b", "b", "b", "c", "a", "d", "a"}); - DoubleArray dar = new DoubleArray(new double[]{ - -121,-100, Double.NaN, 110, 132, -2, 1e30, 132, 1e30, 125}); - IntArray iar = new IntArray(new int[] { - 0, 1, 2, 3, 4, 5, 6, 7, 8, 9}); - Table table = new Table(); - table.addColumn("iar", iar); - table.addColumn("sar", sar); - table.addColumn("dar", dar); - table.orderByClosest("sar, dar, 2 minutes"); - String results = table.dataToString(); - String expected = -"iar,sar,dar\n" + -"9,a,125.0\n" + -"0,b,-121.0\n" + -"5,b,-2.0\n" + -"3,b,110.0\n" + -"6,c,1.0E30\n" + -"8,d,1.0E30\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //2 months: - //note that Jan is the 0th month: so 2 months rounds to Jan 1, Mar 1, May 1 - String2.log("\nTest 2 months"); - sar = new StringArray(new String[]{ - "b", "b", "b", "b", "b", "b", "c", "a", "d", "a"}); - String sa[] = { - "-0002-08-28", //0 b -121 - "-0002-09-28", //1 b -100 - "", //2 b NaN - "2014-06-25", //3 b 110, - "2014-07-25", //4 b 132, - "-912345-12-28", //5 b -2, - "2010-04-05", //6 c 82, - "2016-09-25", //7 a 132, - "2010-04-05", //8 d 82, - "2016-09-10"}; //9 a 125}); - dar = new DoubleArray(); - for (int i = 0; i < 10; i++) - dar.add(Calendar2.safeIsoStringToEpochSeconds(sa[i])); - iar = new IntArray(new int[] { - 0, 1, 2, 3, 4, 5, 6, 7, 8, 9}); - table.clear(); - table.addColumn("iar", iar); - table.addColumn("sar", sar); - table.addColumn("dar", dar); - table.orderByClosest("sar, dar, 2 months"); - StringArray sar2 = new StringArray(); - for (int i = 0; i < dar.size(); i++) - sar2.add(Calendar2.safeEpochSecondsToIsoStringTZ(dar.get(i), "")); - table.setColumn(2, sar2); - results = table.dataToString(); - expected = -"iar,sar,dar\n" + -"9,a,2016-09-10T00:00:00Z\n" + -"5,b,-912345-12-28T00:00:00Z\n" + -"0,b,-0002-08-28T00:00:00Z\n" + -"3,b,2014-06-25T00:00:00Z\n" + -"6,c,2010-04-05T00:00:00Z\n" + -"8,d,2010-04-05T00:00:00Z\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //10 years: beware BC AD transition, see Calendar2.getYear - String2.log("\nTest 10 years"); - sar = new StringArray(new String[]{ - "b", "b", "b", "b", "b", "b", "c", "a", "d", "a"}); - sa = new String[] { - "-0002-12-30", //0 b -121 - "0004-01-14", //1 b -100 - "", //2 b NaN - "2018-06-25", //3 b 110, - "2024-07-25", //4 b 132, - "-912345-12-28",//5 b -2, - "0211-04-05", //6 c 82, - "2024-09-25", //7 a 132, - "0211-04-05", //8 d 82, - "2023-09-10"}; //9 a 125}); - dar = new DoubleArray(); - for (int i = 0; i < 10; i++) - dar.add(Calendar2.safeIsoStringToEpochSeconds(sa[i])); - iar = new IntArray(new int[] { - 0, 1, 2, 3, 4, 5, 6, 7, 8, 9}); - table.clear(); - table.addColumn("iar", iar); - table.addColumn("sar", sar); - table.addColumn("dar", dar); - table.orderByClosest("sar, dar, 10 years"); - sar2 = new StringArray(); - for (int i = 0; i < dar.size(); i++) - sar2.add(Calendar2.safeEpochSecondsToIsoStringTZ(dar.get(i), "")); - table.setColumn(2, sar2); - results = table.dataToString(); - expected = -"iar,sar,dar\n" + -"9,a,2023-09-10T00:00:00Z\n" + -"5,b,-912345-12-28T00:00:00Z\n" + -"0,b,-0002-12-30T00:00:00Z\n" + -"3,b,2018-06-25T00:00:00Z\n" + -"6,c,0211-04-05T00:00:00Z\n" + -"8,d,0211-04-05T00:00:00Z\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - } - - /** * This sorts the table by keyColumns (all ascending) then, * for each block where the nKeyColumns-1 values are constant, @@ -28022,89 +13661,6 @@ public void orderByCount(int keyCols[]) throws Exception { if (someConverted) temporarilySwitchNaNToFakeMissingValues(keyCols); } - - - /** - * This tests orderByCount. - */ - public static void testOrderByCount() throws Exception { - String2.log("\n*** Table.testOrderByCount()"); - - //test 2 orderyBy variables - ShortArray shar = new ShortArray(new short[]{ - 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 2, 2, 2}); - StringArray sar = new StringArray(new String[]{ - "b", "b", "b", "b", "b", "b", "c", "a", "d", "a", "c", "a", ""}); - DoubleArray dar = new DoubleArray(new double[]{ - -121,-100, Double.NaN, 110, 132, -2, 1e30, 132, 1e30,125, 1.1, 1.2, 1.3}); - ByteArray bar = (ByteArray) new ByteArray(new byte[]{ //127=NaN - 0, 127, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}).setMaxIsMV(true); - Table table = new Table(); - table.addColumn("shar",shar); - table.addColumn("bar", bar); - table.addColumn("sar", sar); - table.addColumn("dar", dar); - table.orderByCount(new String[]{"shar","sar"}); - String results = table.toString(); - String expected = -"{\n" + -"dimensions:\n" + -"\trow = 7 ;\n" + -"\tsar_strlen = 1 ;\n" + -"variables:\n" + -"\tshort shar(row) ;\n" + -"\tint bar(row) ;\n" + -"\t\tbar:units = \"count\" ;\n" + -"\tchar sar(row, sar_strlen) ;\n" + -"\tint dar(row) ;\n" + -"\t\tdar:units = \"count\" ;\n" + -"\n" + -"// global attributes:\n" + -"}\n" + -"shar,bar,sar,dar\n" + -"2,1,,1\n" + -"2,1,a,1\n" + -"2,1,c,1\n" + -"100,2,a,2\n" + -"100,5,b,5\n" + -"100,1,c,1\n" + -"100,1,d,1\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - //test 0 orderBy variables - sar = new StringArray(new String[]{ - "b", "b", "b", "b", "b", "b", "c", "a", "d", "a", "c", "a", ""}); - dar = new DoubleArray(new double[]{ - -121,-100, Double.NaN, 110, 132, -2, 1e30, 132, 1e30,125, 1.1, 1.2, 1.3}); - bar = (ByteArray)new ByteArray(new byte[]{ //127=NaN - 0, 127, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12}).setMaxIsMV(true); - table = new Table(); - table.addColumn("bar", bar); - table.addColumn("sar", sar); - table.addColumn("dar", dar); - table.orderByCount(new String[]{}); - results = table.toString(); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 1 ;\n" + -"variables:\n" + -"\tint bar(row) ;\n" + -"\t\tbar:units = \"count\" ;\n" + -"\tint sar(row) ;\n" + -"\t\tsar:units = \"count\" ;\n" + -"\tint dar(row) ;\n" + -"\t\tdar:units = \"count\" ;\n" + -"\n" + -"// global attributes:\n" + -"}\n" + -"bar,sar,dar\n" + -"12,12,12\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - } - - /** * This is a higher level orderByLimit that takes the csv string @@ -28204,33 +13760,6 @@ public void orderByLimit(int keyColumns[], int limitN) throws Exception { temporarilySwitchNaNToFakeMissingValues(keyColumns); } - /** - * This tests orderByLimit. - */ - public static void testOrderByLimit() throws Exception { - String2.log("\n*** Table.testOrderByLimit()"); - - StringArray sar = new StringArray(new String[]{ - "b", "b", "b", "b", "b", "b", "c", "a", "d", "a"}); - IntArray iar = new IntArray(new int[] { - 0, 1, 2, 3, 4, 5, 6, 7, 8, 9}); - Table table = new Table(); - table.addColumn("iar", iar); - table.addColumn("sar", sar); - table.orderByLimit("sar, 2"); - String results = table.dataToString(); - String expected = -"iar,sar\n" + -"7,a\n" + -"9,a\n" + -"0,b\n" + -"1,b\n" + -"6,c\n" + -"8,d\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - } - - /** * This is like the other saveAsMatlab, but writes to a file. * @@ -28463,74 +13992,6 @@ public void saveAsMatlab(OutputStream outputStream, String structureName) } - /** - * This tests saveAsMatlab(). - * - * @throws Exception if trouble - */ - public static void testSaveAsMatlab() throws Exception { - verbose = true; - reallyVerbose = true; - //see gov.noaa.pfel.coastwatch.griddata.Matlab class for summary of Matlab commands - - String2.log("\n***** Table.testSaveAsMatlab"); - Table table = new Table(); - table.addColumn("ints", new IntArray(new int[]{1,2,3})); - table.addColumn("floats", new FloatArray(new float[]{1.1f, 2.2f, 3.3f})); - table.addColumn("Strings", new StringArray(new String[]{"a", "bb", "ccc"})); - table.addColumn("doubles", new DoubleArray(new double[]{1.111, 2.222, 3.333})); - String dir = "c:/temp/"; - File2.delete(dir + "temp.mat"); - table.saveAsMatlab(dir + "temp.mat", "sst"); //names of length 3,4,5 were a challenge - String mhd = File2.hexDump(dir + "temp.mat", 1000); - String2.log(mhd); - //String2.log("\nsst.mat=\n" + File2.hexDump(dir + "sst.mat", 1000)); - Test.ensureEqual( - mhd.substring(0, 71 * 4) + mhd.substring(71 * 7), //remove the creation dateTime -"4d 41 54 4c 41 42 20 35 2e 30 20 4d 41 54 2d 66 MATLAB 5.0 MAT-f |\n" + -"69 6c 65 2c 20 43 72 65 61 74 65 64 20 62 79 3a ile, Created by: |\n" + -"20 67 6f 76 2e 6e 6f 61 61 2e 70 66 65 6c 2e 63 gov.noaa.pfel.c |\n" + -"6f 61 73 74 77 61 74 63 68 2e 4d 61 74 6c 61 62 oastwatch.Matlab |\n" + -//"2c 20 43 72 65 61 74 65 64 20 6f 6e 3a 20 4d 6f , Created on: Mo |\n" + -//"6e 20 46 65 62 20 31 31 20 30 39 3a 31 31 3a 30 n Feb 11 09:11:0 |\n" + -//"30 20 32 30 30 38 20 20 20 20 20 20 20 20 20 20 0 2008 |\n" + -"20 20 20 20 00 00 00 00 00 00 00 00 01 00 4d 49 MI |\n" + -"00 00 00 0e 00 00 01 e8 00 00 00 06 00 00 00 08 |\n" + -"00 00 00 02 00 00 00 00 00 00 00 05 00 00 00 08 |\n" + -"00 00 00 01 00 00 00 01 00 03 00 01 73 73 74 00 sst |\n" + -"00 04 00 05 00 00 00 20 00 00 00 01 00 00 00 80 |\n" + -"69 6e 74 73 00 00 00 00 00 00 00 00 00 00 00 00 ints |\n" + -"00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |\n" + -"66 6c 6f 61 74 73 00 00 00 00 00 00 00 00 00 00 floats |\n" + -"00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |\n" + -"53 74 72 69 6e 67 73 00 00 00 00 00 00 00 00 00 Strings |\n" + -"00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |\n" + -"64 6f 75 62 6c 65 73 00 00 00 00 00 00 00 00 00 doubles |\n" + -"00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |\n" + -"00 00 00 0e 00 00 00 40 00 00 00 06 00 00 00 08 @ |\n" + -"00 00 00 0c 00 00 00 00 00 00 00 05 00 00 00 08 |\n" + -"00 00 00 03 00 00 00 01 00 00 00 01 00 00 00 00 |\n" + -"00 00 00 05 00 00 00 0c 00 00 00 01 00 00 00 02 |\n" + -"00 00 00 03 00 00 00 00 00 00 00 0e 00 00 00 40 @ |\n" + -"00 00 00 06 00 00 00 08 00 00 00 07 00 00 00 00 |\n" + -"00 00 00 05 00 00 00 08 00 00 00 03 00 00 00 01 |\n" + -"00 00 00 01 00 00 00 00 00 00 00 07 00 00 00 0c |\n" + -"3f 8c cc cd 40 0c cc cd 40 53 33 33 00 00 00 00 ? @ @S33 |\n" + -"00 00 00 0e 00 00 00 48 00 00 00 06 00 00 00 08 H |\n" + -"00 00 00 04 00 00 00 00 00 00 00 05 00 00 00 08 |\n" + -"00 00 00 03 00 00 00 03 00 00 00 01 00 00 00 00 |\n" + -"00 00 00 04 00 00 00 12 00 61 00 62 00 63 00 20 a b c |\n" + -"00 62 00 63 00 20 00 20 00 63 00 00 00 00 00 00 b c c |\n" + -"00 00 00 0e 00 00 00 48 00 00 00 06 00 00 00 08 H |\n" + -"00 00 00 06 00 00 00 00 00 00 00 05 00 00 00 08 |\n" + -"00 00 00 03 00 00 00 01 00 00 00 01 00 00 00 00 |\n" + -"00 00 00 09 00 00 00 18 3f f1 c6 a7 ef 9d b2 2d ? - |\n" + -"40 01 c6 a7 ef 9d b2 2d 40 0a a9 fb e7 6c 8b 44 @ -@ l D |\n", -"mhd=" + mhd); - //File2.delete(dir + "temp.mat"); - } - - /** * Save this table of data as a flat netCDF .nc file (a column for each * variable, all referencing one dimension) using the currently @@ -29878,176 +15339,6 @@ public int isoStringToEpochSeconds(int col, int type, return nGood; } - /** - * This tests the readSql and saveAsSql methods. - * @throws Exception if trouble - */ - public static void testSql() throws Exception { - String2.log("\n*** Table.testSql"); - verbose = true; - reallyVerbose = true; - - //load the sql driver (the actual driver .jar must be in the classpath) - Class.forName("org.postgresql.Driver"); - - //set up connection and query - String url = "jdbc:postgresql://otter.pfeg.noaa.gov/posttest"; //database name - String user = "postadmin"; - String password = String2.getPasswordFromSystemIn("Password for '" + user + "'? "); - if (password.length() == 0) { - String2.log("No password, so skipping the test."); - return; - } - long tTime = System.currentTimeMillis(); - Connection con = DriverManager.getConnection(url, user, password); - String2.log("getConnection time=" + (System.currentTimeMillis() - tTime) + "ms"); //often 9s ! - - DatabaseMetaData dm = con.getMetaData(); - String2.log("getMaxRowSize=" + dm.getMaxRowSize()); //1GB - - //get catalog info -- has one col with name(s) of databases for this user - //... - - //test getSqlSchemas - StringArray schemas = getSqlSchemas(con); - Test.ensureTrue(schemas.indexOf("public") >= 0, "schemas=" + schemas.toString()); - - //sometimes: make names table - if (false) { - Table namesTable = new Table(); - namesTable.addColumn("id", PrimitiveArray.factory(new int[]{1,2,3})); - namesTable.addColumn("first_name", PrimitiveArray.factory(new String[]{"Bob", "Nate", "Nancy"})); - namesTable.addColumn("last_name", PrimitiveArray.factory(new String[]{"Smith", "Smith", "Jones"})); - namesTable.saveAsSql( - con, true, //'true' tests dropSqlTable, too - "names", 0, null, null, null, 2); - } - - //test getSqlTableNames - StringArray tableNames = getSqlTableNames(con, "public", new String[]{"TABLE"}); - String2.log("tableNames=" + tableNames); - Test.ensureTrue(tableNames.indexOf("names") >= 0, "tableNames=" + tableNames.toString()); - Test.ensureTrue(tableNames.indexOf("zztop") < 0, "tableNames=" + tableNames.toString()); //doesn't exist - - //test getSqlTableType - Test.ensureEqual(getSqlTableType(con, "public", "names"), "TABLE", ""); - Test.ensureEqual(getSqlTableType(con, "public", "zztop"), null, ""); //doesn't exist - - - //*** test saveAsSql (create a table) (this tests dropSqlTable, too) - if (true) { - String tempTableName = "TempTest"; - String dates[] = {"1960-01-02", "1971-01-02", null, "2020-12-31"}; - double dateDoubles[] = new double[4]; - String timestamps[] = {"1960-01-02 01:02:03", "1971-01-02 07:08:09", null, "2020-12-31 23:59:59"}; - double timestampDoubles[] = new double[4]; - String times[] = {"01:02:03", "07:08:09", null, "23:59:59"}; - for (int i = 0; i < 4; i++) { - dateDoubles[i] = dates[i] == null? Double.NaN : Calendar2.isoStringToEpochSeconds(dates[i]); - timestampDoubles[i] = timestamps[i] == null? Double.NaN : Calendar2.isoStringToEpochSeconds(timestamps[i]); - } - Table tempTable = new Table(); - tempTable.addColumn("uid", PrimitiveArray.factory(new int[]{1,2,3,4})); - tempTable.addColumn("short", PrimitiveArray.factory(new short[]{-10, 0, Short.MAX_VALUE, 10})); - //Math2.random makes this test different every time. ensures old table is dropped and new one created. - tempTable.addColumn("int", PrimitiveArray.factory(new int[]{Math2.random(1000), 0, Integer.MAX_VALUE, 20})); - tempTable.addColumn("long", PrimitiveArray.factory(new long[]{-30, 0, Long.MAX_VALUE, 30})); - tempTable.addColumn("float", PrimitiveArray.factory(new float[]{-44.4f, 0f, Float.NaN, 44.4f})); - tempTable.addColumn("double", PrimitiveArray.factory(new double[]{-55.5, 0, Double.NaN, 55.5})); - tempTable.addColumn("string", PrimitiveArray.factory(new String[]{"ab", "", null, "longer"})); - tempTable.addColumn("date", PrimitiveArray.factory(dateDoubles)); - tempTable.addColumn("timestamp", PrimitiveArray.factory(timestampDoubles)); - tempTable.addColumn("time", PrimitiveArray.factory(times)); - tempTable.saveAsSql( - con, true, //'true' tests dropSqlTable, too - tempTableName, 0, new int[]{7}, new int[]{8}, new int[]{9}, 1.5); - - //test readSql (read a table) - Table tempTable2 = new Table(); - tempTable2.readSql(con, "SELECT * FROM " + tempTableName); - Test.ensureEqual(tempTable, tempTable2, ""); - - - //*** test rollback: add data that causes database to throw exception - tempTable2.setIntData(0, 0, 5); //ok - tempTable2.setIntData(0, 1, 6); //ok - tempTable2.setIntData(0, 2, 7); //ok - tempTable2.setIntData(0, 3, 1); //not ok because not unique - try { //try to add new tempTable2 to database table - tempTable2.saveAsSql( - con, false, //false, so added to previous data - tempTableName, 0, new int[]{7}, new int[]{8}, new int[]{9}, 1.5); - String2.log("Shouldn't get here."); Math2.sleep(60000); - } catch (Exception e) { - //this error is expected - //make sure it has both parts of the error message - String2.log("\nEXPECTED " + String2.ERROR + ":\n" + MustBe.throwableToString(e)); - Test.ensureTrue(e.toString().indexOf( - "PSQLException: " + String2.ERROR + - ": duplicate key violates unique constraint \"temptest_pkey\"") >= 0, - "(A) The error was: " + e.toString()); - Test.ensureTrue(e.toString().indexOf( - "java.sql.BatchUpdateException: Batch entry 3 INSERT INTO TempTest (") >= 0, - "(B)The error was: " + e.toString()); - } - - //and ensure database was rolled back to previous state - tempTable2.readSql(con, "SELECT * FROM " + tempTableName); - Test.ensureEqual(tempTable, tempTable2, ""); - - - //*** test pre-execute errors: add data that causes saveAsSql to throw exception - tempTable2.setIntData(0, 0, 5); //ok, so new rows can be added - tempTable2.setIntData(0, 1, 6); //ok - tempTable2.setIntData(0, 2, 7); //ok - tempTable2.setIntData(0, 3, 8); //ok - int timeCol = tempTable2.findColumnNumber("time"); - //invalid date will be caught before statement is fully prepared - tempTable2.setStringData(timeCol, 3, "20.1/30"); //first 3 rows succeed, this should fail - try { //try to add new tempTable2 to database table - tempTable2.saveAsSql( - con, false, //false, so added to previous data - tempTableName, 0, new int[]{7}, new int[]{8}, new int[]{9}, 1.5); - String2.log("Shouldn't get here."); Math2.sleep(60000); - } catch (Exception e) { - //this error is expected - //make sure it is the right error - String2.log("\nEXPECTED " + String2.ERROR + ":\n" + MustBe.throwableToString(e)); - Test.ensureTrue(e.toString().indexOf( - "java.lang.RuntimeException: ERROR in Table.saveAsSql(TempTest):\n" + - "Time format must be " + - "HH:MM:SS. Bad value=20.1/30 in row=3 col=9") >= 0, - "error=" + e.toString()); - } - - //and ensure it rolls back to previous state - tempTable2.readSql(con, "SELECT * FROM " + tempTableName); - Test.ensureEqual(tempTable, tempTable2, ""); - - - //*** test successfully add data (and ensure previous rollbacks worked - //assign row numbers so new rows can be added (and so different from possibly added 5,6,7,8) - tempTable2.setIntData(0, 0, 9); //ok, - tempTable2.setIntData(0, 1, 10); //ok - tempTable2.setIntData(0, 2, 11); //ok - tempTable2.setIntData(0, 3, 12); //ok - tempTable2.saveAsSql( - con, false, //false, so added to previous data - tempTableName, 0, new int[]{7}, new int[]{8}, new int[]{9}, 1.5); - - //and ensure result has 8 rows - tempTable2.readSql(con, "SELECT uid, string FROM " + tempTableName); - Test.ensureEqual(tempTable2.getColumn(0).toString(), "1, 2, 3, 4, 9, 10, 11, 12", ""); - Test.ensureEqual(tempTable2.getColumn(1).toString(), "ab, , [null], longer, ab, , [null], longer", ""); - } - - //don't drop the table, so I can view it in phpPgAdmin - -//how read just column names and types? query that returns no rows??? - - } - - /** * This is like the other saveAsTabbedASCII that writes to a file, * but this uses the ISO-8859-1 charset. @@ -30893,165 +16184,7 @@ public void writeJsonlCSV(String fullFileName, boolean append) throws Exception } - /** - * The tests readJsonLinesCsv. - */ - public static void testJsonlCSV() throws Exception { - String2.log("\n* String2.testReadJsonlCSV()\n" + - "The WARNING's below are expected..."); - - String source = - "[\"a\",\"\",\"ccc\",\"dddd\"]\n" + - "[2,1.5,\" c3\u00b5\u20acz\\\\q\\f\\n\\r\\t\\u00b5\\u20ac \",true]\n" + - "[\"BAD ROW WITH WRONG NUMBER OF ITEMS\"]\n" + - "[\"BAD ROW with unterminated string ]\n" + - "BAD ROW WITHOUT JSON ARRAY.\n" + - " [null, null, \"1\", null] \n" + - " "; - - //don't simplify - StringReader sr = new StringReader(source); - Table table = new Table(); - table.readJsonlCSV(sr, "[StringReader]", null, null, false); - String results = table.dataToString(); - Test.ensureEqual(results, -"a,,ccc,dddd\n" + -"2,1.5,\"\"\" c3\\u00b5\\u20acz\\\\\\\\q\\\\f\\\\n\\\\r\\\\t\\\\u00b5\\\\u20ac \"\"\",true\n" + //?! not sure if correct -",,\"\"\"1\"\"\",\n", - "results=\n" + results); - - //simplify - sr = new StringReader(source); - table = new Table(); - table.readJsonlCSV(sr, "[StringReader]", null, null, true); - results = table.dataToString(); - Test.ensureEqual(results, -"a,,ccc,dddd\n" + -"2,1.5,\" c3\\u00b5\\u20acz\\\\q\\f\\n\\r\\t\\u00b5\\u20ac \",1\n" + -",,1,\n", - "results=\n" + results); - - //specify colNames and simplify - sr = new StringReader(source); - table = new Table(); - table.readJsonlCSV(sr, "[StringReader]", StringArray.fromCSV("ccc,a,dddd"), null, true); - results = table.dataToString(); - Test.ensureEqual(results, -"ccc,a,dddd\n" + -"\" c3\\u00b5\\u20acz\\\\q\\f\\n\\r\\t\\u00b5\\u20ac \",2,1\n" + -"1,,\n", - "results=\n" + results); - Test.ensureEqual(table.getColumn(0).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(1).elementTypeString(), "byte", ""); - Test.ensureEqual(table.getColumn(2).elementTypeString(), "byte", ""); //boolean -> byte - - //specify colNames and types - sr = new StringReader(source); - table = new Table(); - table.readJsonlCSV(sr, "[StringReader]", StringArray.fromCSV("ccc,a,dddd"), - new String[]{"String", "int", "boolean"}, true); - results = table.dataToString(); - Test.ensureEqual(results, -"ccc,a,dddd\n" + -"\" c3\\u00b5\\u20acz\\\\q\\f\\n\\r\\t\\u00b5\\u20ac \",2,1\n" + -"1,,\n", - "results=\n" + results); - Test.ensureEqual(table.getColumn(0).elementTypeString(), "String", ""); - Test.ensureEqual(table.getColumn(1).elementTypeString(), "int", ""); - Test.ensureEqual(table.getColumn(2).elementTypeString(), "byte", ""); //boolean -> byte - - //tough test table - String fullName = testDir + "testJsonCSV.jsonl"; - File2.delete(fullName); - table = makeToughTestTable(); - results = table.dataToString(); - String expected = -"aString,aChar,aByte,aUByte,aShort,aUShort,anInt,aUInt,aLong,aULong,aFloat,aDouble\n" + -"a\\u00fcb\\nc\\td\\u20ace,\\u00fc,-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308\n" + -"ab,\\u0000,0,127,0,32767,0,7,0,1,2.2,3.3\n" + -",A,99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324\n" + -"cd,\\t,126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308\n" + -",\\u20ac,,,,,,,,,,\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - table.writeJsonlCSV(fullName); - table.clear(); //doubly sure - table.readJsonlCSV(fullName, null, null, true); //simplify - results = table.dataToString(); - expected = //differs in that aULong is now a double column (because simplify doesn't catch unsigned types) -"aString,aChar,aByte,aUByte,aShort,aUShort,anInt,aUInt,aLong,aULong,aFloat,aDouble\n" + -"a\\u00fcb\\nc\\td\\u20ace,\\u00fc,-128,0,-32768,0,-2147483648,0,-9223372036854775808,0.0,-3.4028235E38,-1.7976931348623157E308\n" + -"ab,\\u0000,0,127,0,32767,0,7,0,1.0,2.2,3.3\n" + -",A,99,99,9999,9999,999999999,2147483647,8,9.223372036854776E18,1.4E-45,4.9E-324\n" + -"cd,\\t,126,254,32766,65534,2147483646,4294967294,9223372036854775806,1.8446744073709552E19,3.4028235E38,1.7976931348623157E308\n" + -",\\u20ac,,,,,,,,,,\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - PAType tTypes[] = { - PAType.STRING, PAType.STRING, PAType.BYTE, PAType.SHORT, PAType.SHORT, //char->String, unsigned -> larger signed - PAType.INT, PAType.INT, PAType.LONG, PAType.LONG, PAType.DOUBLE, //ULong -> Double - PAType.DOUBLE, PAType.DOUBLE}; //float->double because lots of decimal digits - for (int col = 0; col < 12; col++) - Test.ensureEqual(table.getColumn(col).elementType(), tTypes[col], "col=" + col); - - //another hard test - fullName = String2.unitTestDataDir + "jsonl/sampleCSV.jsonl"; - table.readJsonlCSV(fullName, null, null, true); //simpify - results = table.dataToString(); - Test.ensureEqual(results, -"ship,time,lat,lon,status,testLong,sst\n" + -"Bell M. Shimada,2017-03-23T00:45:00Z,28.0002,-130.2576,A,-9223372036854775808,10.9\n" + -"Bell M. Shimada,2017-03-23T01:45:00Z,28.0003,-130.3472,\\u20ac,-1234567890123456,\n" + -"Bell M. Shimada,2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,0,10.7\n" + -"Bell M. Shimada,2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",1234567890123456,99.0\n" + -"\" a\\t~\\u00fc,\\n'z\"\"\\u20ac\",2017-03-23T21:45:00Z,28.0003,-132.0014,\\u00fc,9223372036854775806,10.0\n" + -",,,,,,\n", - "results=\n" + results); - - //*** write new file - table = makeToughTestTable(); - fullName = File2.getSystemTempDirectory() + "testJsonlCSV.json"; - table.writeJsonlCSV(fullName); - results = File2.directReadFromUtf8File(fullName); - Test.ensureEqual(results, -"[\"aString\",\"aChar\",\"aByte\",\"aUByte\",\"aShort\",\"aUShort\",\"anInt\",\"aUInt\",\"aLong\",\"aULong\",\"aFloat\",\"aDouble\"]\n" + -"[\"a\\u00fcb\\nc\\td\\u20ace\",\"\\u00fc\",-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308]\n" + -"[\"ab\",\"\\u0000\",0,127,0,32767,0,7,0,1,2.2,3.3]\n" + -"[\"\",\"A\",99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324]\n" + -"[\"cd\",\"\\t\",126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308]\n" + -"[\"\",\"\\u20ac\",null,null,null,null,null,null,null,null,null,null]\n", - "results=\n" + results); - - //*** write/append new file - table = makeToughTestTable(); - File2.delete(fullName); - table.writeJsonlCSV(fullName, true); - results = File2.directReadFromUtf8File(fullName); - Test.ensureEqual(results, -"[\"aString\",\"aChar\",\"aByte\",\"aUByte\",\"aShort\",\"aUShort\",\"anInt\",\"aUInt\",\"aLong\",\"aULong\",\"aFloat\",\"aDouble\"]\n" + -"[\"a\\u00fcb\\nc\\td\\u20ace\",\"\\u00fc\",-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308]\n" + -"[\"ab\",\"\\u0000\",0,127,0,32767,0,7,0,1,2.2,3.3]\n" + -"[\"\",\"A\",99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324]\n" + -"[\"cd\",\"\\t\",126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308]\n" + -"[\"\",\"\\u20ac\",null,null,null,null,null,null,null,null,null,null]\n", - "results=\n" + results); - - //then append - table.writeJsonlCSV(fullName, true); - results = File2.directReadFromUtf8File(fullName); - Test.ensureEqual(results, -"[\"aString\",\"aChar\",\"aByte\",\"aUByte\",\"aShort\",\"aUShort\",\"anInt\",\"aUInt\",\"aLong\",\"aULong\",\"aFloat\",\"aDouble\"]\n" + -"[\"a\\u00fcb\\nc\\td\\u20ace\",\"\\u00fc\",-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308]\n" + -"[\"ab\",\"\\u0000\",0,127,0,32767,0,7,0,1,2.2,3.3]\n" + -"[\"\",\"A\",99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324]\n" + -"[\"cd\",\"\\t\",126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308]\n" + -"[\"\",\"\\u20ac\",null,null,null,null,null,null,null,null,null,null]\n" + -"[\"a\\u00fcb\\nc\\td\\u20ace\",\"\\u00fc\",-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308]\n" + -"[\"ab\",\"\\u0000\",0,127,0,32767,0,7,0,1,2.2,3.3]\n" + -"[\"\",\"A\",99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324]\n" + -"[\"cd\",\"\\t\",126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308]\n" + -"[\"\",\"\\u20ac\",null,null,null,null,null,null,null,null,null,null]\n", - "results=\n" + results); - - } + @@ -31612,84 +16745,6 @@ public String directoryListing(String localDir, String showUrlDir, String userQu return sb.toString(); } - - /** - * Test saveAsJson and readJson. - * - * @throws Exception if trouble - */ - public static void testJson() throws Exception { - String2.log("\n***** Table.testJson"); - verbose = true; - reallyVerbose = true; - - //generate some data - Table table = getTestTable(true, true); - - //write it to a file - String fileName = testDir + "tempTable.json"; - table.saveAsJson(fileName, 0, true); - //String2.log(fileName + "=\n" + File2.readFromFile(fileName)[1]); - //Test.displayInBrowser("file://" + fileName); //.json - - //read it from the file - String results = File2.directReadFromUtf8File(fileName); - Test.ensureEqual(results, -"{\n" + -" \"table\": {\n" + -" \"columnNames\": [\"Time\", \"Longitude\", \"Latitude\", \"Double Data\", \"Long Data\", \"Int Data\", \"Short Data\", \"Byte Data\", \"Char Data\", \"String Data\"],\n" + -" \"columnTypes\": [\"String\", \"int\", \"float\", \"double\", \"long\", \"int\", \"short\", \"byte\", \"char\", \"String\"],\n" + -" \"columnUnits\": [\"UTC\", \"degrees_east\", \"degrees_north\", \"doubles\", \"longs\", \"ints\", \"shorts\", \"bytes\", \"chars\", \"Strings\"],\n" + -" \"rows\": [\n" + -" [\"1970-01-01T00:00:00Z\", -3, 1.0, -1.0E300, -2000000000000000, -2000000000, -32000, -120, \",\", \"a\"],\n" + -" [\"2005-08-31T16:01:02Z\", -2, 1.5, 3.123, 2, 2, 7, 8, \"\\\"\", \"bb\"],\n" + -" [\"2005-11-02T18:04:09Z\", -1, 2.0, 1.0E300, 2000000000000000, 2000000000, 32000, 120, \"\\u20ac\", \"ccc\"],\n" + -" [null, null, null, null, null, null, null, null, \"\", \"\"]\n" + -" ]\n" + -" }\n" + -"}\n", - results); - - //read it - Table table2 = new Table(); - table2.readJson(fileName); - Test.ensureTrue(table.equals(table2), ""); - - //finally - File2.delete(fileName); - - //******************* test readErddapInfo - //String tUrl = "https://coastwatch.pfeg.noaa.gov/erddap2"; - //http://localhost:8080/cwexperimental/info/pmelTaoDySst/index.json - String tUrl = "http://localhost:8080/cwexperimental"; - table.readErddapInfo(tUrl + "/info/pmelTaoDySst/index.json"); - String ncHeader = table.getNCHeader("row"); - Test.ensureEqual(table.globalAttributes.getString("cdm_data_type"), "TimeSeries", ncHeader); - Test.ensureEqual(table.globalAttributes.getString("title"), - "TAO/TRITON, RAMA, and PIRATA Buoys, Daily, 1977-present, Sea Surface Temperature", - ncHeader); - Test.ensureEqual(table.globalAttributes.get("history").size(), 3, ncHeader); - Test.ensureEqual(table.globalAttributes.get("history").getString(0), - "This dataset has data from the TAO/TRITON, RAMA, and PIRATA projects.", - ncHeader); - Test.ensureEqual(table.globalAttributes.get("history").getString(1), - "This dataset is a product of the TAO Project Office at NOAA/PMEL.", - ncHeader); - Test.ensureLinesMatch(table.globalAttributes.get("history").getString(2), - "20\\d{2}-\\d{2}-\\d{2} Bob Simons at NOAA/NMFS/SWFSC/ERD \\(bob.simons@noaa.gov\\) " + - "fully refreshed ERD's copy of this dataset by downloading all of the .cdf files from the PMEL TAO FTP site. " + - "Since then, the dataset has been partially refreshed everyday by downloading and merging the latest version of the last 25 days worth of data.", - ncHeader); - Test.ensureEqual(table.nColumns(), 10, ncHeader); - Test.ensureEqual(table.findColumnNumber("longitude"), 3, ncHeader); - Test.ensureEqual(table.columnAttributes(3).getString("units"), "degrees_east", ncHeader); - int t25Col = table.findColumnNumber("T_25"); - Test.ensureTrue(t25Col > 0, ncHeader); - Test.ensureEqual(table.columnAttributes(t25Col).getString("ioos_category"), "Temperature", ncHeader); - Test.ensureEqual(table.columnAttributes(t25Col).getString("units"), "degree_C", ncHeader); - - } - /** * This saves the current table in some type of file. * If the file already exists, it is touched, and nothing else is done. @@ -31819,106 +16874,6 @@ else if (inType == READ_OPENDAP_SEQUENCE) table.saveAs(outFullName, outType, dimensionName, zipIt); } - - /** - * Test convert. - */ - public static void testConvert() throws Exception { - verbose = true; - reallyVerbose = true; - String url, fileName; - Table table = new Table(); - -// /* - //the original test from Roy - //This is used as an example in various documentation. - //If url changes, do search and replace to change all references to it. - url = "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_bottle?t0,oxygen&month=\"5\""; - String2.log("\ntesting Table.convert \n url=" + url); - fileName = testDir + "convertOriginal.nc"; - convert(url, READ_OPENDAP_SEQUENCE, fileName, SAVE_AS_FLAT_NC, "row", false); - table.readFlatNc(fileName, null, 0); //standardizeWhat=0, should be already unpacked. - String2.log(table.toString(3)); - Test.ensureEqual(table.nColumns(), 2, ""); - Test.ensureEqual(table.nRows(), 190, ""); - Test.ensureEqual(table.getColumnName(0), "t0", ""); - Test.ensureEqual(table.getColumnName(1), "oxygen", ""); - Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Temperature T0", ""); - Test.ensureEqual(table.columnAttributes(1).getString("long_name"), "Oxygen", ""); - Test.ensureEqual(table.getFloatData(0, 0), 12.1185f, ""); - Test.ensureEqual(table.getFloatData(0, 1), 12.1977f, ""); - Test.ensureEqual(table.getFloatData(1, 0), 6.56105f, ""); - Test.ensureEqual(table.getFloatData(1, 1), 6.95252f, ""); - File2.delete(fileName); -// */ - -// /* - //The 8/16/06 test from osu - //Test values below from html ascii request (same as url below, but with .ascii before "?") - //adcp95.yearday, adcp95.depth, adcp95.x, adcp95.y, adcp95.eastv - //row0: 184.45120239257812, 22, -123.8656005859375, 48.287899017333984, -0.31200000643730164 - //last row: 185.99949645996094, 22, -125.98069763183594, 42.844200134277344, -0.15399999916553497 - url = "http://nwioos.coas.oregonstate.edu:8080/dods/drds/1995%20Hake%20Survey%20ADCP?ADCP95.yearday,ADCP95.Z,ADCP95.x,ADCP95.y,ADCP95.EV&ADCP95.yearday<186&ADCP95.Z<25"; - String2.log("\ntesting Table.convert \n url=" + url); - fileName = testDir + "convertOSU.nc"; - convert(url, READ_OPENDAP_SEQUENCE, fileName, SAVE_AS_FLAT_NC, "row", false); - table.readFlatNc(fileName, null, 0); //standardizeWhat=0, should be already unpacked. - String2.log(table.toString(3)); - Test.ensureEqual(table.nColumns(), 5, ""); - Test.ensureEqual(table.nRows(), 446, ""); - Test.ensureEqual(table.getColumnName(0), "yearday", ""); - Test.ensureEqual(table.getColumnName(1), "Z", ""); - Test.ensureEqual(table.getColumnName(2), "x", ""); - Test.ensureEqual(table.getColumnName(3), "y", ""); - Test.ensureEqual(table.getColumnName(4), "EV", ""); - //no attributes - Test.ensureEqual(table.getDoubleData(0, 0), 184.45120239257812, ""); - Test.ensureEqual(table.getDoubleData(1, 0), 22, ""); - Test.ensureEqual(table.getDoubleData(2, 0), -123.8656005859375, ""); - Test.ensureEqual(table.getDoubleData(3, 0), 48.287899017333984, ""); - Test.ensureEqual(table.getDoubleData(4, 0), -0.31200000643730164, ""); - Test.ensureEqual(table.getDoubleData(0, 445), 185.99949645996094, ""); - Test.ensureEqual(table.getDoubleData(1, 445), 22, ""); - Test.ensureEqual(table.getDoubleData(2, 445), -125.98069763183594, ""); - Test.ensureEqual(table.getDoubleData(3, 445), 42.844200134277344, ""); - Test.ensureEqual(table.getDoubleData(4, 445), -0.15399999916553497, ""); - File2.delete(fileName); -// */ - -// /* - //The 8/17/06 test from cimt - //Test values below from html ascii request (same as url below, but with .ascii before "?") - //vCTD.latitude, vCTD.longitude, vCTD.station, vCTD.depth, vCTD.salinity - //first: 36.895, -122.082, "T101", 1.0, 33.9202 - //last: 36.609, -121.989, "T702", 4.0, 33.4914 - url = "http://cimt.dyndns.org:8080/dods/drds/vCTD?vCTD.latitude,vCTD.longitude,vCTD.station,vCTD.depth,vCTD.salinity&vCTD.depth<5"; - String2.log("\ntesting Table.convert \n url=" + url); - fileName = testDir + "convertCIMT.nc"; - convert(url, READ_OPENDAP_SEQUENCE, fileName, SAVE_AS_FLAT_NC, "row", false); - table.readFlatNc(fileName, null, 0); //standardizeWhat=0, should be already unpacked. - String2.log(table.toString(3)); - Test.ensureEqual(table.nColumns(), 5, ""); - //Test.ensureEqual(table.nRows(), 1407, ""); //this changes; file is growing - Test.ensureEqual(table.getColumnName(0), "latitude", ""); - Test.ensureEqual(table.getColumnName(1), "longitude", ""); - Test.ensureEqual(table.getColumnName(2), "station", ""); - Test.ensureEqual(table.getColumnName(3), "depth", ""); - Test.ensureEqual(table.getColumnName(4), "salinity", ""); - //no attributes - Test.ensureEqual(table.getFloatData(0, 0), 36.895f, ""); - Test.ensureEqual(table.getFloatData(1, 0), -122.082f, ""); - Test.ensureEqual(table.getStringData(2, 0), "T101", ""); - Test.ensureEqual(table.getFloatData(3, 0), 1.0f, ""); - Test.ensureEqual(table.getFloatData(4, 0), 33.9202f, ""); - Test.ensureEqual(table.getFloatData(0, 1406), 36.609f, ""); - Test.ensureEqual(table.getFloatData(1, 1406), -121.989f, ""); - Test.ensureEqual(table.getStringData(2, 1406), "T702", ""); - Test.ensureEqual(table.getFloatData(3, 1406), 4.0f, ""); - Test.ensureEqual(table.getFloatData(4, 1406), 33.4914f, ""); - File2.delete(fileName); -// */ - } - /** * This rearranges the columns to be by case-insensitive alphabetical column name. */ @@ -31928,60 +16883,6 @@ public void sortColumnsByName() { reorderColumns(tColNames, false); } - /** - * This tests sortColumnsByName (and reorderColumns). - */ - public static void testSortColumnsByName() { - verbose = true; - reallyVerbose = true; - String2.log("\n***** Table.testSortColumnsByName"); - Table table = getTestTable(true, true); - table.setColumnName(2, "latitude"); //to test case-insensitive - - table.sortColumnsByName(); - - //byte - Test.ensureEqual(table.getColumnName(0), "Byte Data", ""); - Test.ensureEqual(table.columnAttributes(0).getString("units"), "bytes", ""); - - //char - Test.ensureEqual(table.getColumnName(1), "Char Data", ""); - Test.ensureEqual(table.columnAttributes(1).getString("units"), "chars", ""); - - //double - Test.ensureEqual(table.getColumnName(2), "Double Data", ""); - Test.ensureEqual(table.columnAttributes(2).getString("units"), "doubles", ""); - - //int - Test.ensureEqual(table.getColumnName(3), "Int Data", ""); - Test.ensureEqual(table.columnAttributes(3).getString("units"), "ints", ""); - - //Lat - Test.ensureEqual(table.getColumnName(4), "latitude", ""); - Test.ensureEqual(table.columnAttributes(4).getString("units"), "degrees_north", ""); - - //long - Test.ensureEqual(table.getColumnName(5), "Long Data", ""); - Test.ensureEqual(table.columnAttributes(5).getString("units"), "longs", ""); - - //Lon - Test.ensureEqual(table.getColumnName(6), "Longitude", ""); - Test.ensureEqual(table.columnAttributes(6).getString("units"), "degrees_east", ""); - - //short - Test.ensureEqual(table.getColumnName(7), "Short Data", ""); - Test.ensureEqual(table.columnAttributes(7).getString("units"), "shorts", ""); - - //String - Test.ensureEqual(table.getColumnName(8), "String Data", ""); - Test.ensureEqual(table.columnAttributes(8).getString("units"), "Strings", ""); - - //Time - Test.ensureEqual(table.getColumnName(9), "Time", ""); - Test.ensureEqual(table.columnAttributes(9).getString("units"), Calendar2.SECONDS_SINCE_1970, ""); - - } - /** THIS IS NOT FINISHED. * * @param standardizeWhat see Attributes.unpackVariable's standardizeWhat @@ -32248,2455 +17149,15 @@ public void readArgoProfile(String fileName, int standardizeWhat) throws Excepti :comment = "Contains the error on the adjusted values as determined by the delayed mode QC process."; :C_format = "%9.3f"; :FORTRAN_format = "F9.3"; - :resolution = 0.001f; // float - */ - if (reallyVerbose) String2.log(msg + " finished. nColumns=" + nColumns() + - " nRows=" + nRows() + " TIME=" + (System.currentTimeMillis() - tTime) + "ms"); - } finally { - try {if (nc != null) nc.close(); } catch (Exception e9) {} - } - } - - /** - * Make a test Table. - * - * @param includeLongs set this to true if you want a column with longs - * @param includeStrings set this to true if you want a column with Strings - * @return Table - */ - public static Table getTestTable(boolean includeLongs, boolean includeStrings) { - - String testTimes[] = {"1970-01-01T00:00:00", "2005-08-31T16:01:02", "2005-11-02T18:04:09", ""}; - Table table = new Table(); - int nRows = testTimes.length; - - //global attributes - table.globalAttributes().set("global_att1", "a string"); - table.globalAttributes().set("global_att2", new IntArray(new int[]{1,100})); - - //add the data variables (and their attributes) - - //0=seconds - double[] ad = new double[nRows]; - for (int i = 0; i < nRows; i++) - ad[i] = Calendar2.safeIsoStringToEpochSeconds(testTimes[i]); - int col = table.addColumn("Time", new DoubleArray(ad)); - table.columnAttributes(col).set("units", Calendar2.SECONDS_SINCE_1970); - table.columnAttributes(col).set("time_att2", new DoubleArray(new double[]{-1e300, 1e300})); - - //1=lon - int[] ai = {-3, -2, -1, Integer.MAX_VALUE}; - col = table.addColumn("Longitude", new IntArray(ai).setMaxIsMV(true)); - table.columnAttributes(col).set("units", "degrees_east"); - table.columnAttributes(col).set("lon_att2", new IntArray(new int[]{-2000000000, 2000000000})); - - //2=lat - float[] af = {1, 1.5f, 2, Float.NaN}; - col = table.addColumn("Latitude", new FloatArray(af)); - table.columnAttributes(col).set("units", "degrees_north"); - table.columnAttributes(col).set("lat_att2", new FloatArray(new float[]{-1e30f, 1e30f})); - - //3=double - ad = new double[]{-1e300, 3.123, 1e300, Double.NaN}; - col = table.addColumn("Double Data", new DoubleArray(ad)); - table.columnAttributes(col).set("units", "doubles"); - table.columnAttributes(col).set("double_att2", new DoubleArray(new double[]{-1e300, 1e300})); - - //4=long - if (includeLongs) { - long[] al = {-2000000000000000L, 2, 2000000000000000L, Long.MAX_VALUE}; - col = table.addColumn("Long Data", new LongArray(al).setMaxIsMV(true)); - table.columnAttributes(col).set("units", new StringArray(new String[]{"longs"})); - table.columnAttributes(col).set("long_att2", new LongArray(new long[]{-2000000000000000L, 2000000000000000L})); - } - - //5=int - ai = new int[]{-2000000000, 2, 2000000000, Integer.MAX_VALUE}; - col = table.addColumn("Int Data", new IntArray(ai).setMaxIsMV(true)); - table.columnAttributes(col).set("units", new StringArray(new String[]{"ints"})); - table.columnAttributes(col).set("int_att2", new IntArray(new int[]{-2000000000, 2000000000})); - - //6=short - short[] as = {(short)-32000, (short)7, (short)32000, Short.MAX_VALUE}; - col = table.addColumn("Short Data", new ShortArray(as).setMaxIsMV(true)); - table.columnAttributes(col).set("units", new StringArray(new String[]{"shorts"})); - table.columnAttributes(col).set("short_att2", new ShortArray(new short[]{(short)-30000, (short)30000})); - - //7=byte - byte[] ab = {(byte)-120, (byte)8, (byte)120, Byte.MAX_VALUE}; - col = table.addColumn("Byte Data", new ByteArray(ab).setMaxIsMV(true)); - table.columnAttributes(col).set("units", "bytes"); - table.columnAttributes(col).set("byte_att2", new ByteArray(new byte[]{(byte)-120, (byte)120})); - - //8=String - if (includeStrings) { - char[] ac = {',', '"', '\u20ac', '\uffff'}; - col = table.addColumn("Char Data", new CharArray(ac).setMaxIsMV(true)); - table.columnAttributes(col).set("units", "chars"); - table.columnAttributes(col).set("char_att2", new CharArray(new char[]{',', '"', '\u00fc', '\u20ac'})); - - String[] aS = {"a", "bb", "ccc", ""}; - col = table.addColumn("String Data", new StringArray(aS)); - table.columnAttributes(col).set("units", "Strings"); - table.columnAttributes(col).set("String_att2", new StringArray(new String[]{"a string"})); - } - - table.ensureValid(); //throws Exception if not - return table; - } - - /** - * Test the readASCII and saveAsASCII. - * - * @throws Exception if trouble - */ - public static void testASCII() throws Exception { - //*** test read all - String2.log("\n***** Table.testASCII read all"); - verbose = true; - reallyVerbose = true; - - //generate some data - Table table = getTestTable(true, true); - table.removeRow(3); //remove the empty row at the end, since readASCII will remove it - - Table table1 = getTestTable(true, true); - table1.removeRow(3); //remove the empty row at the end, since readASCII will remove it - - //write it to a file - String fileName = testDir + "tempTable.asc"; - table.saveAsTabbedASCII(fileName); - String2.log(fileName + "=\n" + File2.directReadFrom88591File(fileName)); - - //read it from the file - Table table2 = new Table(); - //debugMode = true; - table2.readASCII(fileName); - //debugMode = false; - - //check units on 1st data row - Test.ensureEqual(table2.getStringData(1, 0), "degrees_east", ""); - Test.ensureEqual(table2.getStringData(2, 0), "degrees_north", ""); - - //remove units row - table2.removeRow(0); - table2.simplify(); - - //are they the same (but column types may be different)? - Test.ensureTrue(table1.equals(table2, false), - "\ntable1=" + table1.toString() + "\ntable2=" + table2.toString()); - - //test simplification: see if column types are the same as original table - int n = table.nColumns(); - for (int col = 2; col < n; col++) //skip first 2 columns which are intentionally initially stored in bigger type - if (col != 4 && //LongArray -> StringArray - col != 8) //CharArray -> StringArray - Test.ensureEqual(table.columns.get(col).elementType(), - table2.getColumn(col).elementType(), "test type of col#" + col); - - //*** test read subset - String2.log("\n***** Table.testASCII read subset"); - - //read 2nd row from the file - table2 = new Table(); - table2.readASCII(fileName, File2.ISO_8859_1, - "", "", 0, 1, "", - new String[]{"Int Data"}, new double[]{0}, new double[]{4}, - new String[]{"Short Data", "String Data"}, true); - Test.ensureEqual(table2.nColumns(), 2, ""); - Test.ensureEqual(table2.nRows(), 1, ""); - Test.ensureEqual(table2.getColumnName(0), "Short Data", ""); - Test.ensureEqual(table2.getColumnName(1), "String Data", ""); - Test.ensureEqual(table2.getDoubleData(0, 0), 7, ""); - Test.ensureEqual(table2.getStringData(1, 0), "bb", ""); - - - //*** test read subset with no column names (otherwise same as test above) - String2.log("\n***** Table.testASCII read subset with no column names"); - //read 3rd row from the file - table2 = new Table(); - table2.readASCII(fileName, File2.ISO_8859_1, - "", "", -1, 1, "", //-1=no column names - new String[]{"Column#5"}, new double[]{0}, new double[]{4}, - new String[]{"Column#6", "Column#8", "Column#9"}, true); - Test.ensureEqual(table2.nColumns(), 3, ""); - Test.ensureEqual(table2.nRows(), 1, ""); - Test.ensureEqual(table2.getColumnName(0), "Column#6", ""); - Test.ensureEqual(table2.getColumnName(1), "Column#8", ""); - Test.ensureEqual(table2.getColumnName(2), "Column#9", ""); - Test.ensureEqual(table2.getDoubleData(0, 0), 7, ""); - Test.ensureEqual(table2.getStringData(1, 0), "\"", ""); - Test.ensureEqual(table2.getStringData(2, 0), "bb", ""); - - //** finally - File2.delete(fileName); - } - - /** - * Test readStandardTabbedASCII. - * - * @throws Exception if trouble - */ - public static void testReadStandardTabbedASCII() throws Exception { - //*** test read all - String2.log("\n***** Table.testReadStandardTabbedASCII"); - verbose = true; - reallyVerbose = true; - - //generate some data - String lines = - "colA\tcolB\tcolC\n" + - "1a\t1b\t1c\n" + - "2\n" + - "a\t2\n" + - "b\t2c\n" + - "3a\t3b\t3c"; //no terminal \n - Table table = new Table(); - - //read it from lines - table.readStandardTabbedASCII("tFileName", - new BufferedReader(new StringReader(lines)), null, true); - String2.log("nRows=" + table.nRows() + " nCols=" + table.nColumns()); - Test.ensureEqual(table.dataToString(), - "colA,colB,colC\n" + - "1a,1b,1c\n" + - "2\\na,2\\nb,2c\n" + - "3a,3b,3c\n", - "tFileName toCSVString=\n" + table.dataToString()); - - //write it to a file - String fileName = testDir + "tempTable.asc"; - File2.writeToFile88591(fileName, lines); - - //read all columns from the file - Table table2 = new Table(); - table2.readStandardTabbedASCII(fileName, null, true); - String2.log("nRows=" + table2.nRows() + " nCols=" + table2.nColumns()); - Test.ensureEqual(table2.dataToString(), - "colA,colB,colC\n" + - "1a,1b,1c\n" + - "2\\na,2\\nb,2c\n" + - "3a,3b,3c\n", - "table2 toCSVString=\n" + table2.dataToString()); - - //just read cols B and C from the file - table2 = new Table(); - table2.readStandardTabbedASCII(fileName, new String[]{"colB", "colC"}, true); - String2.log("nRows=" + table2.nRows() + " nCols=" + table2.nColumns()); - Test.ensureEqual(table2.dataToString(), - "colB,colC\n" + - "1b,1c\n" + - "2\\nb,2c\n" + - "3b,3c\n", - "table2 toCSVString=\n" + table2.dataToString()); - - //** finally - File2.delete(fileName); - - } - - /** - * Test the saveAsHtml. - * - * @throws Exception if trouble - */ - public static void testHtml() throws Exception { - String2.log("\n***** Table.testHtml"); - verbose = true; - reallyVerbose = true; - - //generate some data - Table table = getTestTable(true, true); - - //write it to html file - String fileName = testDir + "tempTable.html"; - table.saveAsHtml(fileName, "preTextHtml\n
\n", "postTextHtml\n
", - null, BGCOLOR, 1, true, 0, true, //needEncodingAsHtml - false); - //String2.log(fileName + "=\n" + File2.directReadFromUtf8File(fileName)); - Test.displayInBrowser("file://" + fileName); //.html - - //read it from the file - String results = File2.directReadFromUtf8File(fileName); - Test.ensureEqual(results, -"\n" + -"\n" + -"\n" + -" tempTable\n" + -" \n" + -" \n" + -"\n" + -"\n" + -"preTextHtml\n" + -"
\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"
Time\n" + -"Longitude\n" + -"Latitude\n" + -"Double Data\n" + -"Long Data\n" + -"Int Data\n" + -"Short Data\n" + -"Byte Data\n" + -"Char Data\n" + -"String Data\n" + -"
UTC\n" + -"degrees_east\n" + -"degrees_north\n" + -"doubles\n" + -"longs\n" + -"ints\n" + -"shorts\n" + -"bytes\n" + -"chars\n" + -"Strings\n" + -"
1970-01-01T00:00:00Z\n" + -"-3\n" + -"1.0\n" + -"-1.0E300\n" + -"-2000000000000000\n" + -"-2000000000\n" + -"-32000\n" + -"-120\n" + -",\n" + -"a\n" + -"
2005-08-31T16:01:02Z\n" + -"-2\n" + -"1.5\n" + -"3.123\n" + -"2\n" + -"2\n" + -"7\n" + -"8\n" + -""\n" + -"bb\n" + -"
2005-11-02T18:04:09Z\n" + -"-1\n" + -"2.0\n" + -"1.0E300\n" + -"2000000000000000\n" + -"2000000000\n" + -"32000\n" + -"120\n" + -"€\n" + -"ccc\n" + -"
\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -"\n" + -" \n" + -"
\n" + -"postTextHtml\n" + -"
\n" + -"\n", - results); - - //test readHtml - treat 2nd row as data - Table table2 = new Table(); - table2.readHtml(fileName, results, 0, - false, true); //secondRowHasUnits, simplify - String csv = String2.annotatedString(table2.dataToString()); - Test.ensureEqual(csv, //so units appear here as a row of data -"Time,Longitude,Latitude,Double Data,Long Data,Int Data,Short Data,Byte Data,Char Data,String Data[10]\n" + -"UTC,degrees_east,degrees_north,doubles,longs,ints,shorts,bytes,chars,Strings[10]\n" + -"1970-01-01T00:00:00Z,-3,1.0,-1.0E300,-2000000000000000,-2000000000,-32000,-120,\",\",a[10]\n" + -"2005-08-31T16:01:02Z,-2,1.5,3.123,2,2,7,8,\"\"\"\",bb[10]\n" + -"2005-11-02T18:04:09Z,-1,2.0,1.0E300,2000000000000000,2000000000,32000,120,\\u20ac,ccc[10]\n" + -",,,,,,,,,[10]\n" + -"[end]", - csv); - - //test readHtml - treat 2nd row as units - table2 = new Table(); - table2.readHtml(fileName, results, 0, - true, true); //secondRowHasUnits, simplify - csv = String2.annotatedString(table2.dataToString()); - Test.ensureEqual(csv, //so units correctly stored as units -"Time,Longitude,Latitude,Double Data,Long Data,Int Data,Short Data,Byte Data,Char Data,String Data[10]\n" + -"1970-01-01T00:00:00Z,-3,1.0,-1.0E300,-2000000000000000,-2000000000,-32000,-120,\",\",a[10]\n" + -"2005-08-31T16:01:02Z,-2,1.5,3.123,2,2,7,8,\"\"\"\",bb[10]\n" + -"2005-11-02T18:04:09Z,-1,2.0,1.0E300,2000000000000000,2000000000,32000,120,\\u20ac,ccc[10]\n" + -",,,,,,,,,[10]\n" + -"[end]", - csv); - Test.ensureEqual(table2.columnAttributes(0).getString("units"), "UTC", ""); - Test.ensureEqual(table2.columnAttributes(1).getString("units"), "degrees_east", ""); - Test.ensureEqual(table2.columnAttributes(8).getString("units"), "chars", ""); - Test.ensureEqual(table2.columnAttributes(9).getString("units"), "Strings", ""); - - //** finally - Math2.gc("Table (between tests)", 10000); //in a test. Do something useful while browser gets going to display the file. - File2.delete(fileName); - } - - - /** - * This is a test of readFlatNc and saveAsFlatNc. - * - * @throws Exception of trouble - */ - public static void testFlatNc() throws Exception { - - //********** test reading all data - String2.log("\n*** Table.testFlatNc write and then read all"); - verbose = true; - reallyVerbose = true; - - //generate some data - Table table = getTestTable(false, true); //falses=.nc doesn't seem to take longs - String2.log("*******table=" + table.toString()); - - //write it to a file - String fileName = testDir + "tempTable.nc"; - table.saveAsFlatNc(fileName, "time"); - - //read it from the file - Table table2 = new Table(); - table2.readFlatNc(fileName, null, 0); //standardizeWhat=0 - String2.log("*********table2=" + table2.toString()); - - //replace ' ' with '_' in column names - for (int i = 0; i < table.columnNames.size(); i++) - table.columnNames.set(i, String2.replaceAll(table.columnNames.get(i), " ", "_")); - - //do the test that the tables are equal - String2.log("testFlatNc table.nColAtt=" + table.columnAttributes.size() + //? why columnAtt? - " table2.nColAtt=" + table2.columnAttributes.size()); - //except char \\u20ac becomes "?" in nc file, so reset it - Test.ensureEqual( - table2.columns.get(7).getString(2), "?", ""); - table2.columns.get(7).setString(2, "\u20ac"); - if (table2.columns.get(7).getString(3).equals("?")) - table2.columns.get(7).setString(3, ""); - String t1 = table.dataToString(); - String t2 = table.dataToString(); - String2.log("\nt1=\n" + t1 + "\nt2=\n" + t2); - Test.ensureEqual(t1, t2, ""); - Test.ensureTrue(table.equals(table2), "Test table equality"); - - //test if data types are the same - int n = table.nColumns(); - for (int col = 0; col < n; col++) - Test.ensureEqual(table.columns.get(col).elementType(), - table2.columns.get(col).elementType(), "test type of col#" + col); - - //clean up - table2.clear(); - File2.delete(fileName); - - - //***test unpack options (and global and variable attributes) - String2.log("\n*** Table.testFlatNc test unpack"); - //row of data from 41015h1993.txt - //YY MM DD hh WD WSPD GST WVHT DPD APD MWD BAR ATMP WTMP DEWP VIS - //93 05 24 11 194 02.5 02.8 00.70 04.20 04.90 185 1021.2 17.3 16.4 999.0 18.5 - double seconds = Calendar2.isoStringToEpochSeconds("1993-05-24T11"); - String2.log("seconds=" + seconds); - int[] testColumns = {0}; - double testMin[] = {seconds}; - double testMax[] = {seconds}; - - //don't unpack - table.readFlatNc(testDir + "41015.nc", new String[]{"time", "BAR"}, 0); //standardizeWhat=0 - //String2.log(table.toString(100)); - table.subset(testColumns, testMin, testMax); - Test.ensureEqual(table.nColumns(), 2, ""); - Test.ensureEqual(table.nRows(), 1, ""); - Test.ensureEqual(table.getColumnName(0), "time", ""); - Test.ensureEqual(table.getColumnName(1), "BAR", ""); - Test.ensureEqual(table.getColumn(1).elementType(), PAType.SHORT, ""); //short - Test.ensureEqual(table.getDoubleData(0, 0), seconds, ""); - Test.ensureEqual(table.getDoubleData(1, 0), 10212, ""); - - //test global and variable attributes - Test.ensureEqual(table.globalAttributes().getString("creator_name"), "NOAA National Data Buoy Center", ""); - Test.ensureEqual(table.columnAttributes(1).getString("long_name"), "Sea Level Pressure", ""); - - //unpack, to float if that is recommended - table.readFlatNc(testDir + "41015.nc", new String[]{"time", "BAR"}, 1); //standardizeWhat=1 - table.subset(testColumns, testMin, testMax); - Test.ensureEqual(table.nColumns(), 2, ""); - Test.ensureEqual(table.nRows(), 1, ""); - Test.ensureEqual(table.getColumnName(0), "time", ""); - Test.ensureEqual(table.getColumnName(1), "BAR", ""); - Test.ensureEqual(table.getColumn(1).elementType(), PAType.FLOAT, ""); //float - Test.ensureEqual(table.getDoubleData(0, 0), seconds, ""); - Test.ensureEqual(table.getFloatData(1, 0), 1021.2f, ""); - - - //********** test reading subset of data via bitset (which uses read via firstrow/lastrow) - String2.log("\n*** Table.testFlatNc read subset"); - table.clear(); - NetcdfFile netcdfFile = NcHelper.openFile(testDir + "41015.nc"); - try { - Variable loadVariables[] = NcHelper.findVariables(netcdfFile, new String[]{"time", "BAR"}); - Variable testVariables[] = NcHelper.findVariables(netcdfFile, new String[]{"time"}); - BitSet okRows = NcHelper.testRows(testVariables, testMin, testMax); - table.appendNcRows(loadVariables, okRows); - Test.ensureEqual(okRows.cardinality(), 1, ""); - } finally { - try {if (netcdfFile != null) netcdfFile.close(); } catch (Exception e9) {} - } - - Test.ensureEqual(table.nColumns(), 2, ""); - Test.ensureEqual(table.nRows(), 1, ""); - Test.ensureEqual(table.getColumnName(0), "time", ""); - Test.ensureEqual(table.getColumnName(1), "BAR", ""); - Test.ensureEqual(table.getColumn(1).elementType(), PAType.SHORT, ""); //short - Test.ensureEqual(table.getDoubleData(0, 0), seconds, ""); - Test.ensureEqual(table.getDoubleData(1, 0), 10212, ""); //still packed - - } - - /** - * This is a test of read4DNc and saveAs4DNc. - * - * @throws Exception of trouble - */ - public static void test4DNc() throws Exception { - - //********** test reading all data - String2.log("\n*** Table.test4DNc write and then read all"); - verbose = true; - reallyVerbose = true; - - //generate some data - Table table = new Table(); - DoubleArray xCol = new DoubleArray(); - DoubleArray yCol = new DoubleArray(); - DoubleArray zCol = new DoubleArray(); - DoubleArray tCol = new DoubleArray(); - IntArray data1Col = new IntArray(); - DoubleArray data2Col = new DoubleArray(); - StringArray data3Col = new StringArray(); - table.addColumn("X", xCol); - table.addColumn("Y", yCol); - table.addColumn("Z", zCol); - table.addColumn("T", tCol); - table.addColumn("data1", data1Col); - table.addColumn("data2", data2Col); - table.addColumn("data3", data3Col); - for (int t = 0; t < 2; t++) { - for (int z = 0; z < 3; z++) { - for (int y = 0; y < 3; y++) { - for (int x = 0; x < 4; x++) { - xCol.add(x+1); - yCol.add(y+1); - zCol.add(z+1); - tCol.add(t+1); - int fac = (x+1)*(y+1)*(z+1)*(t+1); - data1Col.add(fac); - data2Col.add(100+ (x+1)*(y+1)*(z+1)*(t+1)); - data3Col.add("" + fac); - } - } - } - } - table.ensureValid(); //throws Exception if not - //String2.log(table.toString("obs", 10)); - - //write it to a file - String fileName = testDir + "temp4DTable.nc"; - Attributes idAttributes = new Attributes(); - idAttributes.set("long_name", "The station's name."); - idAttributes.set("units", DataHelper.UNITLESS); - String stringVariableValue = "My Id Value"; - table.saveAs4DNc(fileName, 0,1,2,3, "ID", stringVariableValue, idAttributes); - - //then insert col 4 filled with "My Id Value" - String sar[] = new String[table.nRows()]; - Arrays.fill(sar, stringVariableValue); - table.addColumn(4, "ID", new StringArray(sar), idAttributes); - - //get the header - //String2.log("table=" + String2.log(NcHelper.ncdump(fileName, "-h"))); - - //read from file - Table table2 = new Table(); - table2.read4DNc(fileName, null, 1, "ID", 4); //standarizeWhat=1 - //String2.log("col6=" + table2.getColumn(6)); - //String2.log("\ntable2 after read4DNc: " + table2.toString("obs", 1000000)); - - //test equality - Test.ensureTrue(table.equals(table2), "test4DNc tables not equal!"); - - File2.delete(fileName); - - } - - - /** - * This is a test of readOpendapSequence. - * Test cases from Roy: - * GLOBEC VPT: - * stn_id=loaddods('https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_vpt?stn_id&unique()'); - * abund=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_vpt?abund_m3&stn_id="NH05"'); - * GLOBEC Bottle: - * month=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_bottle?month&unique()'); - * [oxy temp]=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_bottle?t0,oxygen&month="5"'); - * GLOBEC MOC1: - * [abund,lon,lat]=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1?abund_m3,lat,long'); - * [abund1,lon1,lat1]=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1?abund_m3,lat,long&program="MESO_1"'); - * I note that loaddods documentation is at https://www.opendap.org/user/mgui-html/mgui_36.html - * and -F says to convert all strings to floats. - * "unique()" seems to just return unique values. - * - * @throws Exception of trouble + :resolution = 0.001f; // float */ - public static void testOpendapSequence() throws Exception { - - //2013-03-18 I changed from oceanwatch datasets (no longer available) to coastwatch erddap datasets - String2.log("\n*** Table.testOpendapSequence"); - verbose = true; - reallyVerbose = true; - Table table = new Table(); - int nRows; - String url; - float lon, lat; - String results, expected; - - //2016-07-25 test for Kevin's dataset: from remote erddap - url = "https://ferret.pmel.noaa.gov/pmel/erddap/tabledap/ChukchiSea_454a_037a_fcf4?" + - "prof,id,cast,cruise,time,longitude,lon360,latitude&time%3E=2012-09-04&time%3C=2012-09-07&distinct()"; - table.readOpendapSequence(url, false); //boolean: skipDapSpacerRows - results = table.toString(3); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 2 ;\n" + -"\tid_strlen = 10 ;\n" + -"\tcast_strlen = 3 ;\n" + -"\tcruise_strlen = 6 ;\n" + -"variables:\n" + -"\tdouble prof(row) ;\n" + -"\t\tprof:actual_range = 1.0, 1.0 ;\n" + -"\t\tprof:axis = \"E\" ;\n" + -"\t\tprof:long_name = \"Prof\" ;\n" + -"\t\tprof:point_spacing = \"even\" ;\n" + -"\tchar id(row, id_strlen) ;\n" + -"\t\tid:cf_role = \"profile_id\" ;\n" + -"\t\tid:long_name = \"profile id\" ;\n" + -"\tchar cast(row, cast_strlen) ;\n" + -"\t\tcast:colorBarMaximum = 100.0 ;\n" + -"\t\tcast:colorBarMinimum = 0.0 ;\n" + -"\t\tcast:long_name = \"cast number\" ;\n" + -"\tchar cruise(row, cruise_strlen) ;\n" + -"\t\tcruise:long_name = \"Cruise name\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:_CoordinateAxisType = \"Time\" ;\n" + -"\t\ttime:actual_range = 1.28368572E9, 1.34697582E9 ;\n" + -"\t\ttime:axis = \"T\" ;\n" + -"\t\ttime:ioos_category = \"Time\" ;\n" + -"\t\ttime:long_name = \"Time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:time_origin = \"01-JAN-1970 00:00:00\" ;\n" + -"\t\ttime:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + -"\tfloat longitude(row) ;\n" + -"\t\tlongitude:_CoordinateAxisType = \"Lon\" ;\n" + -"\t\tlongitude:_FillValue = -1.0E34f ;\n" + -"\t\tlongitude:actual_range = -174.6603f, -157.1593f ;\n" + -"\t\tlongitude:axis = \"X\" ;\n" + -"\t\tlongitude:colorBarMaximum = 180.0 ;\n" + -"\t\tlongitude:colorBarMinimum = -180.0 ;\n" + -"\t\tlongitude:ioos_category = \"Location\" ;\n" + -"\t\tlongitude:long_name = \"station longitude\" ;\n" + -"\t\tlongitude:missing_value = -1.0E34f ;\n" + -"\t\tlongitude:standard_name = \"longitude\" ;\n" + -"\t\tlongitude:units = \"degrees_east\" ;\n" + -"\tfloat lon360(row) ;\n" + -"\t\tlon360:_FillValue = -1.0E34f ;\n" + -"\t\tlon360:actual_range = 185.3397f, 202.8407f ;\n" + -"\t\tlon360:colorBarMaximum = 180.0 ;\n" + -"\t\tlon360:colorBarMinimum = -180.0 ;\n" + -"\t\tlon360:long_name = \"station longitude 360\" ;\n" + -"\t\tlon360:missing_value = -1.0E34f ;\n" + -"\t\tlon360:standard_name = \"longitude\" ;\n" + -"\t\tlon360:units = \"degrees_east\" ;\n" + -"\tfloat latitude(row) ;\n" + -"\t\tlatitude:_CoordinateAxisType = \"Lat\" ;\n" + -"\t\tlatitude:_FillValue = -1.0E34f ;\n" + -"\t\tlatitude:actual_range = 54.34184f, 73.11517f ;\n" + -"\t\tlatitude:axis = \"Y\" ;\n" + -"\t\tlatitude:colorBarMaximum = 90.0 ;\n" + -"\t\tlatitude:colorBarMinimum = -90.0 ;\n" + -"\t\tlatitude:history = \"From mb1101c070.nc_copy\" ;\n" + -"\t\tlatitude:ioos_category = \"Location\" ;\n" + -"\t\tlatitude:long_name = \"station latitude\" ;\n" + -"\t\tlatitude:missing_value = -1.0E34f ;\n" + -"\t\tlatitude:standard_name = \"latitude\" ;\n" + -"\t\tlatitude:units = \"degrees_north\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:CAST = \"070\" ;\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"prof, id, cast, cruise, time, longitude, lon360, latitude\" ;\n" + -"\t\t:Conventions = \"CF-1.6, COARDS, ACDD-1.3\" ;\n" + -"\t\t:COORD_SYSTEM = \"GEOGRAPHICAL\" ;\n" + -"\t\t:creation_date = \"14:48 21-JUN-2013\" ;\n" + -"\t\t:creator_email = \"peggy.sullivan@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Phyllis Stabeno, Margaret Sullivan\" ;\n" + -"\t\t:CRUISE = \"Ch2011\" ;\n" + -"\t\t:DATA_CMNT = \"Data from Seasoft File chaoz2011070.cnv\" ;\n" + -"\t\t:DATA_TYPE = \"CTD\" ;\n" + -"\t\t:Easternmost_Easting = -157.1593 ;\n" + -"\t\t:EPIC_FILE_GENERATOR = \"SEASOFT2EPIC_CTD (Version 1.37, 14-Oct-2011)\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 73.11517 ;\n" + -"\t\t:geospatial_lat_min = 54.34184 ;\n" + -"\t\t:geospatial_lat_units = \"degrees_north\" ;\n" + -"\t\t:geospatial_lon_max = -157.1593 ;\n" + -"\t\t:geospatial_lon_min = -174.6603 ;\n" + -"\t\t:geospatial_lon_units = \"degrees_east\" ;\n" + -"\t\t:geospatial_vertical_max = 166.0 ;\n" + -"\t\t:geospatial_vertical_min = 0.0 ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"m\" ;\n" + -"\t\t:history = \"FERRET V7 13-Jun-16\n"; -//2016-10-03T22:25:01Z (local files) -//2016-10-03T22:25:01Z -Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - -expected = -"https://data.pmel.noaa.gov/pmel/erddap/tabledap/ChukchiSea_454a_037a_fcf4.das\" ;\n" + -"\t\t:infoUrl = \"www.ecofoci.noaa.gov\" ;\n" + -"\t\t:INST_TYPE = \"Sea-Bird CTD SBE911\" ;\n" + -"\t\t:institution = \"PMEL EcoFOCI\" ;\n" + -"\t\t:keywords = \"2010-2012, active, ammonia, ammonium, bottle, calibration, cast, chemistry, chlorophyll, chukchi, concentration, concentration_of_chlorophyll_in_sea_water, cooperative, cruise, data, density, depth, dissolved, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > Oxygen, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Ocean Chemistry > Silicate, Earth Science > Oceans > Salinity/Density > Salinity, ecofoci, environmental, factory, fisheries, fisheries-oceanography, flourescence, foci, fraction, fractional, fractional_saturation_of_oxygen_in_sea_water, investigations, laboratory, latitude, lon360, longitude, marine, ml/l, mmoles, mmoles/kg, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, mole_concentration_of_phosphate_in_sea_water, mole_concentration_of_silicate_in_sea_water, molecular, n02, name, nh4, niskin, nitrate, nitrite, no2, no3, noaa, number, nutrients, O2, ocean, ocean_chlorophyll_a_concentration_factoryCal, ocean_chlorophyll_fluorescence_raw, ocean_dissolved_oxygen_concentration_1_mLperL, ocean_dissolved_oxygen_concentration_1_mMperkg, ocean_dissolved_oxygen_concentration_2_mLperL, ocean_dissolved_oxygen_concentration_2_mMperkg, ocean_oxygen_saturation_1, ocean_practical_salinity_1, ocean_practical_salinity_2, ocean_sigma_t, ocean_temperature_1, ocean_temperature_2, oceanography, oceans, oxygen, pacific, percent, phosphate, photosynthetically, photosynthetically_active_radiation, pmel, po4, practical, prof, profile, pss, pss-78, psu, radiation, raw, salinity, saturation, scale, sea, sea_water_ammonium_concentration, sea_water_nitrate_concentration, sea_water_nitrite_concentration, sea_water_nutrient_bottle_number, sea_water_phosphate_concentration, sea_water_practical_salinity, sea_water_silicate_concentration, seawater, sigma, sigma-t, silicate, station, temperature, time, unit, volume, volume_fraction_of_oxygen_in_sea_water, water\" ;\n" + -"\t\t:keywords_vocabulary = \"GCMD Science Keywords\" ;\n" + -"\t\t:license = \"Data Licenses / Data Usage Restrictions\n" + -"The data may be used and redistributed for free but is not intended\n" + -"for legal use, since it may contain inaccuracies. Neither the data\n" + -"Contributor, ERD, NOAA, nor the United States Government, nor any\n" + -"of their employees or contractors, makes any warranty, express or\n" + -"implied, including warranties of merchantability and fitness for a\n" + -"particular purpose, or assumes any legal liability for the accuracy,\n" + -"completeness, or usefulness, of this information.\n" + -"\n" + -"Unless otherwise noted, data served through this ERDDAP server are \n" + -"not quality controlled. Users may need to do quality control when using \n" + -"these data. These data are made available at the users own risk.\" ;\n" + -"\t\t:Northernmost_Northing = 73.11517 ;\n" + -"\t\t:PROG_CMNT1 = \"cat_ctd v1.36 06Aug2010\" ;\n" + -"\t\t:PROG_CMNT2 = \"Variables Extrapolated from 2 db to 0\" ;\n" + -"\t\t:sourceUrl = \"(local files)\" ;\n" + -"\t\t:Southernmost_Northing = 54.34184 ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v29\" ;\n" + -"\t\t:STATION_NAME = \"Unimak3\" ;\n" + -"\t\t:subsetVariables = \"prof, id, cast, cruise, time, longitude, lon360, latitude\" ;\n" + -"\t\t:summary = \"Pacific Marine Environmental Laboratory (PMEL) Fisheries-Oceanography Cooperative Investigations (FOCI) Chukchi Sea. PMEL EcoFOCI data from a local source.\" ;\n" + -"\t\t:time_coverage_end = \"2012-09-06T23:57:00Z\" ;\n" + -"\t\t:time_coverage_start = \"2010-09-05T11:22:00Z\" ;\n" + -"\t\t:title = \"PMEL EcoFOCI Chukchi Sea profile data, 2010-2012\" ;\n" + -"\t\t:WATER_DEPTH = 0 ;\n" + -"\t\t:WATER_MASS = \"A\" ;\n" + -"\t\t:Westernmost_Easting = -174.6603 ;\n" + -"}\n" + -"prof,id,cast,cruise,time,longitude,lon360,latitude\n" + -"1.0,aq1201c069,069,aq1201,1.34697456E9,-164.0447,195.9553,56.866\n" + -"1.0,aq1201c070,070,aq1201,1.34697582E9,-164.049,195.951,56.864\n"; - int po = results.indexOf(expected.substring(0, 60)); - Test.ensureEqual(results.substring(Math.max(0, po)), expected, "results=\n" + results); - - url = "https://data.pmel.noaa.gov/pmel/erddap/tabledap/ChukchiSea_454a_037a_fcf4?" + - "prof,id,cast,cruise,time,longitude,lon360,latitude&time%3E=2012-09-04&time%3C=2012-09-07"; - table.readOpendapSequence(url, false); //boolean: skipDapSpacerRows - results = table.toString(3); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 2 ;\n" + -"\tid_strlen = 10 ;\n" + -"\tcast_strlen = 3 ;\n" + -"\tcruise_strlen = 6 ;\n" + -"variables:\n" + -"\tdouble prof(row) ;\n" + -"\t\tprof:actual_range = 1.0, 1.0 ;\n" + -"\t\tprof:axis = \"E\" ;\n" + -"\t\tprof:long_name = \"Prof\" ;\n" + -"\t\tprof:point_spacing = \"even\" ;\n" + -"\tchar id(row, id_strlen) ;\n" + -"\t\tid:cf_role = \"profile_id\" ;\n" + -"\t\tid:long_name = \"profile id\" ;\n" + -"\tchar cast(row, cast_strlen) ;\n" + -"\t\tcast:colorBarMaximum = 100.0 ;\n" + -"\t\tcast:colorBarMinimum = 0.0 ;\n" + -"\t\tcast:long_name = \"cast number\" ;\n" + -"\tchar cruise(row, cruise_strlen) ;\n" + -"\t\tcruise:long_name = \"Cruise name\" ;\n" + -"\tdouble time(row) ;\n" + -"\t\ttime:_CoordinateAxisType = \"Time\" ;\n" + -"\t\ttime:actual_range = 1.28368572E9, 1.34697582E9 ;\n" + -"\t\ttime:axis = \"T\" ;\n" + -"\t\ttime:ioos_category = \"Time\" ;\n" + -"\t\ttime:long_name = \"Time\" ;\n" + -"\t\ttime:standard_name = \"time\" ;\n" + -"\t\ttime:time_origin = \"01-JAN-1970 00:00:00\" ;\n" + -"\t\ttime:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + -"\tfloat longitude(row) ;\n" + -"\t\tlongitude:_CoordinateAxisType = \"Lon\" ;\n" + -"\t\tlongitude:_FillValue = -1.0E34f ;\n" + -"\t\tlongitude:actual_range = -174.6603f, -157.1593f ;\n" + -"\t\tlongitude:axis = \"X\" ;\n" + -"\t\tlongitude:colorBarMaximum = 180.0 ;\n" + -"\t\tlongitude:colorBarMinimum = -180.0 ;\n" + -"\t\tlongitude:ioos_category = \"Location\" ;\n" + -"\t\tlongitude:long_name = \"station longitude\" ;\n" + -"\t\tlongitude:missing_value = -1.0E34f ;\n" + -"\t\tlongitude:standard_name = \"longitude\" ;\n" + -"\t\tlongitude:units = \"degrees_east\" ;\n" + -"\tfloat lon360(row) ;\n" + -"\t\tlon360:_FillValue = -1.0E34f ;\n" + -"\t\tlon360:actual_range = 185.3397f, 202.8407f ;\n" + -"\t\tlon360:colorBarMaximum = 180.0 ;\n" + -"\t\tlon360:colorBarMinimum = -180.0 ;\n" + -"\t\tlon360:long_name = \"station longitude 360\" ;\n" + -"\t\tlon360:missing_value = -1.0E34f ;\n" + -"\t\tlon360:standard_name = \"longitude\" ;\n" + -"\t\tlon360:units = \"degrees_east\" ;\n" + -"\tfloat latitude(row) ;\n" + -"\t\tlatitude:_CoordinateAxisType = \"Lat\" ;\n" + -"\t\tlatitude:_FillValue = -1.0E34f ;\n" + -"\t\tlatitude:actual_range = 54.34184f, 73.11517f ;\n" + -"\t\tlatitude:axis = \"Y\" ;\n" + -"\t\tlatitude:colorBarMaximum = 90.0 ;\n" + -"\t\tlatitude:colorBarMinimum = -90.0 ;\n" + -"\t\tlatitude:history = \"From mb1101c070.nc_copy\" ;\n" + -"\t\tlatitude:ioos_category = \"Location\" ;\n" + -"\t\tlatitude:long_name = \"station latitude\" ;\n" + -"\t\tlatitude:missing_value = -1.0E34f ;\n" + -"\t\tlatitude:standard_name = \"latitude\" ;\n" + -"\t\tlatitude:units = \"degrees_north\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:CAST = \"070\" ;\n" + -"\t\t:cdm_data_type = \"Profile\" ;\n" + -"\t\t:cdm_profile_variables = \"prof, id, cast, cruise, time, longitude, lon360, latitude\" ;\n" + -"\t\t:Conventions = \"CF-1.6, COARDS, ACDD-1.3\" ;\n" + -"\t\t:COORD_SYSTEM = \"GEOGRAPHICAL\" ;\n" + -"\t\t:creation_date = \"14:48 21-JUN-2013\" ;\n" + -"\t\t:creator_email = \"peggy.sullivan@noaa.gov\" ;\n" + -"\t\t:creator_name = \"Phyllis Stabeno, Margaret Sullivan\" ;\n" + -"\t\t:CRUISE = \"Ch2011\" ;\n" + -"\t\t:DATA_CMNT = \"Data from Seasoft File chaoz2011070.cnv\" ;\n" + -"\t\t:DATA_TYPE = \"CTD\" ;\n" + -"\t\t:Easternmost_Easting = -157.1593 ;\n" + -"\t\t:EPIC_FILE_GENERATOR = \"SEASOFT2EPIC_CTD (Version 1.37, 14-Oct-2011)\" ;\n" + -"\t\t:featureType = \"Profile\" ;\n" + -"\t\t:geospatial_lat_max = 73.11517 ;\n" + -"\t\t:geospatial_lat_min = 54.34184 ;\n" + -"\t\t:geospatial_lat_units = \"degrees_north\" ;\n" + -"\t\t:geospatial_lon_max = -157.1593 ;\n" + -"\t\t:geospatial_lon_min = -174.6603 ;\n" + -"\t\t:geospatial_lon_units = \"degrees_east\" ;\n" + -"\t\t:geospatial_vertical_max = 166.0 ;\n" + -"\t\t:geospatial_vertical_min = 0.0 ;\n" + -"\t\t:geospatial_vertical_positive = \"down\" ;\n" + -"\t\t:geospatial_vertical_units = \"m\" ;\n" + -"\t\t:history = \"FERRET V7 13-Jun-16\n"; -//2016-10-03T22:32:26Z (local files) -//2016-10-03T22:32:26Z - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - - -expected = -"https://data.pmel.noaa.gov/pmel/erddap/tabledap/ChukchiSea_454a_037a_fcf4.das\" ;\n" + -"\t\t:infoUrl = \"www.ecofoci.noaa.gov\" ;\n" + -"\t\t:INST_TYPE = \"Sea-Bird CTD SBE911\" ;\n" + -"\t\t:institution = \"PMEL EcoFOCI\" ;\n" + -"\t\t:keywords = \"2010-2012, active, ammonia, ammonium, bottle, calibration, cast, chemistry, chlorophyll, chukchi, concentration, concentration_of_chlorophyll_in_sea_water, cooperative, cruise, data, density, depth, dissolved, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > Oxygen, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Ocean Chemistry > Silicate, Earth Science > Oceans > Salinity/Density > Salinity, ecofoci, environmental, factory, fisheries, fisheries-oceanography, flourescence, foci, fraction, fractional, fractional_saturation_of_oxygen_in_sea_water, investigations, laboratory, latitude, lon360, longitude, marine, ml/l, mmoles, mmoles/kg, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, mole_concentration_of_phosphate_in_sea_water, mole_concentration_of_silicate_in_sea_water, molecular, n02, name, nh4, niskin, nitrate, nitrite, no2, no3, noaa, number, nutrients, O2, ocean, ocean_chlorophyll_a_concentration_factoryCal, ocean_chlorophyll_fluorescence_raw, ocean_dissolved_oxygen_concentration_1_mLperL, ocean_dissolved_oxygen_concentration_1_mMperkg, ocean_dissolved_oxygen_concentration_2_mLperL, ocean_dissolved_oxygen_concentration_2_mMperkg, ocean_oxygen_saturation_1, ocean_practical_salinity_1, ocean_practical_salinity_2, ocean_sigma_t, ocean_temperature_1, ocean_temperature_2, oceanography, oceans, oxygen, pacific, percent, phosphate, photosynthetically, photosynthetically_active_radiation, pmel, po4, practical, prof, profile, pss, pss-78, psu, radiation, raw, salinity, saturation, scale, sea, sea_water_ammonium_concentration, sea_water_nitrate_concentration, sea_water_nitrite_concentration, sea_water_nutrient_bottle_number, sea_water_phosphate_concentration, sea_water_practical_salinity, sea_water_silicate_concentration, seawater, sigma, sigma-t, silicate, station, temperature, time, unit, volume, volume_fraction_of_oxygen_in_sea_water, water\" ;\n" + -"\t\t:keywords_vocabulary = \"GCMD Science Keywords\" ;\n" + -"\t\t:license = \"Data Licenses / Data Usage Restrictions\n" + -"The data may be used and redistributed for free but is not intended\n" + -"for legal use, since it may contain inaccuracies. Neither the data\n" + -"Contributor, ERD, NOAA, nor the United States Government, nor any\n" + -"of their employees or contractors, makes any warranty, express or\n" + -"implied, including warranties of merchantability and fitness for a\n" + -"particular purpose, or assumes any legal liability for the accuracy,\n" + -"completeness, or usefulness, of this information.\n" + -"\n" + -"Unless otherwise noted, data served through this ERDDAP server are \n" + -"not quality controlled. Users may need to do quality control when using \n" + -"these data. These data are made available at the users own risk.\" ;\n" + -"\t\t:Northernmost_Northing = 73.11517 ;\n" + -"\t\t:PROG_CMNT1 = \"cat_ctd v1.36 06Aug2010\" ;\n" + -"\t\t:PROG_CMNT2 = \"Variables Extrapolated from 2 db to 0\" ;\n" + -"\t\t:sourceUrl = \"(local files)\" ;\n" + -"\t\t:Southernmost_Northing = 54.34184 ;\n" + -"\t\t:standard_name_vocabulary = \"CF Standard Name Table v29\" ;\n" + -"\t\t:STATION_NAME = \"Unimak3\" ;\n" + -"\t\t:subsetVariables = \"prof, id, cast, cruise, time, longitude, lon360, latitude\" ;\n" + -"\t\t:summary = \"Pacific Marine Environmental Laboratory (PMEL) Fisheries-Oceanography Cooperative Investigations (FOCI) Chukchi Sea. PMEL EcoFOCI data from a local source.\" ;\n" + -"\t\t:time_coverage_end = \"2012-09-06T23:57:00Z\" ;\n" + -"\t\t:time_coverage_start = \"2010-09-05T11:22:00Z\" ;\n" + -"\t\t:title = \"PMEL EcoFOCI Chukchi Sea profile data, 2010-2012\" ;\n" + -"\t\t:WATER_DEPTH = 0 ;\n" + -"\t\t:WATER_MASS = \"A\" ;\n" + -"\t\t:Westernmost_Easting = -174.6603 ;\n" + -"}\n" + -"prof,id,cast,cruise,time,longitude,lon360,latitude\n" + -"1.0,aq1201c069,069,aq1201,1.34697456E9,-164.0447,195.9553,56.866\n" + -"1.0,aq1201c070,070,aq1201,1.34697582E9,-164.049,195.951,56.864\n"; - po = results.indexOf(expected.substring(0, 60)); - Test.ensureEqual(results.substring(Math.max(0, po)), expected, "results=\n" + results); - - - //************* SINGLE SEQUENCE ***************************** - //read data from opendap - table.readOpendapSequence( - "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1?abund_m3,latitude,longitude", false); - results = table.toString(5); - String2.log(results); - - nRows = 3763; //2013-0620 was 3779; - Test.ensureEqual(table.nColumns(), 3, ""); - Test.ensureEqual(table.nRows(), nRows, ""); - - expected = -"{\n" + -"dimensions:\n" + -"\trow = 3763 ;\n" + -"variables:\n" + -"\tfloat abund_m3(row) ;\n" + -"\t\tabund_m3:_FillValue = -9999999.0f ;\n" + -"\t\tabund_m3:actual_range = 0.0f, 9852.982f ;\n" + -"\t\tabund_m3:colorBarMaximum = 1000.0 ;\n" + -"\t\tabund_m3:colorBarMinimum = 0.0 ;\n" + -"\t\tabund_m3:comment = \"Density [individuals per m3]\" ;\n" + -"\t\tabund_m3:ioos_category = \"Other\" ;\n" + -"\t\tabund_m3:long_name = \"Abundance\" ;\n" + -"\t\tabund_m3:missing_value = -9999999.0f ;\n" + -"\t\tabund_m3:units = \"count m-3\" ;\n" + -"\tfloat latitude(row) ;\n" + -"\t\tlatitude:_CoordinateAxisType = \"Lat\" ;\n" + -"\t\tlatitude:_FillValue = 214748.36f ;\n" + -"\t\tlatitude:actual_range = 42.4733f, 44.6517f ;\n" + -"\t\tlatitude:axis = \"Y\" ;\n" + -"\t\tlatitude:ioos_category = \"Location\" ;\n" + -"\t\tlatitude:long_name = \"Latitude\" ;\n" + -"\t\tlatitude:missing_value = 214748.36f ;\n" + -"\t\tlatitude:standard_name = \"latitude\" ;\n" + -"\t\tlatitude:units = \"degrees_north\" ;\n" + -"\tfloat longitude(row) ;\n" + -"\t\tlongitude:_CoordinateAxisType = \"Lon\" ;\n" + -"\t\tlongitude:_FillValue = 214748.36f ;\n" + -"\t\tlongitude:actual_range = -125.1167f, -124.175f ;\n" + -"\t\tlongitude:axis = \"X\" ;\n" + -"\t\tlongitude:ioos_category = \"Location\" ;\n" + -"\t\tlongitude:long_name = \"Longitude\" ;\n" + -"\t\tlongitude:missing_value = 214748.36f ;\n" + -"\t\tlongitude:standard_name = \"longitude\" ;\n" + -"\t\tlongitude:units = \"degrees_east\" ;\n" + -"\n" + -"// global attributes:\n" + -"\t\t:cdm_data_type = \"Trajectory\" ;\n" + -"\t\t:cdm_trajectory_variables = \"cruise_id\" ;\n" + -"\t\t:Conventions = \"COARDS, CF-1.6, ACDD-1.3\" ;\n" + -"\t\t:Easternmost_Easting = -124.175 ;\n" + -"\t\t:featureType = \"Trajectory\" ;\n" + -"\t\t:geospatial_lat_max = 44.6517 ;\n" + -"\t\t:geospatial_lat_min = 42.4733 ;\n" + -"\t\t:geospatial_lat_units = \"degrees_north\" ;\n" + -"\t\t:geospatial_lon_max = -124.175 ;\n" + -"\t\t:geospatial_lon_min = -125.1167 ;\n" + -"\t\t:geospatial_lon_units = \"degrees_east\" ;\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - - expected = -"\t\t:time_coverage_end = \"2002-05-30T15:22:00Z\" ;\n" + -"\t\t:time_coverage_start = \"2000-04-12T04:00:00Z\" ;\n" + -"\t\t:title = \"GLOBEC NEP MOCNESS Plankton (MOC1) Data, 2000-2002\" ;\n" + -"\t\t:Westernmost_Easting = -125.1167 ;\n" + -"}\n" + -//" Row abund_m3 latitude longitude\n" + -//" 0 3.698225E-3 44.651699 -124.650002\n" + 2013-06-20 was -//" 1 7.26257E-2 44.651699 -124.650002\n" + -//" 2 1.100231E-3 42.504601 -125.011299\n" + -//" 3 7.889546E-2 42.501801 -124.705803\n" + -//" 4 3.416457 42.5033 -124.845001\n"; -"abund_m3,latitude,longitude\n" + -"0.003688676,44.6517,-124.65\n" + -"0.003688676,44.6517,-124.65\n" + -"0.011066027,44.6517,-124.65\n" + -"0.014754703,44.6517,-124.65\n" + -"0.014754703,44.6517,-124.65\n" + -"...\n"; - po = results.indexOf(expected.substring(0, 19)); - Test.ensureEqual(results.substring(Math.max(po, 0)), expected, "results=\n" + results); -/* on oceanwatch, was -"{\n" + -"dimensions:\n" + -"\trow = 3779 ;\n" + -"variables:\n" + -"\tfloat latitude(row) ;\n" + -"\t\tlat:long_name = \"Latitude\" ;\n" + -"\tfloat long(row) ;\n" + -"\t\tlong:long_name = \"Longitude\" ;\n" + -"\tfloat abund_m3(row) ;\n" + -"\t\tabund_m3:long_name = \"Abundance m3\" ;\n" + -"\n" + -"// global attributes:\n" + -"}\n" + -" Row lat long abund_m3\n" + -" 0 44.651699 -124.650002 3.69822E-3\n" + -" 1 44.651699 -124.650002 7.26257E-2\n" + -" 2 42.504601 -125.011002 1.10023E-3\n" + -" 3 42.501801 -124.706001 7.88955E-2\n" + -" 4 42.5033 -124.845001 3.41646\n"; -*/ - - - - url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecVpt?station_id&distinct()"; - table.readOpendapSequence(url, false); - String2.log(table.toString(3)); - //source has no global metadata - Test.ensureEqual(table.nColumns(), 1, ""); - Test.ensureEqual(table.nRows(), 77, ""); - Test.ensureEqual(table.getColumnName(0), "station_id", ""); - Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Station ID", ""); - Test.ensureEqual(table.getStringData(0, 0), "BO01", ""); - Test.ensureEqual(table.getStringData(0, 1), "BO02", ""); - - - url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecVpt?abund_m3&station_id=%22NH05%22"; - table.readOpendapSequence(url, false); - String2.log(table.toString(3)); - //source has no global metadata - Test.ensureEqual(table.nColumns(), 1, ""); - Test.ensureEqual(table.nRows(), 2400, ""); - Test.ensureEqual(table.getColumnName(0), "abund_m3", ""); - Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Abundance", ""); - Test.ensureEqual(table.getFloatData(0, 0), 11.49f, ""); - Test.ensureEqual(table.getFloatData(0, 1), 74.720001f, ""); - - - url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecBottle?cruise_id&distinct()"; - table.readOpendapSequence(url, false); - String2.log(table.toString(1000000)); - //source has no global metadata - Test.ensureEqual(table.nColumns(), 1, ""); - Test.ensureEqual(table.nRows(), 2, ""); - Test.ensureEqual(table.getColumnName(0), "cruise_id", ""); - Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Cruise ID", ""); - Test.ensureEqual(table.getStringData(0, 0), "nh0207", ""); - Test.ensureEqual(table.getStringData(0, 1), "w0205", ""); - - - url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1?abund_m3,latitude,longitude&program=%22MESO_1%22"; - table.readOpendapSequence(url, false); - results = table.dataToString(); - String2.log(results); - expected = -/* oceanwatch was -... -" Row lat long abund_m3\n" + -" 0 44.651699 -124.650002 10.7463\n" + -" 1 44.651699 -124.650002 1.40056E-2\n" + -" 2 44.651699 -124.650002 0.252101\n"; -*/ -"abund_m3,latitude,longitude\n" + -//"10.746269,44.6517,-124.65\n" + //pre 2013-06-20 was -//"0.014005602,44.6517,-124.65\n" + -//"0.25210083,44.6517,-124.65\n"; -"0.003688676,44.6517,-124.65\n" + -"0.003688676,44.6517,-124.65\n" + -"0.011066027,44.6517,-124.65\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - - //test getting all data - //modified from above so it returns lots of data - //nRows=16507 nColumns=28 readTime=5219 ms processTime=94 ms - url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecVpt"; - table.readOpendapSequence(url, false); - results = table.dataToString(5); - //on oceanwatch, was -// Row datetime datetime_utc datetime_utc_e year program cruise_id cast_no stn_id -//lat long lat1000 lon1000 water_depth sample_id min_sample_dep max_sample_dep month_local day_local -// time_local d_n_flag gear_type gear_area_m2 gear_mesh vol_filt counter_id comments perc_counted lo -//cal_code nodc_code genus_species life_stage abund_m3 -// 0 2001-04-25 21: 2001-04-25 22: 988261731 2001 NH EL010403 2 NH05 44.650 -//002 -124.169998 44650 -124170 60 1 0 55 4 25 -// -9999 -9999 VPT 0.19635 0.202 14.46 WTP -9999 1.1 611 -//8010204# 6118010204 CALANUS_MARSHA 3;_CIII 11.49 - expected = -"cruise_id,longitude,latitude,time,cast_no,station_id,abund_m3,comments,counter_id,d_n_flag,gear_area,gear_mesh,gear_type,genus_species,life_stage,local_code,max_sample_depth,min_sample_depth,nodc_code,perc_counted,program,sample_id,vol_filt,water_depth\n" + -"EL010403,-124.17,44.65,9.88261731E8,0,NH05,11.49,-9999,WTP,-9999,0.19635,0.202,VPT,CALANUS_MARSHALLAE,3;_CIII,6118010204#,55,0,6118010204,1.1,NH,0,14.46,60\n" + -"EL010403,-124.17,44.65,9.88261731E8,0,NH05,74.72,-9999,WTP,-9999,0.19635,0.202,VPT,BIVALVIA,Veliger,55V,55,0,55,1.1,NH,0,14.46,60\n" + -"EL010403,-124.17,44.65,9.88261731E8,0,NH05,57.48,-9999,WTP,-9999,0.19635,0.202,VPT,POLYCHAETA,Larva,5001LV,55,0,5001,1.1,NH,0,14.46,60\n" + -"EL010403,-124.17,44.65,9.88261731E8,0,NH05,74.72,-9999,WTP,-9999,0.19635,0.202,VPT,GASTROPODA,Veliger,51V,55,0,51,1.1,NH,0,14.46,60\n" + -"EL010403,-124.17,44.65,9.88261731E8,0,NH05,11.49,-9999,WTP,-9999,0.19635,0.202,VPT,CALANUS_MARSHALLAE,1;_CI,6118010204!,55,0,6118010204,1.1,NH,0,14.46,60\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); - - - - //************* - String2.log("\n*** Table.testOpendapSequence subset data via tests"); - - //read data from opendap - table = new Table(); - table.readOpendapSequence( - //resulting url (for asc) is: - // https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1.asc?abund_m3,lat,long&abund_m3>=0.248962651&abund_m3<=0.248962653 - // Opera browser changes > to %3E and < to %3C - "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1", - new String[]{"abund_m3"}, - new double[]{0.24896}, //new double[]{0.248962651}, //the last 2 rows only - new double[]{0.24897}, //new double[]{0.248962653}, - new String[]{"abund_m3","latitude","longitude"}, - false); - - results = table.dataToString(); - expected = -"abund_m3,latitude,longitude\n" + -"0.24896266,44.6517,-124.65\n" + -"0.24896266,44.6517,-124.65\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - - //************* TWO-LEVEL SEQUENCE ***************************** - /* 2014-08-06 TEST REMOVED BECAUSE dataset is gone - - - //note that I was UNABLE to get .asc responses for these dapper urls while poking around. - //but straight dods request (without ".dods") works. - //I'm testing Lynn's old ndbc data because I can independently generate test info - // from my ndbc files. - //Starting url from Roy: http://las.pfeg.noaa.gov/dods/ - //See in DChart: http://las.pfeg.noaa.gov/dchart - //Test info from my cached ndbc file /u00/data/points/ndbcMet2HistoricalTxt/46022h2004.txt - //YYYY MM DD hh WD WSPD GST WVHT DPD APD MWD BAR ATMP WTMP DEWP VIS TIDE - //2004 01 01 00 270 2.0 3.1 3.11 16.67 9.80 999 1010.7 999.0 999.0 999.0 99.0 99.00 - //2004 01 01 01 120 5.9 7.3 3.29 16.67 10.12 999 1010.4 999.0 999.0 999.0 99.0 99.00 - //test attributes are from "http://las.pfeg.noaa.gov/dods/ndbc/all_noaa_time_series.cdp.das" - //http://las.pfeg.noaa.gov/dods/ndbc/all_noaa_time_series.cdp?location.LON,location.LAT,location.DEPTH,location.profile.TIME,location.profile.WSPD1,location.profile.BAR1&location.LON>=235.3&location.LON<=235.5&location.LAT>=40.7&location.LAT<=40.8&location.profile.TIME>=1072915200000&location.profile.TIME<=1072920000000 - lon = 235.460007f; //exact values from just get LON and LAT values available - lat = 40.779999f; - long time1 = Calendar2.newGCalendarZulu(2004, 1, 1).getTimeInMillis(); - long time2 = time1 + Calendar2.MILLIS_PER_HOUR; - //was http://las.pfeg.noaa.gov/dods/ndbc/all_noaa_time_series.cdp - //was http://las.pfeg.noaa.gov/dods/ndbcMet/ndbcMet_time_series.cdp?" + - url = "http://oceanview.pfeg.noaa.gov/dods/ndbcMet/ndbcMet_time_series.cdp?" + - "location.LON,location.LAT,location.DEPTH,location.profile.TIME,location.profile.WSPD,location.profile.BAR" + - "&location.LON>=" + (lon - .01f) + "&location.LON<=" + (lon + .01f) + //I couldn't catch lon with "=" - "&location.LAT>=" + (lat - .01f) + "&location.LAT<=" + (lat + .01f) + //I couldn't catch lat with "=" - "&location.profile.TIME>=" + (time1 - 1) + - "&location.profile.TIME<=" + (time2 + 1); - String2.log("url=" + url); - table.readOpendapSequence(url, false); - String2.log(table.toString()); - Test.ensureEqual(table.nColumns(), 6, ""); - Test.ensureEqual(table.nRows(), 2, ""); - int latCol = table.findColumnNumber("LAT"); - int lonCol = table.findColumnNumber("LON"); - Test.ensureTrue(latCol >= 0 && latCol < 2, "latCol=" + latCol); - Test.ensureTrue(lonCol >= 0 && lonCol < 2, "lonCol=" + lonCol); - Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); - Test.ensureEqual(table.getColumnName(3), "TIME", ""); - int barCol = table.findColumnNumber("BAR"); - int wspdCol = table.findColumnNumber("WSPD"); - Test.ensureEqual(table.getColumn(latCol).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(3).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(wspdCol).elementTypeString(), "float", ""); - Test.ensureEqual(table.globalAttributes().getString("Conventions"), "epic-insitu-1.0", ""); - Test.ensureEqual(table.globalAttributes().get("lat_range").toString(), "-27.7000007629395, 70.4000015258789", ""); - Test.ensureEqual(table.getFloatData(latCol, 0), lat, ""); - Test.ensureEqual(table.getFloatData(latCol, 1), lat, ""); - Test.ensureEqual(table.getFloatData(lonCol, 0), lon, ""); - Test.ensureEqual(table.getFloatData(lonCol, 1), lon, ""); - //outer attributes... - Test.ensureEqual(table.columnAttributes(latCol).getString("units"), "degrees_north", ""); - Test.ensureEqual(table.columnAttributes(latCol).getString("long_name"), "latitude", ""); - Test.ensureEqual(table.columnAttributes(latCol).getDouble("missing_value"), Double.NaN, ""); - Test.ensureEqual(table.columnAttributes(latCol).getString("axis"), "Y", ""); - Test.ensureEqual(table.getDoubleData(3, 0), time1, ""); - Test.ensureEqual(table.getDoubleData(3, 1), time2, ""); - //inner attributes... - Test.ensureEqual(table.columnAttributes(3).getString("units"), "msec since 1970-01-01 00:00:00 GMT", ""); - Test.ensureEqual(table.columnAttributes(3).getString("long_name"), "time", ""); - Test.ensureEqual(table.columnAttributes(3).getDouble("missing_value"), Double.NaN, ""); - Test.ensureEqual(table.columnAttributes(3).getString("axis"), "T", ""); - Test.ensureEqual(table.getFloatData(barCol, 0), 1010.7f, ""); //bar - Test.ensureEqual(table.getFloatData(barCol, 1), 1010.4f, ""); - Test.ensureEqual(table.getFloatData(wspdCol, 0), 2.0f, ""); //wspd - Test.ensureEqual(table.getFloatData(wspdCol, 1), 5.9f, ""); - - */ - - - /* 2014-08-06 INACTIVE BECAUSE DATASET NO LONGER AVAILABLE - //This Calcofi test simply verifies that the results now are as they were when - // I wrote the test (circular logic). - //I hope this test is better than ndbc test above, - // since hopefully longer lived (since ndbc data may not be around forever). - //target data - // Row time lat lon depth English_sole_LarvaeCount - // 10 947320140000 32.341667 241.445007 203.800003 NaN - // 11 947320140000 32.341667 241.445007 NaN NaN - lat = 32.341667f; - lon = 241.445f; - long time = 947320140000L; - //Starting url from roy: http://las.pfeg.noaa.gov/dods/ - //see info via url without query, but plus .dds or .das - //was las.pfeg.noaa.gov - url = "http://oceanview.pfeg.noaa.gov/dods/CalCOFI/Biological.cdp?" + - "location.lon,location.lat,location.time,location.profile.depth,location.profile.Line,location.profile.Disintegrated_fish_larvae_LarvaeCount" + - "&location.lon>=" + (lon - .01f) + "&location.lon<=" + (lon + .01f) + //I couldn't catch lon with "=" - "&location.lat>=" + (lat - .01f) + "&location.lat<=" + (lat + .01f) + //I couldn't catch lat with "=" - "&location.time>=" + (time - 1); - table.readOpendapSequence(url, false); - - String2.log(table.toString()); - int latCol = table.findColumnNumber("lat"); - int lonCol = table.findColumnNumber("lon"); - Test.ensureTrue(latCol >= 0, "latCol=" + latCol); - Test.ensureTrue(lonCol >= 0, "lonCol=" + lonCol); - Test.ensureEqual(table.nColumns(), 6, ""); - Test.ensureEqual(table.nRows(), 31, ""); - Test.ensureEqual(table.getColumnName(0), "time", ""); //not in order I requested! they are in dataset order - Test.ensureEqual(table.getColumnName(latCol), "lat", ""); - Test.ensureEqual(table.getColumnName(lonCol), "lon", ""); - Test.ensureEqual(table.getColumnName(3), "Line", ""); - Test.ensureEqual(table.getColumnName(4), "Disintegrated_fish_larvae_LarvaeCount", ""); - Test.ensureEqual(table.getColumnName(5), "depth", ""); - Test.ensureEqual(table.getColumn(0).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(latCol).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(lonCol).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(3).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(4).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(5).elementTypeString(), "float", ""); - //global attributes - Test.ensureEqual(table.globalAttributes().getString("Conventions"), "epic-insitu-1.0", ""); - Test.ensureEqual(table.globalAttributes().getInt("total_profiles_in_dataset"), 6407, ""); - //test of outer attributes - Test.ensureEqual(table.columnAttributes(0).getString("units"), "msec since 1970-01-01 00:00:00 GMT", ""); - Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "time", ""); - Test.ensureEqual(table.columnAttributes(0).getDouble("missing_value"), Double.NaN, ""); - Test.ensureEqual(table.columnAttributes(0).getString("axis"), "T", ""); - //test of inner attributes - Test.ensureEqual(table.columnAttributes(4).getString("long_name"), "disintegrated fish larvae larvae count", ""); - Test.ensureEqual(table.columnAttributes(4).getFloat("missing_value"), Float.NaN, ""); - Test.ensureEqual(table.columnAttributes(4).getString("units"), "number of larvae", ""); - - //test of results - //NOTE that data from different inner sequences is always separated by a row of NaNs - // in the ending inner sequence's info. - // I believe Dapper is doing this. See more comments below. - // Row time lat lon Disintegrated_ Line depth - // 0 947320140000 32.341667 241.445007 NaN 93.300003 203.800003 - // 1 947320140000 32.341667 241.445007 NaN NaN NaN - // 2 955184100000 32.348331 241.448334 NaN 93.300003 215.800003 - // 30 1099482480000 32.345001 241.445007 NaN 93.300003 198.899994 - Test.ensureEqual(table.getDoubleData(0, 0), 947320140000L, ""); - Test.ensureEqual(table.getFloatData(latCol, 0), 32.341667f, ""); - Test.ensureEqual(table.getFloatData(lonCol, 0), 241.445007f, ""); - Test.ensureEqual(table.getFloatData(3, 0), 93.300003f, ""); - Test.ensureEqual(table.getFloatData(4, 0), Float.NaN, ""); - Test.ensureEqual(table.getFloatData(5, 0), 203.800003f, ""); - - Test.ensureEqual(table.getDoubleData(0, 1), 947320140000L, ""); - Test.ensureEqual(table.getFloatData(latCol, 1), 32.341667f, ""); - Test.ensureEqual(table.getFloatData(lonCol, 1), 241.445007f, ""); - Test.ensureEqual(table.getFloatData(3, 1), Float.NaN, ""); - Test.ensureEqual(table.getFloatData(4, 1), Float.NaN, ""); - Test.ensureEqual(table.getFloatData(5, 1), Float.NaN, ""); - - Test.ensureEqual(table.getDoubleData(0, 30), 1099482480000L, ""); - Test.ensureEqual(table.getFloatData(latCol, 30), 32.345001f, ""); - Test.ensureEqual(table.getFloatData(lonCol, 30), 241.445007f, ""); - Test.ensureEqual(table.getFloatData(3, 30), 93.300003f, ""); - Test.ensureEqual(table.getFloatData(4, 30), Float.NaN, ""); - Test.ensureEqual(table.getFloatData(5, 30), 198.899994f, ""); - - - //*** visual test: is dapper returning the NAN row at the end of every innerSequence (true) - // or is that the way it is in the files? (false) - lon = 235.460007f; //exact values from just get LON and LAT values available - lat = 40.779999f; - long time1 = Calendar2.newGCalendarZulu(2004, 1, 1).getTimeInMillis(); - long time2 = time1 + Calendar2.MILLIS_PER_HOUR; - //was http://las.pfeg.noaa.gov/dods/ndbc/all_noaa_time_series.cdp - url = "http://oceanview.pfeg.noaa.gov/dods/ndbcMet/ndbcMet_time_series.cdp?" + - "location.LON,location.LAT,location.DEPTH,location.profile.TIME,location.profile.WSPD,location.profile.BAR" + - "&location.LON>=" + (lon - 5f) + "&location.LON<=" + (lon + 5f) + - "&location.LAT>=" + (lat - 5f) + "&location.LAT<=" + (lat + 5f) + - "&location.profile.TIME>=" + (time1 - 1) + - "&location.profile.TIME<=" + (time2 + 1); - table.readOpendapSequence(url, false); - String2.log(table.toString()); - */ - - /* - //THIS WORKS, BUT TAKES ~40 SECONDS!!! so don't do all the time - //see questions below. - //This gets all the valid English_sole_LarvaeCount data. - //UNFORTUNATELY, you can't put constraint on non-axis variable, - // so I have to get all data and then filter the results. - //This test simply verifies that the results now are as they were when - // I wrote the test (circular logic). - //I had hoped this test would be better than ndbc test above, - // since hopefully longer lived (since ndbc data may not be around forever). - //Starting url from roy: http://las.pfeg.noaa.gov/dods/ - url = "http://las.pfeg.noaa.gov/dods/CalCOFI/Biological.cdp?" + - "location.lon,location.lat,location.time,location.profile.depth,location.profile.English_sole_LarvaeCount"; - table.readOpendapSequence(url); - String2.log("raw results nRows=" + table.nRows()); - //just keep rows with larvaeCounts >= 0 - table.subset(new int[]{4}, new double[]{0}, new double[]{1e300}); - - String2.log(table.toString()); - Test.ensureEqual(table.nColumns(), 5, ""); - Test.ensureEqual(table.nRows(), 98, ""); - Test.ensureEqual(table.getColumnName(0), "time", ""); //not in order I requested! they are in dataset order - Test.ensureEqual(table.getColumnName(1), "lat", ""); - Test.ensureEqual(table.getColumnName(2), "lon", ""); - Test.ensureEqual(table.getColumnName(3), "depth", ""); - Test.ensureEqual(table.getColumnName(4), "English_sole_LarvaeCount", ""); - Test.ensureEqual(table.getColumn(0).elementTypeString(), "double", ""); - Test.ensureEqual(table.getColumn(1).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(2).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(3).elementTypeString(), "float", ""); - Test.ensureEqual(table.getColumn(4).elementTypeString(), "float", ""); - //global attributes - Test.ensureEqual(table.globalAttributes().getString("Conventions"), "epic-insitu-1.0", ""); - Test.ensureEqual(table.globalAttributes().getInt("total_profiles_in_dataset"), 6407, ""); - //test of outer attributes - Test.ensureEqual(table.columnAttributes(0).getString("units"), "msec since 1970-01-01 00:00:00 GMT", ""); - Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "time", ""); - Test.ensureEqual(table.columnAttributes(0).getDouble("missing_value"), Double.NaN, ""); - Test.ensureEqual(table.columnAttributes(0).getString("axis"), "T", ""); - //test of inner attributes - Test.ensureEqual(table.columnAttributes(4).getString("long_name"), "parophrys vetulus larvae count", ""); - Test.ensureEqual(table.columnAttributes(4).getFloat("missing_value"), Float.NaN, ""); - Test.ensureEqual(table.columnAttributes(4).getString("units"), "number of larvae", ""); - - //test of results - Test.ensureEqual(table.getDoubleData(0, 0), 955657380000L, ""); - Test.ensureEqual(table.getFloatData(1, 0), 33.485001f, ""); - Test.ensureEqual(table.getFloatData(2, 0), 242.231659f, ""); - Test.ensureEqual(table.getFloatData(3, 0), 210.800003f, ""); - Test.ensureEqual(table.getFloatData(4, 0), 1, ""); - - Test.ensureEqual(table.getDoubleData(0, 1), 955691700000L, ""); - Test.ensureEqual(table.getFloatData(1, 1), 33.825001f, ""); - Test.ensureEqual(table.getFloatData(2, 1), 241.366669f, ""); - Test.ensureEqual(table.getFloatData(3, 1), 208.5f, ""); - Test.ensureEqual(table.getFloatData(4, 1), 6, ""); - - Test.ensureEqual(table.getDoubleData(0, 97), 923900040000L, ""); - Test.ensureEqual(table.getFloatData(1, 97), 34.976665f, ""); - Test.ensureEqual(table.getFloatData(2, 97), 237.334991f, ""); - Test.ensureEqual(table.getFloatData(3, 97), 24.1f, ""); - Test.ensureEqual(table.getFloatData(4, 97), 4, ""); - -/* */ -/** -[Bob talked to Lynn about this. Conclusions below.] -1) If I just get all lon,lat,time,depth, and English_sole_LarvaeCount - (was http://las.pfeg...) - url = "http://oceanview.pfeg.noaa.gov/dods/CalCOFI/Biological.cdp?" + - "location.lon,location.lat,location.time,location.profile.depth,location.profile.English_sole_LarvaeCount"; - it looks like each time,lat,lon combo has a data row and a NaN row. - ???Is this a real NaN row, or a mistake in my code (e.g., end of sequence beginning of next). - [I believe it is real and added by Dapper.] - Note that some sole counts below are non-NaN. - - Row time lat lon depth English_sole_LarvaeCount - 0 947255160000 32.955002 242.695007 71.5 NaN - 1 947255160000 32.955002 242.695007 NaN NaN - 2 947264520000 32.913334 242.606659 207.600006 NaN - 3 947264520000 32.913334 242.606659 NaN NaN - 4 947275680000 32.848335 242.471664 211.699997 NaN - 5 947275680000 32.848335 242.471664 NaN NaN - 6 947290920000 32.68 242.126663 195.899994 NaN - 7 947290920000 32.68 242.126663 NaN NaN - 8 947306040000 32.513332 241.790009 208.100006 NaN - 9 947306040000 32.513332 241.790009 NaN NaN - 10 947320140000 32.341667 241.445007 203.800003 NaN - 11 947320140000 32.341667 241.445007 NaN NaN - 12 947343360000 32.18 241.110001 209.5 NaN - 13 947343360000 32.18 241.110001 NaN NaN - 14 947359140000 32.006668 240.764999 215.5 NaN - 15 947359140000 32.006668 240.764999 NaN NaN -2) do all time,lat,lon combo's just have one depth? - If so, then why set up this way? - Just to match dapper convention (must have z or t outside and t or z inside)? - [I believe so.] - -3) Since it appears that the 150(?) variables were only measured rarely, - it seems hugely wasteful to allocate space for them. - And worse, since a query use constraints on non-axis variables, - one can't simply ask for ... &English_sole_LarvaeCount>=0 - to find time,lat,lon,depth where there are valid values of English_sole_LarvaeCount. - And requesting all data rows (so I can then filtering on my end) takes ~40 seconds - for 98 rows of data. - [Wasteful, but I believe Roy did it this way to conform to Dapper Conventions so - data easily served by Dapper/DChart, see http://oceanview.pfeg.noaa.gov/dchart (was http://las.pfeg...).] - -4) There are no 0 values for English_sole_LarvaeCount. - So how can one tell if people looked for English_sole_Larvae but didn't find any? - Are NaN's to be treated as 0 for this data set? - [It looks like 0 values are lumped in with NaNs.] - -5) Why is number of larvae (units="number of larvae") a float and not an int? - [Because all variables are floats for simplicity (maybe for matlab or fortran).] - -*/ - } - - /** Test the speed of readASCII */ - public static void testReadASCIISpeed() throws Exception { - - String fileName = "/u00/data/points/ndbcMet2HistoricalTxt/41009h1990.txt"; - long time = 0; - - for (int attempt = 0; attempt < 4; attempt++) { - String2.log("\n*** Table.testReadASCIISpeed attempt #" + attempt + "\n"); - Math2.gcAndWait("Table (between tests)"); //in a test - Math2.sleep(5000); - //time it - long fileLength = File2.length(fileName); //was 1335204 - Test.ensureTrue(fileLength > 1335000, "fileName=" + fileName + " length=" + fileLength); - time = System.currentTimeMillis(); - Table table = new Table(); - table.readASCII(fileName); - time = System.currentTimeMillis() - time; - - String results = table.dataToString(3); - String expected = -"YY,MM,DD,hh,WD,WSPD,GST,WVHT,DPD,APD,MWD,BAR,ATMP,WTMP,DEWP,VIS\n" + -"90,01,01,00,161,08.6,10.7,01.50,05.00,04.80,999,1017.2,22.7,22.0,999.0,99.0\n" + -"90,01,01,01,163,09.3,11.3,01.50,05.00,04.90,999,1017.3,22.7,22.0,999.0,99.0\n" + -"90,01,01,01,164,09.2,10.6,01.60,04.80,04.90,999,1017.3,22.7,22.0,999.0,99.0\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nColumns(), 16, "nColumns=" + table.nColumns()); - Test.ensureEqual(table.nRows(), 17117, "nRows=" + table.nRows()); - - String2.log("********** attempt #" + attempt + " Done.\n" + - "cells/ms=" + (table.nColumns() * table.nRows()/time) + - " (usual=2560 with StringHolder. With String, was 2711 Java 1.7M4700, was 648)" + - "\ntime=" + time + "ms (good=106ms, but slower when computer is busy.\n" + - " (was 101 Java 1.7M4700, was 422, java 1.5 was 719)"); - if (time <= 130) - break; - } - if (time > 130) - throw new SimpleException("readASCII took too long (time=" + time + "ms > 130ms) (but often does when computer is busy)."); - } - - - /** Test the speed of readJson */ - public static void testReadJsonSpeed() throws Exception { - - //warmup - String fileName = String2.unitTestDataDir + "cPostDet3.files.json.gz"; - long time = 0; - String msg = ""; - String expected = -"dirIndex,fileName,lastMod,sortedSpacing,unique_tag_id_min_,unique_tag_id_max_,PI_min_,PI_max_,longitude_min_,longitude_max_,latitude_min_,latitude_max_,time_min_,time_max_,bottom_depth_min_,bottom_depth_max_,common_name_min_,common_name_max_,date_public_min_,date_public_max_,line_min_,line_max_,position_on_subarray_min_,position_on_subarray_max_,project_min_,project_max_,riser_height_min_,riser_height_max_,role_min_,role_max_,scientific_name_min_,scientific_name_max_,serial_number_min_,serial_number_max_,stock_min_,stock_max_,surgery_time_min_,surgery_time_max_,surgery_location_min_,surgery_location_max_,tagger_min_,tagger_max_\n" + -"0,52038_A69-1303_1059305.nc,1.284567715046E12,0.0,52038_A69-1303_1059305,52038_A69-1303_1059305,BARBARA BLOCK,BARBARA BLOCK,-146.36933,-146.1137,60.6426,60.7172,1.2192849E9,1.238062751E9,13.4146341463415,130.487804878049,SALMON SHARK,SALMON SHARK,1.273271649385E9,1.273271649385E9,,PORT GRAVINA,,9,HOPKINS MARINE STATION,HOPKINS MARINE STATION,,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,LAMNA DITROPIS,1059305,1059305,N/A,N/A,1.2192156E9,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\"PORT GRAVINA, PRINCE WILLIAM SOUND\",,\n" + -"1,16955_A69-1303_8685G.nc,1.284567719796E12,-1.0,16955_A69-1303_8685G,16955_A69-1303_8685G,BARRY BEREJIKIAN,BARRY BEREJIKIAN,-122.78316,-122.78316,47.65223,47.65223,1.1466882E9,1.1466882E9,,,STEELHEAD,STEELHEAD,1.222730955645E9,1.222730955645E9,,,,,NOAA|NOAA FISHERIES,NOAA|NOAA FISHERIES,,,BEREJIKIAN_BARRY_ONCORHYNCHUS_MYKISS_BIGBEEFCREEK,BEREJIKIAN_BARRY_ONCORHYNCHUS_MYKISS_BIGBEEFCREEK,ONCORHYNCHUS MYKISS,ONCORHYNCHUS MYKISS,8685G,8685G,BIG BEEF CREEK,BIG BEEF CREEK,1.146528E9,1.146528E9,BIG BEEF CREEK,BIG BEEF CREEK,SKIP TEZAK,SKIP TEZAK\n" + -"1,16956_A69-1303_8686G.nc,1.284567723515E12,-1.0,16956_A69-1303_8686G,16956_A69-1303_8686G,BARRY BEREJIKIAN,BARRY BEREJIKIAN,-122.78316,-122.78316,47.65223,47.65223,1.1466882E9,1.1466882E9,,,STEELHEAD,STEELHEAD,1.222730955653E9,1.222730955653E9,,,,,NOAA|NOAA FISHERIES,NOAA|NOAA FISHERIES,,,BEREJIKIAN_BARRY_ONCORHYNCHUS_MYKISS_BIGBEEFCREEK,BEREJIKIAN_BARRY_ONCORHYNCHUS_MYKISS_BIGBEEFCREEK,ONCORHYNCHUS MYKISS,ONCORHYNCHUS MYKISS,8686G,8686G,BIG BEEF CREEK,BIG BEEF CREEK,1.146528E9,1.146528E9,BIG BEEF CREEK,BIG BEEF CREEK,SKIP TEZAK,SKIP TEZAK\n" + -"...\n"; - - for (int attempt = 0; attempt < 3; attempt++) { - String2.log("\n*** Table.testReadJsonSpeed attempt#" + attempt + "\n"); - - //time it - time = System.currentTimeMillis(); - long fileLength = File2.length(fileName); //before gz was 10,166KB, now 574572 - Test.ensureTrue(fileLength > 574000, "fileName=" + fileName + " length=" + fileLength); - Table table=new Table(); - table.readJson(fileName); - - String results = table.dataToString(3); - Test.ensureEqual(results, expected, "results=" + results); - Test.ensureTrue(results.indexOf("unique_tag_id_max") > 0, "test 1"); - Test.ensureTrue(results.indexOf("surgery_time_min") > 0, "test 2"); - Test.ensureTrue(table.nColumns() > 40, "nColumns=" + table.nColumns()); //was 42 - Test.ensureTrue(table.nRows() > 15000, "nRows=" + table.nRows()); //was 15024 - - time = System.currentTimeMillis() - time; - msg = "*** Done. cells/ms=" + - (table.nColumns() * table.nRows()/time) + " (usual=2881 Java 1.7M4700, was 747)" + - "\ntime=" + time + "ms (usual=300, java 8 was 219, Java 1.7M4700, was 844, java 1.5 was 1687)"; - String2.log(msg); - if (time <= 400) - break; - } - Test.ensureTrue(time < 400, msg + "\nreadJson took too long."); - } - - - /** Test the speed of readNDNc */ - public static void testReadNDNcSpeed() throws Exception { - - String fileName = "c:/u00/data/points/ndbcMet2/historical/NDBC_41004_met.nc"; - Table table = new Table(); - long time = 0; - String2.log(NcHelper.ncdump(fileName, "-h")); - - for (int attempt = 0; attempt < 3; attempt++) { - String2.log("\n*** Table.testReadNDNcSpeed attempt+" + attempt + "\n"); - Math2.gcAndWait("Table (between tests)"); //in a test - - //time it - time = System.currentTimeMillis(); - long fileLength = File2.length(fileName); //was 20580000 - Test.ensureTrue(fileLength > 20570000, "fileName=" + fileName + " length=" + fileLength); - table = new Table(); - table.readNDNc(fileName, null, 0, null, 0, 0); //standardizeWhat=0 - - String results = table.dataToString(3); - String expected = //before 2011-06-14 was 32.31, -75.35, -"TIME,DEPTH,LAT,LON,WD,WSPD,GST,WVHT,DPD,APD,MWD,BAR,ATMP,WTMP,DEWP,VIS,PTDY,TIDE,WSPU,WSPV,ID\n" + -"2.678004E8,0.0,32.501,-79.099,255,1.3,-9999999.0,-9999999.0,-9999999.0,-9999999.0,32767,1020.5,27.2,27.4,-9999999.0,-9999999.0,-9999999.0,-9999999.0,1.3,0.3,41004\n" + -"2.67804E8,0.0,32.501,-79.099,247,6.6,-9999999.0,-9999999.0,-9999999.0,-9999999.0,32767,1020.6,26.8,27.4,-9999999.0,-9999999.0,-9999999.0,-9999999.0,6.1,2.6,41004\n" + -"2.678076E8,0.0,32.501,-79.099,249,7.0,-9999999.0,-9999999.0,-9999999.0,-9999999.0,32767,1020.4,26.8,27.4,-9999999.0,-9999999.0,-9999999.0,-9999999.0,6.5,2.5,41004\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nColumns(), 21, "nColumns=" + table.nColumns()); - Test.ensureTrue(table.nRows() >= 351509, "nRows=" + table.nRows()); - - time = System.currentTimeMillis() - time; - String2.log("********** Done. cells/ms=" + - (table.nColumns() * table.nRows()/time) + " (usual=31414 Java 1.7M4700, was 9679)" + - "\ntime=" + time + "ms (usual=556 Lenovo, was 226 Java 1.7M4700, was 640, java 1.5 was 828, but varies a lot)"); - if (time <= 650) - break; - } - if (time > 650) - throw new SimpleException("readNDNc took too long (time=" + time + "ms (556ms expected))"); - } - - - /** Test the speed of readOpendapSequence */ - public static void testReadOpendapSequenceSpeed() throws Exception { - - String url = - "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/cwwcNDBCMet?" + - "&time%3E=1999-01-01&time%3C=1999-04-01&station=%2241009%22"; - long time = 0; - - for (int attempt = 0; attempt < 3; attempt++) { - String2.log("\n*** Table.testReadOpendapSequenceSpeed\n"); - Math2.gcAndWait("Table (between tests)"); //in a test - - //time it - time = System.currentTimeMillis(); - Table table = new Table(); - table.readOpendapSequence(url); - String results = table.dataToString(3); - String expected = //before 2011-06-14 was -80.17, 28.5 -//"station,longitude,latitude,time,wd,wspd,gst,wvht,dpd,apd,mwd,bar,atmp,wtmp,dewp,vis,ptdy,tide,wspu,wspv\n" + -//"41009,-80.166,28.519,9.151488E8,0,1.9,2.7,1.02,11.11,6.49,32767,1021.0,20.4,24.2,-9999999.0,-9999999.0,-9999999.0,-9999999.0,0.0,-1.9\n" + -//"41009,-80.166,28.519,9.151524E8,53,1.5,2.8,0.99,11.11,6.67,32767,1021.0,20.6,24.5,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-1.2,-0.9\n" + -//"41009,-80.166,28.519,9.15156E8,154,1.0,2.2,1.06,11.11,6.86,32767,1021.2,20.6,24.6,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-0.4,0.9\n" + - -//source ASCII file has: (note 2 rows for ever hour) -//YYYY MM DD hh WD WSPD GST WVHT DPD APD MWD BAR ATMP WTMP DEWP VIS [in EditPlus, the first row of data is here, to right of col names -- screwy line endings?!] -//1999 01 01 00 360 1.9 2.7 1.02 11.11 6.49 999 1021.0 20.4 24.2 999.0 99.0 -//1999 01 01 00 21 1.4 3.4 1.10 11.11 6.82 999 1020.9 20.4 24.5 999.0 99.0 -//1999 01 01 01 53 1.5 2.8 .99 11.11 6.67 999 1021.0 20.6 24.5 999.0 99.0 -//1999 01 01 01 53 1.5 2.6 1.10 11.11 6.97 999 1021.1 20.6 24.5 999.0 99.0 -//1999 01 01 02 154 1.0 2.2 1.06 11.11 6.86 999 1021.2 20.6 24.6 999.0 99.0 -//1999 01 01 02 73 2.5 3.8 1.09 11.11 6.87 999 1021.2 20.7 24.6 999.0 99.0 - -//2020-03-03 this data changed significantly after big changes to processing system/ dealing with duplicate lines (prefer newer data/later in file) -"station,longitude,latitude,time,wd,wspd,gst,wvht,dpd,apd,mwd,bar,atmp,wtmp,dewp,vis,ptdy,tide,wspu,wspv\n" + -"41009,-80.166,28.519,9.151488E8,21,1.4,3.4,1.1,11.11,6.82,32767,1020.9,20.4,24.5,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-0.5,-1.3\n" + //1999-01-01T00:00 -"41009,-80.166,28.519,9.151524E8,53,1.5,2.6,1.1,11.11,6.97,32767,1021.1,20.6,24.5,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-1.2,-0.9\n" + //1999-01-01T01:00 -"41009,-80.166,28.519,9.15156E8,73,2.5,3.8,1.09,11.11,6.87,32767,1021.2,20.7,24.6,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-2.4,-0.7\n" + //1999-01-01T02:00 -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - Test.ensureTrue(table.nRows() > 2100, "nRows=" + table.nRows()); - time = System.currentTimeMillis() - time; - String2.log("********** Done. cells/ms=" + - (table.nColumns() * table.nRows()/time) + " (usual(https)=33, was(http) 337 Java 1.7M4700, was 106)" + - "\ntime=" + time + "ms (usual(https)=1285, was http=600 since remote, was 128 Java 1.7M4700, was 406, java 1.5 was 562)"); - if (time <= 1600) - break; - } - if (time > 1600) - throw new SimpleException("readOpendapSequence took too long (time=" + time + "ms)."); - } - - - /** Test the speed of saveAs speed */ - public static void testSaveAsSpeed() throws Exception { - - //warmup - String2.log("\n*** Table.testSaveAsSpeed\n"); - String sourceName = "/u00/data/points/ndbcMet2HistoricalTxt/41009h1990.txt"; - String destName = File2.getSystemTempDirectory() + "testSaveAsSpeed"; - Table table = new Table(); - table.readASCII(sourceName); - Test.ensureEqual(table.nColumns(), 16, "nColumns=" + table.nColumns()); - Test.ensureEqual(table.nRows(), 17117, "nRows=" + table.nRows()); - table.saveAsCsvASCII(destName + ".csv"); - table.saveAsJson(destName + ".json", table.findColumnNumber("time"), true); //writeUnits - table.saveAsFlatNc(destName + ".nc", "row"); - long time = 0; - - for (int attempt = 0; attempt < 3; attempt++) { - //time it - String2.log("\ntime it\n"); - - //saveAsCsvASCII - time = System.currentTimeMillis(); - table.saveAsCsvASCII(destName + ".csv"); - time = System.currentTimeMillis() - time; - String2.log("saveAsCsvASCII attempt#" + attempt + - " done. cells/ms=" + (table.nColumns() * table.nRows() / time) + //796 - "\ntime=" + time + "ms (expected=344, was 532 for Java 1.5 Dell)"); - File2.delete(destName + ".csv"); - if (time <= 550) - break; - } - if (time > 550) - throw new SimpleException("saveAsCsvASCII (time=" + time + "ms). Expected=~344 for 17117 rows."); - - for (int attempt = 0; attempt < 3; attempt++) { - //saveAsJson - time = System.currentTimeMillis(); - table.saveAsJson(destName + ".json", table.findColumnNumber("time"), true); //writeUnits - time = System.currentTimeMillis() - time; - String2.log("saveAsJson attempt#" + attempt + - " done. cells/ms=" + (table.nColumns() * table.nRows() / time) + //974 - "\ntime=" + time + "ms (expect=281, was 515 for Java 1.5 Dell)"); - File2.delete(destName + ".json"); - if (time <= 450) - break; - } - if (time >= 450) - throw new SimpleException("saveAsJson took too long (time=" + time + "ms). Expected=~281 for 17117 rows."); - - //saveAsFlatNc - for (int attempt = 0; attempt < 3; attempt++) { - time = System.currentTimeMillis(); - table.saveAsFlatNc(destName + ".nc", "row"); - time = System.currentTimeMillis() - time; - String2.log("saveAsFlatNc attempt#" + attempt + - " done. cells/ms=" + (table.nColumns() * table.nRows() / time) + //2190 - "\ntime=" + time + "ms (expected=125, was 172 for Java 1.5 Dell)"); - File2.delete(destName + ".nc"); - if (time <= 200) - break; + if (reallyVerbose) String2.log(msg + " finished. nColumns=" + nColumns() + + " nRows=" + nRows() + " TIME=" + (System.currentTimeMillis() - tTime) + "ms"); + } finally { + try {if (nc != null) nc.close(); } catch (Exception e9) {} } - if (time > 200) - throw new SimpleException("saveAsFlatNc took too long (time=" + time + "ms). Expected=~125 for 17117 rows."); - - } - - - - /** - * This is a test of readOpendap. - * - * @throws Exception of trouble - */ - public static void testOpendap() throws Exception { - //************* - String2.log("\n*** Table.testOpendap"); - verbose = true; - reallyVerbose = true; - - //opendap, even sequence data, can be read via .nc - // but constraints are not supported - Table table = new Table(); - int nRows = 3779; - table.readFlatNc( - //read all via ascii: "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1.asc?abund_m3,lat,long", null); - //or "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1.asc?MOC1.abund_m3,MOC1.lat,MOC1.long", null); - "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1", - new String[]{"MOC1.abund_m3", "MOC1.lat", "MOC1.long"}, //but "MOC1." is required here - 0); //standardizeWhat=0 -//2018-05-12 was unpack to doubles, so these tests will change - String2.log(table.toString(5)); - - Test.ensureEqual(table.nColumns(), 3, ""); - Test.ensureEqual(table.nRows(), nRows, ""); - - Test.ensureEqual(table.getColumnName(0), "abund_m3", ""); - Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Abundance m3", ""); - Test.ensureEqual(table.getDoubleData(0, 0), 0.242688983, ""); - Test.ensureEqual(table.getDoubleData(0, nRows-1), 0.248962652, ""); - - Test.ensureEqual(table.getColumnName(1), "lat", ""); - Test.ensureEqual(table.columnAttributes(1).getString("long_name"), "Latitude", ""); - Test.ensureEqual(table.getDoubleData(1, 0), 44.6517, ""); - Test.ensureEqual(table.getDoubleData(1, nRows-1), 44.6517, ""); - - Test.ensureEqual(table.getColumnName(2), "long", ""); - Test.ensureEqual(table.columnAttributes(2).getString("long_name"), "Longitude", ""); - Test.ensureEqual(table.getDoubleData(2, 0), -124.175, ""); - Test.ensureEqual(table.getDoubleData(2, nRows-1), -124.65, ""); - - //can it read with list of variables? - table.readFlatNc( - "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1?abund_m3,lat,long", - null, //read all variables - 0); //standardizeWhat=0 -//2018-05-12 was unpack to doubles, so these tests will change - String2.log(table.toString(5)); - Test.ensureEqual(table.nColumns(), 3, ""); - Test.ensureEqual(table.nRows(), nRows, ""); - - //!!!HEY, the results are an unexpected order!!! - Test.ensureEqual(table.getColumnName(0), "lat", ""); - Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Latitude", ""); - Test.ensureEqual(table.getDoubleData(0, 0), 44.6517, ""); - Test.ensureEqual(table.getDoubleData(0, nRows-1), 44.6517, ""); - - Test.ensureEqual(table.getColumnName(1), "long", ""); - Test.ensureEqual(table.columnAttributes(1).getString("long_name"), "Longitude", ""); - Test.ensureEqual(table.getDoubleData(1, 0), -124.175, ""); - Test.ensureEqual(table.getDoubleData(1, nRows-1), -124.65, ""); - - Test.ensureEqual(table.getColumnName(2), "abund_m3", ""); - Test.ensureEqual(table.columnAttributes(2).getString("long_name"), "Abundance m3", ""); - Test.ensureEqual(table.getDoubleData(2, 0), 0.242688983, ""); - Test.ensureEqual(table.getDoubleData(2, nRows-1), 0.248962652, ""); - - } - - /** - * This tests the little methods. - */ - public static void testLittleMethods() { - String2.log("\n*** Table.testLittleMethods..."); - verbose = true; - reallyVerbose = true; - - //isValid and findColumnNumber and subset - Table table = getTestTable(true, true); - table.ensureValid(); //throws Exception if not - Test.ensureEqual(table.findColumnNumber("Time"), 0, ""); - Test.ensureEqual(table.findColumnNumber("String Data"), 9, ""); - Test.ensureEqual(table.findColumnNumber("zz"), -1, ""); - - - //toString - table = getTestTable(true, true); - String2.log("toString: " + table.toString()); - - //ensureEqual - Table table2 = getTestTable(true, true); - Test.ensureTrue(table.equals(table2), "test equals a"); - - String2.log("intentional error:\n"); - table2.getColumn(2).setDouble(1, 100); - Test.ensureEqual(table.equals(table2), false, "intentional notEqual b"); - - String2.log("intentional error:\n"); - table2 = getTestTable(true, true); - table2.getColumn(0).setDouble(2, 55); - Test.ensureEqual(table.equals(table2), false, "intentional notEqual c"); - - //getSubset - /*table = getTestTable(); - table.getSubset(new int[]{table.secondsColumn}, - new double[]{stringToSeconds("2005-08-31T16:01:01")}, - new double[]{stringToSeconds("2005-08-31T16:01:03")}); - Test.ensureEqual(table.nRows(), 1, "getSubset a"); - Test.ensureEqual(table.nColumns(), 5, "getSubset b"); - Test.ensureEqual(table.getColumn(table.secondsColumn), new double[]{stringToSeconds("2005-08-31T16:01:02")}, "getSubset c"); - Test.ensureEqual(table.getColumn(table.lonColumn), new double[]{-2}, "getSubset d"); - Test.ensureEqual(table.getColumn(table.latColumn), new double[]{1.5}, "getSubset e"); - Test.ensureEqual(table.getColumn(3)[0], 7, "getSubset f"); - Test.ensureEqual(table.getColumn(4)[0], 8, "getSubset g"); - - table = getTestTable(); - table.getSubset(new int[]{table.latColumn}, - new double[]{1.9}, - new double[]{2.1}); - Test.ensureEqual(table.nRows(), 1, "getSubset b"); - Test.ensureEqual(table.getColumn(table.latColumn), new double[]{2}, "getSubset j"); - */ - - //calculateStats look at array via constants and as array - table = getTestTable(true, true); - Test.ensureEqual(table.getColumnName(1), "Longitude", "columnNames a"); - table.setColumnName(1, "Test"); - Test.ensureEqual(table.getColumnName(1), "Test", "columnNames b"); - table.setColumnName(1, "Longitude"); - Test.ensureEqual(table.getColumnName(1), "Longitude", "columnNames c"); - - double stats[] = table.getColumn(1).calculateStats(); - Test.ensureEqual(stats[PrimitiveArray.STATS_N], 3, "calculateStats n"); - Test.ensureEqual(stats[PrimitiveArray.STATS_MIN], -3, "calculateStats min"); - Test.ensureEqual(stats[PrimitiveArray.STATS_MAX], -1, "calculateStats max"); - - //forceLonPM180(boolean pm180) - table = getTestTable(true, true); - PrimitiveArray lonAr = table.getColumn(1); - forceLonPM180(lonAr, false); - Test.ensureEqual(lonAr.toString(), "357, 358, 359, 2147483647", "forceLonPM180f"); - Table.forceLonPM180(lonAr, true); - Test.ensureEqual(lonAr.toString(), "-3, -2, -1, 2147483647", "forceLonPM180t"); - - //clear - table = getTestTable(true, true); - table.clear(); - Test.ensureEqual(table.nRows(), 0, "clear a"); - Test.ensureEqual(table.nColumns(), 0, "clear b"); - - //getXxxAttribute - table = getTestTable(true, true); - int col = table.findColumnNumber("Double Data"); - Test.ensureEqual(col, 3, ""); - Test.ensureEqual(table.globalAttributes().getString("global_att1"), "a string", ""); - Test.ensureEqual(table.globalAttributes().getString("test"), null, ""); - table.globalAttributes().set("global_att1", "new"); - Test.ensureEqual(table.globalAttributes().getString("global_att1"), "new", ""); - table.globalAttributes().remove("global_att1"); - Test.ensureEqual(table.globalAttributes().getString("global_att1"), null, ""); - - Test.ensureEqual(table.columnAttributes(3).getString("units"), "doubles", ""); - table.columnAttributes(3).set("units", "new"); - Test.ensureEqual(table.columnAttributes(3).getString("units"), "new", ""); - table.columnAttributes(3).remove("units"); - Test.ensureEqual(table.columnAttributes(3).getString("units"), null, ""); - Test.ensureEqual(table.getDoubleData(3,1), 3.123, ""); - Test.ensureEqual(table.getStringData(3,1), "3.123", ""); - table.setColumnName(3, "new3"); - Test.ensureEqual(table.getColumnName(3), "new3", ""); - - //sort - table.sort(new int[]{3}, new boolean[]{false}); - Test.ensureEqual(table.getColumn(2).toString(), "NaN, 2.0, 1.5, 1.0", ""); - Test.ensureEqual(table.getColumn(3).toString(), "NaN, 1.0E300, 3.123, -1.0E300", ""); - - //removeColumn - table.removeColumn(3); - Test.ensureEqual(table.getColumn(3).toString(), "9223372036854775807, 2000000000000000, 2, -2000000000000000", ""); - Test.ensureEqual(table.getColumnName(3), "Long Data", ""); - Test.ensureEqual(table.columnAttributes(3).getString("units"), "longs", ""); - - //addColumn - table.addColumn(3, "test3", new IntArray(new int[]{10,20,30,Integer.MAX_VALUE})); - Test.ensureEqual(table.getColumn(3).toString(), "10, 20, 30, 2147483647", ""); - Test.ensureEqual(table.getColumnName(3), "test3", ""); - Test.ensureEqual(table.getColumn(4).toString(), "9223372036854775807, 2000000000000000, 2, -2000000000000000", ""); - Test.ensureEqual(table.getColumnName(4), "Long Data", ""); - Test.ensureEqual(table.columnAttributes(4).getString("units"), "longs", ""); - - //append - table.append(table); - Test.ensureEqual(table.getColumn(4).toString(), - "9223372036854775807, 2000000000000000, 2, -2000000000000000, 9223372036854775807, 2000000000000000, 2, -2000000000000000", ""); - Test.ensureEqual(table.getColumnName(4), "Long Data", ""); - Test.ensureEqual(table.columnAttributes(4).getString("units"), "longs", ""); - - //average - table = new Table(); - DoubleArray da = new DoubleArray(new double[]{10,20,30,40,50}); - table.addColumn("a", da); - da = new DoubleArray(new double[]{0,0,1,2,2}); - table.addColumn("b", da); - table.average(new int[]{1}); - Test.ensureEqual(table.getColumn(0).toString(), "15.0, 30.0, 45.0", ""); - Test.ensureEqual(table.getColumn(1).toString(), "0.0, 1.0, 2.0", ""); - - } - - /** Test join(). **/ - public static void testJoin() { - - //*** testJoin 1 - String2.log("\n*** Table.testJoin 1 column"); - Table table = new Table(); - table.addColumn("zero", PrimitiveArray.csvFactory(PAType.STRING, "a,b,c,d,,e")); - table.addColumn("one", PrimitiveArray.csvFactory(PAType.INT, "40,10,12,30,,20")); - table.addColumn("two", PrimitiveArray.csvFactory(PAType.STRING, "aa,bb,cc,dd,,ee")); - table.columnAttributes(0).add("long_name", "hey zero"); - table.columnAttributes(1).add("missing_value", -99999); - table.columnAttributes(2).add("long_name", "hey two"); - - Table lut = new Table(); - lut.addColumn("aa", PrimitiveArray.csvFactory(PAType.INT, "10,20,30,40")); - lut.addColumn("bb", PrimitiveArray.csvFactory(PAType.STRING, "11,22,33,44")); - lut.addColumn("cc", PrimitiveArray.csvFactory(PAType.LONG, "111,222,333,444")); - lut.columnAttributes(0).add("missing_value", -99999); - lut.columnAttributes(1).add("long_name", "hey bb"); - lut.columnAttributes(2).add("missing_value", -9999999L); - - //test lut before join - String results = lut.toString(); - String expectedLut = -"{\n" + -"dimensions:\n" + -"\trow = 4 ;\n" + -"\tbb_strlen = 2 ;\n" + -"variables:\n" + -"\tint aa(row) ;\n" + -"\t\taa:missing_value = -99999 ;\n" + -"\tchar bb(row, bb_strlen) ;\n" + -"\t\tbb:long_name = \"hey bb\" ;\n" + -"\tlong cc(row) ;\n" + -"\t\tcc:missing_value = -9999999 ;\n" + -"\n" + -"// global attributes:\n" + -"}\n" + -"aa,bb,cc\n" + -"10,11,111\n" + -"20,22,222\n" + -"30,33,333\n" + -"40,44,444\n"; - Test.ensureEqual(results, expectedLut, "lut results=\n" + results); - - //do the join - table.join(1, 1, "10", lut); - - results = table.toString(); - String expected = -"{\n" + -"dimensions:\n" + -"\trow = 6 ;\n" + -"\tzero_strlen = 1 ;\n" + -"\tbb_strlen = 2 ;\n" + -"\ttwo_strlen = 2 ;\n" + -"variables:\n" + -"\tchar zero(row, zero_strlen) ;\n" + -"\t\tzero:long_name = \"hey zero\" ;\n" + -"\tint one(row) ;\n" + -"\t\tone:missing_value = -99999 ;\n" + -"\tchar bb(row, bb_strlen) ;\n" + -"\t\tbb:long_name = \"hey bb\" ;\n" + -"\tlong cc(row) ;\n" + -"\t\tcc:missing_value = -9999999 ;\n" + -"\tchar two(row, two_strlen) ;\n" + -"\t\ttwo:long_name = \"hey two\" ;\n" + -"\n" + -"// global attributes:\n" + -"}\n" + -"zero,one,bb,cc,two\n" + -"a,40,44,444,aa\n" + -"b,10,11,111,bb\n" + -"c,12,,-9999999,cc\n" + -"d,30,33,333,dd\n" + -",,11,111,\n" + -"e,20,22,222,ee\n"; - Test.ensureEqual(results, expected, "join 1 results=\n" + results); - - //ensure lut unchanged - results = lut.toString(); - Test.ensureEqual(results, expectedLut, "lut 1 results=\n" + results); - - - //*** testJoin 2 columns - String2.log("\n*** Table.testJoin 2 columns"); - table = new Table(); - table.addColumn("zero", PrimitiveArray.csvFactory(PAType.STRING, "a,b,c,d,,e")); - table.addColumn("one", PrimitiveArray.csvFactory(PAType.INT, "40,10,12,30,,20")); - table.addColumn("two", PrimitiveArray.csvFactory(PAType.STRING, "44,bad,1212,33,,22")); - table.addColumn("three",PrimitiveArray.csvFactory(PAType.STRING, "aaa,bbb,ccc,ddd,,eee")); - table.columnAttributes(0).add("long_name", "hey zero"); - table.columnAttributes(1).add("missing_value", -99999); - table.columnAttributes(2).add("long_name", "hey two"); - table.columnAttributes(3).add("long_name", "hey three"); - - //do the join - table.join(2, 1, "10\t11", lut); - - results = table.toString(); - expected = -"{\n" + -"dimensions:\n" + -"\trow = 6 ;\n" + -"\tzero_strlen = 1 ;\n" + -"\ttwo_strlen = 4 ;\n" + -"\tthree_strlen = 3 ;\n" + -"variables:\n" + -"\tchar zero(row, zero_strlen) ;\n" + -"\t\tzero:long_name = \"hey zero\" ;\n" + -"\tint one(row) ;\n" + -"\t\tone:missing_value = -99999 ;\n" + -"\tchar two(row, two_strlen) ;\n" + -"\t\ttwo:long_name = \"hey two\" ;\n" + -"\tlong cc(row) ;\n" + -"\t\tcc:missing_value = -9999999 ;\n" + -"\tchar three(row, three_strlen) ;\n" + -"\t\tthree:long_name = \"hey three\" ;\n" + -"\n" + -"// global attributes:\n" + -"}\n" + -"zero,one,two,cc,three\n" + -"a,40,44,444,aaa\n" + -"b,10,bad,-9999999,bbb\n" + -"c,12,1212,-9999999,ccc\n" + -"d,30,33,333,ddd\n" + -",,,111,\n" + -"e,20,22,222,eee\n"; - Test.ensureEqual(results, expected, "join 2 results=\n" + results); - - //ensure lut unchanged - results = lut.toString(); - Test.ensureEqual(results, expectedLut, "lut 2 results=\n" + results); - } - - /** test update() */ - public static void testUpdate() throws Exception { - Table table = new Table(); - table.addColumn("zero", PrimitiveArray.csvFactory(PAType.STRING, "a, b, c, d, , e")); - table.addColumn("one", PrimitiveArray.csvFactory(PAType.INT, "10, 20, 30, 40, , 50")); - table.addColumn("two", PrimitiveArray.csvFactory(PAType.INT, "111,222,333,444,-99,555")); - table.addColumn("three",PrimitiveArray.csvFactory(PAType.DOUBLE, "1.1,2.2,3.3,4.4,4.6,5.5")); - table.columnAttributes(2).add("missing_value", -99); - - //otherTable rows: matches, matches, partial match, new - //otherTable cols: keys, matches (but different type), doesn't match - Table otherTable = new Table(); - otherTable.addColumn("one", PrimitiveArray.csvFactory(PAType.INT, " 50, , 11, 5")); - otherTable.addColumn("zero", PrimitiveArray.csvFactory(PAType.STRING, " e, , a, f")); - otherTable.addColumn("three",PrimitiveArray.csvFactory(PAType.INT, " 11, 22, 33, 44")); - otherTable.addColumn("five", PrimitiveArray.csvFactory(PAType.INT, " 1, 2, 3, 4")); - - int nMatched = table.update(new String[]{"zero", "one"}, otherTable); - String results = table.dataToString(); - String expected = -"zero,one,two,three\n" + -"a,10,111,1.1\n" + -"b,20,222,2.2\n" + -"c,30,333,3.3\n" + -"d,40,444,4.4\n" + -",,-99,22.0\n" + -"e,50,555,11.0\n" + -"a,11,-99,33.0\n" + //-99 is from missing_value -"f,5,-99,44.0\n"; //-99 is from missing_value - Test.ensureEqual(results, expected, "update results=\n" + results); - Test.ensureEqual(nMatched, 2, "nMatched"); - - } - - public static void testReorderColumns() throws Exception { - String2.log("\n*** Table.testReorderColumns"); - Table table = new Table(); - table.addColumn("ints", new IntArray()); - table.addColumn("floats", new FloatArray()); - table.addColumn("doubles", new DoubleArray()); - - StringArray newOrder = new StringArray(new String[]{ - "hubert", "floats", "doubles", "zztop"}); - table.reorderColumns(newOrder, false); - String results = String2.toCSSVString(table.getColumnNames()); - String expected = "floats, doubles, ints"; - Test.ensureEqual(results, expected, "results=" + results); - - newOrder = new StringArray(new String[]{ - "ints", "doubles"}); - table.reorderColumns(newOrder, true); //discard columns not in list - results = String2.toCSSVString(table.getColumnNames()); - expected = "ints, doubles"; - Test.ensureEqual(results, expected, "results=" + results); - } - - public static void testLastRowWithData() throws Exception { - String2.log("\n*** Table.testLastRowWithData"); - boolean oDebug = debugMode; - debugMode = true; - Table table = new Table(); - String results, expected; - Attributes iAtts = new Attributes(); iAtts.add("missing_value", 99); - iAtts.add("_FillValue", 999); - Attributes fAtts = new Attributes(); fAtts.add("_FillValue", -99f); - Attributes dAtts = new Attributes(); dAtts.add("_FillValue", -99.0); - Attributes sAtts = new Attributes(); sAtts.add("_FillValue", "99"); - - IntArray ia = (IntArray)new IntArray( new int[] {1, 99, 999, Integer.MAX_VALUE}).setMaxIsMV(true); - FloatArray fa = new FloatArray(new float[] {2, -99, -99, Float.NaN}); - DoubleArray da = new DoubleArray(new double[]{3, -99, -99, Double.NaN}); - StringArray sa = new StringArray(new String[]{"4", null,"99",""}); - - table.clear(); - table.addColumn(0, "i", ia, iAtts); - Test.ensureEqual(table.lastRowWithData(), 0, ""); - - table.clear(); - table.addColumn(0, "f", fa, fAtts); - Test.ensureEqual(table.lastRowWithData(), 0, ""); - - table.clear(); - table.addColumn(0, "d", da, dAtts); - Test.ensureEqual(table.lastRowWithData(), 0, ""); - - table.clear(); - table.addColumn(0, "s", sa, sAtts); - Test.ensureEqual(table.lastRowWithData(), 0, ""); - - table.clear(); - table.addColumn(0, "i", ia, iAtts); - table.addColumn(1, "f", fa, fAtts); - table.addColumn(2, "d", da, dAtts); - table.addColumn(3, "s", sa, sAtts); - Test.ensureEqual(table.lastRowWithData(), 0, ""); - - //*** - String2.log("\n*** Table.testRemoveRowsWithoutData"); - table.clear(); - table.addColumn(0, "i", ia, iAtts); - Test.ensureEqual(table.removeRowsWithoutData(), 1, ""); - - table.clear(); - table.addColumn(0, "f", fa, fAtts); - Test.ensureEqual(table.removeRowsWithoutData(), 1, ""); - - table.clear(); - table.addColumn(0, "d", da, dAtts); - Test.ensureEqual(table.removeRowsWithoutData(), 1, ""); - - table.clear(); - table.addColumn(0, "s", sa, sAtts); - Test.ensureEqual(table.removeRowsWithoutData(), 1, ""); - - table.clear(); - table.addColumn(0, "i", ia, iAtts); - table.addColumn(1, "f", fa, fAtts); - table.addColumn(2, "d", da, dAtts); - table.addColumn(3, "s", sa, sAtts); - //good: original row + - // hi 5 there - ia.add(99); ia.add(999); ia.add(Integer.MAX_VALUE); ia.add(99); ia.add(999); - fa.add(-99); fa.add(-99); fa.add(Float.NaN); fa.add(-99); fa.add(-99); - da.add(-99); da.add(-99); da.add(Double.NaN); da.add(5); da.add(-99); - sa.add("hi"); sa.add("99"); sa.add(""); sa.add(""); sa.add("there"); - table.removeRowsWithoutData(); - results = table.dataToString(); -expected = -"i,f,d,s\n" + -"1,2.0,3.0,4\n" + -"99,-99.0,-99.0,hi\n" + -"99,-99.0,5.0,\n" + -"999,-99.0,-99.0,there\n"; - Test.ensureEqual(results, expected, "results=" + results); - - debugMode = oDebug; - - } - - /** - * This tests reading data from a ncCF multidimensional dataset - * where the dimensions are in the discouraged order (e.g., var[time][station]). - * Very large test file has discharge[time=758001][station=18] 4vars[station=18], - * so when flattened 758001 * 18 * 5vars * 8bytes =~545MB - * + 2 indexColumns: 758001 * 18 * 2vars * 4bytes =~109MB - * - * @param readAsNcCF if true, this reads the file via readNcCF. - * If false, this reads the file via readMultidimNc - */ - public static void testReadNcCFMATimeSeriesReversed(boolean readAsNcCF) throws Exception { - String2.log("\n*** Table.testReadNcCFMATimeSeriesReversed readAsNcCF=" + readAsNcCF); - //time is days since 2006-01-01 00:00:00. file has 2007-10-01T04 through 2013-11-14T17:06 - boolean oDebug = debugMode; - debugMode = true; - Table table = new Table(); - String results, expected; - long time; - //was "/data/hunter/USGS_DISCHARGE_STATIONS_SUBSET.nc" - String fileName = String2.unitTestBigDataDir + "nccf/MATimeSeriesReversedDim.nc"; - String2.log(NcHelper.ncdump(fileName, "-h")); - -/* */ - // read all vars when obs is constrained - String2.log("\n* read all vars when obs is constrained"); - time = System.currentTimeMillis(); - if (readAsNcCF) - table.readNcCF(fileName, - null, //all vars - 0, //standardizeWhat=0 - StringArray.fromCSV("time"), StringArray.fromCSV(">"), StringArray.fromCSV("3426.69")); - else - table.readMultidimNc(fileName, - null, null, null, //read default dimensions - true, 0, true, //getMetadata, standardizeWhat, removeMVRows, - StringArray.fromCSV("time"), StringArray.fromCSV(">"), StringArray.fromCSV("3426.69")); - String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); - results = table.dataToString(); - expected = -//EEK! I don't think they should be different. -//I think readMultidimNc is correct, because the -99999.0 values are from -//rows with earlier time than valid data rows from same station at later time. -//I think readNcCF is too aggressive at removing MV rows. -"discharge,station,time,longitude,latitude\n" + -(readAsNcCF? "" : -"-99999.0,1327750.0,3426.691666666651,-73.5958333,43.26944444\n") + -"80.98618241999999,1327750.0,3426.6979166667443,-73.5958333,43.26944444\n" + //same station, later time -(readAsNcCF? "" : -"-99999.0,1357500.0,3426.691666666651,-73.7075,42.78527778\n") + -"181.2278208,1357500.0,3426.6979166667443,-73.7075,42.78527778\n" + //same station, later time -"183.77633703,1357500.0,3426.708333333372,-73.7075,42.78527778\n" + -"-56.06735706,1484085.0,3426.691666666651,-75.3976111,39.05830556\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - // just read station vars (all stations) no constraints - String2.log("\n* just read station vars (all stations) no constraints"); - time = System.currentTimeMillis(); - if (readAsNcCF) - table.readNcCF(fileName, - StringArray.fromCSV("station,latitude,longitude"), - 0, //standardizeWhat=0 - null, null, null); - else - table.readMultidimNc(fileName, - StringArray.fromCSV("station,latitude,longitude"), - null, //dimensions - null, //treatDimensionsAs - true, 0, true, //getMetadata, standardizeWhat, removeMVRows, - null, null, null); - String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); - results = table.dataToString(); - expected = -"station,latitude,longitude\n" + -"1463500.0,40.22166667,-74.7780556\n" + -"1389500.0,40.8847222,-74.2261111\n" + -"1327750.0,43.26944444,-73.5958333\n" + -"1357500.0,42.78527778,-73.7075\n" + -"1403060.0,40.5511111,-74.5483333\n" + -"1474500.0,39.9678905,-75.1885123\n" + -"1477050.0,39.83677934,-75.36630199\n" + -"1480120.0,39.7362245,-75.540172\n" + -"1481500.0,39.7695,-75.5766944\n" + -"1480065.0,39.71063889,-75.6087222\n" + -"1480015.0,39.71575,-75.6399444\n" + -"1482170.0,39.65680556,-75.562\n" + -"1482800.0,39.5009454,-75.5682589\n" + -"1413038.0,39.3836111,-75.35027778\n" + -"1412150.0,39.23166667,-75.0330556\n" + -"1411435.0,39.16166667,-74.8319444\n" + -"1484085.0,39.05830556,-75.3976111\n" + -"1484080.0,39.01061275,-75.45794828\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - // just read station vars (a few stations because lat is constrained) - String2.log("\n* just read station vars (a few stations because lat is constrained)"); - time = System.currentTimeMillis(); - if (readAsNcCF) - table.readNcCF(fileName, - StringArray.fromCSV("station,latitude,longitude"), - 0, //standardizeWhat=0 - StringArray.fromCSV("latitude"), StringArray.fromCSV("<"), StringArray.fromCSV("39.1")); - else - table.readMultidimNc(fileName, - StringArray.fromCSV("station,latitude,longitude"), - null, null, //dimensions, treatDimensionsAs - true, 0, true, //getMetadata, standardizeWhat, removeMVRows, - StringArray.fromCSV("latitude"), StringArray.fromCSV("<"), StringArray.fromCSV("39.1")); - String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); - results = table.dataToString(); - expected = -"station,latitude,longitude\n" + -"1484085.0,39.05830556,-75.3976111\n" + -"1484080.0,39.01061275,-75.45794828\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - - // just read obs vars (obs is constrained) - String2.log("\n* just read obs vars (obs is constrained)"); - time = System.currentTimeMillis(); - if (readAsNcCF) - table.readNcCF(fileName, - StringArray.fromCSV("time,discharge"), - 0, //standardizeWhat=0 - StringArray.fromCSV("discharge"), StringArray.fromCSV(">"), StringArray.fromCSV("5400")); - else - table.readMultidimNc(fileName, - StringArray.fromCSV("time,discharge"), - null, null, //dimensions, treatDimensionsAs - true, 0, true, //getMetadata, standardizeWhat, removeMVRows, - StringArray.fromCSV("discharge"), StringArray.fromCSV(">"), StringArray.fromCSV("5400")); - String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); - results = table.dataToString(); - expected = -"time,discharge\n" + -"2076.5,5408.517777\n" + -"2076.510416666628,5465.151471\n" + -"2076.5208333332557,5493.468318\n" + -"2076.53125,5521.785165\n" + -"2076.541666666628,5521.785165\n" + -"2076.5520833332557,5521.785165\n" + -"2076.5625,5521.785165\n" + -"2076.572916666628,5521.785165\n" + -"2076.5833333332557,5493.468318\n" + -"2076.59375,5465.151471\n" + -"2076.604166666628,5436.834624\n" + -"2076.6145833332557,5408.517777\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - // read all vars when station is constrained, - String2.log("\n* read all vars when station is constrained"); - time = System.currentTimeMillis(); - if (readAsNcCF) - table.readNcCF(fileName, - StringArray.fromCSV("station,latitude,longitude,time,discharge"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station"), StringArray.fromCSV("="), StringArray.fromCSV("1463500.0")); - else - table.readMultidimNc(fileName, - StringArray.fromCSV("station,latitude,longitude,time,discharge"), - null, null, //dimensions, treatDimensionsAs - true, 0, true, //getMetadata, standardizeWhat, removeMVRows, - StringArray.fromCSV("station"), StringArray.fromCSV("="), StringArray.fromCSV("1463500.0")); - String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); - results = table.dataToString(); - expected = -//EEK! Again, readMultidimNc has additional rows with discharge=MV. -//I think readMultidimNc is correct. -"station,latitude,longitude,time,discharge\n" + -"1463500.0,40.22166667,-74.7780556,638.1666666666279,92.02975275\n" + -"1463500.0,40.22166667,-74.7780556,638.1770833332557,92.02975275\n" + -"1463500.0,40.22166667,-74.7780556,638.1875,92.02975275\n" + -"1463500.0,40.22166667,-74.7780556,638.1979166666279,92.87925815999999\n" + -"1463500.0,40.22166667,-74.7780556,638.2083333332557,93.72876357\n" + -(readAsNcCF? "" : -"1463500.0,40.22166667,-74.7780556,638.2083333333721,-99999.0\n" + -"1463500.0,40.22166667,-74.7780556,638.2125000000233,-99999.0\n" + -"1463500.0,40.22166667,-74.7780556,638.2166666666744,-99999.0\n") + -"1463500.0,40.22166667,-74.7780556,638.21875,93.72876357\n" + -(readAsNcCF? "" : -"1463500.0,40.22166667,-74.7780556,638.2208333333256,-99999.0\n" + -"1463500.0,40.22166667,-74.7780556,638.2250000000931,-99999.0\n") + -"1463500.0,40.22166667,-74.7780556,638.2291666666279,94.86143745\n" + -(readAsNcCF? "" : -"1463500.0,40.22166667,-74.7780556,638.2291666667443,-99999.0\n" + -"1463500.0,40.22166667,-74.7780556,638.2333333333954,-99999.0\n" + -"1463500.0,40.22166667,-74.7780556,638.2375000000466,-99999.0\n") + -"1463500.0,40.22166667,-74.7780556,638.2395833332557,95.71094286\n"; //stop there - results = results.substring(0, expected.length()); - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), readAsNcCF? 256610 : 757994, "wrong nRows"); - - // read all data - String2.log("\n* read all data"); - time = System.currentTimeMillis(); - if (readAsNcCF) - table.readNcCF(fileName, - null, 0, //standardizeWhat=0 - null, null, null); - else - table.readMultidimNc(fileName, - null, null, null, //read all dimensions - true, 0, true, //getMetadata, standardizeWhat, removeMVRows, - null, null, null); - String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); - results = table.dataToString(10); - expected = -readAsNcCF? -"discharge,station,time,longitude,latitude\n" + -"92.02975275,1463500.0,638.1666666666279,-74.7780556,40.22166667\n" + -"92.02975275,1463500.0,638.1770833332557,-74.7780556,40.22166667\n" + -"92.02975275,1463500.0,638.1875,-74.7780556,40.22166667\n" + -"92.87925815999999,1463500.0,638.1979166666279,-74.7780556,40.22166667\n" + -"93.72876357,1463500.0,638.2083333332557,-74.7780556,40.22166667\n" + -"93.72876357,1463500.0,638.21875,-74.7780556,40.22166667\n" + -"94.86143745,1463500.0,638.2291666666279,-74.7780556,40.22166667\n" + -"95.71094286,1463500.0,638.2395833332557,-74.7780556,40.22166667\n" + -"95.71094286,1463500.0,638.25,-74.7780556,40.22166667\n" + -"95.71094286,1463500.0,638.2604166666279,-74.7780556,40.22166667\n" + -"...\n" : -"discharge,station,time,longitude,latitude\n" + -"92.02975275,1463500.0,638.1666666666279,-74.7780556,40.22166667\n" + -"92.02975275,1463500.0,638.1770833332557,-74.7780556,40.22166667\n" + -"92.02975275,1463500.0,638.1875,-74.7780556,40.22166667\n" + -"92.87925815999999,1463500.0,638.1979166666279,-74.7780556,40.22166667\n" + -"93.72876357,1463500.0,638.2083333332557,-74.7780556,40.22166667\n" + -"-99999.0,1463500.0,638.2083333333721,-74.7780556,40.22166667\n" + -"-99999.0,1463500.0,638.2125000000233,-74.7780556,40.22166667\n" + -"-99999.0,1463500.0,638.2166666666744,-74.7780556,40.22166667\n" + -"93.72876357,1463500.0,638.21875,-74.7780556,40.22166667\n" + -"-99999.0,1463500.0,638.2208333333256,-74.7780556,40.22166667\n" + -"...\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - Test.ensureEqual(table.nRows(), readAsNcCF? 2315617 : 7539127, "wrong nRows"); - - - // read all vars when obs is constrained, - String2.log("\n* read all vars when obs is constrained"); - time = System.currentTimeMillis(); - if (readAsNcCF) - table.readNcCF(fileName, - StringArray.fromCSV("station,latitude,longitude,time,discharge"), - 0, //standardizeWhat=0 - StringArray.fromCSV("discharge"), StringArray.fromCSV(">"), StringArray.fromCSV("5400")); - else - table.readMultidimNc(fileName, - StringArray.fromCSV("station,latitude,longitude,time,discharge"), - null, null, //dimensions, treatDimensionsAs - true, 0, true, //getMetadata, standardizeWhat, removeMVRows, - StringArray.fromCSV("discharge"), StringArray.fromCSV(">"), StringArray.fromCSV("5400")); - String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); - results = table.dataToString(); - expected = -"station,latitude,longitude,time,discharge\n" + -"1463500.0,40.22166667,-74.7780556,2076.5,5408.517777\n" + -"1463500.0,40.22166667,-74.7780556,2076.510416666628,5465.151471\n" + -"1463500.0,40.22166667,-74.7780556,2076.5208333332557,5493.468318\n" + -"1463500.0,40.22166667,-74.7780556,2076.53125,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.541666666628,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.5520833332557,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.5625,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.572916666628,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.5833333332557,5493.468318\n" + -"1463500.0,40.22166667,-74.7780556,2076.59375,5465.151471\n" + -"1463500.0,40.22166667,-74.7780556,2076.604166666628,5436.834624\n" + -"1463500.0,40.22166667,-74.7780556,2076.6145833332557,5408.517777\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - // read all vars when station and obs are constrained, - String2.log("\n* read all vars when station and obs are constrained"); - time = System.currentTimeMillis(); - if (readAsNcCF) - table.readNcCF(fileName, - StringArray.fromCSV("station,latitude,longitude,time,discharge"), - 0, //standardizeWhat=0 - StringArray.fromCSV("station,discharge"), StringArray.fromCSV("=,>"), StringArray.fromCSV("1463500.0,5400")); - else - table.readMultidimNc(fileName, - StringArray.fromCSV("station,latitude,longitude,time,discharge"), - null, null, //dimensions, treatDimensionsAs - true, 0, true, //getMetadata, standardizeWhat, removeMVRows, - StringArray.fromCSV("station,discharge"), StringArray.fromCSV("=,>"), StringArray.fromCSV("1463500.0,5400")); - String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); - results = table.dataToString(); - expected = -"station,latitude,longitude,time,discharge\n" + -"1463500.0,40.22166667,-74.7780556,2076.5,5408.517777\n" + -"1463500.0,40.22166667,-74.7780556,2076.510416666628,5465.151471\n" + -"1463500.0,40.22166667,-74.7780556,2076.5208333332557,5493.468318\n" + -"1463500.0,40.22166667,-74.7780556,2076.53125,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.541666666628,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.5520833332557,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.5625,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.572916666628,5521.785165\n" + -"1463500.0,40.22166667,-74.7780556,2076.5833333332557,5493.468318\n" + -"1463500.0,40.22166667,-74.7780556,2076.59375,5465.151471\n" + -"1463500.0,40.22166667,-74.7780556,2076.604166666628,5436.834624\n" + -"1463500.0,40.22166667,-74.7780556,2076.6145833332557,5408.517777\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - debugMode = oDebug; - } - /** * Parse the orderByCsv string into an array of strings. If the final string begins with a number (eg. 2days) * it is appended to the last field eg, time/2days. @@ -34814,142 +17275,6 @@ private static Table.Rounder createTimeRounder(final String responsible, String } } - /** - * This tests reading a very large TSV file: 764MB before .gz, 52MB after .gz, - * 33 columns, 3503266 rows. - * I switched to StringHolder in StringArray after complaints this file took ~10GB to load. - * I also made several other significant memory saving changes. - * Now, reading the file into StringArray ~1600MB is the high point. - * While parsing the lines, it shrinks to ~671MB (lots of small strings). - * After convert to binary data types: ~420MB. - * Total time to read and ingest=~33s from gz file (was ~420s before). - */ - public static void testBigAscii() throws Exception { - PrimitiveArray.reallyVerbose = true; - Math2.gcAndWait("Table (between tests)"); Math2.gcAndWait("Table (between tests)"); //in a test - String2.log("\n*** Table.testBigAscii(): " + Math2.memoryString()); - - Table table = new Table(); - long time = System.currentTimeMillis(); - table.readASCII("/data/biddle/3937_v1_CTD_Profiles.tsv.gz"); - time = System.currentTimeMillis() - time; - Math2.gcAndWait("Table (between tests)"); Math2.gcAndWait("Table (between tests)"); //in a test - String2.log(" done. " + Math2.memoryString() + "\n" + - String2.canonicalStatistics()); //in a test - String results = table.dataToString(4); - String2.log(results); - String expected = -"cruise_name,station,cast,ISO_DateTime,Year,Month,Day,timeutc,lon,lat,depth_max,pres_max,Date,timecode,HOT_summary_file_name,parameters,num_bottles,section,nav_code,depth_hgt,EXPOCODE,Ship,comments,CTDPRS,CTDTMP,CTDSAL,CTDOXY,XMISS,CHLPIG,NUMBER,NITRATE,FLUOR,QUALT1\n" + -"001,2,1,1988-10-30T21:34:00,1988,10,30,2134,-157.9967,22.7483,4750,238,103088,BE,cruise.summaries/hot1.sum,NaN,11,PRS2,GPS,4514,32MW001_1,32MW001/1,NaN,0.0,26.2412,35.2615,183.2,4.99,-0.0126,0,,,666666\n" + -"001,2,1,1988-10-30T21:34:00,1988,10,30,2134,-157.9967,22.7483,4750,238,103088,BE,cruise.summaries/hot1.sum,NaN,11,PRS2,GPS,4514,32MW001_1,32MW001/1,NaN,2.0,26.2412,35.2615,183.2,4.99,-0.0126,36,,,222322\n" + -"001,2,1,1988-10-30T21:34:00,1988,10,30,2134,-157.9967,22.7483,4750,238,103088,BE,cruise.summaries/hot1.sum,NaN,11,PRS2,GPS,4514,32MW001_1,32MW001/1,NaN,4.0,26.2554,35.2530,185.5,4.08,0.0026,72,,,223322\n" + -"001,2,1,1988-10-30T21:34:00,1988,10,30,2134,-157.9967,22.7483,4750,238,103088,BE,cruise.summaries/hot1.sum,NaN,11,PRS2,GPS,4514,32MW001_1,32MW001/1,NaN,6.0,26.2377,35.2455,204.8,3.05,0.0167,108,,,222122\n" + -"...\n"; - try { - Test.ensureEqual(results, expected, ""); - } catch (Exception e) { - String2.pressEnterToContinue(MustBe.throwableToString(e)); - } - - Test.ensureEqual(table.nRows(), 3503266, ""); - Test.ensureEqual(table.nColumns(), 33, ""); - - table.removeRows(0, 3503261); - results = table.saveAsNccsv(false, true, 0, Integer.MAX_VALUE); //catchScalars, writeMetadata, firstDataRow, lastDataRow - - expected = //many vars are scalar because they're constant in last 6 rows -"*GLOBAL*,Conventions,\"COARDS, CF-1.10, ACDD-1.3, NCCSV-1.2\"\n" + -"cruise_name,*DATA_TYPE*,String\n" + -"station,*DATA_TYPE*,byte\n" + -"cast,*DATA_TYPE*,byte\n" + -"ISO_DateTime,*DATA_TYPE*,String\n" + -"Year,*DATA_TYPE*,short\n" + -"Month,*DATA_TYPE*,byte\n" + -"Day,*DATA_TYPE*,String\n" + -"timeutc,*DATA_TYPE*,String\n" + -"lon,*DATA_TYPE*,float\n" + -"lat,*DATA_TYPE*,float\n" + -"depth_max,*DATA_TYPE*,short\n" + -"pres_max,*DATA_TYPE*,short\n" + -"Date,*DATA_TYPE*,String\n" + -"timecode,*DATA_TYPE*,String\n" + -"HOT_summary_file_name,*DATA_TYPE*,String\n" + -"parameters,*DATA_TYPE*,String\n" + -"num_bottles,*DATA_TYPE*,byte\n" + -"section,*DATA_TYPE*,String\n" + -"nav_code,*DATA_TYPE*,String\n" + -"depth_hgt,*DATA_TYPE*,short\n" + -"EXPOCODE,*DATA_TYPE*,String\n" + -"Ship,*DATA_TYPE*,String\n" + -"comments,*DATA_TYPE*,String\n" + -"CTDPRS,*DATA_TYPE*,float\n" + -"CTDTMP,*DATA_TYPE*,float\n" + -"CTDSAL,*DATA_TYPE*,String\n" + -"CTDOXY,*DATA_TYPE*,String\n" + -"XMISS,*DATA_TYPE*,float\n" + -"CHLPIG,*DATA_TYPE*,String\n" + -"NUMBER,*DATA_TYPE*,String\n" + -"NITRATE,*DATA_TYPE*,float\n" + -"FLUOR,*DATA_TYPE*,double\n" + -"QUALT1,*DATA_TYPE*,String\n" + -"\n" + -"*END_METADATA*\n" + -"cruise_name,station,cast,ISO_DateTime,Year,Month,Day,timeutc,lon,lat,depth_max,pres_max,Date,timecode,HOT_summary_file_name,parameters,num_bottles,section,nav_code,depth_hgt,EXPOCODE,Ship,comments,CTDPRS,CTDTMP,CTDSAL,CTDOXY,XMISS,CHLPIG,NUMBER,NITRATE,FLUOR,QUALT1\n" + -"288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,194.0,18.2746,34.9098,203.9,,0.0254,144,,,222192\n" + -"288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,196.0,18.159,34.9027,203.8,,0.0257,108,,,222192\n" + -"288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,198.0,17.9686,34.8727,203.8,,0.0257,156,,,222192\n" + -"288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,200.0,17.8751,34.8506,201.8,,0.0248,108,,,222192\n" + -"288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,202.0,17.7435,34.8246,202.1,,0.0248,60,,,222192\n" + -"*END_DATA*\n"; - Test.ensureEqual(results, expected, "results=\n" + results); - - Math2.gcAndWait("Table (between tests)"); //in a test - String msg = Math2.memoryString() + "\n" + - String2.canonicalStatistics() + "\n" + - "testBigAscii time=" + time + - "ms. file read time should be ~60 - 90s in java 17 (but I think it should be faster -- too much gc) (but longer when computer is busy) (Java 8 was 45s. was 36s before v2.10)"; - String2.log(msg); - Test.ensureTrue(time < 60000, "Too slow! " + msg); - } - - /** - * This tests if nc files are closed when "try with resources" approach is taken. - * 2022-09-09 With tryWithResources, ERDDAP crashes every 2 days (like THREDDS)! So go back to: finally {nc.close()} - */ - public static void testNcCloseTryWithResources() throws Throwable { - String2.log("\n*** Table.testNcCloseTryWithResources()"); - - long time = System.currentTimeMillis(); - String fileName = "c:/u00/data/points/erdCalcofiSubsurface/1950/subsurface_19500106_69_144.nc"; - int n = 100000; - for (int i = 0; i < n; i++) { - try (NetcdfFile ncfile = NcHelper.openFile(fileName)) { - if (i % 10000 == 0) - String2.log("" + i); - //} catch (Exception e) { - // String2.log("i=" + i + " " + e.toString()); - } - } - String2.log("Opened the same file " + n + " times and auto-closed them. time=" + (System.currentTimeMillis() - time) + " (exp=35534ms)"); - - //open all of the 10,000 scripps glider files in batch14 after manually: gunzip *.gz - time = System.currentTimeMillis(); - Table table = FileVisitorDNLS.oneStep("/u00/data/points/scrippsGliders/batch14/", - ".*\\.nc", true, "", false); - PrimitiveArray dirs = table.getColumn(0); - PrimitiveArray names = table.getColumn(1); - n = dirs.size(); - String2.log("nFiles found=" + n); - for (int i = 0; i < n; i++) { - try (NetcdfFile ncfile = NcHelper.openFile(dirs.getString(i) + names.getString(i))) { - if (i % 1000 == 0) - String2.log("" + i); - } - } - String2.log("Opened " + n + " files and auto-closed them. time=" + (System.currentTimeMillis() - time) + " (exp=4530ms)"); - } - - /** * This runs all of the interactive or not interactive tests for this class. * @@ -34964,7 +17289,7 @@ public static void testNcCloseTryWithResources() throws Throwable { public static void test(StringBuilder errorSB, boolean interactive, boolean doSlowTestsToo, int firstTest, int lastTest) { if (lastTest < 0) - lastTest = interactive? 2 : 67; + lastTest = interactive? 2 : 0; String msg = "\n^^^ Table.test(" + interactive + ") test="; verbose = true; @@ -34983,78 +17308,6 @@ public static void test(StringBuilder errorSB, boolean interactive, if (test == 2) testReadAudioWriteWaveFiles(0, 1000); } else { - if (test == 0) testLittleMethods(); - if (test == 1) testReorderColumns(); - if (test == 2) testSortColumnsByName(); - if (test == 3) testLastRowWithData(); - if (test == 4) testEnhancedFlatNcFile(); - if (test == 5) testOrderByMinMax(); //tests orderByMin Max MinMax - if (test == 6) testOrderByClosest(); - if (test == 7) testOrderByCount(); - if (test == 8) testOrderByLimit(); - if (test == 9) testGetDapQueryParts(); - if (test == 10) testParseDapQuery(); - if (test == 11) testSubsetViaDapQuery(); - if (test == 12) testAddIndexColumns(); - - //readWrite tests - if (test == 20) testASCII(); - if (test == 21) testReadAsciiCsvFile(); - if (test == 22) testReadAsciiSsvFile(); - if (test == 23) testReadColumnarASCIIFile(); - if (test == 24) testNccsv(); - if (test == 25) testHtml(); - if (test == 26) testJson(); - if (test == 27) testJsonlCSV(); - if (test == 28) testFlatNc(); - if (test == 29) test4DNc(); - if (test == 30) testSaveAsMatlab(); - if (test == 31) testOpendapSequence(); - if (test == 32) testReadAwsXmlFile(); - if (test == 33) testReadNDNc(); - if (test == 34) testReadNDNc2(); - if (test == 35) testJoin(); - if (test == 36) testReadStandardTabbedASCII(); - if (test == 37) testReadMultidimNc(); - if (test == 38) testHardReadMultidimNc(); - if (test == 39) testUnpack(); - //if (test == 40) testReadNcSequence(); //2021 NOT FINISHED - - if (test == 41 && doSlowTestsToo) testReadInvalidCRA(); //very slow - - //readNcCF tests - if (test == 45) testReadNcCFPoint(false); //pauseAfterEachTest - if (test == 46) testReadNcCF1(false); //pauseAfterEachTest - if (test == 47) testReadNcCF2(false); - if (test == 48) testReadNcCFASAProfile(false); - if (test == 49) testReadNcCFASATimeSeries(false); - if (test == 50) testReadNcCFASATrajectory(false); - if (test == 51) testReadNcCFASATimeSeriesProfile(false); - if (test == 52) testReadNcCFASATrajectoryProfile(false); - if (test == 53) testReadNcCFMATimeSeriesReversed(true); //read as ncCF - if (test == 54) testReadNcCFMATimeSeriesReversed(false); //readMultidimNc - if (test == 55) testReadGocdNcCF(); - if (test == 56) testReadNcCF7SampleDims(); - if (test == 57) { - ncCFcc.flip(0, 100); //there are currently 99 code coverage tests - Test.ensureEqual(ncCFcc.toString(), "{}", "Table.readNcCF code coverage"); - ncCFcc = null; //turn off test of readNcCF code coverage - } - - if (test == 60) testReadASCIISpeed(); - if (test == 61) testBigAscii(); - if (test == 62) testReadJsonSpeed(); - if (test == 63) testReadNDNcSpeed(); - if (test == 64) testReadOpendapSequenceSpeed(); - if (test == 65) testSaveAsSpeed(); - if (test == 66) testUpdate(); - if (test == 67) testXml(); - - //if (test == 1000) testConvert(); //2013-04-03 Needs work. Not active. This test needs to be updated to test a new source DAP server - //if (test == 1001) testSql(); //Needs work. Not active. - //if (test == 1002) testIobis(); // Needs work. Not active. It needs work to deal with sessions. - //if (test == 1003) testOpendap(); //not done yet, see opendapSequence - //if (test == 1004) testNcCloseTryWithResources(); //2022-09-09 With tryWithResources, ERDDAP crashes every 2 days (like THREDDS)! So go back to: finally {nc.close()} } String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); @@ -35068,6 +17321,4 @@ public static void test(StringBuilder errorSB, boolean interactive, } } } - - } diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/util/RegexFilenameFilter.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/util/RegexFilenameFilter.java index 7733060c4..159b18371 100644 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/util/RegexFilenameFilter.java +++ b/WEB-INF/classes/gov/noaa/pfel/coastwatch/util/RegexFilenameFilter.java @@ -8,12 +8,9 @@ import com.cohort.array.PrimitiveArray; import com.cohort.array.StringArray; -import com.cohort.util.Calendar2; -import com.cohort.util.Math2; import com.cohort.util.File2; import com.cohort.util.MustBe; import com.cohort.util.String2; -import com.cohort.util.Test; import java.io.File; import java.io.FilenameFilter; @@ -21,7 +18,6 @@ import java.util.Arrays; import java.util.Collections; import java.util.regex.Pattern; -import java.util.regex.Matcher; /** * A filter to find files (and directories!) whose names match a specified @@ -380,136 +376,4 @@ public static boolean touchFileAndRelated(String fullName) { } return true; } - - - /** - * This tests the methods of RegexFilenameFilter. - * - * @throws Exception if trouble - */ - public static void basicTest() throws Exception { - String2.log("\n* RegexFilenameFilter.basicTest ..."); - String coastwatchDir = File2.webInfParentDirectory() + //with / separator and / at the end - "WEB-INF/classes/gov/noaa/pfel/coastwatch/"; - - //test list - String[] sar = list(coastwatchDir, "S.+\\.java"); - String[] shouldBe = { - "Screen.java", - "Shared.java"}; - Test.ensureEqual(sar, shouldBe, "RegexFilenameFilter.list"); - - //test fullNameList - sar = fullNameList(coastwatchDir, "S.+\\.java"); - shouldBe = new String[] { - coastwatchDir + "Screen.java", - coastwatchDir + "Shared.java" - }; - Test.ensureEqual(sar, shouldBe, "RegexFilenameFilter.fullNameList"); - - //test recursiveList - sar = recursiveFullNameList(coastwatchDir, "S.+\\.java", true); - shouldBe = new String[] { - coastwatchDir + "Screen.java", - coastwatchDir + "Shared.java", - coastwatchDir + "griddata/", - coastwatchDir + "griddata/SaveOpendap.java", - coastwatchDir + "hdf/", - coastwatchDir + "hdf/SdsReader.java", - coastwatchDir + "hdf/SdsWriter.java", - coastwatchDir + "netcheck/", - coastwatchDir + "pointdata/", - coastwatchDir + "pointdata/ScriptRow.java", - coastwatchDir + "pointdata/StationVariableNc4D.java", - coastwatchDir + "pointdata/StoredIndex.java", - coastwatchDir + "sgt/", - coastwatchDir + "sgt/SGTPointsVector.java", - coastwatchDir + "sgt/SgtGraph.java", - coastwatchDir + "sgt/SgtMap.java", - coastwatchDir + "sgt/SgtUtil.java", - coastwatchDir + "util/", - coastwatchDir + "util/SSR.java", - coastwatchDir + "util/SimpleXMLReader.java", - coastwatchDir + "util/StringObject.java" - }; - Test.ensureEqual(sar, shouldBe, "RegexFilenameFilter.recursiveFullNameList"); - - //test recursiveList no directories - sar = recursiveFullNameList(coastwatchDir, "S.+\\.java", false); - shouldBe = new String[] { - coastwatchDir + "Screen.java", - coastwatchDir + "Shared.java", - coastwatchDir + "griddata/SaveOpendap.java", - coastwatchDir + "hdf/SdsReader.java", - coastwatchDir + "hdf/SdsWriter.java", - coastwatchDir + "pointdata/ScriptRow.java", - coastwatchDir + "pointdata/StationVariableNc4D.java", - coastwatchDir + "pointdata/StoredIndex.java", - coastwatchDir + "sgt/SGTPointsVector.java", - coastwatchDir + "sgt/SgtGraph.java", - coastwatchDir + "sgt/SgtMap.java", - coastwatchDir + "sgt/SgtUtil.java", - coastwatchDir + "util/SSR.java", - coastwatchDir + "util/SimpleXMLReader.java", - coastwatchDir + "util/StringObject.java" - }; - Test.ensureEqual(sar, shouldBe, "RegexFilenameFilter.recursiveFullNameList"); - - //gatherInfo - PrimitiveArray info[] = gatherInfo("C:\\programs\\digir", "obis.*"); - int tn = info[1].size(); - StringArray lastMod = new StringArray(); - for (int i = 0; i < tn; i++) - lastMod.add(Calendar2.safeEpochSecondsToIsoStringTZ(info[2].getLong(i) / 1000.0, "ERROR")); - Test.ensureEqual(info[0].toString(), - "BiotaDiGIRProvider, DiGIR_Portal_Engine, DiGIRprov", ""); - Test.ensureEqual(info[1].toString(), - "obis.xsd, obisInventory.txt", ""); - //lastMod and size verified by using DOS dir command - Test.ensureEqual(lastMod.toString(), - "2007-04-23T18:24:38Z, 2007-05-02T19:18:32Z", ""); //2018-08-07 was :33Z on M4700, but :32 on Lenovo! - Test.ensureEqual(info[3].toString(), - "21509, 3060", ""); - } - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? -1 : 0; - String msg = "\n^^^ RegexFilenameFilter.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - //if (test == 0) ...; - - } else { - if (test == 0) basicTest(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } } \ No newline at end of file diff --git a/WEB-INF/classes/gov/noaa/pfel/coastwatch/util/TestSSR.java b/WEB-INF/classes/gov/noaa/pfel/coastwatch/util/TestSSR.java deleted file mode 100644 index 696356ac7..000000000 --- a/WEB-INF/classes/gov/noaa/pfel/coastwatch/util/TestSSR.java +++ /dev/null @@ -1,726 +0,0 @@ -/* - * TestSSR Copyright 2005, NOAA. - * See the LICENSE.txt file in this file's directory. - */ -package gov.noaa.pfel.coastwatch.util; - -import com.cohort.util.Calendar2; -import com.cohort.util.File2; -import com.cohort.util.Math2; -import com.cohort.util.MustBe; -import com.cohort.util.String2; -import com.cohort.util.Test; -import com.cohort.util.XML; - -import java.awt.Color; -import java.awt.Image; -import java.awt.image.PixelGrabber; -import java.io.BufferedInputStream; -import java.io.BufferedOutputStream; -import java.io.BufferedReader; -import java.io.File; -import java.io.FileOutputStream; -import java.io.InputStreamReader; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.GregorianCalendar; -import java.util.Properties; - -/** - * This is a Java program to test all of the methods in SSR. - * - * @author Robert Simons was bob.simons@noaa.gov, now BobSimons2.00@gmail.com January 2005 - */ -public class TestSSR { - - static String classPath = File2.getClassPath(); //with / separator and / at the end - - /** - * Run all of the tests which are operating system independent. - */ - public static void runNonUnixTests() throws Throwable { - String sar[]; - - String2.log("\n*** TestSSR"); - String2.log("This must be run in a command line window so passwords can be entered!"); - - /* - //sendSoap - String soap = SSR.sendSoap( - "http://services.xmethods.net:80/soap/servlet/rpcrouter", - " \n" + - " 93950\n" + - " \n", - ""); - String2.log(soap); - System.exit(0); - */ - - //percentDecode(String query) - String s = "~`!@#$%^&*()_-+=|\\{[}]:;\"'<,>.?/ a\nA°1"; //after A is degree #176/B0 - Test.ensureEqual(SSR.percentEncode(s), //it is utf-8'd then % encoded - //note that I modified Java code so ' ' becomes %20, not + - "%7E%60%21%40%23%24%25%5E%26*%28%29_-%2B%3D%7C%5C%7B%5B%7D%5D%3A%3B%22%27%3C%2C%3E.%3F%2F%20a%0AA%C2%B01", - ""); //It encodes ~!*()' - Test.ensureEqual(SSR.minimalPercentEncode(s),// - "~%60!%40%23%24%25%5E%26*()_-%2B%3D%7C%5C%7B%5B%7D%5D%3A%3B%22%27%3C%2C%3E.%3F%2F%20a%0AA%C2%B01", ""); - Test.ensureEqual(SSR.percentDecode("%2B%20%3Aq*~%3F%3D%26%25"), "+ :q*~?=&%", ""); - - s = "AZaz09 \t\r\n`"; - Test.ensureEqual(SSR.minimalPercentEncode(s), - "AZaz09%20%09%0D%0A%60", ""); - Test.ensureEqual(SSR.percentEncode(s), - "AZaz09%20%09%0D%0A%60", ""); - Test.ensureEqual(SSR.percentDecode("AZaz09%20%09%0D%0A%60"), s, ""); - - s = "~!@#$%^&*()"; - Test.ensureEqual(SSR.minimalPercentEncode(s), - "~!%40%23%24%25%5E%26*()", ""); - Test.ensureEqual(SSR.percentEncode(s), - "%7E%21%40%23%24%25%5E%26*%28%29", ""); - Test.ensureEqual(SSR.percentDecode("%7E%21%40%23%24%25%5E%26*%28%29"), s, ""); - - s = "-_=+\\|[{]};"; - Test.ensureEqual(SSR.minimalPercentEncode(s), - "-_%3D%2B%5C%7C%5B%7B%5D%7D%3B", ""); - Test.ensureEqual(SSR.percentEncode(s), - "-_%3D%2B%5C%7C%5B%7B%5D%7D%3B", ""); - Test.ensureEqual(SSR.percentDecode("-_%3D%2B%5C%7C%5B%7B%5D%7D%3B"), s, ""); - - s = ":'\",<.>/?"; - Test.ensureEqual(SSR.minimalPercentEncode(s), - "%3A%27%22%2C%3C.%3E%2F%3F", ""); - Test.ensureEqual(SSR.percentEncode(s), - "%3A%27%22%2C%3C.%3E%2F%3F", ""); - Test.ensureEqual(SSR.percentDecode("%3A%27%22%2C%3C.%3E%2F%3F"), s, ""); - - /* 2014-08-05 DEACTIVATED BECAUSE NOT USED. IF NEEDED, SWITCH TO Apache commons-net??? - //sftp - String2.log("test sftp"); - String password = String2.getPasswordFromSystemIn(//String2.beep(1) + - "cwatch password for coastwatch computer (enter \"\" to skip the test)? "); - if (password.length() > 0) { - String fileName = "Rainbow.cpt"; - StringBuilder cmds = new StringBuilder( - "lcd " + SSR.getTempDirectory() + "\n" + - "cd /u00/cwatch/bobtemp\n" + //on coastwatch computer; don't use String2.testU00Dir - "get " + fileName); - File2.delete(SSR.getTempDirectory() + fileName); - SSR.sftp("coastwatch.pfeg.noaa.gov", "cwatch", password, cmds.toString()); - Test.ensureEqual(File2.length(SSR.getTempDirectory() + fileName), 214, "a"); - File2.delete(SSR.getTempDirectory() + fileName); - } - Math2.sleep(3000); //allow j2ssh to finish closing and writing messages - */ - - //SSR.windowsSftp never worked (authentication trouble) and SSR.sftp is - // better anyway because it is Java-based and therefore platform independent. - //SSR.windowsSftp("coastwatch.pfeg.noaa.gov", "cwatch", password, - // "\\temp\\", "/usr/local/jakarta-tomcat-5.5.4/webapps/cwexperimental/WEB-INF/secure/", - // new String[]{"btemplate.xml"}, //send - // new String[]{}, 10); //receive - - //dosShell - String2.log("test dosShell"); - String tempGif = File2.webInfParentDirectory() + //with / separator and / at the end - "images/temp.gif"; - File2.delete(tempGif); - try { - Test.ensureEqual( - String2.toNewlineString(SSR.dosShell( - "\"C:\\Program Files (x86)\\ImageMagick-6.8.0-Q16\\convert\" " + - File2.webInfParentDirectory() + //with / separator and / at the end - "images/subtitle.jpg " + - tempGif, 10).toArray()), - "", "dosShell a"); - Test.ensureTrue(File2.isFile(tempGif), "dosShell b"); - } catch (Exception e) { - Test.knownProblem( - "IMAGEMAGICK NOT SET UP ON BOB'S DELL M4700 or Lenovo.", - MustBe.throwableToString(e)); - } - File2.delete(tempGif); - - //cutChar - String2.log("test cutChar"); - Test.ensureEqual( SSR.cutChar("abcd", 2, 3), "bc", "a"); - Test.ensureEqual( SSR.cutChar("abcd", 1, 4), "abcd", "b"); - Test.ensureEqual( SSR.cutChar("abcd", 0, 4), "abcd", "c"); - Test.ensureEqual( SSR.cutChar("abcd", 1, 5), "abcd", "d"); - Test.ensureEqual( SSR.cutChar("abcd", 3, 3), "c", "e"); - Test.ensureEqual( SSR.cutChar("abcd", 4, 1), "", "f"); - Test.ensureEqual( SSR.cutChar("abcd", -2, 0), "", "g"); - - Test.ensureEqual( SSR.cutChar("abcd", 1), "abcd", "a"); - Test.ensureEqual( SSR.cutChar("abcd", 0), "abcd", "b"); - Test.ensureEqual( SSR.cutChar("abcd", -1), "abcd", "c"); - Test.ensureEqual( SSR.cutChar("abcd", 2), "bcd", "d"); - Test.ensureEqual( SSR.cutChar("abcd", 4), "d", "e"); - Test.ensureEqual( SSR.cutChar("abcd", 5), "", "f"); - - //make a big chunk of text - StringBuilder sb = new StringBuilder(); - for (int i = 0; i < 1000000; i++) - sb.append("This is a really, really, long line of text to text compression speed.\n"); - String longText = sb.toString(); - sb = null; - String testMB = " " + (longText.length() / Math2.BytesPerMB) + " MB"; - - //zip without directory info - String2.log("\n* test zip without dir info" + testMB); - String middleDir = "gov/noaa/pfel/coastwatch/"; - String zipDir = classPath + middleDir; - String zipName = "TestSSR.zip"; - String fileName = "TestSSR.txt"; - //write a longText file - Test.ensureEqual(File2.writeToFile88591(zipDir + fileName, longText), "", "SSR.zip a"); - //make the zip file - File2.delete(zipDir + zipName); - long time1 = System.currentTimeMillis(); - SSR.zip(zipDir + zipName, new String[]{zipDir + fileName}, 10); - time1 = System.currentTimeMillis() - time1; - File2.delete(zipDir + fileName); - //unzip the zip file - long time2 = System.currentTimeMillis(); - SSR.unzip(zipDir + zipName, zipDir, //note: extract to zipDir, since it doesn't include dir - false, 10, null); //false 'ignoreDirectoryInfo', but there is none - time2 = System.currentTimeMillis() - time2; - //ensure results are as expected - String[] results = File2.readFromFile88591(zipDir + fileName); - Test.ensureEqual(results[0], "", "SSR.zip b"); - Test.ensureEqual(results[1], longText, "SSR.zip c"); - String2.log("zip+unzip time=" + (time1 + time2) + "ms (Java 1.7M4700 967ms, 1.6 4000-11000ms)"); - File2.delete(zipDir + zipName); - File2.delete(zipDir + fileName); - - //zip with directory info - String2.log("\n* test zip with dir info" + testMB); - //write a longText file - Test.ensureEqual(File2.writeToFile88591(zipDir + fileName, longText), "", "SSR.zip a"); - //make the zip file - File2.delete(zipDir + zipName); - time1 = System.currentTimeMillis(); - SSR.zip(zipDir + zipName, new String[]{zipDir + fileName}, 10, classPath); - time1 = System.currentTimeMillis() - time1; - File2.delete(zipDir + fileName); - //unzip the zip file - time2 = System.currentTimeMillis(); - SSR.unzip(zipDir + zipName, classPath, //note: extract to classPath, since includes dir - false, 10, null); //false 'ignoreDirectoryInfo' - time2 = System.currentTimeMillis() - time2; - //ensure results are as expected - results = File2.readFromFile88591(zipDir + fileName); - Test.ensureEqual(results[0], "", "SSR.zip b"); - Test.ensureEqual(results[1], longText, "SSR.zip c"); - String2.log("zip+unzip (w directory info) time=" + (time1 + time2) + - "ms (Java 1.7M4700 937, 1.6 ~4000-11000ms)"); - File2.delete(zipDir + zipName); - File2.delete(zipDir + fileName); - - //gzip without directory info - for (int rep = 0; rep < 2; rep++) { - String2.log("\n* test gzip without dir info" + testMB); - middleDir = "gov/noaa/pfel/coastwatch/"; - String gzipDir = classPath + middleDir; - String gzipName = "TestSSRG.txt.gz"; - fileName = "TestSSRG.txt"; - //write a longText file - Test.ensureEqual(File2.writeToFile88591(gzipDir + fileName, longText), "", "SSR.gz a"); - //make the gzip file - File2.delete(gzipDir + gzipName); - time1 = System.currentTimeMillis(); - SSR.gzip(gzipDir + gzipName, new String[]{gzipDir + fileName}, 10); //don't include dir info - time1 = System.currentTimeMillis() - time1; - File2.delete(gzipDir + fileName); - //unzip the gzip file - time2 = System.currentTimeMillis(); - SSR.unGzip(gzipDir + gzipName, gzipDir, //note: extract to classPath, since doesn't include dir - true, 10); //false 'ignoreDirectoryInfo' - time2 = System.currentTimeMillis() - time2; - //ensure results are as expected - results = File2.readFromFile88591(gzipDir + fileName); - Test.ensureEqual(results[0], "", "SSR.gz b"); - Test.ensureEqual(results[1], longText, "SSR.z c"); - String2.log("gzip+ungzip time=" + (time1 + time2) + - "ms (Java 1.7M4700 780-880ms, 1.6 ~4000-11000ms)"); - File2.delete(gzipDir + gzipName); - File2.delete(gzipDir + fileName); - } - - //getURLResponse (which uses getURLInputStream) - //FUTURE: test various compressed url's - String2.log("test getURLResponse"); - try { - sar = SSR.getUrlResponseLines("https://coastwatch.pfeg.noaa.gov/erddap/index.html"); - Test.ensureEqual( - String2.lineContaining(sar, "ERDDAP is a data server that gives you a simple, consistent way") == -1, - false, "Response=" + String2.toNewlineString(sar)); - } catch (Exception e) { - String2.log(MustBe.throwableToString(e)); - String2.pressEnterToContinue("\nRecover from failure?"); - } - - //test non-existent file - long rTime = System.currentTimeMillis(); - try { - sar = SSR.getUrlResponseLines("https://coastwatch.pfeg.noaa.gov/zzz.html"); - throw new Throwable("shouldn't get here."); - } catch (Exception e) { //not throwable - String2.log("SSR.getUrlResponse for non existent url time=" + (System.currentTimeMillis() - rTime) + "ms"); - //String2.pressEnterToContinue(); - } catch (Throwable t) { - Test.error(t.toString()); //converts it to Exception and stops the testing - } - - //note there is no continuity (session cookie isn't being sent) - //but you can put as many params on one line as needed (from any screen) - //and put edit=... to determine which screen gets returned - sar = SSR.getUrlResponseLines("https://coastwatch.pfeg.noaa.gov/coastwatch/CWBrowser.jsp?edit=Grid+Data"); - String2.log("****beginResponse\n" + String2.toNewlineString(sar) + "\n****endResponse"); - Test.ensureNotEqual(String2.lineContaining(sar, "Download the grid data:"), -1, "e"); - - //postHTMLForm (always right after contact the website above) - //I NEVER GOT THIS WORKING. JUST USE 'GET' TESTS ABOVE -// String2.log("test postHTMLForm"); - - //for apache commons version -// sar = SSR.postHTMLForm("https://coastwatch.pfeg.noaa.gov/cwexperimental/", "CWBrowser.jsp", -// new String[]{"edit", "Bathymetry"}); - - //for devx version - //sar = SSR.postHTMLForm("https://coastwatch.pfeg.noaa.gov/cwexperimental/CWBrowser.jsp", - // new Object[]{"bathymetry", "false", "edit", "Bathymetry"}); - - //for java almanac version - //sar = SSR.postHTMLForm("coastwatch.pfeg.noaa.gov", "/cwexperimental/CWBrowser.jsp", - // "edit=Bathymetry"); - -// String2.log("****beginResponse\n" + String2.toNewlineString(sar) + "\n****endResponse"); -// Test.ensureNotEqual(String2.lineContaining(sar, "1) Draw bathymetry lines:"), -1, "a"); - - //getFirstLineStartsWith - String2.log("test getFirstLineStartsWith"); - String tFileName = classPath + "testSSR.txt"; - File2.writeToFile88591(tFileName, "This is\na file\nwith a few lines."); - Test.ensureEqual(SSR.getFirstLineStartsWith(tFileName, File2.ISO_8859_1, "with "), "with a few lines.", "a"); - Test.ensureEqual(SSR.getFirstLineStartsWith(tFileName, File2.ISO_8859_1, "hi "), null, "b"); - - //getFirstLineMatching - String2.log("test getFirstLineMatching"); - Test.ensureEqual(SSR.getFirstLineMatching(tFileName, File2.ISO_8859_1, ".*?i.*"), "This is", "a"); //find first of many matches - Test.ensureEqual(SSR.getFirstLineMatching(tFileName, File2.ISO_8859_1, "^a.*"), "a file", "b"); //start of line - Test.ensureEqual(SSR.getFirstLineMatching(tFileName, File2.ISO_8859_1, ".*?\\sfew\\s.*"),"with a few lines.", "c"); //containing - Test.ensureEqual(SSR.getFirstLineMatching(tFileName, File2.ISO_8859_1, "q"), null, "d"); //no match - - Test.ensureTrue(File2.delete(tFileName), "delete " + tFileName); - - //getContextDirectory - String2.log("test getContextDirectory current=" + - File2.webInfParentDirectory()); //with / separator and / at the end - //there is no way to test this and have it work with different installations - //test for my computer (comment out on other computers): - //ensureEqual(String2.getContextDirectory(), //with / separator and / at the end - // "C:/programs/_tomcat/webapps/cwexperimental/", "a"); - //wimpy test, but works on all computers - Test.ensureNotNull(File2.webInfParentDirectory(), //with / separator and / at the end - "contextDirectory"); - - //getTempDirectory - String2.log("test getTempDirectory current=" + SSR.getTempDirectory()); - //wimpy test - Test.ensureEqual(SSR.getTempDirectory(), File2.webInfParentDirectory() + "WEB-INF/temp/", "a"); - - - //done - String2.log("\nDone. All non-Unix tests passed!"); - - } - - /** - * If this fails with "Connection refused" error, make sure McAffee "Virus Scan Console : - * Access Protection Properties : Anti Virus Standard Protections : - * Prevent mass mailing worms from sending mail" is un-checked. - */ - public static void testEmail() throws Exception { - - String emailServer, emailPort, emailProperties, emailUser, - emailPassword, emailReplyToAddress, emailToAddresses; - SSR.debugMode = true; - - //*** sendEmail via Google uses starttls authentication - emailServer = String2.getStringFromSystemIn( - "\n\n***gmail email server (e.g., smtp.gmail.com)? "); - if (emailServer.length() == 0) emailServer = "smtp.gmail.com"; - - emailPort = String2.getStringFromSystemIn( - "gmail email port (e.g., 465 or 587 (default))? "); - if (emailPort.length() == 0) emailPort = "587"; - - emailUser = String2.getStringFromSystemIn( - "gmail email user (e.g., erd.data@noaa.gov)? "); - if (emailUser.length() == 0) emailUser = "erd.data@noaa.gov"; - - emailPassword = String2.getPasswordFromSystemIn( - "gmail email password\n" + - "(e.g., password (or \"\" to skip this test. Bob: use 'application specific password')? "); - - if (emailPassword.length() > 0) { - emailReplyToAddress = String2.getStringFromSystemIn( - "gmail email Reply To address (e.g., erd.data@noaa.gov)? "); - if (emailReplyToAddress.length() == 0) emailReplyToAddress = "erd.data@noaa.gov"; - - emailToAddresses = String2.getStringFromSystemIn( - "1+ email To addresses (e.g., BobSimons2.00@gmail.com,CoHortSoftware@gmail.com)? "); - if (emailToAddresses.length() == 0) emailToAddresses = "BobSimons2.00@gmail.com,CoHortSoftware@gmail.com"; - - try { - String2.log("test gmail email " + emailToAddresses); - SSR.sendEmail(emailServer, String2.parseInt(emailPort), emailUser, emailPassword, - "mail.smtp.starttls.enable|true", - emailReplyToAddress, emailToAddresses, - "gmail email test", //Euro - "This is a gmail email test from TestSSR with embedded special characters < > & û \u20ac .\nSecond line."); - } catch (Exception e) { - String2.pressEnterToContinue(MustBe.throwableToString(e)); - } - } - SSR.debugMode = false; - } - - - /** - * Test email. - * If this fails with "Connection refused" error, make sure McAffee "Virus Scan Console : - * Access Protection Properties : Anti Virus Standard Protections : - * Prevent mass mailing worms from sending mail" is un-checked. - * - */ - public static void testEmail(String emailUser, String password) throws Exception { - - String title = "Email Test from TestSSR"; - String content = "This is an email test (local) from user=" + emailUser + " in TestSSR."; - String2.log("\n*** " + content); - SSR.debugMode = true; - if (true) { - String emailServer = "smtp.gmail.com"; - //Thunderbird used 465. 587 is what we're supposed to use. Dave Nordello opened it up. - int emailPort = 587; - SSR.sendEmail(emailServer, emailPort, emailUser, password, - "mail.smtp.starttls.enable|true", - emailUser, "erd.data@noaa.gov,CoHortSoftware@gmail.com,null", title, content); - } - SSR.debugMode = false; - } - - /** - * Test posting info and getting response. - */ - public static void testPostFormGetResponseString() throws Exception { - for (int i = 0; i < 2; i++) { - try { - String s = SSR.postFormGetResponseString( - "https://coastwatch.pfeg.noaa.gov/erddap/search/index.html?page=1&itemsPerPage=1000&searchFor=jplmursst41"); - String2.log("\nSSR.testPostFormGetResponseString() result:\n" + s); - Test.ensureTrue(s.indexOf("Do a Full Text Search for Datasets:") >= 0, ""); - Test.ensureTrue(s.indexOf("Multi-scale Ultra-high Resolution (MUR) SST Analysis fv04.1, Global") >= 0, ""); - Test.ensureTrue(s.indexOf("ERDDAP, Version") >= 0, ""); - - //2018-10-24 I verified that - //* This request appears as a POST (not GET) in tomcat's localhost_access_lot[date].txt - //* The parameters don't appear in that file (whereas they do for GET requests) - //* The parameters don't appear in ERDDAP log (whereas they do for GET requests), - //* and it is labelled as a POST request. - s = SSR.postFormGetResponseString( - "http://localhost:8080/cwexperimental/search/index.html?page=1&itemsPerPage=1000&searchFor=jplmursst41"); - String2.log("\nSSR.testPostFormGetResponseString() result:\n" + s); - Test.ensureTrue(s.indexOf("Do a Full Text Search for Datasets:") >= 0, ""); - Test.ensureTrue(s.indexOf("Multi-scale Ultra-high Resolution (MUR) SST Analysis fv04.1, Global") >= 0, - "This test requires MUR 4.1 in the local host ERDDAP."); - Test.ensureTrue(s.indexOf("ERDDAP, Version") >= 0, ""); - break; //if successful, don't do i=1 loop - } catch (Exception e) { - String2.pressEnterToContinue(MustBe.throwableToString(e) + - "This requires localhost ERDDAP.\nPress Enter to " + - (i == 0? "try again." : "skip this test.")); - } - } - } - - /** - * Run all of the tests which are dependent on Unix. - */ - public static void runUnixTests() throws Exception { - //cShell - String2.log("test cShell"); - //Test.ensureEqual(toNewlineString(SSR.cShell("")), "", "a"); - - String2.log("Done. All Unix tests passed!"); - } - - /** - * Runs some AWS S3-related tests. - */ - public static void testAwsS3() throws Exception { - - String2.log("\n*** TestSSR.testAwsS3() -- THIS TEST REQUIRES testPrivateAwsS3MediaFiles in localhost erddap."); - String localFile20 = "/u00/data/points/testMediaFiles/ShouldWork/noaa20.gif"; - String privateAwsSource20 = "https://bobsimonsdata.s3.us-east-1.amazonaws.com/testMediaFiles/noaa20.gif"; - String privateErddapSource20 = "http://localhost:8080/cwexperimental/files/testPrivateAwsS3MediaFiles/noaa20.gif"; - BufferedInputStream bis; - BufferedOutputStream bos; - String dest = File2.getSystemTempDirectory() + "testS3"; - String results, expected; - - //String2.isRemote() and String2.isTrulyRemote() - Test.ensureEqual(String2.isRemote( localFile20), false, ""); - Test.ensureEqual(String2.isTrulyRemote(localFile20), false, ""); - Test.ensureEqual(String2.isRemote( privateAwsSource20), true, ""); - Test.ensureEqual(String2.isTrulyRemote(privateAwsSource20), false, ""); - Test.ensureEqual(String2.isRemote( privateErddapSource20), true, ""); - Test.ensureEqual(String2.isTrulyRemote(privateErddapSource20), true, ""); - - String bro[] = String2.parseAwsS3Url(privateAwsSource20); - Test.ensureEqual(bro[0], "bobsimonsdata", ""); - Test.ensureEqual(bro[1], "us-east-1", ""); - Test.ensureEqual(bro[2], "testMediaFiles/noaa20.gif", ""); - - bro = String2.parseAwsS3Url("http://some.bucket.s3-website-us-east-1.amazonaws.com/some/object.gif"); - Test.ensureEqual(bro[0], "some.bucket", ""); - Test.ensureEqual(bro[1], "us-east-1", ""); - Test.ensureEqual(bro[2], "some/object.gif", ""); - - //private file length - Test.ensureEqual(File2.length(localFile20), 1043, ""); - Test.ensureEqual(File2.length(privateAwsSource20), 1043, ""); - - //private file lastModified - Test.ensureEqual(File2.getLastModified(localFile20), 1302534310000L, ""); - Test.ensureEqual(File2.getLastModified(privateAwsSource20), 1620243246000L, ""); //the instant I put it in S3 - - //a public bucket/file should allow access via a simple https request - results = "okay"; - try { - SSR.touchUrl("https://nasanex.s3.us-west-2.amazonaws.com/NEX-DCP30/doi.txt", 5000, false); //handleS3ViaSDK=false - } catch (Exception e) { - results = e.toString(); - } - Test.ensureEqual(results, "okay", - "A public S3 file should be accessible (e.g., touchUrl) via a simple URL."); - - //a private bucket/file shouldn't allow access via a simple https request - results = "shouldn't happen"; - try { - SSR.touchUrl(privateAwsSource20, 5000, false); //handleS3ViaSDK=false - } catch (Exception e) { - results = e.toString(); - } - expected = "java.io.IOException: HTTP status code=403 for URL: https://bobsimonsdata.s3.us-east-1.amazonaws.com/testMediaFiles/noaa20.gif\n"; - Test.ensureEqual(results.substring(0, expected.length()), expected, - "A private S3 file shouldn't be accessible (e.g., touchUrl) via a simple URL (even with credentials on this computer). results=" + results); - - //byte range private - Test.ensureTrue(File2.copy(privateAwsSource20, dest + "1a"), ""); - results = File2.hexDump(dest + "1a", 96); - String expected1 = -"47 49 46 38 39 61 14 00 14 00 f7 00 00 14 3a 8c GIF89a : |\n" + -"2c a2 d4 94 d2 ec 4c 6e a4 8c a2 c4 04 86 d4 34 , Ln 4 |\n" + -"56 9c cc ea f4 6c 86 b4 64 ba e4 84 c6 e4 24 4a V l d $J |\n" + -"94 44 aa dc 14 96 d4 e4 f6 fc ac ba d4 cc d2 e4 D |\n" + -"64 7e ac 44 62 9c 34 a6 dc 7c 92 bc bc ca dc 14 d~ Db 4 | |\n" + -"42 8c 5c 76 ac 9c ae cc 74 c2 e4 14 96 dc fc fe B \\v t |\n"; - Test.ensureEqual(results, expected1, "results=\n" + results); - - //range request - Test.ensureTrue(File2.copy(privateAwsSource20, dest + "2a", 16, 95), ""); - results = File2.hexDump(dest + "2a", 1000); //read all - String expected2 = //same but without 1st row (16 bytes) -"2c a2 d4 94 d2 ec 4c 6e a4 8c a2 c4 04 86 d4 34 , Ln 4 |\n" + -"56 9c cc ea f4 6c 86 b4 64 ba e4 84 c6 e4 24 4a V l d $J |\n" + -"94 44 aa dc 14 96 d4 e4 f6 fc ac ba d4 cc d2 e4 D |\n" + -"64 7e ac 44 62 9c 34 a6 dc 7c 92 bc bc ca dc 14 d~ Db 4 | |\n" + -"42 8c 5c 76 ac 9c ae cc 74 c2 e4 14 96 dc fc fe B \\v t |\n"; - Test.ensureEqual(results, expected2, "results=\n" + results); - - //byte range private - bis = (BufferedInputStream)SSR.getUrlConnBufferedInputStream(privateErddapSource20, - 30000, false, false, 0, -1, false)[1]; - bos = new BufferedOutputStream(new FileOutputStream(dest + "1b")); - File2.copy(bis, bos, 0, -1); - bis.close(); - bos.close(); - results = File2.hexDump(dest + "1b", 96); - Test.ensureEqual(results, expected1, "results=\n" + results); - - //range request - bis = (BufferedInputStream)SSR.getUrlConnBufferedInputStream(privateErddapSource20, - 30000, false, false, 16, 95, false)[1]; //16 to 95 - bos = new BufferedOutputStream(new FileOutputStream(dest + "2b")); - File2.copy(bis, bos, 0, -1); - bis.close(); - bos.close(); - results = File2.hexDump(dest + "2b", 1000); //all - Test.ensureEqual(results, expected2, "results=\n" + results); - - //range request - bis = (BufferedInputStream)SSR.getUrlConnBufferedInputStream(privateErddapSource20, - 30000, false, false, 16, -1, false)[1]; //16 to end - bos = new BufferedOutputStream(new FileOutputStream(dest + "2b2")); - File2.copy(bis, bos, 0, -1); - bis.close(); - bos.close(); - results = File2.hexDump(dest + "2b2", 80); - Test.ensureEqual(results, expected2, "results=\n" + results); - } - - /** - * Tests Aws TransferManager. - */ - public static void testAwsTransferManager() throws Exception { - - //*** test a lot of AWS S3 actions on a private AWS bucket - //delete a file on S3 to ensure it doesn't exist (ignore result) - String origLocal = String2.unitTestDataDir + "ascii/standardizeWhat1.csv"; - String tempLocal = File2.getSystemTempDirectory() + "testAwsS3.csv"; - String awsUrl = "https://bobsimonsdata.s3.us-east-1.amazonaws.com/testMediaFiles/testAwsS3.csv"; - //bucket is publicly readible in a browser via http but not https - String awsUrl2 = "http://bob.simons.public.output.s3-website-us-east-1.amazonaws.com/testAwsS3.csv"; - String content; - - //delete files I will create - File2.deleteAwsS3File(awsUrl); - File2.delete(tempLocal); - - //isAwsS3File - Test.ensureEqual(File2.isAwsS3File(awsUrl), false, ""); - - //upload a file to S3 - SSR.uploadFileToAwsS3(null, origLocal, awsUrl, "text/csv"); - - //length of Aws S3 file - Test.ensureEqual(File2.length(awsUrl), 44, ""); - - //isAwsS3File - Test.ensureEqual(File2.isAwsS3File(awsUrl), true, ""); - - //download a file from S3 - SSR.downloadFile(awsUrl, tempLocal, false); //tryToUseCompression is ignored - - //read local file - content = File2.directReadFrom88591File(tempLocal); - Test.ensureEqual(content, - "date,data\n" + - "20100101000000,1\n" + - "20100102000000,2\n", - "content=" + String2.annotatedString(content)); - - //delete files I created - File2.deleteAwsS3File(awsUrl); - File2.delete(tempLocal); - - //isAwsS3File - Test.ensureEqual(File2.isAwsS3File(awsUrl ), false, ""); - - - //************** again but with awsUrl2 - //delete files I will create - File2.deleteAwsS3File(awsUrl2); - File2.delete(tempLocal); - - //isAwsS3File - Test.ensureEqual(File2.isAwsS3File(awsUrl2), false, ""); - - //upload a file to S3 - //fails here. - //"software.amazon.awssdk.crt.s3.CrtS3RuntimeException: Retry cannot be attempted - // because the maximum number of retries has been exceeded. AWS_IO_MAX_RETRIES_EXCEEDED(1069) - // at com.amazonaws.s3.S3NativeClient$3.onFinished(S3NativeClient.java:313)" - //a permissions problem? - SSR.uploadFileToAwsS3(null, origLocal, awsUrl2, "text/csv"); - - //length of Aws S3 file - Test.ensureEqual(File2.length(awsUrl2), 44, ""); - - //isAwsS3File - Test.ensureEqual(File2.isAwsS3File(awsUrl2), true, ""); - - //download a file from S3 - SSR.downloadFile(awsUrl2, tempLocal, false); //tryToUseCompression is ignored - - //read local file - content = File2.directReadFrom88591File(tempLocal); - Test.ensureEqual(content, - "date,data\n" + - "20100101000000,1\n" + - "20100102000000,2\n", - "content=" + String2.annotatedString(content)); - - //delete files I created - File2.deleteAwsS3File(awsUrl2); - File2.delete(tempLocal); - - //isAwsS3File - Test.ensureEqual(File2.isAwsS3File(awsUrl2), false, ""); - } - - - /** - * This runs all of the interactive or not interactive tests for this class. - * - * @param errorSB all caught exceptions are logged to this. - * @param interactive If true, this runs all of the interactive tests; - * otherwise, this runs all of the non-interactive tests. - * @param doSlowTestsToo If true, this runs the slow tests, too. - * @param firstTest The first test to be run (0...). Test numbers may change. - * @param lastTest The last test to be run, inclusive (0..., or -1 for the last test). - * Test numbers may change. - */ - public static void test(StringBuilder errorSB, boolean interactive, - boolean doSlowTestsToo, int firstTest, int lastTest) { - if (lastTest < 0) - lastTest = interactive? 2 : 1; - String msg = "\n^^^ TestSSR.test(" + interactive + ") test="; - - for (int test = firstTest; test <= lastTest; test++) { - try { - long time = System.currentTimeMillis(); - String2.log(msg + test); - - if (interactive) { - if (test == 0) runNonUnixTests(); - if (test == 1) testEmail(); - if (test == 2) testPostFormGetResponseString(); - - if (test == 1000) runUnixTests(); - - } else { - if (test == 0) testAwsS3(); - if (test == 1) testAwsTransferManager(); - } - - String2.log(msg + test + " finished successfully in " + (System.currentTimeMillis() - time) + " ms."); - } catch (Throwable testThrowable) { - String eMsg = msg + test + " caught throwable:\n" + - MustBe.throwableToString(testThrowable); - errorSB.append(eMsg); - String2.log(eMsg); - if (interactive) - String2.pressEnterToContinue(""); - } - } - } - - - /** - * Run all of the tests - */ - public static void main(String args[]) throws Throwable { - SSR.verbose = true; - -// runUnixTests(); - } - -} - - diff --git a/pom.xml b/pom.xml index c364a69e5..048f2cf57 100644 --- a/pom.xml +++ b/pom.xml @@ -237,6 +237,9 @@ maven-surefire-plugin 3.2.1 + + AWS, LocalERDDAP, Password, Thredds, ExternalERDDAP, MissingFile, LargeFile, ExternalOther, IncompleteTest, WebInfStructureDependency + diff --git a/src/test/java/WEB-INF/classes/com/cohort/array/ByteArrayTests.java b/src/test/java/WEB-INF/classes/com/cohort/array/ByteArrayTests.java deleted file mode 100644 index 8dbdf61de..000000000 --- a/src/test/java/WEB-INF/classes/com/cohort/array/ByteArrayTests.java +++ /dev/null @@ -1,467 +0,0 @@ -package com.cohort.array; - -import com.cohort.util.*; - -import java.io.DataInputStream; -import java.io.DataOutputStream; -import java.io.InputStream; -import java.io.IOException; -import java.io.RandomAccessFile; -import java.math.BigInteger; -import java.text.MessageFormat; -import java.util.Arrays; -import java.util.BitSet; -import java.util.HashMap; -import java.util.Iterator; -import java.util.Set; - -import ucar.ma2.StructureData; - -class ByteArrayTests { - @org.junit.jupiter.api.Test - /** - * This tests the methods of this class. - * - * @throws Throwable if trouble. - */ - void basicTest() throws Throwable { - String2.log("*** ByteArray.basicTest"); - - ByteArray anArray = ByteArray.fromCSV(" -128, -1, 0, 126, , 127, 200 "); - Test.ensureEqual(anArray.toString(), "-128, -1, 0, 126, 127, 127, 127", ""); - Test.ensureEqual(anArray.toNccsvAttString(), "-128b,-1b,0b,126b,127b,127b,127b", ""); - Test.ensureEqual(anArray.toNccsv127AttString(), "-128b,-1b,0b,126b,127b,127b,127b", ""); - - // ** test default constructor and many of the methods - anArray = new ByteArray(); - Test.ensureEqual(anArray.isIntegerType(), true, ""); - Test.ensureEqual(anArray.missingValue().getRawDouble(), Byte.MAX_VALUE, ""); - anArray.addString(""); - Test.ensureEqual(anArray.get(0), Byte.MAX_VALUE, ""); - Test.ensureEqual(anArray.getRawInt(0), Byte.MAX_VALUE, ""); - Test.ensureEqual(anArray.getRawDouble(0), Byte.MAX_VALUE, ""); - Test.ensureEqual(anArray.getUnsignedDouble(0), Byte.MAX_VALUE, ""); - Test.ensureEqual(anArray.getRawString(0), "" + Byte.MAX_VALUE, ""); - Test.ensureEqual(anArray.getRawNiceDouble(0), Byte.MAX_VALUE, ""); - Test.ensureEqual(anArray.getInt(0), Integer.MAX_VALUE, ""); - Test.ensureEqual(anArray.getDouble(0), Double.NaN, ""); - Test.ensureEqual(anArray.getString(0), "", ""); - Test.ensureEqual(anArray.toString(), "127", ""); - - anArray.set(0, (byte) -128); - Test.ensureEqual(anArray.getUnsignedDouble(0), 128, ""); - anArray.set(0, (byte) -127); - Test.ensureEqual(anArray.getUnsignedDouble(0), 129, ""); - anArray.set(0, (byte) -1); - Test.ensureEqual(anArray.getUnsignedDouble(0), 255, ""); - anArray.clear(); - - Test.ensureEqual(anArray.size(), 0, ""); - anArray.add((byte) 120); - Test.ensureEqual(anArray.size(), 1, ""); - Test.ensureEqual(anArray.get(0), 120, ""); - Test.ensureEqual(anArray.getInt(0), 120, ""); - Test.ensureEqual(anArray.getFloat(0), 120, ""); - Test.ensureEqual(anArray.getDouble(0), 120, ""); - Test.ensureEqual(anArray.getString(0), "120", ""); - Test.ensureEqual(anArray.elementType(), PAType.BYTE, ""); - byte tArray[] = anArray.toArray(); - Test.ensureEqual(tArray, new byte[] { (byte) 120 }, ""); - - // intentional errors - try { - anArray.get(1); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); - } - try { - anArray.set(1, (byte) 100); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); - } - try { - anArray.getInt(1); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); - } - try { - anArray.setInt(1, 100); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); - } - try { - anArray.getLong(1); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); - } - try { - anArray.setLong(1, 100); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); - } - try { - anArray.getFloat(1); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); - } - try { - anArray.setFloat(1, 100); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); - } - try { - anArray.getDouble(1); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); - } - try { - anArray.setDouble(1, 100); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); - } - try { - anArray.getString(1); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); - } - try { - anArray.setString(1, "100"); - throw new Throwable("It should have failed."); - } catch (Exception e) { - Test.ensureEqual(e.toString(), - "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); - } - - // set NaN returned as NaN - anArray.setDouble(0, Double.NaN); - Test.ensureEqual(anArray.getDouble(0), Double.NaN, ""); - anArray.setDouble(0, -1e300); - Test.ensureEqual(anArray.getDouble(0), Double.NaN, ""); - anArray.setDouble(0, 2.2); - Test.ensureEqual(anArray.getDouble(0), 2, ""); - anArray.setFloat(0, Float.NaN); - Test.ensureEqual(anArray.getFloat(0), Float.NaN, ""); - anArray.setFloat(0, -1e33f); - Test.ensureEqual(anArray.getFloat(0), Float.NaN, ""); - anArray.setFloat(0, 3.3f); - Test.ensureEqual(anArray.getFloat(0), 3, ""); - anArray.setLong(0, Long.MAX_VALUE); - Test.ensureEqual(anArray.getLong(0), Long.MAX_VALUE, ""); - anArray.setLong(0, 9123456789L); - Test.ensureEqual(anArray.getLong(0), Long.MAX_VALUE, ""); - anArray.setLong(0, 4); - Test.ensureEqual(anArray.getLong(0), 4, ""); - anArray.setInt(0, Integer.MAX_VALUE); - Test.ensureEqual(anArray.getInt(0), Integer.MAX_VALUE, ""); - anArray.setInt(0, 1123456789); - Test.ensureEqual(anArray.getInt(0), Integer.MAX_VALUE, ""); - anArray.setInt(0, 5); - Test.ensureEqual(anArray.getInt(0), 5, ""); - - // makeUnsignedPA - anArray = new ByteArray(new byte[] { -128, -2, -1, 0, 1, 126, 127 }); - UByteArray uArray = (UByteArray) anArray.makeUnsignedPA(); - Test.ensureEqual(uArray.toString(), "128, 254, 255, 0, 1, 126, 127", ""); // -1 -> mv - anArray.clear(); - - // ** test capacity constructor, test expansion, test clear - anArray = new ByteArray(2, false); - Test.ensureEqual(anArray.size(), 0, ""); - for (int i = 0; i < 10; i++) { - anArray.add((byte) i); - Test.ensureEqual(anArray.get(i), i, ""); - Test.ensureEqual(anArray.size(), i + 1, ""); - } - Test.ensureEqual(anArray.size(), 10, ""); - anArray.clear(); - Test.ensureEqual(anArray.size(), 0, ""); - - // active - anArray = new ByteArray(3, true); - Test.ensureEqual(anArray.size(), 3, ""); - Test.ensureEqual(anArray.get(2), 0, ""); - - // ** test array constructor - anArray = new ByteArray(new byte[] { 0, 2, 4, 6, 8 }); - Test.ensureEqual(anArray.size(), 5, ""); - Test.ensureEqual(anArray.get(0), 0, ""); - Test.ensureEqual(anArray.get(1), 2, ""); - Test.ensureEqual(anArray.get(2), 4, ""); - Test.ensureEqual(anArray.get(3), 6, ""); - Test.ensureEqual(anArray.get(4), 8, ""); - - // test compare - Test.ensureEqual(anArray.compare(1, 3), -1, ""); - Test.ensureEqual(anArray.compare(1, 1), 0, ""); - Test.ensureEqual(anArray.compare(3, 1), 1, ""); - - // test toString - Test.ensureEqual(anArray.toString(), "0, 2, 4, 6, 8", ""); - - // test calculateStats - anArray.addString(""); - double stats[] = anArray.calculateStats(); - anArray.remove(5); - Test.ensureEqual(stats[PrimitiveArray.STATS_N], 5, ""); - Test.ensureEqual(stats[PrimitiveArray.STATS_MIN], 0, ""); - Test.ensureEqual(stats[PrimitiveArray.STATS_MAX], 8, ""); - Test.ensureEqual(stats[PrimitiveArray.STATS_SUM], 20, ""); - - // test indexOf(int) indexOf(String) - Test.ensureEqual(anArray.indexOf((byte) 0, 0), 0, ""); - Test.ensureEqual(anArray.indexOf((byte) 0, 1), -1, ""); - Test.ensureEqual(anArray.indexOf((byte) 8, 0), 4, ""); - Test.ensureEqual(anArray.indexOf((byte) 9, 0), -1, ""); - - Test.ensureEqual(anArray.indexOf("0", 0), 0, ""); - Test.ensureEqual(anArray.indexOf("0", 1), -1, ""); - Test.ensureEqual(anArray.indexOf("8", 0), 4, ""); - Test.ensureEqual(anArray.indexOf("9", 0), -1, ""); - - // test remove - anArray.remove(1); - Test.ensureEqual(anArray.size(), 4, ""); - Test.ensureEqual(anArray.get(0), 0, ""); - Test.ensureEqual(anArray.get(1), 4, ""); - Test.ensureEqual(anArray.get(3), 8, ""); - - // test atInsert(index, value) - anArray.atInsert(1, (byte) 22); - Test.ensureEqual(anArray.size(), 5, ""); - Test.ensureEqual(anArray.get(0), 0, ""); - Test.ensureEqual(anArray.get(1), 22, ""); - Test.ensureEqual(anArray.get(2), 4, ""); - Test.ensureEqual(anArray.get(4), 8, ""); - anArray.remove(1); - - // test removeRange - anArray.removeRange(4, 4); // make sure it is allowed - anArray.removeRange(1, 3); - Test.ensureEqual(anArray.size(), 2, ""); - Test.ensureEqual(anArray.get(0), 0, ""); - Test.ensureEqual(anArray.get(1), 8, ""); - - // test (before trimToSize) that toString, toDoubleArray, and toStringArray use - // 'size' - Test.ensureEqual(anArray.toString(), "0, 8", ""); - Test.ensureEqual(anArray.toDoubleArray(), new double[] { 0, 8 }, ""); - Test.ensureEqual(anArray.toStringArray(), new String[] { "0", "8" }, ""); - - // test trimToSize - anArray.trimToSize(); - Test.ensureEqual(anArray.array.length, 2, ""); - - // test equals - ByteArray anArray2 = new ByteArray(); - anArray2.add((byte) 0); - Test.ensureEqual(anArray.testEquals(null), - "The two objects aren't equal: this object is a ByteArray; the other is a null.", ""); - Test.ensureEqual(anArray.testEquals("A String"), - "The two objects aren't equal: this object is a ByteArray; the other is a java.lang.String.", ""); - Test.ensureEqual(anArray.testEquals(anArray2), - "The two ByteArrays aren't equal: one has 2 value(s); the other has 1 value(s).", ""); - Test.ensureTrue(!anArray.equals(anArray2), ""); - anArray2.addString("7"); - Test.ensureEqual(anArray.testEquals(anArray2), - "The two ByteArrays aren't equal: this[1]=8; other[1]=7.", ""); - Test.ensureTrue(!anArray.equals(anArray2), ""); - anArray2.setString(1, "8"); - Test.ensureEqual(anArray.testEquals(anArray2), "", ""); - Test.ensureTrue(anArray.equals(anArray2), ""); - - // test toObjectArray - Test.ensureEqual(anArray.toArray(), anArray.toObjectArray(), ""); - - // test toDoubleArray - Test.ensureEqual(anArray.toDoubleArray(), new double[] { 0, 8 }, ""); - - // test reorder - int rank[] = { 1, 0 }; - anArray.reorder(rank); - Test.ensureEqual(anArray.toDoubleArray(), new double[] { 8, 0 }, ""); - - // ** test append and clone - anArray = new ByteArray(new byte[] { 1 }); - anArray.append(new ByteArray(new byte[] { 5, -5 })); - Test.ensureEqual(anArray.toDoubleArray(), new double[] { 1, 5, -5 }, ""); - anArray.append(new StringArray(new String[] { "a", "9" })); - Test.ensureEqual(anArray.getMaxIsMV(), true, ""); - Test.ensureEqual(anArray.toString(), "1, 5, -5, 127, 9", ""); // toString shows numbers as is, regardless of - // maxIsMV - Test.ensureEqual(anArray.toDoubleArray(), new double[] { 1, 5, -5, Double.NaN, 9 }, ""); - anArray2 = (ByteArray) anArray.clone(); - Test.ensureEqual(anArray2.toDoubleArray(), new double[] { 1, 5, -5, Double.NaN, 9 }, ""); - - // test move - anArray = new ByteArray(new byte[] { 0, 1, 2, 3, 4 }); - anArray.move(1, 3, 0); - Test.ensureEqual(anArray.toArray(), new byte[] { 1, 2, 0, 3, 4 }, ""); - - anArray = new ByteArray(new byte[] { 0, 1, 2, 3, 4 }); - anArray.move(1, 2, 4); - Test.ensureEqual(anArray.toArray(), new byte[] { 0, 2, 3, 1, 4 }, ""); - - // move does nothing, but is allowed - anArray = new ByteArray(new byte[] { 0, 1, 2, 3, 4 }); - anArray.move(1, 1, 0); - Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); - anArray.move(1, 2, 1); - Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); - anArray.move(1, 2, 2); - Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); - anArray.move(5, 5, 0); - Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); - anArray.move(3, 5, 5); - Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); - - // makeIndices - anArray = new ByteArray(new byte[] { 25, 1, 1, 10 }); - IntArray indices = new IntArray(); - Test.ensureEqual(anArray.makeIndices(indices).toString(), "1, 10, 25", ""); - Test.ensureEqual(indices.toString(), "2, 0, 0, 1", ""); - - anArray = new ByteArray(new byte[] { 35, 35, Byte.MAX_VALUE, 1, 2 }); - indices = new IntArray(); - Test.ensureEqual(anArray.makeIndices(indices).toString(), "1, 2, 35, 127", ""); - Test.ensureEqual(indices.toString(), "2, 2, 3, 0, 1", ""); - - anArray = new ByteArray(new byte[] { 10, 20, 30, 40 }); - Test.ensureEqual(anArray.makeIndices(indices).toString(), "10, 20, 30, 40", ""); - Test.ensureEqual(indices.toString(), "0, 1, 2, 3", ""); - - // switchToFakeMissingValue - anArray = new ByteArray(new byte[] { Byte.MAX_VALUE, 1, 2, Byte.MAX_VALUE, 3, Byte.MAX_VALUE }); - Test.ensureEqual(anArray.switchFromTo("", "75"), 3, ""); - Test.ensureEqual(anArray.toString(), "75, 1, 2, 75, 3, 75", ""); - anArray.switchFromTo("75", ""); - Test.ensureEqual(anArray.toString(), "127, 1, 2, 127, 3, 127", ""); - Test.ensureEqual(anArray.getNMinMaxIndex(), new int[] { 3, 1, 4 }, ""); - - // addN - anArray = new ByteArray(new byte[] { 25 }); - anArray.addN(2, (byte) 5); - Test.ensureEqual(anArray.toString(), "25, 5, 5", ""); - Test.ensureEqual(anArray.getNMinMaxIndex(), new int[] { 3, 2, 0 }, ""); - - // add array - anArray.add(new byte[] { 17, 19 }); - Test.ensureEqual(anArray.toString(), "25, 5, 5, 17, 19", ""); - - // subset - PrimitiveArray ss = anArray.subset(1, 3, 4); - Test.ensureEqual(ss.toString(), "5, 19", ""); - ss = anArray.subset(0, 1, 0); - Test.ensureEqual(ss.toString(), "25", ""); - ss = anArray.subset(0, 1, -1); - Test.ensureEqual(ss.toString(), "", ""); - ss = anArray.subset(1, 1, 0); - Test.ensureEqual(ss.toString(), "", ""); - - ss.trimToSize(); - anArray.subset(ss, 1, 3, 4); - Test.ensureEqual(ss.toString(), "5, 19", ""); - anArray.subset(ss, 0, 1, 0); - Test.ensureEqual(ss.toString(), "25", ""); - anArray.subset(ss, 0, 1, -1); - Test.ensureEqual(ss.toString(), "", ""); - anArray.subset(ss, 1, 1, 0); - Test.ensureEqual(ss.toString(), "", ""); - - // evenlySpaced - anArray = new ByteArray(new byte[] { 10, 20, 30 }); - Test.ensureEqual(anArray.isEvenlySpaced(), "", ""); - anArray.set(2, (byte) 31); - Test.ensureEqual(anArray.isEvenlySpaced(), - "ByteArray isn't evenly spaced: [0]=10.0, [1]=20.0, spacing=10.0, expected spacing=10.5.", ""); - Test.ensureEqual(anArray.smallestBiggestSpacing(), - " smallest spacing=10.0: [0]=10.0, [1]=20.0\n" + - " biggest spacing=11.0: [1]=20.0, [2]=31.0", - ""); - - // isAscending - anArray = new ByteArray(new byte[] { 10, 10, 30 }); - Test.ensureEqual(anArray.isAscending(), "", ""); - anArray.set(2, Byte.MAX_VALUE); - Test.ensureEqual(anArray.isAscending(), "", ""); - anArray.setMaxIsMV(true); - Test.ensureEqual(anArray.isAscending(), - "ByteArray isn't sorted in ascending order: [2]=(missing value).", ""); - anArray.set(1, (byte) 9); - Test.ensureEqual(anArray.isAscending(), - "ByteArray isn't sorted in ascending order: [0]=10 > [1]=9.", ""); - - // isDescending - anArray = new ByteArray(new byte[] { 30, 10, 10 }); - Test.ensureEqual(anArray.isDescending(), "", ""); - anArray.set(2, Byte.MAX_VALUE); - anArray.setMaxIsMV(true); - Test.ensureEqual(anArray.isDescending(), - "ByteArray isn't sorted in descending order: [1]=10 < [2]=127.", ""); - anArray.set(1, (byte) 35); - Test.ensureEqual(anArray.isDescending(), - "ByteArray isn't sorted in descending order: [0]=30 < [1]=35.", ""); - - // firstTie - anArray = new ByteArray(new byte[] { 30, 35, 10 }); - Test.ensureEqual(anArray.firstTie(), -1, ""); - anArray.set(1, (byte) 30); - Test.ensureEqual(anArray.firstTie(), 0, ""); - - // hashcode - anArray = new ByteArray(); - for (int i = 5; i < 1000; i++) - anArray.add((byte) i); - String2.log("hashcode1=" + anArray.hashCode()); - anArray2 = (ByteArray) anArray.clone(); - Test.ensureEqual(anArray.hashCode(), anArray2.hashCode(), ""); - anArray.atInsert(0, (byte) 2); - Test.ensureTrue(anArray.hashCode() != anArray2.hashCode(), ""); - - // justKeep - BitSet bitset = new BitSet(); - anArray = new ByteArray(new byte[] { 0, 11, 22, 33, 44 }); - bitset.set(1); - bitset.set(4); - anArray.justKeep(bitset); - Test.ensureEqual(anArray.toString(), "11, 44", ""); - - // min max - anArray = new ByteArray(); - anArray.addPAOne(anArray.MINEST_VALUE()); - anArray.addPAOne(anArray.MAXEST_VALUE()); - Test.ensureEqual(anArray.getString(0), anArray.MINEST_VALUE().toString(), ""); - Test.ensureEqual(anArray.getString(0), "-128", ""); - Test.ensureEqual(anArray.getString(1), anArray.MAXEST_VALUE().toString(), ""); - Test.ensureEqual(anArray.getString(1), "126", ""); - - // tryToFindNumericMissingValue() - Test.ensureEqual((new ByteArray(new byte[] {})).tryToFindNumericMissingValue(), null, ""); - Test.ensureEqual((new ByteArray(new byte[] { 1, 2 })).tryToFindNumericMissingValue(), null, ""); - Test.ensureEqual((new ByteArray(new byte[] { -128 })).tryToFindNumericMissingValue(), -128, ""); - Test.ensureEqual((new ByteArray(new byte[] { 127 })).tryToFindNumericMissingValue(), 127, ""); - Test.ensureEqual((new ByteArray(new byte[] { 1, 99 })).tryToFindNumericMissingValue(), 99, ""); - - } -} diff --git a/src/test/java/com/cohort/array/ByteArrayTests.java b/src/test/java/com/cohort/array/ByteArrayTests.java new file mode 100644 index 000000000..2fad15b63 --- /dev/null +++ b/src/test/java/com/cohort/array/ByteArrayTests.java @@ -0,0 +1,454 @@ +package com.cohort.array; + +import com.cohort.util.*; + +import java.util.BitSet; + +class ByteArrayTests { + @org.junit.jupiter.api.Test + /** + * This tests the methods of this class. + * + * @throws Throwable if trouble. + */ + void basicTest() throws Throwable { + String2.log("*** ByteArray.basicTest"); + + ByteArray anArray = ByteArray.fromCSV(" -128, -1, 0, 126, , 127, 200 "); + Test.ensureEqual(anArray.toString(), "-128, -1, 0, 126, 127, 127, 127", ""); + Test.ensureEqual(anArray.toNccsvAttString(), "-128b,-1b,0b,126b,127b,127b,127b", ""); + Test.ensureEqual(anArray.toNccsv127AttString(), "-128b,-1b,0b,126b,127b,127b,127b", ""); + + // ** test default constructor and many of the methods + anArray = new ByteArray(); + Test.ensureEqual(anArray.isIntegerType(), true, ""); + Test.ensureEqual(anArray.missingValue().getRawDouble(), Byte.MAX_VALUE, ""); + anArray.addString(""); + Test.ensureEqual(anArray.get(0), Byte.MAX_VALUE, ""); + Test.ensureEqual(anArray.getRawInt(0), Byte.MAX_VALUE, ""); + Test.ensureEqual(anArray.getRawDouble(0), Byte.MAX_VALUE, ""); + Test.ensureEqual(anArray.getUnsignedDouble(0), Byte.MAX_VALUE, ""); + Test.ensureEqual(anArray.getRawString(0), "" + Byte.MAX_VALUE, ""); + Test.ensureEqual(anArray.getRawNiceDouble(0), Byte.MAX_VALUE, ""); + Test.ensureEqual(anArray.getInt(0), Integer.MAX_VALUE, ""); + Test.ensureEqual(anArray.getDouble(0), Double.NaN, ""); + Test.ensureEqual(anArray.getString(0), "", ""); + Test.ensureEqual(anArray.toString(), "127", ""); + + anArray.set(0, (byte) -128); + Test.ensureEqual(anArray.getUnsignedDouble(0), 128, ""); + anArray.set(0, (byte) -127); + Test.ensureEqual(anArray.getUnsignedDouble(0), 129, ""); + anArray.set(0, (byte) -1); + Test.ensureEqual(anArray.getUnsignedDouble(0), 255, ""); + anArray.clear(); + + Test.ensureEqual(anArray.size(), 0, ""); + anArray.add((byte) 120); + Test.ensureEqual(anArray.size(), 1, ""); + Test.ensureEqual(anArray.get(0), 120, ""); + Test.ensureEqual(anArray.getInt(0), 120, ""); + Test.ensureEqual(anArray.getFloat(0), 120, ""); + Test.ensureEqual(anArray.getDouble(0), 120, ""); + Test.ensureEqual(anArray.getString(0), "120", ""); + Test.ensureEqual(anArray.elementType(), PAType.BYTE, ""); + byte tArray[] = anArray.toArray(); + Test.ensureEqual(tArray, new byte[] { (byte) 120 }, ""); + + // intentional errors + try { + anArray.get(1); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); + } + try { + anArray.set(1, (byte) 100); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); + } + try { + anArray.getInt(1); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); + } + try { + anArray.setInt(1, 100); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); + } + try { + anArray.getLong(1); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); + } + try { + anArray.setLong(1, 100); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); + } + try { + anArray.getFloat(1); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); + } + try { + anArray.setFloat(1, 100); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); + } + try { + anArray.getDouble(1); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); + } + try { + anArray.setDouble(1, 100); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); + } + try { + anArray.getString(1); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.get: index (1) >= size (1).", ""); + } + try { + anArray.setString(1, "100"); + throw new Throwable("It should have failed."); + } catch (Exception e) { + Test.ensureEqual(e.toString(), + "java.lang.IllegalArgumentException: ERROR in ByteArray.set: index (1) >= size (1).", ""); + } + + // set NaN returned as NaN + anArray.setDouble(0, Double.NaN); + Test.ensureEqual(anArray.getDouble(0), Double.NaN, ""); + anArray.setDouble(0, -1e300); + Test.ensureEqual(anArray.getDouble(0), Double.NaN, ""); + anArray.setDouble(0, 2.2); + Test.ensureEqual(anArray.getDouble(0), 2, ""); + anArray.setFloat(0, Float.NaN); + Test.ensureEqual(anArray.getFloat(0), Float.NaN, ""); + anArray.setFloat(0, -1e33f); + Test.ensureEqual(anArray.getFloat(0), Float.NaN, ""); + anArray.setFloat(0, 3.3f); + Test.ensureEqual(anArray.getFloat(0), 3, ""); + anArray.setLong(0, Long.MAX_VALUE); + Test.ensureEqual(anArray.getLong(0), Long.MAX_VALUE, ""); + anArray.setLong(0, 9123456789L); + Test.ensureEqual(anArray.getLong(0), Long.MAX_VALUE, ""); + anArray.setLong(0, 4); + Test.ensureEqual(anArray.getLong(0), 4, ""); + anArray.setInt(0, Integer.MAX_VALUE); + Test.ensureEqual(anArray.getInt(0), Integer.MAX_VALUE, ""); + anArray.setInt(0, 1123456789); + Test.ensureEqual(anArray.getInt(0), Integer.MAX_VALUE, ""); + anArray.setInt(0, 5); + Test.ensureEqual(anArray.getInt(0), 5, ""); + + // makeUnsignedPA + anArray = new ByteArray(new byte[] { -128, -2, -1, 0, 1, 126, 127 }); + UByteArray uArray = (UByteArray) anArray.makeUnsignedPA(); + Test.ensureEqual(uArray.toString(), "128, 254, 255, 0, 1, 126, 127", ""); // -1 -> mv + anArray.clear(); + + // ** test capacity constructor, test expansion, test clear + anArray = new ByteArray(2, false); + Test.ensureEqual(anArray.size(), 0, ""); + for (int i = 0; i < 10; i++) { + anArray.add((byte) i); + Test.ensureEqual(anArray.get(i), i, ""); + Test.ensureEqual(anArray.size(), i + 1, ""); + } + Test.ensureEqual(anArray.size(), 10, ""); + anArray.clear(); + Test.ensureEqual(anArray.size(), 0, ""); + + // active + anArray = new ByteArray(3, true); + Test.ensureEqual(anArray.size(), 3, ""); + Test.ensureEqual(anArray.get(2), 0, ""); + + // ** test array constructor + anArray = new ByteArray(new byte[] { 0, 2, 4, 6, 8 }); + Test.ensureEqual(anArray.size(), 5, ""); + Test.ensureEqual(anArray.get(0), 0, ""); + Test.ensureEqual(anArray.get(1), 2, ""); + Test.ensureEqual(anArray.get(2), 4, ""); + Test.ensureEqual(anArray.get(3), 6, ""); + Test.ensureEqual(anArray.get(4), 8, ""); + + // test compare + Test.ensureEqual(anArray.compare(1, 3), -1, ""); + Test.ensureEqual(anArray.compare(1, 1), 0, ""); + Test.ensureEqual(anArray.compare(3, 1), 1, ""); + + // test toString + Test.ensureEqual(anArray.toString(), "0, 2, 4, 6, 8", ""); + + // test calculateStats + anArray.addString(""); + double stats[] = anArray.calculateStats(); + anArray.remove(5); + Test.ensureEqual(stats[PrimitiveArray.STATS_N], 5, ""); + Test.ensureEqual(stats[PrimitiveArray.STATS_MIN], 0, ""); + Test.ensureEqual(stats[PrimitiveArray.STATS_MAX], 8, ""); + Test.ensureEqual(stats[PrimitiveArray.STATS_SUM], 20, ""); + + // test indexOf(int) indexOf(String) + Test.ensureEqual(anArray.indexOf((byte) 0, 0), 0, ""); + Test.ensureEqual(anArray.indexOf((byte) 0, 1), -1, ""); + Test.ensureEqual(anArray.indexOf((byte) 8, 0), 4, ""); + Test.ensureEqual(anArray.indexOf((byte) 9, 0), -1, ""); + + Test.ensureEqual(anArray.indexOf("0", 0), 0, ""); + Test.ensureEqual(anArray.indexOf("0", 1), -1, ""); + Test.ensureEqual(anArray.indexOf("8", 0), 4, ""); + Test.ensureEqual(anArray.indexOf("9", 0), -1, ""); + + // test remove + anArray.remove(1); + Test.ensureEqual(anArray.size(), 4, ""); + Test.ensureEqual(anArray.get(0), 0, ""); + Test.ensureEqual(anArray.get(1), 4, ""); + Test.ensureEqual(anArray.get(3), 8, ""); + + // test atInsert(index, value) + anArray.atInsert(1, (byte) 22); + Test.ensureEqual(anArray.size(), 5, ""); + Test.ensureEqual(anArray.get(0), 0, ""); + Test.ensureEqual(anArray.get(1), 22, ""); + Test.ensureEqual(anArray.get(2), 4, ""); + Test.ensureEqual(anArray.get(4), 8, ""); + anArray.remove(1); + + // test removeRange + anArray.removeRange(4, 4); // make sure it is allowed + anArray.removeRange(1, 3); + Test.ensureEqual(anArray.size(), 2, ""); + Test.ensureEqual(anArray.get(0), 0, ""); + Test.ensureEqual(anArray.get(1), 8, ""); + + // test (before trimToSize) that toString, toDoubleArray, and toStringArray use + // 'size' + Test.ensureEqual(anArray.toString(), "0, 8", ""); + Test.ensureEqual(anArray.toDoubleArray(), new double[] { 0, 8 }, ""); + Test.ensureEqual(anArray.toStringArray(), new String[] { "0", "8" }, ""); + + // test trimToSize + anArray.trimToSize(); + Test.ensureEqual(anArray.array.length, 2, ""); + + // test equals + ByteArray anArray2 = new ByteArray(); + anArray2.add((byte) 0); + Test.ensureEqual(anArray.testEquals(null), + "The two objects aren't equal: this object is a ByteArray; the other is a null.", ""); + Test.ensureEqual(anArray.testEquals("A String"), + "The two objects aren't equal: this object is a ByteArray; the other is a java.lang.String.", ""); + Test.ensureEqual(anArray.testEquals(anArray2), + "The two ByteArrays aren't equal: one has 2 value(s); the other has 1 value(s).", ""); + Test.ensureTrue(!anArray.equals(anArray2), ""); + anArray2.addString("7"); + Test.ensureEqual(anArray.testEquals(anArray2), + "The two ByteArrays aren't equal: this[1]=8; other[1]=7.", ""); + Test.ensureTrue(!anArray.equals(anArray2), ""); + anArray2.setString(1, "8"); + Test.ensureEqual(anArray.testEquals(anArray2), "", ""); + Test.ensureTrue(anArray.equals(anArray2), ""); + + // test toObjectArray + Test.ensureEqual(anArray.toArray(), anArray.toObjectArray(), ""); + + // test toDoubleArray + Test.ensureEqual(anArray.toDoubleArray(), new double[] { 0, 8 }, ""); + + // test reorder + int rank[] = { 1, 0 }; + anArray.reorder(rank); + Test.ensureEqual(anArray.toDoubleArray(), new double[] { 8, 0 }, ""); + + // ** test append and clone + anArray = new ByteArray(new byte[] { 1 }); + anArray.append(new ByteArray(new byte[] { 5, -5 })); + Test.ensureEqual(anArray.toDoubleArray(), new double[] { 1, 5, -5 }, ""); + anArray.append(new StringArray(new String[] { "a", "9" })); + Test.ensureEqual(anArray.getMaxIsMV(), true, ""); + Test.ensureEqual(anArray.toString(), "1, 5, -5, 127, 9", ""); // toString shows numbers as is, regardless of + // maxIsMV + Test.ensureEqual(anArray.toDoubleArray(), new double[] { 1, 5, -5, Double.NaN, 9 }, ""); + anArray2 = (ByteArray) anArray.clone(); + Test.ensureEqual(anArray2.toDoubleArray(), new double[] { 1, 5, -5, Double.NaN, 9 }, ""); + + // test move + anArray = new ByteArray(new byte[] { 0, 1, 2, 3, 4 }); + anArray.move(1, 3, 0); + Test.ensureEqual(anArray.toArray(), new byte[] { 1, 2, 0, 3, 4 }, ""); + + anArray = new ByteArray(new byte[] { 0, 1, 2, 3, 4 }); + anArray.move(1, 2, 4); + Test.ensureEqual(anArray.toArray(), new byte[] { 0, 2, 3, 1, 4 }, ""); + + // move does nothing, but is allowed + anArray = new ByteArray(new byte[] { 0, 1, 2, 3, 4 }); + anArray.move(1, 1, 0); + Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); + anArray.move(1, 2, 1); + Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); + anArray.move(1, 2, 2); + Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); + anArray.move(5, 5, 0); + Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); + anArray.move(3, 5, 5); + Test.ensureEqual(anArray.toArray(), new byte[] { 0, 1, 2, 3, 4 }, ""); + + // makeIndices + anArray = new ByteArray(new byte[] { 25, 1, 1, 10 }); + IntArray indices = new IntArray(); + Test.ensureEqual(anArray.makeIndices(indices).toString(), "1, 10, 25", ""); + Test.ensureEqual(indices.toString(), "2, 0, 0, 1", ""); + + anArray = new ByteArray(new byte[] { 35, 35, Byte.MAX_VALUE, 1, 2 }); + indices = new IntArray(); + Test.ensureEqual(anArray.makeIndices(indices).toString(), "1, 2, 35, 127", ""); + Test.ensureEqual(indices.toString(), "2, 2, 3, 0, 1", ""); + + anArray = new ByteArray(new byte[] { 10, 20, 30, 40 }); + Test.ensureEqual(anArray.makeIndices(indices).toString(), "10, 20, 30, 40", ""); + Test.ensureEqual(indices.toString(), "0, 1, 2, 3", ""); + + // switchToFakeMissingValue + anArray = new ByteArray(new byte[] { Byte.MAX_VALUE, 1, 2, Byte.MAX_VALUE, 3, Byte.MAX_VALUE }); + Test.ensureEqual(anArray.switchFromTo("", "75"), 3, ""); + Test.ensureEqual(anArray.toString(), "75, 1, 2, 75, 3, 75", ""); + anArray.switchFromTo("75", ""); + Test.ensureEqual(anArray.toString(), "127, 1, 2, 127, 3, 127", ""); + Test.ensureEqual(anArray.getNMinMaxIndex(), new int[] { 3, 1, 4 }, ""); + + // addN + anArray = new ByteArray(new byte[] { 25 }); + anArray.addN(2, (byte) 5); + Test.ensureEqual(anArray.toString(), "25, 5, 5", ""); + Test.ensureEqual(anArray.getNMinMaxIndex(), new int[] { 3, 2, 0 }, ""); + + // add array + anArray.add(new byte[] { 17, 19 }); + Test.ensureEqual(anArray.toString(), "25, 5, 5, 17, 19", ""); + + // subset + PrimitiveArray ss = anArray.subset(1, 3, 4); + Test.ensureEqual(ss.toString(), "5, 19", ""); + ss = anArray.subset(0, 1, 0); + Test.ensureEqual(ss.toString(), "25", ""); + ss = anArray.subset(0, 1, -1); + Test.ensureEqual(ss.toString(), "", ""); + ss = anArray.subset(1, 1, 0); + Test.ensureEqual(ss.toString(), "", ""); + + ss.trimToSize(); + anArray.subset(ss, 1, 3, 4); + Test.ensureEqual(ss.toString(), "5, 19", ""); + anArray.subset(ss, 0, 1, 0); + Test.ensureEqual(ss.toString(), "25", ""); + anArray.subset(ss, 0, 1, -1); + Test.ensureEqual(ss.toString(), "", ""); + anArray.subset(ss, 1, 1, 0); + Test.ensureEqual(ss.toString(), "", ""); + + // evenlySpaced + anArray = new ByteArray(new byte[] { 10, 20, 30 }); + Test.ensureEqual(anArray.isEvenlySpaced(), "", ""); + anArray.set(2, (byte) 31); + Test.ensureEqual(anArray.isEvenlySpaced(), + "ByteArray isn't evenly spaced: [0]=10.0, [1]=20.0, spacing=10.0, expected spacing=10.5.", ""); + Test.ensureEqual(anArray.smallestBiggestSpacing(), + " smallest spacing=10.0: [0]=10.0, [1]=20.0\n" + + " biggest spacing=11.0: [1]=20.0, [2]=31.0", + ""); + + // isAscending + anArray = new ByteArray(new byte[] { 10, 10, 30 }); + Test.ensureEqual(anArray.isAscending(), "", ""); + anArray.set(2, Byte.MAX_VALUE); + Test.ensureEqual(anArray.isAscending(), "", ""); + anArray.setMaxIsMV(true); + Test.ensureEqual(anArray.isAscending(), + "ByteArray isn't sorted in ascending order: [2]=(missing value).", ""); + anArray.set(1, (byte) 9); + Test.ensureEqual(anArray.isAscending(), + "ByteArray isn't sorted in ascending order: [0]=10 > [1]=9.", ""); + + // isDescending + anArray = new ByteArray(new byte[] { 30, 10, 10 }); + Test.ensureEqual(anArray.isDescending(), "", ""); + anArray.set(2, Byte.MAX_VALUE); + anArray.setMaxIsMV(true); + Test.ensureEqual(anArray.isDescending(), + "ByteArray isn't sorted in descending order: [1]=10 < [2]=127.", ""); + anArray.set(1, (byte) 35); + Test.ensureEqual(anArray.isDescending(), + "ByteArray isn't sorted in descending order: [0]=30 < [1]=35.", ""); + + // firstTie + anArray = new ByteArray(new byte[] { 30, 35, 10 }); + Test.ensureEqual(anArray.firstTie(), -1, ""); + anArray.set(1, (byte) 30); + Test.ensureEqual(anArray.firstTie(), 0, ""); + + // hashcode + anArray = new ByteArray(); + for (int i = 5; i < 1000; i++) + anArray.add((byte) i); + String2.log("hashcode1=" + anArray.hashCode()); + anArray2 = (ByteArray) anArray.clone(); + Test.ensureEqual(anArray.hashCode(), anArray2.hashCode(), ""); + anArray.atInsert(0, (byte) 2); + Test.ensureTrue(anArray.hashCode() != anArray2.hashCode(), ""); + + // justKeep + BitSet bitset = new BitSet(); + anArray = new ByteArray(new byte[] { 0, 11, 22, 33, 44 }); + bitset.set(1); + bitset.set(4); + anArray.justKeep(bitset); + Test.ensureEqual(anArray.toString(), "11, 44", ""); + + // min max + anArray = new ByteArray(); + anArray.addPAOne(anArray.MINEST_VALUE()); + anArray.addPAOne(anArray.MAXEST_VALUE()); + Test.ensureEqual(anArray.getString(0), anArray.MINEST_VALUE().toString(), ""); + Test.ensureEqual(anArray.getString(0), "-128", ""); + Test.ensureEqual(anArray.getString(1), anArray.MAXEST_VALUE().toString(), ""); + Test.ensureEqual(anArray.getString(1), "126", ""); + + // tryToFindNumericMissingValue() + Test.ensureEqual((new ByteArray(new byte[] {})).tryToFindNumericMissingValue(), null, ""); + Test.ensureEqual((new ByteArray(new byte[] { 1, 2 })).tryToFindNumericMissingValue(), null, ""); + Test.ensureEqual((new ByteArray(new byte[] { -128 })).tryToFindNumericMissingValue(), -128, ""); + Test.ensureEqual((new ByteArray(new byte[] { 127 })).tryToFindNumericMissingValue(), 127, ""); + Test.ensureEqual((new ByteArray(new byte[] { 1, 99 })).tryToFindNumericMissingValue(), 99, ""); + + } +} diff --git a/src/test/java/com/cohort/util/HashDigestTests.java b/src/test/java/com/cohort/util/HashDigestTests.java new file mode 100644 index 000000000..f0c21ad04 --- /dev/null +++ b/src/test/java/com/cohort/util/HashDigestTests.java @@ -0,0 +1,31 @@ +package com.cohort.util; + +class HashDigestTests { + @org.junit.jupiter.api.Test + /** + * This tests this class. + */ + void basicTest() throws Throwable { + System.out.println("*** HashDigest.basicTest"); + String tName = HashDigestTests.class.getResource("LICENSE.txt").getPath(); + Test.ensureEqual(HashDigest.doIt(new String[] { "type:MD5" }), + "Neither password or filename was specified.\n" + HashDigest.usage, ""); + Test.ensureEqual(HashDigest.doIt(new String[] { "password:myPassword", "type:MD-5" }), + "Invalid algorithm.\n" + HashDigest.usage, ""); + Test.ensureEqual(HashDigest.doIt(new String[] { "password:myPassword", "type:MD5" }), + "deb1536f480475f7d593219aa1afd74c", ""); + Test.ensureEqual(HashDigest.doIt(new String[] { "password:myPassword", "type:SHA-1" }), + "5413ee24723bba2c5a6ba2d0196c78b3ee4628d1", ""); + Test.ensureEqual(HashDigest.doIt(new String[] { "password:myPassword", "type:SHA-256" }), + "76549b827ec46e705fd03831813fa52172338f0dfcbd711ed44b81a96dac51c6", ""); + Test.ensureEqual(HashDigest.doIt(new String[] { "filename:" + tName, "type:MD5" }), + "96e9b4d974b734874a66f433b276a41a", ""); + Test.ensureEqual(HashDigest.doIt(new String[] { "filename:" + tName, "type:SHA-256" }), + "f6afea3f5fa69c8e54b14b3fdb86a9aa261a423cea957c9c87b55b92441d56bb", ""); + Test.ensureEqual(HashDigest.doIt(new String[] { "filename:" + tName, "type:SHA-256", "-file" }), + "Created " + tName + ".sha256", ""); + Test.ensureEqual(File2.readFromFileUtf8(tName + ".sha256")[1], + "f6afea3f5fa69c8e54b14b3fdb86a9aa261a423cea957c9c87b55b92441d56bb LICENSE.txt\n", ""); + File2.delete(tName + ".sha256"); + } +} diff --git a/src/test/java/com/cohort/util/Image2Tests.java b/src/test/java/com/cohort/util/Image2Tests.java new file mode 100644 index 000000000..8fcd89c99 --- /dev/null +++ b/src/test/java/com/cohort/util/Image2Tests.java @@ -0,0 +1,90 @@ +package com.cohort.util; + +import java.awt.Color; +import java.awt.Graphics; +import java.awt.Image; +import java.awt.image.BufferedImage; +import java.io.File; +import java.nio.file.Path; + +import javax.imageio.ImageIO; + +import org.junit.jupiter.api.io.TempDir; + +class Image2Tests { + + @TempDir + private static Path TEMP_DIR; + + @org.junit.jupiter.api.Test + /** + * This intentionally throws an Exception to test testImagesIdentical(). + */ + void testTestImagesIdentical() throws Exception { + String2.log("\n*** Image2.testTestImagesIdentical"); + + // test images which are identical + String testDir = Image2Tests.class.getResource("/images/").getPath(); + String tempDir = TEMP_DIR.toAbsolutePath().toString(); + Image2.testImagesIdentical( + testDir + "/testImagesIdentical_1.png", + testDir + "/testImagesIdentical_1.png", + tempDir + "/testImagesIdentical_diff.png"); + + // test images which aren't identical + try { + + // one time: createImage with transparent background + // BufferedImage image2 = Image2.getImage(testDir + "testImagesIdentical_1.png", + // 2000, false); + // image2 = Image2.makeImageBackgroundTransparent(image2, Color.white, 10000); + // Image2.saveAsPng(image2, testDir + "testImagesIdentical_2.png"); + + // test images which aren't identical + Image2.testImagesIdentical( + testDir + "/testImagesIdentical_1.png", + testDir + "/testImagesIdentical_2.png", + tempDir + "/testImagesIdentical_diff.png"); + } catch (Exception e) { + return; + } + throw new RuntimeException("shouldn't get here"); + } + + @org.junit.jupiter.api.Test + /** + * Test the methods in Image2. + */ + void basicTest() throws Exception { + String2.log("\n*** Image2.basicTest"); + + String imageDir = Image2Tests.class.getResource("/images/").getPath(); + + // test ImageIO + BufferedImage bi = ImageIO.read(new File(imageDir + "testmap.gif")); + Graphics g = bi.getGraphics(); + ImageIO.write(bi, "png", new File(imageDir + "temp.png")); + Image2.saveAsGif(bi, imageDir + "temp.gif"); + + long localTime = System.currentTimeMillis(); + String2.log("test() here 1"); + Color gray = new Color(128, 128, 128); + String2.log("test() here 2=" + (System.currentTimeMillis() - localTime)); + Image image = Image2.getImage(imageDir + "temp.gif", + 10000, false); // javaShouldCache + String2.log("test() here 3=" + (System.currentTimeMillis() - localTime)); + + // convert 128,128,128 to transparent + image = Image2.makeImageBackgroundTransparent(image, gray, 10000); + String2.log("test() here 4=" + (System.currentTimeMillis() - localTime)); + + // save as gif again + Image2.saveAsGif(image, imageDir + "temp2.gif"); + String2.log("test() here 5=" + (System.currentTimeMillis() - localTime)); + + File2.delete(imageDir + "temp.png"); + File2.delete(imageDir + "temp.gif"); + File2.delete(imageDir + "temp2.gif"); + + } +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetAnomalyTests.java b/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetAnomalyTests.java new file mode 100644 index 000000000..638793e6a --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetAnomalyTests.java @@ -0,0 +1,112 @@ +package gov.noaa.pfel.coastwatch.griddata; + +import java.nio.file.Path; + +import org.junit.jupiter.api.io.TempDir; + +import com.cohort.util.File2; +import com.cohort.util.String2; +import com.cohort.util.Test; + +import tags.TagThredds; + +class GridDataSetAnomalyTests { + + @TempDir + private static Path TEMP_DIR; + + /** + * This tests this class. + */ + @org.junit.jupiter.api.Test + @TagThredds + void basicTest() throws Exception { + String2.log("\n*** GridDataSetAnomaly.basicTest NOTE: this requires data in C:/u00/data/QC/mday/grd/ "); + FileNameUtility.verbose = true; + FileNameUtility fnu = new FileNameUtility("gov.noaa.pfel.coastwatch.CWBrowser"); + Grid.verbose = true; + GridDataSet.verbose = true; + Opendap.verbose = true; + String dir = TEMP_DIR.toAbsolutePath().toString(); + File2.deleteAllFiles(dir); + + // make the regular, climatology and anomaly datasets + GridDataSet gridDataSet = new GridDataSetThredds(fnu, "TQSux10", + // was "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatQS/ux10/", + // //was :8081 + "https://thredds1.pfeg.noaa.gov/thredds/catalog/Satellite/aggregsatQS/ux10/", + "BlueWhiteRed", "Linear", "-10", "10", -1, "", null, null, "S", 1, 1, "", 1, 1); + GridDataSetCWLocalClimatology climatologyDataSet = new GridDataSetCWLocalClimatology( + fnu, "CQCux10", "c:/u00/data/", dir); + GridDataSetAnomaly anomalyDataSet = new GridDataSetAnomaly( + "AQSuxan", fnu, gridDataSet, climatologyDataSet, + "Wind Anomaly, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal", + "*", "1"); + + // get data from each dataset + String timePeriod = "1 month"; + String centeredTime = "2006-01-16 12:00:00"; + String climatologyCenteredTime = "0001-01-16 12:00:00"; + + Grid gdsGrid = gridDataSet.makeGrid(timePeriod, centeredTime, + -135, -135, 22, 51, 1, 29); + String2.log("\ngdsGrid lon(" + gdsGrid.lon.length + ")=" + String2.toCSSVString(gdsGrid.lon) + + "\n lat(" + gdsGrid.lat.length + ")=" + String2.toCSSVString(gdsGrid.lat) + + "\n data(" + gdsGrid.data.length + ")=" + String2.toCSSVString(gdsGrid.data)); + + Grid climatologyGrid = climatologyDataSet.makeGrid("monthly", climatologyCenteredTime, + -135, -135, 22, 51, 1, 29); + String2 + .log("\nclimatologyGrid lon(" + climatologyGrid.lon.length + ")=" + String2.toCSSVString(climatologyGrid.lon) + + "\n lat(" + climatologyGrid.lat.length + ")=" + String2.toCSSVString(climatologyGrid.lat) + + "\n data(" + climatologyGrid.data.length + ")=" + String2.toCSSVString(climatologyGrid.data)); + + Grid anomalyGrid = anomalyDataSet.makeGrid(timePeriod, centeredTime, + -135, -135, 22, 51, 1, 29); + String2.log("\nanomalyGrid lon(" + anomalyGrid.lon.length + ")=" + String2.toCSSVString(anomalyGrid.lon) + + "\n lat(" + anomalyGrid.lat.length + ")=" + String2.toCSSVString(anomalyGrid.lat) + + "\n data(" + anomalyGrid.data.length + ")=" + String2.toCSSVString(anomalyGrid.data)); + + Test.ensureEqual(anomalyGrid.lon.length, 1, ""); + Test.ensureEqual(anomalyGrid.lon[0], -135, ""); + Test.ensureEqual(gdsGrid.lon, anomalyGrid.lon, ""); + Test.ensureEqual(climatologyGrid.lon, anomalyGrid.lon, ""); + + Test.ensureEqual(anomalyGrid.lat.length, 30, ""); + Test.ensureEqual(anomalyGrid.lat[0], 22, ""); + Test.ensureEqual(anomalyGrid.lat[29], 51, ""); + Test.ensureEqual(gdsGrid.lat, anomalyGrid.lat, ""); + Test.ensureEqual(climatologyGrid.lat, anomalyGrid.lat, ""); + + for (int i = 0; i < 29; i++) { + // I had some problems, so as additional test, + // get the climatology points 1 by 1 (which avoids possible stride-related + // problems) + // and ensure they match + Grid cGrid1 = climatologyDataSet.makeGrid("monthly", climatologyCenteredTime, + -135, -135, 22 + i, 22 + i, 1, 1); + Test.ensureEqual(climatologyGrid.data[i], cGrid1.data[0], "i=" + i); + } + + for (int i = 0; i < 29; i++) { + String2.log("data[" + i + "] gds=" + gdsGrid.data[i] + + " cli=" + climatologyGrid.data[i] + " ano=" + anomalyGrid.data[i]); + Test.ensureEqual((float) (gdsGrid.data[i] - climatologyGrid.data[i]), (float) anomalyGrid.data[i], "i=" + i); + } + + /* + * data[0] gds=-6.918294429779053 cli=-6.036570072174072 ano=-0.8817243576049805 + * data[28] gds=3.990844964981079 cli=1.5286099910736084 ano=2.4622349739074707 + */ + + Test.ensureEqual(gdsGrid.data[0], -6.918294429779053, ""); + Test.ensureEqual(climatologyGrid.data[0], -6.036570072174072, ""); + Test.ensureEqual(anomalyGrid.data[0], -0.8817243576049805, ""); + + Test.ensureEqual(gdsGrid.data[28], 3.990844964981079, ""); + Test.ensureEqual(climatologyGrid.data[28], 1.5286099910736084, ""); + Test.ensureEqual(anomalyGrid.data[28], 2.4622349739074707, ""); + + } + +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetOpenDataTests.java b/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetOpenDataTests.java new file mode 100644 index 000000000..ec17f28bb --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetOpenDataTests.java @@ -0,0 +1,389 @@ +package gov.noaa.pfel.coastwatch.griddata; + +import java.nio.file.Path; + +import org.junit.jupiter.api.io.TempDir; + +import com.cohort.array.DoubleArray; +import com.cohort.array.FloatArray; +import com.cohort.array.IntArray; +import com.cohort.array.PrimitiveArray; +import com.cohort.array.StringArray; +import com.cohort.util.Calendar2; +import com.cohort.util.File2; +import com.cohort.util.String2; +import com.cohort.util.Test; + +import gov.noaa.pfel.coastwatch.pointdata.Table; +import tags.TagThredds; + +class GridDataSetOpenDataTests { + + @TempDir + private static Path TEMP_DIR; + + /** + * This does a test of getTimeSeries using a data set on West Coast + * cwexperimental. + */ + @org.junit.jupiter.api.Test + @TagThredds + void testGetTimeSeries() throws Exception { + String2.log("\n*** start TestBrowsers.testGetTimeSeries"); + String url = "https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/GA/ssta/"; // oceanwatch + + DataHelper.verbose = true; + GridDataSetOpendap.verbose = true; + + String tempDir = TEMP_DIR.toAbsolutePath().toString(); + Table table = null; + + GridDataSetOpendap gdst = new GridDataSetOpendap( + "OGAssta", "GAssta", null, url, + new String[] { "hday", "1day", "3day", "5day", "8day", "14day", "mday" }, + new int[] { 0, 24, 3 * 24, 5 * 24, 8 * 24, 14 * 24, 30 * 24, }, + "Rainbow", "Linear", "8", "32", -1, "", null, // fgdc, + null, + "S", 1.8, 32, "degree_F", 45, 90); + + // *** test the GridDataSetOpendap version of getTimeSeries + // test individual makeGrid to get the values tested below in getTimeSeries + double rLon = -128.975; + double rLat = 36.025; + + Grid grid = gdst.makeGrid("1 day", + "2007-12-01 12:00:00", + rLon, rLon, rLat, rLat, 1, 1); + Test.ensureEqual(grid.lon[0], rLon, ""); + Test.ensureEqual(grid.lat[0], rLat, ""); + Test.ensureEqual((float) grid.data[0], 16.35f, ""); + + grid = gdst.makeGrid("1 day", + "2007-12-02 12:00:00", + rLon, rLon, rLat, rLat, 1, 1); + Test.ensureEqual(grid.lon[0], rLon, ""); + Test.ensureEqual(grid.lat[0], rLat, ""); + Test.ensureEqual((float) grid.data[0], 16.05f, ""); + + // first just test if it gets correct answers + table = gdst.getTimeSeries(tempDir, rLon, rLat, + "2007-12-01 12:00:00", "2007-12-20 12:00:00", "1 day"); + // String2.log("timeSeriesTable=" + table); + Test.ensureEqual(table.nRows(), 20, ""); + Test.ensureEqual(table.nColumns(), 6, ""); + Test.ensureEqual(table.getColumnName(0), "LON", ""); + Test.ensureEqual(table.getColumnName(1), "LAT", ""); + Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); + Test.ensureEqual(table.getColumnName(3), "TIME", ""); + Test.ensureEqual(table.getColumnName(4), "ID", ""); + Test.ensureEqual(table.getColumnName(5), "OGAssta", ""); + + Test.ensureEqual(table.getColumn(0).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(1).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(2).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(3).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(4).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(5).elementTypeString(), "float", ""); + + Test.ensureEqual(table.getDoubleData(0, 0), rLon, ""); + Test.ensureEqual(table.getDoubleData(1, 0), rLat, ""); + Test.ensureEqual(table.getDoubleData(2, 0), 0, ""); + Test.ensureEqual(table.getDoubleData(3, 0), Calendar2.isoStringToEpochSeconds("2007-12-01 12:00:00"), ""); + Test.ensureEqual(table.getStringData(4, 0), "OGAssta", ""); + Test.ensureEqual(table.getFloatData(5, 0), 16.35f, ""); + + Test.ensureEqual(table.getDoubleData(0, 1), rLon, ""); + Test.ensureEqual(table.getDoubleData(1, 1), rLat, ""); + Test.ensureEqual(table.getDoubleData(2, 1), 0, ""); + Test.ensureEqual(table.getDoubleData(3, 1), Calendar2.isoStringToEpochSeconds("2007-12-02 12:00:00"), ""); + Test.ensureEqual(table.getStringData(4, 1), "OGAssta", ""); + Test.ensureEqual(table.getFloatData(5, 1), 16.05f, ""); + + // HARDER TEST: data for all time does it crash? 35s first run, then 12s + // for (int i = 30; i <= 36; i++) + // table = gdst.getTimeSeries(tempDir, rLon, i, + // "1980-01-01", "2099-12-31", gdst.activeTimePeriodOptions[0]); + + // *** test the GridDataSet (superclass) version of getTimeSeries + // this is the only test of superclass' getTimeSeries + table = null; + table = gdst.getSuperTimeSeries(tempDir, rLon, rLat, + "2007-12-01 12:00:00", "2007-12-20 12:00:00", "1 day"); + // String2.log("super timeSeriesTable=" + table); + Test.ensureEqual(table.nRows(), 20, ""); + Test.ensureEqual(table.nColumns(), 6, ""); + Test.ensureEqual(table.getColumnName(0), "LON", ""); + Test.ensureEqual(table.getColumnName(1), "LAT", ""); + Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); + Test.ensureEqual(table.getColumnName(3), "TIME", ""); + Test.ensureEqual(table.getColumnName(4), "ID", ""); + Test.ensureEqual(table.getColumnName(5), "OGAssta", ""); + + Test.ensureEqual(table.getDoubleData(0, 0), rLon, ""); + Test.ensureEqual(table.getDoubleData(1, 0), rLat, ""); + Test.ensureEqual(table.getDoubleData(2, 0), 0, ""); + Test.ensureEqual(table.getDoubleData(3, 0), Calendar2.isoStringToEpochSeconds("2007-12-01 12:00:00"), ""); + Test.ensureEqual(table.getStringData(4, 0), "OGAssta", ""); + Test.ensureEqual(table.getFloatData(5, 0), 16.35f, ""); + + Test.ensureEqual(table.getDoubleData(0, 1), rLon, ""); + Test.ensureEqual(table.getDoubleData(1, 1), rLat, ""); + Test.ensureEqual(table.getDoubleData(2, 1), 0, ""); + Test.ensureEqual(table.getDoubleData(3, 1), Calendar2.isoStringToEpochSeconds("2007-12-02 12:00:00"), ""); + Test.ensureEqual(table.getStringData(4, 1), "OGAssta", ""); + Test.ensureEqual(table.getFloatData(5, 1), 16.05f, ""); + + // *** test of centering time periods + // test individual makeGrid to get the values tested below in getTimeSeries + grid = gdst.makeGrid("3 day", "2006-08-13 12:00:00", // centered time + -130.02, -130.02, 36.02, 36.02, // close, not exact + 1, 1); + Test.ensureEqual(grid.lon[0], -130.025, ""); // 3 day grid is offset by .025!! + Test.ensureEqual(grid.lat[0], 36.025, ""); + Test.ensureEqual((float) grid.data[0], 19.8f, ""); + + grid = gdst.makeGrid("3 day", "2006-08-08 12:00:00", // centered time + -130.02, -130.02, 36.02, 36.02, + 1, 1); + Test.ensureEqual(grid.lon[0], -130.025, ""); + Test.ensureEqual(grid.lat[0], 36.025, ""); + Test.ensureEqual((float) grid.data[0], 18.75f, ""); + + // first just test if it gets correct answers + table = gdst.getTimeSeries(tempDir, -130.02, 36.02, + "2006-08-08", "2006-08-14", // begin and end centered times + "3 day"); + // String2.log("timeSeriesTable=" + table); + PrimitiveArray timePA = table.getColumn(3); + PrimitiveArray dataPA = table.getColumn(5); + + // find the row corresponding to the desired time + double seconds = Calendar2.isoStringToEpochSeconds("2006-08-13 12:00:00"); // centered time + int row = timePA.binaryFindClosest(seconds); + Test.ensureEqual(timePA.getDouble(row), seconds, ""); // ensure exact match 2006-08-13T23:59:59 + Test.ensureEqual(dataPA.getFloat(row), 19.8f, ""); + + seconds = Calendar2.isoStringToEpochSeconds("2006-08-08 12:00:00"); // centered time + row = timePA.binaryFindClosest(seconds); + Test.ensureEqual(timePA.getDouble(row), seconds, ""); // ensure exact match + Test.ensureEqual(dataPA.getFloat(row), 18.75f, ""); + } + + /** + * This performs a simple test of this class. + */ + @org.junit.jupiter.api.Test + @TagThredds + void basicTest() throws Exception { + // FileNameUtility.verbose = true; + // FileNameUtility fnu = new + // FileNameUtility("gov.noaa.pfel.coastwatch.CWBrowser"); + + String2.log("\n*** GridDataSetOpendap.basicTest"); + GridDataSetOpendap gridDataSet; + + // variables + String internalName, sixName; + GridDataSetOpendap.verbose = true; + Opendap.verbose = true; + String dir = File2.getClassPath() + // with / separator and / at the end + "gov/noaa/pfel/coastwatch/griddata/"; + + // ********************************************************************* + internalName = "OQSux10"; + sixName = internalName.substring(1); + String url = "https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/QS/ux10/"; // oceanwatch + gridDataSet = new GridDataSetOpendap( + internalName, "QSux10", null, url, + new String[] { "1day", "3day", "4day", "8day", "14day", "mday" }, + new int[] { 24, 3 * 24, 4 * 24, 8 * 24, 14 * 24, 30 * 24 }, + "BlueWhiteRed", "Linear", "-10", "10", -1, "", null, null, "S", 1, 0, "", 1, 1); + + Grid grid = gridDataSet.makeGrid( + "1 day", "2006-06-10 12:00:00", -135, -105, 22, 50, 300, 300); + + // set attributes + String fileName = "TQSux10S1day_20060610_x-135_X-105_y22_Y50"; + gridDataSet.setAttributes(grid, fileName); + grid.setStatsAttributes(false); // false -> floats + + // see if it has the expected values + int nLat = grid.lat.length; + int nLon = grid.lon.length; + Test.ensureEqual(grid.globalAttributes().get("Conventions"), + new StringArray(new String[] { "COARDS, CF-1.6, ACDD-1.3, CWHDF" }), "Conventions"); + Test.ensureEqual(grid.globalAttributes().get("title"), + new StringArray(new String[] { "Wind, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal" }), + "title"); + Test.ensureEqual(grid.globalAttributes().get("summary"), new StringArray(new String[] { + "Remote Sensing Inc. distributes science quality wind velocity data from the SeaWinds instrument onboard NASA's QuikSCAT satellite. SeaWinds is a microwave scatterometer designed to measure surface winds over the global ocean. Wind velocity fields are provided in zonal, meridional, and modulus sets. The reference height for all wind velocities is 10 meters." }), + "summary"); + Test.ensureEqual(grid.globalAttributes().get("keywords"), + new StringArray(new String[] { "EARTH SCIENCE > Oceans > Ocean Winds > Surface Winds" }), "keywords"); + // !!!! thredds id differs from opendap at first letter + Test.ensureEqual(grid.globalAttributes().get("id"), new StringArray(new String[] { "TQSux10S1day" }), "id"); + Test.ensureEqual(grid.globalAttributes().get("naming_authority"), + new StringArray(new String[] { "gov.noaa.pfeg.coastwatch" }), "naming_authority"); + Test.ensureEqual(grid.globalAttributes().get("keywords_vocabulary"), + new StringArray(new String[] { "GCMD Science Keywords" }), "keywords_vocabulary"); + Test.ensureEqual(grid.globalAttributes().get("cdm_data_type"), new StringArray(new String[] { "Grid" }), + "cdm_data_typ"); + Test.ensureTrue(grid.globalAttributes().getString("history").startsWith("Remote Sensing Systems, Inc."), + "history=" + grid.globalAttributes().getString("history")); + Test.ensureEqual(grid.globalAttributes().get("date_created"), + new StringArray(new String[] { Calendar2.formatAsISODate(Calendar2.newGCalendarZulu()) }), "date_created"); + Test.ensureEqual(grid.globalAttributes().get("creator_name"), + new StringArray(new String[] { "NOAA CoastWatch, West Coast Node" }), "creator_name"); + Test.ensureEqual(grid.globalAttributes().get("creator_url"), + new StringArray(new String[] { "http://coastwatch.pfel.noaa.gov" }), "creator_url"); + Test.ensureEqual(grid.globalAttributes().get("creator_email"), + new StringArray(new String[] { "dave.foley@noaa.gov" }), "creator_email"); + Test.ensureEqual(grid.globalAttributes().getString("institution"), "NOAA CoastWatch, West Coast Node", + "institution=" + grid.globalAttributes().getString("institution")); + Test.ensureEqual(grid.globalAttributes().get("project"), + new StringArray(new String[] { "CoastWatch (http://coastwatch.noaa.gov/)" }), "project"); + Test.ensureEqual(grid.globalAttributes().get("processing_level"), new StringArray(new String[] { "3" }), + "processing_level"); + Test.ensureEqual(grid.globalAttributes().get("acknowledgement"), + new StringArray(new String[] { "NOAA NESDIS COASTWATCH, NOAA SWFSC ERD" }), "acknowledgement"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_min"), new DoubleArray(new double[] { 22 }), + "geospatial_lat_min"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_max"), new DoubleArray(new double[] { 50 }), + "geospatial_lat_max"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_min"), new DoubleArray(new double[] { -135 }), + "geospatial_lon_min"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_max"), new DoubleArray(new double[] { -105 }), + "geospatial_lon_max"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_units"), + new StringArray(new String[] { "degrees_north" }), "geospatial_lat_units"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_resolution"), new DoubleArray(new double[] { 0.125 }), + "geospatial_lat_resolution"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_units"), + new StringArray(new String[] { "degrees_east" }), "geospatial_lon_units"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_resolution"), new DoubleArray(new double[] { 0.125 }), + "geospatial_lon_resolution"); + Test.ensureEqual(grid.globalAttributes().get("time_coverage_start"), + new StringArray(new String[] { "2006-06-10T00:00:00Z" }), "time_coverage_start"); + Test.ensureEqual(grid.globalAttributes().get("time_coverage_end"), + new StringArray(new String[] { "2006-06-11T00:00:00Z" }), "time_coverage_end"); + // Test.ensureEqual(grid.globalAttributes().get("time_coverage_resolution", new + // StringArray(new String[]{""}), "time_coverage_resolution"); + Test.ensureEqual(grid.globalAttributes().get("standard_name_vocabulary"), + new StringArray(new String[] { "CF Standard Name Table v70" }), "standard_name_vocabulary"); + Test.ensureEqual(grid.globalAttributes().get("license"), new StringArray(new String[] { + "The data may be used and redistributed for free but is not intended for legal use, since it may contain inaccuracies. Neither the data Contributor, CoastWatch, NOAA, nor the United States Government, nor any of their employees or contractors, makes any warranty, express or implied, including warranties of merchantability and fitness for a particular purpose, or assumes any legal liability for the accuracy, completeness, or usefulness, of this information." }), + "license"); + Test.ensureEqual(grid.globalAttributes().get("contributor_name"), + new StringArray(new String[] { "Remote Sensing Systems, Inc." }), "contributor_name"); + Test.ensureEqual(grid.globalAttributes().get("contributor_role"), + new StringArray(new String[] { "Source of level 2 data." }), "contributor_role"); + Test.ensureEqual(grid.globalAttributes().get("date_issued"), + new StringArray(new String[] { Calendar2.formatAsISODate(Calendar2.newGCalendarZulu()) }), "date_issued"); + Test.ensureEqual(grid.globalAttributes().get("references"), + new StringArray(new String[] { "RSS Inc. Winds: http://www.remss.com/ ." }), "references"); + Test.ensureEqual(grid.globalAttributes().get("source"), + new StringArray(new String[] { "satellite observation: QuikSCAT, SeaWinds" }), "source"); + // Google Earth + Test.ensureEqual(grid.globalAttributes().get("Southernmost_Northing"), new DoubleArray(new double[] { 22 }), + "southernmost"); + Test.ensureEqual(grid.globalAttributes().get("Northernmost_Northing"), new DoubleArray(new double[] { 50 }), + "northernmost"); + Test.ensureEqual(grid.globalAttributes().get("Westernmost_Easting"), new DoubleArray(new double[] { -135 }), + "westernmost"); + Test.ensureEqual(grid.globalAttributes().get("Easternmost_Easting"), new DoubleArray(new double[] { -105 }), + "easternmost"); + + // cwhdf attributes + Test.ensureEqual(grid.globalAttributes().get("cwhdf_version"), new StringArray(new String[] { "3.4" }), + "cwhdf_version"); // string + Test.ensureEqual(grid.globalAttributes().get("satellite"), new StringArray(new String[] { "QuikSCAT" }), + "satellite"); // string + Test.ensureEqual(grid.globalAttributes().get("sensor"), new StringArray(new String[] { "SeaWinds" }), "sensor"); // string + Test.ensureEqual(grid.globalAttributes().get("composite"), new StringArray(new String[] { "true" }), "composite"); // string + + Test.ensureEqual(grid.globalAttributes().get("pass_date"), new IntArray(new int[] { 13309 }), "pass_date"); // int32[nDays] + Test.ensureEqual(grid.globalAttributes().get("start_time"), new DoubleArray(new double[] { 0 }), "start_time"); // float64[nDays] + Test.ensureEqual(grid.globalAttributes().get("origin"), + new StringArray(new String[] { "Remote Sensing Systems, Inc." }), "origin"); // string + // Test.ensureEqual(grid.globalAttributes().get("history"), new StringArray(new + // String[]{"unknown"}), "history"); //string + + Test.ensureEqual(grid.globalAttributes().get("projection_type"), new StringArray(new String[] { "mapped" }), + "projection_type"); // string + Test.ensureEqual(grid.globalAttributes().get("projection"), new StringArray(new String[] { "geographic" }), + "projection"); // string + Test.ensureEqual(grid.globalAttributes().get("gctp_sys"), new IntArray(new int[] { 0 }), "gctp_sys"); // int32 + Test.ensureEqual(grid.globalAttributes().get("gctp_zone"), new IntArray(new int[] { 0 }), "gctp_zone"); // int32 + Test.ensureEqual(grid.globalAttributes().get("gctp_parm"), new DoubleArray(new double[15]), "gctp_parm"); // float64[15 + // 0's] + Test.ensureEqual(grid.globalAttributes().get("gctp_datum"), new IntArray(new int[] { 12 }), "gctp_datum");// int32 + // 12=WGS84 + + double matrix[] = { 0, -grid.latSpacing, grid.lonSpacing, 0, grid.lon[0], grid.lat[nLat - 1] }; // up side down + Test.ensureEqual(grid.globalAttributes().get("et_affine"), new DoubleArray(matrix), "et_affine"); // right side up + + Test.ensureEqual(grid.globalAttributes().get("rows"), new IntArray(new int[] { grid.lat.length }), "rows");// int32 + // number + // of + // rows + Test.ensureEqual(grid.globalAttributes().get("cols"), new IntArray(new int[] { grid.lon.length }), "cols");// int32 + // number + // of + // columns + Test.ensureEqual(grid.globalAttributes().get("polygon_latitude"), new DoubleArray(new double[] { + grid.lat[0], grid.lat[nLat - 1], grid.lat[nLat - 1], grid.lat[0], grid.lat[0] }), "polygon_latitude"); + Test.ensureEqual(grid.globalAttributes().get("polygon_longitude"), new DoubleArray(new double[] { + grid.lon[0], grid.lon[0], grid.lon[nLon - 1], grid.lon[nLon - 1], grid.lon[0] }), "polygon_longitude"); + + // lat attributes + Test.ensureEqual(grid.latAttributes().get("long_name"), new StringArray(new String[] { "Latitude" }), + "lat long_name"); + Test.ensureEqual(grid.latAttributes().get("standard_name"), new StringArray(new String[] { "latitude" }), + "lat standard_name"); + Test.ensureEqual(grid.latAttributes().get("units"), new StringArray(new String[] { "degrees_north" }), "lat units"); + Test.ensureEqual(grid.latAttributes().get("point_spacing"), new StringArray(new String[] { "even" }), + "lat point_spacing"); + Test.ensureEqual(grid.latAttributes().get("actual_range"), new DoubleArray(new double[] { 22, 50 }), + "lat actual_range"); + + // CWHDF metadata/attributes for Latitude + Test.ensureEqual(grid.latAttributes().get("coordsys"), new StringArray(new String[] { "geographic" }), "coordsys");// string + Test.ensureEqual(grid.latAttributes().get("fraction_digits"), new IntArray(new int[] { 2 }), "fraction_digits"); // int32 + + // lon attributes + Test.ensureEqual(grid.lonAttributes().get("long_name"), new StringArray(new String[] { "Longitude" }), + "lon long_name"); + Test.ensureEqual(grid.lonAttributes().get("standard_name"), new StringArray(new String[] { "longitude" }), + "lon standard_name"); + Test.ensureEqual(grid.lonAttributes().get("units"), new StringArray(new String[] { "degrees_east" }), "lon units"); + Test.ensureEqual(grid.lonAttributes().get("point_spacing"), new StringArray(new String[] { "even" }), + "lon point_spacing"); + Test.ensureEqual(grid.lonAttributes().get("actual_range"), new DoubleArray(new double[] { -135, -105 }), + "lon actual_range"); + + // CWHDF metadata/attributes for Longitude + Test.ensureEqual(grid.lonAttributes().get("coordsys"), new StringArray(new String[] { "geographic" }), "coordsys"); // string + Test.ensureEqual(grid.lonAttributes().get("fraction_digits"), new IntArray(new int[] { 2 }), "fraction_digits"); // int32 + + // data attributes it's 0.125 in DataSet.properties, but files need to be + // reprocessed to catch that + Test.ensureEqual(grid.dataAttributes().get("long_name"), + new StringArray(new String[] { "Wind, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal" }), + "data long_name"); + Test.ensureEqual(grid.dataAttributes().get("standard_name"), new StringArray(new String[] { "x_wind" }), + "data standard_name"); + Test.ensureEqual(grid.dataAttributes().get("units"), new StringArray(new String[] { "m s-1" }), "data units"); + Test.ensureEqual(grid.dataAttributes().get("_FillValue"), new FloatArray(new float[] { -9999999 }), + "data _FillValue"); + Test.ensureEqual(grid.dataAttributes().get("missing_value"), new FloatArray(new float[] { -9999999 }), + "data missing_value"); + Test.ensureEqual(grid.dataAttributes().get("numberOfObservations"), new IntArray(new int[] { 25021 }), + "data numberOfObservations"); + Test.ensureEqual(grid.dataAttributes().get("percentCoverage"), + new DoubleArray(new double[] { 0.46142923005993547 }), "data percentCoverage"); + + // CWHDF metadata/attributes for the data: varName + Test.ensureEqual(grid.dataAttributes().get("coordsys"), new StringArray(new String[] { "geographic" }), "coordsys"); // string + Test.ensureEqual(grid.dataAttributes().get("fraction_digits"), new IntArray(new int[] { 1 }), "fraction_digits"); // int32 + } +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetThreddsTests.java b/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetThreddsTests.java new file mode 100644 index 000000000..b0b958d7b --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/griddata/GridDataSetThreddsTests.java @@ -0,0 +1,465 @@ +package gov.noaa.pfel.coastwatch.griddata; + +import java.nio.file.Path; + +import org.junit.jupiter.api.io.TempDir; + +import com.cohort.array.DoubleArray; +import com.cohort.array.FloatArray; +import com.cohort.array.IntArray; +import com.cohort.array.PrimitiveArray; +import com.cohort.array.StringArray; +import com.cohort.util.Calendar2; +import com.cohort.util.File2; +import com.cohort.util.String2; +import com.cohort.util.Test; + +import gov.noaa.pfel.coastwatch.pointdata.Table; +import gov.noaa.pfel.coastwatch.util.SSR; +import tags.TagThredds; + +class GridDataSetThreddsTests { + + @TempDir + private static Path TEMP_DIR; + + /** + * This performs a simple test of this class. + */ + @org.junit.jupiter.api.Test + @TagThredds + void basicTest() throws Exception { + FileNameUtility.verbose = true; + FileNameUtility fnu = new FileNameUtility("gov.noaa.pfel.coastwatch.CWBrowser"); + +// String baseUrl = "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMO/k490/"; +// String2.log("getUrlString for " + baseUrl + "catalog.xml"); +// String2.log(SSR.getURLResponseStringUnchanged(baseUrl + "catalog.xml")); + +// Opendap opendap = new Opendap( +// //"https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMO/k490/hday", +// //"https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMO/k490/hday", +// "https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/MO/k490/hday.das", +// acceptDeflate); //throws Exception if trouble + +// public GridDataSetThredds(FileNameUtility fileNameUtility, String internalName, String baseUrl, +// String tPalette, String tPaletteScale, String tPaletteMin, String tPaletteMax, +// int tDaysTillDataAccessAllowed, String tAnomalyDataSet, String fgdc, +// String flagDirectory, +// String tDefaultUnits, double tAltScaleFactor, double tAltOffset, +// String tAltUnits, double tAltMin, double tAltMax) throws Exception { + + String2.log("\n*** GridDataSetThredds.basicTest"); + GridDataSetThredds gridDataSet; + + //variables + String internalName, sixName; + GridDataSetThredds.verbose = true; + Opendap.verbose = true; + String dir = File2.getClassPath() + //with / separator and / at the end + "gov/noaa/pfel/coastwatch/griddata/"; + + //**************************** + //ensure J1ugeo loads (it has 1 level: ) + /* //Comment out this line with /* to comment out this test. + //J1 datasets are no longer available as of March 2009 + internalName = "TJ1ugeo"; + sixName = internalName.substring(1); + gridDataSet = new GridDataSetThredds(fnu, internalName, + //was "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatJ1/ugeo/", //was :8081 + "https://thredds1.pfeg.noaa.gov/thredds/Satellite/aggregsatJ1/ugeo/", + "BlueWhiteRed", "Linear", "-10", "10", -1, "", null, null, + "S", 1, 0, "", 1, 1); + String2.log("TJ1ugeo activeTimePeriodOptions.length=" + gridDataSet.activeTimePeriodOptions.length); + Test.ensureNotEqual(gridDataSet.activeTimePeriodOptions.length, 0, + "TJ1ugeo activeTimePeriodOptions.length"); + /* */ + + //********************************************************************* + //large test of TQSux10 (it has 2 levels: ) + //Comment out this line with /* to comment out this test. + internalName = "TQSux10"; + sixName = internalName.substring(1); + gridDataSet = new GridDataSetThredds(fnu, internalName, + "https://thredds1.pfeg.noaa.gov/thredds/catalog/Satellite/aggregsatQS/ux10/", + "BlueWhiteRed", "Linear", "-10", "10", -1, "", null, null, "S", 1, 0, "", 1, 1); + + Grid grid = gridDataSet.makeGrid( + "1 day", "2006-06-10 12:00:00", -135, -105, 22, 50, 300, 300); + + //set attributes + String fileName = "TQSux10S1day_20060610_x-135_X-105_y22_Y50"; + gridDataSet.setAttributes(grid, fileName); + grid.setStatsAttributes(false); //false -> floats + + //see if it has the expected values + int nLat = grid.lat.length; + int nLon = grid.lon.length; + Test.ensureEqual(grid.globalAttributes().get("Conventions"), new StringArray(new String[]{"COARDS, CF-1.6, ACDD-1.3, CWHDF"}), "Conventions"); + Test.ensureEqual(grid.globalAttributes().get("title"), new StringArray(new String[]{"Wind, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal"}), "title"); + Test.ensureEqual(grid.globalAttributes().get("summary"), new StringArray(new String[]{"Remote Sensing Inc. distributes science quality wind velocity data from the SeaWinds instrument onboard NASA's QuikSCAT satellite. SeaWinds is a microwave scatterometer designed to measure surface winds over the global ocean. Wind velocity fields are provided in zonal, meridional, and modulus sets. The reference height for all wind velocities is 10 meters."}), "summary"); + Test.ensureEqual(grid.globalAttributes().get("keywords"), new StringArray(new String[]{"EARTH SCIENCE > Oceans > Ocean Winds > Surface Winds"}), "keywords"); + //!!!! thredds id differs from opendap at first letter + Test.ensureEqual(grid.globalAttributes().get("id"), new StringArray(new String[]{"TQSux10S1day"}), "id"); + Test.ensureEqual(grid.globalAttributes().get("naming_authority"), new StringArray(new String[]{"gov.noaa.pfeg.coastwatch"}), "naming_authority"); + Test.ensureEqual(grid.globalAttributes().get("keywords_vocabulary"), new StringArray(new String[]{"GCMD Science Keywords"}), "keywords_vocabulary"); + Test.ensureEqual(grid.globalAttributes().get("cdm_data_type"), new StringArray(new String[]{"Grid"}), "cdm_data_typ"); + Test.ensureTrue(grid.globalAttributes().getString("history").startsWith("Remote Sensing Systems, Inc."), "history=" + grid.globalAttributes().getString("history")); + Test.ensureEqual(grid.globalAttributes().get("date_created"), new StringArray(new String[]{Calendar2.formatAsISODate(Calendar2.newGCalendarZulu())}), "date_created"); + Test.ensureEqual(grid.globalAttributes().get("creator_name"), new StringArray(new String[]{"NOAA CoastWatch, West Coast Node"}), "creator_name"); + Test.ensureEqual(grid.globalAttributes().get("creator_url"), new StringArray(new String[]{"http://coastwatch.pfel.noaa.gov"}), "creator_url"); + Test.ensureEqual(grid.globalAttributes().get("creator_email"), new StringArray(new String[]{"dave.foley@noaa.gov"}), "creator_email"); + Test.ensureEqual(grid.globalAttributes().getString("institution"), "NOAA CoastWatch, West Coast Node", "institution=" + grid.globalAttributes().getString("institution")); + Test.ensureEqual(grid.globalAttributes().get("project"), new StringArray(new String[]{"CoastWatch (http://coastwatch.noaa.gov/)"}), "project"); + Test.ensureEqual(grid.globalAttributes().get("processing_level"), new StringArray(new String[]{"3"}), "processing_level"); + Test.ensureEqual(grid.globalAttributes().get("acknowledgement"), new StringArray(new String[]{"NOAA NESDIS COASTWATCH, NOAA SWFSC ERD"}), "acknowledgement"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_min"), new DoubleArray(new double[]{22}), "geospatial_lat_min"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_max"), new DoubleArray(new double[]{50}), "geospatial_lat_max"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_min"), new DoubleArray(new double[]{-135}), "geospatial_lon_min"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_max"), new DoubleArray(new double[]{-105}), "geospatial_lon_max"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_units"), new StringArray(new String[]{"degrees_north"}), "geospatial_lat_units"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lat_resolution"), new DoubleArray(new double[]{0.125}), "geospatial_lat_resolution"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_units"), new StringArray(new String[]{"degrees_east"}), "geospatial_lon_units"); + Test.ensureEqual(grid.globalAttributes().get("geospatial_lon_resolution"), new DoubleArray(new double[]{0.125}), "geospatial_lon_resolution"); + Test.ensureEqual(grid.globalAttributes().get("time_coverage_start"), new StringArray(new String[]{"2006-06-10T00:00:00Z"}), "time_coverage_start"); + Test.ensureEqual(grid.globalAttributes().get("time_coverage_end"), new StringArray(new String[]{"2006-06-11T00:00:00Z"}), "time_coverage_end"); + //Test.ensureEqual(grid.globalAttributes().get("time_coverage_resolution", new StringArray(new String[]{""}), "time_coverage_resolution"); + Test.ensureEqual(grid.globalAttributes().get("standard_name_vocabulary"), new StringArray(new String[]{"CF Standard Name Table v70"}), "standard_name_vocabulary"); + Test.ensureEqual(grid.globalAttributes().get("license"), new StringArray(new String[]{"The data may be used and redistributed for free but is not intended for legal use, since it may contain inaccuracies. Neither the data Contributor, CoastWatch, NOAA, nor the United States Government, nor any of their employees or contractors, makes any warranty, express or implied, including warranties of merchantability and fitness for a particular purpose, or assumes any legal liability for the accuracy, completeness, or usefulness, of this information."}), "license"); + Test.ensureEqual(grid.globalAttributes().get("contributor_name"), new StringArray(new String[]{"Remote Sensing Systems, Inc."}), "contributor_name"); + Test.ensureEqual(grid.globalAttributes().get("contributor_role"), new StringArray(new String[]{"Source of level 2 data."}), "contributor_role"); + Test.ensureEqual(grid.globalAttributes().get("date_issued"), new StringArray(new String[]{Calendar2.formatAsISODate(Calendar2.newGCalendarZulu())}), "date_issued"); + Test.ensureEqual(grid.globalAttributes().get("references"), new StringArray(new String[]{"RSS Inc. Winds: http://www.remss.com/ ."}), "references"); + Test.ensureEqual(grid.globalAttributes().get("source"), new StringArray(new String[]{"satellite observation: QuikSCAT, SeaWinds"}), "source"); + //Google Earth + Test.ensureEqual(grid.globalAttributes().get("Southernmost_Northing"), new DoubleArray(new double[]{22}), "southernmost"); + Test.ensureEqual(grid.globalAttributes().get("Northernmost_Northing"), new DoubleArray(new double[]{50}), "northernmost"); + Test.ensureEqual(grid.globalAttributes().get("Westernmost_Easting"), new DoubleArray(new double[]{-135}), "westernmost"); + Test.ensureEqual(grid.globalAttributes().get("Easternmost_Easting"), new DoubleArray(new double[]{-105}), "easternmost"); + + //cwhdf attributes + Test.ensureEqual(grid.globalAttributes().get("cwhdf_version"), new StringArray(new String[]{"3.4"}), "cwhdf_version"); //string + Test.ensureEqual(grid.globalAttributes().get("satellite"), new StringArray(new String[]{"QuikSCAT"}), "satellite"); //string + Test.ensureEqual(grid.globalAttributes().get("sensor"), new StringArray(new String[]{"SeaWinds"}), "sensor"); //string + Test.ensureEqual(grid.globalAttributes().get("composite"), new StringArray(new String[]{"true"}), "composite"); //string + + Test.ensureEqual(grid.globalAttributes().get("pass_date"), new IntArray(new int[]{13309}), "pass_date"); //int32[nDays] + Test.ensureEqual(grid.globalAttributes().get("start_time"), new DoubleArray(new double[]{0}), "start_time"); //float64[nDays] + Test.ensureEqual(grid.globalAttributes().get("origin"), new StringArray(new String[]{"Remote Sensing Systems, Inc."}), "origin"); //string + //Test.ensureEqual(grid.globalAttributes().get("history"), new StringArray(new String[]{"unknown"}), "history"); //string + + Test.ensureEqual(grid.globalAttributes().get("projection_type"), new StringArray(new String[]{"mapped"}), "projection_type"); //string + Test.ensureEqual(grid.globalAttributes().get("projection"), new StringArray(new String[]{"geographic"}), "projection"); //string + Test.ensureEqual(grid.globalAttributes().get("gctp_sys"), new IntArray(new int[]{0}), "gctp_sys"); //int32 + Test.ensureEqual(grid.globalAttributes().get("gctp_zone"), new IntArray(new int[]{0}), "gctp_zone"); //int32 + Test.ensureEqual(grid.globalAttributes().get("gctp_parm"), new DoubleArray(new double[15]), "gctp_parm"); //float64[15 0's] + Test.ensureEqual(grid.globalAttributes().get("gctp_datum"), new IntArray(new int[]{12}), "gctp_datum");//int32 12=WGS84 + + double matrix[] = {0, -grid.latSpacing, grid.lonSpacing, 0, grid.lon[0], grid.lat[nLat-1]}; //up side down + Test.ensureEqual(grid.globalAttributes().get("et_affine"), new DoubleArray(matrix), "et_affine"); //right side up + + Test.ensureEqual(grid.globalAttributes().get("rows"), new IntArray(new int[]{grid.lat.length}), "rows");//int32 number of rows + Test.ensureEqual(grid.globalAttributes().get("cols"), new IntArray(new int[]{grid.lon.length}), "cols");//int32 number of columns + Test.ensureEqual(grid.globalAttributes().get("polygon_latitude"), new DoubleArray(new double[]{ + grid.lat[0], grid.lat[nLat - 1], grid.lat[nLat - 1], grid.lat[0], grid.lat[0]}), "polygon_latitude"); + Test.ensureEqual(grid.globalAttributes().get("polygon_longitude"), new DoubleArray(new double[]{ + grid.lon[0], grid.lon[0], grid.lon[nLon - 1], grid.lon[nLon - 1], grid.lon[0]}), "polygon_longitude"); + + //lat attributes + Test.ensureEqual(grid.latAttributes().get("long_name"), new StringArray(new String[]{"Latitude"}), "lat long_name"); + Test.ensureEqual(grid.latAttributes().get("standard_name"), new StringArray(new String[]{"latitude"}), "lat standard_name"); + Test.ensureEqual(grid.latAttributes().get("units"), new StringArray(new String[]{"degrees_north"}), "lat units"); + Test.ensureEqual(grid.latAttributes().get("point_spacing"), new StringArray(new String[]{"even"}), "lat point_spacing"); + Test.ensureEqual(grid.latAttributes().get("actual_range"), new DoubleArray(new double[]{22, 50}), "lat actual_range"); + + //CWHDF metadata/attributes for Latitude + Test.ensureEqual(grid.latAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys");//string + Test.ensureEqual(grid.latAttributes().get("fraction_digits"), new IntArray(new int[]{2}), "fraction_digits"); //int32 + + + //lon attributes + Test.ensureEqual(grid.lonAttributes().get("long_name"), new StringArray(new String[]{"Longitude"}), "lon long_name"); + Test.ensureEqual(grid.lonAttributes().get("standard_name"), new StringArray(new String[]{"longitude"}), "lon standard_name"); + Test.ensureEqual(grid.lonAttributes().get("units"), new StringArray(new String[]{"degrees_east"}), "lon units"); + Test.ensureEqual(grid.lonAttributes().get("point_spacing"), new StringArray(new String[]{"even"}), "lon point_spacing"); + Test.ensureEqual(grid.lonAttributes().get("actual_range"), new DoubleArray(new double[]{-135, -105}), "lon actual_range"); + + //CWHDF metadata/attributes for Longitude + Test.ensureEqual(grid.lonAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys"); //string + Test.ensureEqual(grid.lonAttributes().get("fraction_digits"), new IntArray(new int[]{2}), "fraction_digits"); //int32 + + + //data attributes DataSet.properties has 0.125, but files need to be reprocessed to catch that + Test.ensureEqual(grid.dataAttributes().get("long_name"), new StringArray(new String[]{"Wind, QuikSCAT SeaWinds, 0.25 degrees, Global, Science Quality, Zonal"}), "data long_name"); + Test.ensureEqual(grid.dataAttributes().get("standard_name"), new StringArray(new String[]{"x_wind"}), "data standard_name"); + Test.ensureEqual(grid.dataAttributes().get("units"), new StringArray(new String[]{"m s-1"}), "data units"); + Test.ensureEqual(grid.dataAttributes().get("_FillValue"), new FloatArray(new float[]{-9999999}), "data _FillValue"); + Test.ensureEqual(grid.dataAttributes().get("missing_value"), new FloatArray(new float[]{-9999999}), "data missing_value"); + Test.ensureEqual(grid.dataAttributes().get("numberOfObservations"), new IntArray(new int[]{25021}), "data numberOfObservations"); + Test.ensureEqual(grid.dataAttributes().get("percentCoverage"), new DoubleArray(new double[]{0.46142923005993547}), "data percentCoverage"); + + //CWHDF metadata/attributes for the data: varName + Test.ensureEqual(grid.dataAttributes().get("coordsys"), new StringArray(new String[]{"geographic"}), "coordsys"); //string + Test.ensureEqual(grid.dataAttributes().get("fraction_digits"), new IntArray(new int[]{1}), "fraction_digits"); //int32 + + /* */ + + //*************************************** + //large test of TMBchla which covers has odd x range ~ 110 to 320 + //actual dataset minX=120.0 maxX=320.0 minY=-45.0 maxY=65.0 xInc=0.025 yInc=0.025 + //These mimic tests in Grid.testReadGrdSubset(). + //Comment out this line with /* to comment out this test. + gridDataSet = new GridDataSetThredds(fnu, "TMBchla", + //was "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMB/chla/", //was :8081 + "https://thredds1.pfeg.noaa.gov/thredds/catalog/Satellite/aggregsatMB/chla/", + "Rainbow", "Log", ".001", "30", -1, "", null, null, "S", 1, 0, "", 1, 1); + fileName = "temp"; + + //get 4 points individually + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315, 315, 30, 30, 1, 1); + Test.ensureEqual(grid.lon, new double[]{315}, ""); + Test.ensureEqual(grid.lat, new double[]{30}, ""); + Test.ensureEqual((float)grid.data[0], (float)0.039, ""); + + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 135, 30, 30, 1, 1); + Test.ensureEqual(grid.lon, new double[]{135}, ""); + Test.ensureEqual(grid.lat, new double[]{30}, ""); + Test.ensureEqual((float)grid.data[0], (float)0.200333, ""); + + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315, 315, -41, -41, 1, 1); + Test.ensureEqual(grid.lon, new double[]{315}, ""); + Test.ensureEqual(grid.lat, new double[]{-41}, ""); + Test.ensureEqual((float)grid.data[0], (float)0.968, ""); + + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 135, -41, -41, 1, 1); + Test.ensureEqual(grid.lon, new double[]{135}, ""); + Test.ensureEqual(grid.lat, new double[]{-41}, ""); + Test.ensureEqual((float)grid.data[0], (float) 0.431, ""); + + //test 2 wide, 1 high + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 315, 30, 30, 2, 1); + Test.ensureEqual(grid.lon, new double[]{135, 315}, ""); + Test.ensureEqual(grid.lat, new double[]{30}, ""); + Test.ensureEqual((float)grid.data[0], (float)0.200333, ""); + Test.ensureEqual((float)grid.data[1], (float)0.039, ""); + + //test 37 wide, 1 high test most of the data rotated around to right + //This is a little contrived: getting every 5 degrees of lon allows it to + // cleanly align at 0 and still get my two test points exactly. + // But that is part of the nature of having to move the data columns around. + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", -45, 135, 30, 30, 37, 1); //180 range / 5 = 36 + 1 + String2.log("lon=" + String2.toCSSVString(grid.lon)); + Test.ensureEqual(grid.lon, DataHelper.getRegularArray(37, -45, 5), ""); + Test.ensureEqual(grid.lat, new double[]{30}, ""); + Test.ensureEqual((float)grid.data[0], (float)0.039, ""); + Test.ensureEqual((float)grid.data[36], (float)0.200333, ""); + + //test 1 wide, 2 high x in 0.. 180 + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 135, -41, 30, 1, 2); + Test.ensureEqual(grid.lon, new double[]{135}, ""); + Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); + Test.ensureEqual((float)grid.data[0], (float) 0.431, ""); + Test.ensureEqual((float)grid.data[1], (float)0.200333, ""); + + //test 1 wide, 2 high in x>180 + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315, 315, -41, 30, 1, 2); + Test.ensureEqual(grid.lon, new double[]{315}, ""); + Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); + Test.ensureEqual((float)grid.data[0], (float)0.968, ""); + Test.ensureEqual((float)grid.data[1], (float)0.039, ""); + + //test 1 wide, 2 high in x<0 + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315-360, 315-360, -41, 30, 1, 2); + Test.ensureEqual(grid.lon, new double[]{315-360}, ""); + Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); + Test.ensureEqual((float)grid.data[0], (float)0.968, ""); + Test.ensureEqual((float)grid.data[1], (float)0.039, ""); + + //test 2 wide, 2 high in x<0 + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 135, 315, -41, 30, 2, 2); + Test.ensureEqual(grid.lon, new double[]{135, 315}, ""); + Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); + Test.ensureEqual((float)grid.data[0], (float) 0.431, ""); + Test.ensureEqual((float)grid.data[1], (float)0.200333, ""); + Test.ensureEqual((float)grid.data[2], (float)0.968, ""); + Test.ensureEqual((float)grid.data[3], (float)0.039, ""); + + //test 37 wide, 2 high in x<0 + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 315-360, 135, -41, 30, 37, 2); + Test.ensureEqual(grid.lon, DataHelper.getRegularArray(37, -45, 5), ""); + Test.ensureEqual(grid.lat, new double[]{-41, 30}, ""); + Test.ensureEqual((float)grid.data[0], (float)0.968, ""); + Test.ensureEqual((float)grid.data[1], (float)0.039, ""); + Test.ensureEqual((float)grid.data[72], (float)0.431, ""); + Test.ensureEqual((float)grid.data[73], (float)0.200333, ""); + + /* */ + + /* + //*************************************** + //one time only: get one of these files for testing readGrd + //actual dataset minX=120.0 maxX=320.0 minY=-45.0 maxY=65.0 xInc=0.025 yInc=0.025 + gridDataSet = new GridDataSetThredds(fnu, "TMBchla", + "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatMB/chla/", //was :8081 + "Rainbow", "Log", ".001", "30", -1, "", null, null); + fileName = "TestReadGrgTMBchla"; + + //get 4 points individually + grid = gridDataSet.makeGrid("8 day", "2007-01-12 00:00:00", 120, 320, -45, 65, 201, 111); //1 x 1 degree + String2.log("resultingFileName=" + resultingFileName); + //result is TestReadGrgTMBchla_x120_X320_y-45_Y65_nx201_ny111.grd + */ + } + + /** + * This does a test of getTimeSeries using a data set on West Coast cwexperimental. + */ + @org.junit.jupiter.api.Test + @TagThredds + void testGetTimeSeries() throws Exception { + String2.log("\n*** start TestBrowsers.testGetTimeSeries"); + String url = + //was "https://oceanwatch.pfeg.noaa.gov/thredds/Satellite/aggregsatGA/ssta/"; //oceanwatch + "https://thredds1.pfeg.noaa.gov/thredds/catalog/Satellite/aggregsatGA/ssta/"; + + DataHelper.verbose = true; + GridDataSetThredds.verbose = true; + + String tempDir = TEMP_DIR.toAbsolutePath().toString(); + Table table = null; + + GridDataSetThredds gdst = new GridDataSetThredds( + new FileNameUtility("gov.noaa.pfel.coastwatch.CWBrowser"), + "TGAssta", //String internalName, + url, + "Rainbow", "Linear", "8", "32", -1, "", null, //fgdc, + null, + "S", 1.8, 32, "degree_F", 45, 90); + + //*** test the GridDataSetThredds version of getTimeSeries + //test individual makeGrid to get the values tested below in getTimeSeries + double rLon = -128.975; + double rLat = 36.025; + + Grid grid = gdst.makeGrid("1 day", + "2007-12-01 12:00:00", + rLon, rLon, rLat, rLat, 1, 1); + Test.ensureEqual(grid.lon[0], rLon, ""); + Test.ensureEqual(grid.lat[0], rLat, ""); + Test.ensureEqual((float)grid.data[0], 16.35f, ""); + + grid = gdst.makeGrid("1 day", + "2007-12-02 12:00:00", + rLon, rLon, rLat, rLat, 1, 1); + Test.ensureEqual(grid.lon[0], rLon, ""); + Test.ensureEqual(grid.lat[0], rLat, ""); + Test.ensureEqual((float)grid.data[0], 16.05f, ""); + + //first just test if it gets correct answers + table = gdst.getTimeSeries(tempDir, rLon, rLat, + "2007-12-01 12:00:00", "2007-12-20 12:00:00", "1 day"); + //String2.log("timeSeriesTable=" + table); + Test.ensureEqual(table.nRows(), 20, ""); + Test.ensureEqual(table.nColumns(), 6, ""); + Test.ensureEqual(table.getColumnName(0), "LON", ""); + Test.ensureEqual(table.getColumnName(1), "LAT", ""); + Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); + Test.ensureEqual(table.getColumnName(3), "TIME", ""); + Test.ensureEqual(table.getColumnName(4), "ID", ""); + Test.ensureEqual(table.getColumnName(5), "TGAssta", ""); + + Test.ensureEqual(table.getColumn(0).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(1).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(2).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(3).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(4).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(5).elementTypeString(), "float", ""); + + Test.ensureEqual(table.getDoubleData(0,0), rLon, ""); + Test.ensureEqual(table.getDoubleData(1,0), rLat, ""); + Test.ensureEqual(table.getDoubleData(2,0), 0, ""); + Test.ensureEqual(table.getDoubleData(3,0), Calendar2.isoStringToEpochSeconds("2007-12-01 12:00:00"), ""); + Test.ensureEqual(table.getStringData(4,0), "TGAssta", ""); + Test.ensureEqual(table.getFloatData(5,0), 16.35f, ""); + + Test.ensureEqual(table.getDoubleData(0,1), rLon, ""); + Test.ensureEqual(table.getDoubleData(1,1), rLat, ""); + Test.ensureEqual(table.getDoubleData(2,1), 0, ""); + Test.ensureEqual(table.getDoubleData(3,1), Calendar2.isoStringToEpochSeconds("2007-12-02 12:00:00"), ""); + Test.ensureEqual(table.getStringData(4,1), "TGAssta", ""); + Test.ensureEqual(table.getFloatData( 5,1), 16.05f, ""); + + + //HARDER TEST: data for all time does it crash? 35s first run, then 12s + //for (int i = 30; i <= 36; i++) + // table = gdst.getTimeSeries(tempDir, rLon, i, + // "1980-01-01", "2099-12-31", gdst.activeTimePeriodOptions[0]); + + + //*** test the GridDataSet (superclass) version of getTimeSeries + //this is the only test of superclass' getTimeSeries + table = null; + table = gdst.getSuperTimeSeries(tempDir, rLon, rLat, + "2007-12-01 12:00:00", "2007-12-20 12:00:00", "1 day"); + //String2.log("super timeSeriesTable=" + table); + Test.ensureEqual(table.nRows(), 20, ""); + Test.ensureEqual(table.nColumns(), 6, ""); + Test.ensureEqual(table.getColumnName(0), "LON", ""); + Test.ensureEqual(table.getColumnName(1), "LAT", ""); + Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); + Test.ensureEqual(table.getColumnName(3), "TIME", ""); + Test.ensureEqual(table.getColumnName(4), "ID", ""); + Test.ensureEqual(table.getColumnName(5), "TGAssta", ""); + + Test.ensureEqual(table.getDoubleData(0,0), rLon, ""); + Test.ensureEqual(table.getDoubleData(1,0), rLat, ""); + Test.ensureEqual(table.getDoubleData(2,0), 0, ""); + Test.ensureEqual(table.getDoubleData(3,0), Calendar2.isoStringToEpochSeconds("2007-12-01 12:00:00"), ""); + Test.ensureEqual(table.getStringData(4,0), "TGAssta", ""); + Test.ensureEqual(table.getFloatData(5,0), 16.35f, ""); + + Test.ensureEqual(table.getDoubleData(0,1), rLon, ""); + Test.ensureEqual(table.getDoubleData(1,1), rLat, ""); + Test.ensureEqual(table.getDoubleData(2,1), 0, ""); + Test.ensureEqual(table.getDoubleData(3,1), Calendar2.isoStringToEpochSeconds("2007-12-02 12:00:00"), ""); + Test.ensureEqual(table.getStringData(4,1), "TGAssta", ""); + Test.ensureEqual(table.getFloatData(5,1), 16.05f, ""); + + + //*** test of centering time periods + //test individual makeGrid to get the values tested below in getTimeSeries + grid = gdst.makeGrid("3 day", "2006-08-13 12:00:00", //centered time + -130.02, -130.02, 36.02, 36.02, //close, not exact + 1, 1); + Test.ensureEqual(grid.lon[0], -130.025, ""); //3 day grid is offset by .025!! + Test.ensureEqual(grid.lat[0], 36.025, ""); + Test.ensureEqual((float)grid.data[0], 19.8f, ""); + + grid = gdst.makeGrid("3 day", "2006-08-08 12:00:00", //centered time + -130.02, -130.02, 36.02, 36.02, + 1, 1); + Test.ensureEqual(grid.lon[0], -130.025, ""); + Test.ensureEqual(grid.lat[0], 36.025, ""); + Test.ensureEqual((float)grid.data[0], 18.75f, ""); + + //first just test if it gets correct answers + table = gdst.getTimeSeries(tempDir, -130.02, 36.02, + "2006-08-08", "2006-08-14", //begin and end centered times + "3 day"); + //String2.log("timeSeriesTable=" + table); + PrimitiveArray timePA = table.getColumn(3); + PrimitiveArray dataPA = table.getColumn(5); + + //find the row corresponding to the desired time + double seconds = Calendar2.isoStringToEpochSeconds("2006-08-13 12:00:00"); //centered time + int row = timePA.binaryFindClosest(seconds); + Test.ensureEqual(timePA.getDouble(row), seconds, ""); //ensure exact match 2006-08-13T23:59:59 + Test.ensureEqual(dataPA.getFloat(row), 19.8f, ""); + + seconds = Calendar2.isoStringToEpochSeconds("2006-08-08 12:00:00"); //centered time + row = timePA.binaryFindClosest(seconds); + Test.ensureEqual(timePA.getDouble(row), seconds, ""); //ensure exact match + Test.ensureEqual(dataPA.getFloat(row), 18.75f, ""); + } + +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/griddata/NcHelperTests.java b/src/test/java/gov/noaa/pfel/coastwatch/griddata/NcHelperTests.java new file mode 100644 index 000000000..45808a307 --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/griddata/NcHelperTests.java @@ -0,0 +1,722 @@ +package gov.noaa.pfel.coastwatch.griddata; + +import java.nio.file.Path; +import java.util.ArrayList; + +import org.junit.jupiter.api.io.TempDir; + +import com.cohort.array.Attributes; +import com.cohort.array.ByteArray; +import com.cohort.array.CharArray; +import com.cohort.array.DoubleArray; +import com.cohort.array.FloatArray; +import com.cohort.array.IntArray; +import com.cohort.array.LongArray; +import com.cohort.array.PAType; +import com.cohort.array.PrimitiveArray; +import com.cohort.array.ShortArray; +import com.cohort.array.StringArray; +import com.cohort.util.File2; +import com.cohort.util.Math2; +import com.cohort.util.MustBe; +import com.cohort.util.String2; +import com.cohort.util.Test; + +import ucar.ma2.Array; +import ucar.ma2.ArrayByte; +import ucar.ma2.ArrayChar; +import ucar.ma2.ArrayDouble; +import ucar.ma2.DataType; +import ucar.ma2.StructureData; +import ucar.ma2.StructureDataIterator; +import ucar.ma2.StructureMembers; +import ucar.nc2.Attribute; +import ucar.nc2.Dimension; +import ucar.nc2.Group; +import ucar.nc2.NetcdfFile; +import ucar.nc2.NetcdfFiles; +import ucar.nc2.Structure; +import ucar.nc2.Variable; +import ucar.nc2.write.NetcdfFormatWriter; + +class NcHelperTests { + + @TempDir + private static Path TEMP_DIR; + + /** + * This tests the methods in this class. + */ + @org.junit.jupiter.api.Test + void testBasic() throws Throwable { + String2.log("\n*** NcHelper.testBasic..."); + String fullName; + + // getArray get1DArray, get1DArrayLength + Object o; + o = new String[] { "5.5", "7.77" }; + Array array = NcHelper.get1DArray(o, false); + Test.ensureTrue(array instanceof ArrayChar.D2, "get1DArray a"); + Test.ensureEqual(NcHelper.get1DArrayLength(array), 2, "get1DArrayLength a"); + o = NcHelper.getPrimitiveArray(array); + Test.ensureTrue(o instanceof StringArray, "getArray a; o=" + o.toString()); + StringArray sar = (StringArray) o; + Test.ensureEqual(sar.size(), 2, ""); + Test.ensureEqual(sar.get(0), "5.5", ""); + Test.ensureEqual(sar.get(1), "7.77", ""); + + /* + * ArrayChar.D3 ac3 = new ArrayChar.D3(2, 3, 5); + * Index index = ac3.getIndex(); + * index.set(0, 0); ac3.setString(index, "a"); + * index.set(0, 1); ac3.setString(index, "bb"); + * index.set(0, 2); ac3.setString(index, "ccc"); + * index.set(1, 0); ac3.setString(index, "dddd"); + * index.set(1, 1); ac3.setString(index, "e"); + * index.set(1, 2); ac3.setString(index, "f"); + * o = getArray(ac3); + * Test.ensureTrue(o instanceof String[], "getArray a; o=" + o.toString()); + * sar = (String[])o; + * Test.ensureEqual(sar.length, 6, ""); + * Test.ensureEqual(sar[0], "a", ""); + * Test.ensureEqual(sar[1], "bb", ""); + * Test.ensureEqual(sar[2], "ccc", ""); + * Test.ensureEqual(sar[3], "dddd", ""); + * Test.ensureEqual(sar[4], "e", ""); + * Test.ensureEqual(sar[5], "f", ""); + */ + + o = new byte[] { (byte) 2, (byte) 9 }; + array = NcHelper.get1DArray(o, false); + Test.ensureTrue(array instanceof ArrayByte.D1, "get1DArray b"); + Test.ensureEqual(NcHelper.get1DArrayLength(array), 2, "get1DArrayLength a"); + o = NcHelper.getPrimitiveArray(array); + Test.ensureTrue(o instanceof ByteArray, "getArray b"); + ByteArray bar = (ByteArray) o; + Test.ensureEqual(bar.size(), 2, ""); + Test.ensureEqual(bar.get(0), 2, ""); + Test.ensureEqual(bar.get(1), 9, ""); + + o = new double[] { 2.2, 9.9 }; + array = NcHelper.get1DArray(o, false); + Test.ensureTrue(array instanceof ArrayDouble.D1, "get1DArray c"); + Test.ensureEqual(NcHelper.get1DArrayLength(array), 2, "get1DArrayLength a"); + o = NcHelper.getPrimitiveArray(array); + Test.ensureTrue(o instanceof DoubleArray, "getArray c"); + DoubleArray dar = (DoubleArray) o; + Test.ensureEqual(dar.size(), 2, ""); + Test.ensureEqual(dar.get(0), 2.2, ""); + Test.ensureEqual(dar.get(1), 9.9, ""); + + // test readWritePAsInNc + ByteArray ba = new ByteArray(new byte[] { 1, 2, 4, 7 }); + ShortArray sha = new ShortArray(new short[] { 100, 200, 400, 700 }); + IntArray ia = new IntArray(new int[] { -1, 0, 1 }); + LongArray la = new LongArray(new long[] { -10L, 0, 10L }); + char charAr[] = new char[65536]; + for (int i = 0; i < 65536; i++) + charAr[i] = (char) i; + CharArray ca = new CharArray(charAr); + FloatArray fa = new FloatArray(new float[] { -1.1f, 2.2f, 5.5f, Float.NaN }); + DoubleArray da = new DoubleArray(new double[] { 1.1, 2.2, 9.9, Double.NaN }); + StringArray sa = new StringArray(); + for (int i = 0; i < 65536; i++) + sa.add("a" + (i == 8 ? " " : (char) i) + "z"); // backspace not saved + // write to file + fullName = TEMP_DIR.toAbsolutePath().toString() + "/PAsInNc.nc"; + File2.delete(fullName); // for test, make double sure it doesn't already exist + StringArray varNames = new StringArray(new String[] { + "ba", "sha", "ia", "la", "ca", "fa", "da", "sa" }); + PrimitiveArray pas[] = new PrimitiveArray[] { + ba, sha, ia, la, ca, fa, da, sa }; + NcHelper.writePAsInNc3(fullName, varNames, pas); + // read from file + StringArray varNames2 = new StringArray(); + PrimitiveArray pas2[] = NcHelper.readPAsInNc3(fullName, null, varNames2); + Test.ensureEqual(varNames, varNames2, ""); + Test.ensureEqual(pas.length, pas2.length, ""); + for (int i = 0; i < pas.length; i++) { + int which = varNames2.indexOf(varNames.get(i)); + PrimitiveArray pa2 = pas2[which]; + Test.ensureEqual(pas[i].elementTypeString(), pa2.elementTypeString(), "i=" + i); + if (pas[i].elementType() == PAType.STRING) { + for (int j = 0; j < pas[i].size(); j++) + Test.ensureEqual(String2.toJson(pas[i].getString(j)), + String2.toJson(pa2.getString(j)), "i=" + i + " j=" + j); + } else { + Test.ensureEqual(pas[i].toJsonCsvString(), pa2.toJsonCsvString(), "i=" + i); + } + } + + pas2 = NcHelper.readPAsInNc3(fullName, new String[] { "sa" }, varNames2); + Test.ensureEqual(varNames2.size(), 1, ""); + Test.ensureEqual(varNames2.get(0), "sa", ""); + Test.ensureEqual(pas2.length, 1, ""); + Test.ensureEqual(pas[varNames.indexOf("sa")].toJsonCsvString(), pas2[0].toJsonCsvString(), ""); + + // test writeAttributesToNc + fullName = TEMP_DIR.toAbsolutePath().toString() + "/AttsInNc.nc"; + Attributes atts = new Attributes(); + for (int i = 0; i < pas.length; i++) + atts.set(varNames.get(i), pas[i]); + NcHelper.writeAttributesToNc3(fullName, atts); + // read 1 + PrimitiveArray pa = NcHelper.readAttributeFromNc(fullName, "sa"); + Test.ensureEqual(sa.elementTypeString(), pa.elementTypeString(), ""); + Test.ensureEqual(sa, pa, ""); + pa = NcHelper.readAttributeFromNc(fullName, "ia"); + Test.ensureEqual(ia.elementTypeString(), pa.elementTypeString(), ""); + Test.ensureEqual(ia, pa, ""); + // read many + pas2 = NcHelper.readAttributesFromNc3(fullName, varNames.toArray()); + for (int i = 0; i < pas.length; i++) { + Test.ensureEqual(pas[i].elementTypeString(), pas2[i].elementTypeString(), "i=" + i); + Test.ensureEqual(pas[i].toJsonCsvString(), pas2[i].toJsonCsvString(), "i=" + i); + } + // read all + atts = NcHelper.readAttributesFromNc3(fullName); + for (int i = 0; i < varNames.size(); i++) { + pa = atts.get(varNames.get(i)); + Test.ensureEqual(pas[i].elementTypeString(), pa.elementTypeString(), "i=" + i); + Test.ensureEqual(pas[i].toJsonCsvString(), pa.toJsonCsvString(), "i=" + i); + } + // test fail to read non-existent file + try { + pa = NcHelper.readAttributeFromNc(fullName + "zztop", "sa"); + throw new RuntimeException("shouldn't get here"); + } catch (Exception e) { + if (e.toString().indexOf( + "java.io.FileNotFoundException: " + TEMP_DIR.toAbsolutePath().toString() + "\\AttsInNc.nczztop " + + "(The system cannot find the file specified)") < 0) + throw e; + } + + try { + pas2 = NcHelper.readAttributesFromNc3(fullName + "zztop", varNames.toArray()); + throw new RuntimeException("shouldn't get here"); + } catch (Exception e) { + if (e.toString().indexOf( + "java.io.FileNotFoundException: " + TEMP_DIR.toAbsolutePath().toString() + "\\AttsInNc.nczztop " + + "(The system cannot find the file specified)") < 0) + throw e; + } + + try { + atts = NcHelper.readAttributesFromNc3(fullName + "zztop"); + throw new RuntimeException("shouldn't get here"); + } catch (Exception e) { + if (e.toString().indexOf( + "java.io.FileNotFoundException: " + TEMP_DIR.toAbsolutePath().toString() + "\\AttsInNc.nczztop " + + "(The system cannot find the file specified)") < 0) + throw e; + } + + // test fail to read non-existent var + try { + pa = NcHelper.readAttributeFromNc(fullName, "zztop"); + throw new RuntimeException("shouldn't get here"); + } catch (Exception e) { + if (e.toString().indexOf( + String2.ERROR + ": Expected variable #0 not found while reading " + + TEMP_DIR.toAbsolutePath().toString() + "/AttsInNc.nc (loadVarNames=zztop).") < 0) + throw e; + } + + try { + pas2 = NcHelper.readAttributesFromNc3(fullName, new String[] { "zztop" }); + throw new RuntimeException("shouldn't get here"); + } catch (Exception e) { + if (e.toString().indexOf( + String2.ERROR + ": Expected variable #0 not found while reading " + + TEMP_DIR.toAbsolutePath().toString() + "/AttsInNc.nc (loadVarNames=zztop).") < 0) + throw e; + } + + // test if defining >2GB throws exception + fullName = TEMP_DIR.toAbsolutePath().toString() + "/TooBig.nc"; + File2.delete(fullName); + NetcdfFormatWriter ncWriter = null; + + // *** test writing Strings to nc files + fullName = TEMP_DIR.toAbsolutePath().toString() + "/StringsInNc.nc"; + File2.delete(fullName); + ncWriter = null; + try { + NetcdfFormatWriter.Builder ncOut = NetcdfFormatWriter.createNewNetcdf3(fullName); + // "define" mode + Group.Builder rootGroup = ncOut.getRootGroup(); + ncOut.setFill(false); + Dimension dim0 = NcHelper.addDimension(rootGroup, "dim0", 2); + Dimension dim1 = NcHelper.addDimension(rootGroup, "dim1", 3); + ArrayList dims = new ArrayList(); + dims.add(dim0); + dims.add(dim1); + NcHelper.addNc3StringVariable(rootGroup, "s1", dims, 4); // test strLength not long enough for all strings! + Array ar; + + // "create" mode + ncWriter = ncOut.build(); + String sa6[] = { "", "a", "abcd", "abc", "abcd", "abcd" }; + Variable s1Var = ncWriter.findVariable("s1"); + + // this fails (as expected and desired): + // so origin and ar must be correct nDimensions and size + // ar = Array.factory(DataType.STRING, new int[]{6}, sa6); + // ncOut.writeStringDataToChar(s1, new int[]{0}, ar); + + ar = Array.factory(DataType.STRING, new int[] { 2, 3 }, sa6); + ncWriter.writeStringDataToChar(s1Var, new int[] { 0, 0 }, ar); + ncWriter.close(); + ncWriter = null; + } catch (Exception e) { + String2.log(NcHelper.ERROR_WHILE_CREATING_NC_FILE + MustBe.throwableToString(e)); + if (ncWriter != null) { + try { + ncWriter.abort(); + } catch (Exception e9) { + } + File2.delete(fullName); + ncWriter = null; + } + } + + // Strings are truncated to maxCharLength specified in "define" mode. + String results = NcHelper.ncdump(fullName, ""); + String expected = "netcdf StringsInNc.nc {\n" + + " dimensions:\n" + + " dim0 = 2;\n" + + " dim1 = 3;\n" + + " s1_strlen = 4;\n" + + " variables:\n" + + " char s1(dim0=2, dim1=3, s1_strlen=4);\n" + + "\n" + + "\n" + + " data:\n" + + " s1 = \n" + + " { \"\", \"a\", \"abcd\", \"abc\", \"abcd\", \"abcd\"\n" + + " }\n" + + "}\n"; + // String2.log("results=\n" + results); + Test.ensureEqual(results, expected, ""); + File2.delete(fullName); + + // *** test writing too-long Strings to nc files + // Must the char[][] be the exact right size? What if too long? + fullName = TEMP_DIR.toAbsolutePath().toString() + "/StringsInNc2.nc"; + File2.delete(fullName); + ncWriter = null; + try { + NetcdfFormatWriter.Builder ncOut = NetcdfFormatWriter.createNewNetcdf3(fullName); + // "define" mode + Group.Builder rootGroup = ncOut.getRootGroup(); + ncOut.setFill(false); + Dimension dim0 = NcHelper.addDimension(rootGroup, "dim0", 2); + Dimension dim1 = NcHelper.addDimension(rootGroup, "dim1", 3); + ArrayList dims = new ArrayList(); + dims.add(dim0); + dims.add(dim1); + NcHelper.addNc3StringVariable(rootGroup, "s1", dims, 4); // test strLength not long enough for all strings! + Array ar; + + // "create" mode + ncWriter = ncOut.build(); + String sa6[] = { "", "a", "abcde", "abc", "abcd", "abcde" }; + Variable s1Var = ncWriter.findVariable("s1"); + + // this fails (as expected and desired): + // so origin and ar must be correct nDimensions and size + // ar = Array.factory(DataType.STRING, new int[]{6}, sa6); + // ncOut.writeStringDataToChar(s1, new int[]{0}, ar); + + ar = Array.factory(DataType.STRING, new int[] { 2, 3 }, sa6); + ncWriter.writeStringDataToChar(s1Var, new int[] { 0, 0 }, ar); + ncWriter.close(); + ncWriter = null; + } catch (Exception e) { + String2.log(NcHelper.ERROR_WHILE_CREATING_NC_FILE + MustBe.throwableToString(e)); + if (ncWriter != null) { + try { + ncWriter.abort(); + } catch (Exception e9) { + } + File2.delete(fullName); + ncWriter = null; + } + } + + // Strings are truncated to maxCharLength specified in "define" mode. + results = NcHelper.ncdump(fullName, ""); + expected = "netcdf StringsInNc2.nc {\n" + + " dimensions:\n" + + " dim0 = 2;\n" + + " dim1 = 3;\n" + + " s1_strlen = 4;\n" + + " variables:\n" + + " char s1(dim0=2, dim1=3, s1_strlen=4);\n" + + "\n" + + "\n" + + " data:\n" + + " s1 = \n" + + " { \"\", \"a\", \"abcd\", \"abc\", \"abcd\", \"abcd\"\n" + + " }\n" + + "}\n"; + // String2.log("results=\n" + results); + Test.ensureEqual(results, expected, ""); + + // nc chars are essentially unsigned bytes! + // String2.log(File2.hexDump(fullName, 1000000)); + File2.delete(fullName); + + // 2021-01-06 This worked (ie netcdf-java refused to create the file) + // until netcdf-java v5.4.1. I reported to Sean Arms. + // (Chris) I'm commenting out the below during the move to JUnit. Based on my + // reading of the NetCDF Users Guide, + // https://docs.unidata.ucar.edu/nug/current/file_structure_and_performance.html + // I don't think this is really an error. Besides that, this is testing the + // NetCDF + // library, not the ERDDAP code. + // if (true) { // this is normally true + // try { + // NetcdfFormatWriter.Builder ncOut = NetcdfFormatWriter.createNewNetcdf3( + // fullName) + // .setFormat(NetcdfFileFormat.NETCDF3) // this is default. I'm just testing. + // .setFill(false); + + // // "define" mode 2vars * 3000*50000*8bytes = 2,400,000,000 + // Group.Builder rootGroup = ncOut.getRootGroup(); + + // Dimension dim0 = NcHelper.addDimension(rootGroup, "dim0", 3000); + // Dimension dim1 = NcHelper.addDimension(rootGroup, "dim1", 50000); + // List dims = Arrays.asList(dim0, dim1); + // NcHelper.addVariable(rootGroup, "d1", DataType.DOUBLE, dims); + // NcHelper.addVariable(rootGroup, "d2", DataType.DOUBLE, dims); + + // // define a var above 2GB (This causes the exception.) + // NcHelper.addVariable(rootGroup, "b3", DataType.BYTE, Arrays.asList(dim0)); + + // // "create" mode (and error isn't triggered till here) + // ncWriter = ncOut.build(); + + // ncWriter.close(); // it calls flush() and doesn't like flush called + // separately + // ncWriter = null; + // if (true) + // throw new RuntimeException( + // "Shouldn't get here (It let me create nc3 file >2GB!) . fileSize=" + + // File2.length(fullName)); + + // } catch (Throwable t) { + // String2.log(NcHelper.ERROR_WHILE_CREATING_NC_FILE + + // MustBe.throwableToString(t)); + // if (ncWriter != null) { + // try { + // ncWriter.abort(); + // } catch (Exception e9) { + // } + // File2.delete(fullName); + // ncWriter = null; + // } + + // String msg = t.toString(); + // String2.log("Intentional error (should be: not allowed to create nc3 file + // >2GB):\n" + msg); + + // if (!msg.equals( + // "java.lang.IllegalArgumentException: Variable starting pos=2400000172 " + + // "may not exceed 2147483647")) + // Test.knownProblem("netcdf-java 5.4.1+ allows creation of nc3 files >2GB!\n" + + // "I reported this to Sean Arms 2021-01-06.", t); + // } finally { + // File2.delete(fullName); + // } + // } + + } + + /** + * Test findAllVariablesWithDims. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testFindAllVariablesWithDims() throws Exception { + StringArray sa = new StringArray(); + NetcdfFile ncFile = NcHelper.openFile(NcHelperTests.class.getResource("/nodcTemplates/ncCFMA2a.nc").getFile()); + try { + Variable vars[] = NcHelper.findAllVariablesWithDims(ncFile); + for (int v = 0; v < vars.length; v++) + sa.add(vars[v].getFullName()); + sa.sort(); + } finally { + ncFile.close(); + } + String results = sa.toString(); + String expected = "bottle_posn, cast, cruise_id, latitude, longitude, ship, temperature0, time"; + Test.ensureEqual(results, expected, "results=" + results); + + } + + /** + * This is the test that Bob sent to Sean. It only uses netcdf-java methods, not + * NcHelper. + */ + @org.junit.jupiter.api.Test + void testReadStructure() throws Throwable { + String fileName = NcHelperTests.class.getResource("/nc/SDScompound.h5").getFile(); + // System.out.println(NcHelper.ncdump(fileName, "-v ArrayOfStructures")); + NetcdfFile nc = NetcdfFiles.open(fileName); + try { + // System.out.println(nc.toString()); + Variable v = nc.findVariable("ArrayOfStructures"); + if (v instanceof Structure s) { + // System.out.println("v=" + v); + StructureMembers sm = s.makeStructureMembers(); + // System.out.println("sm=" + sm); + StructureMembers.Member smma = sm.findMember("a_name"); + StructureMembers.Member smmb = sm.findMember("b_name"); + StructureMembers.Member smmc = sm.findMember("c_name"); + // boolean buildStringsFromChars = false; + // boolean isUnsigned = false; + StructureDataIterator it = s.getStructureIterator(); + int recNo = 0; + try { + while (it.hasNext()) { + StructureData sd = it.next(); + // System.out.println("byName recNo=" + recNo + + // " a_name=" + sd.getScalarInt("a_name") + + // " b_name=" + sd.getScalarFloat("b_name") + + // " c_name=" + sd.getScalarDouble("c_name")); + // System.out.println("byMem recNo=" + recNo + + // " a_name=" + sd.getScalarInt(smma) + + // " b_name=" + sd.getScalarFloat(smmb) + + // " c_name=" + sd.getScalarDouble(smmc)); + recNo++; + } + } finally { + it.close(); + } + } + + } finally { + nc.close(); + } + } + + /** + * ERDDAP: require that all vars be in same structure + */ + @org.junit.jupiter.api.Test + void testReadStructure2() throws Throwable { + String fileName = NcHelperTests.class.getResource("/nc/SDScompound.h5").getFile(); + // System.out.println(NcHelper.ncdump(fileName, "-v ArrayOfStructures")); + NetcdfFile nc = NetcdfFiles.open(fileName); + try { + String memberNames[] = new String[] { "a_name", "b_name", "c_name" }; + PrimitiveArray pa[] = NcHelper.readStructure(nc, "ArrayOfStructures", + memberNames, IntArray.fromCSV("0,1,9")); + Test.ensureEqual(pa[0].toString(), "0, 1, 2, 3, 4, 5, 6, 7, 8, 9", "a_name"); + Test.ensureEqual(pa[1].toString(), "0.0, 1.0, 4.0, 9.0, 16.0, 25.0, 36.0, 49.0, 64.0, 81.0", "b_name"); + Test.ensureEqual(pa[2].toString(), + "1.0, 0.5, 0.3333333333333333, 0.25, 0.2, 0.16666666666666666, 0.14285714285714285, 0.125, 0.1111111111111111, 0.1", + "c_name"); + + pa = NcHelper.readStructure(nc, "ArrayOfStructures", memberNames, IntArray.fromCSV("2,3,9")); + Test.ensureEqual(pa[0].toString(), "2, 5, 8", "a_name"); + Test.ensureEqual(pa[1].toString(), "4.0, 25.0, 64.0", "b_name"); + Test.ensureEqual(pa[2].toString(), "0.3333333333333333, 0.16666666666666666, 0.1111111111111111", "c_name"); + + pa = NcHelper.readStructure(nc, "ArrayOfStructures", memberNames, IntArray.fromCSV("2,3,8")); + Test.ensureEqual(pa[0].toString(), "2, 5, 8", "a_name"); + Test.ensureEqual(pa[1].toString(), "4.0, 25.0, 64.0", "b_name"); + Test.ensureEqual(pa[2].toString(), "0.3333333333333333, 0.16666666666666666, 0.1111111111111111", "c_name"); + } finally { + nc.close(); + } + } + + /** + * This is a test of unlimitedDimension + */ + @org.junit.jupiter.api.Test + void testUnlimited() throws Exception { + String testUnlimitedFileName = "/temp/unlimited.nc"; + String2.log("\n* Projects.testUnlimited() " + testUnlimitedFileName); + int strlen = 6; + int row = -1; + String results, expected; + NetcdfFormatWriter ncWriter = null; + try { + NetcdfFormatWriter.Builder file = NetcdfFormatWriter.createNewNetcdf3( + testUnlimitedFileName); + Group.Builder rootGroup = file.getRootGroup(); + + // add the unlimited time dimension + // Dimension timeDim = file.addUnlimitedDimension("time"); + + // alternative way to add the unlimited dimension + Dimension timeDim = Dimension.builder().setName("time").setIsUnlimited(true).setLength(0).build(); + rootGroup.addDimension(timeDim); + + ArrayList dims = new ArrayList(); + dims.add(timeDim); + + // define Variables + Variable.Builder timeVar = NcHelper.addVariable(rootGroup, "time", DataType.DOUBLE, dims); + timeVar.addAttribute(new Attribute("units", "seconds since 1970-01-01")); + + Variable.Builder latVar = NcHelper.addVariable(rootGroup, "lat", DataType.DOUBLE, dims); + latVar.addAttribute(new Attribute("units", "degrees_north")); + + Variable.Builder lonVar = NcHelper.addVariable(rootGroup, "lon", DataType.DOUBLE, dims); + lonVar.addAttribute(new Attribute("units", "degrees_east")); + + Variable.Builder sstVar = NcHelper.addVariable(rootGroup, "sst", DataType.DOUBLE, dims); + sstVar.addAttribute(new Attribute("units", "degree_C")); + + Variable.Builder commentVar = NcHelper.addNc3StringVariable(rootGroup, "comment", dims, strlen); + + // create the file + ncWriter = file.build(); + + // optional + ncWriter.close(); + ncWriter = null; + + // ncdump it + // String2.log("\nInitially:\n" + NcHelper.ncdump(testUnlimitedFileName, "")); + + // write 1 row at a time to the file + for (row = 0; row < 5; row++) { + Math2.sleep(20); + if (ncWriter == null) + ncWriter = NetcdfFormatWriter.openExisting(testUnlimitedFileName).build(); + // String2.log("writing row=" + row); + + int[] origin1 = new int[] { row }; + int[] origin2 = new int[] { row, 0 }; + Array array; + ArrayChar.D2 ac = new ArrayChar.D2(1, strlen); + + double cTime = System.currentTimeMillis() / 1000.0; + array = NcHelper.get1DArray(new double[] { row }, false); + ncWriter.write(ncWriter.findVariable("time"), origin1, array); + // String2.log(">> array=" + array.toString()); + array = NcHelper.get1DArray(new double[] { 33.33 }, false); + ncWriter.write(ncWriter.findVariable("lat"), origin1, array); + array = NcHelper.get1DArray(new double[] { -123.45 }, false); + ncWriter.write(ncWriter.findVariable("lon"), origin1, array); + array = NcHelper.get1DArray(new double[] { 10 + row / 10.0 }, false); + ncWriter.write(ncWriter.findVariable("sst"), origin1, array); + ac.setString(0, row + " comment"); + ncWriter.write(ncWriter.findVariable("comment"), origin2, ac); + ncWriter.close(); + ncWriter = null; + + // String2.log("\nrow=" + row + ":\n" + NcHelper.ncdump(testUnlimitedFileName, + // "")); + + /* + * if (row == 1) { + * results = NcHelper.ncdump(testUnlimitedFileName, ""); + * String2.log(results); + * expected = + * "netcdf unlimited.nc {\n" + //2013-09-03 netcdf-java 4.3 added blank lines + * " dimensions:\n" + + * " time = UNLIMITED; // (2 currently)\n" + + * " comment_strlen = 6;\n" + + * " variables:\n" + + * " double time(time=2);\n" + + * " :units = \"seconds since 1970-01-01\";\n" + + * "\n" + + * " double lat(time=2);\n" + + * " :units = \"degrees_north\";\n" + + * "\n" + + * " double lon(time=2);\n" + + * " :units = \"degrees_east\";\n" + + * "\n" + + * " double sst(time=2);\n" + + * " :units = \"degree_C\";\n" + + * "\n" + + * " char comment(time=2, comment_strlen=6);\n" + + * "\n" + + * "\n" + + * " data:\n" + + * " time = \n" + + * " {0.0, 1.0}\n" + + * " lat = \n" + + * " {33.33, 33.33}\n" + + * " lon = \n" + + * " {-123.45, -123.45}\n" + + * " sst = \n" + + * " {10.0, 10.1}\n" + + * " comment = \"0 comm\", \"1 comm\"\n" + + * "}\n"; + * if (!results.equals(expected)) { + * ncWriter.close(); + * ncWriter = null; + * Test.ensureEqual(results, expected, "trouble when i==1"); + * } + * } + */ + } + + // NOTE: instead of closing the ncWriter to write changes to disk, you can use + // ncWriter.flush(). + if (ncWriter != null) { + try { + ncWriter.abort(); + } catch (Exception e9) { + } + File2.delete(testUnlimitedFileName); + ncWriter = null; + } + } catch (Exception e9) { + String2.log("row=" + row + " " + NcHelper.ERROR_WHILE_CREATING_NC_FILE + MustBe.throwableToString(e9)); + if (ncWriter != null) { + try { + ncWriter.abort(); + } catch (Exception e8) { + } + File2.delete(testUnlimitedFileName); + ncWriter = null; + } + throw e9; + } + + results = NcHelper.ncdump(testUnlimitedFileName, ""); + // String2.log(results); + expected = "netcdf unlimited.nc {\n" + // 2013-09-03 netcdf-java 4.3 added blank lines + " dimensions:\n" + + " time = UNLIMITED; // (5 currently)\n" + + " comment_strlen = 6;\n" + + " variables:\n" + + " double time(time=5);\n" + + " :units = \"seconds since 1970-01-01\";\n" + + "\n" + + " double lat(time=5);\n" + + " :units = \"degrees_north\";\n" + + "\n" + + " double lon(time=5);\n" + + " :units = \"degrees_east\";\n" + + "\n" + + " double sst(time=5);\n" + + " :units = \"degree_C\";\n" + + "\n" + + " char comment(time=5, comment_strlen=6);\n" + + "\n" + + "\n" + + " data:\n" + + " time = \n" + + " {0.0, 1.0, 2.0, 3.0, 4.0}\n" + + " lat = \n" + + " {33.33, 33.33, 33.33, 33.33, 33.33}\n" + + " lon = \n" + + " {-123.45, -123.45, -123.45, -123.45, -123.45}\n" + + " sst = \n" + + " {10.0, 10.1, 10.2, 10.3, 10.4}\n" + + " comment = \"0 comm\", \"1 comm\", \"2 comm\", \"3 comm\", \"4 comm\"\n" + + "}\n"; + Test.ensureEqual(results, expected, ""); + + } +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/griddata/OpendapHelperTests.java b/src/test/java/gov/noaa/pfel/coastwatch/griddata/OpendapHelperTests.java new file mode 100644 index 000000000..ad2f98f12 --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/griddata/OpendapHelperTests.java @@ -0,0 +1,1232 @@ +package gov.noaa.pfel.coastwatch.griddata; + +import java.nio.file.Path; + +import org.junit.jupiter.api.io.TempDir; + +import com.cohort.array.Attributes; +import com.cohort.util.Calendar2; +import com.cohort.util.File2; +import com.cohort.util.MustBe; +import com.cohort.util.String2; +import com.cohort.util.Test; + +/** The Java DAP classes. */ +import dods.dap.DAS; +import dods.dap.DConnect; +import dods.dap.DDS; +import tags.TagExternalERDDAP; +import tags.TagThredds; + +class OpendapHelperTests { + + @TempDir + private static Path TEMP_DIR; + + @org.junit.jupiter.api.Test + /** This tests getting attibutes, notably the DODS_strlen attribute. */ + void testGetAttributes() throws Throwable { + String url = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; + String2.log("\n* OpendapHelper.testGetAttributes\n" + url); + DConnect dConnect = new DConnect(url, true, 1, 1); + DAS das = dConnect.getDAS(OpendapHelper.DEFAULT_TIMEOUT); + Attributes atts = new Attributes(); + OpendapHelper.getAttributes(das, "flag", atts); + + String results = atts.toString(); + String expected = // the DODS_ attributes are from an attribute that is a container. + " A=Units added\n" + + " B=Data out of range\n" + + " C=Non-sequential time\n" + + " D=Failed T>=Tw>=Td\n" + + " DODS_dimName=f_string\n" + + " DODS_strlen=13i\n" + + " E=True wind error\n" + + " F=Velocity unrealistic\n" + + " G=Value > 4 s. d. from climatology\n" + + " H=Discontinuity\n" + + " I=Interesting feature\n" + + " J=Erroneous\n" + + " K=Suspect - visual\n" + + " L=Ocean platform over land\n" + + " long_name=quality control flags\n" + + " M=Instrument malfunction\n" + + " N=In Port\n" + + " O=Multiple original units\n" + + " P=Movement uncertain\n" + + " Q=Pre-flagged as suspect\n" + + " R=Interpolated data\n" + + " S=Spike - visual\n" + + " T=Time duplicate\n" + + " U=Suspect - statistial\n" + + " V=Spike - statistical\n" + + " X=Step - statistical\n" + + " Y=Suspect between X-flags\n" + + " Z=Good data\n"; + Test.ensureEqual(results, expected, "results=" + results); + } + + /** This tests dapToNc DArray. */ + @org.junit.jupiter.api.Test + @TagThredds + void testDapToNcDArray() throws Throwable { + String2.log("\n\n*** OpendapHelper.testDapToNcDArray()"); + String fileName, expected, results; + String today = Calendar2.getCurrentISODateTimeStringLocalTZ().substring(0, 10); + + fileName = TEMP_DIR.toAbsolutePath() + "/testDapToNcDArray.nc"; + String dArrayUrl = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; + OpendapHelper.dapToNc(dArrayUrl, + // note that request for zztop is ignored (because not found) + new String[] { "zztop", "time", "lat", "lon", "PL_HD", "flag" }, null, // projection + fileName, false); // jplMode + results = NcHelper.ncdump(fileName, ""); // printData + expected = "netcdf testDapToNcDArray.nc {\n" + + " dimensions:\n" + + " time = 144;\n" + + " flag_strlen = 13;\n" + + " variables:\n" + + " int time(time=144);\n" + + " :actual_range = 16870896, 16871039; // int\n" + + " :data_interval = 60; // int\n" + + " :long_name = \"time\";\n" + + " :observation_type = \"calculated\";\n" + + " :original_units = \"hhmmss UTC\";\n" + + " :qcindex = 1; // int\n" + + " :units = \"minutes since 1-1-1980 00:00 UTC\";\n" + + "\n" + + " float lat(time=144);\n" + + " :actual_range = 44.6f, 44.75f; // float\n" + + " :average_center = \"time at end of period\";\n" + + " :average_length = 60S; // short\n" + + " :average_method = \"average\";\n" + + " :data_precision = -9999.0f; // float\n" + + " :instrument = \"unknown\";\n" + + " :long_name = \"latitude\";\n" + + " :observation_type = \"measured\";\n" + + " :original_units = \"degrees (+N)\";\n" + + " :qcindex = 2; // int\n" + + " :sampling_rate = 1.0f; // float\n" + + " :units = \"degrees (+N)\";\n" + + "\n" + + " float lon(time=144);\n" + + " :actual_range = 235.82f, 235.95f; // float\n" + + " :average_center = \"time at end of period\";\n" + + " :average_length = 60S; // short\n" + + " :average_method = \"average\";\n" + + " :data_precision = -9999.0f; // float\n" + + " :instrument = \"unknown\";\n" + + " :long_name = \"longitude\";\n" + + " :observation_type = \"measured\";\n" + + " :original_units = \"degrees (-W/+E)\";\n" + + " :qcindex = 3; // int\n" + + " :sampling_rate = 1.0f; // float\n" + + " :units = \"degrees (+E)\";\n" + + "\n" + + " float PL_HD(time=144);\n" + + " :actual_range = 37.89f, 355.17f; // float\n" + + " :average_center = \"time at end of period\";\n" + + " :average_length = 60S; // short\n" + + " :average_method = \"average\";\n" + + " :data_precision = -9999.0f; // float\n" + + " :instrument = \"unknown\";\n" + + " :long_name = \"platform heading\";\n" + + " :missing_value = -9999.0f; // float\n" + + " :observation_type = \"calculated\";\n" + + " :original_units = \"degrees (clockwise towards true north)\";\n" + + " :qcindex = 4; // int\n" + + " :sampling_rate = 1.0f; // float\n" + + " :special_value = -8888.0f; // float\n" + + " :units = \"degrees (clockwise towards true north)\";\n" + + "\n" + + " char flag(time=144, flag_strlen=13);\n" + + " :A = \"Units added\";\n" + + " :B = \"Data out of range\";\n" + + " :C = \"Non-sequential time\";\n" + + " :D = \"Failed T>=Tw>=Td\";\n" + + " :DODS_dimName = \"f_string\";\n" + + " :DODS_strlen = 13; // int\n" + + " :E = \"True wind error\";\n" + + " :F = \"Velocity unrealistic\";\n" + + " :G = \"Value > 4 s. d. from climatology\";\n" + + " :H = \"Discontinuity\";\n" + + " :I = \"Interesting feature\";\n" + + " :J = \"Erroneous\";\n" + + " :K = \"Suspect - visual\";\n" + + " :L = \"Ocean platform over land\";\n" + + " :long_name = \"quality control flags\";\n" + + " :M = \"Instrument malfunction\";\n" + + " :N = \"In Port\";\n" + + " :O = \"Multiple original units\";\n" + + " :P = \"Movement uncertain\";\n" + + " :Q = \"Pre-flagged as suspect\";\n" + + " :R = \"Interpolated data\";\n" + + " :S = \"Spike - visual\";\n" + + " :T = \"Time duplicate\";\n" + + " :U = \"Suspect - statistial\";\n" + + " :V = \"Spike - statistical\";\n" + + " :X = \"Step - statistical\";\n" + + " :Y = \"Suspect between X-flags\";\n" + + " :Z = \"Good data\";\n" + + "\n" + + " // global attributes:\n" + + " :contact_email = \"samos@coaps.fsu.edu\";\n" + + " :contact_info = \"Center for Ocean-Atmospheric Prediction Studies, The Florida State University, Tallahassee, FL, 32306-2840, USA\";\n" + + + " :Cruise_id = \"Cruise_id undefined for now\";\n" + + " :Data_modification_date = \"02/07/2012 10:03:37 EST\";\n" + + " :data_provider = \"Timothy Salisbury\";\n" + + " :elev = 0S; // short\n" + + " :end_date_time = \"2012/01/28 -- 23:59 UTC\";\n" + + " :EXPOCODE = \"EXPOCODE undefined for now\";\n" + + " :facility = \"NOAA\";\n" + + " :fsu_version = \"300\";\n" + + " :ID = \"WTEP\";\n" + + " :IMO = \"009270335\";\n" + + " :Metadata_modification_date = \"02/07/2012 10:03:37 EST\";\n" + + " :platform = \"SCS\";\n" + + " :platform_version = \"4.0\";\n" + + " :receipt_order = \"01\";\n" + + " :site = \"OSCAR DYSON\";\n" + + " :start_date_time = \"2012/01/28 -- 21:36 UTC\";\n" + + " :title = \"OSCAR DYSON Meteorological Data\";\n" + + "\n" + + " data:\n" + + " time = \n" + + " {16870896, 16870897, 16870898, 16870899, 16870900, 16870901, 16870902, 16870903, 16870904, 16870905, 16870906, 16870907, 16870908, 16870909, 16870910, 16870911, 16870912, 16870913, 16870914, 16870915, 16870916, 16870917, 16870918, 16870919, 16870920, 16870921, 16870922, 16870923, 16870924, 16870925, 16870926, 16870927, 16870928, 16870929, 16870930, 16870931, 16870932, 16870933, 16870934, 16870935, 16870936, 16870937, 16870938, 16870939, 16870940, 16870941, 16870942, 16870943, 16870944, 16870945, 16870946, 16870947, 16870948, 16870949, 16870950, 16870951, 16870952, 16870953, 16870954, 16870955, 16870956, 16870957, 16870958, 16870959, 16870960, 16870961, 16870962, 16870963, 16870964, 16870965, 16870966, 16870967, 16870968, 16870969, 16870970, 16870971, 16870972, 16870973, 16870974, 16870975, 16870976, 16870977, 16870978, 16870979, 16870980, 16870981, 16870982, 16870983, 16870984, 16870985, 16870986, 16870987, 16870988, 16870989, 16870990, 16870991, 16870992, 16870993, 16870994, 16870995, 16870996, 16870997, 16870998, 16870999, 16871000, 16871001, 16871002, 16871003, 16871004, 16871005, 16871006, 16871007, 16871008, 16871009, 16871010, 16871011, 16871012, 16871013, 16871014, 16871015, 16871016, 16871017, 16871018, 16871019, 16871020, 16871021, 16871022, 16871023, 16871024, 16871025, 16871026, 16871027, 16871028, 16871029, 16871030, 16871031, 16871032, 16871033, 16871034, 16871035, 16871036, 16871037, 16871038, 16871039}\n" + + + " lat = \n" + + " {44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.62, 44.62, 44.62, 44.62, 44.62, 44.62, 44.62, 44.61, 44.61, 44.61, 44.61, 44.61, 44.61, 44.61, 44.61, 44.6, 44.6, 44.6, 44.6, 44.6, 44.6, 44.61, 44.61, 44.61, 44.61, 44.62, 44.62, 44.62, 44.62, 44.63, 44.63, 44.63, 44.64, 44.64, 44.64, 44.65, 44.65, 44.65, 44.66, 44.66, 44.66, 44.67, 44.67, 44.67, 44.68, 44.68, 44.68, 44.69, 44.69, 44.69, 44.7, 44.7, 44.7, 44.71, 44.71, 44.71, 44.72, 44.72, 44.72, 44.73, 44.73, 44.73, 44.73, 44.74, 44.74, 44.74, 44.75}\n" + + + " lon = \n" + + " {235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.94, 235.94, 235.94, 235.94, 235.94, 235.94, 235.93, 235.93, 235.93, 235.92, 235.92, 235.92, 235.91, 235.91, 235.91, 235.9, 235.9, 235.9, 235.89, 235.89, 235.88, 235.88, 235.88, 235.88, 235.88, 235.88, 235.87, 235.87, 235.87, 235.87, 235.87, 235.87, 235.87, 235.86, 235.86, 235.86, 235.86, 235.86, 235.86, 235.86, 235.85, 235.85, 235.85, 235.85, 235.85, 235.85, 235.85, 235.85, 235.85, 235.84, 235.84, 235.84, 235.84, 235.84, 235.84, 235.83, 235.83, 235.83, 235.83, 235.83, 235.82, 235.82, 235.82, 235.82, 235.82, 235.82, 235.82}\n" + + + " PL_HD = \n" + + " {75.53, 75.57, 75.97, 76.0, 75.81, 75.58, 75.99, 75.98, 75.77, 75.61, 75.72, 75.75, 75.93, 75.96, 76.01, 75.64, 75.65, 75.94, 75.93, 76.12, 76.65, 76.42, 76.25, 75.81, 76.5, 76.09, 76.35, 76.0, 76.16, 76.36, 76.43, 75.99, 75.93, 76.41, 75.85, 76.07, 76.15, 76.33, 76.7, 76.37, 76.58, 76.89, 77.14, 76.81, 74.73, 75.24, 74.52, 81.04, 80.64, 73.21, 63.34, 37.89, 347.02, 309.93, 290.99, 285.0, 279.38, 276.45, 270.26, 266.33, 266.49, 266.08, 263.59, 261.41, 259.05, 259.82, 260.35, 262.78, 258.73, 249.71, 246.52, 245.78, 246.16, 245.88, 243.52, 231.62, 223.09, 221.08, 221.01, 221.08, 220.81, 223.64, 234.12, 239.55, 241.08, 242.09, 242.04, 242.33, 242.06, 242.22, 242.11, 242.3, 242.07, 247.35, 285.6, 287.02, 287.96, 288.37, 321.32, 344.82, 346.91, 344.78, 347.95, 344.75, 344.66, 344.78, 344.7, 344.76, 343.89, 336.73, 334.01, 340.23, 344.76, 348.25, 348.74, 348.63, 351.97, 344.55, 343.77, 343.71, 347.04, 349.06, 349.45, 349.79, 349.66, 349.7, 349.74, 344.2, 343.22, 341.79, 339.11, 334.12, 334.47, 334.62, 334.7, 334.66, 327.06, 335.74, 348.25, 351.05, 355.17, 343.66, 346.85, 347.28}\n" + + + " flag = \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZEZZSZZZZ\", \"ZZZZZEZZSZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\", \"ZZZZZZZZZZZZZ\"\n" + + + "}\n"; + Test.ensureEqual(results, expected, "results=" + results); + File2.delete(fileName); + + // test subset + try { + String2.log("\n* testDapToNcDArray Subset"); + fileName = TEMP_DIR.toAbsolutePath() + "/testDapToNcDArraySubset.nc"; + System.out.println(fileName); + String dArraySubsetUrl = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; + OpendapHelper.dapToNc(dArraySubsetUrl, + new String[] { "zztop", "time", "lat", "lon", "PL_HD", "flag" }, "[0:10:99]", // projection + fileName, false); // jplMode + results = NcHelper.ncdump(fileName, ""); // printData + expected = "netcdf testDapToNcDArraySubset.nc {\n" + + " dimensions:\n" + + " time = 10;\n" + + " variables:\n" + + " int time(time=10);\n" + + " :actual_range = 16870896, 16871039; // int\n" + + " :data_interval = 60; // int\n" + + " :long_name = \"time\";\n" + + " :observation_type = \"calculated\";\n" + + " :original_units = \"hhmmss UTC\";\n" + + " :qcindex = 1; // int\n" + + " :units = \"minutes since 1-1-1980 00:00 UTC\";\n" + + " float lat(time=10);\n" + + " :actual_range = 44.6f, 44.75f; // float\n" + + " :average_center = \"time at end of period\";\n" + + " :average_length = 60S; // short\n" + + " :average_method = \"average\";\n" + + " :data_precision = -9999.0f; // float\n" + + " :instrument = \"unknown\";\n" + + " :long_name = \"latitude\";\n" + + " :observation_type = \"measured\";\n" + + " :original_units = \"degrees (+N)\";\n" + + " :qcindex = 2; // int\n" + + " :sampling_rate = 1.0f; // float\n" + + " :units = \"degrees (+N)\";\n" + + " float lon(time=10);\n" + + " :actual_range = 235.82f, 235.95f; // float\n" + + " :average_center = \"time at end of period\";\n" + + " :average_length = 60S; // short\n" + + " :average_method = \"average\";\n" + + " :data_precision = -9999.0f; // float\n" + + " :instrument = \"unknown\";\n" + + " :long_name = \"longitude\";\n" + + " :observation_type = \"measured\";\n" + + " :original_units = \"degrees (-W/+E)\";\n" + + " :qcindex = 3; // int\n" + + " :sampling_rate = 1.0f; // float\n" + + " :units = \"degrees (+E)\";\n" + + " float PL_HD(time=10);\n" + + " :actual_range = 37.89f, 355.17f; // float\n" + + " :average_center = \"time at end of period\";\n" + + " :average_length = 60S; // short\n" + + " :average_method = \"average\";\n" + + " :data_precision = -9999.0f; // float\n" + + " :instrument = \"unknown\";\n" + + " :long_name = \"platform heading\";\n" + + " :missing_value = -9999.0f; // float\n" + + " :observation_type = \"calculated\";\n" + + " :original_units = \"degrees (clockwise towards true north)\";\n" + + " :qcindex = 4; // int\n" + + " :sampling_rate = 1.0f; // float\n" + + " :special_value = -8888.0f; // float\n" + + " :units = \"degrees (clockwise towards true north)\";\n" + + "\n" + + " :contact_email = \"samos@coaps.fsu.edu\";\n" + + " :contact_info = \"Center for Ocean-Atmospheric Prediction Studies, The Florida State University, Tallahassee, FL, 32306-2840, USA\";\n" + + + " :Cruise_id = \"Cruise_id undefined for now\";\n" + + " :Data_modification_date = \"02/07/2012 10:03:37 EST\";\n" + + " :data_provider = \"Timothy Salisbury\";\n" + + " :elev = 0S; // short\n" + + " :end_date_time = \"2012/01/28 -- 23:59 UTC\";\n" + + " :EXPOCODE = \"EXPOCODE undefined for now\";\n" + + " :facility = \"NOAA\";\n" + + " :fsu_version = \"300\";\n" + + " :ID = \"WTEP\";\n" + + " :IMO = \"009270335\";\n" + + " :Metadata_modification_date = \"02/07/2012 10:03:37 EST\";\n" + + " :platform = \"SCS\";\n" + + " :platform_version = \"4.0\";\n" + + " :receipt_order = \"01\";\n" + + " :site = \"OSCAR DYSON\";\n" + + " :start_date_time = \"2012/01/28 -- 21:36 UTC\";\n" + + " :title = \"OSCAR DYSON Meteorological Data\";\n" + + " data:\n" + + "time =\n" + + " {16870896, 16870906, 16870916, 16870926, 16870936, 16870946, 16870956, 16870966, 16870976, 16870986}\n" + + "lat =\n" + + " {44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.62, 44.61}\n" + + "lon =\n" + + " {235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.94, 235.91}\n" + + "PL_HD =\n" + + " {75.53, 75.72, 76.65, 76.43, 76.58, 63.34, 266.49, 246.52, 220.81, 242.11}\n" + + "}\n"; + /* + * from + * https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/ + * WTEP_20120128v30001.nc.ascii?time[0:10:99],lat[0:10:99],lon[0:10:99],PL_HD[0: + * 10:99] + * time[10] 16870896, 16870906, 16870916, 16870926, 16870936, 16870946, + * 16870956, 16870966, 16870976, 16870986 + * lat[10] 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.63, 44.62, 44.61 + * lon[10] 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, 235.95, + * 235.94, 235.91 + * PL_HD[10] 75.53, 75.72, 76.65, 76.43, 76.58, 63.34, 266.49, 246.52, 220.81, + * 242.11 + */ + Test.ensureEqual(results, expected, "results=" + results); + File2.delete(fileName); + if (true) + throw new RuntimeException("shouldn't get here"); + } catch (OutOfMemoryError oome) { + Test.knownProblem( + "THREDDS OutOfMemoryError. I reported it to John Caron.", + "2012-03-02 A TDS problem. I reported it to John Caron:\n" + + MustBe.throwableToString(oome)); + // OpendapHelper.getPrimitiveArrays ?flag[0:10:99] + // Exception in thread "main" java.lang.OutOfMemoryError: Java heap space + // at + // dods.dap.BaseTypePrimitiveVector.setLength(BaseTypePrimitiveVector.java:69) + // at dods.dap.DVector.deserialize(DVector.java:221) + // at dods.dap.DataDDS.readData(DataDDS.java:75) + // at dods.dap.DConnect.getDataFromUrl(DConnect.java:523) + // at dods.dap.DConnect.getData(DConnect.java:450) + // at dods.dap.DConnect.getData(DConnect.java:633) + // at + // gov.noaa.pfel.coastwatch.griddata.OpendapHelper.getPrimitiveArrays(OpendapHelper.java:458) + // at + // gov.noaa.pfel.coastwatch.griddata.OpendapHelper.dapToNc(OpendapHelper.java:1398) + // at + // gov.noaa.pfel.coastwatch.griddata.OpendapHelper.testDapToNcDArray(OpendapHelper.java:1628) + // at gov.noaa.pfel.coastwatch.TestAll.main(TestAll.java:723) + } catch (Throwable t) { + Test.knownProblem( + "\nOutOfMememoryError from TDS bug was expected (but 404 Not Found/ 'Connection cannont be read' is also common)." + + + "\n(server timed out 2013-10-24)", + t); + } + + // test DArray error caused by history having different dimensions + String2.log("\n*** test DArray error cause by history having different dimensions"); + try { + OpendapHelper.dapToNc(dArrayUrl, + new String[] { "zztop", "time", "lat", "lon", "PL_HD", "history" }, null, // projection + fileName, false); // jplMode + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + results = t.toString(); + expected = "java.lang.RuntimeException: ERROR in OpendapHelper.dapToNc\n" + + " url=https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc\n" + + " varNames=zztop,time,lat,lon,PL_HD,history projection=null\n" + + " file=C:/programs/_tomcat/webapps/cwexperimental/WEB-INF/temp/testDapToNcDArraySubset.nc\n" + + "var=history has different dimensions than previous vars."; + if (results.indexOf("java.net.ConnectException: Connection timed out: connect") >= 0) + String2.pressEnterToContinue(MustBe.throwableToString(t) + + "\nurl=" + dArrayUrl + + "\n(The server timed out 2013-10-24.)"); + else if (results.startsWith("dods.dap.DODSException: Connection cannot be opened")) + String2.pressEnterToContinue(MustBe.throwableToString(t) + + "\nurl=" + dArrayUrl + + "\n(The connection can't be opened 2019-11-25.)"); + else + Test.ensureEqual(results, expected, "results=" + results); + } + + String2.log("\n*** OpendapHelper.testDapToNcDArray finished."); + } + + /** This tests dapToNc DGrid. */ + @org.junit.jupiter.api.Test + @TagExternalERDDAP + void testDapToNcDGrid() throws Throwable { + String2.log("\n\n*** OpendapHelper.testDapToNcDGrid"); + String fileName, expected, results; + String today = Calendar2.getCurrentISODateTimeStringZulu().substring(0, 10); + + fileName = TEMP_DIR.toAbsolutePath() + "/testDapToNcDGrid.nc"; + System.out.println(fileName); + String dGridUrl = "https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday"; + OpendapHelper.dapToNc(dGridUrl, + // note that request for zztop is ignored (because not found) + new String[] { "zztop", "x_wind", "y_wind" }, "[5][0][0:200:1200][0:200:2880]", // projection + fileName, false); // jplMode + results = NcHelper.ncdump(fileName, ""); // printData + expected = "netcdf testDapToNcDGrid.nc {\n" + + " dimensions:\n" + + " time = 1;\n" + + " altitude = 1;\n" + + " latitude = 7;\n" + + " longitude = 15;\n" + + " variables:\n" + + " double time(time=1);\n" + + " :_CoordinateAxisType = \"Time\";\n" + + " :actual_range = 9.348048E8, 1.2556944E9; // double\n" + + " :axis = \"T\";\n" + + " :fraction_digits = 0; // int\n" + + " :ioos_category = \"Time\";\n" + + " :long_name = \"Centered Time\";\n" + + " :standard_name = \"time\";\n" + + " :time_origin = \"01-JAN-1970 00:00:00\";\n" + + " :units = \"seconds since 1970-01-01T00:00:00Z\";\n" + + "\n" + + " double altitude(altitude=1);\n" + + " :_CoordinateAxisType = \"Height\";\n" + + " :_CoordinateZisPositive = \"up\";\n" + + " :actual_range = 10.0, 10.0; // double\n" + + " :axis = \"Z\";\n" + + " :fraction_digits = 0; // int\n" + + " :ioos_category = \"Location\";\n" + + " :long_name = \"Altitude\";\n" + + " :positive = \"up\";\n" + + " :standard_name = \"altitude\";\n" + + " :units = \"m\";\n" + + "\n" + + " double latitude(latitude=7);\n" + + " :_CoordinateAxisType = \"Lat\";\n" + + " :actual_range = -75.0, 75.0; // double\n" + + " :axis = \"Y\";\n" + + " :coordsys = \"geographic\";\n" + + " :fraction_digits = 2; // int\n" + + " :ioos_category = \"Location\";\n" + + " :long_name = \"Latitude\";\n" + + " :point_spacing = \"even\";\n" + + " :standard_name = \"latitude\";\n" + + " :units = \"degrees_north\";\n" + + "\n" + + " double longitude(longitude=15);\n" + + " :_CoordinateAxisType = \"Lon\";\n" + + " :actual_range = 0.0, 360.0; // double\n" + + " :axis = \"X\";\n" + + " :coordsys = \"geographic\";\n" + + " :fraction_digits = 2; // int\n" + + " :ioos_category = \"Location\";\n" + + " :long_name = \"Longitude\";\n" + + " :point_spacing = \"even\";\n" + + " :standard_name = \"longitude\";\n" + + " :units = \"degrees_east\";\n" + + "\n" + + " float x_wind(time=1, altitude=1, latitude=7, longitude=15);\n" + + " :_FillValue = -9999999.0f; // float\n" + + " :colorBarMaximum = 15.0; // double\n" + + " :colorBarMinimum = -15.0; // double\n" + + " :coordsys = \"geographic\";\n" + + " :fraction_digits = 1; // int\n" + + " :ioos_category = \"Wind\";\n" + + " :long_name = \"Zonal Wind\";\n" + + " :missing_value = -9999999.0f; // float\n" + + " :standard_name = \"x_wind\";\n" + + " :units = \"m s-1\";\n" + + "\n" + + " float y_wind(time=1, altitude=1, latitude=7, longitude=15);\n" + + " :_FillValue = -9999999.0f; // float\n" + + " :colorBarMaximum = 15.0; // double\n" + + " :colorBarMinimum = -15.0; // double\n" + + " :coordsys = \"geographic\";\n" + + " :fraction_digits = 1; // int\n" + + " :ioos_category = \"Wind\";\n" + + " :long_name = \"Meridional Wind\";\n" + + " :missing_value = -9999999.0f; // float\n" + + " :standard_name = \"y_wind\";\n" + + " :units = \"m s-1\";\n" + + "\n" + + " // global attributes:\n" + + " :acknowledgement = \"NOAA NESDIS COASTWATCH, NOAA SWFSC ERD\";\n" + + " :cdm_data_type = \"Grid\";\n" + + " :composite = \"true\";\n" + + " :contributor_name = \"Remote Sensing Systems, Inc.\";\n" + + " :contributor_role = \"Source of level 2 data.\";\n" + + " :Conventions = \"COARDS, CF-1.6, ACDD-1.3\";\n" + + " :creator_email = \"erd.data@noaa.gov\";\n" + + " :creator_name = \"NOAA NMFS SWFSC ERD\";\n" + + " :creator_type = \"institution\";\n" + + " :creator_url = \"https://www.pfeg.noaa.gov\";\n" + + " :date_created = \"2010-07-02\";\n" + + " :date_issued = \"2010-07-02\";\n" + + " :defaultGraphQuery = \"&.draw=vectors\";\n" + + " :Easternmost_Easting = 360.0; // double\n" + + " :geospatial_lat_max = 75.0; // double\n" + + " :geospatial_lat_min = -75.0; // double\n" + + " :geospatial_lat_resolution = 0.125; // double\n" + + " :geospatial_lat_units = \"degrees_north\";\n" + + " :geospatial_lon_max = 360.0; // double\n" + + " :geospatial_lon_min = 0.0; // double\n" + + " :geospatial_lon_resolution = 0.125; // double\n" + + " :geospatial_lon_units = \"degrees_east\";\n" + + " :geospatial_vertical_max = 10.0; // double\n" + + " :geospatial_vertical_min = 10.0; // double\n" + + " :geospatial_vertical_positive = \"up\";\n" + + " :geospatial_vertical_units = \"m\";\n" + + " :history = \"Remote Sensing Systems, Inc.\n" + + "2010-07-02T15:36:22Z NOAA CoastWatch (West Coast Node) and NOAA SFSC ERD\n" + + today + "T"; // + time " + // https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/QS/ux10/mday\n" + + // today + " + // https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday.das\";\n" + + String expected2 = " :infoUrl = \"https://coastwatch.pfeg.noaa.gov/infog/QS_ux10_las.html\";\n" + + " :institution = \"NOAA NMFS SWFSC ERD\";\n" + + " :keywords = \"altitude, atmosphere, atmospheric, coast, coastwatch, data, degrees, Earth Science > Atmosphere > Atmospheric Winds > Surface Winds, Earth Science > Oceans > Ocean Winds > Surface Winds, global, noaa, node, ocean, oceans, QSux10, quality, quikscat, science, science quality, seawinds, surface, time, wcn, west, wind, winds, x_wind, zonal\";\n" + + + " :keywords_vocabulary = \"GCMD Science Keywords\";\n" + + " :license = \"The data may be used and redistributed for free but is not intended\n" + + "for legal use, since it may contain inaccuracies. Neither the data\n" + + "Contributor, ERD, NOAA, nor the United States Government, nor any\n" + + "of their employees or contractors, makes any warranty, express or\n" + + "implied, including warranties of merchantability and fitness for a\n" + + "particular purpose, or assumes any legal liability for the accuracy,\n" + + "completeness, or usefulness, of this information.\";\n" + + " :naming_authority = \"gov.noaa.pfeg.coastwatch\";\n" + + " :Northernmost_Northing = 75.0; // double\n" + + " :origin = \"Remote Sensing Systems, Inc.\";\n" + + " :processing_level = \"3\";\n" + + " :project = \"CoastWatch (https://coastwatch.noaa.gov/)\";\n" + + " :projection = \"geographic\";\n" + + " :projection_type = \"mapped\";\n" + + " :publisher_email = \"erd.data@noaa.gov\";\n" + + " :publisher_name = \"NOAA NMFS SWFSC ERD\";\n" + + " :publisher_type = \"institution\";\n" + + " :publisher_url = \"https://www.pfeg.noaa.gov\";\n" + + " :references = \"RSS Inc. Winds: http://www.remss.com/ .\";\n" + + " :satellite = \"QuikSCAT\";\n" + + " :sensor = \"SeaWinds\";\n" + + " :source = \"satellite observation: QuikSCAT, SeaWinds\";\n" + + " :sourceUrl = \"(local files)\";\n" + + " :Southernmost_Northing = -75.0; // double\n" + + " :standard_name_vocabulary = \"CF Standard Name Table v70\";\n" + + " :summary = \"Remote Sensing Inc. distributes science quality wind velocity data from the SeaWinds instrument onboard NASA's QuikSCAT satellite. SeaWinds is a microwave scatterometer designed to measure surface winds over the global ocean. Wind velocity fields are provided in zonal, meridional, and modulus sets. The reference height for all wind velocities is 10 meters. (This is a monthly composite.)\";\n" + + + " :time_coverage_end = \"2009-10-16T12:00:00Z\";\n" + + " :time_coverage_start = \"1999-08-16T12:00:00Z\";\n" + + " :title = \"Wind, QuikSCAT SeaWinds, 0.125°, Global, Science Quality, 1999-2009 (Monthly)\";\n" + + " :Westernmost_Easting = 0.0; // double\n" + + "\n" + + " data:\n" + + " time = \n" + + " {9.48024E8}\n" + + " altitude = \n" + + " {10.0}\n" + + " latitude = \n" + + " {-75.0, -50.0, -25.0, 0.0, 25.0, 50.0, 75.0}\n" + + " longitude = \n" + + " {0.0, 25.0, 50.0, 75.0, 100.0, 125.0, 150.0, 175.0, 200.0, 225.0, 250.0, 275.0, 300.0, 325.0, 350.0}\n" + + " x_wind = \n" + + " {\n" + + " {\n" + + " {\n" + + " {-9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 0.76867574, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0},\n" + + + " {6.903795, 7.7432585, 8.052648, 7.375461, 8.358787, 7.5664454, 4.537408, 4.349131, 2.4506109, 2.1340106, 6.4230127, 8.5656395, 5.679372, 5.775274, 6.8520603},\n" + + + " {-3.513153, -9999999.0, -5.7222853, -4.0249896, -4.6091595, -9999999.0, -9999999.0, -3.9060166, -1.821446, -2.0546885, -2.349195, -4.2188687, -9999999.0, -0.7905332, -3.715024},\n" + + + " {0.38850072, -9999999.0, -2.8492346, 0.7843591, -9999999.0, -0.353197, -0.93183184, -5.3337674, -7.8715024, -5.2341905, -2.1567967, 0.46681255, -9999999.0, -3.7223456, -1.3264368},\n" + + + " {-9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -4.250928, -1.9779109, -2.3081408, -6.070514, -3.4209945, 2.3732827, -3.4732149, -3.2282434, -3.99131, -9999999.0},\n" + + + " {2.3816996, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 1.9863724, 1.746363, 5.305478, 2.3346918, -9999999.0, -9999999.0, 2.0079596, 3.4320266, 1.8692436},\n" + + + " {0.83961326, -3.4395192, -3.1952338, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -2.9099085}\n" + + + " }\n" + + " }\n" + + " }\n" + + " y_wind = \n" + + " {\n" + + " {\n" + + " {\n" + + " {-9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, 3.9745862, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0},\n" + + + " {-1.6358501, -2.1310546, -1.672539, -2.8083494, -1.7282568, -2.5679686, -0.032763753, 0.6524638, 0.9784334, -2.4545083, 0.6344165, -0.5887741, -0.6837046, -0.92711323, -1.9981208},\n" + + + " {3.7522712, -9999999.0, -0.04178731, 1.6603879, 5.321683, -9999999.0, -9999999.0, 1.5633415, -0.50912154, -2.964269, -0.92438585, 3.959174, -9999999.0, -2.2249718, 0.46982485},\n" + + + " {4.8992314, -9999999.0, -4.7178936, -3.2770228, -9999999.0, -2.8111093, -0.9852706, 0.46997508, 0.0683085, 0.46172503, 1.2998049, 3.5235379, -9999999.0, 1.1354263, 4.7139735},\n" + + + " {-9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -5.092368, -3.3667018, -0.60028434, -0.7609817, -1.114303, -3.6573937, -0.934499, -0.40036556, -2.5770886, -9999999.0},\n" + + + " {0.56877106, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -3.2394278, 0.45922723, -0.8394715, 0.7333555, -9999999.0, -9999999.0, -2.3936603, 3.725975, 0.09879057},\n" + + + " {-6.128998, 2.379096, 7.463917, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -11.026609}\n" + + + " }\n" + + " }\n" + + " }\n" + + "}\n"; + /* + * From .asc request: + * https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday.asc?x_wind[5][0 + * ][0:200:1200][0:200:2880],y_wind[5][0][0:200:1200][0:200:2880] + * x_wind.x_wind[1][1][7][15] + * [0][0][0], -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, -9999999.0, 0.76867574, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, -9999999.0, -9999999.0, -9999999.0 + * [0][0][1], 6.903795, 7.7432585, 8.052648, 7.375461, 8.358787, 7.5664454, + * 4.537408, 4.349131, 2.4506109, 2.1340106, 6.4230127, 8.5656395, 5.679372, + * 5.775274, 6.8520603 + * [0][0][2], -3.513153, -9999999.0, -5.7222853, -4.0249896, -4.6091595, + * -9999999.0, -9999999.0, -3.9060166, -1.821446, -2.0546885, -2.349195, + * -4.2188687, -9999999.0, -0.7905332, -3.715024 + * [0][0][3], 0.38850072, -9999999.0, -2.8492346, 0.7843591, -9999999.0, + * -0.353197, -0.93183184, -5.3337674, -7.8715024, -5.2341905, -2.1567967, + * 0.46681255, -9999999.0, -3.7223456, -1.3264368 + * [0][0][4], -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, + * -4.250928, -1.9779109, -2.3081408, -6.070514, -3.4209945, 2.3732827, + * -3.4732149, -3.2282434, -3.99131, -9999999.0 + * [0][0][5], 2.3816996, -9999999.0, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, 1.9863724, 1.746363, 5.305478, 2.3346918, -9999999.0, -9999999.0, + * 2.0079596, 3.4320266, 1.8692436 + * [0][0][6], 0.83961326, -3.4395192, -3.1952338, -9999999.0, -9999999.0, + * -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, -9999999.0, -9999999.0, -2.9099085 + * y_wind.y_wind[1][1][7][15] + * [0][0][0], -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, -9999999.0, 3.9745862, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, -9999999.0, -9999999.0, -9999999.0 + * [0][0][1], -1.6358501, -2.1310546, -1.672539, -2.8083494, -1.7282568, + * -2.5679686, -0.032763753, 0.6524638, 0.9784334, -2.4545083, 0.6344165, + * -0.5887741, -0.6837046, -0.92711323, -1.9981208 + * [0][0][2], 3.7522712, -9999999.0, -0.04178731, 1.6603879, 5.321683, + * -9999999.0, -9999999.0, 1.5633415, -0.50912154, -2.964269, -0.92438585, + * 3.959174, -9999999.0, -2.2249718, 0.46982485 + * [0][0][3], 4.8992314, -9999999.0, -4.7178936, -3.2770228, -9999999.0, + * -2.8111093, -0.9852706, 0.46997508, 0.0683085, 0.46172503, 1.2998049, + * 3.5235379, -9999999.0, 1.1354263, 4.7139735 + * [0][0][4], -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, + * -5.092368, -3.3667018, -0.60028434, -0.7609817, -1.114303, -3.6573937, + * -0.934499, -0.40036556, -2.5770886, -9999999.0 + * [0][0][5], 0.56877106, -9999999.0, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, -3.2394278, 0.45922723, -0.8394715, 0.7333555, -9999999.0, + * -9999999.0, -2.3936603, 3.725975, 0.09879057 + * [0][0][6], -6.128998, 2.379096, 7.463917, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, -9999999.0, + * -9999999.0, -9999999.0, -11.026609 + */ + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=" + results); + int po = results.indexOf(" :infoUrl ="); + Test.ensureEqual(results.substring(po), expected2, "results=" + results); + File2.delete(fileName); + + // test 1D var should be ignored if others are 2+D + String2.log("\n*** test 1D var should be ignored if others are 2+D"); + fileName = TEMP_DIR.toAbsolutePath() + "/testDapToNcDGrid1D2D.nc"; + OpendapHelper.dapToNc(dGridUrl, + new String[] { "zztop", "x_wind", "y_wind", "latitude" }, + "[5][0][0:200:1200][0:200:2880]", // projection + fileName, false); // jplMode + results = NcHelper.ncdump(fileName, "-h"); // printData + expected = "netcdf testDapToNcDGrid1D2D.nc {\n" + + " dimensions:\n" + + " time = 1;\n" + + " altitude = 1;\n" + + " latitude = 7;\n" + + " longitude = 15;\n" + + " variables:\n" + + " double time(time=1);\n" + + " :_CoordinateAxisType = \"Time\";\n" + + " :actual_range = 9.348048E8, 1.2556944E9; // double\n" + + " :axis = \"T\";\n" + + " :fraction_digits = 0; // int\n" + + " :ioos_category = \"Time\";\n" + + " :long_name = \"Centered Time\";\n" + + " :standard_name = \"time\";\n" + + " :time_origin = \"01-JAN-1970 00:00:00\";\n" + + " :units = \"seconds since 1970-01-01T00:00:00Z\";\n" + + "\n" + + " double altitude(altitude=1);\n" + + " :_CoordinateAxisType = \"Height\";\n" + + " :_CoordinateZisPositive = \"up\";\n" + + " :actual_range = 10.0, 10.0; // double\n" + + " :axis = \"Z\";\n" + + " :fraction_digits = 0; // int\n" + + " :ioos_category = \"Location\";\n" + + " :long_name = \"Altitude\";\n" + + " :positive = \"up\";\n" + + " :standard_name = \"altitude\";\n" + + " :units = \"m\";\n" + + "\n" + + " double latitude(latitude=7);\n" + + " :_CoordinateAxisType = \"Lat\";\n" + + " :actual_range = -75.0, 75.0; // double\n" + + " :axis = \"Y\";\n" + + " :coordsys = \"geographic\";\n" + + " :fraction_digits = 2; // int\n" + + " :ioos_category = \"Location\";\n" + + " :long_name = \"Latitude\";\n" + + " :point_spacing = \"even\";\n" + + " :standard_name = \"latitude\";\n" + + " :units = \"degrees_north\";\n" + + "\n" + + " double longitude(longitude=15);\n" + + " :_CoordinateAxisType = \"Lon\";\n" + + " :actual_range = 0.0, 360.0; // double\n" + + " :axis = \"X\";\n" + + " :coordsys = \"geographic\";\n" + + " :fraction_digits = 2; // int\n" + + " :ioos_category = \"Location\";\n" + + " :long_name = \"Longitude\";\n" + + " :point_spacing = \"even\";\n" + + " :standard_name = \"longitude\";\n" + + " :units = \"degrees_east\";\n" + + "\n" + + " float x_wind(time=1, altitude=1, latitude=7, longitude=15);\n" + + " :_FillValue = -9999999.0f; // float\n" + + " :colorBarMaximum = 15.0; // double\n" + + " :colorBarMinimum = -15.0; // double\n" + + " :coordsys = \"geographic\";\n" + + " :fraction_digits = 1; // int\n" + + " :ioos_category = \"Wind\";\n" + + " :long_name = \"Zonal Wind\";\n" + + " :missing_value = -9999999.0f; // float\n" + + " :standard_name = \"x_wind\";\n" + + " :units = \"m s-1\";\n" + + "\n" + + " float y_wind(time=1, altitude=1, latitude=7, longitude=15);\n" + + " :_FillValue = -9999999.0f; // float\n" + + " :colorBarMaximum = 15.0; // double\n" + + " :colorBarMinimum = -15.0; // double\n" + + " :coordsys = \"geographic\";\n" + + " :fraction_digits = 1; // int\n" + + " :ioos_category = \"Wind\";\n" + + " :long_name = \"Meridional Wind\";\n" + + " :missing_value = -9999999.0f; // float\n" + + " :standard_name = \"y_wind\";\n" + + " :units = \"m s-1\";\n" + + "\n" + + " // global attributes:\n" + + " :acknowledgement = \"NOAA NESDIS COASTWATCH, NOAA SWFSC ERD\";\n" + + " :cdm_data_type = \"Grid\";\n" + + " :composite = \"true\";\n" + + " :contributor_name = \"Remote Sensing Systems, Inc.\";\n" + + " :contributor_role = \"Source of level 2 data.\";\n" + + " :Conventions = \"COARDS, CF-1.6, ACDD-1.3\";\n" + + " :creator_email = \"erd.data@noaa.gov\";\n" + + " :creator_name = \"NOAA NMFS SWFSC ERD\";\n" + + " :creator_type = \"institution\";\n" + + " :creator_url = \"https://www.pfeg.noaa.gov\";\n" + + " :date_created = \"2010-07-02\";\n" + + " :date_issued = \"2010-07-02\";\n" + + " :defaultGraphQuery = \"&.draw=vectors\";\n" + + " :Easternmost_Easting = 360.0; // double\n" + + " :geospatial_lat_max = 75.0; // double\n" + + " :geospatial_lat_min = -75.0; // double\n" + + " :geospatial_lat_resolution = 0.125; // double\n" + + " :geospatial_lat_units = \"degrees_north\";\n" + + " :geospatial_lon_max = 360.0; // double\n" + + " :geospatial_lon_min = 0.0; // double\n" + + " :geospatial_lon_resolution = 0.125; // double\n" + + " :geospatial_lon_units = \"degrees_east\";\n" + + " :geospatial_vertical_max = 10.0; // double\n" + + " :geospatial_vertical_min = 10.0; // double\n" + + " :geospatial_vertical_positive = \"up\";\n" + + " :geospatial_vertical_units = \"m\";\n" + + " :history = \"Remote Sensing Systems, Inc.\n" + + "2010-07-02T15:36:22Z NOAA CoastWatch (West Coast Node) and NOAA SFSC ERD\n" + + today + "T"; // time https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/QS/ux10/mday\n" + // + + // today + time " + // https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday.das\";\n" + + expected2 = " :infoUrl = \"https://coastwatch.pfeg.noaa.gov/infog/QS_ux10_las.html\";\n" + + " :institution = \"NOAA NMFS SWFSC ERD\";\n" + + " :keywords = \"altitude, atmosphere, atmospheric, coast, coastwatch, data, degrees, Earth Science > Atmosphere > Atmospheric Winds > Surface Winds, Earth Science > Oceans > Ocean Winds > Surface Winds, global, noaa, node, ocean, oceans, QSux10, quality, quikscat, science, science quality, seawinds, surface, time, wcn, west, wind, winds, x_wind, zonal\";\n" + + + " :keywords_vocabulary = \"GCMD Science Keywords\";\n" + + " :license = \"The data may be used and redistributed for free but is not intended\n" + + "for legal use, since it may contain inaccuracies. Neither the data\n" + + "Contributor, ERD, NOAA, nor the United States Government, nor any\n" + + "of their employees or contractors, makes any warranty, express or\n" + + "implied, including warranties of merchantability and fitness for a\n" + + "particular purpose, or assumes any legal liability for the accuracy,\n" + + "completeness, or usefulness, of this information.\";\n" + + " :naming_authority = \"gov.noaa.pfeg.coastwatch\";\n" + + " :Northernmost_Northing = 75.0; // double\n" + + " :origin = \"Remote Sensing Systems, Inc.\";\n" + + " :processing_level = \"3\";\n" + + " :project = \"CoastWatch (https://coastwatch.noaa.gov/)\";\n" + + " :projection = \"geographic\";\n" + + " :projection_type = \"mapped\";\n" + + " :publisher_email = \"erd.data@noaa.gov\";\n" + + " :publisher_name = \"NOAA NMFS SWFSC ERD\";\n" + + " :publisher_type = \"institution\";\n" + + " :publisher_url = \"https://www.pfeg.noaa.gov\";\n" + + " :references = \"RSS Inc. Winds: http://www.remss.com/ .\";\n" + + " :satellite = \"QuikSCAT\";\n" + + " :sensor = \"SeaWinds\";\n" + + " :source = \"satellite observation: QuikSCAT, SeaWinds\";\n" + + " :sourceUrl = \"(local files)\";\n" + + " :Southernmost_Northing = -75.0; // double\n" + + " :standard_name_vocabulary = \"CF Standard Name Table v70\";\n" + + " :summary = \"Remote Sensing Inc. distributes science quality wind velocity data from the SeaWinds instrument onboard NASA's QuikSCAT satellite. SeaWinds is a microwave scatterometer designed to measure surface winds over the global ocean. Wind velocity fields are provided in zonal, meridional, and modulus sets. The reference height for all wind velocities is 10 meters. (This is a monthly composite.)\";\n" + + + " :time_coverage_end = \"2009-10-16T12:00:00Z\";\n" + + " :time_coverage_start = \"1999-08-16T12:00:00Z\";\n" + + " :title = \"Wind, QuikSCAT SeaWinds, 0.125°, Global, Science Quality, 1999-2009 (Monthly)\";\n" + + " :Westernmost_Easting = 0.0; // double\n" + + "}\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=" + results); + po = results.indexOf(" :infoUrl ="); + Test.ensureEqual(results.substring(po), expected2, "results=" + results); + File2.delete(fileName); + + /* */ + String2.log("\n*** OpendapHelper.testDapToNcDGrid finished."); + + } + + /** This tests parseStartStrideStop and throws exception if trouble. */ + @org.junit.jupiter.api.Test + void testParseStartStrideStop() { + + Test.ensureEqual(String2.toCSSVString(OpendapHelper.parseStartStrideStop(null)), "", ""); + Test.ensureEqual(String2.toCSSVString(OpendapHelper.parseStartStrideStop("")), "", ""); + Test.ensureEqual(String2.toCSSVString(OpendapHelper.parseStartStrideStop("[6:7:8]")), + "6, 7, 8", ""); + Test.ensureEqual(String2.toCSSVString(OpendapHelper.parseStartStrideStop("[5][3:4][6:7:8]")), + "5, 1, 5, 3, 1, 4, 6, 7, 8", ""); + try { + OpendapHelper.parseStartStrideStop("a"); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"a\": '[' expected at projection position #0", + ""); + } + try { + OpendapHelper.parseStartStrideStop("["); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[\": End ']' not found.", + ""); + } + try { + OpendapHelper.parseStartStrideStop("[5"); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[5\": End ']' not found.", + ""); + } + try { + OpendapHelper.parseStartStrideStop("[5:t]"); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.NumberFormatException: For input string: \"t\"", + ""); + } + try { + OpendapHelper.parseStartStrideStop("[-1]"); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[-1]\": Negative number=-1 at projection position #1", + ""); + } + try { + OpendapHelper.parseStartStrideStop("[0:1:2:3]"); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.NumberFormatException: For input string: \"2:3\"", + ""); + } + try { + OpendapHelper.parseStartStrideStop("[4:3]"); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[4:3]\": start=4 must be less than or equal to stop=3", + ""); + } + try { + OpendapHelper.parseStartStrideStop("[4:2:3]"); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.RuntimeException: ERROR parsing OPENDAP constraint=\"[4:2:3]\": start=4 must be less than or equal to stop=3", + ""); + } + + // test calculateNValues + Test.ensureEqual(OpendapHelper.calculateNValues(1, 1, 3), 3, ""); + Test.ensureEqual(OpendapHelper.calculateNValues(1, 2, 3), 2, ""); + Test.ensureEqual(OpendapHelper.calculateNValues(1, 2, 4), 2, ""); + try { + OpendapHelper.calculateNValues(4, 2, 3); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.RuntimeException: start=4 must be less than or equal to stop=3", + ""); + } + try { + OpendapHelper.calculateNValues(3, 0, 5); + Test.ensureEqual(0, 1, ""); + } catch (Throwable t) { + Test.ensureEqual(t.toString(), + "java.lang.RuntimeException: stride=0 must be greater than 0", + ""); + } + } + + /** This tests findVarsWithSharedDimensions. */ + @org.junit.jupiter.api.Test + void testFindVarsWithSharedDimensions() throws Throwable { + String2.log("\n\n*** OpendapHelper.findVarsWithSharedDimensions"); + String expected, results; + DConnect dConnect; + DDS dds; + + /* + * //test of Sequence DAP dataset + * String2.log("\n*** test of Sequence DAP dataset"); + * String sequenceUrl = + * "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1"; + * dConnect = new DConnect(sequenceUrl, true, 1, 1); + * dds = dConnect.getDDS(DEFAULT_TIMEOUT); + * results = String2.toCSSVString(findVarsWithSharedDimensions(dds)); + * expected = + * "zztop"; + * Test.ensureEqual(results, expected, "results=" + results); + */ + + // test of DArray DAP dataset + // 2018-09-13 https: works in browser by not yet in Java + String dArrayUrl = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; + String2.log("\n*** test of DArray DAP dataset\n" + dArrayUrl); + dConnect = new DConnect(dArrayUrl, true, 1, 1); + dds = dConnect.getDDS(OpendapHelper.DEFAULT_TIMEOUT); + results = String2.toCSSVString(OpendapHelper.findVarsWithSharedDimensions(dds)); + expected = "time, lat, lon, PL_HD, PL_CRS, DIR, PL_WDIR, PL_SPD, SPD, PL_WSPD, P, T, RH, date, time_of_day, flag"; + Test.ensureEqual(results, expected, "results=" + results); + + // ***** test of DGrid DAP dataset + String2.log("\n*** test of DGrid DAP dataset"); + String dGridUrl = "https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday"; + dConnect = new DConnect(dGridUrl, true, 1, 1); + dds = dConnect.getDDS(OpendapHelper.DEFAULT_TIMEOUT); + results = String2.toCSSVString(OpendapHelper.findVarsWithSharedDimensions(dds)); + expected = "x_wind, y_wind"; + Test.ensureEqual(results, expected, "results=" + results); + + /* */ + String2.log("\n*** OpendapHelper.testFindVarsWithSharedDimensions finished."); + + } + + /** This tests findAllVars. */ + @org.junit.jupiter.api.Test + void testFindAllScalarOrMultiDimVars() throws Throwable { + String2.log("\n\n*** OpendapHelper.testFindAllScalarOrMultiDimVars"); + String expected, results; + DConnect dConnect; + DDS dds; + String url; + + /* + * //test of Sequence DAP dataset + * String2.log("\n*** test of Sequence DAP dataset"); + * url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1"; + * dConnect = new DConnect(url, true, 1, 1); + * dds = dConnect.getDDS(DEFAULT_TIMEOUT); + * results = String2.toCSSVString(findVarsWithSharedDimensions(dds)); + * expected = + * "zztop"; + * Test.ensureEqual(results, expected, "results=" + results); + */ + + // test of DArray DAP dataset + // 2018-09-13 https: works in browser by not yet in Java. 2019-06-28 https works + // in Java + url = "https://tds.coaps.fsu.edu/thredds/dodsC/samos/data/research/WTEP/2012/WTEP_20120128v30001.nc"; + String2.log("\n*** test of DArray DAP dataset\n" + url); + dConnect = new DConnect(url, true, 1, 1); + dds = dConnect.getDDS(OpendapHelper.DEFAULT_TIMEOUT); + results = String2.toCSSVString(OpendapHelper.findAllScalarOrMultiDimVars(dds)); + expected = "time, lat, lon, PL_HD, PL_CRS, DIR, PL_WDIR, PL_SPD, SPD, PL_WSPD, P, T, RH, date, time_of_day, flag, history"; + Test.ensureEqual(results, expected, "results=" + results); + + // ***** test of DGrid DAP dataset + String2.log("\n*** test of DGrid DAP dataset"); + url = "https://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwindmday"; + dConnect = new DConnect(url, true, 1, 1); + dds = dConnect.getDDS(OpendapHelper.DEFAULT_TIMEOUT); + results = String2.toCSSVString(OpendapHelper.findAllScalarOrMultiDimVars(dds)); + expected = "time, altitude, latitude, longitude, x_wind, y_wind"; + Test.ensureEqual(results, expected, "results=" + results); + + // ***** test of NODC template dataset + /** + * 2020-10-26 disabled because source is unreliable + * String2.log("\n*** test of NODC template dataset"); + * url = + * "https://data.nodc.noaa.gov/thredds/dodsC/testdata/netCDFTemplateExamples/timeSeries/BodegaMarineLabBuoyCombined.nc"; + * dConnect = new DConnect(url, true, 1, 1); + * dds = dConnect.getDDS(DEFAULT_TIMEOUT); + * results = String2.toCSSVString(findAllScalarOrMultiDimVars(dds)); + * expected = + * "time, lat, lon, alt, station_name, temperature, salinity, density, + * conductivity, " + + * "turbidity, fluorescence, platform1, temperature_qc, salinity_qc, density_qc, + * " + + * "conductivity_qc, turbidity_qc, fluorescence_qc, instrument1, instrument2, " + * + + * "instrument3, ht_wgs84, ht_mllw, crs"; + * Test.ensureEqual(results, expected, "results=" + results); + */ + + // ***** test of sequence dataset (no vars should be found + String2.log("\n*** test of sequence dataset"); + url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCAMarCatLY"; + dConnect = new DConnect(url, true, 1, 1); + dds = dConnect.getDDS(OpendapHelper.DEFAULT_TIMEOUT); + results = String2.toCSSVString(OpendapHelper.findAllScalarOrMultiDimVars(dds)); + expected = ""; + Test.ensureEqual(results, expected, "results=" + results); + + /* */ + String2.log("\n*** OpendapHelper.testFindAllScalarOrMultiDimVars finished."); + + } + + /** + * Test allDapToNc. + * + * @param whichTests -1 for all, or 0.. for specific ones + */ + @org.junit.jupiter.api.Test + @TagThredds + void testAllDapToNc() throws Throwable { + // tests from nodc template examples https://www.ncei.noaa.gov/netcdf-templates + String2.log("\n*** OpendapHelper.testAllDapToNc()"); + String dir = OpendapHelperTests.class.getResource("/nodcTemplates/").getPath(); + // 2023-02-15 This method hadn't been run since 2020 because tdsUrl often + // stalled, so I had commented it out. + // tdsUrl was + // "https://data.nodc.noaa.gov/thredds/dodsC/testdata/netCDFTemplateExamples/"; + // //+e.g., point/KachemakBay.nc"; + String tdsUrl = "https://www.ncei.noaa.gov/thredds-ocean/dodsC/example/v1.0/"; // +e.g., point/KachemakBay.nc"; + String fileName; + String url, results, expected; + + // this tests numeric scalars, and numeric and String 1D arrays + fileName = "pointKachemakBay.nc"; + url = tdsUrl + "point/KachemakBay.nc"; + OpendapHelper.allDapToNc(url, dir + fileName); + results = NcHelper.dds(dir + fileName); + // String2.log(results); + // expected = "zztop"; + // Test.ensureEqual(results, expected, ""); + + // this tests numeric and String scalars, and numeric 1D arrays + fileName = "timeSeriesBodegaMarineLabBuoy.nc"; + url = tdsUrl + "timeSeries/BodegaMarineLabBuoy.nc"; + OpendapHelper.allDapToNc(url, dir + fileName); + results = NcHelper.dds(dir + fileName); + expected = "netcdf " + dir + "timeSeriesBodegaMarineLabBuoy.nc {\n" + + " dimensions:\n" + + " time = 63242;\n" + + " string1 = 1;\n" + + " station_name_strlen = 17;\n" + + " variables:\n" + + " double time(time=63242);\n" + + " float lat;\n" + + " float lon;\n" + + " double alt;\n" + + " char station_name(string1=1, station_name_strlen=17);\n" + + " double temperature(time=63242);\n" + + " double salinity(time=63242);\n" + + " double density(time=63242);\n" + + " double conductivity(time=63242);\n" + + " int platform1;\n" + + " int temperature_qc(time=63242);\n" + + " int salinity_qc(time=63242);\n" + + " int density_qc(time=63242);\n" + + " int conductivity_qc(time=63242);\n" + + " int instrument1;\n" + + " int instrument2;\n" + + " double ht_wgs84;\n" + + " double ht_mllw;\n" + + " int crs;\n" + + " // global attributes:\n" + + "}\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // this tests numeric scalars, and grids + fileName = "trajectoryAoml_tsg.nc"; + url = tdsUrl + "trajectory/aoml_tsg.nc"; + OpendapHelper.allDapToNc(url, dir + fileName); + results = NcHelper.dds(dir + fileName); + // String2.log(results); + expected = "netcdf " + dir + "trajectoryAoml_tsg.nc {\n" + + " dimensions:\n" + + " trajectory = 1;\n" + + " obs = 2880;\n" + + " variables:\n" + + " int trajectory(trajectory=1);\n" + + " int time(trajectory=1, obs=2880);\n" + + " double lat(trajectory=1, obs=2880);\n" + + " double lon(trajectory=1, obs=2880);\n" + + " double intp(trajectory=1, obs=2880);\n" + + " double sal(trajectory=1, obs=2880);\n" + + " double cond(trajectory=1, obs=2880);\n" + + " double ext(trajectory=1, obs=2880);\n" + + " double sst(trajectory=1, obs=2880);\n" + + " byte plt(trajectory=1);\n" + + " byte tsg(trajectory=1);\n" + + " byte tmsr(trajectory=1);\n" + + " byte sstr(trajectory=1);\n" + + " byte flag_a(trajectory=1, obs=2880);\n" + + " byte flag_b(trajectory=1, obs=2880);\n" + + " byte flag_c(trajectory=1, obs=2880);\n" + + " byte flag_d(trajectory=1, obs=2880);\n" + + " byte flag_e(trajectory=1, obs=2880);\n" + + " byte flag_f(trajectory=1, obs=2880);\n" + + " byte flag_g(trajectory=1, obs=2880);\n" + + " byte flag_h(trajectory=1, obs=2880);\n" + + " byte flag_i(trajectory=1, obs=2880);\n" + + " byte flag_j(trajectory=1, obs=2880);\n" + + " byte flag_k(trajectory=1, obs=2880);\n" + + " byte flag_l(trajectory=1, obs=2880);\n" + + " byte crs(trajectory=1);\n" + + " // global attributes:\n" + + "}\n"; + Test.ensureEqual(results, expected, ""); + + // this tests numeric scalars, and byte/numeric arrays + fileName = "trajectoryJason2_satelliteAltimeter.nc"; + url = tdsUrl + "trajectory/jason2_satelliteAltimeter.nc"; + OpendapHelper.allDapToNc(url, dir + fileName); + results = NcHelper.dds(dir + fileName); + // String2.log(results); + expected = "netcdf " + dir + "trajectoryJason2_satelliteAltimeter.nc {\n" + + " dimensions:\n" + + " trajectory = 1;\n" + + " obs = 3;\n" + + " meas_ind = 20;\n" + + " variables:\n" + + " double time(trajectory=1, obs=3);\n" + + " byte meas_ind(trajectory=1, meas_ind=20);\n" + + " int lat(trajectory=1, obs=3);\n" + + " int lon(trajectory=1, obs=3);\n" + + " byte surface_type(trajectory=1, obs=3);\n" + + " byte orb_state_flag_rest(trajectory=1, obs=3);\n" + + " byte ecmwf_meteo_map_avail(trajectory=1, obs=3);\n" + + " byte interp_flag_meteo(trajectory=1, obs=3);\n" + + " int alt(trajectory=1, obs=3);\n" + + " byte range_numval_ku(trajectory=1, obs=3);\n" + + " short model_wet_tropo_corr(trajectory=1, obs=3);\n" + + " byte atmos_corr_sig0_ku(trajectory=1, obs=3);\n" + + " short tb_187(trajectory=1, obs=3);\n" + + " short rad_water_vapor(trajectory=1, obs=3);\n" + + " short ssha(trajectory=1, obs=3);\n" + + " // global attributes:\n" + + "}\n"; + Test.ensureEqual(results, expected, ""); + + /* + * if (whichTests == -1 || whichTests == 4) { + * //JDAP fails to read/parse the .dds: + * //Exception in thread "main" com.cohort.util.SimpleException: Error while + * getting DDS from https://data.nodc.noaa.gov/thredds/dodsC/testdata/ne + * //tCDFTemplateExamples/profile/wodObservedLevels.nc.dds . + * // + * //Parse Error on token: String + * //In the dataset descriptor object: + * //Expected a variable declaration (e.g., Int32 i;). + * // at + * gov.noaa.pfel.coastwatch.griddata.OpendapHelper.allDapToNc(OpendapHelper.java + * :1239) + * // at + * gov.noaa.pfel.coastwatch.griddata.OpendapHelper.testAllDapToNc(OpendapHelper. + * java:1716) + * // at gov.noaa.pfel.coastwatch.TestAll.main(TestAll.java:741) + * //this tests numeric scalars, and numeric and string arrays + * fileName = "profileWodObservedLevels.nc"; + * url = tdsUrl + "profile/wodObservedLevels.nc"; + * allDapToNc(url, dir + fileName); + * results = NcHelper.ncdump(dir + fileName, "-h"); + * String2.log(results); + * //expected = "zztop"; + * //Test.ensureEqual(results, expected, ""); + * } + */ + // this tests numeric scalars, and numeric arrays + fileName = "timeSeriesProfileUsgs_internal_wave_timeSeries.nc"; + url = tdsUrl + "timeSeriesProfile/usgs_internal_wave_timeSeries.nc"; + OpendapHelper.allDapToNc(url, dir + fileName); + results = NcHelper.dds(dir + fileName); + // String2.log(results); + expected = "netcdf " + dir + "timeSeriesProfileUsgs_internal_wave_timeSeries.nc {\n" + + " dimensions:\n" + + " station = 1;\n" + + " time = 38990;\n" + + " z = 5;\n" + + " variables:\n" + + " int station_id(station=1);\n" + + " double time(time=38990);\n" + + " double z(z=5);\n" + + " double lon(station=1);\n" + + " double lat(station=1);\n" + + " double T_20(station=1, time=38990, z=5);\n" + + " double C_51(station=1, time=38990, z=5);\n" + + " double S_40(station=1, time=38990, z=5);\n" + + " double STH_71(station=1, time=38990, z=5);\n" + + " int instrument_1(station=1, z=5);\n" + + " int instrument_2(station=1);\n" + + " int platform;\n" + + " int crs;\n" + + " // global attributes:\n" + + "}\n"; + Test.ensureEqual(results, expected, ""); + + // currently no trajectoryProfile example + + // currently no swath example + + } + +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/griddata/OpendapTests.java b/src/test/java/gov/noaa/pfel/coastwatch/griddata/OpendapTests.java new file mode 100644 index 000000000..2a66283ef --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/griddata/OpendapTests.java @@ -0,0 +1,98 @@ +package gov.noaa.pfel.coastwatch.griddata; + +import com.cohort.util.String2; +import com.cohort.util.Test; + +import dods.dap.DConnect; +import gov.noaa.pfel.coastwatch.util.SSR; +import tags.TagThredds; + +class OpendapTests { + + @org.junit.jupiter.api.Test + @TagThredds + void basicTest() throws Exception { + + Grid.verbose = true; + Opendap.verbose = true; + Opendap opendap; + + /* + * //test Oceanwatch Opendap no longer active + * opendap = new Opendap( + * // + * "http://las.pfeg.noaa.gov/cgi-bin/nph-dods/data/oceanwatch/nrt/gac/AG1day.nc", + * "http://192.168.31.13/cgi-bin/nph-dods/data/oceanwatch/nrt/qscat/QNuy108day.nc", + * true, null); + * //opendap.getGridInfo("ssta", "-1.0e34"); + * opendap.getGridInfo("uy10", "-1.0e34"); + * opendap.numberOfObservations = + * DataHelper.getDoubleArray(opendap.dConnect, + * "?numberOfObservations.numberOfObservations"); + * opendap.getTimeOptions(true, Calendar2.SECONDS_PER_DAY, + * Calendar2.isoStringToEpochSeconds("1985-01-01")); + * File2.delete(SSR.getTempDirectory() + "OpendapTest.grd"); + * opendap.makeGrid(SSR.getTempDirectory(), "OpendapTest.grd", + * opendap.timeOptions[0], + * -135 + 360, -105 + 360, 22, 50, //US+Mexico + * Integer.MAX_VALUE, Integer.MAX_VALUE, null); + */ + + // test THREDDS //was :8081 + opendap = new Opendap("https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/GA/ssta/3day", true, null); + DConnect dConnect = new DConnect(opendap.url, opendap.acceptDeflate, 1, 1); + opendap.getGridInfo(dConnect.getDAS(OpendapHelper.DEFAULT_TIMEOUT), + dConnect.getDDS(OpendapHelper.DEFAULT_TIMEOUT), "GAssta", "-1.0e34"); + Test.ensureEqual(opendap.getLat(0), -44.975, ""); // I'm not sure about exact range, should be global data + Test.ensureEqual(opendap.getLat(opendap.gridNLatValues - 1), 59.975, ""); + Test.ensureEqual(opendap.gridLatIncrement, .05, ""); + Test.ensureEqual(opendap.getLon(0), 180.025, ""); + Test.ensureEqual(opendap.getLon(opendap.gridNLonValues - 1), 329.975, ""); + Test.ensureEqual(opendap.gridLonIncrement, .05, ""); + + // test THREDDS + opendap = new Opendap( // was :8081 + "https://oceanwatch.pfeg.noaa.gov/thredds/dodsC/satellite/AG/ssta/3day", + true, null); + dConnect = new DConnect(opendap.url, opendap.acceptDeflate, 1, 1); + opendap.getGridInfo(dConnect.getDAS(60000), dConnect.getDDS(60000), "AGssta", "-1.0e34"); + Test.ensureEqual(opendap.getLat(0), -75, ""); + Test.ensureEqual(opendap.getLat(opendap.gridNLatValues - 1), 75, ""); + Test.ensureEqual(opendap.gridLatIncrement, .1, ""); + Test.ensureEqual(opendap.getLon(0), 0, ""); + Test.ensureEqual(opendap.getLon(opendap.gridNLonValues - 1), 360, ""); + Test.ensureEqual(opendap.gridLonIncrement, .1, ""); + opendap.getTimeOptions(false, + opendap.gridTimeFactorToGetSeconds, + opendap.gridTimeBaseSeconds, + 3 * 24); + + // ensure not oddly spaced after makeLonPM180 + // data is 0..360, so ask for ~-180 to ~180 + String dir = SSR.getTempDirectory(); + Grid grid = opendap.makeGrid(opendap.timeOptions[0], + -170, 170, 22, 50, 53, 37); + String2.log("lon values: " + String2.toCSSVString(grid.lon)); + DataHelper.ensureEvenlySpaced(grid.lon, "The lon values aren't evenly spaced:\n"); + DataHelper.ensureEvenlySpaced(grid.lat, "The lat values aren't evenly spaced:\n"); + int nLon = grid.lon.length; + int nLat = grid.lat.length; + String lonString = "lon values: " + String2.toCSSVString(grid.lon); + String latString = "lat values: " + String2.toCSSVString(grid.lat); + // ???the results seem to flip flop, perhaps based on some intermediate file + // that isn't being deleted every time + // but both answers are ok (179.2 is preferred?) + // if (nLon == 55) { + Test.ensureEqual(grid.lon[0], -172.8, lonString); + Test.ensureEqual(grid.lon[nLon - 1], 172.8, lonString); + // } else if (nLon == 57) { + // Test.ensureEqual(grid.lon[0], -179.2, lonString); + // Test.ensureEqual(grid.lon[nLon-1], 179.2, lonString); + // } else + // Test.error(grid.lonInfoString()); + Test.ensureEqual(nLat, 41, latString); + Test.ensureEqual(grid.lat[0], 22, latString); + Test.ensureEqual(grid.lat[nLat - 1], 50, latString); + + } +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/pointdata/TableTests.java b/src/test/java/gov/noaa/pfel/coastwatch/pointdata/TableTests.java new file mode 100644 index 000000000..2d7179b65 --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/pointdata/TableTests.java @@ -0,0 +1,17718 @@ +package gov.noaa.pfel.coastwatch.pointdata; + +import java.io.BufferedReader; +import java.io.ByteArrayOutputStream; +import java.io.StringReader; +import java.nio.file.Path; +import java.sql.Connection; +import java.sql.DatabaseMetaData; +import java.sql.DriverManager; +import java.util.Arrays; +import java.util.BitSet; + +import org.junit.jupiter.api.io.TempDir; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.ValueSource; + +import com.cohort.array.Attributes; +import com.cohort.array.ByteArray; +import com.cohort.array.CharArray; +import com.cohort.array.DoubleArray; +import com.cohort.array.FloatArray; +import com.cohort.array.IntArray; +import com.cohort.array.LongArray; +import com.cohort.array.PAType; +import com.cohort.array.PrimitiveArray; +import com.cohort.array.ShortArray; +import com.cohort.array.StringArray; +import com.cohort.array.UByteArray; +import com.cohort.array.UIntArray; +import com.cohort.array.ULongArray; +import com.cohort.array.UShortArray; +import com.cohort.util.Calendar2; +import com.cohort.util.File2; +import com.cohort.util.Math2; +import com.cohort.util.MustBe; +import com.cohort.util.SimpleException; +import com.cohort.util.String2; +import com.cohort.util.Test; + +import gov.noaa.pfel.coastwatch.griddata.DataHelper; +import gov.noaa.pfel.coastwatch.griddata.NcHelper; +import gov.noaa.pfel.coastwatch.util.FileVisitorDNLS; +import tags.TagExternalOther; +import tags.TagIncompleteTest; +import tags.TagLargeFile; +import tags.TagLocalERDDAP; +import tags.TagMissingFile; +import tags.TagPassword; +import tags.TagWebInfStructureDependency; +import ucar.nc2.NetcdfFile; +import ucar.nc2.Variable; + +class TableTests { + + @TempDir + private static Path TEMP_DIR; + + /** + * This tests the little methods. + */ + @org.junit.jupiter.api.Test + void testLittleMethods() { + // String2.log("\n*** Table.testLittleMethods..."); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // isValid and findColumnNumber and subset + Table table = getTestTable(true, true); + table.ensureValid(); // throws Exception if not + Test.ensureEqual(table.findColumnNumber("Time"), 0, ""); + Test.ensureEqual(table.findColumnNumber("String Data"), 9, ""); + Test.ensureEqual(table.findColumnNumber("zz"), -1, ""); + + // toString + table = getTestTable(true, true); + // String2.log("toString: " + table.toString()); + + // ensureEqual + Table table2 = getTestTable(true, true); + Test.ensureTrue(table.equals(table2), "test equals a"); + + String2.log("intentional error:\n"); + table2.getColumn(2).setDouble(1, 100); + Test.ensureEqual(table.equals(table2), false, "intentional notEqual b"); + + String2.log("intentional error:\n"); + table2 = getTestTable(true, true); + table2.getColumn(0).setDouble(2, 55); + Test.ensureEqual(table.equals(table2), false, "intentional notEqual c"); + + // getSubset + /* + * table = getTestTable(); + * table.getSubset(new int[]{table.secondsColumn}, + * new double[]{stringToSeconds("2005-08-31T16:01:01")}, + * new double[]{stringToSeconds("2005-08-31T16:01:03")}); + * Test.ensureEqual(table.nRows(), 1, "getSubset a"); + * Test.ensureEqual(table.nColumns(), 5, "getSubset b"); + * Test.ensureEqual(table.getColumn(table.secondsColumn), new + * double[]{stringToSeconds("2005-08-31T16:01:02")}, "getSubset c"); + * Test.ensureEqual(table.getColumn(table.lonColumn), new double[]{-2}, + * "getSubset d"); + * Test.ensureEqual(table.getColumn(table.latColumn), new double[]{1.5}, + * "getSubset e"); + * Test.ensureEqual(table.getColumn(3)[0], 7, "getSubset f"); + * Test.ensureEqual(table.getColumn(4)[0], 8, "getSubset g"); + * + * table = getTestTable(); + * table.getSubset(new int[]{table.latColumn}, + * new double[]{1.9}, + * new double[]{2.1}); + * Test.ensureEqual(table.nRows(), 1, "getSubset b"); + * Test.ensureEqual(table.getColumn(table.latColumn), new double[]{2}, + * "getSubset j"); + */ + + // calculateStats look at array via constants and as array + table = getTestTable(true, true); + Test.ensureEqual(table.getColumnName(1), "Longitude", "columnNames a"); + table.setColumnName(1, "Test"); + Test.ensureEqual(table.getColumnName(1), "Test", "columnNames b"); + table.setColumnName(1, "Longitude"); + Test.ensureEqual(table.getColumnName(1), "Longitude", "columnNames c"); + + double stats[] = table.getColumn(1).calculateStats(); + Test.ensureEqual(stats[PrimitiveArray.STATS_N], 3, "calculateStats n"); + Test.ensureEqual(stats[PrimitiveArray.STATS_MIN], -3, "calculateStats min"); + Test.ensureEqual(stats[PrimitiveArray.STATS_MAX], -1, "calculateStats max"); + + // forceLonPM180(boolean pm180) + table = getTestTable(true, true); + PrimitiveArray lonAr = table.getColumn(1); + Table.forceLonPM180(lonAr, false); + Test.ensureEqual(lonAr.toString(), "357, 358, 359, 2147483647", "forceLonPM180f"); + Table.forceLonPM180(lonAr, true); + Test.ensureEqual(lonAr.toString(), "-3, -2, -1, 2147483647", "forceLonPM180t"); + + // clear + table = getTestTable(true, true); + table.clear(); + Test.ensureEqual(table.nRows(), 0, "clear a"); + Test.ensureEqual(table.nColumns(), 0, "clear b"); + + // getXxxAttribute + table = getTestTable(true, true); + int col = table.findColumnNumber("Double Data"); + Test.ensureEqual(col, 3, ""); + Test.ensureEqual(table.globalAttributes().getString("global_att1"), "a string", ""); + Test.ensureEqual(table.globalAttributes().getString("test"), null, ""); + table.globalAttributes().set("global_att1", "new"); + Test.ensureEqual(table.globalAttributes().getString("global_att1"), "new", ""); + table.globalAttributes().remove("global_att1"); + Test.ensureEqual(table.globalAttributes().getString("global_att1"), null, ""); + + Test.ensureEqual(table.columnAttributes(3).getString("units"), "doubles", ""); + table.columnAttributes(3).set("units", "new"); + Test.ensureEqual(table.columnAttributes(3).getString("units"), "new", ""); + table.columnAttributes(3).remove("units"); + Test.ensureEqual(table.columnAttributes(3).getString("units"), null, ""); + Test.ensureEqual(table.getDoubleData(3, 1), 3.123, ""); + Test.ensureEqual(table.getStringData(3, 1), "3.123", ""); + table.setColumnName(3, "new3"); + Test.ensureEqual(table.getColumnName(3), "new3", ""); + + // sort + table.sort(new int[] { 3 }, new boolean[] { false }); + Test.ensureEqual(table.getColumn(2).toString(), "NaN, 2.0, 1.5, 1.0", ""); + Test.ensureEqual(table.getColumn(3).toString(), "NaN, 1.0E300, 3.123, -1.0E300", ""); + + // removeColumn + table.removeColumn(3); + Test.ensureEqual(table.getColumn(3).toString(), "9223372036854775807, 2000000000000000, 2, -2000000000000000", ""); + Test.ensureEqual(table.getColumnName(3), "Long Data", ""); + Test.ensureEqual(table.columnAttributes(3).getString("units"), "longs", ""); + + // addColumn + table.addColumn(3, "test3", new IntArray(new int[] { 10, 20, 30, Integer.MAX_VALUE })); + Test.ensureEqual(table.getColumn(3).toString(), "10, 20, 30, 2147483647", ""); + Test.ensureEqual(table.getColumnName(3), "test3", ""); + Test.ensureEqual(table.getColumn(4).toString(), "9223372036854775807, 2000000000000000, 2, -2000000000000000", ""); + Test.ensureEqual(table.getColumnName(4), "Long Data", ""); + Test.ensureEqual(table.columnAttributes(4).getString("units"), "longs", ""); + + // append + table.append(table); + Test.ensureEqual(table.getColumn(4).toString(), + "9223372036854775807, 2000000000000000, 2, -2000000000000000, 9223372036854775807, 2000000000000000, 2, -2000000000000000", + ""); + Test.ensureEqual(table.getColumnName(4), "Long Data", ""); + Test.ensureEqual(table.columnAttributes(4).getString("units"), "longs", ""); + + // average + table = new Table(); + DoubleArray da = new DoubleArray(new double[] { 10, 20, 30, 40, 50 }); + table.addColumn("a", da); + da = new DoubleArray(new double[] { 0, 0, 1, 2, 2 }); + table.addColumn("b", da); + table.average(new int[] { 1 }); + Test.ensureEqual(table.getColumn(0).toString(), "15.0, 30.0, 45.0", ""); + Test.ensureEqual(table.getColumn(1).toString(), "0.0, 1.0, 2.0", ""); + + } + + @org.junit.jupiter.api.Test + void testReorderColumns() throws Exception { + // String2.log("\n*** Table.testReorderColumns"); + Table table = new Table(); + table.addColumn("ints", new IntArray()); + table.addColumn("floats", new FloatArray()); + table.addColumn("doubles", new DoubleArray()); + + StringArray newOrder = new StringArray(new String[] { + "hubert", "floats", "doubles", "zztop" }); + table.reorderColumns(newOrder, false); + String results = String2.toCSSVString(table.getColumnNames()); + String expected = "floats, doubles, ints"; + Test.ensureEqual(results, expected, "results=" + results); + + newOrder = new StringArray(new String[] { + "ints", "doubles" }); + table.reorderColumns(newOrder, true); // discard columns not in list + results = String2.toCSSVString(table.getColumnNames()); + expected = "ints, doubles"; + Test.ensureEqual(results, expected, "results=" + results); + } + + @org.junit.jupiter.api.Test + void testLastRowWithData() throws Exception { + // String2.log("\n*** Table.testLastRowWithData"); + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + Table table = new Table(); + String results, expected; + Attributes iAtts = new Attributes(); + iAtts.add("missing_value", 99); + iAtts.add("_FillValue", 999); + Attributes fAtts = new Attributes(); + fAtts.add("_FillValue", -99f); + Attributes dAtts = new Attributes(); + dAtts.add("_FillValue", -99.0); + Attributes sAtts = new Attributes(); + sAtts.add("_FillValue", "99"); + + IntArray ia = (IntArray) new IntArray(new int[] { 1, 99, 999, Integer.MAX_VALUE }).setMaxIsMV(true); + FloatArray fa = new FloatArray(new float[] { 2, -99, -99, Float.NaN }); + DoubleArray da = new DoubleArray(new double[] { 3, -99, -99, Double.NaN }); + StringArray sa = new StringArray(new String[] { "4", null, "99", "" }); + + table.clear(); + table.addColumn(0, "i", ia, iAtts); + Test.ensureEqual(table.lastRowWithData(), 0, ""); + + table.clear(); + table.addColumn(0, "f", fa, fAtts); + Test.ensureEqual(table.lastRowWithData(), 0, ""); + + table.clear(); + table.addColumn(0, "d", da, dAtts); + Test.ensureEqual(table.lastRowWithData(), 0, ""); + + table.clear(); + table.addColumn(0, "s", sa, sAtts); + Test.ensureEqual(table.lastRowWithData(), 0, ""); + + table.clear(); + table.addColumn(0, "i", ia, iAtts); + table.addColumn(1, "f", fa, fAtts); + table.addColumn(2, "d", da, dAtts); + table.addColumn(3, "s", sa, sAtts); + Test.ensureEqual(table.lastRowWithData(), 0, ""); + + // *** + // String2.log("\n*** Table.testRemoveRowsWithoutData"); + table.clear(); + table.addColumn(0, "i", ia, iAtts); + Test.ensureEqual(table.removeRowsWithoutData(), 1, ""); + + table.clear(); + table.addColumn(0, "f", fa, fAtts); + Test.ensureEqual(table.removeRowsWithoutData(), 1, ""); + + table.clear(); + table.addColumn(0, "d", da, dAtts); + Test.ensureEqual(table.removeRowsWithoutData(), 1, ""); + + table.clear(); + table.addColumn(0, "s", sa, sAtts); + Test.ensureEqual(table.removeRowsWithoutData(), 1, ""); + + table.clear(); + table.addColumn(0, "i", ia, iAtts); + table.addColumn(1, "f", fa, fAtts); + table.addColumn(2, "d", da, dAtts); + table.addColumn(3, "s", sa, sAtts); + // good: original row + + // hi 5 there + ia.add(99); + ia.add(999); + ia.add(Integer.MAX_VALUE); + ia.add(99); + ia.add(999); + fa.add(-99); + fa.add(-99); + fa.add(Float.NaN); + fa.add(-99); + fa.add(-99); + da.add(-99); + da.add(-99); + da.add(Double.NaN); + da.add(5); + da.add(-99); + sa.add("hi"); + sa.add("99"); + sa.add(""); + sa.add(""); + sa.add("there"); + table.removeRowsWithoutData(); + results = table.dataToString(); + expected = "i,f,d,s\n" + + "1,2.0,3.0,4\n" + + "99,-99.0,-99.0,hi\n" + + "99,-99.0,5.0,\n" + + "999,-99.0,-99.0,there\n"; + Test.ensureEqual(results, expected, "results=" + results); + + // Table.debugMode = oDebug; + + } + + /** + * This tests reading data from a ncCF multidimensional dataset + * where the dimensions are in the discouraged order (e.g., var[time][station]). + * Very large test file has discharge[time=758001][station=18] + * 4vars[station=18], + * so when flattened 758001 * 18 * 5vars * 8bytes =~545MB + * + 2 indexColumns: 758001 * 18 * 2vars * 4bytes =~109MB + * + * @param readAsNcCF if true, this reads the file via readNcCF. + * If false, this reads the file via readMultidimNc + */ + @org.junit.jupiter.api.Test + @ParameterizedTest + @ValueSource(booleans = { true, false }) + @TagLargeFile + void testReadNcCFMATimeSeriesReversed(boolean readAsNcCF) throws Exception { + // String2.log("\n*** Table.testReadNcCFMATimeSeriesReversed readAsNcCF=" + readAsNcCF); + // time is days since 2006-01-01 00:00:00. file has 2007-10-01T04 through + // 2013-11-14T17:06 + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + Table table = new Table(); + String results, expected; + long time; + // was "/data/hunter/USGS_DISCHARGE_STATIONS_SUBSET.nc" + String fileName = String2.unitTestBigDataDir + "nccf/MATimeSeriesReversedDim.nc"; + NcHelper.ncdump(fileName, "-h") + // String2.log(NcHelper.ncdump(fileName, "-h")); + + /* */ + // read all vars when obs is constrained + // String2.log("\n* read all vars when obs is constrained"); + time = System.currentTimeMillis(); + if (readAsNcCF) + table.readNcCF(fileName, + null, // all vars + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), StringArray.fromCSV(">"), StringArray.fromCSV("3426.69")); + else + table.readMultidimNc(fileName, + null, null, null, // read default dimensions + true, 0, true, // getMetadata, standardizeWhat, removeMVRows, + StringArray.fromCSV("time"), StringArray.fromCSV(">"), StringArray.fromCSV("3426.69")); + String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); + results = table.dataToString(); + expected = + // EEK! I don't think they should be different. + // I think readMultidimNc is correct, because the -99999.0 values are from + // rows with earlier time than valid data rows from same station at later time. + // I think readNcCF is too aggressive at removing MV rows. + "discharge,station,time,longitude,latitude\n" + + (readAsNcCF ? "" : "-99999.0,1327750.0,3426.691666666651,-73.5958333,43.26944444\n") + + "80.98618241999999,1327750.0,3426.6979166667443,-73.5958333,43.26944444\n" + // same station, later time + (readAsNcCF ? "" : "-99999.0,1357500.0,3426.691666666651,-73.7075,42.78527778\n") + + "181.2278208,1357500.0,3426.6979166667443,-73.7075,42.78527778\n" + // same station, later time + "183.77633703,1357500.0,3426.708333333372,-73.7075,42.78527778\n" + + "-56.06735706,1484085.0,3426.691666666651,-75.3976111,39.05830556\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // just read station vars (all stations) no constraints + // String2.log("\n* just read station vars (all stations) no constraints"); + time = System.currentTimeMillis(); + if (readAsNcCF) + table.readNcCF(fileName, + StringArray.fromCSV("station,latitude,longitude"), + 0, // standardizeWhat=0 + null, null, null); + else + table.readMultidimNc(fileName, + StringArray.fromCSV("station,latitude,longitude"), + null, // dimensions + null, // treatDimensionsAs + true, 0, true, // getMetadata, standardizeWhat, removeMVRows, + null, null, null); + String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); + results = table.dataToString(); + expected = "station,latitude,longitude\n" + + "1463500.0,40.22166667,-74.7780556\n" + + "1389500.0,40.8847222,-74.2261111\n" + + "1327750.0,43.26944444,-73.5958333\n" + + "1357500.0,42.78527778,-73.7075\n" + + "1403060.0,40.5511111,-74.5483333\n" + + "1474500.0,39.9678905,-75.1885123\n" + + "1477050.0,39.83677934,-75.36630199\n" + + "1480120.0,39.7362245,-75.540172\n" + + "1481500.0,39.7695,-75.5766944\n" + + "1480065.0,39.71063889,-75.6087222\n" + + "1480015.0,39.71575,-75.6399444\n" + + "1482170.0,39.65680556,-75.562\n" + + "1482800.0,39.5009454,-75.5682589\n" + + "1413038.0,39.3836111,-75.35027778\n" + + "1412150.0,39.23166667,-75.0330556\n" + + "1411435.0,39.16166667,-74.8319444\n" + + "1484085.0,39.05830556,-75.3976111\n" + + "1484080.0,39.01061275,-75.45794828\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // just read station vars (a few stations because lat is constrained) + // String2.log("\n* just read station vars (a few stations because lat is constrained)"); + time = System.currentTimeMillis(); + if (readAsNcCF) + table.readNcCF(fileName, + StringArray.fromCSV("station,latitude,longitude"), + 0, // standardizeWhat=0 + StringArray.fromCSV("latitude"), StringArray.fromCSV("<"), StringArray.fromCSV("39.1")); + else + table.readMultidimNc(fileName, + StringArray.fromCSV("station,latitude,longitude"), + null, null, // dimensions, treatDimensionsAs + true, 0, true, // getMetadata, standardizeWhat, removeMVRows, + StringArray.fromCSV("latitude"), StringArray.fromCSV("<"), StringArray.fromCSV("39.1")); + String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); + results = table.dataToString(); + expected = "station,latitude,longitude\n" + + "1484085.0,39.05830556,-75.3976111\n" + + "1484080.0,39.01061275,-75.45794828\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // just read obs vars (obs is constrained) + // String2.log("\n* just read obs vars (obs is constrained)"); + time = System.currentTimeMillis(); + if (readAsNcCF) + table.readNcCF(fileName, + StringArray.fromCSV("time,discharge"), + 0, // standardizeWhat=0 + StringArray.fromCSV("discharge"), StringArray.fromCSV(">"), StringArray.fromCSV("5400")); + else + table.readMultidimNc(fileName, + StringArray.fromCSV("time,discharge"), + null, null, // dimensions, treatDimensionsAs + true, 0, true, // getMetadata, standardizeWhat, removeMVRows, + StringArray.fromCSV("discharge"), StringArray.fromCSV(">"), StringArray.fromCSV("5400")); + String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); + results = table.dataToString(); + expected = "time,discharge\n" + + "2076.5,5408.517777\n" + + "2076.510416666628,5465.151471\n" + + "2076.5208333332557,5493.468318\n" + + "2076.53125,5521.785165\n" + + "2076.541666666628,5521.785165\n" + + "2076.5520833332557,5521.785165\n" + + "2076.5625,5521.785165\n" + + "2076.572916666628,5521.785165\n" + + "2076.5833333332557,5493.468318\n" + + "2076.59375,5465.151471\n" + + "2076.604166666628,5436.834624\n" + + "2076.6145833332557,5408.517777\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read all vars when station is constrained, + // String2.log("\n* read all vars when station is constrained"); + time = System.currentTimeMillis(); + if (readAsNcCF) + table.readNcCF(fileName, + StringArray.fromCSV("station,latitude,longitude,time,discharge"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station"), StringArray.fromCSV("="), StringArray.fromCSV("1463500.0")); + else + table.readMultidimNc(fileName, + StringArray.fromCSV("station,latitude,longitude,time,discharge"), + null, null, // dimensions, treatDimensionsAs + true, 0, true, // getMetadata, standardizeWhat, removeMVRows, + StringArray.fromCSV("station"), StringArray.fromCSV("="), StringArray.fromCSV("1463500.0")); + String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); + results = table.dataToString(); + expected = + // EEK! Again, readMultidimNc has additional rows with discharge=MV. + // I think readMultidimNc is correct. + "station,latitude,longitude,time,discharge\n" + + "1463500.0,40.22166667,-74.7780556,638.1666666666279,92.02975275\n" + + "1463500.0,40.22166667,-74.7780556,638.1770833332557,92.02975275\n" + + "1463500.0,40.22166667,-74.7780556,638.1875,92.02975275\n" + + "1463500.0,40.22166667,-74.7780556,638.1979166666279,92.87925815999999\n" + + "1463500.0,40.22166667,-74.7780556,638.2083333332557,93.72876357\n" + + (readAsNcCF ? "" + : "1463500.0,40.22166667,-74.7780556,638.2083333333721,-99999.0\n" + + "1463500.0,40.22166667,-74.7780556,638.2125000000233,-99999.0\n" + + "1463500.0,40.22166667,-74.7780556,638.2166666666744,-99999.0\n") + + + "1463500.0,40.22166667,-74.7780556,638.21875,93.72876357\n" + + (readAsNcCF ? "" + : "1463500.0,40.22166667,-74.7780556,638.2208333333256,-99999.0\n" + + "1463500.0,40.22166667,-74.7780556,638.2250000000931,-99999.0\n") + + + "1463500.0,40.22166667,-74.7780556,638.2291666666279,94.86143745\n" + + (readAsNcCF ? "" + : "1463500.0,40.22166667,-74.7780556,638.2291666667443,-99999.0\n" + + "1463500.0,40.22166667,-74.7780556,638.2333333333954,-99999.0\n" + + "1463500.0,40.22166667,-74.7780556,638.2375000000466,-99999.0\n") + + + "1463500.0,40.22166667,-74.7780556,638.2395833332557,95.71094286\n"; // stop there + results = results.substring(0, expected.length()); + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), readAsNcCF ? 256610 : 757994, "wrong nRows"); + + // read all data + // String2.log("\n* read all data"); + time = System.currentTimeMillis(); + if (readAsNcCF) + table.readNcCF(fileName, + null, 0, // standardizeWhat=0 + null, null, null); + else + table.readMultidimNc(fileName, + null, null, null, // read all dimensions + true, 0, true, // getMetadata, standardizeWhat, removeMVRows, + null, null, null); + String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); + results = table.dataToString(10); + expected = readAsNcCF ? "discharge,station,time,longitude,latitude\n" + + "92.02975275,1463500.0,638.1666666666279,-74.7780556,40.22166667\n" + + "92.02975275,1463500.0,638.1770833332557,-74.7780556,40.22166667\n" + + "92.02975275,1463500.0,638.1875,-74.7780556,40.22166667\n" + + "92.87925815999999,1463500.0,638.1979166666279,-74.7780556,40.22166667\n" + + "93.72876357,1463500.0,638.2083333332557,-74.7780556,40.22166667\n" + + "93.72876357,1463500.0,638.21875,-74.7780556,40.22166667\n" + + "94.86143745,1463500.0,638.2291666666279,-74.7780556,40.22166667\n" + + "95.71094286,1463500.0,638.2395833332557,-74.7780556,40.22166667\n" + + "95.71094286,1463500.0,638.25,-74.7780556,40.22166667\n" + + "95.71094286,1463500.0,638.2604166666279,-74.7780556,40.22166667\n" + + "...\n" + : "discharge,station,time,longitude,latitude\n" + + "92.02975275,1463500.0,638.1666666666279,-74.7780556,40.22166667\n" + + "92.02975275,1463500.0,638.1770833332557,-74.7780556,40.22166667\n" + + "92.02975275,1463500.0,638.1875,-74.7780556,40.22166667\n" + + "92.87925815999999,1463500.0,638.1979166666279,-74.7780556,40.22166667\n" + + "93.72876357,1463500.0,638.2083333332557,-74.7780556,40.22166667\n" + + "-99999.0,1463500.0,638.2083333333721,-74.7780556,40.22166667\n" + + "-99999.0,1463500.0,638.2125000000233,-74.7780556,40.22166667\n" + + "-99999.0,1463500.0,638.2166666666744,-74.7780556,40.22166667\n" + + "93.72876357,1463500.0,638.21875,-74.7780556,40.22166667\n" + + "-99999.0,1463500.0,638.2208333333256,-74.7780556,40.22166667\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), readAsNcCF ? 2315617 : 7539127, "wrong nRows"); + + // read all vars when obs is constrained, + // String2.log("\n* read all vars when obs is constrained"); + time = System.currentTimeMillis(); + if (readAsNcCF) + table.readNcCF(fileName, + StringArray.fromCSV("station,latitude,longitude,time,discharge"), + 0, // standardizeWhat=0 + StringArray.fromCSV("discharge"), StringArray.fromCSV(">"), StringArray.fromCSV("5400")); + else + table.readMultidimNc(fileName, + StringArray.fromCSV("station,latitude,longitude,time,discharge"), + null, null, // dimensions, treatDimensionsAs + true, 0, true, // getMetadata, standardizeWhat, removeMVRows, + StringArray.fromCSV("discharge"), StringArray.fromCSV(">"), StringArray.fromCSV("5400")); + String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); + results = table.dataToString(); + expected = "station,latitude,longitude,time,discharge\n" + + "1463500.0,40.22166667,-74.7780556,2076.5,5408.517777\n" + + "1463500.0,40.22166667,-74.7780556,2076.510416666628,5465.151471\n" + + "1463500.0,40.22166667,-74.7780556,2076.5208333332557,5493.468318\n" + + "1463500.0,40.22166667,-74.7780556,2076.53125,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.541666666628,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.5520833332557,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.5625,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.572916666628,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.5833333332557,5493.468318\n" + + "1463500.0,40.22166667,-74.7780556,2076.59375,5465.151471\n" + + "1463500.0,40.22166667,-74.7780556,2076.604166666628,5436.834624\n" + + "1463500.0,40.22166667,-74.7780556,2076.6145833332557,5408.517777\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read all vars when station and obs are constrained, + // String2.log("\n* read all vars when station and obs are constrained"); + time = System.currentTimeMillis(); + if (readAsNcCF) + table.readNcCF(fileName, + StringArray.fromCSV("station,latitude,longitude,time,discharge"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station,discharge"), StringArray.fromCSV("=,>"), StringArray.fromCSV("1463500.0,5400")); + else + table.readMultidimNc(fileName, + StringArray.fromCSV("station,latitude,longitude,time,discharge"), + null, null, // dimensions, treatDimensionsAs + true, 0, true, // getMetadata, standardizeWhat, removeMVRows, + StringArray.fromCSV("station,discharge"), StringArray.fromCSV("=,>"), StringArray.fromCSV("1463500.0,5400")); + String2.log("time=" + (System.currentTimeMillis() - time) + "ms"); + results = table.dataToString(); + expected = "station,latitude,longitude,time,discharge\n" + + "1463500.0,40.22166667,-74.7780556,2076.5,5408.517777\n" + + "1463500.0,40.22166667,-74.7780556,2076.510416666628,5465.151471\n" + + "1463500.0,40.22166667,-74.7780556,2076.5208333332557,5493.468318\n" + + "1463500.0,40.22166667,-74.7780556,2076.53125,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.541666666628,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.5520833332557,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.5625,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.572916666628,5521.785165\n" + + "1463500.0,40.22166667,-74.7780556,2076.5833333332557,5493.468318\n" + + "1463500.0,40.22166667,-74.7780556,2076.59375,5465.151471\n" + + "1463500.0,40.22166667,-74.7780556,2076.604166666628,5436.834624\n" + + "1463500.0,40.22166667,-74.7780556,2076.6145833332557,5408.517777\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // Table.debugMode = oDebug; + + } + + /** + * This tests sortColumnsByName (and reorderColumns). + */ + @org.junit.jupiter.api.Test + void testSortColumnsByName() { + // Table.verbose = true; + // Table.reallyVerbose = true; + // String2.log("\n***** Table.testSortColumnsByName"); + Table table = getTestTable(true, true); + table.setColumnName(2, "latitude"); // to test case-insensitive + + table.sortColumnsByName(); + + // byte + Test.ensureEqual(table.getColumnName(0), "Byte Data", ""); + Test.ensureEqual(table.columnAttributes(0).getString("units"), "bytes", ""); + + // char + Test.ensureEqual(table.getColumnName(1), "Char Data", ""); + Test.ensureEqual(table.columnAttributes(1).getString("units"), "chars", ""); + + // double + Test.ensureEqual(table.getColumnName(2), "Double Data", ""); + Test.ensureEqual(table.columnAttributes(2).getString("units"), "doubles", ""); + + // int + Test.ensureEqual(table.getColumnName(3), "Int Data", ""); + Test.ensureEqual(table.columnAttributes(3).getString("units"), "ints", ""); + + // Lat + Test.ensureEqual(table.getColumnName(4), "latitude", ""); + Test.ensureEqual(table.columnAttributes(4).getString("units"), "degrees_north", ""); + + // long + Test.ensureEqual(table.getColumnName(5), "Long Data", ""); + Test.ensureEqual(table.columnAttributes(5).getString("units"), "longs", ""); + + // Lon + Test.ensureEqual(table.getColumnName(6), "Longitude", ""); + Test.ensureEqual(table.columnAttributes(6).getString("units"), "degrees_east", ""); + + // short + Test.ensureEqual(table.getColumnName(7), "Short Data", ""); + Test.ensureEqual(table.columnAttributes(7).getString("units"), "shorts", ""); + + // String + Test.ensureEqual(table.getColumnName(8), "String Data", ""); + Test.ensureEqual(table.columnAttributes(8).getString("units"), "Strings", ""); + + // Time + Test.ensureEqual(table.getColumnName(9), "Time", ""); + Test.ensureEqual(table.columnAttributes(9).getString("units"), Calendar2.SECONDS_SINCE_1970, ""); + + } + + /** + * This tests saveAsEnhancedFlatNcFile and readEnhancedFlatNcFile. + */ + @org.junit.jupiter.api.Test + void testEnhancedFlatNcFile() throws Exception { + + // String2.log("\n*** Table.testEnhancedFlatNcFile()"); + String results, expected; + String fileName = File2.getSystemTempDirectory() + "enhancedFlatNcFile.nc"; + + Table table = makeToughTestTable(); + expected = String2.annotatedString(table.toString()); + // String2.log("expected=\n" + expected); + + table.saveAsEnhancedFlatNc(fileName); + results = String2.annotatedString(table.toString()); + Test.ensureEqual(results, expected, "a"); // saveAsEnhancedFlatNc didn't change anything + table.clear(); + + table.readEnhancedFlatNc(fileName, null); + table.globalAttributes().remove("id"); + results = String2.annotatedString(table.toString()); + expected = "{[10]\n" + + "dimensions:[10]\n" + + "[9]row = 5 ;[10]\n" + + "[9]aString_strlen = 9 ;[10]\n" + + "variables:[10]\n" + + "[9]char aString(row, aString_strlen) ;[10]\n" + + "[9][9]aString:test = \"a[252]b[10]\n" + + "c\\td[8364]e\" ;[10]\n" + + "[9]char aChar(row) ;[10]\n" + + "[9][9]aChar:test = \"[252]\" ;[10]\n" + + "[9]byte aByte(row) ;[10]\n" + + "[9][9]aByte:_FillValue = 99 ;[10]\n" + + "[9][9]aByte:test = -128, 127 ;[10]\n" + + "[9]ubyte aUByte(row) ;[10]\n" + + "[9][9]aUByte:_FillValue = 99 ;[10]\n" + + "[9][9]aUByte:test = 0, 255 ;[10]\n" + + "[9]short aShort(row) ;[10]\n" + + "[9][9]aShort:_FillValue = 9999 ;[10]\n" + + "[9][9]aShort:test = -32768, 32767 ;[10]\n" + + "[9]ushort aUShort(row) ;[10]\n" + + "[9][9]aUShort:_FillValue = 9999 ;[10]\n" + + "[9][9]aUShort:test = 0, 65535 ;[10]\n" + + "[9]int anInt(row) ;[10]\n" + + "[9][9]anInt:_FillValue = 999999999 ;[10]\n" + + "[9][9]anInt:test = -2147483648, 2147483647 ;[10]\n" + + "[9]uint aUInt(row) ;[10]\n" + + "[9][9]aUInt:_FillValue = 999999999 ;[10]\n" + + "[9][9]aUInt:test = 0, 4294967295 ;[10]\n" + + "[9]long aLong(row) ;[10]\n" + + "[9][9]aLong:_FillValue = 999999999999 ;[10]\n" + + "[9][9]aLong:test = -9223372036854775808, 9223372036854775807 ;[10]\n" + + "[9]ulong aULong(row) ;[10]\n" + + "[9][9]aULong:_FillValue = 999999999999 ;[10]\n" + + "[9][9]aULong:test = 0, 18446744073709551615 ;[10]\n" + + "[9]float aFloat(row) ;[10]\n" + + "[9][9]aFloat:_FillValue = 1.0E36f ;[10]\n" + + "[9][9]aFloat:test = -3.4028235E38f, NaNf ;[10]\n" + + "[9]double aDouble(row) ;[10]\n" + + "[9][9]aDouble:_FillValue = 1.0E300 ;[10]\n" + + "[9][9]aDouble:test = -1.7976931348623157E308, NaN ;[10]\n" + + "[10]\n" + + "// global attributes:[10]\n" + + "[9][9]:testc = \"[252]\" ;[10]\n" + + "[9][9]:testi = -2147483648, 2147483647 ;[10]\n" + + "[9][9]:testl = -9223372036854775808, 9223372036854775807 ;[10]\n" + + "[9][9]:tests = \"a[252]b[10]\n" + + "c\\td[8364]z\" ;[10]\n" + + "[9][9]:testub = 0, 255 ;[10]\n" + + "[9][9]:testui = 0, 4294967295 ;[10]\n" + + "[9][9]:testul = 0, 9223372036854775807, 18446744073709551615 ;[10]\n" + + "[9][9]:testus = 0, 65535 ;[10]\n" + + "}[10]\n" + + "aString,aChar,aByte,aUByte,aShort,aUShort,anInt,aUInt,aLong,aULong,aFloat,aDouble[10]\n" + + "a\\u00fcb\\nc\\td\\u20ace,\\u00fc,-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308[10]\n" + + + "ab,\\u0000,0,127,0,32767,0,7,0,1,2.2,3.3[10]\n" + + ",A,99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324[10]\n" + + "cd,\\t,126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308[10]\n" + + + ",\\u20ac,,,,,,,,,,[10]\n" + + "[end]"; + Test.ensureEqual(results, expected, "b"); + } + + /** + * The tests readJsonLinesCsv. + */ + @org.junit.jupiter.api.Test + void testJsonlCSV() throws Exception { + // String2.log("\n* String2.testReadJsonlCSV()\n" + + // "The WARNING's below are expected..."); + + String source = "[\"a\",\"\",\"ccc\",\"dddd\"]\n" + + "[2,1.5,\" c3\u00b5\u20acz\\\\q\\f\\n\\r\\t\\u00b5\\u20ac \",true]\n" + + "[\"BAD ROW WITH WRONG NUMBER OF ITEMS\"]\n" + + "[\"BAD ROW with unterminated string ]\n" + + "BAD ROW WITHOUT JSON ARRAY.\n" + + " [null, null, \"1\", null] \n" + + " "; + + // don't simplify + StringReader sr = new StringReader(source); + Table table = new Table(); + table.readJsonlCSV(sr, "[StringReader]", null, null, false); + String results = table.dataToString(); + Test.ensureEqual(results, + "a,,ccc,dddd\n" + + "2,1.5,\"\"\" c3\\u00b5\\u20acz\\\\\\\\q\\\\f\\\\n\\\\r\\\\t\\\\u00b5\\\\u20ac \"\"\",true\n" + // ?! not + // sure if + // correct + ",,\"\"\"1\"\"\",\n", + "results=\n" + results); + + // simplify + sr = new StringReader(source); + table = new Table(); + table.readJsonlCSV(sr, "[StringReader]", null, null, true); + results = table.dataToString(); + Test.ensureEqual(results, + "a,,ccc,dddd\n" + + "2,1.5,\" c3\\u00b5\\u20acz\\\\q\\f\\n\\r\\t\\u00b5\\u20ac \",1\n" + + ",,1,\n", + "results=\n" + results); + + // specify colNames and simplify + sr = new StringReader(source); + table = new Table(); + table.readJsonlCSV(sr, "[StringReader]", StringArray.fromCSV("ccc,a,dddd"), null, true); + results = table.dataToString(); + Test.ensureEqual(results, + "ccc,a,dddd\n" + + "\" c3\\u00b5\\u20acz\\\\q\\f\\n\\r\\t\\u00b5\\u20ac \",2,1\n" + + "1,,\n", + "results=\n" + results); + Test.ensureEqual(table.getColumn(0).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(1).elementTypeString(), "byte", ""); + Test.ensureEqual(table.getColumn(2).elementTypeString(), "byte", ""); // boolean -> byte + + // specify colNames and types + sr = new StringReader(source); + table = new Table(); + table.readJsonlCSV(sr, "[StringReader]", StringArray.fromCSV("ccc,a,dddd"), + new String[] { "String", "int", "boolean" }, true); + results = table.dataToString(); + Test.ensureEqual(results, + "ccc,a,dddd\n" + + "\" c3\\u00b5\\u20acz\\\\q\\f\\n\\r\\t\\u00b5\\u20ac \",2,1\n" + + "1,,\n", + "results=\n" + results); + Test.ensureEqual(table.getColumn(0).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(1).elementTypeString(), "int", ""); + Test.ensureEqual(table.getColumn(2).elementTypeString(), "byte", ""); // boolean -> byte + + // tough test table + String fullName = TEMP_DIR.toAbsolutePath().toString() + "/testJsonCSV.jsonl"; + File2.delete(fullName); + table = makeToughTestTable(); + results = table.dataToString(); + String expected = "aString,aChar,aByte,aUByte,aShort,aUShort,anInt,aUInt,aLong,aULong,aFloat,aDouble\n" + + "a\\u00fcb\\nc\\td\\u20ace,\\u00fc,-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308\n" + + + "ab,\\u0000,0,127,0,32767,0,7,0,1,2.2,3.3\n" + + ",A,99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324\n" + + "cd,\\t,126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308\n" + + + ",\\u20ac,,,,,,,,,,\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + table.writeJsonlCSV(fullName); + table.clear(); // doubly sure + table.readJsonlCSV(fullName, null, null, true); // simplify + results = table.dataToString(); + expected = // differs in that aULong is now a double column (because simplify doesn't catch + // unsigned types) + "aString,aChar,aByte,aUByte,aShort,aUShort,anInt,aUInt,aLong,aULong,aFloat,aDouble\n" + + "a\\u00fcb\\nc\\td\\u20ace,\\u00fc,-128,0,-32768,0,-2147483648,0,-9223372036854775808,0.0,-3.4028235E38,-1.7976931348623157E308\n" + + + "ab,\\u0000,0,127,0,32767,0,7,0,1.0,2.2,3.3\n" + + ",A,99,99,9999,9999,999999999,2147483647,8,9.223372036854776E18,1.4E-45,4.9E-324\n" + + "cd,\\t,126,254,32766,65534,2147483646,4294967294,9223372036854775806,1.8446744073709552E19,3.4028235E38,1.7976931348623157E308\n" + + + ",\\u20ac,,,,,,,,,,\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + PAType tTypes[] = { + PAType.STRING, PAType.STRING, PAType.BYTE, PAType.SHORT, PAType.SHORT, // char->String, unsigned -> larger + // signed + PAType.INT, PAType.INT, PAType.LONG, PAType.LONG, PAType.DOUBLE, // ULong -> Double + PAType.DOUBLE, PAType.DOUBLE }; // float->double because lots of decimal digits + for (int col = 0; col < 12; col++) + Test.ensureEqual(table.getColumn(col).elementType(), tTypes[col], "col=" + col); + + // another hard test + fullName = TableTests.class.getResource("/jsonl/sampleCSV.jsonl").getPath(); + table.readJsonlCSV(fullName, null, null, true); // simpify + results = table.dataToString(); + Test.ensureEqual(results, + "ship,time,lat,lon,status,testLong,sst\n" + + "Bell M. Shimada,2017-03-23T00:45:00Z,28.0002,-130.2576,A,-9223372036854775808,10.9\n" + + "Bell M. Shimada,2017-03-23T01:45:00Z,28.0003,-130.3472,\\u20ac,-1234567890123456,\n" + + "Bell M. Shimada,2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,0,10.7\n" + + "Bell M. Shimada,2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",1234567890123456,99.0\n" + + "\" a\\t~\\u00fc,\\n'z\"\"\\u20ac\",2017-03-23T21:45:00Z,28.0003,-132.0014,\\u00fc,9223372036854775806,10.0\n" + + + ",,,,,,\n", + "results=\n" + results); + + // *** write new file + table = makeToughTestTable(); + fullName = File2.getSystemTempDirectory() + "testJsonlCSV.json"; + table.writeJsonlCSV(fullName); + results = File2.directReadFromUtf8File(fullName); + Test.ensureEqual(results, + "[\"aString\",\"aChar\",\"aByte\",\"aUByte\",\"aShort\",\"aUShort\",\"anInt\",\"aUInt\",\"aLong\",\"aULong\",\"aFloat\",\"aDouble\"]\n" + + + "[\"a\\u00fcb\\nc\\td\\u20ace\",\"\\u00fc\",-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308]\n" + + + "[\"ab\",\"\\u0000\",0,127,0,32767,0,7,0,1,2.2,3.3]\n" + + "[\"\",\"A\",99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324]\n" + + "[\"cd\",\"\\t\",126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308]\n" + + + "[\"\",\"\\u20ac\",null,null,null,null,null,null,null,null,null,null]\n", + "results=\n" + results); + + // *** write/append new file + table = makeToughTestTable(); + File2.delete(fullName); + table.writeJsonlCSV(fullName, true); + results = File2.directReadFromUtf8File(fullName); + Test.ensureEqual(results, + "[\"aString\",\"aChar\",\"aByte\",\"aUByte\",\"aShort\",\"aUShort\",\"anInt\",\"aUInt\",\"aLong\",\"aULong\",\"aFloat\",\"aDouble\"]\n" + + + "[\"a\\u00fcb\\nc\\td\\u20ace\",\"\\u00fc\",-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308]\n" + + + "[\"ab\",\"\\u0000\",0,127,0,32767,0,7,0,1,2.2,3.3]\n" + + "[\"\",\"A\",99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324]\n" + + "[\"cd\",\"\\t\",126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308]\n" + + + "[\"\",\"\\u20ac\",null,null,null,null,null,null,null,null,null,null]\n", + "results=\n" + results); + + // then append + table.writeJsonlCSV(fullName, true); + results = File2.directReadFromUtf8File(fullName); + Test.ensureEqual(results, + "[\"aString\",\"aChar\",\"aByte\",\"aUByte\",\"aShort\",\"aUShort\",\"anInt\",\"aUInt\",\"aLong\",\"aULong\",\"aFloat\",\"aDouble\"]\n" + + + "[\"a\\u00fcb\\nc\\td\\u20ace\",\"\\u00fc\",-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308]\n" + + + "[\"ab\",\"\\u0000\",0,127,0,32767,0,7,0,1,2.2,3.3]\n" + + "[\"\",\"A\",99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324]\n" + + "[\"cd\",\"\\t\",126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308]\n" + + + "[\"\",\"\\u20ac\",null,null,null,null,null,null,null,null,null,null]\n" + + "[\"a\\u00fcb\\nc\\td\\u20ace\",\"\\u00fc\",-128,0,-32768,0,-2147483648,0,-9223372036854775808,0,-3.4028235E38,-1.7976931348623157E308]\n" + + + "[\"ab\",\"\\u0000\",0,127,0,32767,0,7,0,1,2.2,3.3]\n" + + "[\"\",\"A\",99,99,9999,9999,999999999,2147483647,8,9223372036854775807,1.4E-45,4.9E-324]\n" + + "[\"cd\",\"\\t\",126,254,32766,65534,2147483646,4294967294,9223372036854775806,18446744073709551614,3.4028235E38,1.7976931348623157E308]\n" + + + "[\"\",\"\\u20ac\",null,null,null,null,null,null,null,null,null,null]\n", + "results=\n" + results); + + } + + /** + * Test saveAsJson and readJson. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + @TagLocalERDDAP + void testJson() throws Exception { + // String2.log("\n***** Table.testJson"); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // generate some data + Table table = getTestTable(true, true); + + // write it to a file + String fileName = TEMP_DIR.toAbsolutePath().toString() + "/tempTable.json"; + table.saveAsJson(fileName, 0, true); + // String2.log(fileName + "=\n" + File2.readFromFile(fileName)[1]); + // Test.displayInBrowser("file://" + fileName); //.json + + // read it from the file + String results = File2.directReadFromUtf8File(fileName); + Test.ensureEqual(results, + "{\n" + + " \"table\": {\n" + + " \"columnNames\": [\"Time\", \"Longitude\", \"Latitude\", \"Double Data\", \"Long Data\", \"Int Data\", \"Short Data\", \"Byte Data\", \"Char Data\", \"String Data\"],\n" + + + " \"columnTypes\": [\"String\", \"int\", \"float\", \"double\", \"long\", \"int\", \"short\", \"byte\", \"char\", \"String\"],\n" + + + " \"columnUnits\": [\"UTC\", \"degrees_east\", \"degrees_north\", \"doubles\", \"longs\", \"ints\", \"shorts\", \"bytes\", \"chars\", \"Strings\"],\n" + + + " \"rows\": [\n" + + " [\"1970-01-01T00:00:00Z\", -3, 1.0, -1.0E300, -2000000000000000, -2000000000, -32000, -120, \",\", \"a\"],\n" + + + " [\"2005-08-31T16:01:02Z\", -2, 1.5, 3.123, 2, 2, 7, 8, \"\\\"\", \"bb\"],\n" + + " [\"2005-11-02T18:04:09Z\", -1, 2.0, 1.0E300, 2000000000000000, 2000000000, 32000, 120, \"\\u20ac\", \"ccc\"],\n" + + + " [null, null, null, null, null, null, null, null, \"\", \"\"]\n" + + " ]\n" + + " }\n" + + "}\n", + results); + + // read it + Table table2 = new Table(); + table2.readJson(fileName); + Test.ensureTrue(table.equals(table2), ""); + + // finally + File2.delete(fileName); + + // ******************* test readErddapInfo + // String tUrl = "https://coastwatch.pfeg.noaa.gov/erddap2"; + // http://localhost:8080/cwexperimental/info/pmelTaoDySst/index.json + String tUrl = "http://localhost:8080/cwexperimental"; + table.readErddapInfo(tUrl + "/info/pmelTaoDySst/index.json"); + String ncHeader = table.getNCHeader("row"); + Test.ensureEqual(table.globalAttributes.getString("cdm_data_type"), "TimeSeries", ncHeader); + Test.ensureEqual(table.globalAttributes.getString("title"), + "TAO/TRITON, RAMA, and PIRATA Buoys, Daily, 1977-present, Sea Surface Temperature", + ncHeader); + Test.ensureEqual(table.globalAttributes.get("history").size(), 3, ncHeader); + Test.ensureEqual(table.globalAttributes.get("history").getString(0), + "This dataset has data from the TAO/TRITON, RAMA, and PIRATA projects.", + ncHeader); + Test.ensureEqual(table.globalAttributes.get("history").getString(1), + "This dataset is a product of the TAO Project Office at NOAA/PMEL.", + ncHeader); + Test.ensureLinesMatch(table.globalAttributes.get("history").getString(2), + "20\\d{2}-\\d{2}-\\d{2} Bob Simons at NOAA/NMFS/SWFSC/ERD \\(bob.simons@noaa.gov\\) " + + "fully refreshed ERD's copy of this dataset by downloading all of the .cdf files from the PMEL TAO FTP site. " + + + "Since then, the dataset has been partially refreshed everyday by downloading and merging the latest version of the last 25 days worth of data.", + ncHeader); + Test.ensureEqual(table.nColumns(), 10, ncHeader); + Test.ensureEqual(table.findColumnNumber("longitude"), 3, ncHeader); + Test.ensureEqual(table.columnAttributes(3).getString("units"), "degrees_east", ncHeader); + int t25Col = table.findColumnNumber("T_25"); + Test.ensureTrue(t25Col > 0, ncHeader); + Test.ensureEqual(table.columnAttributes(t25Col).getString("ioos_category"), "Temperature", ncHeader); + Test.ensureEqual(table.columnAttributes(t25Col).getString("units"), "degree_C", ncHeader); + + } + + /** + * Test convert. + */ + @org.junit.jupiter.api.Test + @TagExternalOther + void testConvert() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + String url, fileName; + Table table = new Table(); + + // /* + // the original test from Roy + // This is used as an example in various documentation. + // If url changes, do search and replace to change all references to it. + url = "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_bottle?t0,oxygen&month=\"5\""; + // String2.log("\ntesting Table.convert \n url=" + url); + fileName = TEMP_DIR.toAbsolutePath().toString() + "/convertOriginal.nc"; + Table.convert(url, Table.READ_OPENDAP_SEQUENCE, fileName, Table.SAVE_AS_FLAT_NC, "row", false); + table.readFlatNc(fileName, null, 0); // standardizeWhat=0, should be already unpacked. + // String2.log(table.toString(3)); + Test.ensureEqual(table.nColumns(), 2, ""); + Test.ensureEqual(table.nRows(), 190, ""); + Test.ensureEqual(table.getColumnName(0), "t0", ""); + Test.ensureEqual(table.getColumnName(1), "oxygen", ""); + Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Temperature T0", ""); + Test.ensureEqual(table.columnAttributes(1).getString("long_name"), "Oxygen", ""); + Test.ensureEqual(table.getFloatData(0, 0), 12.1185f, ""); + Test.ensureEqual(table.getFloatData(0, 1), 12.1977f, ""); + Test.ensureEqual(table.getFloatData(1, 0), 6.56105f, ""); + Test.ensureEqual(table.getFloatData(1, 1), 6.95252f, ""); + File2.delete(fileName); + // */ + + // /* + // The 8/16/06 test from osu + // Test values below from html ascii request (same as url below, but with .ascii + // before "?") + // adcp95.yearday, adcp95.depth, adcp95.x, adcp95.y, adcp95.eastv + // row0: 184.45120239257812, 22, -123.8656005859375, 48.287899017333984, + // -0.31200000643730164 + // last row: 185.99949645996094, 22, -125.98069763183594, 42.844200134277344, + // -0.15399999916553497 + url = "http://nwioos.coas.oregonstate.edu:8080/dods/drds/1995%20Hake%20Survey%20ADCP?ADCP95.yearday,ADCP95.Z,ADCP95.x,ADCP95.y,ADCP95.EV&ADCP95.yearday<186&ADCP95.Z<25"; + // String2.log("\ntesting Table.convert \n url=" + url); + fileName = TEMP_DIR.toAbsolutePath().toString() + "/convertOSU.nc"; + Table.convert(url, Table.READ_OPENDAP_SEQUENCE, fileName, Table.SAVE_AS_FLAT_NC, "row", false); + table.readFlatNc(fileName, null, 0); // standardizeWhat=0, should be already unpacked. + // String2.log(table.toString(3)); + Test.ensureEqual(table.nColumns(), 5, ""); + Test.ensureEqual(table.nRows(), 446, ""); + Test.ensureEqual(table.getColumnName(0), "yearday", ""); + Test.ensureEqual(table.getColumnName(1), "Z", ""); + Test.ensureEqual(table.getColumnName(2), "x", ""); + Test.ensureEqual(table.getColumnName(3), "y", ""); + Test.ensureEqual(table.getColumnName(4), "EV", ""); + // no attributes + Test.ensureEqual(table.getDoubleData(0, 0), 184.45120239257812, ""); + Test.ensureEqual(table.getDoubleData(1, 0), 22, ""); + Test.ensureEqual(table.getDoubleData(2, 0), -123.8656005859375, ""); + Test.ensureEqual(table.getDoubleData(3, 0), 48.287899017333984, ""); + Test.ensureEqual(table.getDoubleData(4, 0), -0.31200000643730164, ""); + Test.ensureEqual(table.getDoubleData(0, 445), 185.99949645996094, ""); + Test.ensureEqual(table.getDoubleData(1, 445), 22, ""); + Test.ensureEqual(table.getDoubleData(2, 445), -125.98069763183594, ""); + Test.ensureEqual(table.getDoubleData(3, 445), 42.844200134277344, ""); + Test.ensureEqual(table.getDoubleData(4, 445), -0.15399999916553497, ""); + File2.delete(fileName); + // */ + + // /* + // The 8/17/06 test from cimt + // Test values below from html ascii request (same as url below, but with .ascii + // before "?") + // vCTD.latitude, vCTD.longitude, vCTD.station, vCTD.depth, vCTD.salinity + // first: 36.895, -122.082, "T101", 1.0, 33.9202 + // last: 36.609, -121.989, "T702", 4.0, 33.4914 + url = "http://cimt.dyndns.org:8080/dods/drds/vCTD?vCTD.latitude,vCTD.longitude,vCTD.station,vCTD.depth,vCTD.salinity&vCTD.depth<5"; + // String2.log("\ntesting Table.convert \n url=" + url); + fileName = TEMP_DIR.toAbsolutePath().toString() + "/convertCIMT.nc"; + Table.convert(url, Table.READ_OPENDAP_SEQUENCE, fileName, Table.SAVE_AS_FLAT_NC, "row", false); + table.readFlatNc(fileName, null, 0); // standardizeWhat=0, should be already unpacked. + // String2.log(table.toString(3)); + Test.ensureEqual(table.nColumns(), 5, ""); + // Test.ensureEqual(table.nRows(), 1407, ""); //this changes; file is growing + Test.ensureEqual(table.getColumnName(0), "latitude", ""); + Test.ensureEqual(table.getColumnName(1), "longitude", ""); + Test.ensureEqual(table.getColumnName(2), "station", ""); + Test.ensureEqual(table.getColumnName(3), "depth", ""); + Test.ensureEqual(table.getColumnName(4), "salinity", ""); + // no attributes + Test.ensureEqual(table.getFloatData(0, 0), 36.895f, ""); + Test.ensureEqual(table.getFloatData(1, 0), -122.082f, ""); + Test.ensureEqual(table.getStringData(2, 0), "T101", ""); + Test.ensureEqual(table.getFloatData(3, 0), 1.0f, ""); + Test.ensureEqual(table.getFloatData(4, 0), 33.9202f, ""); + Test.ensureEqual(table.getFloatData(0, 1406), 36.609f, ""); + Test.ensureEqual(table.getFloatData(1, 1406), -121.989f, ""); + Test.ensureEqual(table.getStringData(2, 1406), "T702", ""); + Test.ensureEqual(table.getFloatData(3, 1406), 4.0f, ""); + Test.ensureEqual(table.getFloatData(4, 1406), 33.4914f, ""); + File2.delete(fileName); + // */ + } + + /** + * Test the readASCII and saveAsASCII. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testASCII() throws Exception { + // *** test read all + // String2.log("\n***** Table.testASCII read all"); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // generate some data + Table table = getTestTable(true, true); + table.removeRow(3); // remove the empty row at the end, since readASCII will remove it + + Table table1 = getTestTable(true, true); + table1.removeRow(3); // remove the empty row at the end, since readASCII will remove it + + // write it to a file + String fileName = TEMP_DIR.toAbsolutePath().toString() + "/tempTable.asc"; + table.saveAsTabbedASCII(fileName); + // String2.log(fileName + "=\n" + File2.directReadFrom88591File(fileName)); + + // read it from the file + Table table2 = new Table(); + // // Table.debugMode = true; + table2.readASCII(fileName); + // // Table.debugMode = false; + + // check units on 1st data row + Test.ensureEqual(table2.getStringData(1, 0), "degrees_east", ""); + Test.ensureEqual(table2.getStringData(2, 0), "degrees_north", ""); + + // remove units row + table2.removeRow(0); + table2.simplify(); + + // are they the same (but column types may be different)? + Test.ensureTrue(table1.equals(table2, false), + "\ntable1=" + table1.toString() + "\ntable2=" + table2.toString()); + + // test simplification: see if column types are the same as original table + int n = table.nColumns(); + for (int col = 2; col < n; col++) // skip first 2 columns which are intentionally initially stored in bigger type + if (col != 4 && // LongArray -> StringArray + col != 8) // CharArray -> StringArray + Test.ensureEqual(table.columns.get(col).elementType(), + table2.getColumn(col).elementType(), "test type of col#" + col); + + // *** test read subset + // String2.log("\n***** Table.testASCII read subset"); + + // read 2nd row from the file + table2 = new Table(); + table2.readASCII(fileName, File2.ISO_8859_1, + "", "", 0, 1, "", + new String[] { "Int Data" }, new double[] { 0 }, new double[] { 4 }, + new String[] { "Short Data", "String Data" }, true); + Test.ensureEqual(table2.nColumns(), 2, ""); + Test.ensureEqual(table2.nRows(), 1, ""); + Test.ensureEqual(table2.getColumnName(0), "Short Data", ""); + Test.ensureEqual(table2.getColumnName(1), "String Data", ""); + Test.ensureEqual(table2.getDoubleData(0, 0), 7, ""); + Test.ensureEqual(table2.getStringData(1, 0), "bb", ""); + + // *** test read subset with no column names (otherwise same as test above) + // String2.log("\n***** Table.testASCII read subset with no column names"); + // read 3rd row from the file + table2 = new Table(); + table2.readASCII(fileName, File2.ISO_8859_1, + "", "", -1, 1, "", // -1=no column names + new String[] { "Column#5" }, new double[] { 0 }, new double[] { 4 }, + new String[] { "Column#6", "Column#8", "Column#9" }, true); + Test.ensureEqual(table2.nColumns(), 3, ""); + Test.ensureEqual(table2.nRows(), 1, ""); + Test.ensureEqual(table2.getColumnName(0), "Column#6", ""); + Test.ensureEqual(table2.getColumnName(1), "Column#8", ""); + Test.ensureEqual(table2.getColumnName(2), "Column#9", ""); + Test.ensureEqual(table2.getDoubleData(0, 0), 7, ""); + Test.ensureEqual(table2.getStringData(1, 0), "\"", ""); + Test.ensureEqual(table2.getStringData(2, 0), "bb", ""); + + // ** finally + File2.delete(fileName); + } + + /** + * Test readStandardTabbedASCII. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testReadStandardTabbedASCII() throws Exception { + // *** test read all + // String2.log("\n***** Table.testReadStandardTabbedASCII"); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // generate some data + String lines = "colA\tcolB\tcolC\n" + + "1a\t1b\t1c\n" + + "2\n" + + "a\t2\n" + + "b\t2c\n" + + "3a\t3b\t3c"; // no terminal \n + Table table = new Table(); + + // read it from lines + table.readStandardTabbedASCII("tFileName", + new BufferedReader(new StringReader(lines)), null, true); + // String2.log("nRows=" + table.nRows() + " nCols=" + table.nColumns()); + Test.ensureEqual(table.dataToString(), + "colA,colB,colC\n" + + "1a,1b,1c\n" + + "2\\na,2\\nb,2c\n" + + "3a,3b,3c\n", + "tFileName toCSVString=\n" + table.dataToString()); + + // write it to a file + String fileName = TEMP_DIR.toAbsolutePath().toString() + "/tempTable.asc"; + File2.writeToFile88591(fileName, lines); + + // read all columns from the file + Table table2 = new Table(); + table2.readStandardTabbedASCII(fileName, null, true); + // String2.log("nRows=" + table2.nRows() + " nCols=" + table2.nColumns()); + Test.ensureEqual(table2.dataToString(), + "colA,colB,colC\n" + + "1a,1b,1c\n" + + "2\\na,2\\nb,2c\n" + + "3a,3b,3c\n", + "table2 toCSVString=\n" + table2.dataToString()); + + // just read cols B and C from the file + table2 = new Table(); + table2.readStandardTabbedASCII(fileName, new String[] { "colB", "colC" }, true); + // String2.log("nRows=" + table2.nRows() + " nCols=" + table2.nColumns()); + Test.ensureEqual(table2.dataToString(), + "colB,colC\n" + + "1b,1c\n" + + "2\\nb,2c\n" + + "3b,3c\n", + "table2 toCSVString=\n" + table2.dataToString()); + + // ** finally + File2.delete(fileName); + + } + + /** + * Test the saveAsHtml. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testHtml() throws Exception { + // String2.log("\n***** Table.testHtml"); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // generate some data + Table table = getTestTable(true, true); + + // write it to html file + String fileName = TEMP_DIR.toAbsolutePath().toString() + "/tempTable.html"; + table.saveAsHtml(fileName, "preTextHtml\n
\n", "postTextHtml\n
", + null, Table.BGCOLOR, 1, true, 0, true, // needEncodingAsHtml + false); + // String2.log(fileName + "=\n" + File2.directReadFromUtf8File(fileName)); + Test.displayInBrowser("file://" + fileName); // .html + + // read it from the file + String results = File2.directReadFromUtf8File(fileName); + Test.ensureEqual(results, + "\n" + + "\n" + + "\n" + + " tempTable\n" + + " \n" + + " \n" + + + "\n" + + "\n" + + "preTextHtml\n" + + "
\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "
Time\n" + + "Longitude\n" + + "Latitude\n" + + "Double Data\n" + + "Long Data\n" + + "Int Data\n" + + "Short Data\n" + + "Byte Data\n" + + "Char Data\n" + + "String Data\n" + + "
UTC\n" + + "degrees_east\n" + + "degrees_north\n" + + "doubles\n" + + "longs\n" + + "ints\n" + + "shorts\n" + + "bytes\n" + + "chars\n" + + "Strings\n" + + "
1970-01-01T00:00:00Z\n" + + "-3\n" + + "1.0\n" + + "-1.0E300\n" + + "-2000000000000000\n" + + "-2000000000\n" + + "-32000\n" + + "-120\n" + + ",\n" + + "a\n" + + "
2005-08-31T16:01:02Z\n" + + "-2\n" + + "1.5\n" + + "3.123\n" + + "2\n" + + "2\n" + + "7\n" + + "8\n" + + ""\n" + + "bb\n" + + "
2005-11-02T18:04:09Z\n" + + "-1\n" + + "2.0\n" + + "1.0E300\n" + + "2000000000000000\n" + + "2000000000\n" + + "32000\n" + + "120\n" + + "€\n" + + "ccc\n" + + "
\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + " \n" + + "
\n" + + "postTextHtml\n" + + "
\n" + + "\n", + results); + + // test readHtml - treat 2nd row as data + Table table2 = new Table(); + table2.readHtml(fileName, results, 0, + false, true); // secondRowHasUnits, simplify + String csv = String2.annotatedString(table2.dataToString()); + Test.ensureEqual(csv, // so units appear here as a row of data + "Time,Longitude,Latitude,Double Data,Long Data,Int Data,Short Data,Byte Data,Char Data,String Data[10]\n" + + "UTC,degrees_east,degrees_north,doubles,longs,ints,shorts,bytes,chars,Strings[10]\n" + + "1970-01-01T00:00:00Z,-3,1.0,-1.0E300,-2000000000000000,-2000000000,-32000,-120,\",\",a[10]\n" + + "2005-08-31T16:01:02Z,-2,1.5,3.123,2,2,7,8,\"\"\"\",bb[10]\n" + + "2005-11-02T18:04:09Z,-1,2.0,1.0E300,2000000000000000,2000000000,32000,120,\\u20ac,ccc[10]\n" + + ",,,,,,,,,[10]\n" + + "[end]", + csv); + + // test readHtml - treat 2nd row as units + table2 = new Table(); + table2.readHtml(fileName, results, 0, + true, true); // secondRowHasUnits, simplify + csv = String2.annotatedString(table2.dataToString()); + Test.ensureEqual(csv, // so units correctly stored as units + "Time,Longitude,Latitude,Double Data,Long Data,Int Data,Short Data,Byte Data,Char Data,String Data[10]\n" + + "1970-01-01T00:00:00Z,-3,1.0,-1.0E300,-2000000000000000,-2000000000,-32000,-120,\",\",a[10]\n" + + "2005-08-31T16:01:02Z,-2,1.5,3.123,2,2,7,8,\"\"\"\",bb[10]\n" + + "2005-11-02T18:04:09Z,-1,2.0,1.0E300,2000000000000000,2000000000,32000,120,\\u20ac,ccc[10]\n" + + ",,,,,,,,,[10]\n" + + "[end]", + csv); + Test.ensureEqual(table2.columnAttributes(0).getString("units"), "UTC", ""); + Test.ensureEqual(table2.columnAttributes(1).getString("units"), "degrees_east", ""); + Test.ensureEqual(table2.columnAttributes(8).getString("units"), "chars", ""); + Test.ensureEqual(table2.columnAttributes(9).getString("units"), "Strings", ""); + + // ** finally + Math2.gc("Table (between tests)", 10000); // in a test. Do something useful while browser gets going to display the + // file. + File2.delete(fileName); + } + + /** + * This is a test of readFlatNc and saveAsFlatNc. + * + * @throws Exception of trouble + */ + @org.junit.jupiter.api.Test + @TagMissingFile + void testFlatNc() throws Exception { + + // ********** test reading all data + // String2.log("\n*** Table.testFlatNc write and then read all"); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // generate some data + Table table = getTestTable(false, true); // falses=.nc doesn't seem to take longs + // String2.log("*******table=" + table.toString()); + + // write it to a file + String fileName = TEMP_DIR.toAbsolutePath().toString() + "/tempTable.nc"; + table.saveAsFlatNc(fileName, "time"); + + // read it from the file + Table table2 = new Table(); + table2.readFlatNc(fileName, null, 0); // standardizeWhat=0 + // String2.log("*********table2=" + table2.toString()); + + // replace ' ' with '_' in column names + for (int i = 0; i < table.columnNames.size(); i++) + table.columnNames.set(i, String2.replaceAll(table.columnNames.get(i), " ", "_")); + + // do the test that the tables are equal + // String2.log("testFlatNc table.nColAtt=" + table.columnAttributes.size() + // ? why columnAtt? + // " table2.nColAtt=" + table2.columnAttributes.size()); + // except char \\u20ac becomes "?" in nc file, so reset it + Test.ensureEqual( + table2.columns.get(7).getString(2), "?", ""); + table2.columns.get(7).setString(2, "\u20ac"); + if (table2.columns.get(7).getString(3).equals("?")) + table2.columns.get(7).setString(3, ""); + String t1 = table.dataToString(); + String t2 = table.dataToString(); + // String2.log("\nt1=\n" + t1 + "\nt2=\n" + t2); + Test.ensureEqual(t1, t2, ""); + Test.ensureTrue(table.equals(table2), "Test table equality"); + + // test if data types are the same + int n = table.nColumns(); + for (int col = 0; col < n; col++) + Test.ensureEqual(table.columns.get(col).elementType(), + table2.columns.get(col).elementType(), "test type of col#" + col); + + // clean up + table2.clear(); + File2.delete(fileName); + + // ***test unpack options (and global and variable attributes) + // String2.log("\n*** Table.testFlatNc test unpack"); + // row of data from 41015h1993.txt + // YY MM DD hh WD WSPD GST WVHT DPD APD MWD BAR ATMP WTMP DEWP VIS + // 93 05 24 11 194 02.5 02.8 00.70 04.20 04.90 185 1021.2 17.3 16.4 999.0 18.5 + double seconds = Calendar2.isoStringToEpochSeconds("1993-05-24T11"); + // String2.log("seconds=" + seconds); + int[] testColumns = { 0 }; + double testMin[] = { seconds }; + double testMax[] = { seconds }; + + // don't unpack + table.readFlatNc(TEMP_DIR.toAbsolutePath().toString() + "/41015.nc", new String[] { "time", "BAR" }, 0); // standardizeWhat=0 + // String2.log(table.toString(100)); + table.subset(testColumns, testMin, testMax); + Test.ensureEqual(table.nColumns(), 2, ""); + Test.ensureEqual(table.nRows(), 1, ""); + Test.ensureEqual(table.getColumnName(0), "time", ""); + Test.ensureEqual(table.getColumnName(1), "BAR", ""); + Test.ensureEqual(table.getColumn(1).elementType(), PAType.SHORT, ""); // short + Test.ensureEqual(table.getDoubleData(0, 0), seconds, ""); + Test.ensureEqual(table.getDoubleData(1, 0), 10212, ""); + + // test global and variable attributes + Test.ensureEqual(table.globalAttributes().getString("creator_name"), "NOAA National Data Buoy Center", ""); + Test.ensureEqual(table.columnAttributes(1).getString("long_name"), "Sea Level Pressure", ""); + + // unpack, to float if that is recommended + table.readFlatNc(TEMP_DIR.toAbsolutePath().toString() + "/41015.nc", new String[] { "time", "BAR" }, 1); // standardizeWhat=1 + table.subset(testColumns, testMin, testMax); + Test.ensureEqual(table.nColumns(), 2, ""); + Test.ensureEqual(table.nRows(), 1, ""); + Test.ensureEqual(table.getColumnName(0), "time", ""); + Test.ensureEqual(table.getColumnName(1), "BAR", ""); + Test.ensureEqual(table.getColumn(1).elementType(), PAType.FLOAT, ""); // float + Test.ensureEqual(table.getDoubleData(0, 0), seconds, ""); + Test.ensureEqual(table.getFloatData(1, 0), 1021.2f, ""); + + // ********** test reading subset of data via bitset (which uses read via + // firstrow/lastrow) + // String2.log("\n*** Table.testFlatNc read subset"); + table.clear(); + NetcdfFile netcdfFile = NcHelper.openFile(TEMP_DIR.toAbsolutePath().toString() + "/41015.nc"); + try { + Variable loadVariables[] = NcHelper.findVariables(netcdfFile, new String[] { "time", "BAR" }); + Variable testVariables[] = NcHelper.findVariables(netcdfFile, new String[] { "time" }); + BitSet okRows = NcHelper.testRows(testVariables, testMin, testMax); + table.appendNcRows(loadVariables, okRows); + Test.ensureEqual(okRows.cardinality(), 1, ""); + } finally { + try { + if (netcdfFile != null) + netcdfFile.close(); + } catch (Exception e9) { + } + } + + Test.ensureEqual(table.nColumns(), 2, ""); + Test.ensureEqual(table.nRows(), 1, ""); + Test.ensureEqual(table.getColumnName(0), "time", ""); + Test.ensureEqual(table.getColumnName(1), "BAR", ""); + Test.ensureEqual(table.getColumn(1).elementType(), PAType.SHORT, ""); // short + Test.ensureEqual(table.getDoubleData(0, 0), seconds, ""); + Test.ensureEqual(table.getDoubleData(1, 0), 10212, ""); // still packed + + } + + /** + * This is a test of read4DNc and saveAs4DNc. + * + * @throws Exception of trouble + */ + @org.junit.jupiter.api.Test + void test4DNc() throws Exception { + + // ********** test reading all data + // String2.log("\n*** Table.test4DNc write and then read all"); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // generate some data + Table table = new Table(); + DoubleArray xCol = new DoubleArray(); + DoubleArray yCol = new DoubleArray(); + DoubleArray zCol = new DoubleArray(); + DoubleArray tCol = new DoubleArray(); + IntArray data1Col = new IntArray(); + DoubleArray data2Col = new DoubleArray(); + StringArray data3Col = new StringArray(); + table.addColumn("X", xCol); + table.addColumn("Y", yCol); + table.addColumn("Z", zCol); + table.addColumn("T", tCol); + table.addColumn("data1", data1Col); + table.addColumn("data2", data2Col); + table.addColumn("data3", data3Col); + for (int t = 0; t < 2; t++) { + for (int z = 0; z < 3; z++) { + for (int y = 0; y < 3; y++) { + for (int x = 0; x < 4; x++) { + xCol.add(x + 1); + yCol.add(y + 1); + zCol.add(z + 1); + tCol.add(t + 1); + int fac = (x + 1) * (y + 1) * (z + 1) * (t + 1); + data1Col.add(fac); + data2Col.add(100 + (x + 1) * (y + 1) * (z + 1) * (t + 1)); + data3Col.add("" + fac); + } + } + } + } + table.ensureValid(); // throws Exception if not + // String2.log(table.toString("obs", 10)); + + // write it to a file + String fileName = TEMP_DIR.toAbsolutePath().toString() + "/temp4DTable.nc"; + Attributes idAttributes = new Attributes(); + idAttributes.set("long_name", "The station's name."); + idAttributes.set("units", DataHelper.UNITLESS); + String stringVariableValue = "My Id Value"; + table.saveAs4DNc(fileName, 0, 1, 2, 3, "ID", stringVariableValue, idAttributes); + + // then insert col 4 filled with "My Id Value" + String sar[] = new String[table.nRows()]; + Arrays.fill(sar, stringVariableValue); + table.addColumn(4, "ID", new StringArray(sar), idAttributes); + + // get the header + // String2.log("table=" + String2.log(NcHelper.ncdump(fileName, "-h"))); + + // read from file + Table table2 = new Table(); + table2.read4DNc(fileName, null, 1, "ID", 4); // standarizeWhat=1 + // String2.log("col6=" + table2.getColumn(6)); + // String2.log("\ntable2 after read4DNc: " + table2.toString("obs", 1000000)); + + // test equality + Test.ensureTrue(table.equals(table2), "test4DNc tables not equal!"); + + File2.delete(fileName); + + } + + /** + * This is a test of readOpendapSequence. + * Test cases from Roy: + * GLOBEC VPT: + * stn_id=loaddods('https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_vpt?stn_id&unique()'); + * abund=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_vpt?abund_m3&stn_id="NH05"'); + * GLOBEC Bottle: + * month=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_bottle?month&unique()'); + * [oxy + * temp]=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_bottle?t0,oxygen&month="5"'); + * GLOBEC MOC1: + * [abund,lon,lat]=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1?abund_m3,lat,long'); + * [abund1,lon1,lat1]=loaddods('-F','https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1?abund_m3,lat,long&program="MESO_1"'); + * I note that loaddods documentation is at + * https://www.opendap.org/user/mgui-html/mgui_36.html + * and -F says to convert all strings to floats. + * "unique()" seems to just return unique values. + * + * @throws Exception of trouble + */ + @org.junit.jupiter.api.Test + void testOpendapSequence() throws Exception { + + // 2013-03-18 I changed from oceanwatch datasets (no longer available) to + // coastwatch erddap datasets + // String2.log("\n*** Table.testOpendapSequence"); + // Table.verbose = true; + // Table.reallyVerbose = true; + Table table = new Table(); + int nRows; + String url; + float lon, lat; + String results, expected; + + // 2016-07-25 test for Kevin's dataset: from remote erddap + url = "https://ferret.pmel.noaa.gov/pmel/erddap/tabledap/ChukchiSea_454a_037a_fcf4?" + + "prof,id,cast,cruise,time,longitude,lon360,latitude&time%3E=2012-09-04&time%3C=2012-09-07&distinct()"; + table.readOpendapSequence(url, false); // boolean: skipDapSpacerRows + results = table.toString(3); + expected = "{\n" + + "dimensions:\n" + + "\trow = 2 ;\n" + + "\tid_strlen = 10 ;\n" + + "\tcast_strlen = 3 ;\n" + + "\tcruise_strlen = 6 ;\n" + + "variables:\n" + + "\tdouble prof(row) ;\n" + + "\t\tprof:actual_range = 1.0, 1.0 ;\n" + + "\t\tprof:axis = \"E\" ;\n" + + "\t\tprof:long_name = \"Prof\" ;\n" + + "\t\tprof:point_spacing = \"even\" ;\n" + + "\tchar id(row, id_strlen) ;\n" + + "\t\tid:cf_role = \"profile_id\" ;\n" + + "\t\tid:long_name = \"profile id\" ;\n" + + "\tchar cast(row, cast_strlen) ;\n" + + "\t\tcast:colorBarMaximum = 100.0 ;\n" + + "\t\tcast:colorBarMinimum = 0.0 ;\n" + + "\t\tcast:long_name = \"cast number\" ;\n" + + "\tchar cruise(row, cruise_strlen) ;\n" + + "\t\tcruise:long_name = \"Cruise name\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:_CoordinateAxisType = \"Time\" ;\n" + + "\t\ttime:actual_range = 1.28368572E9, 1.34697582E9 ;\n" + + "\t\ttime:axis = \"T\" ;\n" + + "\t\ttime:ioos_category = \"Time\" ;\n" + + "\t\ttime:long_name = \"Time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:time_origin = \"01-JAN-1970 00:00:00\" ;\n" + + "\t\ttime:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + + "\tfloat longitude(row) ;\n" + + "\t\tlongitude:_CoordinateAxisType = \"Lon\" ;\n" + + "\t\tlongitude:_FillValue = -1.0E34f ;\n" + + "\t\tlongitude:actual_range = -174.6603f, -157.1593f ;\n" + + "\t\tlongitude:axis = \"X\" ;\n" + + "\t\tlongitude:colorBarMaximum = 180.0 ;\n" + + "\t\tlongitude:colorBarMinimum = -180.0 ;\n" + + "\t\tlongitude:ioos_category = \"Location\" ;\n" + + "\t\tlongitude:long_name = \"station longitude\" ;\n" + + "\t\tlongitude:missing_value = -1.0E34f ;\n" + + "\t\tlongitude:standard_name = \"longitude\" ;\n" + + "\t\tlongitude:units = \"degrees_east\" ;\n" + + "\tfloat lon360(row) ;\n" + + "\t\tlon360:_FillValue = -1.0E34f ;\n" + + "\t\tlon360:actual_range = 185.3397f, 202.8407f ;\n" + + "\t\tlon360:colorBarMaximum = 180.0 ;\n" + + "\t\tlon360:colorBarMinimum = -180.0 ;\n" + + "\t\tlon360:long_name = \"station longitude 360\" ;\n" + + "\t\tlon360:missing_value = -1.0E34f ;\n" + + "\t\tlon360:standard_name = \"longitude\" ;\n" + + "\t\tlon360:units = \"degrees_east\" ;\n" + + "\tfloat latitude(row) ;\n" + + "\t\tlatitude:_CoordinateAxisType = \"Lat\" ;\n" + + "\t\tlatitude:_FillValue = -1.0E34f ;\n" + + "\t\tlatitude:actual_range = 54.34184f, 73.11517f ;\n" + + "\t\tlatitude:axis = \"Y\" ;\n" + + "\t\tlatitude:colorBarMaximum = 90.0 ;\n" + + "\t\tlatitude:colorBarMinimum = -90.0 ;\n" + + "\t\tlatitude:history = \"From mb1101c070.nc_copy\" ;\n" + + "\t\tlatitude:ioos_category = \"Location\" ;\n" + + "\t\tlatitude:long_name = \"station latitude\" ;\n" + + "\t\tlatitude:missing_value = -1.0E34f ;\n" + + "\t\tlatitude:standard_name = \"latitude\" ;\n" + + "\t\tlatitude:units = \"degrees_north\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:CAST = \"070\" ;\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"prof, id, cast, cruise, time, longitude, lon360, latitude\" ;\n" + + "\t\t:Conventions = \"CF-1.6, COARDS, ACDD-1.3\" ;\n" + + "\t\t:COORD_SYSTEM = \"GEOGRAPHICAL\" ;\n" + + "\t\t:creation_date = \"14:48 21-JUN-2013\" ;\n" + + "\t\t:creator_email = \"peggy.sullivan@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Phyllis Stabeno, Margaret Sullivan\" ;\n" + + "\t\t:CRUISE = \"Ch2011\" ;\n" + + "\t\t:DATA_CMNT = \"Data from Seasoft File chaoz2011070.cnv\" ;\n" + + "\t\t:DATA_TYPE = \"CTD\" ;\n" + + "\t\t:Easternmost_Easting = -157.1593 ;\n" + + "\t\t:EPIC_FILE_GENERATOR = \"SEASOFT2EPIC_CTD (Version 1.37, 14-Oct-2011)\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 73.11517 ;\n" + + "\t\t:geospatial_lat_min = 54.34184 ;\n" + + "\t\t:geospatial_lat_units = \"degrees_north\" ;\n" + + "\t\t:geospatial_lon_max = -157.1593 ;\n" + + "\t\t:geospatial_lon_min = -174.6603 ;\n" + + "\t\t:geospatial_lon_units = \"degrees_east\" ;\n" + + "\t\t:geospatial_vertical_max = 166.0 ;\n" + + "\t\t:geospatial_vertical_min = 0.0 ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"m\" ;\n" + + "\t\t:history = \"FERRET V7 13-Jun-16\n"; + // 2016-10-03T22:25:01Z (local files) + // 2016-10-03T22:25:01Z + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + + expected = "https://data.pmel.noaa.gov/pmel/erddap/tabledap/ChukchiSea_454a_037a_fcf4.das\" ;\n" + + "\t\t:infoUrl = \"www.ecofoci.noaa.gov\" ;\n" + + "\t\t:INST_TYPE = \"Sea-Bird CTD SBE911\" ;\n" + + "\t\t:institution = \"PMEL EcoFOCI\" ;\n" + + "\t\t:keywords = \"2010-2012, active, ammonia, ammonium, bottle, calibration, cast, chemistry, chlorophyll, chukchi, concentration, concentration_of_chlorophyll_in_sea_water, cooperative, cruise, data, density, depth, dissolved, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > Oxygen, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Ocean Chemistry > Silicate, Earth Science > Oceans > Salinity/Density > Salinity, ecofoci, environmental, factory, fisheries, fisheries-oceanography, flourescence, foci, fraction, fractional, fractional_saturation_of_oxygen_in_sea_water, investigations, laboratory, latitude, lon360, longitude, marine, ml/l, mmoles, mmoles/kg, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, mole_concentration_of_phosphate_in_sea_water, mole_concentration_of_silicate_in_sea_water, molecular, n02, name, nh4, niskin, nitrate, nitrite, no2, no3, noaa, number, nutrients, O2, ocean, ocean_chlorophyll_a_concentration_factoryCal, ocean_chlorophyll_fluorescence_raw, ocean_dissolved_oxygen_concentration_1_mLperL, ocean_dissolved_oxygen_concentration_1_mMperkg, ocean_dissolved_oxygen_concentration_2_mLperL, ocean_dissolved_oxygen_concentration_2_mMperkg, ocean_oxygen_saturation_1, ocean_practical_salinity_1, ocean_practical_salinity_2, ocean_sigma_t, ocean_temperature_1, ocean_temperature_2, oceanography, oceans, oxygen, pacific, percent, phosphate, photosynthetically, photosynthetically_active_radiation, pmel, po4, practical, prof, profile, pss, pss-78, psu, radiation, raw, salinity, saturation, scale, sea, sea_water_ammonium_concentration, sea_water_nitrate_concentration, sea_water_nitrite_concentration, sea_water_nutrient_bottle_number, sea_water_phosphate_concentration, sea_water_practical_salinity, sea_water_silicate_concentration, seawater, sigma, sigma-t, silicate, station, temperature, time, unit, volume, volume_fraction_of_oxygen_in_sea_water, water\" ;\n" + + + "\t\t:keywords_vocabulary = \"GCMD Science Keywords\" ;\n" + + "\t\t:license = \"Data Licenses / Data Usage Restrictions\n" + + "The data may be used and redistributed for free but is not intended\n" + + "for legal use, since it may contain inaccuracies. Neither the data\n" + + "Contributor, ERD, NOAA, nor the United States Government, nor any\n" + + "of their employees or contractors, makes any warranty, express or\n" + + "implied, including warranties of merchantability and fitness for a\n" + + "particular purpose, or assumes any legal liability for the accuracy,\n" + + "completeness, or usefulness, of this information.\n" + + "\n" + + "Unless otherwise noted, data served through this ERDDAP server are \n" + + "not quality controlled. Users may need to do quality control when using \n" + + "these data. These data are made available at the users own risk.\" ;\n" + + "\t\t:Northernmost_Northing = 73.11517 ;\n" + + "\t\t:PROG_CMNT1 = \"cat_ctd v1.36 06Aug2010\" ;\n" + + "\t\t:PROG_CMNT2 = \"Variables Extrapolated from 2 db to 0\" ;\n" + + "\t\t:sourceUrl = \"(local files)\" ;\n" + + "\t\t:Southernmost_Northing = 54.34184 ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v29\" ;\n" + + "\t\t:STATION_NAME = \"Unimak3\" ;\n" + + "\t\t:subsetVariables = \"prof, id, cast, cruise, time, longitude, lon360, latitude\" ;\n" + + "\t\t:summary = \"Pacific Marine Environmental Laboratory (PMEL) Fisheries-Oceanography Cooperative Investigations (FOCI) Chukchi Sea. PMEL EcoFOCI data from a local source.\" ;\n" + + + "\t\t:time_coverage_end = \"2012-09-06T23:57:00Z\" ;\n" + + "\t\t:time_coverage_start = \"2010-09-05T11:22:00Z\" ;\n" + + "\t\t:title = \"PMEL EcoFOCI Chukchi Sea profile data, 2010-2012\" ;\n" + + "\t\t:WATER_DEPTH = 0 ;\n" + + "\t\t:WATER_MASS = \"A\" ;\n" + + "\t\t:Westernmost_Easting = -174.6603 ;\n" + + "}\n" + + "prof,id,cast,cruise,time,longitude,lon360,latitude\n" + + "1.0,aq1201c069,069,aq1201,1.34697456E9,-164.0447,195.9553,56.866\n" + + "1.0,aq1201c070,070,aq1201,1.34697582E9,-164.049,195.951,56.864\n"; + int po = results.indexOf(expected.substring(0, 60)); + Test.ensureEqual(results.substring(Math.max(0, po)), expected, "results=\n" + results); + + url = "https://data.pmel.noaa.gov/pmel/erddap/tabledap/ChukchiSea_454a_037a_fcf4?" + + "prof,id,cast,cruise,time,longitude,lon360,latitude&time%3E=2012-09-04&time%3C=2012-09-07"; + table.readOpendapSequence(url, false); // boolean: skipDapSpacerRows + results = table.toString(3); + expected = "{\n" + + "dimensions:\n" + + "\trow = 2 ;\n" + + "\tid_strlen = 10 ;\n" + + "\tcast_strlen = 3 ;\n" + + "\tcruise_strlen = 6 ;\n" + + "variables:\n" + + "\tdouble prof(row) ;\n" + + "\t\tprof:actual_range = 1.0, 1.0 ;\n" + + "\t\tprof:axis = \"E\" ;\n" + + "\t\tprof:long_name = \"Prof\" ;\n" + + "\t\tprof:point_spacing = \"even\" ;\n" + + "\tchar id(row, id_strlen) ;\n" + + "\t\tid:cf_role = \"profile_id\" ;\n" + + "\t\tid:long_name = \"profile id\" ;\n" + + "\tchar cast(row, cast_strlen) ;\n" + + "\t\tcast:colorBarMaximum = 100.0 ;\n" + + "\t\tcast:colorBarMinimum = 0.0 ;\n" + + "\t\tcast:long_name = \"cast number\" ;\n" + + "\tchar cruise(row, cruise_strlen) ;\n" + + "\t\tcruise:long_name = \"Cruise name\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:_CoordinateAxisType = \"Time\" ;\n" + + "\t\ttime:actual_range = 1.28368572E9, 1.34697582E9 ;\n" + + "\t\ttime:axis = \"T\" ;\n" + + "\t\ttime:ioos_category = \"Time\" ;\n" + + "\t\ttime:long_name = \"Time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:time_origin = \"01-JAN-1970 00:00:00\" ;\n" + + "\t\ttime:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + + "\tfloat longitude(row) ;\n" + + "\t\tlongitude:_CoordinateAxisType = \"Lon\" ;\n" + + "\t\tlongitude:_FillValue = -1.0E34f ;\n" + + "\t\tlongitude:actual_range = -174.6603f, -157.1593f ;\n" + + "\t\tlongitude:axis = \"X\" ;\n" + + "\t\tlongitude:colorBarMaximum = 180.0 ;\n" + + "\t\tlongitude:colorBarMinimum = -180.0 ;\n" + + "\t\tlongitude:ioos_category = \"Location\" ;\n" + + "\t\tlongitude:long_name = \"station longitude\" ;\n" + + "\t\tlongitude:missing_value = -1.0E34f ;\n" + + "\t\tlongitude:standard_name = \"longitude\" ;\n" + + "\t\tlongitude:units = \"degrees_east\" ;\n" + + "\tfloat lon360(row) ;\n" + + "\t\tlon360:_FillValue = -1.0E34f ;\n" + + "\t\tlon360:actual_range = 185.3397f, 202.8407f ;\n" + + "\t\tlon360:colorBarMaximum = 180.0 ;\n" + + "\t\tlon360:colorBarMinimum = -180.0 ;\n" + + "\t\tlon360:long_name = \"station longitude 360\" ;\n" + + "\t\tlon360:missing_value = -1.0E34f ;\n" + + "\t\tlon360:standard_name = \"longitude\" ;\n" + + "\t\tlon360:units = \"degrees_east\" ;\n" + + "\tfloat latitude(row) ;\n" + + "\t\tlatitude:_CoordinateAxisType = \"Lat\" ;\n" + + "\t\tlatitude:_FillValue = -1.0E34f ;\n" + + "\t\tlatitude:actual_range = 54.34184f, 73.11517f ;\n" + + "\t\tlatitude:axis = \"Y\" ;\n" + + "\t\tlatitude:colorBarMaximum = 90.0 ;\n" + + "\t\tlatitude:colorBarMinimum = -90.0 ;\n" + + "\t\tlatitude:history = \"From mb1101c070.nc_copy\" ;\n" + + "\t\tlatitude:ioos_category = \"Location\" ;\n" + + "\t\tlatitude:long_name = \"station latitude\" ;\n" + + "\t\tlatitude:missing_value = -1.0E34f ;\n" + + "\t\tlatitude:standard_name = \"latitude\" ;\n" + + "\t\tlatitude:units = \"degrees_north\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:CAST = \"070\" ;\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"prof, id, cast, cruise, time, longitude, lon360, latitude\" ;\n" + + "\t\t:Conventions = \"CF-1.6, COARDS, ACDD-1.3\" ;\n" + + "\t\t:COORD_SYSTEM = \"GEOGRAPHICAL\" ;\n" + + "\t\t:creation_date = \"14:48 21-JUN-2013\" ;\n" + + "\t\t:creator_email = \"peggy.sullivan@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Phyllis Stabeno, Margaret Sullivan\" ;\n" + + "\t\t:CRUISE = \"Ch2011\" ;\n" + + "\t\t:DATA_CMNT = \"Data from Seasoft File chaoz2011070.cnv\" ;\n" + + "\t\t:DATA_TYPE = \"CTD\" ;\n" + + "\t\t:Easternmost_Easting = -157.1593 ;\n" + + "\t\t:EPIC_FILE_GENERATOR = \"SEASOFT2EPIC_CTD (Version 1.37, 14-Oct-2011)\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 73.11517 ;\n" + + "\t\t:geospatial_lat_min = 54.34184 ;\n" + + "\t\t:geospatial_lat_units = \"degrees_north\" ;\n" + + "\t\t:geospatial_lon_max = -157.1593 ;\n" + + "\t\t:geospatial_lon_min = -174.6603 ;\n" + + "\t\t:geospatial_lon_units = \"degrees_east\" ;\n" + + "\t\t:geospatial_vertical_max = 166.0 ;\n" + + "\t\t:geospatial_vertical_min = 0.0 ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"m\" ;\n" + + "\t\t:history = \"FERRET V7 13-Jun-16\n"; + // 2016-10-03T22:32:26Z (local files) + // 2016-10-03T22:32:26Z + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + + expected = "https://data.pmel.noaa.gov/pmel/erddap/tabledap/ChukchiSea_454a_037a_fcf4.das\" ;\n" + + "\t\t:infoUrl = \"www.ecofoci.noaa.gov\" ;\n" + + "\t\t:INST_TYPE = \"Sea-Bird CTD SBE911\" ;\n" + + "\t\t:institution = \"PMEL EcoFOCI\" ;\n" + + "\t\t:keywords = \"2010-2012, active, ammonia, ammonium, bottle, calibration, cast, chemistry, chlorophyll, chukchi, concentration, concentration_of_chlorophyll_in_sea_water, cooperative, cruise, data, density, depth, dissolved, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > Oxygen, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Ocean Chemistry > Silicate, Earth Science > Oceans > Salinity/Density > Salinity, ecofoci, environmental, factory, fisheries, fisheries-oceanography, flourescence, foci, fraction, fractional, fractional_saturation_of_oxygen_in_sea_water, investigations, laboratory, latitude, lon360, longitude, marine, ml/l, mmoles, mmoles/kg, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_dissolved_molecular_oxygen_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, mole_concentration_of_phosphate_in_sea_water, mole_concentration_of_silicate_in_sea_water, molecular, n02, name, nh4, niskin, nitrate, nitrite, no2, no3, noaa, number, nutrients, O2, ocean, ocean_chlorophyll_a_concentration_factoryCal, ocean_chlorophyll_fluorescence_raw, ocean_dissolved_oxygen_concentration_1_mLperL, ocean_dissolved_oxygen_concentration_1_mMperkg, ocean_dissolved_oxygen_concentration_2_mLperL, ocean_dissolved_oxygen_concentration_2_mMperkg, ocean_oxygen_saturation_1, ocean_practical_salinity_1, ocean_practical_salinity_2, ocean_sigma_t, ocean_temperature_1, ocean_temperature_2, oceanography, oceans, oxygen, pacific, percent, phosphate, photosynthetically, photosynthetically_active_radiation, pmel, po4, practical, prof, profile, pss, pss-78, psu, radiation, raw, salinity, saturation, scale, sea, sea_water_ammonium_concentration, sea_water_nitrate_concentration, sea_water_nitrite_concentration, sea_water_nutrient_bottle_number, sea_water_phosphate_concentration, sea_water_practical_salinity, sea_water_silicate_concentration, seawater, sigma, sigma-t, silicate, station, temperature, time, unit, volume, volume_fraction_of_oxygen_in_sea_water, water\" ;\n" + + + "\t\t:keywords_vocabulary = \"GCMD Science Keywords\" ;\n" + + "\t\t:license = \"Data Licenses / Data Usage Restrictions\n" + + "The data may be used and redistributed for free but is not intended\n" + + "for legal use, since it may contain inaccuracies. Neither the data\n" + + "Contributor, ERD, NOAA, nor the United States Government, nor any\n" + + "of their employees or contractors, makes any warranty, express or\n" + + "implied, including warranties of merchantability and fitness for a\n" + + "particular purpose, or assumes any legal liability for the accuracy,\n" + + "completeness, or usefulness, of this information.\n" + + "\n" + + "Unless otherwise noted, data served through this ERDDAP server are \n" + + "not quality controlled. Users may need to do quality control when using \n" + + "these data. These data are made available at the users own risk.\" ;\n" + + "\t\t:Northernmost_Northing = 73.11517 ;\n" + + "\t\t:PROG_CMNT1 = \"cat_ctd v1.36 06Aug2010\" ;\n" + + "\t\t:PROG_CMNT2 = \"Variables Extrapolated from 2 db to 0\" ;\n" + + "\t\t:sourceUrl = \"(local files)\" ;\n" + + "\t\t:Southernmost_Northing = 54.34184 ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v29\" ;\n" + + "\t\t:STATION_NAME = \"Unimak3\" ;\n" + + "\t\t:subsetVariables = \"prof, id, cast, cruise, time, longitude, lon360, latitude\" ;\n" + + "\t\t:summary = \"Pacific Marine Environmental Laboratory (PMEL) Fisheries-Oceanography Cooperative Investigations (FOCI) Chukchi Sea. PMEL EcoFOCI data from a local source.\" ;\n" + + + "\t\t:time_coverage_end = \"2012-09-06T23:57:00Z\" ;\n" + + "\t\t:time_coverage_start = \"2010-09-05T11:22:00Z\" ;\n" + + "\t\t:title = \"PMEL EcoFOCI Chukchi Sea profile data, 2010-2012\" ;\n" + + "\t\t:WATER_DEPTH = 0 ;\n" + + "\t\t:WATER_MASS = \"A\" ;\n" + + "\t\t:Westernmost_Easting = -174.6603 ;\n" + + "}\n" + + "prof,id,cast,cruise,time,longitude,lon360,latitude\n" + + "1.0,aq1201c069,069,aq1201,1.34697456E9,-164.0447,195.9553,56.866\n" + + "1.0,aq1201c070,070,aq1201,1.34697582E9,-164.049,195.951,56.864\n"; + po = results.indexOf(expected.substring(0, 60)); + Test.ensureEqual(results.substring(Math.max(0, po)), expected, "results=\n" + results); + + // ************* SINGLE SEQUENCE ***************************** + // read data from opendap + table.readOpendapSequence( + "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1?abund_m3,latitude,longitude", false); + results = table.toString(5); + // String2.log(results); + + nRows = 3763; // 2013-0620 was 3779; + Test.ensureEqual(table.nColumns(), 3, ""); + Test.ensureEqual(table.nRows(), nRows, ""); + + expected = "{\n" + + "dimensions:\n" + + "\trow = 3763 ;\n" + + "variables:\n" + + "\tfloat abund_m3(row) ;\n" + + "\t\tabund_m3:_FillValue = -9999999.0f ;\n" + + "\t\tabund_m3:actual_range = 0.0f, 9852.982f ;\n" + + "\t\tabund_m3:colorBarMaximum = 1000.0 ;\n" + + "\t\tabund_m3:colorBarMinimum = 0.0 ;\n" + + "\t\tabund_m3:comment = \"Density [individuals per m3]\" ;\n" + + "\t\tabund_m3:ioos_category = \"Other\" ;\n" + + "\t\tabund_m3:long_name = \"Abundance\" ;\n" + + "\t\tabund_m3:missing_value = -9999999.0f ;\n" + + "\t\tabund_m3:units = \"count m-3\" ;\n" + + "\tfloat latitude(row) ;\n" + + "\t\tlatitude:_CoordinateAxisType = \"Lat\" ;\n" + + "\t\tlatitude:_FillValue = 214748.36f ;\n" + + "\t\tlatitude:actual_range = 42.4733f, 44.6517f ;\n" + + "\t\tlatitude:axis = \"Y\" ;\n" + + "\t\tlatitude:ioos_category = \"Location\" ;\n" + + "\t\tlatitude:long_name = \"Latitude\" ;\n" + + "\t\tlatitude:missing_value = 214748.36f ;\n" + + "\t\tlatitude:standard_name = \"latitude\" ;\n" + + "\t\tlatitude:units = \"degrees_north\" ;\n" + + "\tfloat longitude(row) ;\n" + + "\t\tlongitude:_CoordinateAxisType = \"Lon\" ;\n" + + "\t\tlongitude:_FillValue = 214748.36f ;\n" + + "\t\tlongitude:actual_range = -125.1167f, -124.175f ;\n" + + "\t\tlongitude:axis = \"X\" ;\n" + + "\t\tlongitude:ioos_category = \"Location\" ;\n" + + "\t\tlongitude:long_name = \"Longitude\" ;\n" + + "\t\tlongitude:missing_value = 214748.36f ;\n" + + "\t\tlongitude:standard_name = \"longitude\" ;\n" + + "\t\tlongitude:units = \"degrees_east\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Trajectory\" ;\n" + + "\t\t:cdm_trajectory_variables = \"cruise_id\" ;\n" + + "\t\t:Conventions = \"COARDS, CF-1.6, ACDD-1.3\" ;\n" + + "\t\t:Easternmost_Easting = -124.175 ;\n" + + "\t\t:featureType = \"Trajectory\" ;\n" + + "\t\t:geospatial_lat_max = 44.6517 ;\n" + + "\t\t:geospatial_lat_min = 42.4733 ;\n" + + "\t\t:geospatial_lat_units = \"degrees_north\" ;\n" + + "\t\t:geospatial_lon_max = -124.175 ;\n" + + "\t\t:geospatial_lon_min = -125.1167 ;\n" + + "\t\t:geospatial_lon_units = \"degrees_east\" ;\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + + expected = "\t\t:time_coverage_end = \"2002-05-30T15:22:00Z\" ;\n" + + "\t\t:time_coverage_start = \"2000-04-12T04:00:00Z\" ;\n" + + "\t\t:title = \"GLOBEC NEP MOCNESS Plankton (MOC1) Data, 2000-2002\" ;\n" + + "\t\t:Westernmost_Easting = -125.1167 ;\n" + + "}\n" + + // " Row abund_m3 latitude longitude\n" + + // " 0 3.698225E-3 44.651699 -124.650002\n" + 2013-06-20 was + // " 1 7.26257E-2 44.651699 -124.650002\n" + + // " 2 1.100231E-3 42.504601 -125.011299\n" + + // " 3 7.889546E-2 42.501801 -124.705803\n" + + // " 4 3.416457 42.5033 -124.845001\n"; + "abund_m3,latitude,longitude\n" + + "0.003688676,44.6517,-124.65\n" + + "0.003688676,44.6517,-124.65\n" + + "0.011066027,44.6517,-124.65\n" + + "0.014754703,44.6517,-124.65\n" + + "0.014754703,44.6517,-124.65\n" + + "...\n"; + po = results.indexOf(expected.substring(0, 19)); + Test.ensureEqual(results.substring(Math.max(po, 0)), expected, "results=\n" + results); + /* + * on oceanwatch, was + * "{\n" + + * "dimensions:\n" + + * "\trow = 3779 ;\n" + + * "variables:\n" + + * "\tfloat latitude(row) ;\n" + + * "\t\tlat:long_name = \"Latitude\" ;\n" + + * "\tfloat long(row) ;\n" + + * "\t\tlong:long_name = \"Longitude\" ;\n" + + * "\tfloat abund_m3(row) ;\n" + + * "\t\tabund_m3:long_name = \"Abundance m3\" ;\n" + + * "\n" + + * "// global attributes:\n" + + * "}\n" + + * " Row lat long abund_m3\n" + + * " 0 44.651699 -124.650002 3.69822E-3\n" + + * " 1 44.651699 -124.650002 7.26257E-2\n" + + * " 2 42.504601 -125.011002 1.10023E-3\n" + + * " 3 42.501801 -124.706001 7.88955E-2\n" + + * " 4 42.5033 -124.845001 3.41646\n"; + */ + + url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecVpt?station_id&distinct()"; + table.readOpendapSequence(url, false); + // String2.log(table.toString(3)); + // source has no global metadata + Test.ensureEqual(table.nColumns(), 1, ""); + Test.ensureEqual(table.nRows(), 77, ""); + Test.ensureEqual(table.getColumnName(0), "station_id", ""); + Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Station ID", ""); + Test.ensureEqual(table.getStringData(0, 0), "BO01", ""); + Test.ensureEqual(table.getStringData(0, 1), "BO02", ""); + + url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecVpt?abund_m3&station_id=%22NH05%22"; + table.readOpendapSequence(url, false); + // String2.log(table.toString(3)); + // source has no global metadata + Test.ensureEqual(table.nColumns(), 1, ""); + Test.ensureEqual(table.nRows(), 2400, ""); + Test.ensureEqual(table.getColumnName(0), "abund_m3", ""); + Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Abundance", ""); + Test.ensureEqual(table.getFloatData(0, 0), 11.49f, ""); + Test.ensureEqual(table.getFloatData(0, 1), 74.720001f, ""); + + url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecBottle?cruise_id&distinct()"; + table.readOpendapSequence(url, false); + // String2.log(table.toString(1000000)); + // source has no global metadata + Test.ensureEqual(table.nColumns(), 1, ""); + Test.ensureEqual(table.nRows(), 2, ""); + Test.ensureEqual(table.getColumnName(0), "cruise_id", ""); + Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Cruise ID", ""); + Test.ensureEqual(table.getStringData(0, 0), "nh0207", ""); + Test.ensureEqual(table.getStringData(0, 1), "w0205", ""); + + url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1?abund_m3,latitude,longitude&program=%22MESO_1%22"; + table.readOpendapSequence(url, false); + results = table.dataToString(); + // String2.log(results); + expected = + /* + * oceanwatch was + * ... + * " Row lat long abund_m3\n" + + * " 0 44.651699 -124.650002 10.7463\n" + + * " 1 44.651699 -124.650002 1.40056E-2\n" + + * " 2 44.651699 -124.650002 0.252101\n"; + */ + "abund_m3,latitude,longitude\n" + + // "10.746269,44.6517,-124.65\n" + //pre 2013-06-20 was + // "0.014005602,44.6517,-124.65\n" + + // "0.25210083,44.6517,-124.65\n"; + "0.003688676,44.6517,-124.65\n" + + "0.003688676,44.6517,-124.65\n" + + "0.011066027,44.6517,-124.65\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + + // test getting all data + // modified from above so it returns lots of data + // nRows=16507 nColumns=28 readTime=5219 ms processTime=94 ms + url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecVpt"; + table.readOpendapSequence(url, false); + results = table.dataToString(5); + // on oceanwatch, was + // Row datetime datetime_utc datetime_utc_e year program cruise_id cast_no + // stn_id + // lat long lat1000 lon1000 water_depth sample_id min_sample_dep max_sample_dep + // month_local day_local + // time_local d_n_flag gear_type gear_area_m2 gear_mesh vol_filt counter_id + // comments perc_counted lo + // cal_code nodc_code genus_species life_stage abund_m3 + // 0 2001-04-25 21: 2001-04-25 22: 988261731 2001 NH EL010403 2 NH05 44.650 + // 002 -124.169998 44650 -124170 60 1 0 55 4 25 + // -9999 -9999 VPT 0.19635 0.202 14.46 WTP -9999 1.1 611 + // 8010204# 6118010204 CALANUS_MARSHA 3;_CIII 11.49 + expected = "cruise_id,longitude,latitude,time,cast_no,station_id,abund_m3,comments,counter_id,d_n_flag,gear_area,gear_mesh,gear_type,genus_species,life_stage,local_code,max_sample_depth,min_sample_depth,nodc_code,perc_counted,program,sample_id,vol_filt,water_depth\n" + + + "EL010403,-124.17,44.65,9.88261731E8,0,NH05,11.49,-9999,WTP,-9999,0.19635,0.202,VPT,CALANUS_MARSHALLAE,3;_CIII,6118010204#,55,0,6118010204,1.1,NH,0,14.46,60\n" + + + "EL010403,-124.17,44.65,9.88261731E8,0,NH05,74.72,-9999,WTP,-9999,0.19635,0.202,VPT,BIVALVIA,Veliger,55V,55,0,55,1.1,NH,0,14.46,60\n" + + + "EL010403,-124.17,44.65,9.88261731E8,0,NH05,57.48,-9999,WTP,-9999,0.19635,0.202,VPT,POLYCHAETA,Larva,5001LV,55,0,5001,1.1,NH,0,14.46,60\n" + + + "EL010403,-124.17,44.65,9.88261731E8,0,NH05,74.72,-9999,WTP,-9999,0.19635,0.202,VPT,GASTROPODA,Veliger,51V,55,0,51,1.1,NH,0,14.46,60\n" + + + "EL010403,-124.17,44.65,9.88261731E8,0,NH05,11.49,-9999,WTP,-9999,0.19635,0.202,VPT,CALANUS_MARSHALLAE,1;_CI,6118010204!,55,0,6118010204,1.1,NH,0,14.46,60\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + + // ************* + // String2.log("\n*** Table.testOpendapSequence subset data via tests"); + + // read data from opendap + table = new Table(); + table.readOpendapSequence( + // resulting url (for asc) is: + // https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1.asc?abund_m3,lat,long&abund_m3>=0.248962651&abund_m3<=0.248962653 + // Opera browser changes > to %3E and < to %3C + "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdGlobecMoc1", + new String[] { "abund_m3" }, + new double[] { 0.24896 }, // new double[]{0.248962651}, //the last 2 rows only + new double[] { 0.24897 }, // new double[]{0.248962653}, + new String[] { "abund_m3", "latitude", "longitude" }, + false); + + results = table.dataToString(); + expected = "abund_m3,latitude,longitude\n" + + "0.24896266,44.6517,-124.65\n" + + "0.24896266,44.6517,-124.65\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // ************* TWO-LEVEL SEQUENCE ***************************** + /* + * 2014-08-06 TEST REMOVED BECAUSE dataset is gone + * + * + * //note that I was UNABLE to get .asc responses for these dapper urls while + * poking around. + * //but straight dods request (without ".dods") works. + * //I'm testing Lynn's old ndbc data because I can independently generate test + * info + * // from my ndbc files. + * //Starting url from Roy: http://las.pfeg.noaa.gov/dods/ + * //See in DChart: http://las.pfeg.noaa.gov/dchart + * //Test info from my cached ndbc file + * /u00/data/points/ndbcMet2HistoricalTxt/46022h2004.txt + * //YYYY MM DD hh WD WSPD GST WVHT DPD APD MWD BAR ATMP WTMP DEWP VIS TIDE + * //2004 01 01 00 270 2.0 3.1 3.11 16.67 9.80 999 1010.7 999.0 999.0 999.0 99.0 + * 99.00 + * //2004 01 01 01 120 5.9 7.3 3.29 16.67 10.12 999 1010.4 999.0 999.0 999.0 + * 99.0 99.00 + * //test attributes are from + * "http://las.pfeg.noaa.gov/dods/ndbc/all_noaa_time_series.cdp.das" + * //http://las.pfeg.noaa.gov/dods/ndbc/all_noaa_time_series.cdp?location.LON, + * location.LAT,location.DEPTH,location.profile.TIME,location.profile.WSPD1, + * location.profile.BAR1&location.LON>=235.3&location.LON<=235.5&location.LAT>= + * 40.7&location.LAT<=40.8&location.profile.TIME>=1072915200000&location.profile + * .TIME<=1072920000000 + * lon = 235.460007f; //exact values from just get LON and LAT values available + * lat = 40.779999f; + * long time1 = Calendar2.newGCalendarZulu(2004, 1, 1).getTimeInMillis(); + * long time2 = time1 + Calendar2.MILLIS_PER_HOUR; + * //was http://las.pfeg.noaa.gov/dods/ndbc/all_noaa_time_series.cdp + * //was http://las.pfeg.noaa.gov/dods/ndbcMet/ndbcMet_time_series.cdp?" + + * url = "http://oceanview.pfeg.noaa.gov/dods/ndbcMet/ndbcMet_time_series.cdp?" + * + + * "location.LON,location.LAT,location.DEPTH,location.profile.TIME,location.profile.WSPD,location.profile.BAR" + * + + * "&location.LON>=" + (lon - .01f) + "&location.LON<=" + (lon + .01f) + //I + * couldn't catch lon with "=" + * "&location.LAT>=" + (lat - .01f) + "&location.LAT<=" + (lat + .01f) + //I + * couldn't catch lat with "=" + * "&location.profile.TIME>=" + (time1 - 1) + + * "&location.profile.TIME<=" + (time2 + 1); + * String2.log("url=" + url); + * table.readOpendapSequence(url, false); + * String2.log(table.toString()); + * Test.ensureEqual(table.nColumns(), 6, ""); + * Test.ensureEqual(table.nRows(), 2, ""); + * int latCol = table.findColumnNumber("LAT"); + * int lonCol = table.findColumnNumber("LON"); + * Test.ensureTrue(latCol >= 0 && latCol < 2, "latCol=" + latCol); + * Test.ensureTrue(lonCol >= 0 && lonCol < 2, "lonCol=" + lonCol); + * Test.ensureEqual(table.getColumnName(2), "DEPTH", ""); + * Test.ensureEqual(table.getColumnName(3), "TIME", ""); + * int barCol = table.findColumnNumber("BAR"); + * int wspdCol = table.findColumnNumber("WSPD"); + * Test.ensureEqual(table.getColumn(latCol).elementTypeString(), "float", ""); + * Test.ensureEqual(table.getColumn(3).elementTypeString(), "double", ""); + * Test.ensureEqual(table.getColumn(wspdCol).elementTypeString(), "float", ""); + * Test.ensureEqual(table.globalAttributes().getString("Conventions"), + * "epic-insitu-1.0", ""); + * Test.ensureEqual(table.globalAttributes().get("lat_range").toString(), + * "-27.7000007629395, 70.4000015258789", ""); + * Test.ensureEqual(table.getFloatData(latCol, 0), lat, ""); + * Test.ensureEqual(table.getFloatData(latCol, 1), lat, ""); + * Test.ensureEqual(table.getFloatData(lonCol, 0), lon, ""); + * Test.ensureEqual(table.getFloatData(lonCol, 1), lon, ""); + * //outer attributes... + * Test.ensureEqual(table.columnAttributes(latCol).getString("units"), + * "degrees_north", ""); + * Test.ensureEqual(table.columnAttributes(latCol).getString("long_name"), + * "latitude", ""); + * Test.ensureEqual(table.columnAttributes(latCol).getDouble("missing_value"), + * Double.NaN, ""); + * Test.ensureEqual(table.columnAttributes(latCol).getString("axis"), "Y", ""); + * Test.ensureEqual(table.getDoubleData(3, 0), time1, ""); + * Test.ensureEqual(table.getDoubleData(3, 1), time2, ""); + * //inner attributes... + * Test.ensureEqual(table.columnAttributes(3).getString("units"), + * "msec since 1970-01-01 00:00:00 GMT", ""); + * Test.ensureEqual(table.columnAttributes(3).getString("long_name"), "time", + * ""); + * Test.ensureEqual(table.columnAttributes(3).getDouble("missing_value"), + * Double.NaN, ""); + * Test.ensureEqual(table.columnAttributes(3).getString("axis"), "T", ""); + * Test.ensureEqual(table.getFloatData(barCol, 0), 1010.7f, ""); //bar + * Test.ensureEqual(table.getFloatData(barCol, 1), 1010.4f, ""); + * Test.ensureEqual(table.getFloatData(wspdCol, 0), 2.0f, ""); //wspd + * Test.ensureEqual(table.getFloatData(wspdCol, 1), 5.9f, ""); + * + */ + + /* + * 2014-08-06 INACTIVE BECAUSE DATASET NO LONGER AVAILABLE + * //This Calcofi test simply verifies that the results now are as they were + * when + * // I wrote the test (circular logic). + * //I hope this test is better than ndbc test above, + * // since hopefully longer lived (since ndbc data may not be around forever). + * //target data + * // Row time lat lon depth English_sole_LarvaeCount + * // 10 947320140000 32.341667 241.445007 203.800003 NaN + * // 11 947320140000 32.341667 241.445007 NaN NaN + * lat = 32.341667f; + * lon = 241.445f; + * long time = 947320140000L; + * //Starting url from roy: http://las.pfeg.noaa.gov/dods/ + * //see info via url without query, but plus .dds or .das + * //was las.pfeg.noaa.gov + * url = "http://oceanview.pfeg.noaa.gov/dods/CalCOFI/Biological.cdp?" + + * "location.lon,location.lat,location.time,location.profile.depth,location.profile.Line,location.profile.Disintegrated_fish_larvae_LarvaeCount" + * + + * "&location.lon>=" + (lon - .01f) + "&location.lon<=" + (lon + .01f) + //I + * couldn't catch lon with "=" + * "&location.lat>=" + (lat - .01f) + "&location.lat<=" + (lat + .01f) + //I + * couldn't catch lat with "=" + * "&location.time>=" + (time - 1); + * table.readOpendapSequence(url, false); + * + * String2.log(table.toString()); + * int latCol = table.findColumnNumber("lat"); + * int lonCol = table.findColumnNumber("lon"); + * Test.ensureTrue(latCol >= 0, "latCol=" + latCol); + * Test.ensureTrue(lonCol >= 0, "lonCol=" + lonCol); + * Test.ensureEqual(table.nColumns(), 6, ""); + * Test.ensureEqual(table.nRows(), 31, ""); + * Test.ensureEqual(table.getColumnName(0), "time", ""); //not in order I + * requested! they are in dataset order + * Test.ensureEqual(table.getColumnName(latCol), "lat", ""); + * Test.ensureEqual(table.getColumnName(lonCol), "lon", ""); + * Test.ensureEqual(table.getColumnName(3), "Line", ""); + * Test.ensureEqual(table.getColumnName(4), + * "Disintegrated_fish_larvae_LarvaeCount", ""); + * Test.ensureEqual(table.getColumnName(5), "depth", ""); + * Test.ensureEqual(table.getColumn(0).elementTypeString(), "double", ""); + * Test.ensureEqual(table.getColumn(latCol).elementTypeString(), "float", ""); + * Test.ensureEqual(table.getColumn(lonCol).elementTypeString(), "float", ""); + * Test.ensureEqual(table.getColumn(3).elementTypeString(), "float", ""); + * Test.ensureEqual(table.getColumn(4).elementTypeString(), "float", ""); + * Test.ensureEqual(table.getColumn(5).elementTypeString(), "float", ""); + * //global attributes + * Test.ensureEqual(table.globalAttributes().getString("Conventions"), + * "epic-insitu-1.0", ""); + * Test.ensureEqual(table.globalAttributes().getInt("total_profiles_in_dataset") + * , 6407, ""); + * //test of outer attributes + * Test.ensureEqual(table.columnAttributes(0).getString("units"), + * "msec since 1970-01-01 00:00:00 GMT", ""); + * Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "time", + * ""); + * Test.ensureEqual(table.columnAttributes(0).getDouble("missing_value"), + * Double.NaN, ""); + * Test.ensureEqual(table.columnAttributes(0).getString("axis"), "T", ""); + * //test of inner attributes + * Test.ensureEqual(table.columnAttributes(4).getString("long_name"), + * "disintegrated fish larvae larvae count", ""); + * Test.ensureEqual(table.columnAttributes(4).getFloat("missing_value"), + * Float.NaN, ""); + * Test.ensureEqual(table.columnAttributes(4).getString("units"), + * "number of larvae", ""); + * + * //test of results + * //NOTE that data from different inner sequences is always separated by a row + * of NaNs + * // in the ending inner sequence's info. + * // I believe Dapper is doing this. See more comments below. + * // Row time lat lon Disintegrated_ Line depth + * // 0 947320140000 32.341667 241.445007 NaN 93.300003 203.800003 + * // 1 947320140000 32.341667 241.445007 NaN NaN NaN + * // 2 955184100000 32.348331 241.448334 NaN 93.300003 215.800003 + * // 30 1099482480000 32.345001 241.445007 NaN 93.300003 198.899994 + * Test.ensureEqual(table.getDoubleData(0, 0), 947320140000L, ""); + * Test.ensureEqual(table.getFloatData(latCol, 0), 32.341667f, ""); + * Test.ensureEqual(table.getFloatData(lonCol, 0), 241.445007f, ""); + * Test.ensureEqual(table.getFloatData(3, 0), 93.300003f, ""); + * Test.ensureEqual(table.getFloatData(4, 0), Float.NaN, ""); + * Test.ensureEqual(table.getFloatData(5, 0), 203.800003f, ""); + * + * Test.ensureEqual(table.getDoubleData(0, 1), 947320140000L, ""); + * Test.ensureEqual(table.getFloatData(latCol, 1), 32.341667f, ""); + * Test.ensureEqual(table.getFloatData(lonCol, 1), 241.445007f, ""); + * Test.ensureEqual(table.getFloatData(3, 1), Float.NaN, ""); + * Test.ensureEqual(table.getFloatData(4, 1), Float.NaN, ""); + * Test.ensureEqual(table.getFloatData(5, 1), Float.NaN, ""); + * + * Test.ensureEqual(table.getDoubleData(0, 30), 1099482480000L, ""); + * Test.ensureEqual(table.getFloatData(latCol, 30), 32.345001f, ""); + * Test.ensureEqual(table.getFloatData(lonCol, 30), 241.445007f, ""); + * Test.ensureEqual(table.getFloatData(3, 30), 93.300003f, ""); + * Test.ensureEqual(table.getFloatData(4, 30), Float.NaN, ""); + * Test.ensureEqual(table.getFloatData(5, 30), 198.899994f, ""); + * + * + * //*** visual test: is dapper returning the NAN row at the end of every + * innerSequence (true) + * // or is that the way it is in the files? (false) + * lon = 235.460007f; //exact values from just get LON and LAT values available + * lat = 40.779999f; + * long time1 = Calendar2.newGCalendarZulu(2004, 1, 1).getTimeInMillis(); + * long time2 = time1 + Calendar2.MILLIS_PER_HOUR; + * //was http://las.pfeg.noaa.gov/dods/ndbc/all_noaa_time_series.cdp + * url = "http://oceanview.pfeg.noaa.gov/dods/ndbcMet/ndbcMet_time_series.cdp?" + * + + * "location.LON,location.LAT,location.DEPTH,location.profile.TIME,location.profile.WSPD,location.profile.BAR" + * + + * "&location.LON>=" + (lon - 5f) + "&location.LON<=" + (lon + 5f) + + * "&location.LAT>=" + (lat - 5f) + "&location.LAT<=" + (lat + 5f) + + * "&location.profile.TIME>=" + (time1 - 1) + + * "&location.profile.TIME<=" + (time2 + 1); + * table.readOpendapSequence(url, false); + * String2.log(table.toString()); + */ + + /* + * //THIS WORKS, BUT TAKES ~40 SECONDS!!! so don't do all the time + * //see questions below. + * //This gets all the valid English_sole_LarvaeCount data. + * //UNFORTUNATELY, you can't put constraint on non-axis variable, + * // so I have to get all data and then filter the results. + * //This test simply verifies that the results now are as they were when + * // I wrote the test (circular logic). + * //I had hoped this test would be better than ndbc test above, + * // since hopefully longer lived (since ndbc data may not be around forever). + * //Starting url from roy: http://las.pfeg.noaa.gov/dods/ + * url = "http://las.pfeg.noaa.gov/dods/CalCOFI/Biological.cdp?" + + * "location.lon,location.lat,location.time,location.profile.depth,location.profile.English_sole_LarvaeCount"; + * table.readOpendapSequence(url); + * String2.log("raw results nRows=" + table.nRows()); + * //just keep rows with larvaeCounts >= 0 + * table.subset(new int[]{4}, new double[]{0}, new double[]{1e300}); + * + * String2.log(table.toString()); + * Test.ensureEqual(table.nColumns(), 5, ""); + * Test.ensureEqual(table.nRows(), 98, ""); + * Test.ensureEqual(table.getColumnName(0), "time", ""); //not in order I + * requested! they are in dataset order + * Test.ensureEqual(table.getColumnName(1), "lat", ""); + * Test.ensureEqual(table.getColumnName(2), "lon", ""); + * Test.ensureEqual(table.getColumnName(3), "depth", ""); + * Test.ensureEqual(table.getColumnName(4), "English_sole_LarvaeCount", ""); + * Test.ensureEqual(table.getColumn(0).elementTypeString(), "double", ""); + * Test.ensureEqual(table.getColumn(1).elementTypeString(), "float", ""); + * Test.ensureEqual(table.getColumn(2).elementTypeString(), "float", ""); + * Test.ensureEqual(table.getColumn(3).elementTypeString(), "float", ""); + * Test.ensureEqual(table.getColumn(4).elementTypeString(), "float", ""); + * //global attributes + * Test.ensureEqual(table.globalAttributes().getString("Conventions"), + * "epic-insitu-1.0", ""); + * Test.ensureEqual(table.globalAttributes().getInt("total_profiles_in_dataset") + * , 6407, ""); + * //test of outer attributes + * Test.ensureEqual(table.columnAttributes(0).getString("units"), + * "msec since 1970-01-01 00:00:00 GMT", ""); + * Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "time", + * ""); + * Test.ensureEqual(table.columnAttributes(0).getDouble("missing_value"), + * Double.NaN, ""); + * Test.ensureEqual(table.columnAttributes(0).getString("axis"), "T", ""); + * //test of inner attributes + * Test.ensureEqual(table.columnAttributes(4).getString("long_name"), + * "parophrys vetulus larvae count", ""); + * Test.ensureEqual(table.columnAttributes(4).getFloat("missing_value"), + * Float.NaN, ""); + * Test.ensureEqual(table.columnAttributes(4).getString("units"), + * "number of larvae", ""); + * + * //test of results + * Test.ensureEqual(table.getDoubleData(0, 0), 955657380000L, ""); + * Test.ensureEqual(table.getFloatData(1, 0), 33.485001f, ""); + * Test.ensureEqual(table.getFloatData(2, 0), 242.231659f, ""); + * Test.ensureEqual(table.getFloatData(3, 0), 210.800003f, ""); + * Test.ensureEqual(table.getFloatData(4, 0), 1, ""); + * + * Test.ensureEqual(table.getDoubleData(0, 1), 955691700000L, ""); + * Test.ensureEqual(table.getFloatData(1, 1), 33.825001f, ""); + * Test.ensureEqual(table.getFloatData(2, 1), 241.366669f, ""); + * Test.ensureEqual(table.getFloatData(3, 1), 208.5f, ""); + * Test.ensureEqual(table.getFloatData(4, 1), 6, ""); + * + * Test.ensureEqual(table.getDoubleData(0, 97), 923900040000L, ""); + * Test.ensureEqual(table.getFloatData(1, 97), 34.976665f, ""); + * Test.ensureEqual(table.getFloatData(2, 97), 237.334991f, ""); + * Test.ensureEqual(table.getFloatData(3, 97), 24.1f, ""); + * Test.ensureEqual(table.getFloatData(4, 97), 4, ""); + * + * /* + */ + /** + * [Bob talked to Lynn about this. Conclusions below.] + * 1) If I just get all lon,lat,time,depth, and English_sole_LarvaeCount + * (was http://las.pfeg...) + * url = "http://oceanview.pfeg.noaa.gov/dods/CalCOFI/Biological.cdp?" + + * "location.lon,location.lat,location.time,location.profile.depth,location.profile.English_sole_LarvaeCount"; + * it looks like each time,lat,lon combo has a data row and a NaN row. + * ???Is this a real NaN row, or a mistake in my code (e.g., end of sequence + * beginning of next). + * [I believe it is real and added by Dapper.] + * Note that some sole counts below are non-NaN. + * + * Row time lat lon depth English_sole_LarvaeCount + * 0 947255160000 32.955002 242.695007 71.5 NaN + * 1 947255160000 32.955002 242.695007 NaN NaN + * 2 947264520000 32.913334 242.606659 207.600006 NaN + * 3 947264520000 32.913334 242.606659 NaN NaN + * 4 947275680000 32.848335 242.471664 211.699997 NaN + * 5 947275680000 32.848335 242.471664 NaN NaN + * 6 947290920000 32.68 242.126663 195.899994 NaN + * 7 947290920000 32.68 242.126663 NaN NaN + * 8 947306040000 32.513332 241.790009 208.100006 NaN + * 9 947306040000 32.513332 241.790009 NaN NaN + * 10 947320140000 32.341667 241.445007 203.800003 NaN + * 11 947320140000 32.341667 241.445007 NaN NaN + * 12 947343360000 32.18 241.110001 209.5 NaN + * 13 947343360000 32.18 241.110001 NaN NaN + * 14 947359140000 32.006668 240.764999 215.5 NaN + * 15 947359140000 32.006668 240.764999 NaN NaN + * 2) do all time,lat,lon combo's just have one depth? + * If so, then why set up this way? + * Just to match dapper convention (must have z or t outside and t or z inside)? + * [I believe so.] + * + * 3) Since it appears that the 150(?) variables were only measured rarely, + * it seems hugely wasteful to allocate space for them. + * And worse, since a query use constraints on non-axis variables, + * one can't simply ask for ... &English_sole_LarvaeCount>=0 + * to find time,lat,lon,depth where there are valid values of + * English_sole_LarvaeCount. + * And requesting all data rows (so I can then filtering on my end) takes ~40 + * seconds + * for 98 rows of data. + * [Wasteful, but I believe Roy did it this way to conform to Dapper Conventions + * so + * data easily served by Dapper/DChart, see + * http://oceanview.pfeg.noaa.gov/dchart (was http://las.pfeg...).] + * + * 4) There are no 0 values for English_sole_LarvaeCount. + * So how can one tell if people looked for English_sole_Larvae but didn't find + * any? + * Are NaN's to be treated as 0 for this data set? + * [It looks like 0 values are lumped in with NaNs.] + * + * 5) Why is number of larvae (units="number of larvae") a float and not an int? + * [Because all variables are floats for simplicity (maybe for matlab or + * fortran).] + * + */ + } + + /** Test the speed of readASCII */ + @org.junit.jupiter.api.Test + void testReadASCIISpeed() throws Exception { + + String fileName = TableTests.class.getResource("/points/ndbcMet2HistoricalTxt/41009h1990.txt").getPath(); + long time = 0; + + for (int attempt = 0; attempt < 4; attempt++) { + // String2.log("\n*** Table.testReadASCIISpeed attempt #" + attempt + "\n"); + Math2.gcAndWait("Table (between tests)"); // in a test + Math2.sleep(5000); + // time it + long fileLength = File2.length(fileName); // was 1335204 + Test.ensureTrue(fileLength > 1335000, "fileName=" + fileName + " length=" + fileLength); + time = System.currentTimeMillis(); + Table table = new Table(); + table.readASCII(fileName); + time = System.currentTimeMillis() - time; + + String results = table.dataToString(3); + String expected = "YY,MM,DD,hh,WD,WSPD,GST,WVHT,DPD,APD,MWD,BAR,ATMP,WTMP,DEWP,VIS\n" + + "90,01,01,00,161,08.6,10.7,01.50,05.00,04.80,999,1017.2,22.7,22.0,999.0,99.0\n" + + "90,01,01,01,163,09.3,11.3,01.50,05.00,04.90,999,1017.3,22.7,22.0,999.0,99.0\n" + + "90,01,01,01,164,09.2,10.6,01.60,04.80,04.90,999,1017.3,22.7,22.0,999.0,99.0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nColumns(), 16, "nColumns=" + table.nColumns()); + Test.ensureEqual(table.nRows(), 17117, "nRows=" + table.nRows()); + + String2.log("********** attempt #" + attempt + " Done.\n" + + "cells/ms=" + (table.nColumns() * table.nRows() / time) + + " (usual=2560 with StringHolder. With String, was 2711 Java 1.7M4700, was 648)" + + "\ntime=" + time + "ms (good=106ms, but slower when computer is busy.\n" + + " (was 101 Java 1.7M4700, was 422, java 1.5 was 719)"); + if (time <= 130) + break; + } + if (time > 130) + throw new SimpleException( + "readASCII took too long (time=" + time + "ms > 130ms) (but often does when computer is busy)."); + } + + /** Test the speed of readJson */ + @org.junit.jupiter.api.Test + void testReadJsonSpeed() throws Exception { + + // warmup + String fileName = TableTests.class.getResource("/cPostDet3.files.json.gz").getPath(); + long time = 0; + String msg = ""; + String expected = "dirIndex,fileName,lastMod,sortedSpacing,unique_tag_id_min_,unique_tag_id_max_,PI_min_,PI_max_,longitude_min_,longitude_max_,latitude_min_,latitude_max_,time_min_,time_max_,bottom_depth_min_,bottom_depth_max_,common_name_min_,common_name_max_,date_public_min_,date_public_max_,line_min_,line_max_,position_on_subarray_min_,position_on_subarray_max_,project_min_,project_max_,riser_height_min_,riser_height_max_,role_min_,role_max_,scientific_name_min_,scientific_name_max_,serial_number_min_,serial_number_max_,stock_min_,stock_max_,surgery_time_min_,surgery_time_max_,surgery_location_min_,surgery_location_max_,tagger_min_,tagger_max_\n" + + + "0,52038_A69-1303_1059305.nc,1.284567715046E12,0.0,52038_A69-1303_1059305,52038_A69-1303_1059305,BARBARA BLOCK,BARBARA BLOCK,-146.36933,-146.1137,60.6426,60.7172,1.2192849E9,1.238062751E9,13.4146341463415,130.487804878049,SALMON SHARK,SALMON SHARK,1.273271649385E9,1.273271649385E9,,PORT GRAVINA,,9,HOPKINS MARINE STATION,HOPKINS MARINE STATION,,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,LAMNA DITROPIS,1059305,1059305,N/A,N/A,1.2192156E9,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\"PORT GRAVINA, PRINCE WILLIAM SOUND\",,\n" + + + "1,16955_A69-1303_8685G.nc,1.284567719796E12,-1.0,16955_A69-1303_8685G,16955_A69-1303_8685G,BARRY BEREJIKIAN,BARRY BEREJIKIAN,-122.78316,-122.78316,47.65223,47.65223,1.1466882E9,1.1466882E9,,,STEELHEAD,STEELHEAD,1.222730955645E9,1.222730955645E9,,,,,NOAA|NOAA FISHERIES,NOAA|NOAA FISHERIES,,,BEREJIKIAN_BARRY_ONCORHYNCHUS_MYKISS_BIGBEEFCREEK,BEREJIKIAN_BARRY_ONCORHYNCHUS_MYKISS_BIGBEEFCREEK,ONCORHYNCHUS MYKISS,ONCORHYNCHUS MYKISS,8685G,8685G,BIG BEEF CREEK,BIG BEEF CREEK,1.146528E9,1.146528E9,BIG BEEF CREEK,BIG BEEF CREEK,SKIP TEZAK,SKIP TEZAK\n" + + + "1,16956_A69-1303_8686G.nc,1.284567723515E12,-1.0,16956_A69-1303_8686G,16956_A69-1303_8686G,BARRY BEREJIKIAN,BARRY BEREJIKIAN,-122.78316,-122.78316,47.65223,47.65223,1.1466882E9,1.1466882E9,,,STEELHEAD,STEELHEAD,1.222730955653E9,1.222730955653E9,,,,,NOAA|NOAA FISHERIES,NOAA|NOAA FISHERIES,,,BEREJIKIAN_BARRY_ONCORHYNCHUS_MYKISS_BIGBEEFCREEK,BEREJIKIAN_BARRY_ONCORHYNCHUS_MYKISS_BIGBEEFCREEK,ONCORHYNCHUS MYKISS,ONCORHYNCHUS MYKISS,8686G,8686G,BIG BEEF CREEK,BIG BEEF CREEK,1.146528E9,1.146528E9,BIG BEEF CREEK,BIG BEEF CREEK,SKIP TEZAK,SKIP TEZAK\n" + + + "...\n"; + + for (int attempt = 0; attempt < 3; attempt++) { + // String2.log("\n*** Table.testReadJsonSpeed attempt#" + attempt + "\n"); + + // time it + time = System.currentTimeMillis(); + long fileLength = File2.length(fileName); // before gz was 10,166KB, now 574572 + Test.ensureTrue(fileLength > 574000, "fileName=" + fileName + " length=" + fileLength); + Table table = new Table(); + table.readJson(fileName); + + String results = table.dataToString(3); + Test.ensureEqual(results, expected, "results=" + results); + Test.ensureTrue(results.indexOf("unique_tag_id_max") > 0, "test 1"); + Test.ensureTrue(results.indexOf("surgery_time_min") > 0, "test 2"); + Test.ensureTrue(table.nColumns() > 40, "nColumns=" + table.nColumns()); // was 42 + Test.ensureTrue(table.nRows() > 15000, "nRows=" + table.nRows()); // was 15024 + + time = System.currentTimeMillis() - time; + msg = "*** Done. cells/ms=" + + (table.nColumns() * table.nRows() / time) + " (usual=2881 Java 1.7M4700, was 747)" + + "\ntime=" + time + "ms (usual=300, java 8 was 219, Java 1.7M4700, was 844, java 1.5 was 1687)"; + String2.log(msg); + if (time <= 400) + break; + } + Test.ensureTrue(time < 400, msg + "\nreadJson took too long."); + } + + /** Test the speed of readNDNc */ + @org.junit.jupiter.api.Test + @TagLargeFile + void testReadNDNcSpeed() throws Exception { + + String fileName = "c:/u00/data/points/ndbcMet2/historical/NDBC_41004_met.nc"; + Table table = new Table(); + long time = 0; + NcHelper.ncdump(fileName, "-h") + // String2.log(NcHelper.ncdump(fileName, "-h")); + + for (int attempt = 0; attempt < 3; attempt++) { + // String2.log("\n*** Table.testReadNDNcSpeed attempt+" + attempt + "\n"); + Math2.gcAndWait("Table (between tests)"); // in a test + + // time it + time = System.currentTimeMillis(); + long fileLength = File2.length(fileName); // was 20580000 + Test.ensureTrue(fileLength > 20570000, "fileName=" + fileName + " length=" + fileLength); + table = new Table(); + table.readNDNc(fileName, null, 0, null, 0, 0); // standardizeWhat=0 + + String results = table.dataToString(3); + String expected = // before 2011-06-14 was 32.31, -75.35, + "TIME,DEPTH,LAT,LON,WD,WSPD,GST,WVHT,DPD,APD,MWD,BAR,ATMP,WTMP,DEWP,VIS,PTDY,TIDE,WSPU,WSPV,ID\n" + + "2.678004E8,0.0,32.501,-79.099,255,1.3,-9999999.0,-9999999.0,-9999999.0,-9999999.0,32767,1020.5,27.2,27.4,-9999999.0,-9999999.0,-9999999.0,-9999999.0,1.3,0.3,41004\n" + + + "2.67804E8,0.0,32.501,-79.099,247,6.6,-9999999.0,-9999999.0,-9999999.0,-9999999.0,32767,1020.6,26.8,27.4,-9999999.0,-9999999.0,-9999999.0,-9999999.0,6.1,2.6,41004\n" + + + "2.678076E8,0.0,32.501,-79.099,249,7.0,-9999999.0,-9999999.0,-9999999.0,-9999999.0,32767,1020.4,26.8,27.4,-9999999.0,-9999999.0,-9999999.0,-9999999.0,6.5,2.5,41004\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nColumns(), 21, "nColumns=" + table.nColumns()); + Test.ensureTrue(table.nRows() >= 351509, "nRows=" + table.nRows()); + + time = System.currentTimeMillis() - time; + String2.log("********** Done. cells/ms=" + + (table.nColumns() * table.nRows() / time) + " (usual=31414 Java 1.7M4700, was 9679)" + + "\ntime=" + time + + "ms (usual=556 Lenovo, was 226 Java 1.7M4700, was 640, java 1.5 was 828, but varies a lot)"); + if (time <= 650) + break; + } + if (time > 650) + throw new SimpleException("readNDNc took too long (time=" + time + "ms (556ms expected))"); + } + + /** Test the speed of readOpendapSequence */ + @org.junit.jupiter.api.Test + void testReadOpendapSequenceSpeed() throws Exception { + + String url = "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/cwwcNDBCMet?" + + "&time%3E=1999-01-01&time%3C=1999-04-01&station=%2241009%22"; + long time = 0; + + for (int attempt = 0; attempt < 3; attempt++) { + // String2.log("\n*** Table.testReadOpendapSequenceSpeed\n"); + Math2.gcAndWait("Table (between tests)"); // in a test + + // time it + time = System.currentTimeMillis(); + Table table = new Table(); + table.readOpendapSequence(url); + String results = table.dataToString(3); + String expected = // before 2011-06-14 was -80.17, 28.5 + // "station,longitude,latitude,time,wd,wspd,gst,wvht,dpd,apd,mwd,bar,atmp,wtmp,dewp,vis,ptdy,tide,wspu,wspv\n" + // + + // "41009,-80.166,28.519,9.151488E8,0,1.9,2.7,1.02,11.11,6.49,32767,1021.0,20.4,24.2,-9999999.0,-9999999.0,-9999999.0,-9999999.0,0.0,-1.9\n" + // + + // "41009,-80.166,28.519,9.151524E8,53,1.5,2.8,0.99,11.11,6.67,32767,1021.0,20.6,24.5,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-1.2,-0.9\n" + // + + // "41009,-80.166,28.519,9.15156E8,154,1.0,2.2,1.06,11.11,6.86,32767,1021.2,20.6,24.6,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-0.4,0.9\n" + // + + + // source ASCII file has: (note 2 rows for ever hour) + // YYYY MM DD hh WD WSPD GST WVHT DPD APD MWD BAR ATMP WTMP DEWP VIS [in + // EditPlus, the first row of data is here, to right of col names -- screwy line + // endings?!] + // 1999 01 01 00 360 1.9 2.7 1.02 11.11 6.49 999 1021.0 20.4 24.2 999.0 99.0 + // 1999 01 01 00 21 1.4 3.4 1.10 11.11 6.82 999 1020.9 20.4 24.5 999.0 99.0 + // 1999 01 01 01 53 1.5 2.8 .99 11.11 6.67 999 1021.0 20.6 24.5 999.0 99.0 + // 1999 01 01 01 53 1.5 2.6 1.10 11.11 6.97 999 1021.1 20.6 24.5 999.0 99.0 + // 1999 01 01 02 154 1.0 2.2 1.06 11.11 6.86 999 1021.2 20.6 24.6 999.0 99.0 + // 1999 01 01 02 73 2.5 3.8 1.09 11.11 6.87 999 1021.2 20.7 24.6 999.0 99.0 + + // 2020-03-03 this data changed significantly after big changes to processing + // system/ dealing with duplicate lines (prefer newer data/later in file) + "station,longitude,latitude,time,wd,wspd,gst,wvht,dpd,apd,mwd,bar,atmp,wtmp,dewp,vis,ptdy,tide,wspu,wspv\n" + + "41009,-80.166,28.519,9.151488E8,21,1.4,3.4,1.1,11.11,6.82,32767,1020.9,20.4,24.5,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-0.5,-1.3\n" + + // 1999-01-01T00:00 + "41009,-80.166,28.519,9.151524E8,53,1.5,2.6,1.1,11.11,6.97,32767,1021.1,20.6,24.5,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-1.2,-0.9\n" + + // 1999-01-01T01:00 + "41009,-80.166,28.519,9.15156E8,73,2.5,3.8,1.09,11.11,6.87,32767,1021.2,20.7,24.6,-9999999.0,-9999999.0,-9999999.0,-9999999.0,-2.4,-0.7\n" + + // 1999-01-01T02:00 + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + Test.ensureTrue(table.nRows() > 2100, "nRows=" + table.nRows()); + time = System.currentTimeMillis() - time; + String2.log("********** Done. cells/ms=" + + (table.nColumns() * table.nRows() / time) + " (usual(https)=33, was(http) 337 Java 1.7M4700, was 106)" + + "\ntime=" + time + + "ms (usual(https)=1285, was http=600 since remote, was 128 Java 1.7M4700, was 406, java 1.5 was 562)"); + if (time <= 1600) + break; + } + if (time > 1600) + throw new SimpleException("readOpendapSequence took too long (time=" + time + "ms)."); + } + + /** Test the speed of saveAs speed */ + @org.junit.jupiter.api.Test + void testSaveAsSpeed() throws Exception { + + // warmup + // String2.log("\n*** Table.testSaveAsSpeed\n"); + String sourceName = TableTests.class.getResource("/points/ndbcMet2HistoricalTxt/41009h1990.txt").getPath(); + String destName = File2.getSystemTempDirectory() + "testSaveAsSpeed"; + Table table = new Table(); + table.readASCII(sourceName); + Test.ensureEqual(table.nColumns(), 16, "nColumns=" + table.nColumns()); + Test.ensureEqual(table.nRows(), 17117, "nRows=" + table.nRows()); + table.saveAsCsvASCII(destName + ".csv"); + table.saveAsJson(destName + ".json", table.findColumnNumber("time"), true); // writeUnits + table.saveAsFlatNc(destName + ".nc", "row"); + long time = 0; + + for (int attempt = 0; attempt < 3; attempt++) { + // time it + // String2.log("\ntime it\n"); + + // saveAsCsvASCII + time = System.currentTimeMillis(); + table.saveAsCsvASCII(destName + ".csv"); + time = System.currentTimeMillis() - time; + String2.log("saveAsCsvASCII attempt#" + attempt + + " done. cells/ms=" + (table.nColumns() * table.nRows() / time) + // 796 + "\ntime=" + time + "ms (expected=344, was 532 for Java 1.5 Dell)"); + File2.delete(destName + ".csv"); + if (time <= 550) + break; + } + if (time > 550) + throw new SimpleException("saveAsCsvASCII (time=" + time + "ms). Expected=~344 for 17117 rows."); + + for (int attempt = 0; attempt < 3; attempt++) { + // saveAsJson + time = System.currentTimeMillis(); + table.saveAsJson(destName + ".json", table.findColumnNumber("time"), true); // writeUnits + time = System.currentTimeMillis() - time; + String2.log("saveAsJson attempt#" + attempt + + " done. cells/ms=" + (table.nColumns() * table.nRows() / time) + // 974 + "\ntime=" + time + "ms (expect=281, was 515 for Java 1.5 Dell)"); + File2.delete(destName + ".json"); + if (time <= 450) + break; + } + if (time >= 450) + throw new SimpleException("saveAsJson took too long (time=" + time + "ms). Expected=~281 for 17117 rows."); + + // saveAsFlatNc + for (int attempt = 0; attempt < 3; attempt++) { + time = System.currentTimeMillis(); + table.saveAsFlatNc(destName + ".nc", "row"); + time = System.currentTimeMillis() - time; + String2.log("saveAsFlatNc attempt#" + attempt + + " done. cells/ms=" + (table.nColumns() * table.nRows() / time) + // 2190 + "\ntime=" + time + "ms (expected=125, was 172 for Java 1.5 Dell)"); + File2.delete(destName + ".nc"); + if (time <= 200) + break; + } + if (time > 200) + throw new SimpleException("saveAsFlatNc took too long (time=" + time + "ms). Expected=~125 for 17117 rows."); + + } + + /** + * This is a test of readOpendap. + * + * @throws Exception of trouble + */ + @org.junit.jupiter.api.Test + @TagExternalOther + void testOpendap() throws Exception { + // ************* + // String2.log("\n*** Table.testOpendap"); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // opendap, even sequence data, can be read via .nc + // but constraints are not supported + Table table = new Table(); + int nRows = 3779; + table.readFlatNc( + // read all via ascii: + // "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1.asc?abund_m3,lat,long", + // null); + // or + // "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1.asc?MOC1.abund_m3,MOC1.lat,MOC1.long", + // null); + "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1", + new String[] { "MOC1.abund_m3", "MOC1.lat", "MOC1.long" }, // but "MOC1." is required here + 0); // standardizeWhat=0 + // 2018-05-12 was unpack to doubles, so these tests will change + // String2.log(table.toString(5)); + + Test.ensureEqual(table.nColumns(), 3, ""); + Test.ensureEqual(table.nRows(), nRows, ""); + + Test.ensureEqual(table.getColumnName(0), "abund_m3", ""); + Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Abundance m3", ""); + Test.ensureEqual(table.getDoubleData(0, 0), 0.242688983, ""); + Test.ensureEqual(table.getDoubleData(0, nRows - 1), 0.248962652, ""); + + Test.ensureEqual(table.getColumnName(1), "lat", ""); + Test.ensureEqual(table.columnAttributes(1).getString("long_name"), "Latitude", ""); + Test.ensureEqual(table.getDoubleData(1, 0), 44.6517, ""); + Test.ensureEqual(table.getDoubleData(1, nRows - 1), 44.6517, ""); + + Test.ensureEqual(table.getColumnName(2), "long", ""); + Test.ensureEqual(table.columnAttributes(2).getString("long_name"), "Longitude", ""); + Test.ensureEqual(table.getDoubleData(2, 0), -124.175, ""); + Test.ensureEqual(table.getDoubleData(2, nRows - 1), -124.65, ""); + + // can it read with list of variables? + table.readFlatNc( + "https://oceanwatch.pfeg.noaa.gov/opendap/GLOBEC/GLOBEC_MOC1?abund_m3,lat,long", + null, // read all variables + 0); // standardizeWhat=0 + // 2018-05-12 was unpack to doubles, so these tests will change + // String2.log(table.toString(5)); + Test.ensureEqual(table.nColumns(), 3, ""); + Test.ensureEqual(table.nRows(), nRows, ""); + + // !!!HEY, the results are an unexpected order!!! + Test.ensureEqual(table.getColumnName(0), "lat", ""); + Test.ensureEqual(table.columnAttributes(0).getString("long_name"), "Latitude", ""); + Test.ensureEqual(table.getDoubleData(0, 0), 44.6517, ""); + Test.ensureEqual(table.getDoubleData(0, nRows - 1), 44.6517, ""); + + Test.ensureEqual(table.getColumnName(1), "long", ""); + Test.ensureEqual(table.columnAttributes(1).getString("long_name"), "Longitude", ""); + Test.ensureEqual(table.getDoubleData(1, 0), -124.175, ""); + Test.ensureEqual(table.getDoubleData(1, nRows - 1), -124.65, ""); + + Test.ensureEqual(table.getColumnName(2), "abund_m3", ""); + Test.ensureEqual(table.columnAttributes(2).getString("long_name"), "Abundance m3", ""); + Test.ensureEqual(table.getDoubleData(2, 0), 0.242688983, ""); + Test.ensureEqual(table.getDoubleData(2, nRows - 1), 0.248962652, ""); + + } + + /** Test join(). **/ + @org.junit.jupiter.api.Test + void testJoin() { + + // *** testJoin 1 + // String2.log("\n*** Table.testJoin 1 column"); + Table table = new Table(); + table.addColumn("zero", PrimitiveArray.csvFactory(PAType.STRING, "a,b,c,d,,e")); + table.addColumn("one", PrimitiveArray.csvFactory(PAType.INT, "40,10,12,30,,20")); + table.addColumn("two", PrimitiveArray.csvFactory(PAType.STRING, "aa,bb,cc,dd,,ee")); + table.columnAttributes(0).add("long_name", "hey zero"); + table.columnAttributes(1).add("missing_value", -99999); + table.columnAttributes(2).add("long_name", "hey two"); + + Table lut = new Table(); + lut.addColumn("aa", PrimitiveArray.csvFactory(PAType.INT, "10,20,30,40")); + lut.addColumn("bb", PrimitiveArray.csvFactory(PAType.STRING, "11,22,33,44")); + lut.addColumn("cc", PrimitiveArray.csvFactory(PAType.LONG, "111,222,333,444")); + lut.columnAttributes(0).add("missing_value", -99999); + lut.columnAttributes(1).add("long_name", "hey bb"); + lut.columnAttributes(2).add("missing_value", -9999999L); + + // test lut before join + String results = lut.toString(); + String expectedLut = "{\n" + + "dimensions:\n" + + "\trow = 4 ;\n" + + "\tbb_strlen = 2 ;\n" + + "variables:\n" + + "\tint aa(row) ;\n" + + "\t\taa:missing_value = -99999 ;\n" + + "\tchar bb(row, bb_strlen) ;\n" + + "\t\tbb:long_name = \"hey bb\" ;\n" + + "\tlong cc(row) ;\n" + + "\t\tcc:missing_value = -9999999 ;\n" + + "\n" + + "// global attributes:\n" + + "}\n" + + "aa,bb,cc\n" + + "10,11,111\n" + + "20,22,222\n" + + "30,33,333\n" + + "40,44,444\n"; + Test.ensureEqual(results, expectedLut, "lut results=\n" + results); + + // do the join + table.join(1, 1, "10", lut); + + results = table.toString(); + String expected = "{\n" + + "dimensions:\n" + + "\trow = 6 ;\n" + + "\tzero_strlen = 1 ;\n" + + "\tbb_strlen = 2 ;\n" + + "\ttwo_strlen = 2 ;\n" + + "variables:\n" + + "\tchar zero(row, zero_strlen) ;\n" + + "\t\tzero:long_name = \"hey zero\" ;\n" + + "\tint one(row) ;\n" + + "\t\tone:missing_value = -99999 ;\n" + + "\tchar bb(row, bb_strlen) ;\n" + + "\t\tbb:long_name = \"hey bb\" ;\n" + + "\tlong cc(row) ;\n" + + "\t\tcc:missing_value = -9999999 ;\n" + + "\tchar two(row, two_strlen) ;\n" + + "\t\ttwo:long_name = \"hey two\" ;\n" + + "\n" + + "// global attributes:\n" + + "}\n" + + "zero,one,bb,cc,two\n" + + "a,40,44,444,aa\n" + + "b,10,11,111,bb\n" + + "c,12,,-9999999,cc\n" + + "d,30,33,333,dd\n" + + ",,11,111,\n" + + "e,20,22,222,ee\n"; + Test.ensureEqual(results, expected, "join 1 results=\n" + results); + + // ensure lut unchanged + results = lut.toString(); + Test.ensureEqual(results, expectedLut, "lut 1 results=\n" + results); + + // *** testJoin 2 columns + // String2.log("\n*** Table.testJoin 2 columns"); + table = new Table(); + table.addColumn("zero", PrimitiveArray.csvFactory(PAType.STRING, "a,b,c,d,,e")); + table.addColumn("one", PrimitiveArray.csvFactory(PAType.INT, "40,10,12,30,,20")); + table.addColumn("two", PrimitiveArray.csvFactory(PAType.STRING, "44,bad,1212,33,,22")); + table.addColumn("three", PrimitiveArray.csvFactory(PAType.STRING, "aaa,bbb,ccc,ddd,,eee")); + table.columnAttributes(0).add("long_name", "hey zero"); + table.columnAttributes(1).add("missing_value", -99999); + table.columnAttributes(2).add("long_name", "hey two"); + table.columnAttributes(3).add("long_name", "hey three"); + + // do the join + table.join(2, 1, "10\t11", lut); + + results = table.toString(); + expected = "{\n" + + "dimensions:\n" + + "\trow = 6 ;\n" + + "\tzero_strlen = 1 ;\n" + + "\ttwo_strlen = 4 ;\n" + + "\tthree_strlen = 3 ;\n" + + "variables:\n" + + "\tchar zero(row, zero_strlen) ;\n" + + "\t\tzero:long_name = \"hey zero\" ;\n" + + "\tint one(row) ;\n" + + "\t\tone:missing_value = -99999 ;\n" + + "\tchar two(row, two_strlen) ;\n" + + "\t\ttwo:long_name = \"hey two\" ;\n" + + "\tlong cc(row) ;\n" + + "\t\tcc:missing_value = -9999999 ;\n" + + "\tchar three(row, three_strlen) ;\n" + + "\t\tthree:long_name = \"hey three\" ;\n" + + "\n" + + "// global attributes:\n" + + "}\n" + + "zero,one,two,cc,three\n" + + "a,40,44,444,aaa\n" + + "b,10,bad,-9999999,bbb\n" + + "c,12,1212,-9999999,ccc\n" + + "d,30,33,333,ddd\n" + + ",,,111,\n" + + "e,20,22,222,eee\n"; + Test.ensureEqual(results, expected, "join 2 results=\n" + results); + + // ensure lut unchanged + results = lut.toString(); + Test.ensureEqual(results, expectedLut, "lut 2 results=\n" + results); + } + + /** test update() */ + @org.junit.jupiter.api.Test + void testUpdate() throws Exception { + Table table = new Table(); + table.addColumn("zero", PrimitiveArray.csvFactory(PAType.STRING, "a, b, c, d, , e")); + table.addColumn("one", PrimitiveArray.csvFactory(PAType.INT, "10, 20, 30, 40, , 50")); + table.addColumn("two", PrimitiveArray.csvFactory(PAType.INT, "111,222,333,444,-99,555")); + table.addColumn("three", PrimitiveArray.csvFactory(PAType.DOUBLE, "1.1,2.2,3.3,4.4,4.6,5.5")); + table.columnAttributes(2).add("missing_value", -99); + + // otherTable rows: matches, matches, partial match, new + // otherTable cols: keys, matches (but different type), doesn't match + Table otherTable = new Table(); + otherTable.addColumn("one", PrimitiveArray.csvFactory(PAType.INT, " 50, , 11, 5")); + otherTable.addColumn("zero", PrimitiveArray.csvFactory(PAType.STRING, " e, , a, f")); + otherTable.addColumn("three", PrimitiveArray.csvFactory(PAType.INT, " 11, 22, 33, 44")); + otherTable.addColumn("five", PrimitiveArray.csvFactory(PAType.INT, " 1, 2, 3, 4")); + + int nMatched = table.update(new String[] { "zero", "one" }, otherTable); + String results = table.dataToString(); + String expected = "zero,one,two,three\n" + + "a,10,111,1.1\n" + + "b,20,222,2.2\n" + + "c,30,333,3.3\n" + + "d,40,444,4.4\n" + + ",,-99,22.0\n" + + "e,50,555,11.0\n" + + "a,11,-99,33.0\n" + // -99 is from missing_value + "f,5,-99,44.0\n"; // -99 is from missing_value + Test.ensureEqual(results, expected, "update results=\n" + results); + Test.ensureEqual(nMatched, 2, "nMatched"); + + } + + /** This tests orderByMax, orderByMin, orderByMinMax */ + @org.junit.jupiter.api.Test + void testOrderByMinMax() throws Exception { + + for (int proc = 0; proc < 3; proc++) { + // String2.log("Table.testOrderBy" + + // (proc == 1 ? "" : "Max") + + // (proc == 0 ? "" : "Min")); + + // *** test #1 + PrimitiveArray substation = PrimitiveArray.csvFactory(PAType.INT, + "10, 20, 20, 30, 10, 10, 10"); + PrimitiveArray station = PrimitiveArray.csvFactory(PAType.STRING, + " a, a, a, b, c, c, c"); + PrimitiveArray time = PrimitiveArray.csvFactory(PAType.INT, + " 1, 1, 2, 1, 1, 2, 3"); + PrimitiveArray other = PrimitiveArray.csvFactory(PAType.INT, + "99, 95, 92, 91, 93, 98, 90"); + Table table = new Table(); + table.addColumn("substation", substation); + table.addColumn("station", station); + table.addColumn("time", time); + table.addColumn("other", other); + + // unsort by sorting on 'other' + table.ascendingSort(new int[] { 3 }); + + // orderBy... + String vars[] = new String[] { "station", "substation", "time" }; + if (proc == 0) + table.orderByMax(vars); + if (proc == 1) + table.orderByMin(vars); + if (proc == 2) + table.orderByMinMax(vars); + String results = table.dataToString(); + String expected[] = new String[] { + "substation,station,time,other\n" + + "10,a,1,99\n" + + "20,a,2,92\n" + + "30,b,1,91\n" + + "10,c,3,90\n", + "substation,station,time,other\n" + + "10,a,1,99\n" + + "20,a,1,95\n" + + "30,b,1,91\n" + + "10,c,1,93\n", + "substation,station,time,other\n" + + "10,a,1,99\n" + // note duplicate of 1 row of data + "10,a,1,99\n" + + "20,a,1,95\n" + + "20,a,2,92\n" + + "30,b,1,91\n" + // note duplicate + "30,b,1,91\n" + + "10,c,1,93\n" + + "10,c,3,90\n" }; + Test.ensureEqual(results, expected[proc], "proc=" + proc + " results=\n" + results); + + // *** test #2 + PrimitiveArray time2 = PrimitiveArray.csvFactory(PAType.INT, + " 1, 1, 2, 1, 1, 2, 3"); + PrimitiveArray other2 = PrimitiveArray.csvFactory(PAType.INT, + "99, 95, 92, 91, 93, 98, 90"); + table = new Table(); + table.addColumn("time", time2); + table.addColumn("other", other2); + + // unsort by sorting on 'other' + table.ascendingSort(new int[] { 1 }); + + // orderBy... + vars = new String[] { "time" }; + if (proc == 0) + table.orderByMax(vars); + if (proc == 1) + table.orderByMin(vars); + if (proc == 2) + table.orderByMinMax(vars); + results = table.dataToString(); + expected = new String[] { + "time,other\n" + + "3,90\n", + "time,other\n" + + "1,91\n", // for ties, the one that is picked isn't specified. unsort above causes 91 to + // be first. + "time,other\n" + + "1,91\n" + // for ties, the one that is picked isn't specified. unsort above causes 91 to + // be first. + "3,90\n" }; + + Test.ensureEqual(results, expected[proc], "proc=" + proc + " results=\n" + results); + + // *** test #3 + PrimitiveArray time3 = PrimitiveArray.csvFactory(PAType.INT, + " 1"); + PrimitiveArray other3 = PrimitiveArray.csvFactory(PAType.INT, + "99"); + table = new Table(); + table.addColumn("time", time3); + table.addColumn("other", other3); + + // unsort by sorting on 'other' + table.ascendingSort(new int[] { 1 }); + + // orderBy... + vars = new String[] { "time" }; + if (proc == 0) + table.orderByMax(vars); + if (proc == 1) + table.orderByMin(vars); + if (proc == 2) + table.orderByMinMax(vars); + results = table.dataToString(); + expected = new String[] { + "time,other\n" + + "1,99\n", + "time,other\n" + + "1,99\n", + "time,other\n" + + "1,99\n" + + "1,99\n" }; + Test.ensureEqual(results, expected[proc], "proc=" + proc + " results=\n" + results); + + // *** test #4 + PrimitiveArray time4 = new IntArray(); + PrimitiveArray other4 = new IntArray(); + table = new Table(); + table.addColumn("time", time4); + table.addColumn("other", other4); + + // orderBy... + vars = new String[] { "time" }; + if (proc == 0) + table.orderByMax(vars); + if (proc == 1) + table.orderByMin(vars); + if (proc == 2) + table.orderByMinMax(vars); + results = table.dataToString(); + String expected4 = "time,other\n"; + Test.ensureEqual(results, expected4, "proc=" + proc + " results=\n" + results); + } + + } + + /** + * This tests orderByClosest. + */ + @org.junit.jupiter.api.Test + void testOrderByClosest() throws Exception { + // String2.log("\n*** Table.testOrderByClosest()"); + + // regular: 2 minutes + // String2.log("\nTest 2 minutes"); + StringArray sar = new StringArray(new String[] { + "b", "b", "b", "b", "b", "b", "c", "a", "d", "a" }); + DoubleArray dar = new DoubleArray(new double[] { + -121, -100, Double.NaN, 110, 132, -2, 1e30, 132, 1e30, 125 }); + IntArray iar = new IntArray(new int[] { + 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 }); + Table table = new Table(); + table.addColumn("iar", iar); + table.addColumn("sar", sar); + table.addColumn("dar", dar); + table.orderByClosest("sar, dar, 2 minutes"); + String results = table.dataToString(); + String expected = "iar,sar,dar\n" + + "9,a,125.0\n" + + "0,b,-121.0\n" + + "5,b,-2.0\n" + + "3,b,110.0\n" + + "6,c,1.0E30\n" + + "8,d,1.0E30\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // 2 months: + // note that Jan is the 0th month: so 2 months rounds to Jan 1, Mar 1, May 1 + // String2.log("\nTest 2 months"); + sar = new StringArray(new String[] { + "b", "b", "b", "b", "b", "b", "c", "a", "d", "a" }); + String sa[] = { + "-0002-08-28", // 0 b -121 + "-0002-09-28", // 1 b -100 + "", // 2 b NaN + "2014-06-25", // 3 b 110, + "2014-07-25", // 4 b 132, + "-912345-12-28", // 5 b -2, + "2010-04-05", // 6 c 82, + "2016-09-25", // 7 a 132, + "2010-04-05", // 8 d 82, + "2016-09-10" }; // 9 a 125}); + dar = new DoubleArray(); + for (int i = 0; i < 10; i++) + dar.add(Calendar2.safeIsoStringToEpochSeconds(sa[i])); + iar = new IntArray(new int[] { + 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 }); + table.clear(); + table.addColumn("iar", iar); + table.addColumn("sar", sar); + table.addColumn("dar", dar); + table.orderByClosest("sar, dar, 2 months"); + StringArray sar2 = new StringArray(); + for (int i = 0; i < dar.size(); i++) + sar2.add(Calendar2.safeEpochSecondsToIsoStringTZ(dar.get(i), "")); + table.setColumn(2, sar2); + results = table.dataToString(); + expected = "iar,sar,dar\n" + + "9,a,2016-09-10T00:00:00Z\n" + + "5,b,-912345-12-28T00:00:00Z\n" + + "0,b,-0002-08-28T00:00:00Z\n" + + "3,b,2014-06-25T00:00:00Z\n" + + "6,c,2010-04-05T00:00:00Z\n" + + "8,d,2010-04-05T00:00:00Z\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // 10 years: beware BC AD transition, see Calendar2.getYear + // String2.log("\nTest 10 years"); + sar = new StringArray(new String[] { + "b", "b", "b", "b", "b", "b", "c", "a", "d", "a" }); + sa = new String[] { + "-0002-12-30", // 0 b -121 + "0004-01-14", // 1 b -100 + "", // 2 b NaN + "2018-06-25", // 3 b 110, + "2024-07-25", // 4 b 132, + "-912345-12-28", // 5 b -2, + "0211-04-05", // 6 c 82, + "2024-09-25", // 7 a 132, + "0211-04-05", // 8 d 82, + "2023-09-10" }; // 9 a 125}); + dar = new DoubleArray(); + for (int i = 0; i < 10; i++) + dar.add(Calendar2.safeIsoStringToEpochSeconds(sa[i])); + iar = new IntArray(new int[] { + 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 }); + table.clear(); + table.addColumn("iar", iar); + table.addColumn("sar", sar); + table.addColumn("dar", dar); + table.orderByClosest("sar, dar, 10 years"); + sar2 = new StringArray(); + for (int i = 0; i < dar.size(); i++) + sar2.add(Calendar2.safeEpochSecondsToIsoStringTZ(dar.get(i), "")); + table.setColumn(2, sar2); + results = table.dataToString(); + expected = "iar,sar,dar\n" + + "9,a,2023-09-10T00:00:00Z\n" + + "5,b,-912345-12-28T00:00:00Z\n" + + "0,b,-0002-12-30T00:00:00Z\n" + + "3,b,2018-06-25T00:00:00Z\n" + + "6,c,0211-04-05T00:00:00Z\n" + + "8,d,0211-04-05T00:00:00Z\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + } + + /** + * This tests orderByCount. + */ + @org.junit.jupiter.api.Test + void testOrderByCount() throws Exception { + // String2.log("\n*** Table.testOrderByCount()"); + + // test 2 orderyBy variables + ShortArray shar = new ShortArray(new short[] { + 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 2, 2, 2 }); + StringArray sar = new StringArray(new String[] { + "b", "b", "b", "b", "b", "b", "c", "a", "d", "a", "c", "a", "" }); + DoubleArray dar = new DoubleArray(new double[] { + -121, -100, Double.NaN, 110, 132, -2, 1e30, 132, 1e30, 125, 1.1, 1.2, 1.3 }); + ByteArray bar = (ByteArray) new ByteArray(new byte[] { // 127=NaN + 0, 127, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 }).setMaxIsMV(true); + Table table = new Table(); + table.addColumn("shar", shar); + table.addColumn("bar", bar); + table.addColumn("sar", sar); + table.addColumn("dar", dar); + table.orderByCount(new String[] { "shar", "sar" }); + String results = table.toString(); + String expected = "{\n" + + "dimensions:\n" + + "\trow = 7 ;\n" + + "\tsar_strlen = 1 ;\n" + + "variables:\n" + + "\tshort shar(row) ;\n" + + "\tint bar(row) ;\n" + + "\t\tbar:units = \"count\" ;\n" + + "\tchar sar(row, sar_strlen) ;\n" + + "\tint dar(row) ;\n" + + "\t\tdar:units = \"count\" ;\n" + + "\n" + + "// global attributes:\n" + + "}\n" + + "shar,bar,sar,dar\n" + + "2,1,,1\n" + + "2,1,a,1\n" + + "2,1,c,1\n" + + "100,2,a,2\n" + + "100,5,b,5\n" + + "100,1,c,1\n" + + "100,1,d,1\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test 0 orderBy variables + sar = new StringArray(new String[] { + "b", "b", "b", "b", "b", "b", "c", "a", "d", "a", "c", "a", "" }); + dar = new DoubleArray(new double[] { + -121, -100, Double.NaN, 110, 132, -2, 1e30, 132, 1e30, 125, 1.1, 1.2, 1.3 }); + bar = (ByteArray) new ByteArray(new byte[] { // 127=NaN + 0, 127, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 }).setMaxIsMV(true); + table = new Table(); + table.addColumn("bar", bar); + table.addColumn("sar", sar); + table.addColumn("dar", dar); + table.orderByCount(new String[] {}); + results = table.toString(); + expected = "{\n" + + "dimensions:\n" + + "\trow = 1 ;\n" + + "variables:\n" + + "\tint bar(row) ;\n" + + "\t\tbar:units = \"count\" ;\n" + + "\tint sar(row) ;\n" + + "\t\tsar:units = \"count\" ;\n" + + "\tint dar(row) ;\n" + + "\t\tdar:units = \"count\" ;\n" + + "\n" + + "// global attributes:\n" + + "}\n" + + "bar,sar,dar\n" + + "12,12,12\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + } + + /** + * This tests orderByLimit. + */ + @org.junit.jupiter.api.Test + void testOrderByLimit() throws Exception { + // String2.log("\n*** Table.testOrderByLimit()"); + + StringArray sar = new StringArray(new String[] { + "b", "b", "b", "b", "b", "b", "c", "a", "d", "a" }); + IntArray iar = new IntArray(new int[] { + 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 }); + Table table = new Table(); + table.addColumn("iar", iar); + table.addColumn("sar", sar); + table.orderByLimit("sar, 2"); + String results = table.dataToString(); + String expected = "iar,sar\n" + + "7,a\n" + + "9,a\n" + + "0,b\n" + + "1,b\n" + + "6,c\n" + + "8,d\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + /** This tests getDapQueryParts. */ + @org.junit.jupiter.api.Test + void testGetDapQueryParts() throws Exception { + // String2.log("\n*** Table.testGetDapQueryParts"); + + // test Table.getDapQueryParts + Test.ensureEqual(Table.getDapQueryParts(null), new String[] { "" }, ""); + Test.ensureEqual(Table.getDapQueryParts(""), new String[] { "" }, ""); + Test.ensureEqual(Table.getDapQueryParts(" "), new String[] { " " }, ""); + Test.ensureEqual(Table.getDapQueryParts("ab%3dc"), new String[] { "ab=c" }, ""); + Test.ensureEqual(Table.getDapQueryParts("a&b&c"), new String[] { "a", "b", "c" }, ""); + Test.ensureEqual(Table.getDapQueryParts("&&"), new String[] { "", "", "" }, ""); + Test.ensureEqual(Table.getDapQueryParts("a&b=R%26D"), new String[] { "a", "b=R&D" }, ""); // & visible + Test.ensureEqual(Table.getDapQueryParts("a%26b=\"R%26D\""), new String[] { "a", "b=\"R&D\"" }, ""); // & encoded + Test.ensureEqual(Table.getDapQueryParts("a%26b=\"R%26D\"%26c"), new String[] { "a", "b=\"R&D\"", "c" }, ""); // & + // encoded + Test.ensureEqual(Table.getDapQueryParts("a%26b%3dR-D"), new String[] { "a", "b=R-D" }, ""); + + // *** test getDapQueryParts (decoded) with invalid queries + String error = ""; + try { + Table.getDapQueryParts("a%26b=\"R%26D"); // decoded. unclosed " + + } catch (Throwable t) { + error = MustBe.throwableToString(t); + } + + Test.ensureEqual(String2.split(error, '\n')[0], + "SimpleException: Query error: A closing doublequote is missing.", + "error=" + error); + + // String2.log("\n*** Table.testGetDapQueryParts succeeded"); + } + + /** + * This tests subsetViaDapQuery. + */ + @org.junit.jupiter.api.Test + void testSubsetViaDapQuery() throws Exception { + // String2.log("\n*** Table.testSubsetViaDapQuery"); + String results, expected; + Table table; + + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery(""); + results = table.dataToString(); + expected = "Time,Longitude,Latitude,Double Data,Int Data,Short Data,Byte Data,Char Data,String Data\n" + + "0.0,-3,1.0,-1.0E300,-2000000000,-32000,-120,\",\",a\n" + + "1.125504062E9,-2,1.5,3.123,2,7,8,\"\"\"\",bb\n" + + "1.130954649E9,-1,2.0,1.0E300,2000000000,32000,120,\\u20ac,ccc\n" + + ",,,,,,,,\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // !=NaN + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery("&Latitude!=NaN"); + results = table.dataToString(); + expected = "Time,Longitude,Latitude,Double Data,Int Data,Short Data,Byte Data,Char Data,String Data\n" + + "0.0,-3,1.0,-1.0E300,-2000000000,-32000,-120,\",\",a\n" + + "1.125504062E9,-2,1.5,3.123,2,7,8,\"\"\"\",bb\n" + + "1.130954649E9,-1,2.0,1.0E300,2000000000,32000,120,\\u20ac,ccc\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // =NaN + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery("&Latitude=NaN"); + results = table.dataToString(); + expected = "Time,Longitude,Latitude,Double Data,Int Data,Short Data,Byte Data,Char Data,String Data\n" + + ",,,,,,,,\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // 1125504062 seconds since 1970-01-01T00:00:00Z = 2005-08-31T16:01:02Z + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery("&Time>2005-08-31T16:01:02Z"); + results = table.dataToString(); + expected = "Time,Longitude,Latitude,Double Data,Int Data,Short Data,Byte Data,Char Data,String Data\n" + + "1.130954649E9,-1,2.0,1.0E300,2000000000,32000,120,\\u20ac,ccc\n"; + // mv row removed because tests related to NaN (except NaN=NaN) return false. + Test.ensureEqual(results, expected, "results=\n" + results); + + // 1125504062 seconds since 1970-01-01T00:00:00Z = 2005-08-31T16:01:02Z + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery("String Data,Time&Time>=2005-08-31T16:01:02Z"); + results = table.dataToString(); + expected = "String Data,Time\n" + + "bb,1.125504062E9\n" + + "ccc,1.130954649E9\n"; + // mv row removed because tests related to NaN (except NaN=NaN) return false. + Test.ensureEqual(results, expected, "results=\n" + results); + + // constraint var needn't be in resultsVars + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery("String Data&Time>=2005-08-31T16:01:02Z"); + results = table.dataToString(); + expected = "String Data\n" + + "bb\n" + + "ccc\n"; + // mv row removed because tests related to NaN (except NaN=NaN) return false. + Test.ensureEqual(results, expected, "results=\n" + results); + + // return 0 rows + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery("Longitude,Time&Time=2005-08-31"); + results = table.dataToString(); + expected = "Longitude,Time\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // string + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery("String Data,Time&Time>1970-01-01&String Data=\"bb\""); + results = table.dataToString(); + expected = "String Data,Time\n" + + "bb,1.125504062E9\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // regex + table = getTestTable(false, true); // includeLongs, Strings + table.subsetViaDapQuery("String Data,Time&String Data=~\"b{1,5}\""); + results = table.dataToString(); + expected = "String Data,Time\n" + + "bb,1.125504062E9\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // String2.log("\n*** Table.testSubsetViaDapQuery finished successfully"); + } + + /** + * This tests parseDapQuery. + */ + @org.junit.jupiter.api.Test + void testParseDapQuery() throws Exception { + // String2.log("\n*** Table.testParseDapQuery"); + + Table table = Table.makeEmptyTable( + new String[] { "myDouble", "myString", "time", "myInt" }, + new String[] { "double", "String", "double", "int" }); + table.columnAttributes("time").add("units", Calendar2.SECONDS_SINCE_1970); + StringArray rVar = new StringArray(); + StringArray cVar = new StringArray(); + StringArray cOp = new StringArray(); + StringArray cVal = new StringArray(); + String results; + + // *** test valid queries + table.parseDapQuery("", rVar, cVar, cOp, cVal, false); // fix + Test.ensureEqual(rVar.toString(), "myDouble, myString, time, myInt", ""); + Test.ensureEqual(cVar.toString(), "", ""); + Test.ensureEqual(cOp.toString(), "", ""); + Test.ensureEqual(cVal.toString(), "", ""); + + table.parseDapQuery("myString,myDouble", rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myString, myDouble", ""); + Test.ensureEqual(cVar.toString(), "", ""); + Test.ensureEqual(cOp.toString(), "", ""); + Test.ensureEqual(cVal.toString(), "", ""); + + table.parseDapQuery("myDouble&myString=\"something\"", rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myDouble", ""); + Test.ensureEqual(cVar.toString(), "myString", ""); + Test.ensureEqual(cOp.toString(), "=", ""); + Test.ensureEqual(cVal.toString(), "something", ""); + + table.parseDapQuery("myDouble&myInt=~\"regex\"", rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myDouble", ""); + Test.ensureEqual(cVar.toString(), "myInt", ""); + Test.ensureEqual(cOp.toString(), "=~", ""); + Test.ensureEqual(cVal.toString(), "regex", ""); + + table.parseDapQuery("myDouble&time>=1.4229216E9", rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myDouble", ""); + Test.ensureEqual(cVar.toString(), "time", ""); + Test.ensureEqual(cOp.toString(), ">=", ""); + Test.ensureEqual(cVal.toString(), "1.4229216E9", ""); + + table.parseDapQuery("myDouble&time>=2015-02-03", rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myDouble", ""); + Test.ensureEqual(cVar.toString(), "time", ""); + Test.ensureEqual(cOp.toString(), ">=", ""); + Test.ensureEqual(cVal.toString(), "1.4229216E9", ""); + + table.parseDapQuery("myDouble&myInt=NaN", rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myDouble", ""); + Test.ensureEqual(cVar.toString(), "myInt", ""); + Test.ensureEqual(cOp.toString(), "=", ""); + Test.ensureEqual(cVal.toString(), "NaN", ""); + + table.parseDapQuery( + "&time!=2015-02-03&myInt<5.1&myString=\"Nate\"&orderBy(\"myString,myInt\")&distinct()", + rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myDouble, myString, time, myInt", ""); + Test.ensureEqual(cVar.toString(), "time, myInt, myString", ""); + Test.ensureEqual(cOp.toString(), "!=, <, =", ""); + Test.ensureEqual(cVal.toString(), "1.4229216E9, 5.1, Nate", ""); + + // s + table.parseDapQuery("s", rVar, cVar, cOp, cVal, false); // fix + Test.ensureEqual(rVar.toString(), "myDouble, myString, time, myInt", ""); + Test.ensureEqual(cVar.toString(), "", ""); + Test.ensureEqual(cOp.toString(), "", ""); + Test.ensureEqual(cVal.toString(), "", ""); + + table.parseDapQuery("s.myDouble&s.time>=2015-02-03", rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myDouble", ""); + Test.ensureEqual(cVar.toString(), "time", ""); + Test.ensureEqual(cOp.toString(), ">=", ""); + Test.ensureEqual(cVal.toString(), "1.4229216E9", ""); + + table.parseDapQuery( + "&s.time!=2015-02-03&s.myInt<5.1&s.myString=\"Nate\"&orderBy(\"s.myString,s.myInt\")&distinct()", + rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "myDouble, myString, time, myInt", ""); + Test.ensureEqual(cVar.toString(), "time, myInt, myString", ""); + Test.ensureEqual(cOp.toString(), "!=, <, =", ""); + Test.ensureEqual(cVal.toString(), "1.4229216E9, 5.1, Nate", ""); + + // Tests of time related to "now" + double now = System.currentTimeMillis() / 1000.0; + // String2.log("epochSecondsNow=" + now); + table.parseDapQuery("time&time>now&time>now%2Bsecond&time>now-minute&time>now-44days", + rVar, cVar, cOp, cVal, false); + Test.ensureEqual(rVar.toString(), "time", ""); + Test.ensureEqual(cVar.toString(), "time, time, time, time", ""); + Test.ensureEqual(cOp.toString(), ">, >, >, >", ""); + Test.ensureTrue(Math.abs(cVal.getDouble(0) - (now)) < 20, cVal.get(0)); + Test.ensureTrue(Math.abs(cVal.getDouble(1) - (now + 1)) < 20, cVal.get(1)); + Test.ensureTrue(Math.abs(cVal.getDouble(2) - (now - 60)) < 20, cVal.get(2)); + Test.ensureTrue(Math.abs(cVal.getDouble(3) - (now - 44 * 86400)) < 20, cVal.get(3)); + + // ********* tests that fail + results = "invalid request var"; + try { + table.parseDapQuery("time,MyInt", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Unrecognized variable=\"MyInt\".", ""); + + results = "listed twice"; + try { + table.parseDapQuery("time,myInt,time", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: variable=time is listed twice in the results variables list.", + ""); + + results = "invalid constraint var"; + try { + table.parseDapQuery("time&MyDouble>5", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Unrecognized constraint variable=\"MyDouble\".", ""); + + results = "missing &"; + try { + table.parseDapQuery("myInt>5", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: All constraints (including \"myInt>...\") must be preceded by '&'.", + ""); + + results = "missing & with date with double col"; + try { + table.parseDapQuery("myDouble>2014-01-01T00:00:00Z", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: All constraints (including \"myDouble>...\") must be preceded by '&'.", + ""); + + results = "invalid op"; + try { + table.parseDapQuery("&myInt==5", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Use '=' instead of '==' in constraints.", ""); + + results = "invalid NAN value"; + try { + table.parseDapQuery("&myInt=NAN", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Numeric tests of NaN must use \"NaN\", not value=\"NAN\".", ""); + + results = "invalid NaN value, something"; + try { + table.parseDapQuery("&myInt=something", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Numeric tests of NaN must use \"NaN\", not value=\"something\".", + ""); + + results = "invalid NaN value"; + try { + table.parseDapQuery("&myInt=1e1000", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Numeric tests of NaN must use \"NaN\", not value=\"1e1000\".", + ""); + + results = "invalid regex op"; + try { + table.parseDapQuery("&myInt~=\"regex\"", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Use '=~' instead of '~=' in constraints.", ""); + + results = "missing \"\" for string"; + try { + table.parseDapQuery("&myString=something", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: For constraints of String variables, the right-hand-side value must be surrounded by double quotes.\n" + + + "Bad constraint: myString=something", + "results=" + results); + + results = "missing \"\" for regex"; + try { + table.parseDapQuery("&myInt=~something", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: For =~ constraints of numeric variables, the right-hand-side value must be surrounded by double quotes.\n" + + + "Bad constraint: myInt=~something", + "results=" + results); + + results = "invalid now units"; + try { + table.parseDapQuery("&time>now-2dayss", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Invalid \"now\" constraint: \"now-2dayss\". " + + "Timestamp constraints with \"now\" must be in the form \"now[+|-positiveInteger[millis|seconds|minutes|hours|days|months|years]]\" (or singular units).", + "results=" + results); + + results = "invalid now option -"; + try { + table.parseDapQuery("&time>now-", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Invalid \"now\" constraint: \"now-\". " + + "Timestamp constraints with \"now\" must be in the form \"now[+|-positiveInteger[millis|seconds|minutes|hours|days|months|years]]\" (or singular units).", + "results=" + results); + + results = "invalid now option -+"; + try { + table.parseDapQuery("&time>now-%2B4seconds", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Invalid \"now\" constraint: \"now-+4seconds\". " + + "Timestamp constraints with \"now\" must be in the form \"now[+|-positiveInteger[millis|seconds|minutes|hours|days|months|years]]\" (or singular units).", + "results=" + results); + + results = "invalid now option +-"; + try { + table.parseDapQuery("&time>now%2B-4seconds", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Invalid \"now\" constraint: \"now+-4seconds\". " + + "Timestamp constraints with \"now\" must be in the form \"now[+|-positiveInteger[millis|seconds|minutes|hours|days|months|years]]\" (or singular units).", + "results=" + results); + + results = "invalid now option"; + try { + table.parseDapQuery("&time>now=2days", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: Unrecognized constraint variable=\"time>now\".", + "results=" + results); + + results = "unknown filter"; + try { + table.parseDapQuery("&Distinct()", rVar, cVar, cOp, cVal, false); + } catch (Throwable t) { + results = t.toString(); + } + Test.ensureEqual(results, + "com.cohort.util.SimpleException: Query error: No operator found in constraint=\"Distinct()\".", ""); + + // String2.log("\n*** Table.testParseDapQuery finished successfully."); + } + + @org.junit.jupiter.api.Test + void testAddIndexColumns() throws Exception { + Table table = new Table(); + table.addIndexColumns(new int[] { 3, 2, 4 }); + String results = table.dataToString(); + String expected = "_index_0,_index_1,_index_2\n" + + "0,0,0\n" + + "0,0,1\n" + + "0,0,2\n" + + "0,0,3\n" + + "0,1,0\n" + + "0,1,1\n" + + "0,1,2\n" + + "0,1,3\n" + + "1,0,0\n" + + "1,0,1\n" + + "1,0,2\n" + + "1,0,3\n" + + "1,1,0\n" + + "1,1,1\n" + + "1,1,2\n" + + "1,1,3\n" + + "2,0,0\n" + + "2,0,1\n" + + "2,0,2\n" + + "2,0,3\n" + + "2,1,0\n" + + "2,1,1\n" + + "2,1,2\n" + + "2,1,3\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + /** This tests readMultidimNc by reading an Argo Profile file. */ + @org.junit.jupiter.api.Test + void testReadMultidimNc() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebugMode = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadMultidimNc"); + Table table = new Table(); + // ftp://ftp.ifremer.fr/ifremer/argo/dac/csio/2901175/2901175_prof.nc + String fiName = TableTests.class.getResource("/nc/2901175_prof.nc").getPath(); + // String2.log(NcHelper.ncdump(fiName, "-h")); + String results, expectedStart, expectedEnd; + /* */ + + // ** don't specify varNames or dimNames -- it find vars with most dims + table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, + true, 0, false, // readMetadata, standardizeWhat=0, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + expectedStart = + // static vars and vars like char SCIENTIFIC_CALIB_COEFFICIENT(N_PROF=254, + // N_CALIB=1, N_PARAM=3, STRING256=256); + "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + + + "...\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 762, "nRows"); // 254*3 + + // * same but quick reject based on constraint + table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, + true, 0, false, // readMetadata, standardizeWhat=0, removeMVRows + StringArray.fromCSV("FORMAT_VERSION,FORMAT_VERSION"), // conVars + StringArray.fromCSV("=,="), // conOps + StringArray.fromCSV("3.1,3.2")); // conVals + Test.ensureEqual(table.nRows(), 0, "nRows"); + + // * test don't removeMVRows + table.readMultidimNc(fiName, null, + StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), + null, + true, 0, false, // readMetadata, standardizeWhat=0, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.toString(3); + expectedStart = "{\n" + + "dimensions:\n" + + "\trow = 18034 ;\n" + + "\tDATA_TYPE_strlen = 12 ;\n" + + "\tFORMAT_VERSION_strlen = 3 ;\n" + + "\tHANDBOOK_VERSION_strlen = 3 ;\n" + + "\tREFERENCE_DATE_TIME_strlen = 14 ;\n" + + "\tDATE_CREATION_strlen = 14 ;\n" + + "\tDATE_UPDATE_strlen = 14 ;\n" + + "\tPLATFORM_NUMBER_strlen = 7 ;\n" + + "\tPROJECT_NAME_strlen = 18 ;\n" + + "\tPI_NAME_strlen = 11 ;\n" + + "\tDATA_CENTRE_strlen = 2 ;\n" + + "\tDC_REFERENCE_strlen = 14 ;\n" + + "\tDATA_STATE_INDICATOR_strlen = 2 ;\n" + + "\tPLATFORM_TYPE_strlen = 4 ;\n" + + "\tFLOAT_SERIAL_NO_strlen = 13 ;\n" + + "\tFIRMWARE_VERSION_strlen = 6 ;\n" + + "\tWMO_INST_TYPE_strlen = 3 ;\n" + + "\tPOSITIONING_SYSTEM_strlen = 5 ;\n" + + "\tVERTICAL_SAMPLING_SCHEME_strlen = 26 ;\n" + + "variables:\n" + + "\tchar DATA_TYPE(row, DATA_TYPE_strlen) ;\n" + + "\t\tDATA_TYPE:conventions = \"Argo reference table 1\" ;\n" + + "\t\tDATA_TYPE:long_name = \"Data type\" ;\n" + + "\tchar FORMAT_VERSION(row, FORMAT_VERSION_strlen) ;\n" + + "\t\tFORMAT_VERSION:long_name = \"File format version\" ;\n" + + "\tchar HANDBOOK_VERSION(row, HANDBOOK_VERSION_strlen) ;\n" + + "\t\tHANDBOOK_VERSION:long_name = \"Data handbook version\" ;\n" + + "\tchar REFERENCE_DATE_TIME(row, REFERENCE_DATE_TIME_strlen) ;\n" + + "\t\tREFERENCE_DATE_TIME:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tREFERENCE_DATE_TIME:long_name = \"Date of reference for Julian days\" ;\n" + + "\tchar DATE_CREATION(row, DATE_CREATION_strlen) ;\n" + + "\t\tDATE_CREATION:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tDATE_CREATION:long_name = \"Date of file creation\" ;\n" + + "\tchar DATE_UPDATE(row, DATE_UPDATE_strlen) ;\n" + + "\t\tDATE_UPDATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tDATE_UPDATE:long_name = \"Date of update of this file\" ;\n" + + "\tchar PLATFORM_NUMBER(row, PLATFORM_NUMBER_strlen) ;\n" + + "\t\tPLATFORM_NUMBER:conventions = \"WMO float identifier : A9IIIII\" ;\n" + + "\t\tPLATFORM_NUMBER:long_name = \"Float unique identifier\" ;\n" + + "\tchar PROJECT_NAME(row, PROJECT_NAME_strlen) ;\n" + + "\t\tPROJECT_NAME:long_name = \"Name of the project\" ;\n" + + "\tchar PI_NAME(row, PI_NAME_strlen) ;\n" + + "\t\tPI_NAME:long_name = \"Name of the principal investigator\" ;\n" + + "\tint CYCLE_NUMBER(row) ;\n" + + "\t\tCYCLE_NUMBER:_FillValue = 99999 ;\n" + + "\t\tCYCLE_NUMBER:conventions = \"0...N, 0 : launch cycle (if exists), 1 : first complete cycle\" ;\n" + + "\t\tCYCLE_NUMBER:long_name = \"Float cycle number\" ;\n" + + "\tchar DIRECTION(row) ;\n" + + "\t\tDIRECTION:conventions = \"A: ascending profiles, D: descending profiles\" ;\n" + + "\t\tDIRECTION:long_name = \"Direction of the station profiles\" ;\n" + + "\tchar DATA_CENTRE(row, DATA_CENTRE_strlen) ;\n" + + "\t\tDATA_CENTRE:conventions = \"Argo reference table 4\" ;\n" + + "\t\tDATA_CENTRE:long_name = \"Data centre in charge of float data processing\" ;\n" + + "\tchar DC_REFERENCE(row, DC_REFERENCE_strlen) ;\n" + + "\t\tDC_REFERENCE:conventions = \"Data centre convention\" ;\n" + + "\t\tDC_REFERENCE:long_name = \"Station unique identifier in data centre\" ;\n" + + "\tchar DATA_STATE_INDICATOR(row, DATA_STATE_INDICATOR_strlen) ;\n" + + "\t\tDATA_STATE_INDICATOR:conventions = \"Argo reference table 6\" ;\n" + + "\t\tDATA_STATE_INDICATOR:long_name = \"Degree of processing the data have passed through\" ;\n" + + "\tchar DATA_MODE(row) ;\n" + + "\t\tDATA_MODE:conventions = \"R : real time; D : delayed mode; A : real time with adjustment\" ;\n" + + "\t\tDATA_MODE:long_name = \"Delayed mode or real time data\" ;\n" + + "\tchar PLATFORM_TYPE(row, PLATFORM_TYPE_strlen) ;\n" + + "\t\tPLATFORM_TYPE:conventions = \"Argo reference table 23\" ;\n" + + "\t\tPLATFORM_TYPE:long_name = \"Type of float\" ;\n" + + "\tchar FLOAT_SERIAL_NO(row, FLOAT_SERIAL_NO_strlen) ;\n" + + "\t\tFLOAT_SERIAL_NO:long_name = \"Serial number of the float\" ;\n" + + "\tchar FIRMWARE_VERSION(row, FIRMWARE_VERSION_strlen) ;\n" + + "\t\tFIRMWARE_VERSION:long_name = \"Instrument firmware version\" ;\n" + + "\tchar WMO_INST_TYPE(row, WMO_INST_TYPE_strlen) ;\n" + + "\t\tWMO_INST_TYPE:conventions = \"Argo reference table 8\" ;\n" + + "\t\tWMO_INST_TYPE:long_name = \"Coded instrument type\" ;\n" + + "\tdouble JULD(row) ;\n" + + "\t\tJULD:_FillValue = 999999.0 ;\n" + + "\t\tJULD:axis = \"T\" ;\n" + + "\t\tJULD:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + + "\t\tJULD:long_name = \"Julian day (UTC) of the station relative to REFERENCE_DATE_TIME\" ;\n" + + "\t\tJULD:resolution = 0.0 ;\n" + + "\t\tJULD:standard_name = \"time\" ;\n" + + "\t\tJULD:units = \"days since 1950-01-01 00:00:00 UTC\" ;\n" + + "\tchar JULD_QC(row) ;\n" + + "\t\tJULD_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tJULD_QC:long_name = \"Quality on date and time\" ;\n" + + "\tdouble JULD_LOCATION(row) ;\n" + + "\t\tJULD_LOCATION:_FillValue = 999999.0 ;\n" + + "\t\tJULD_LOCATION:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + + "\t\tJULD_LOCATION:long_name = \"Julian day (UTC) of the location relative to REFERENCE_DATE_TIME\" ;\n" + + "\t\tJULD_LOCATION:resolution = 0.0 ;\n" + + "\t\tJULD_LOCATION:units = \"days since 1950-01-01 00:00:00 UTC\" ;\n" + + "\tdouble LATITUDE(row) ;\n" + + "\t\tLATITUDE:_FillValue = 99999.0 ;\n" + + "\t\tLATITUDE:axis = \"Y\" ;\n" + + "\t\tLATITUDE:long_name = \"Latitude of the station, best estimate\" ;\n" + + "\t\tLATITUDE:standard_name = \"latitude\" ;\n" + + "\t\tLATITUDE:units = \"degree_north\" ;\n" + + "\t\tLATITUDE:valid_max = 90.0 ;\n" + + "\t\tLATITUDE:valid_min = -90.0 ;\n" + + "\tdouble LONGITUDE(row) ;\n" + + "\t\tLONGITUDE:_FillValue = 99999.0 ;\n" + + "\t\tLONGITUDE:axis = \"X\" ;\n" + + "\t\tLONGITUDE:long_name = \"Longitude of the station, best estimate\" ;\n" + + "\t\tLONGITUDE:standard_name = \"longitude\" ;\n" + + "\t\tLONGITUDE:units = \"degree_east\" ;\n" + + "\t\tLONGITUDE:valid_max = 180.0 ;\n" + + "\t\tLONGITUDE:valid_min = -180.0 ;\n" + + "\tchar POSITION_QC(row) ;\n" + + "\t\tPOSITION_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tPOSITION_QC:long_name = \"Quality on position (latitude and longitude)\" ;\n" + + "\tchar POSITIONING_SYSTEM(row, POSITIONING_SYSTEM_strlen) ;\n" + + "\t\tPOSITIONING_SYSTEM:long_name = \"Positioning system\" ;\n" + + "\tchar PROFILE_PRES_QC(row) ;\n" + + "\t\tPROFILE_PRES_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_PRES_QC:long_name = \"Global quality flag of PRES profile\" ;\n" + + "\tchar PROFILE_TEMP_QC(row) ;\n" + + "\t\tPROFILE_TEMP_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_TEMP_QC:long_name = \"Global quality flag of TEMP profile\" ;\n" + + "\tchar PROFILE_PSAL_QC(row) ;\n" + + "\t\tPROFILE_PSAL_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_PSAL_QC:long_name = \"Global quality flag of PSAL profile\" ;\n" + + "\tchar VERTICAL_SAMPLING_SCHEME(row, VERTICAL_SAMPLING_SCHEME_strlen) ;\n" + + "\t\tVERTICAL_SAMPLING_SCHEME:conventions = \"Argo reference table 16\" ;\n" + + "\t\tVERTICAL_SAMPLING_SCHEME:long_name = \"Vertical sampling scheme\" ;\n" + + "\tint CONFIG_MISSION_NUMBER(row) ;\n" + + "\t\tCONFIG_MISSION_NUMBER:_FillValue = 99999 ;\n" + + "\t\tCONFIG_MISSION_NUMBER:conventions = \"1...N, 1 : first complete mission\" ;\n" + + "\t\tCONFIG_MISSION_NUMBER:long_name = \"Unique number denoting the missions performed by the float\" ;\n" + + "\tfloat PRES(row) ;\n" + + "\t\tPRES:_FillValue = 99999.0f ;\n" + + "\t\tPRES:axis = \"Z\" ;\n" + + "\t\tPRES:C_format = \"%7.1f\" ;\n" + + "\t\tPRES:FORTRAN_format = \"F7.1\" ;\n" + + "\t\tPRES:long_name = \"Sea water pressure, equals 0 at sea-level\" ;\n" + + "\t\tPRES:resolution = 1.0f ;\n" + + "\t\tPRES:standard_name = \"sea_water_pressure\" ;\n" + + "\t\tPRES:units = \"decibar\" ;\n" + + "\t\tPRES:valid_max = 12000.0f ;\n" + + "\t\tPRES:valid_min = 0.0f ;\n" + + "\tchar PRES_QC(row) ;\n" + + "\t\tPRES_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tPRES_QC:long_name = \"quality flag\" ;\n" + + "\tfloat PRES_ADJUSTED(row) ;\n" + + "\t\tPRES_ADJUSTED:_FillValue = 99999.0f ;\n" + + "\t\tPRES_ADJUSTED:axis = \"Z\" ;\n" + + "\t\tPRES_ADJUSTED:C_format = \"%7.1f\" ;\n" + + "\t\tPRES_ADJUSTED:FORTRAN_format = \"F7.1\" ;\n" + + "\t\tPRES_ADJUSTED:long_name = \"Sea water pressure, equals 0 at sea-level\" ;\n" + + "\t\tPRES_ADJUSTED:resolution = 1.0f ;\n" + + "\t\tPRES_ADJUSTED:standard_name = \"sea_water_pressure\" ;\n" + + "\t\tPRES_ADJUSTED:units = \"decibar\" ;\n" + + "\t\tPRES_ADJUSTED:valid_max = 12000.0f ;\n" + + "\t\tPRES_ADJUSTED:valid_min = 0.0f ;\n" + + "\tchar PRES_ADJUSTED_QC(row) ;\n" + + "\t\tPRES_ADJUSTED_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tPRES_ADJUSTED_QC:long_name = \"quality flag\" ;\n" + + "\tfloat PRES_ADJUSTED_ERROR(row) ;\n" + + "\t\tPRES_ADJUSTED_ERROR:_FillValue = 99999.0f ;\n" + + "\t\tPRES_ADJUSTED_ERROR:C_format = \"%7.1f\" ;\n" + + "\t\tPRES_ADJUSTED_ERROR:FORTRAN_format = \"F7.1\" ;\n" + + "\t\tPRES_ADJUSTED_ERROR:long_name = \"Contains the error on the adjusted values as determined by the delayed mode QC process\" ;\n" + + + "\t\tPRES_ADJUSTED_ERROR:resolution = 1.0f ;\n" + + "\t\tPRES_ADJUSTED_ERROR:units = \"decibar\" ;\n" + + "\tfloat TEMP(row) ;\n" + + "\t\tTEMP:_FillValue = 99999.0f ;\n" + + "\t\tTEMP:C_format = \"%9.3f\" ;\n" + + "\t\tTEMP:FORTRAN_format = \"F9.3\" ;\n" + + "\t\tTEMP:long_name = \"Sea temperature in-situ ITS-90 scale\" ;\n" + + "\t\tTEMP:resolution = 0.001f ;\n" + + "\t\tTEMP:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTEMP:units = \"degree_Celsius\" ;\n" + + "\t\tTEMP:valid_max = 40.0f ;\n" + + "\t\tTEMP:valid_min = -2.5f ;\n" + + "\tchar TEMP_QC(row) ;\n" + + "\t\tTEMP_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tTEMP_QC:long_name = \"quality flag\" ;\n" + + "\tfloat TEMP_ADJUSTED(row) ;\n" + + "\t\tTEMP_ADJUSTED:_FillValue = 99999.0f ;\n" + + "\t\tTEMP_ADJUSTED:C_format = \"%9.3f\" ;\n" + + "\t\tTEMP_ADJUSTED:FORTRAN_format = \"F9.3\" ;\n" + + "\t\tTEMP_ADJUSTED:long_name = \"Sea temperature in-situ ITS-90 scale\" ;\n" + + "\t\tTEMP_ADJUSTED:resolution = 0.001f ;\n" + + "\t\tTEMP_ADJUSTED:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTEMP_ADJUSTED:units = \"degree_Celsius\" ;\n" + + "\t\tTEMP_ADJUSTED:valid_max = 40.0f ;\n" + + "\t\tTEMP_ADJUSTED:valid_min = -2.5f ;\n" + + "\tchar TEMP_ADJUSTED_QC(row) ;\n" + + "\t\tTEMP_ADJUSTED_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tTEMP_ADJUSTED_QC:long_name = \"quality flag\" ;\n" + + "\tfloat TEMP_ADJUSTED_ERROR(row) ;\n" + + "\t\tTEMP_ADJUSTED_ERROR:_FillValue = 99999.0f ;\n" + + "\t\tTEMP_ADJUSTED_ERROR:C_format = \"%9.3f\" ;\n" + + "\t\tTEMP_ADJUSTED_ERROR:FORTRAN_format = \"F9.3\" ;\n" + + "\t\tTEMP_ADJUSTED_ERROR:long_name = \"Contains the error on the adjusted values as determined by the delayed mode QC process\" ;\n" + + + "\t\tTEMP_ADJUSTED_ERROR:resolution = 0.001f ;\n" + + "\t\tTEMP_ADJUSTED_ERROR:units = \"degree_Celsius\" ;\n" + + "\tfloat PSAL(row) ;\n" + + "\t\tPSAL:_FillValue = 99999.0f ;\n" + + "\t\tPSAL:C_format = \"%9.3f\" ;\n" + + "\t\tPSAL:FORTRAN_format = \"F9.3\" ;\n" + + "\t\tPSAL:long_name = \"Practical salinity\" ;\n" + + "\t\tPSAL:resolution = 0.001f ;\n" + + "\t\tPSAL:standard_name = \"sea_water_salinity\" ;\n" + + "\t\tPSAL:units = \"psu\" ;\n" + + "\t\tPSAL:valid_max = 41.0f ;\n" + + "\t\tPSAL:valid_min = 2.0f ;\n" + + "\tchar PSAL_QC(row) ;\n" + + "\t\tPSAL_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tPSAL_QC:long_name = \"quality flag\" ;\n" + + "\tfloat PSAL_ADJUSTED(row) ;\n" + + "\t\tPSAL_ADJUSTED:_FillValue = 99999.0f ;\n" + + "\t\tPSAL_ADJUSTED:C_format = \"%9.3f\" ;\n" + + "\t\tPSAL_ADJUSTED:FORTRAN_format = \"F9.3\" ;\n" + + "\t\tPSAL_ADJUSTED:long_name = \"Practical salinity\" ;\n" + + "\t\tPSAL_ADJUSTED:resolution = 0.001f ;\n" + + "\t\tPSAL_ADJUSTED:standard_name = \"sea_water_salinity\" ;\n" + + "\t\tPSAL_ADJUSTED:units = \"psu\" ;\n" + + "\t\tPSAL_ADJUSTED:valid_max = 41.0f ;\n" + + "\t\tPSAL_ADJUSTED:valid_min = 2.0f ;\n" + + "\tchar PSAL_ADJUSTED_QC(row) ;\n" + + "\t\tPSAL_ADJUSTED_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tPSAL_ADJUSTED_QC:long_name = \"quality flag\" ;\n" + + "\tfloat PSAL_ADJUSTED_ERROR(row) ;\n" + + "\t\tPSAL_ADJUSTED_ERROR:_FillValue = 99999.0f ;\n" + + "\t\tPSAL_ADJUSTED_ERROR:C_format = \"%9.3f\" ;\n" + + "\t\tPSAL_ADJUSTED_ERROR:FORTRAN_format = \"F9.3\" ;\n" + + "\t\tPSAL_ADJUSTED_ERROR:long_name = \"Contains the error on the adjusted values as determined by the delayed mode QC process\" ;\n" + + + "\t\tPSAL_ADJUSTED_ERROR:resolution = 0.001f ;\n" + + "\t\tPSAL_ADJUSTED_ERROR:units = \"psu\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:Conventions = \"Argo-3.1 CF-1.6\" ;\n" + + "\t\t:featureType = \"trajectoryProfile\" ;\n" + + "\t\t:history = \"2016-04-15T20:47:22Z creation\" ;\n" + + "\t\t:institution = \"Coriolis GDAC\" ;\n" + + "\t\t:references = \"http://www.argodatamgt.org/Documentation\" ;\n" + + "\t\t:source = \"Argo float\" ;\n" + + "\t\t:title = \"Argo float vertical profile\" ;\n" + + "\t\t:user_manual_version = \"3.1\" ;\n" + + "}\n"; + Test.ensureEqual(results.substring(0, expectedStart.length()), expectedStart, "results=\n" + results); + + results = table.dataToString(3); + expectedStart = "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,5.9,1,5.8,1,2.4,24.989,1,24.989,1,0.002,34.555,1,34.55511,1,0.01\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,10.0,1,9.9,1,2.4,24.99,1,24.99,1,0.002,34.554,1,34.55505,1,0.01\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,20.1,1,20.0,1,2.4,24.69,1,24.69,1,0.002,34.56,1,34.56191,1,0.01\n" + + + "...\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 18034, "nRows"); // 254*71 + + // and the end of that table + table.removeRows(0, table.nRows() - 3); + results = table.dataToString(5); + expectedEnd = "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1899.9,1,1899.3,1,99999.0,2.055,1,2.055,1,99999.0,34.612,1,34.612,1,99999.0\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1950.0,1,1949.4,1,99999.0,2.014,1,2.014,1,99999.0,34.617,1,34.617,1,99999.0\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,99999.0,\" \",99999.0,\" \",99999.0,99999.0,\" \",99999.0,\" \",99999.0,99999.0,\" \",99999.0,\" \",99999.0\n"; + Test.ensureEqual(results, expectedEnd, "results=\n" + results); + + // * test do removeMVRows + table.readMultidimNc(fiName, null, StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 17266, "nRows"); + + // and test data at the end of that table + table.removeRows(0, table.nRows() - 3); + results = table.dataToString(5); + expectedEnd = "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1850.0,1,1849.4,1,99999.0,2.106,1,2.106,1,99999.0,34.604,1,34.604,1,99999.0\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1899.9,1,1899.3,1,99999.0,2.055,1,2.055,1,99999.0,34.612,1,34.612,1,99999.0\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1950.0,1,1949.4,1,99999.0,2.014,1,2.014,1,99999.0,34.617,1,34.617,1,99999.0\n"; + Test.ensureEqual(results, expectedEnd, "results=\n" + results); + + // * same but quick reject based on constraint LAT,LON 26.587,154.853 + // *** this takes 9ms while test above takes 99ms! + table.readMultidimNc(fiName, null, StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + StringArray.fromCSV("LATITUDE"), // conVars + StringArray.fromCSV("="), // conOps + StringArray.fromCSV("45")); // conVals + Test.ensureEqual(table.nRows(), 0, "nRows"); + + // * test different dim order (should be rearranged so the same) + table.readMultidimNc(fiName, null, StringArray.fromCSV("N_LEVELS, ZZTOP, N_PROF"), null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 17266, "nRows"); + + // and test data at the end of that table + table.removeRows(0, table.nRows() - 3); + results = table.dataToString(5); + Test.ensureEqual(results, expectedEnd, "results=\n" + results); + + // * test read all and constrain PLATFORM_NUMBER + // Roland reported this problem 2016-06-21: returned 0 rows, saying: + // "Returning an empty table because var=PLATFORM_NUMBER failed its constraints, + // including =2901175. time=0" + + table.readMultidimNc(fiName, StringArray.fromCSV( + "DATA_TYPE, FORMAT_VERSION, HANDBOOK_VERSION, REFERENCE_DATE_TIME, DATE_CREATION, " + + "DATE_UPDATE, PLATFORM_NUMBER, PROJECT_NAME, PI_NAME, CYCLE_NUMBER, DIRECTION, " + + "DATA_CENTRE, DC_REFERENCE, DATA_STATE_INDICATOR, DATA_MODE, PLATFORM_TYPE, " + + "FLOAT_SERIAL_NO, FIRMWARE_VERSION, WMO_INST_TYPE, JULD, JULD_QC, JULD_LOCATION, " + + "LATITUDE, LONGITUDE, POSITION_QC, POSITIONING_SYSTEM, PROFILE_PRES_QC, " + + "PROFILE_TEMP_QC, PROFILE_PSAL_QC, VERTICAL_SAMPLING_SCHEME, " + + "CONFIG_MISSION_NUMBER, PRES, PRES_QC, PRES_ADJUSTED, PRES_ADJUSTED_QC, " + + "PRES_ADJUSTED_ERROR, TEMP, TEMP_QC, TEMP_ADJUSTED, TEMP_ADJUSTED_QC, " + + "TEMP_ADJUSTED_ERROR, PSAL, PSAL_QC, PSAL_ADJUSTED, PSAL_ADJUSTED_QC, " + + "PSAL_ADJUSTED_ERROR"), + null, null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + StringArray.fromCSV("PLATFORM_NUMBER"), // conVars, conOps, conVals + StringArray.fromCSV("="), + StringArray.fromCSV("2901175")); + results = table.dataToString(3); + expectedStart = "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION," + + "DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE," + + "DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO," + + "FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE," + + "POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC," + + "VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED," + + "PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC," + + "TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175," + + "CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846," + + "21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1," + + "ARGOS,A,A,A,,1,5.9,1,5.8,1,2.4,24.989,1,24.989,1,0.002,34.555,1,34.55511," + + "1,0.01\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175," + + "CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846," + + "21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1," + + "ARGOS,A,A,A,,1,10.0,1,9.9,1,2.4,24.99,1,24.99,1,0.002,34.554,1,34.55505," + + "1,0.01\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175," + + "CHINA ARGO PROJECT,JIANPING XU,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846," + + "21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1," + + "ARGOS,A,A,A,,1,20.1,1,20.0,1,2.4,24.69,1,24.69,1,0.002,34.56,1,34.56191," + + "1,0.01\n" + + "...\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 17266, "nRows"); // same as when all variables were explicitly loaded + + // * test different varNames + table.readMultidimNc(fiName, + StringArray.fromCSV( + "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR"), + null, null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 17266, "nRows"); + + // and test data at the end of that table + table.removeRows(0, table.nRows() - 3); + results = table.dataToString(5); + Test.ensureEqual(results, expectedEnd, "results=\n" + results); + + // * test do removeMVRows when loadVariables is limited (to ensure all are + // loaded for the test) + table.readMultidimNc(fiName, StringArray.fromCSV("LONGITUDE,PRES,PSAL_ADJUSTED_ERROR"), + null, null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + expectedStart = "LONGITUDE,PRES,PSAL_ADJUSTED_ERROR\n" + + "123.36499786376953,5.9,0.01\n" + + "123.36499786376953,10.0,0.01\n" + + "123.36499786376953,20.1,0.01\n" + + "...\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 17266, "nRows"); // same as when all variables were explicitly loaded + + // and test data at the end of that table + table.removeRows(0, table.nRows() - 3); + results = table.dataToString(5); + expectedEnd = "LONGITUDE,PRES,PSAL_ADJUSTED_ERROR\n" + + "154.853,1850.0,99999.0\n" + // these rows were're removed because other full-dim vars had values + "154.853,1899.9,99999.0\n" + + "154.853,1950.0,99999.0\n"; + Test.ensureEqual(results, expectedEnd, "results=\n" + results); + + // * test read JULD + table.readMultidimNc(fiName, StringArray.fromCSV("JULD"), null, null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + expectedStart = "JULD\n" + + "21660.34238425926\n" + + "21670.351828703704\n" + + "21680.386898148146\n" + + "...\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 254, "nRows"); // same as when all variables were explicitly loaded + + table.removeRows(0, 251); + results = table.dataToString(1000); + expectedStart = "JULD\n" + + "24190.451828703703\n" + + "24200.381412037037\n" + + "24210.44662037037\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + + // * test read JULD && PRES + table.readMultidimNc(fiName, StringArray.fromCSV("JULD,PRES"), null, null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + expectedStart = "JULD,PRES\n" + + "21660.34238425926,5.9\n" + // JULD is correctly JOINed + "21660.34238425926,10.0\n" + + "21660.34238425926,20.1\n" + + "...\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 17266, "nRows"); // same as when all variables were explicitly loaded + + table.removeRows(0, 17263); + results = table.dataToString(1000); + expectedStart = "JULD,PRES\n" + + "24210.44662037037,1850.0\n" + // JULD is correctly JOINed + "24210.44662037037,1899.9\n" + + "24210.44662037037,1950.0\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + + // * test read just static vars, in a different order + table.readMultidimNc(fiName, + StringArray.fromCSV("HANDBOOK_VERSION,FORMAT_VERSION,DATA_TYPE"), + null, null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + expectedStart = "HANDBOOK_VERSION,FORMAT_VERSION,DATA_TYPE\n" + + "1.2,3.1,Argo profile\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + + // * test read 0 dim variable -> empty table + table.readMultidimNc(fiName, + StringArray.fromCSV("HISTORY_INSTITUTION"), + null, null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // * test read non-existent dim -> just scalar vars + table.readMultidimNc(fiName, + null, StringArray.fromCSV("ZZTOP"), null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + expectedStart = "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE\n" + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + + // * test read non-existent Var -> empty table + table.readMultidimNc(fiName, + StringArray.fromCSV("ZZTOP"), null, null, + true, 0, true, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // done + /* */ + // Table.debugMode = oDebugMode; + } + + /** + * Test readASCII with csv file. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testReadAsciiCsvFile() throws Exception { + + // String2.log("\nTable.testReadAsciiCsvASCIIFile"); + String results, expected; + StringArray sa = new StringArray(); + String fileName = TableTests.class.getResource("/csvAscii.txt").getPath(); + String skipHeaderToRegex = "\\*\\*\\* END OF HEADER.*"; + String skipLinesRegex = "#.*"; + + Table table; + + // public void readASCII(String fullFileName, int columnNamesLine, int + // dataStartLine, + // String testColumns[], double testMin[], double testMax[], + // String loadColumns[], boolean simplify) throws Exception { + + // read as Strings + table = new Table(); + table.allowRaggedRightInReadASCII = true; + table.readASCII(fileName, File2.ISO_8859_1, + skipHeaderToRegex, skipLinesRegex, + 0, 1, "", null, null, null, null, false); + results = table.dataToString(); + expected = "aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat,aDouble\n" + + "\" b,d \",Ab,t,24,24000,24000000,240000000000,2.4,2.412345678987654\n" + + "needs,1comma:,,,,,,,\n" + + "fg,F,true,11,12001,1200000,12000000000,1.21,1e200\n" + + "h,H,1,12,12002,120000,1200000000,1.22,2e200\n" + + "i,I,TRUE,13,12003,12000,120000000,1.23,3e200\n" + + "j,J,f,14,12004,1200,12000000,1.24,4e200\n" + + "k,K,false,15,12005,120,1200000,1.25,5e200\n" + + "\"BAD LINE: UNCLOSED QUOTE,K,false,15,12005,120,1200000,1.25, 5.5e200\",,,,,,,,\n" + + "l,L,0,16,12006,12,120000,1.26,6e200\n" + + "m,M,FALSE,17,12007,121,12000,1.27,7e200\n" + + "n,N,8,18,12008,122,1200,1.28,8e200\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // test types + sa.clear(); + for (int col = 0; col < table.nColumns(); col++) + sa.add(table.getColumn(col).elementTypeString()); + results = sa.toString(); + expected = "String, String, String, String, String, String, String, String, String"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test simplify + table = new Table(); + table.allowRaggedRightInReadASCII = false; + table.readASCII(fileName, File2.ISO_8859_1, + skipHeaderToRegex, skipLinesRegex, + 0, 1, "", null, null, null, null, true); + results = table.dataToString(); + expected = // bad lines are removed + "aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat,aDouble\n" + + "\" b,d \",Ab,t,24,24000,24000000,240000000000,2.4,2.412345678987654\n" + + "fg,F,true,11,12001,1200000,12000000000,1.21,1.0E200\n" + + "h,H,1,12,12002,120000,1200000000,1.22,2.0E200\n" + + "i,I,TRUE,13,12003,12000,120000000,1.23,3.0E200\n" + + "j,J,f,14,12004,1200,12000000,1.24,4.0E200\n" + + "k,K,false,15,12005,120,1200000,1.25,5.0E200\n" + + "l,L,0,16,12006,12,120000,1.26,6.0E200\n" + + "m,M,FALSE,17,12007,121,12000,1.27,7.0E200\n" + + "n,N,8,18,12008,122,1200,1.28,8.0E200\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // test types + sa.clear(); + for (int col = 0; col < table.nColumns(); col++) + sa.add(table.getColumn(col).elementTypeString()); + results = sa.toString(); + expected = "String, String, String, byte, short, int, long, float, double"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read subset + table = new Table(); + table.allowRaggedRightInReadASCII = false; + table.readASCII(fileName, File2.ISO_8859_1, + skipHeaderToRegex, skipLinesRegex, + 0, 1, "", + new String[] { "aByte" }, new double[] { 14 }, new double[] { 16 }, + new String[] { "aDouble", "aString", "aByte" }, true); // load cols + results = table.dataToString(); + expected = // bad lines are removed + "aDouble,aString,aByte\n" + + "4.0E200,j,14\n" + + "5.0E200,k,15\n" + + "6.0E200,l,16\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + /** + * Test readASCII with ssv file. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testReadAsciiSsvFile() throws Exception { + + // String2.log("\nTable.testReadAsciiSsvASCIIFile"); + String results, expected; + StringArray sa = new StringArray(); + String fileName = TableTests.class.getResource("/ssvAscii.txt").getPath(); + Table table; + + // public void readASCII(String fullFileName, int columnNamesLine, int + // dataStartLine, + // String testColumns[], double testMin[], double testMax[], + // String loadColumns[], boolean simplify) throws Exception { + + // read as Strings + table = new Table(); + table.allowRaggedRightInReadASCII = true; + table.readASCII(fileName, File2.ISO_8859_1, + "", "", 0, 1, "", null, null, null, null, false); + results = table.dataToString(); + expected = "aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat,aDouble\n" + + "\" b d \",Ab,t,24,24000,24000000,240000000000,2.4,2.412345678987654\n" + + "needs1space,E,,,,,,,\n" + + "fg,F,true,11,12001,1200000,12000000000,1.21,1e200\n" + + "h,H,1,12,12002,120000,1200000000,1.22,2e200\n" + + "i,I,TRUE,13,12003,12000,120000000,1.23,3e200\n" + + "j,J,f,14,12004,1200,12000000,1.24,4e200\n" + + "k,K,false,15,12005,120,1200000,1.25,5e200\n" + + "l,L,0,16,12006,12,120000,1.26,6e200\n" + + "m,M,FALSE,17,12007,121,12000,1.27,7e200\n" + + "n,N,8,18,12008,122,1200,1.28,8e200\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // test types + sa.clear(); + for (int col = 0; col < table.nColumns(); col++) + sa.add(table.getColumn(col).elementTypeString()); + results = sa.toString(); + expected = "String, String, String, String, String, String, String, String, String"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test simplify + table = new Table(); + table.allowRaggedRightInReadASCII = true; + table.readASCII(fileName, File2.ISO_8859_1, + "", "", 0, 1, "", null, null, null, null, true); + results = table.dataToString(); + expected = "aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat,aDouble\n" + + "\" b d \",Ab,t,24,24000,24000000,240000000000,2.4,2.412345678987654\n" + + "needs1space,E,,,,,,,\n" + + "fg,F,true,11,12001,1200000,12000000000,1.21,1.0E200\n" + + "h,H,1,12,12002,120000,1200000000,1.22,2.0E200\n" + + "i,I,TRUE,13,12003,12000,120000000,1.23,3.0E200\n" + + "j,J,f,14,12004,1200,12000000,1.24,4.0E200\n" + + "k,K,false,15,12005,120,1200000,1.25,5.0E200\n" + + "l,L,0,16,12006,12,120000,1.26,6.0E200\n" + + "m,M,FALSE,17,12007,121,12000,1.27,7.0E200\n" + + "n,N,8,18,12008,122,1200,1.28,8.0E200\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // test types + sa.clear(); + for (int col = 0; col < table.nColumns(); col++) + sa.add(table.getColumn(col).elementTypeString()); + results = sa.toString(); + expected = "String, String, String, byte, short, int, long, float, double"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read subset + table = new Table(); + table.allowRaggedRightInReadASCII = true; + table.readASCII(fileName, File2.ISO_8859_1, + "", "", 0, 1, "", + new String[] { "aByte" }, new double[] { 14 }, new double[] { 16 }, + new String[] { "aDouble", "aString", "aByte" }, true); // load cols + results = table.dataToString(); + expected = "aDouble,aString,aByte\n" + + ",needs1space,\n" + + "4.0E200,j,14\n" + + "5.0E200,k,15\n" + + "6.0E200,l,16\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + /** + * Test readColumnarASCII. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testReadColumnarASCIIFile() throws Exception { + + // String2.log("\nTable.testReadColumnarASCIIFile"); + String results, expected; + StringArray sa = new StringArray(); + String fullFileName = TableTests.class.getResource("/columnarAsciiWithComments.txt").getPath(); + String skipHeaderToRegex = "END OF HEADER.*"; + String skipLinesRegex = "%.*"; + String colNames[] = { + "aDouble", "aString", "aChar", "aBoolean", "aByte", "aShort", "anInt", "aLong", "aFloat" }; + int start[] = { + 66, 0, 9, 15, 24, 30, 37, 45, 57 }; + int end[] = { + 86, 9, 15, 24, 30, 37, 45, 57, 66 }; + + // 012345678911234567892123456789312345678941234567895123456789612345678971234567898123456 + // aString aChar aBoolean aByte aShort anInt aLong aFloat aDouble + // abc a true 24 24000 240000002400000000002.4 2.412345678987654 + + // read as Strings + PAType colPAType[] = new PAType[9]; + Arrays.fill(colPAType, PAType.STRING); + Table table = new Table(); + table.readColumnarASCIIFile(fullFileName, "", + skipHeaderToRegex, skipLinesRegex, 3, colNames, start, end, colPAType); + results = table.dataToString(); + expected = "aDouble,aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat\n" + + "2.412345678987654,abcdef,Ab,t,24,24000,24000000,240000000000,2.4\n" + + ",short:,,,,,,,\n" + + "1e200,fg,F,true,11,12001,1200000,12000000000,1.21\n" + + "2e200,h,H,1,12,12002,120000,1200000000,1.22\n" + + "3e200,i,I,TRUE,13,12003,12000,120000000,1.23\n" + + "4e200,j,J,f,14,12004,1200,12000000,1.24\n" + + "5e200,k,K,false,15,12005,120,1200000,1.25\n" + + "6e200,l,L,0,16,12006,12,120000,1.26\n" + + "7e200,m,M,FALSE,17,12007,121,12000,1.27\n" + + "8e200,n,N,8,18,12008,122,1200,1.28\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // test types + sa.clear(); + for (int col = 0; col < table.nColumns(); col++) + sa.add(table.getColumn(col).elementTypeString()); + results = sa.toString(); + expected = "String, String, String, String, String, String, String, String, String"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // simplify + table.readColumnarASCIIFile(fullFileName, "", + skipHeaderToRegex, skipLinesRegex, 3, colNames, start, end, null); + results = table.dataToString(); + expected = "aDouble,aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat\n" + + "2.412345678987654,abcdef,Ab,t,24,24000,24000000,240000000000,2.4\n" + + ",short:,,,,,,,\n" + + "1.0E200,fg,F,true,11,12001,1200000,12000000000,1.21\n" + + "2.0E200,h,H,1,12,12002,120000,1200000000,1.22\n" + + "3.0E200,i,I,TRUE,13,12003,12000,120000000,1.23\n" + + "4.0E200,j,J,f,14,12004,1200,12000000,1.24\n" + + "5.0E200,k,K,false,15,12005,120,1200000,1.25\n" + + "6.0E200,l,L,0,16,12006,12,120000,1.26\n" + + "7.0E200,m,M,FALSE,17,12007,121,12000,1.27\n" + + "8.0E200,n,N,8,18,12008,122,1200,1.28\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // test types + sa.clear(); + for (int col = 0; col < table.nColumns(); col++) + sa.add(table.getColumn(col).elementTypeString()); + results = sa.toString(); + expected = "double, String, String, String, byte, short, int, long, float"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read as types + colPAType = new PAType[] { + PAType.DOUBLE, PAType.STRING, PAType.CHAR, PAType.BOOLEAN, PAType.BYTE, + PAType.SHORT, PAType.INT, PAType.LONG, PAType.FLOAT }; + table.readColumnarASCIIFile(fullFileName, "", + skipHeaderToRegex, skipLinesRegex, 3, colNames, start, end, colPAType); + results = table.dataToString(); + expected = "aDouble,aString,aChar,aBoolean,aByte,aShort,anInt,aLong,aFloat\n" + + "2.412345678987654,abcdef,A,1,24,24000,24000000,240000000000,2.4\n" + + ",short:,,,,,,,\n" + + "1.0E200,fg,F,1,11,12001,1200000,12000000000,1.21\n" + + "2.0E200,h,H,1,12,12002,120000,1200000000,1.22\n" + + "3.0E200,i,I,1,13,12003,12000,120000000,1.23\n" + + "4.0E200,j,J,0,14,12004,1200,12000000,1.24\n" + + "5.0E200,k,K,0,15,12005,120,1200000,1.25\n" + + "6.0E200,l,L,0,16,12006,12,120000,1.26\n" + + "7.0E200,m,M,0,17,12007,121,12000,1.27\n" + + "8.0E200,n,N,1,18,12008,122,1200,1.28\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // test types + sa.clear(); + for (int col = 0; col < table.nColumns(); col++) + sa.add(table.getColumn(col).elementTypeString()); + results = sa.toString(); + expected = "double, String, char, byte, byte, short, int, long, float"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + /** + * This tests readNccsv(), readNccsvMetadata(), + */ + @org.junit.jupiter.api.Test + @TagMissingFile + void testNccsv() throws Exception { + // String2.log("\n**** Table.testNccsv()\n"); + String dir = TableTests.class.getResource("/nccsv/").getPath(); + + // read/write scalar + String fileName = dir + "testScalar_1.1.csv"; + Table table = new Table(); + table.readNccsv(fileName); + for (int c = 0; c < table.nColumns(); c++) { + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) == null, "col=" + c); + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE) == null, "col=" + c); + } + String results = table.saveAsNccsv(); + String expected1 = "*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + + "*GLOBAL*,cdm_trajectory_variables,ship\n" + + "*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + + "*GLOBAL*,creator_name,Bob Simons\n" + + "*GLOBAL*,creator_type,person\n" + + "*GLOBAL*,creator_url,https://www.pfeg.noaa.gov\n" + + "*GLOBAL*,featureType,trajectory\n" + + "*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html\n" + + "*GLOBAL*,institution,\"NOAA NMFS SWFSC ERD, NOAA PMEL\"\n" + + "*GLOBAL*,keywords,\"NOAA, sea, ship, sst, surface, temperature, trajectory\"\n" + + "*GLOBAL*,license,\"\"\"NCCSV Demonstration\"\" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ .\"\n" + + + "*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55\n" + + "*GLOBAL*,subsetVariables,ship\n" + + "*GLOBAL*,summary,This is a paragraph or two describing the dataset.\n" + + "*GLOBAL*,title,NCCSV Demonstration\n" + + "ship,*SCALAR*,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + + "ship,cf_role,trajectory_id\n" + + "time,*DATA_TYPE*,String\n" + + "time,standard_name,time\n" + + "time,units,yyyy-MM-dd'T'HH:mm:ssZ\n" + + "lat,*DATA_TYPE*,double\n" + + "lat,units,degrees_north\n" + + "lon,*DATA_TYPE*,double\n" + + "lon,units,degrees_east\n" + + "status,*DATA_TYPE*,char\n" + + "status,comment,\"From http://some.url.gov/someProjectDocument , Table C\"\n" + + "testByte,*DATA_TYPE*,byte\n" + + "testByte,units,\"1\"\n" + + "testUByte,*DATA_TYPE*,ubyte\n" + + "testUByte,units,\"1\"\n" + + "testLong,*DATA_TYPE*,long\n" + + "testLong,units,\"1\"\n" + + "testULong,*DATA_TYPE*,ulong\n" + + "testULong,units,\"1\"\n" + + "sst,*DATA_TYPE*,float\n" + + "sst,actual_range,0.17f,23.58f\n" + + "sst,missing_value,99.0f\n" + + "sst,standard_name,sea_surface_temperature\n" + + "sst,testBytes,-128b,0b,127b\n" + + "sst,testChars,\"','\",\"'\"\"'\",\"'\u20ac'\"\n" + + "sst,testDoubles,-1.7976931348623157E308d,0.0d,1.7976931348623157E308d\n" + + "sst,testFloats,-3.4028235E38f,0.0f,3.4028235E38f\n" + + "sst,testInts,-2147483648i,0i,2147483647i\n" + + "sst,testLongs,-9223372036854775808L,-9007199254740992L,9007199254740992L,9223372036854775806L,9223372036854775807L\n" + + + "sst,testShorts,-32768s,0s,32767s\n" + + "sst,testStrings,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + + "sst,testUBytes,0ub,127ub,255ub\n" + + "sst,testUInts,0ui,2147483647ui,4294967295ui\n" + + "sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL\n" + + "sst,testUShorts,0us,32767us,65535us\n" + + "sst,units,degree_C\n" + + "\n" + + "*END_METADATA*\n" + + "time,lat,lon,status,testByte,testUByte,testLong,testULong,sst\n" + + "2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128,0,-9223372036854775808L,0uL,10.9\n" + + "2017-03-23T01:45:00Z,28.0003,-130.3472,\u20ac,0,127,-9007199254740992L,9223372036854775807uL,10.0\n" + + "2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,126,254,9223372036854775806L,18446744073709551614uL,99.0\n" + + "2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",,,,,\n" + + "2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,,,,,\n" + + "2017-03-23T23:45:00Z,28.0002,-132.1591,?,,,,,\n" + + "*END_DATA*\n"; + Test.ensureEqual(results, expected1, "results=\n" + results); + + results = table.saveAsNccsv(false, true, 0, Integer.MAX_VALUE); // don't catch scalar + String expected2 = "*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + + "*GLOBAL*,cdm_trajectory_variables,ship\n" + + "*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + + "*GLOBAL*,creator_name,Bob Simons\n" + + "*GLOBAL*,creator_type,person\n" + + "*GLOBAL*,creator_url,https://www.pfeg.noaa.gov\n" + + "*GLOBAL*,featureType,trajectory\n" + + "*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html\n" + + "*GLOBAL*,institution,\"NOAA NMFS SWFSC ERD, NOAA PMEL\"\n" + + "*GLOBAL*,keywords,\"NOAA, sea, ship, sst, surface, temperature, trajectory\"\n" + + "*GLOBAL*,license,\"\"\"NCCSV Demonstration\"\" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ .\"\n" + + + "*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55\n" + + "*GLOBAL*,subsetVariables,ship\n" + + "*GLOBAL*,summary,This is a paragraph or two describing the dataset.\n" + + "*GLOBAL*,title,NCCSV Demonstration\n" + + "ship,*DATA_TYPE*,String\n" + + "ship,cf_role,trajectory_id\n" + + "time,*DATA_TYPE*,String\n" + + "time,standard_name,time\n" + + "time,units,yyyy-MM-dd'T'HH:mm:ssZ\n" + + "lat,*DATA_TYPE*,double\n" + + "lat,units,degrees_north\n" + + "lon,*DATA_TYPE*,double\n" + + "lon,units,degrees_east\n" + + "status,*DATA_TYPE*,char\n" + + "status,comment,\"From http://some.url.gov/someProjectDocument , Table C\"\n" + + "testByte,*DATA_TYPE*,byte\n" + + "testByte,units,\"1\"\n" + + "testUByte,*DATA_TYPE*,ubyte\n" + + "testUByte,units,\"1\"\n" + + "testLong,*DATA_TYPE*,long\n" + + "testLong,units,\"1\"\n" + + "testULong,*DATA_TYPE*,ulong\n" + + "testULong,units,\"1\"\n" + + "sst,*DATA_TYPE*,float\n" + + "sst,actual_range,0.17f,23.58f\n" + + "sst,missing_value,99.0f\n" + + "sst,standard_name,sea_surface_temperature\n" + + "sst,testBytes,-128b,0b,127b\n" + + "sst,testChars,\"','\",\"'\"\"'\",\"'\u20ac'\"\n" + + "sst,testDoubles,-1.7976931348623157E308d,0.0d,1.7976931348623157E308d\n" + + "sst,testFloats,-3.4028235E38f,0.0f,3.4028235E38f\n" + + "sst,testInts,-2147483648i,0i,2147483647i\n" + + "sst,testLongs,-9223372036854775808L,-9007199254740992L,9007199254740992L,9223372036854775806L,9223372036854775807L\n" + + + "sst,testShorts,-32768s,0s,32767s\n" + + "sst,testStrings,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + + "sst,testUBytes,0ub,127ub,255ub\n" + + "sst,testUInts,0ui,2147483647ui,4294967295ui\n" + + "sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL\n" + + "sst,testUShorts,0us,32767us,65535us\n" + + "sst,units,degree_C\n" + + "\n" + + "*END_METADATA*\n" + + "ship,time,lat,lon,status,testByte,testUByte,testLong,testULong,sst\n" + + "\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128,0,-9223372036854775808L,0uL,10.9\n" + + + "\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T01:45:00Z,28.0003,-130.3472,\u20ac,0,127,-9007199254740992L,9223372036854775807uL,10.0\n" + + + "\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,126,254,9223372036854775806L,18446744073709551614uL,99.0\n" + + + "\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",,,,,\n" + + "\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,,,,,\n" + + "\" a\\t~\u00fc,\\n'z\"\"\u20ac\",2017-03-23T23:45:00Z,28.0002,-132.1591,?,,,,,\n" + + "*END_DATA*\n"; + Test.ensureEqual(results, expected2, "results=\n" + results); + + // non scalar + fileName = dir + "sample_1.1.csv"; + table.readNccsv(fileName); + for (int c = 0; c < table.nColumns(); c++) { + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) == null, "col=" + c); + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE) == null, "col=" + c); + } + // String2.log(table.toString()); + Attributes atts = table.columnAttributes("sst"); + PrimitiveArray pa = atts.get("testChars"); + // String2.log(">> sample_1.1.csv testChars isCharArray?" + (pa instanceof CharArray) + " isStringArray?" + // + (pa instanceof StringArray)); + results = table.saveAsNccsv(false, true, 0, Integer.MAX_VALUE); // don't catch scalars + expected1 = "*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + + "*GLOBAL*,cdm_trajectory_variables,ship\n" + + "*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + + "*GLOBAL*,creator_name,Bob Simons\n" + + "*GLOBAL*,creator_type,person\n" + + "*GLOBAL*,creator_url,https://www.pfeg.noaa.gov\n" + + "*GLOBAL*,featureType,trajectory\n" + + "*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html\n" + + "*GLOBAL*,institution,\"NOAA NMFS SWFSC ERD, NOAA PMEL\"\n" + + "*GLOBAL*,keywords,\"NOAA, sea, ship, sst, surface, temperature, trajectory\"\n" + + "*GLOBAL*,license,\"\"\"NCCSV Demonstration\"\" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ .\"\n" + + + "*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55\n" + + "*GLOBAL*,subsetVariables,ship\n" + + "*GLOBAL*,summary,This is a paragraph or two describing the dataset.\n" + + "*GLOBAL*,title,NCCSV Demonstration\n" + + "ship,*DATA_TYPE*,String\n" + + "ship,cf_role,trajectory_id\n" + + "time,*DATA_TYPE*,String\n" + + "time,standard_name,time\n" + + "time,units,yyyy-MM-dd'T'HH:mm:ssZ\n" + + "lat,*DATA_TYPE*,double\n" + + "lat,units,degrees_north\n" + + "lon,*DATA_TYPE*,double\n" + + "lon,units,degrees_east\n" + + "status,*DATA_TYPE*,char\n" + + "status,comment,\"From http://some.url.gov/someProjectDocument , Table C\"\n" + + "testByte,*DATA_TYPE*,byte\n" + + "testByte,units,\"1\"\n" + + "testUByte,*DATA_TYPE*,ubyte\n" + + "testUByte,units,\"1\"\n" + + "testLong,*DATA_TYPE*,long\n" + + "testLong,units,\"1\"\n" + + "testULong,*DATA_TYPE*,ulong\n" + + "testULong,units,\"1\"\n" + + "sst,*DATA_TYPE*,float\n" + + "sst,actual_range,0.17f,23.58f\n" + + "sst,missing_value,99.0f\n" + + "sst,standard_name,sea_surface_temperature\n" + + "sst,testBytes,-128b,0b,127b\n" + + "sst,testChars,\"','\",\"'\"\"'\",\"'\u20ac'\"\n" + + "sst,testDoubles,-1.7976931348623157E308d,0.0d,1.7976931348623157E308d\n" + + "sst,testFloats,-3.4028235E38f,0.0f,3.4028235E38f\n" + + "sst,testInts,-2147483648i,0i,2147483647i\n" + + "sst,testLongs,-9223372036854775808L,0L,9223372036854775807L\n" + + "sst,testShorts,-32768s,0s,32767s\n" + + "sst,testStrings,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + + "sst,testUBytes,0ub,127ub,255ub\n" + + "sst,testUInts,0ui,2147483647ui,4294967295ui\n" + + "sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL\n" + + "sst,testUShorts,0us,32767us,65535us\n" + + "sst,units,degree_C\n" + + "\n" + + "*END_METADATA*\n" + + "ship,time,lat,lon,status,testByte,testUByte,testLong,testULong,sst\n" + + "Bell M. Shimada,2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128,0,-9223372036854775808L,0uL,10.9\n" + + "Bell M. Shimada,2017-03-23T01:45:00Z,28.0003,-130.3472,\u20ac,0,127,-9007199254740992L,9223372036854775807uL,10.0\n" + + + "Bell M. Shimada,2017-03-23T02:45:00Z,28.0001,-130.4305,\\t,126,254,9223372036854775806L,18446744073709551614uL,99.0\n" + + + "Bell M. Shimada,2017-03-23T12:45:00Z,27.9998,-131.5578,\"\"\"\",,,,,\n" + + "Bell M. Shimada,2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,,,,,\n" + + "Bell M. Shimada,2017-03-23T23:45:00Z,28.0002,-132.1591,?,,,,,\n" + + "*END_DATA*\n"; + Test.ensureEqual(results, expected1, "results=\n" + results); + + // non scalar + fileName = dir + "sample_1.2.csv"; + table.readNccsv(fileName); + for (int c = 0; c < table.nColumns(); c++) { + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) == null, "col=" + c); + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE) == null, "col=" + c); + } + // String2.log(table.toString()); + atts = table.columnAttributes("sst"); + pa = atts.get("testChars"); + String2.log(">> sample_1.2.csv testChars isCharArray?" + (pa instanceof CharArray) + " isStringArray?" + + (pa instanceof StringArray)); + results = table.saveAsNccsv(false, true, 0, Integer.MAX_VALUE); // don't catch scalars + // we expect the same results + Test.ensureEqual(results, expected1, "results=\n" + results); + + // just metadata + fileName = dir + "sampleMetadata_1.1.csv"; + table = new Table(); + table.readNccsv(fileName, false); // readData? + for (int c = 0; c < table.nColumns(); c++) { + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) == null, "col=" + c); + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE) == null, "col=" + c); + } + results = table.saveAsNccsv(true, true, 0, 0); // catch scalar, writeMetadata, don't write data + String expected3 = "*GLOBAL*,Conventions,\"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.2\"\n" + + "*GLOBAL*,cdm_trajectory_variables,ship\n" + + "*GLOBAL*,creator_email,bob.simons@noaa.gov\n" + + "*GLOBAL*,creator_name,Bob Simons\n" + + "*GLOBAL*,creator_type,person\n" + + "*GLOBAL*,creator_url,https://www.pfeg.noaa.gov\n" + + "*GLOBAL*,featureType,trajectory\n" + + "*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html\n" + + "*GLOBAL*,institution,\"NOAA NMFS SWFSC ERD, NOAA PMEL\"\n" + + "*GLOBAL*,keywords,\"NOAA, sea, ship, sst, surface, temperature, trajectory\"\n" + + "*GLOBAL*,license,\"\"\"NCCSV Demonstration\"\" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ .\"\n" + + + "*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55\n" + + "*GLOBAL*,subsetVariables,ship\n" + + "*GLOBAL*,summary,This is a paragraph or two describing the dataset.\n" + + "*GLOBAL*,title,NCCSV Demonstration\n" + + "ship,*SCALAR*,Bell M. Shimada\n" + + "ship,cf_role,trajectory_id\n" + + "time,*DATA_TYPE*,String\n" + + "time,standard_name,time\n" + + "time,units,yyyy-MM-dd'T'HH:mm:ssZ\n" + + "lat,*DATA_TYPE*,double\n" + + "lat,units,degrees_north\n" + + "lon,*DATA_TYPE*,double\n" + + "lon,units,degrees_east\n" + + "status,*DATA_TYPE*,char\n" + + "status,comment,\"From http://some.url.gov/someProjectDocument , Table C\"\n" + + "testLong,*DATA_TYPE*,long\n" + + "testLong,units,\"1\"\n" + + "sst,*DATA_TYPE*,float\n" + + "sst,actual_range,0.17f,23.58f\n" + + "sst,missing_value,99.0f\n" + + "sst,standard_name,sea_surface_temperature\n" + + "sst,testBytes,-128b,0b,127b\n" + + "sst,testChars,\"','\",\"'\"\"'\",\"'\u20ac'\"\n" + + "sst,testDoubles,-1.7976931348623157E308d,0.0d,1.7976931348623157E308d\n" + + "sst,testFloats,-3.4028235E38f,0.0f,3.4028235E38f\n" + + "sst,testInts,-2147483648i,0i,2147483647i\n" + + "sst,testLongs,-9223372036854775808L,0L,9223372036854775807L\n" + + "sst,testShorts,-32768s,0s,32767s\n" + + "sst,testStrings,\" a\\t~\u00fc,\\n'z\"\"\u20ac\"\n" + + "sst,testUBytes,0ub,127ub,255ub\n" + + "sst,testUInts,0ui,2147483647ui,4294967295ui\n" + + "sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL\n" + + "sst,testUShorts,0us,32767us,65535us\n" + + "sst,units,degree_C\n" + + "\n" + + "*END_METADATA*\n"; + Test.ensureEqual(results, expected3, "results=\n" + results); + + // just metadata + fileName = dir + "sampleMetadata_1.2.csv"; + table = new Table(); + table.readNccsv(fileName, false); // readData? + for (int c = 0; c < table.nColumns(); c++) { + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_SCALAR) == null, "col=" + c); + Test.ensureTrue(table.columnAttributes(c).get(String2.NCCSV_DATATYPE) == null, "col=" + c); + } + results = table.saveAsNccsv(true, true, 0, 0); // catch scalar, writeMetadata, don't write data + Test.ensureEqual(results, expected3, "results=\n" + results); + + } + + /** + * This tests saveAsMatlab(). + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testSaveAsMatlab() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + // see gov.noaa.pfel.coastwatch.griddata.Matlab class for summary of Matlab + // commands + + // String2.log("\n***** Table.testSaveAsMatlab"); + Table table = new Table(); + table.addColumn("ints", new IntArray(new int[] { 1, 2, 3 })); + table.addColumn("floats", new FloatArray(new float[] { 1.1f, 2.2f, 3.3f })); + table.addColumn("Strings", new StringArray(new String[] { "a", "bb", "ccc" })); + table.addColumn("doubles", new DoubleArray(new double[] { 1.111, 2.222, 3.333 })); + String dir = TEMP_DIR.toAbsolutePath().toString() + "/"; + File2.delete(dir + "temp.mat"); + table.saveAsMatlab(dir + "temp.mat", "sst"); // names of length 3,4,5 were a challenge + String mhd = File2.hexDump(dir + "temp.mat", 1000); + // String2.log(mhd); + // String2.log("\nsst.mat=\n" + File2.hexDump(dir + "sst.mat", 1000)); + Test.ensureEqual( + mhd.substring(0, 71 * 4) + mhd.substring(71 * 7), // remove the creation dateTime + "4d 41 54 4c 41 42 20 35 2e 30 20 4d 41 54 2d 66 MATLAB 5.0 MAT-f |\n" + + "69 6c 65 2c 20 43 72 65 61 74 65 64 20 62 79 3a ile, Created by: |\n" + + "20 67 6f 76 2e 6e 6f 61 61 2e 70 66 65 6c 2e 63 gov.noaa.pfel.c |\n" + + "6f 61 73 74 77 61 74 63 68 2e 4d 61 74 6c 61 62 oastwatch.Matlab |\n" + + // "2c 20 43 72 65 61 74 65 64 20 6f 6e 3a 20 4d 6f , Created on: Mo |\n" + + // "6e 20 46 65 62 20 31 31 20 30 39 3a 31 31 3a 30 n Feb 11 09:11:0 |\n" + + // "30 20 32 30 30 38 20 20 20 20 20 20 20 20 20 20 0 2008 |\n" + + "20 20 20 20 00 00 00 00 00 00 00 00 01 00 4d 49 MI |\n" + + "00 00 00 0e 00 00 01 e8 00 00 00 06 00 00 00 08 |\n" + + "00 00 00 02 00 00 00 00 00 00 00 05 00 00 00 08 |\n" + + "00 00 00 01 00 00 00 01 00 03 00 01 73 73 74 00 sst |\n" + + "00 04 00 05 00 00 00 20 00 00 00 01 00 00 00 80 |\n" + + "69 6e 74 73 00 00 00 00 00 00 00 00 00 00 00 00 ints |\n" + + "00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |\n" + + "66 6c 6f 61 74 73 00 00 00 00 00 00 00 00 00 00 floats |\n" + + "00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |\n" + + "53 74 72 69 6e 67 73 00 00 00 00 00 00 00 00 00 Strings |\n" + + "00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |\n" + + "64 6f 75 62 6c 65 73 00 00 00 00 00 00 00 00 00 doubles |\n" + + "00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 |\n" + + "00 00 00 0e 00 00 00 40 00 00 00 06 00 00 00 08 @ |\n" + + "00 00 00 0c 00 00 00 00 00 00 00 05 00 00 00 08 |\n" + + "00 00 00 03 00 00 00 01 00 00 00 01 00 00 00 00 |\n" + + "00 00 00 05 00 00 00 0c 00 00 00 01 00 00 00 02 |\n" + + "00 00 00 03 00 00 00 00 00 00 00 0e 00 00 00 40 @ |\n" + + "00 00 00 06 00 00 00 08 00 00 00 07 00 00 00 00 |\n" + + "00 00 00 05 00 00 00 08 00 00 00 03 00 00 00 01 |\n" + + "00 00 00 01 00 00 00 00 00 00 00 07 00 00 00 0c |\n" + + "3f 8c cc cd 40 0c cc cd 40 53 33 33 00 00 00 00 ? @ @S33 |\n" + + "00 00 00 0e 00 00 00 48 00 00 00 06 00 00 00 08 H |\n" + + "00 00 00 04 00 00 00 00 00 00 00 05 00 00 00 08 |\n" + + "00 00 00 03 00 00 00 03 00 00 00 01 00 00 00 00 |\n" + + "00 00 00 04 00 00 00 12 00 61 00 62 00 63 00 20 a b c |\n" + + "00 62 00 63 00 20 00 20 00 63 00 00 00 00 00 00 b c c |\n" + + "00 00 00 0e 00 00 00 48 00 00 00 06 00 00 00 08 H |\n" + + "00 00 00 06 00 00 00 00 00 00 00 05 00 00 00 08 |\n" + + "00 00 00 03 00 00 00 01 00 00 00 01 00 00 00 00 |\n" + + "00 00 00 09 00 00 00 18 3f f1 c6 a7 ef 9d b2 2d ? - |\n" + + "40 01 c6 a7 ef 9d b2 2d 40 0a a9 fb e7 6c 8b 44 @ -@ l D |\n", + "mhd=" + mhd); + // File2.delete(dir + "temp.mat"); + } + + /** + * Test readAwsXmlFile. Automatic Weather Station + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void testReadAwsXmlFile() throws Exception { + // String2.log("\nTable.testReadAwsXmlFile"); + Table table = new Table(); + table.readAwsXmlFile(TableTests.class.getResource("/aws/xml/SNFLS-2012-11-03T20_30_01Z.xml").getPath()); + String results = table.toString(); + String expected = "{\n" + + "dimensions:\n" + + "\trow = 1 ;\n" + + "\tob-date_strlen = 11 ;\n" + + "\tstation-id_strlen = 5 ;\n" + + "\tstation_strlen = 13 ;\n" + + "\tcity-state-zip_strlen = 5 ;\n" + + "\tcity-state_strlen = 17 ;\n" + + "\tsite-url_strlen = 0 ;\n" + + "\taux-temp_strlen = 2 ;\n" + + "\taux-temp-rate_strlen = 1 ;\n" + + "\tdew-point_strlen = 2 ;\n" + + "\televation_strlen = 1 ;\n" + + "\tfeels-like_strlen = 2 ;\n" + + "\tgust-time_strlen = 11 ;\n" + + "\tgust-direction_strlen = 1 ;\n" + + "\tgust-speed_strlen = 1 ;\n" + + "\thumidity_strlen = 2 ;\n" + + "\thumidity-high_strlen = 3 ;\n" + + "\thumidity-low_strlen = 2 ;\n" + + "\thumidity-rate_strlen = 2 ;\n" + + "\tindoor-temp_strlen = 2 ;\n" + + "\tindoor-temp-rate_strlen = 4 ;\n" + + "\tlight_strlen = 4 ;\n" + + "\tlight-rate_strlen = 4 ;\n" + + "\tmoon-phase-moon-phase-img_strlen = 12 ;\n" + + "\tmoon-phase_strlen = 2 ;\n" + + "\tpressure_strlen = 4 ;\n" + + "\tpressure-high_strlen = 5 ;\n" + + "\tpressure-low_strlen = 5 ;\n" + + "\tpressure-rate_strlen = 5 ;\n" + + "\train-month_strlen = 4 ;\n" + + "\train-rate_strlen = 1 ;\n" + + "\train-rate-max_strlen = 1 ;\n" + + "\train-today_strlen = 1 ;\n" + + "\train-year_strlen = 4 ;\n" + + "\ttemp_strlen = 4 ;\n" + + "\ttemp-high_strlen = 2 ;\n" + + "\ttemp-low_strlen = 2 ;\n" + + "\ttemp-rate_strlen = 3 ;\n" + + "\tsunrise_strlen = 13 ;\n" + + "\tsunset_strlen = 13 ;\n" + + "\twet-bulb_strlen = 6 ;\n" + + "\twind-speed_strlen = 1 ;\n" + + "\twind-speed-avg_strlen = 1 ;\n" + + "\twind-direction_strlen = 3 ;\n" + + "\twind-direction-avg_strlen = 1 ;\n" + + "variables:\n" + + "\tchar ob-date(row, ob-date_strlen) ;\n" + + "\t\tob-date:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + + "\tchar station-id(row, station-id_strlen) ;\n" + + "\tchar station(row, station_strlen) ;\n" + + "\tchar city-state-zip(row, city-state-zip_strlen) ;\n" + + "\tchar city-state(row, city-state_strlen) ;\n" + + "\tchar site-url(row, site-url_strlen) ;\n" + + "\tchar aux-temp(row, aux-temp_strlen) ;\n" + + "\t\taux-temp:units = \"degree_F\" ;\n" + + "\tchar aux-temp-rate(row, aux-temp-rate_strlen) ;\n" + + "\t\taux-temp-rate:units = \"degree_F\" ;\n" + + "\tchar dew-point(row, dew-point_strlen) ;\n" + + "\t\tdew-point:units = \"degree_F\" ;\n" + + "\tchar elevation(row, elevation_strlen) ;\n" + + "\t\televation:units = \"ft\" ;\n" + + "\tchar feels-like(row, feels-like_strlen) ;\n" + + "\t\tfeels-like:units = \"degree_F\" ;\n" + + "\tchar gust-time(row, gust-time_strlen) ;\n" + + "\t\tgust-time:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + + "\tchar gust-direction(row, gust-direction_strlen) ;\n" + + "\tchar gust-speed(row, gust-speed_strlen) ;\n" + + "\t\tgust-speed:units = \"mph\" ;\n" + + "\tchar humidity(row, humidity_strlen) ;\n" + + "\t\thumidity:units = \"%\" ;\n" + + "\tchar humidity-high(row, humidity-high_strlen) ;\n" + + "\t\thumidity-high:units = \"%\" ;\n" + + "\tchar humidity-low(row, humidity-low_strlen) ;\n" + + "\t\thumidity-low:units = \"%\" ;\n" + + "\tchar humidity-rate(row, humidity-rate_strlen) ;\n" + + "\tchar indoor-temp(row, indoor-temp_strlen) ;\n" + + "\t\tindoor-temp:units = \"degree_F\" ;\n" + + "\tchar indoor-temp-rate(row, indoor-temp-rate_strlen) ;\n" + + "\t\tindoor-temp-rate:units = \"degree_F\" ;\n" + + "\tchar light(row, light_strlen) ;\n" + + "\tchar light-rate(row, light-rate_strlen) ;\n" + + "\tchar moon-phase-moon-phase-img(row, moon-phase-moon-phase-img_strlen) ;\n" + + "\tchar moon-phase(row, moon-phase_strlen) ;\n" + + "\tchar pressure(row, pressure_strlen) ;\n" + + "\t\tpressure:units = \"inch_Hg\" ;\n" + + "\tchar pressure-high(row, pressure-high_strlen) ;\n" + + "\t\tpressure-high:units = \"inch_Hg\" ;\n" + + "\tchar pressure-low(row, pressure-low_strlen) ;\n" + + "\t\tpressure-low:units = \"inch_Hg\" ;\n" + + "\tchar pressure-rate(row, pressure-rate_strlen) ;\n" + + "\t\tpressure-rate:units = \"inch_Hg/h\" ;\n" + + "\tchar rain-month(row, rain-month_strlen) ;\n" + + "\t\train-month:units = \"inches\" ;\n" + + "\tchar rain-rate(row, rain-rate_strlen) ;\n" + + "\t\train-rate:units = \"inches/h\" ;\n" + + "\tchar rain-rate-max(row, rain-rate-max_strlen) ;\n" + + "\t\train-rate-max:units = \"inches/h\" ;\n" + + "\tchar rain-today(row, rain-today_strlen) ;\n" + + "\t\train-today:units = \"inches\" ;\n" + + "\tchar rain-year(row, rain-year_strlen) ;\n" + + "\t\train-year:units = \"inches\" ;\n" + + "\tchar temp(row, temp_strlen) ;\n" + + "\t\ttemp:units = \"degree_F\" ;\n" + + "\tchar temp-high(row, temp-high_strlen) ;\n" + + "\t\ttemp-high:units = \"degree_F\" ;\n" + + "\tchar temp-low(row, temp-low_strlen) ;\n" + + "\t\ttemp-low:units = \"degree_F\" ;\n" + + "\tchar temp-rate(row, temp-rate_strlen) ;\n" + + "\t\ttemp-rate:units = \"degree_F\" ;\n" + + "\tchar sunrise(row, sunrise_strlen) ;\n" + + "\t\tsunrise:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + + "\tchar sunset(row, sunset_strlen) ;\n" + + "\t\tsunset:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + + "\tchar wet-bulb(row, wet-bulb_strlen) ;\n" + + "\t\twet-bulb:units = \"degree_F\" ;\n" + + "\tchar wind-speed(row, wind-speed_strlen) ;\n" + + "\t\twind-speed:units = \"mph\" ;\n" + + "\tchar wind-speed-avg(row, wind-speed-avg_strlen) ;\n" + + "\t\twind-speed-avg:units = \"mph\" ;\n" + + "\tchar wind-direction(row, wind-direction_strlen) ;\n" + + "\tchar wind-direction-avg(row, wind-direction-avg_strlen) ;\n" + + "\n" + + "// global attributes:\n" + + "}\n" + + "ob-date,station-id,station,city-state-zip,city-state,site-url,aux-temp,aux-temp-rate,dew-point,elevation,feels-like,gust-time,gust-direction,gust-speed,humidity,humidity-high,humidity-low,humidity-rate,indoor-temp,indoor-temp-rate,light,light-rate,moon-phase-moon-phase-img,moon-phase,pressure,pressure-high,pressure-low,pressure-rate,rain-month,rain-rate,rain-rate-max,rain-today,rain-year,temp,temp-high,temp-low,temp-rate,sunrise,sunset,wet-bulb,wind-speed,wind-speed-avg,wind-direction,wind-direction-avg\n" + + + "1.3519746E9,SNFLS,Exploratorium,94123,\"San Francisco, CA\",,32,0,54,0,67,1.3519746E9,E,8,63,100,63,-6,90,+4.6,67.9,-0.3,mphase16.gif,82,30.1,30.14,30.06,-0.01,0.21,0,0,0,1.76,66.9,67,52,3.8,1.351953497E9,1.351991286E9,59.162,0,2,ENE,E\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + Test.ensureEqual(Calendar2.epochSecondsToIsoStringTZ(1.3519746E9), "2012-11-03T20:30:00Z", ""); + Test.ensureEqual(Calendar2.epochSecondsToIsoStringTZ(1.3519746E9), "2012-11-03T20:30:00Z", ""); + Test.ensureEqual(Calendar2.epochSecondsToIsoStringTZ(1.351953497E9), "2012-11-03T14:38:17Z", ""); + Test.ensureEqual(Calendar2.epochSecondsToIsoStringTZ(1.351991286E9), "2012-11-04T01:08:06Z", ""); + } + + /** This tests readNDNC. */ + @org.junit.jupiter.api.Test + @TagMissingFile + @TagLargeFile + void testReadNDNc() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + // String2.log("\n*** Table.testReadNDNc"); + Table table = new Table(); + String results, expected; + + // test no vars specified, 4D, only 2nd dim has >1 value, getMetadata + String fiName = TableTests.class.getResource("/points/erdCalcofiSubsurface/1950/subsurface_19500106_69_144.nc") + .getPath(); + table.readNDNc(fiName, null, 0, // standardizeWhat=0 + null, 0, 0); + results = table.toString(); + expected = "{\n" + + "dimensions:\n" + + "\trow = 16 ;\n" + + "variables:\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:units = \"seconds since 1948-1-1\" ;\n" + + "\tfloat depth(row) ;\n" + + "\t\tdepth:long_name = \"depth index\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:_FillValue = -999.0f ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:missing_value = -999.0f ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:_FillValue = -999.0f ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:missing_value = -999.0f ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tint stationyear(row) ;\n" + + "\t\tstationyear:_FillValue = -9999 ;\n" + + "\t\tstationyear:long_name = \"Station Year\" ;\n" + + "\t\tstationyear:missing_value = -9999 ;\n" + + "\t\tstationyear:units = \"years\" ;\n" + + "\tint stationmonth(row) ;\n" + + "\t\tstationmonth:_FillValue = -9999 ;\n" + + "\t\tstationmonth:long_name = \"Station Month\" ;\n" + + "\t\tstationmonth:missing_value = -9999 ;\n" + + "\t\tstationmonth:units = \"months\" ;\n" + + "\tint stationday(row) ;\n" + + "\t\tstationday:_FillValue = -9999 ;\n" + + "\t\tstationday:long_name = \"Station Day\" ;\n" + + "\t\tstationday:missing_value = -9999 ;\n" + + "\t\tstationday:units = \"days\" ;\n" + + "\tint stime(row) ;\n" + + "\t\tstime:_FillValue = -9999 ;\n" + + "\t\tstime:long_name = \"Cast Time (GMT)\" ;\n" + + "\t\tstime:missing_value = -9999 ;\n" + + "\t\tstime:units = \"GMT\" ;\n" + + "\tfloat stationline(row) ;\n" + + "\t\tstationline:_FillValue = -999.0f ;\n" + + "\t\tstationline:long_name = \"CALCOFI Line Number\" ;\n" + + "\t\tstationline:missing_value = -999.0f ;\n" + + "\t\tstationline:units = \"number\" ;\n" + + "\tfloat stationnum(row) ;\n" + + "\t\tstationnum:_FillValue = -999.0f ;\n" + + "\t\tstationnum:long_name = \"CALCOFI Station Number\" ;\n" + + "\t\tstationnum:missing_value = -999.0f ;\n" + + "\t\tstationnum:units = \"number\" ;\n" + + "\tfloat temperature(row) ;\n" + + "\t\ttemperature:_FillValue = -999.0f ;\n" + + "\t\ttemperature:has_data = 1 ;\n" + + "\t\ttemperature:long_name = \"Temperature\" ;\n" + + "\t\ttemperature:missing_value = -999.0f ;\n" + + "\t\ttemperature:units = \"degC\" ;\n" + + "\tfloat salinity(row) ;\n" + + "\t\tsalinity:_FillValue = -999.0f ;\n" + + "\t\tsalinity:has_data = 1 ;\n" + + "\t\tsalinity:long_name = \"Salinity\" ;\n" + + "\t\tsalinity:missing_value = -999.0f ;\n" + + "\t\tsalinity:units = \"PSU\" ;\n" + + "\tfloat pressure(row) ;\n" + + "\t\tpressure:_FillValue = -999.0f ;\n" + + "\t\tpressure:has_data = 0 ;\n" + + "\t\tpressure:long_name = \"Pressure\" ;\n" + + "\t\tpressure:missing_value = -999.0f ;\n" + + "\t\tpressure:units = \"decibars\" ;\n" + + "\tfloat oxygen(row) ;\n" + + "\t\toxygen:_FillValue = -999.0f ;\n" + + "\t\toxygen:has_data = 1 ;\n" + + "\t\toxygen:long_name = \"Oxygen\" ;\n" + + "\t\toxygen:missing_value = -999.0f ;\n" + + "\t\toxygen:units = \"milliliters/liter\" ;\n" + + "\tfloat po4(row) ;\n" + + "\t\tpo4:_FillValue = -999.0f ;\n" + + "\t\tpo4:has_data = 1 ;\n" + + "\t\tpo4:long_name = \"Phosphate\" ;\n" + + "\t\tpo4:missing_value = -999.0f ;\n" + + "\t\tpo4:units = \"ugram-atoms/liter\" ;\n" + + "\tfloat silicate(row) ;\n" + + "\t\tsilicate:_FillValue = -999.0f ;\n" + + "\t\tsilicate:has_data = 0 ;\n" + + "\t\tsilicate:long_name = \"Silicate\" ;\n" + + "\t\tsilicate:missing_value = -999.0f ;\n" + + "\t\tsilicate:units = \"ugram-atoms/liter\" ;\n" + + "\tfloat no2(row) ;\n" + + "\t\tno2:_FillValue = -999.0f ;\n" + + "\t\tno2:has_data = 0 ;\n" + + "\t\tno2:long_name = \"Nitrite\" ;\n" + + "\t\tno2:missing_value = -999.0f ;\n" + + "\t\tno2:units = \"ugram-atoms/liter\" ;\n" + + "\tfloat no3(row) ;\n" + + "\t\tno3:_FillValue = -999.0f ;\n" + + "\t\tno3:has_data = 0 ;\n" + + "\t\tno3:long_name = \"Nitrate\" ;\n" + + "\t\tno3:missing_value = -999.0f ;\n" + + "\t\tno3:units = \"ugram-atoms/liter\" ;\n" + + "\tfloat nh3(row) ;\n" + + "\t\tnh3:_FillValue = -999.0f ;\n" + + "\t\tnh3:has_data = 0 ;\n" + + "\t\tnh3:long_name = \"Ammonia\" ;\n" + + "\t\tnh3:missing_value = -999.0f ;\n" + + "\t\tnh3:units = \"ugram-atoms/liter\" ;\n" + + "\tfloat chl(row) ;\n" + + "\t\tchl:_FillValue = -999.0f ;\n" + + "\t\tchl:has_data = 0 ;\n" + + "\t\tchl:long_name = \"Chlorophyll-a\" ;\n" + + "\t\tchl:missing_value = -999.0f ;\n" + + "\t\tchl:units = \"milligrams/meter**3\" ;\n" + + "\tfloat dark(row) ;\n" + + "\t\tdark:_FillValue = -999.0f ;\n" + + "\t\tdark:has_data = 0 ;\n" + + "\t\tdark:long_name = \"Dark Bottle C14 Assimilation\" ;\n" + + "\t\tdark:missing_value = -999.0f ;\n" + + "\t\tdark:units = \"milligrams/meter**3/experiment\" ;\n" + + "\tfloat primprod(row) ;\n" + + "\t\tprimprod:_FillValue = -999.0f ;\n" + + "\t\tprimprod:has_data = 0 ;\n" + + "\t\tprimprod:long_name = \"Mean Primary Production (C14 Assimilation)\" ;\n" + + "\t\tprimprod:missing_value = -999.0f ;\n" + + "\t\tprimprod:units = \"milligrams/meter**3/experiment\" ;\n" + + "\tfloat lightpercent(row) ;\n" + + "\t\tlightpercent:_FillValue = -999.0f ;\n" + + "\t\tlightpercent:has_data = 0 ;\n" + + "\t\tlightpercent:long_name = \"Percent Light (for incubations)\" ;\n" + + "\t\tlightpercent:missing_value = -999.0f ;\n" + + "\t\tlightpercent:units = \"milligrams/meter**3/experiment\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:history = \"created by ERD from Matlab database created by Andrew Leising from the CalCOFI Physical data\" ;\n" + + + "\t\t:title = \"CalCOFI Physical Observations, 1949-2001\" ;\n" + + "}\n" + + "time,depth,lat,lon,stationyear,stationmonth,stationday,stime,stationline,stationnum,temperature,salinity,pressure,oxygen,po4,silicate,no2,no3,nh3,chl,dark,primprod,lightpercent\n" + + + "6.3612E7,0.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,16.19,33.6,-999.0,5.3,0.42,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,22.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,16.18,33.6,-999.0,5.26,0.38,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,49.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,16.2,33.6,-999.0,5.3,0.36,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,72.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,14.95,33.58,-999.0,5.51,0.37,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,98.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,13.02,33.35,-999.0,5.35,0.45,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,147.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,11.45,33.36,-999.0,4.99,0.81,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,194.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,9.32,33.55,-999.0,4.47,1.19,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,241.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,8.51,33.85,-999.0,4.02,1.51,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,287.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,7.74,33.95,-999.0,3.48,1.76,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,384.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,6.42,33.97,-999.0,2.55,2.15,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,477.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,5.35,34.04,-999.0,1.29,2.48,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,576.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,4.83,34.14,-999.0,0.73,2.73,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,673.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,4.44,34.22,-999.0,0.48,2.9,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,768.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,4.15,34.31,-999.0,0.37,2.87,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,969.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,3.67,34.43,-999.0,0.49,2.8,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n" + + + "6.3612E7,1167.0,33.31667,-128.53333,1950,1,6,600,69.0,144.0,3.3,34.49,-999.0,0.66,2.7,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0,-999.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test specify vars (including out-of-order axis var, and nonsense var), + // !getMetadata + table.readNDNc(fiName, new String[] { "temperature", "lat", "salinity", "junk" }, 0, // standardizeWhat=0 + "depth", 100, 200); + results = table.dataToString(); + expected = "time,depth,lat,lon,temperature,salinity\n" + + "6.3612E7,147.0,33.31667,-128.53333,11.45,33.36\n" + + "6.3612E7,194.0,33.31667,-128.53333,9.32,33.55\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test String vars + fiName = "c:/erddapBPD/copy/cPostDet3/BARBARAx20BLOCK/LAMNAx20DITROPIS/Nx2fA/52038_A69-1303_1059305.nc"; + table.readNDNc(fiName, null, 0, // standardizeWhat=0 + null, 0, 0); + results = table.dataToString(4); + expected = "row,unique_tag_id,PI,longitude,latitude,time,bottom_depth,common_name,date_public,line,position_on_subarray,project,riser_height,role,scientific_name,serial_number,stock,surgery_time,surgery_location,tagger\n" + + + "0,52038_A69-1303_1059305,BARBARA BLOCK,-146.1137,60.7172,1.2192849E9,,SALMON SHARK,1.273271649385E9,,,HOPKINS MARINE STATION,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,1059305,N/A,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\n" + + + "1,52038_A69-1303_1059305,BARBARA BLOCK,-146.32355,60.66713,1.233325298E9,127.743902439024,SALMON SHARK,1.273271649385E9,PORT GRAVINA,6,HOPKINS MARINE STATION,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,1059305,N/A,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\n" + + + "2,52038_A69-1303_1059305,BARBARA BLOCK,-146.32355,60.66713,1.233325733E9,127.743902439024,SALMON SHARK,1.273271649385E9,PORT GRAVINA,6,HOPKINS MARINE STATION,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,1059305,N/A,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\n" + + + "3,52038_A69-1303_1059305,BARBARA BLOCK,-146.32355,60.66713,1.233325998E9,127.743902439024,SALMON SHARK,1.273271649385E9,PORT GRAVINA,6,HOPKINS MARINE STATION,,BLOCK_BARBARA_LAMNA_DITROPIS_N/A,LAMNA DITROPIS,1059305,N/A,1.2192156E9,\"PORT GRAVINA, PRINCE WILLIAM SOUND\",\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test 4D but request axis vars only, with constraints + fiName = TableTests.class.getResource("/points/ndbcMet2/historical/NDBC_51001_met.nc").getPath(); // implied c: + table.readNDNc(fiName, new String[] { "LON", "LAT", "TIME" }, 0, // standardizeWhat=0 + "TIME", 1.2051936e9, 1.20528e9); + results = table.dataToString(4); + expected = "LON,LAT,TIME\n" + + "-162.279,23.445,1.2051894E9\n" + + "-162.279,23.445,1.205193E9\n" + + "-162.279,23.445,1.2051966E9\n" + + "-162.279,23.445,1.2052002E9\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + } + + /** This tests readNDNC. */ + @org.junit.jupiter.api.Test + void testReadNDNc2() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + // String2.log("\n*** Table.testReadNDNc2"); + String fiName = TableTests.class.getResource("/wodSample/wod_008015632O.nc").getPath(); + Table table = new Table(); + String results, expected; + + // test no vars specified + table.readNDNc(fiName, null, 0, // standardizeWhat=0 + null, 0, 0); + results = table.toString(); + expected = "{\n" + + "dimensions:\n" + + "\trow = 11 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\tProject_strlen = 49 ;\n" + + "\tdataset_strlen = 14 ;\n" + + "variables:\n" + + "\tfloat z(row) ;\n" + + "\t\tz:long_name = \"depth_below_sea_level\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"altitude\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:flag_definitions = \"WODfp\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:Instrument_(WOD_code) = \"UNDERWAY: MK3 data recording tag (Wildlife Computers) mounted on elephant seal\" ;\n" + + + "\t\tTemperature:long_name = \"Temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\t\tTemperature:WODprofile_flag = 9 ;\n" + + "\tint Temperature_sigfigs(row) ;\n" + + "\tint Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_definitions = \"WODf\" ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:country = \"UNITED STATES\" ;\n" + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:axis = \"Y\" ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:axis = \"X\" ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:axis = \"T\" ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units = \"NODC_code\" ;\n" + + "\tchar Project(row, Project_strlen) ;\n" + + "\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + + "\t\tProject:long_name = \"Project_name\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tfloat ARGOS_last_fix(row) ;\n" + + "\t\tARGOS_last_fix:units = \"hours\" ;\n" + + "\tfloat ARGOS_next_fix(row) ;\n" + + "\t\tARGOS_next_fix:units = \"hours\" ;\n" + + "\tint crs(row) ;\n" + + "\t\tcrs:epsg_code = \"EPSG:4326\" ;\n" + + "\t\tcrs:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\tcrs:inverse_flattening = 298.25723f ;\n" + + "\t\tcrs:longitude_of_prime_meridian = 0.0f ;\n" + + "\t\tcrs:semi_major_axis = 6378137.0f ;\n" + + "\tint profile(row) ;\n" + + "\tint WODf(row) ;\n" + + "\t\tWODf:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tWODf:flag_values = \"0 1 2 3 4 5 6 7 8 9\" ;\n" + + "\t\tWODf:long_name = \"WOD_observation_flag\" ;\n" + + "\tint WODfp(row) ;\n" + + "\t\tWODfp:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tWODfp:flag_values = \"0 1 2 3 4 5 6 7 8 9\" ;\n" + + "\t\tWODfp:long_name = \"WOD_profile_flag\" ;\n" + + "\tint WODfd(row) ;\n" + + "\t\tWODfd:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tWODfd:flag_values = \"0 1 2\" ;\n" + + "\t\tWODfd:long_name = \"WOD_depth_level_\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cf_role = \"profile_id\" ;\n" + + "\t\t:Conventions = \"CF-1.5\" ;\n" + + "\t\t:featureType = \"profile\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:Metadata_Conventions = \"Unidata Dataset Discovery v1.0\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF-1.5\" ;\n" + + "}\n" + + "z,Temperature,Temperature_sigfigs,Temperature_WODflag,WOD_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,dataset,ARGOS_last_fix,ARGOS_next_fix,crs,profile,WODf,WODfp,WODfd\n" + + + "0.0,7.9,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "10.0,7.9,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "42.0,7.8,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "76.0,7.8,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "120.0,7.8,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "166.0,7.5,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "212.0,7.0,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "260.0,6.5,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "308.0,5.8,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "354.0,5.2,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n" + + + "402.0,4.9,2,0,US025547,8015632,45.28,-142.24,83369.90625,19980403,21.81665,573,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES),animal mounted,4.836731,14.149658,-2147483647,-2147483647,-2147483647,-2147483647,-2147483647\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test specify 0D and 1D data vars (out-of-order, implied axis var, and + // nonsense var), !getMetadata + table.readNDNc(fiName, new String[] { + "lon", "lat", "time", "Temperature", "WOD_cruise_identifier", "junk" }, 0, // standardizeWhat=0 + "z", 100, 200); + results = table.dataToString(); + expected = "z,Temperature,WOD_cruise_identifier,lat,lon,time\n" + + "120.0,7.8,US025547,45.28,-142.24,83369.90625\n" + + "166.0,7.5,US025547,45.28,-142.24,83369.90625\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // request axis vars only, with constraints + table.readNDNc(fiName, new String[] { "z" }, 0, // standardizeWhat=0 + "z", 100, 200); + results = table.dataToString(); + expected = "z\n" + + "120.0\n" + + "166.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // request 0D vars only, with constraints (ignored) + table.readNDNc(fiName, new String[] { + "WOD_cruise_identifier", "Project", "junk", "lon", "lat" }, 0, // standardizeWhat=0 + "z", 100, 200); + results = table.dataToString(); + expected = "WOD_cruise_identifier,lat,lon,Project\n" + + "US025547,45.28,-142.24,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES)\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // request axis var and 0D vars only, with constraints + table.readNDNc(fiName, new String[] { + "WOD_cruise_identifier", "Project", "z", "junk", "lon", "lat" }, 0, // standardizeWhat=0 + "z", 100, 200); + results = table.dataToString(); + expected = "z,WOD_cruise_identifier,lat,lon,Project\n" + + "120.0,US025547,45.28,-142.24,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES)\n" + + "166.0,US025547,45.28,-142.24,AUTONOMOUS PINNIPED ENVIRONMENTAL SAMPLERS (APES)\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + } + + /** + * Test readMultidimNc with treatDimensionsAs specified. + */ + @org.junit.jupiter.api.Test + @TagWebInfStructureDependency + void testHardReadMultidimNc() throws Exception { + String fileName = TableTests.class.getResource("/nc/GLsubdir/GL_201207_TS_DB_44761.nc").getPath(); + // String2.log("\n*** Table.testHardReadMultidimNc(" + fileName + ")"); + // Table.debugMode = true; + Table table = new Table(); + NcHelper.ncdump(fileName, "-h") + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readMultidimNc(fileName, + StringArray.fromCSV("TIME,LATITUDE,LONGITUDE,DEPTH,TEMP,TEMP_DM"), // loadVarNames, + null, // loadDimNames, + new String[][] { { "LATITUDE", "LONGITUDE", "TIME" } }, // treatDimensionsAs + true, // getMetadata, + 0, // standardizeWhat, + true, // removeMVRows, + null, null, null); // conVars, conOps, conVals + // String2.log(table.toString(5)); + String results = table.dataToString(5); + String expected = "TIME,LATITUDE,LONGITUDE,DEPTH,TEMP,TEMP_DM\n" + + "22837.541666666668,48.309,-44.112,-99999.0,12.6,R\n" + + "22837.583333333332,48.313,-44.111,-99999.0,12.6,R\n" + + "22837.625,48.317,-44.107,-99999.0,12.7,R\n" + + "22837.666666666668,48.318,-44.103,-99999.0,13.0,R\n" + + "22837.708333333332,48.315,-44.097,-99999.0,13.1,R\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // time + Test.ensureEqual(table.getColumnName(0), "TIME", ""); + Test.ensureEqual(table.columnAttributes(0).getString("units"), + "days since 1950-01-01T00:00:00Z", "results=\n" + results); + Test.ensureEqual(table.columnAttributes(0).getDouble("valid_min"), + 0.0, "results=\n" + results); + Test.ensureEqual(table.columnAttributes(0).getDouble("valid_max"), + 90000.0, "results=\n" + results); + // depth + Test.ensureEqual(table.getColumnName(3), "DEPTH", ""); + Test.ensureEqual(table.columnAttributes(3).getFloat("_FillValue"), + -99999f, "results=\n" + results); + Test.ensureEqual(table.columnAttributes(3).getString("units"), + "meter", "results=\n" + results); + // temp + Test.ensureEqual(table.getColumnName(4), "TEMP", ""); + Test.ensureEqual(table.columnAttributes(4).getFloat("_FillValue"), + 9.96921E36f, "results=\n" + results); + Test.ensureEqual(table.columnAttributes(4).getString("units"), + "degree_Celsius", "results=\n" + results); + + // standardizeWhat + table.clear(); + table.readMultidimNc(fileName, + StringArray.fromCSV("TIME,LATITUDE,LONGITUDE,DEPTH,TEMP,TEMP_DM"), // loadVarNames, + null, // loadDimNames, + new String[][] { { "LATITUDE", "LONGITUDE", "TIME" } }, // treatDimensionsAs + true, // getMetadata, + 1 + 2 + 4096, // standardizeWhat, + true, // removeMVRows, + null, null, null); // conVars, conOps, conVals + // String2.log(table.toString(5)); + results = table.dataToString(5); + expected = "TIME,LATITUDE,LONGITUDE,DEPTH,TEMP,TEMP_DM\n" + + "1.3420116E9,48.309,-44.112,,12.6,R\n" + + "1.3420152E9,48.313,-44.111,,12.6,R\n" + + "1.3420188E9,48.317,-44.107,,12.7,R\n" + + "1.3420224E9,48.318,-44.103,,13.0,R\n" + + "1.342026E9,48.315,-44.097,,13.1,R\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // time + Test.ensureEqual(table.getColumnName(0), "TIME", ""); + Test.ensureEqual(table.columnAttributes(0).getString("units"), + "seconds since 1970-01-01T00:00:00Z", "results=\n" + results); + Test.ensureEqual(table.columnAttributes(0).getDouble("valid_min"), + -6.31152E8, "results=\n" + results); + Test.ensureEqual(table.columnAttributes(0).getDouble("valid_max"), + 7.144848E9, "results=\n" + results); + // depth + Test.ensureEqual(table.getColumnName(3), "DEPTH", ""); + Test.ensureEqual(table.columnAttributes(3).getFloat("_FillValue"), + Float.NaN, "results=\n" + results); + Test.ensureEqual(table.columnAttributes(3).getString("units"), + "m", "results=\n" + results); + // temp + Test.ensureEqual(table.getColumnName(4), "TEMP", ""); + Test.ensureEqual(table.columnAttributes(4).getFloat("_FillValue"), + Float.NaN, "results=\n" + results); + Test.ensureEqual(table.columnAttributes(4).getString("units"), + "degree_C", "results=\n" + results); + + // Table.debugMode = false; + } + + /** This tests unpack by reading an Argo Profile file. */ + @org.junit.jupiter.api.Test + void testUnpack() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebugMode = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testUnpack"); + Table table = new Table(); + // ftp://ftp.ifremer.fr/ifremer/argo/dac/csio/2901175/2901175_prof.nc + String fiName = TableTests.class.getResource("/nc/2901175_prof.nc").getPath(); + String results, expected; + + // ** test the original packed format for comparison + table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, + true, 0, false, // readMetadata, unpack, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.toString(3); + expected = "{\n" + + "dimensions:\n" + + "\trow = 762 ;\n" + + "\tDATA_TYPE_strlen = 12 ;\n" + + "\tFORMAT_VERSION_strlen = 3 ;\n" + + "\tHANDBOOK_VERSION_strlen = 3 ;\n" + + "\tREFERENCE_DATE_TIME_strlen = 14 ;\n" + + "\tDATE_CREATION_strlen = 14 ;\n" + + "\tDATE_UPDATE_strlen = 14 ;\n" + + "\tPLATFORM_NUMBER_strlen = 7 ;\n" + + "\tPROJECT_NAME_strlen = 18 ;\n" + + "\tPI_NAME_strlen = 11 ;\n" + + "\tSTATION_PARAMETERS_strlen = 4 ;\n" + + "\tDATA_CENTRE_strlen = 2 ;\n" + + "\tDC_REFERENCE_strlen = 14 ;\n" + + "\tDATA_STATE_INDICATOR_strlen = 2 ;\n" + + "\tPLATFORM_TYPE_strlen = 4 ;\n" + + "\tFLOAT_SERIAL_NO_strlen = 13 ;\n" + + "\tFIRMWARE_VERSION_strlen = 6 ;\n" + + "\tWMO_INST_TYPE_strlen = 3 ;\n" + + "\tPOSITIONING_SYSTEM_strlen = 5 ;\n" + + "\tVERTICAL_SAMPLING_SCHEME_strlen = 26 ;\n" + + "\tPARAMETER_strlen = 4 ;\n" + + "\tSCIENTIFIC_CALIB_EQUATION_strlen = 153 ;\n" + + "\tSCIENTIFIC_CALIB_COEFFICIENT_strlen = 55 ;\n" + + "\tSCIENTIFIC_CALIB_COMMENT_strlen = 124 ;\n" + + "\tSCIENTIFIC_CALIB_DATE_strlen = 14 ;\n" + + "variables:\n" + + "\tchar DATA_TYPE(row, DATA_TYPE_strlen) ;\n" + + "\t\tDATA_TYPE:conventions = \"Argo reference table 1\" ;\n" + + "\t\tDATA_TYPE:long_name = \"Data type\" ;\n" + + "\tchar FORMAT_VERSION(row, FORMAT_VERSION_strlen) ;\n" + + "\t\tFORMAT_VERSION:long_name = \"File format version\" ;\n" + + "\tchar HANDBOOK_VERSION(row, HANDBOOK_VERSION_strlen) ;\n" + + "\t\tHANDBOOK_VERSION:long_name = \"Data handbook version\" ;\n" + + "\tchar REFERENCE_DATE_TIME(row, REFERENCE_DATE_TIME_strlen) ;\n" + + "\t\tREFERENCE_DATE_TIME:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tREFERENCE_DATE_TIME:long_name = \"Date of reference for Julian days\" ;\n" + + "\tchar DATE_CREATION(row, DATE_CREATION_strlen) ;\n" + + "\t\tDATE_CREATION:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tDATE_CREATION:long_name = \"Date of file creation\" ;\n" + + "\tchar DATE_UPDATE(row, DATE_UPDATE_strlen) ;\n" + + "\t\tDATE_UPDATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tDATE_UPDATE:long_name = \"Date of update of this file\" ;\n" + + "\tchar PLATFORM_NUMBER(row, PLATFORM_NUMBER_strlen) ;\n" + + "\t\tPLATFORM_NUMBER:conventions = \"WMO float identifier : A9IIIII\" ;\n" + + "\t\tPLATFORM_NUMBER:long_name = \"Float unique identifier\" ;\n" + + "\tchar PROJECT_NAME(row, PROJECT_NAME_strlen) ;\n" + + "\t\tPROJECT_NAME:long_name = \"Name of the project\" ;\n" + + "\tchar PI_NAME(row, PI_NAME_strlen) ;\n" + + "\t\tPI_NAME:long_name = \"Name of the principal investigator\" ;\n" + + "\tchar STATION_PARAMETERS(row, STATION_PARAMETERS_strlen) ;\n" + + "\t\tSTATION_PARAMETERS:conventions = \"Argo reference table 3\" ;\n" + + "\t\tSTATION_PARAMETERS:long_name = \"List of available parameters for the station\" ;\n" + + "\tint CYCLE_NUMBER(row) ;\n" + + "\t\tCYCLE_NUMBER:_FillValue = 99999 ;\n" + + "\t\tCYCLE_NUMBER:conventions = \"0...N, 0 : launch cycle (if exists), 1 : first complete cycle\" ;\n" + + "\t\tCYCLE_NUMBER:long_name = \"Float cycle number\" ;\n" + + "\tchar DIRECTION(row) ;\n" + + "\t\tDIRECTION:conventions = \"A: ascending profiles, D: descending profiles\" ;\n" + + "\t\tDIRECTION:long_name = \"Direction of the station profiles\" ;\n" + + "\tchar DATA_CENTRE(row, DATA_CENTRE_strlen) ;\n" + + "\t\tDATA_CENTRE:conventions = \"Argo reference table 4\" ;\n" + + "\t\tDATA_CENTRE:long_name = \"Data centre in charge of float data processing\" ;\n" + + "\tchar DC_REFERENCE(row, DC_REFERENCE_strlen) ;\n" + + "\t\tDC_REFERENCE:conventions = \"Data centre convention\" ;\n" + + "\t\tDC_REFERENCE:long_name = \"Station unique identifier in data centre\" ;\n" + + "\tchar DATA_STATE_INDICATOR(row, DATA_STATE_INDICATOR_strlen) ;\n" + + "\t\tDATA_STATE_INDICATOR:conventions = \"Argo reference table 6\" ;\n" + + "\t\tDATA_STATE_INDICATOR:long_name = \"Degree of processing the data have passed through\" ;\n" + + "\tchar DATA_MODE(row) ;\n" + + "\t\tDATA_MODE:conventions = \"R : real time; D : delayed mode; A : real time with adjustment\" ;\n" + + "\t\tDATA_MODE:long_name = \"Delayed mode or real time data\" ;\n" + + "\tchar PLATFORM_TYPE(row, PLATFORM_TYPE_strlen) ;\n" + + "\t\tPLATFORM_TYPE:conventions = \"Argo reference table 23\" ;\n" + + "\t\tPLATFORM_TYPE:long_name = \"Type of float\" ;\n" + + "\tchar FLOAT_SERIAL_NO(row, FLOAT_SERIAL_NO_strlen) ;\n" + + "\t\tFLOAT_SERIAL_NO:long_name = \"Serial number of the float\" ;\n" + + "\tchar FIRMWARE_VERSION(row, FIRMWARE_VERSION_strlen) ;\n" + + "\t\tFIRMWARE_VERSION:long_name = \"Instrument firmware version\" ;\n" + + "\tchar WMO_INST_TYPE(row, WMO_INST_TYPE_strlen) ;\n" + + "\t\tWMO_INST_TYPE:conventions = \"Argo reference table 8\" ;\n" + + "\t\tWMO_INST_TYPE:long_name = \"Coded instrument type\" ;\n" + + "\tdouble JULD(row) ;\n" + + "\t\tJULD:_FillValue = 999999.0 ;\n" + + "\t\tJULD:axis = \"T\" ;\n" + + "\t\tJULD:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + + "\t\tJULD:long_name = \"Julian day (UTC) of the station relative to REFERENCE_DATE_TIME\" ;\n" + + "\t\tJULD:resolution = 0.0 ;\n" + + "\t\tJULD:standard_name = \"time\" ;\n" + + "\t\tJULD:units = \"days since 1950-01-01 00:00:00 UTC\" ;\n" + + "\tchar JULD_QC(row) ;\n" + + "\t\tJULD_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tJULD_QC:long_name = \"Quality on date and time\" ;\n" + + "\tdouble JULD_LOCATION(row) ;\n" + + "\t\tJULD_LOCATION:_FillValue = 999999.0 ;\n" + + "\t\tJULD_LOCATION:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + + "\t\tJULD_LOCATION:long_name = \"Julian day (UTC) of the location relative to REFERENCE_DATE_TIME\" ;\n" + + "\t\tJULD_LOCATION:resolution = 0.0 ;\n" + + "\t\tJULD_LOCATION:units = \"days since 1950-01-01 00:00:00 UTC\" ;\n" + + "\tdouble LATITUDE(row) ;\n" + + "\t\tLATITUDE:_FillValue = 99999.0 ;\n" + + "\t\tLATITUDE:axis = \"Y\" ;\n" + + "\t\tLATITUDE:long_name = \"Latitude of the station, best estimate\" ;\n" + + "\t\tLATITUDE:standard_name = \"latitude\" ;\n" + + "\t\tLATITUDE:units = \"degree_north\" ;\n" + + "\t\tLATITUDE:valid_max = 90.0 ;\n" + + "\t\tLATITUDE:valid_min = -90.0 ;\n" + + "\tdouble LONGITUDE(row) ;\n" + + "\t\tLONGITUDE:_FillValue = 99999.0 ;\n" + + "\t\tLONGITUDE:axis = \"X\" ;\n" + + "\t\tLONGITUDE:long_name = \"Longitude of the station, best estimate\" ;\n" + + "\t\tLONGITUDE:standard_name = \"longitude\" ;\n" + + "\t\tLONGITUDE:units = \"degree_east\" ;\n" + + "\t\tLONGITUDE:valid_max = 180.0 ;\n" + + "\t\tLONGITUDE:valid_min = -180.0 ;\n" + + "\tchar POSITION_QC(row) ;\n" + + "\t\tPOSITION_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tPOSITION_QC:long_name = \"Quality on position (latitude and longitude)\" ;\n" + + "\tchar POSITIONING_SYSTEM(row, POSITIONING_SYSTEM_strlen) ;\n" + + "\t\tPOSITIONING_SYSTEM:long_name = \"Positioning system\" ;\n" + + "\tchar PROFILE_PRES_QC(row) ;\n" + + "\t\tPROFILE_PRES_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_PRES_QC:long_name = \"Global quality flag of PRES profile\" ;\n" + + "\tchar PROFILE_TEMP_QC(row) ;\n" + + "\t\tPROFILE_TEMP_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_TEMP_QC:long_name = \"Global quality flag of TEMP profile\" ;\n" + + "\tchar PROFILE_PSAL_QC(row) ;\n" + + "\t\tPROFILE_PSAL_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_PSAL_QC:long_name = \"Global quality flag of PSAL profile\" ;\n" + + "\tchar VERTICAL_SAMPLING_SCHEME(row, VERTICAL_SAMPLING_SCHEME_strlen) ;\n" + + "\t\tVERTICAL_SAMPLING_SCHEME:conventions = \"Argo reference table 16\" ;\n" + + "\t\tVERTICAL_SAMPLING_SCHEME:long_name = \"Vertical sampling scheme\" ;\n" + + "\tint CONFIG_MISSION_NUMBER(row) ;\n" + + "\t\tCONFIG_MISSION_NUMBER:_FillValue = 99999 ;\n" + + "\t\tCONFIG_MISSION_NUMBER:conventions = \"1...N, 1 : first complete mission\" ;\n" + + "\t\tCONFIG_MISSION_NUMBER:long_name = \"Unique number denoting the missions performed by the float\" ;\n" + + "\tchar PARAMETER(row, PARAMETER_strlen) ;\n" + + "\t\tPARAMETER:conventions = \"Argo reference table 3\" ;\n" + + "\t\tPARAMETER:long_name = \"List of parameters with calibration information\" ;\n" + + "\tchar SCIENTIFIC_CALIB_EQUATION(row, SCIENTIFIC_CALIB_EQUATION_strlen) ;\n" + + "\t\tSCIENTIFIC_CALIB_EQUATION:long_name = \"Calibration equation for this parameter\" ;\n" + + "\tchar SCIENTIFIC_CALIB_COEFFICIENT(row, SCIENTIFIC_CALIB_COEFFICIENT_strlen) ;\n" + + "\t\tSCIENTIFIC_CALIB_COEFFICIENT:long_name = \"Calibration coefficients for this equation\" ;\n" + + "\tchar SCIENTIFIC_CALIB_COMMENT(row, SCIENTIFIC_CALIB_COMMENT_strlen) ;\n" + + "\t\tSCIENTIFIC_CALIB_COMMENT:long_name = \"Comment applying to this parameter calibration\" ;\n" + + "\tchar SCIENTIFIC_CALIB_DATE(row, SCIENTIFIC_CALIB_DATE_strlen) ;\n" + + "\t\tSCIENTIFIC_CALIB_DATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tSCIENTIFIC_CALIB_DATE:long_name = \"Date of calibration\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:Conventions = \"Argo-3.1 CF-1.6\" ;\n" + + "\t\t:featureType = \"trajectoryProfile\" ;\n" + + "\t\t:history = \"2016-04-15T20:47:22Z creation\" ;\n" + + "\t\t:institution = \"Coriolis GDAC\" ;\n" + + "\t\t:references = \"http://www.argodatamgt.org/Documentation\" ;\n" + + "\t\t:source = \"Argo float\" ;\n" + + "\t\t:title = \"Argo float vertical profile\" ;\n" + + "\t\t:user_manual_version = \"3.1\" ;\n" + + "}\n" + + "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // ** don't specify varNames or dimNames -- it find vars with most dims + table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, + true, 3, false, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.toString(3); + expected = "{\n" + + "dimensions:\n" + + "\trow = 762 ;\n" + + "\tDATA_TYPE_strlen = 12 ;\n" + + "\tFORMAT_VERSION_strlen = 3 ;\n" + + "\tHANDBOOK_VERSION_strlen = 3 ;\n" + + "\tREFERENCE_DATE_TIME_strlen = 14 ;\n" + + "\tDATE_CREATION_strlen = 14 ;\n" + + "\tDATE_UPDATE_strlen = 14 ;\n" + + "\tPLATFORM_NUMBER_strlen = 7 ;\n" + + "\tPROJECT_NAME_strlen = 18 ;\n" + + "\tPI_NAME_strlen = 11 ;\n" + + "\tSTATION_PARAMETERS_strlen = 4 ;\n" + + "\tDATA_CENTRE_strlen = 2 ;\n" + + "\tDC_REFERENCE_strlen = 14 ;\n" + + "\tDATA_STATE_INDICATOR_strlen = 2 ;\n" + + "\tPLATFORM_TYPE_strlen = 4 ;\n" + + "\tFLOAT_SERIAL_NO_strlen = 13 ;\n" + + "\tFIRMWARE_VERSION_strlen = 6 ;\n" + + "\tWMO_INST_TYPE_strlen = 3 ;\n" + + "\tPOSITIONING_SYSTEM_strlen = 5 ;\n" + + "\tVERTICAL_SAMPLING_SCHEME_strlen = 26 ;\n" + + "\tPARAMETER_strlen = 4 ;\n" + + "\tSCIENTIFIC_CALIB_EQUATION_strlen = 153 ;\n" + + "\tSCIENTIFIC_CALIB_COEFFICIENT_strlen = 55 ;\n" + + "\tSCIENTIFIC_CALIB_COMMENT_strlen = 124 ;\n" + + "\tSCIENTIFIC_CALIB_DATE_strlen = 14 ;\n" + + "variables:\n" + + "\tchar DATA_TYPE(row, DATA_TYPE_strlen) ;\n" + + "\t\tDATA_TYPE:conventions = \"Argo reference table 1\" ;\n" + + "\t\tDATA_TYPE:long_name = \"Data type\" ;\n" + + "\tchar FORMAT_VERSION(row, FORMAT_VERSION_strlen) ;\n" + + "\t\tFORMAT_VERSION:long_name = \"File format version\" ;\n" + + "\tchar HANDBOOK_VERSION(row, HANDBOOK_VERSION_strlen) ;\n" + + "\t\tHANDBOOK_VERSION:long_name = \"Data handbook version\" ;\n" + + "\tchar REFERENCE_DATE_TIME(row, REFERENCE_DATE_TIME_strlen) ;\n" + + "\t\tREFERENCE_DATE_TIME:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tREFERENCE_DATE_TIME:long_name = \"Date of reference for Julian days\" ;\n" + + "\tchar DATE_CREATION(row, DATE_CREATION_strlen) ;\n" + + "\t\tDATE_CREATION:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tDATE_CREATION:long_name = \"Date of file creation\" ;\n" + + "\tchar DATE_UPDATE(row, DATE_UPDATE_strlen) ;\n" + + "\t\tDATE_UPDATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tDATE_UPDATE:long_name = \"Date of update of this file\" ;\n" + + "\tchar PLATFORM_NUMBER(row, PLATFORM_NUMBER_strlen) ;\n" + + "\t\tPLATFORM_NUMBER:conventions = \"WMO float identifier : A9IIIII\" ;\n" + + "\t\tPLATFORM_NUMBER:long_name = \"Float unique identifier\" ;\n" + + "\tchar PROJECT_NAME(row, PROJECT_NAME_strlen) ;\n" + + "\t\tPROJECT_NAME:long_name = \"Name of the project\" ;\n" + + "\tchar PI_NAME(row, PI_NAME_strlen) ;\n" + + "\t\tPI_NAME:long_name = \"Name of the principal investigator\" ;\n" + + "\tchar STATION_PARAMETERS(row, STATION_PARAMETERS_strlen) ;\n" + + "\t\tSTATION_PARAMETERS:conventions = \"Argo reference table 3\" ;\n" + + "\t\tSTATION_PARAMETERS:long_name = \"List of available parameters for the station\" ;\n" + + "\tint CYCLE_NUMBER(row) ;\n" + + "\t\tCYCLE_NUMBER:_FillValue = 2147483647 ;\n" + + "\t\tCYCLE_NUMBER:conventions = \"0...N, 0 : launch cycle (if exists), 1 : first complete cycle\" ;\n" + + "\t\tCYCLE_NUMBER:long_name = \"Float cycle number\" ;\n" + + "\tchar DIRECTION(row) ;\n" + + "\t\tDIRECTION:conventions = \"A: ascending profiles, D: descending profiles\" ;\n" + + "\t\tDIRECTION:long_name = \"Direction of the station profiles\" ;\n" + + "\tchar DATA_CENTRE(row, DATA_CENTRE_strlen) ;\n" + + "\t\tDATA_CENTRE:conventions = \"Argo reference table 4\" ;\n" + + "\t\tDATA_CENTRE:long_name = \"Data centre in charge of float data processing\" ;\n" + + "\tchar DC_REFERENCE(row, DC_REFERENCE_strlen) ;\n" + + "\t\tDC_REFERENCE:conventions = \"Data centre convention\" ;\n" + + "\t\tDC_REFERENCE:long_name = \"Station unique identifier in data centre\" ;\n" + + "\tchar DATA_STATE_INDICATOR(row, DATA_STATE_INDICATOR_strlen) ;\n" + + "\t\tDATA_STATE_INDICATOR:conventions = \"Argo reference table 6\" ;\n" + + "\t\tDATA_STATE_INDICATOR:long_name = \"Degree of processing the data have passed through\" ;\n" + + "\tchar DATA_MODE(row) ;\n" + + "\t\tDATA_MODE:conventions = \"R : real time; D : delayed mode; A : real time with adjustment\" ;\n" + + "\t\tDATA_MODE:long_name = \"Delayed mode or real time data\" ;\n" + + "\tchar PLATFORM_TYPE(row, PLATFORM_TYPE_strlen) ;\n" + + "\t\tPLATFORM_TYPE:conventions = \"Argo reference table 23\" ;\n" + + "\t\tPLATFORM_TYPE:long_name = \"Type of float\" ;\n" + + "\tchar FLOAT_SERIAL_NO(row, FLOAT_SERIAL_NO_strlen) ;\n" + + "\t\tFLOAT_SERIAL_NO:long_name = \"Serial number of the float\" ;\n" + + "\tchar FIRMWARE_VERSION(row, FIRMWARE_VERSION_strlen) ;\n" + + "\t\tFIRMWARE_VERSION:long_name = \"Instrument firmware version\" ;\n" + + "\tchar WMO_INST_TYPE(row, WMO_INST_TYPE_strlen) ;\n" + + "\t\tWMO_INST_TYPE:conventions = \"Argo reference table 8\" ;\n" + + "\t\tWMO_INST_TYPE:long_name = \"Coded instrument type\" ;\n" + + "\tdouble JULD(row) ;\n" + + "\t\tJULD:_FillValue = NaN ;\n" + + "\t\tJULD:axis = \"T\" ;\n" + + "\t\tJULD:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + + "\t\tJULD:long_name = \"Julian day (UTC) of the station relative to REFERENCE_DATE_TIME\" ;\n" + + "\t\tJULD:resolution = 0.0 ;\n" + + "\t\tJULD:standard_name = \"time\" ;\n" + + "\t\tJULD:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + + "\tchar JULD_QC(row) ;\n" + + "\t\tJULD_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tJULD_QC:long_name = \"Quality on date and time\" ;\n" + + "\tdouble JULD_LOCATION(row) ;\n" + + "\t\tJULD_LOCATION:_FillValue = NaN ;\n" + + "\t\tJULD_LOCATION:conventions = \"Relative julian days with decimal part (as parts of day)\" ;\n" + + "\t\tJULD_LOCATION:long_name = \"Julian day (UTC) of the location relative to REFERENCE_DATE_TIME\" ;\n" + + "\t\tJULD_LOCATION:resolution = 0.0 ;\n" + + "\t\tJULD_LOCATION:units = \"seconds since 1970-01-01T00:00:00Z\" ;\n" + + "\tdouble LATITUDE(row) ;\n" + + "\t\tLATITUDE:_FillValue = NaN ;\n" + + "\t\tLATITUDE:axis = \"Y\" ;\n" + + "\t\tLATITUDE:long_name = \"Latitude of the station, best estimate\" ;\n" + + "\t\tLATITUDE:standard_name = \"latitude\" ;\n" + + "\t\tLATITUDE:units = \"degree_north\" ;\n" + + "\t\tLATITUDE:valid_max = 90.0 ;\n" + + "\t\tLATITUDE:valid_min = -90.0 ;\n" + + "\tdouble LONGITUDE(row) ;\n" + + "\t\tLONGITUDE:_FillValue = NaN ;\n" + + "\t\tLONGITUDE:axis = \"X\" ;\n" + + "\t\tLONGITUDE:long_name = \"Longitude of the station, best estimate\" ;\n" + + "\t\tLONGITUDE:standard_name = \"longitude\" ;\n" + + "\t\tLONGITUDE:units = \"degree_east\" ;\n" + + "\t\tLONGITUDE:valid_max = 180.0 ;\n" + + "\t\tLONGITUDE:valid_min = -180.0 ;\n" + + "\tchar POSITION_QC(row) ;\n" + + "\t\tPOSITION_QC:conventions = \"Argo reference table 2\" ;\n" + + "\t\tPOSITION_QC:long_name = \"Quality on position (latitude and longitude)\" ;\n" + + "\tchar POSITIONING_SYSTEM(row, POSITIONING_SYSTEM_strlen) ;\n" + + "\t\tPOSITIONING_SYSTEM:long_name = \"Positioning system\" ;\n" + + "\tchar PROFILE_PRES_QC(row) ;\n" + + "\t\tPROFILE_PRES_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_PRES_QC:long_name = \"Global quality flag of PRES profile\" ;\n" + + "\tchar PROFILE_TEMP_QC(row) ;\n" + + "\t\tPROFILE_TEMP_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_TEMP_QC:long_name = \"Global quality flag of TEMP profile\" ;\n" + + "\tchar PROFILE_PSAL_QC(row) ;\n" + + "\t\tPROFILE_PSAL_QC:conventions = \"Argo reference table 2a\" ;\n" + + "\t\tPROFILE_PSAL_QC:long_name = \"Global quality flag of PSAL profile\" ;\n" + + "\tchar VERTICAL_SAMPLING_SCHEME(row, VERTICAL_SAMPLING_SCHEME_strlen) ;\n" + + "\t\tVERTICAL_SAMPLING_SCHEME:conventions = \"Argo reference table 16\" ;\n" + + "\t\tVERTICAL_SAMPLING_SCHEME:long_name = \"Vertical sampling scheme\" ;\n" + + "\tint CONFIG_MISSION_NUMBER(row) ;\n" + + "\t\tCONFIG_MISSION_NUMBER:_FillValue = 2147483647 ;\n" + + "\t\tCONFIG_MISSION_NUMBER:conventions = \"1...N, 1 : first complete mission\" ;\n" + + "\t\tCONFIG_MISSION_NUMBER:long_name = \"Unique number denoting the missions performed by the float\" ;\n" + + "\tchar PARAMETER(row, PARAMETER_strlen) ;\n" + + "\t\tPARAMETER:conventions = \"Argo reference table 3\" ;\n" + + "\t\tPARAMETER:long_name = \"List of parameters with calibration information\" ;\n" + + "\tchar SCIENTIFIC_CALIB_EQUATION(row, SCIENTIFIC_CALIB_EQUATION_strlen) ;\n" + + "\t\tSCIENTIFIC_CALIB_EQUATION:long_name = \"Calibration equation for this parameter\" ;\n" + + "\tchar SCIENTIFIC_CALIB_COEFFICIENT(row, SCIENTIFIC_CALIB_COEFFICIENT_strlen) ;\n" + + "\t\tSCIENTIFIC_CALIB_COEFFICIENT:long_name = \"Calibration coefficients for this equation\" ;\n" + + "\tchar SCIENTIFIC_CALIB_COMMENT(row, SCIENTIFIC_CALIB_COMMENT_strlen) ;\n" + + "\t\tSCIENTIFIC_CALIB_COMMENT:long_name = \"Comment applying to this parameter calibration\" ;\n" + + "\tchar SCIENTIFIC_CALIB_DATE(row, SCIENTIFIC_CALIB_DATE_strlen) ;\n" + + "\t\tSCIENTIFIC_CALIB_DATE:conventions = \"YYYYMMDDHHMISS\" ;\n" + + "\t\tSCIENTIFIC_CALIB_DATE:long_name = \"Date of calibration\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:Conventions = \"Argo-3.1 CF-1.6\" ;\n" + + "\t\t:featureType = \"trajectoryProfile\" ;\n" + + "\t\t:history = \"2016-04-15T20:47:22Z creation\" ;\n" + + "\t\t:institution = \"Coriolis GDAC\" ;\n" + + "\t\t:references = \"http://www.argodatamgt.org/Documentation\" ;\n" + + "\t\t:source = \"Argo float\" ;\n" + + "\t\t:title = \"Argo float vertical profile\" ;\n" + + "\t\t:user_manual_version = \"3.1\" ;\n" + + "}\n" + + "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + + + // from raw file dif JULD_LOCATION dif JULD_LOCATION + // "Argo + // profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA + // ARGO PROJECT,JIANPING + // XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED + // = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the + // sea surface. The quoted error is manufacturer specified accuracy in + // dbar.,20110628060155\n" + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,1.240301582E9,1,1.240301812E9,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,1.240301582E9,1,1.240301812E9,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,1.240301582E9,1,1.240301812E9,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // done + /* */ + // Table.debugMode = oDebugMode; + } + + /** This tests readVlenNc. */ + @org.junit.jupiter.api.Test + @TagLargeFile + void testReadVlenNc() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebugMode = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadVlenNc"); + Table table = new Table(); + String fiName = String2.unitTestBigDataDir + "nccf/vlen/rr2_vlen_test.nc"; + String2.log(NcHelper.ncdump(fiName, "-h") + // String2.log(NcHelper.ncdump(fiName, "-h")); + String results, expectedStart, expectedEnd; + /* */ + + // ** don't specify varNames or dimNames -- it find vars with most dims + table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, + true, 0, false, // readMetadata, standardizeWhat, removeMVRows + null, null, null); // conVars, conOps, conVals + results = table.dataToString(3); + expectedStart = + // static vars and vars like char SCIENTIFIC_CALIB_COEFFICIENT(N_PROF=254, + // N_CALIB=1, N_PARAM=3, STRING256=256); + "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + + + "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + + + "...\n"; + Test.ensureEqual(results, expectedStart, "results=\n" + results); + Test.ensureEqual(table.nRows(), 762, "nRows"); // 254*3 + /* + * //* same but quick reject based on constraint + * table.readVlenNc(fiName, new StringArray(), new StringArray(), + * true, false, //readMetadata, removeMVRows + * StringArray.fromCSV("FORMAT_VERSION,FORMAT_VERSION"), //conVars + * StringArray.fromCSV("=,="), //conOps + * StringArray.fromCSV("3.1,3.2")); //conVals + * Test.ensureEqual(table.nRows(), 0, "nRows"); + * + * + * + * //* test do removeMVRows + * table.readVlenNc(fiName, null, + * StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), + * true, false, //readMetadata, removeMVRows + * null, null, null); //conVars, conOps, conVals + * results = table.dataToString(3, true); + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * Test.ensureEqual(table.nRows(), 17266, "nRows"); + * + * //and test data at the end of that table + * table.removeRows(0, table.nRows() - 3); + * results = table.dataToString(5); + * expectedEnd = + * "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR\n" + * + + * "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1850.0,1,1849.4,1,99999.0,2.106,1,2.106,1,99999.0,34.604,1,34.604,1,99999.0\n" + * + + * "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1899.9,1,1899.3,1,99999.0,2.055,1,2.055,1,99999.0,34.612,1,34.612,1,99999.0\n" + * + + * "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,256,A,HZ,0066_80617_256,2B,A,APEX,4136,013108,846,24210.44662037037,1,24210.44662037037,26.587,154.853,1,ARGOS,A,A,A,Primary sampling: discrete,1,1950.0,1,1949.4,1,99999.0,2.014,1,2.014,1,99999.0,34.617,1,34.617,1,99999.0\n" + * ; + * Test.ensureEqual(results, expectedEnd, "results=\n" + results); + * + * //* same but quick reject based on constraint LAT,LON 26.587,154.853 + * //*** this takes 9ms while test above takes 99ms! + * table.readVlenNc(fiName, null, + * StringArray.fromCSV("ZZTOP, N_PROF, N_LEVELS"), + * true, //readMetadata, + * StringArray.fromCSV("LATITUDE"), //conVars + * StringArray.fromCSV("="), //conOps + * StringArray.fromCSV("45")); //conVals + * Test.ensureEqual(table.nRows(), 0, "nRows"); + * + * //* test different dim order (should be rearranged so the same) + * table.readVlenNc(fiName, null, + * StringArray.fromCSV("N_LEVELS, ZZTOP, N_PROF"), + * true, //readMetadata, + * null, null, null); //conVars, conOps, conVals + * results = table.dataToString(3, true); + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * Test.ensureEqual(table.nRows(), 17266, "nRows"); + * + * //and test data at the end of that table + * table.removeRows(0, table.nRows() - 3); + * results = table.dataToString(5, true); + * Test.ensureEqual(results, expectedEnd, "results=\n" + results); + * + * + * //* test different varNames + * table.readVlenNc(fiName, + * StringArray.fromCSV( + * "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PRES,PRES_QC,PRES_ADJUSTED,PRES_ADJUSTED_QC,PRES_ADJUSTED_ERROR,TEMP,TEMP_QC,TEMP_ADJUSTED,TEMP_ADJUSTED_QC,TEMP_ADJUSTED_ERROR,PSAL,PSAL_QC,PSAL_ADJUSTED,PSAL_ADJUSTED_QC,PSAL_ADJUSTED_ERROR" + * ), + * null, + * true, //readMetadata, + * null, null, null); //conVars, conOps, conVals + * results = table.dataToString(3, true); + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * Test.ensureEqual(table.nRows(), 17266, "nRows"); + * + * //and test data at the end of that table + * table.removeRows(0, table.nRows() - 3); + * results = table.dataToString(5, true); + * Test.ensureEqual(results, expectedEnd, "results=\n" + results); + * + * + * //* test read JULD + * table.readVlenNc(fiName, StringArray.fromCSV("JULD"), null, + * true, //readMetadata, + * null, null, null); //conVars, conOps, conVals + * results = table.dataToString(3); + * expectedStart = + * "JULD\n" + + * "21660.34238425926\n" + + * "21670.351828703704\n" + + * "21680.386898148146\n" + + * "...\n"; + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * Test.ensureEqual(table.nRows(), 254, "nRows"); //same as when all variables + * were explicitly loaded + * + * table.removeRows(0, 251); + * results = table.dataToString(1000); + * expectedStart = + * "JULD\n" + + * "24190.451828703703\n" + + * "24200.381412037037\n" + + * "24210.44662037037\n"; + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * + * + * //* test read JULD && PRES + * table.readVlenNc(fiName, StringArray.fromCSV("JULD,PRES"), null, + * true, //readMetadata, + * null, null, null); //conVars, conOps, conVals + * results = table.dataToString(3); + * expectedStart = + * "JULD,PRES\n" + + * "21660.34238425926,5.9\n" + //JULD is correctly JOINed + * "21660.34238425926,10.0\n" + + * "21660.34238425926,20.1\n" + + * "...\n"; + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * Test.ensureEqual(table.nRows(), 17266, "nRows"); //same as when all variables + * were explicitly loaded + * + * table.removeRows(0, 17263); + * results = table.dataToString(1000); + * expectedStart = + * "JULD,PRES\n" + + * "24210.44662037037,1850.0\n" + //JULD is correctly JOINed + * "24210.44662037037,1899.9\n" + + * "24210.44662037037,1950.0\n"; + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * + * + * //* test read just static vars, in a different order + * table.readVlenNc(fiName, + * StringArray.fromCSV("HANDBOOK_VERSION,FORMAT_VERSION,DATA_TYPE"), + * null, + * true, //readMetadata, + * null, null, null); //conVars, conOps, conVals + * results = table.dataToString(3); + * expectedStart = + * "HANDBOOK_VERSION,FORMAT_VERSION,DATA_TYPE\n" + + * "1.2,3.1,Argo profile\n"; + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * + * + * //* test read 0 dim variable -> empty table + * table.readVlenNc(fiName, + * StringArray.fromCSV("HISTORY_INSTITUTION"), + * null, + * true, //readMetadata, + * null, null, null); //conVars, conOps, conVals + * Test.ensureEqual(table.nRows(), 0, ""); + * Test.ensureEqual(table.nColumns(), 0, ""); + * + * //* test read non-existent dim -> just scalar vars + * table.readVlenNc(fiName, + * null, + * StringArray.fromCSV("ZZTOP"), + * true, //readMetadata, + * null, null, null); //conVars, conOps, conVals + * results = table.dataToString(3); + * expectedStart = + * "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE\n" + * + + * "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722\n"; + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * + * //* test read non-existent Var -> empty table + * table.readVlenNc(fiName, + * StringArray.fromCSV("ZZTOP"), + * null, + * true, //readMetadata, + * null, null, null); //conVars, conOps, conVals + * Test.ensureEqual(table.nRows(), 0, ""); + * Test.ensureEqual(table.nColumns(), 0, ""); + * + * + * //done + * /* + */ + // Table.debugMode = oDebugMode; + } + + /** NOT FINISHED. This tests readNcSequence. */ + /* + * public static void testReadNcSequence() throws Exception { + * // Table.verbose = true; + * // Table.reallyVerbose = true; + * boolean oDebugMode = Table.debugMode; + * // Table.debugMode = true; + * String2.log("\n*** Table.testReadNcSequence"); + * Table table = new Table(); + * String fiName = "/data/andy/pilot_20210818202736_IUPA50_EGRR_181930.bufr"; + * //String2.unitTestDataDir + ""; + * String2.log(NcHelper.ncdump(fiName, "")); + * String results, expectedStart, expectedEnd; + * + * //** don't specify varNames or dimNames -- it find vars with most dims + * table.readNcSequence(fiName, new StringArray(), new StringArray(), + * true, 0, //readMetadata, standardizeWhat=0 + * null, null, null); //conVars, conOps, conVals + * results = table.dataToString(3); + * expectedStart = + * //static vars and vars like char SCIENTIFIC_CALIB_COEFFICIENT(N_PROF=254, + * N_CALIB=1, N_PARAM=3, STRING256=256); + * "DATA_TYPE,FORMAT_VERSION,HANDBOOK_VERSION,REFERENCE_DATE_TIME,DATE_CREATION,DATE_UPDATE,PLATFORM_NUMBER,PROJECT_NAME,PI_NAME,STATION_PARAMETERS,CYCLE_NUMBER,DIRECTION,DATA_CENTRE,DC_REFERENCE,DATA_STATE_INDICATOR,DATA_MODE,PLATFORM_TYPE,FLOAT_SERIAL_NO,FIRMWARE_VERSION,WMO_INST_TYPE,JULD,JULD_QC,JULD_LOCATION,LATITUDE,LONGITUDE,POSITION_QC,POSITIONING_SYSTEM,PROFILE_PRES_QC,PROFILE_TEMP_QC,PROFILE_PSAL_QC,VERTICAL_SAMPLING_SCHEME,CONFIG_MISSION_NUMBER,PARAMETER,SCIENTIFIC_CALIB_EQUATION,SCIENTIFIC_CALIB_COEFFICIENT,SCIENTIFIC_CALIB_COMMENT,SCIENTIFIC_CALIB_DATE\n" + * + + * "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PRES,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PRES,PRES_ADJUSTED = PRES - dP,dP = 0.1 dbar.,Pressures adjusted by using pressure offset at the sea surface. The quoted error is manufacturer specified accuracy in dbar.,20110628060155\n" + * + + * "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,TEMP,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,TEMP,none,none,The quoted error is manufacturer specified accuracy with respect to ITS-90 at time of laboratory calibration.,20110628060155\n" + * + + * "Argo profile,3.1,1.2,19500101000000,20090422121913,20160415204722,2901175,CHINA ARGO PROJECT,JIANPING XU,PSAL,1,A,HZ,0066_80617_001,2C,D,,APEX_SBE_4136,,846,21660.34238425926,1,21660.345046296297,21.513999938964844,123.36499786376953,1,ARGOS,A,A,A,,1,PSAL,\"PSAL_ADJUSTED = sw_salt( sw_cndr(PSAL,TEMP,PRES), TEMP, PRES_ADJUSTED ); PSAL_ADJ corrects conductivity cell therm mass (CTM), Johnson et al, 2007, JAOT;\",\"same as for PRES_ADJUSTED; CTL: alpha=0.0267, tau=18.6;\",No significant salinity drift detected; SBE sensor accuracy,20110628060155\n" + * + + * "...\n"; + * Test.ensureEqual(results, expectedStart, "results=\n" + results); + * Test.ensureEqual(table.nRows(), 762, "nRows"); //254*3 + * + * //* same but quick reject based on constraint + * table.readMultidimNc(fiName, new StringArray(), new StringArray(), null, + * true, 0, false, //readMetadata, standardizeWhat=0, removeMVRows + * StringArray.fromCSV("FORMAT_VERSION,FORMAT_VERSION"), //conVars + * StringArray.fromCSV("=,="), //conOps + * StringArray.fromCSV("3.1,3.2")); //conVals + * Test.ensureEqual(table.nRows(), 0, "nRows"); + * + * //done + * // Table.debugMode = oDebugMode; + * } + */ + + @org.junit.jupiter.api.Test + @TagLargeFile + void testReadInvalidCRA() throws Exception { + // String2.log("\n*** Table.testReadInvalidCRA()"); + StringArray colNames, conNames, conOps, conVals; + Table table = new Table(); + table.debugMode = true; + String dir = String2.unitTestBigDataDir + "nccf/wod/"; + String fullName, results, expected; + // String doAllString = String2.getStringFromSystemIn( + // "Do all the tests, including ones that are slow and take lots of memory + // (y/n)?"); + boolean doAll = true; // doAllString.startsWith("y"); + /* */ + // read all + fullName = dir + "wod_apb_2005.nc"; + if (doAll) { + table.readInvalidCRA(fullName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.toString(5); + expected = "{\n" + + "dimensions:\n" + + "\trow = 19223385 ;\n" + + "\tcountry_strlen = 13 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\toriginators_cruise_identifier_strlen = 15 ;\n" + + "\tProject_strlen = 60 ;\n" + + "\tPlatform_strlen = 19 ;\n" + + "\tdataset_strlen = 14 ;\n" + + "\tOcean_Vehicle_strlen = 13 ;\n" + + "\tTemperature_Instrument_strlen = 73 ;\n" + + "\tSalinity_Instrument_strlen = 73 ;\n" + + "\tPrimary_Investigator_strlen = 20 ;\n" + + "\tPrimary_Investigator_VAR_strlen = 13 ;\n" + + "variables:\n" + + "\tchar country(row, country_strlen) ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\t\tGMT_time:units = \"hours\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:_FillValue = -99999 ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + + "\tchar Project(row, Project_strlen) ;\n" + + "\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + + "\t\tProject:long_name = \"Project_name\" ;\n" + + "\tchar Platform(row, Platform_strlen) ;\n" + + "\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + + "\t\tPlatform:long_name = \"Platform_name\" ;\n" + + "\tint Orig_Stat_Num(row) ;\n" + + "\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + + "\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + + "\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tchar Ocean_Vehicle(row, Ocean_Vehicle_strlen) ;\n" + + "\t\tOcean_Vehicle:comment = \"Ocean_vehicle\" ;\n" + + "\tbyte Temperature_WODprofileflag(row) ;\n" + + "\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + + "\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + + "\tint Temperature_uncalibrated(row) ;\n" + + "\t\tTemperature_uncalibrated:_FillValue = -99999 ;\n" + + "\t\tTemperature_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + + "\tbyte Salinity_WODprofileflag(row) ;\n" + + "\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + + "\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + + "\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + + "\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + + "\tfloat z(row) ;\n" + + "\t\tz:ancillary_variables = \"z_sigfigs z_WODflag\" ;\n" + + "\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"depth\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tbyte z_WODflag(row) ;\n" + + "\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + + "\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + + "\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_sigfigs(row) ;\n" + + "\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag\" ;\n" + + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\tbyte Temperature_sigfigs(row) ;\n" + + "\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + + "\tbyte Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tfloat Pressure(row) ;\n" + + "\t\tPressure:_FillValue = -1.0E10f ;\n" + + "\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag\" ;\n" + + "\t\tPressure:coordinates = \"time lat lon z\" ;\n" + + "\t\tPressure:grid_mapping = \"crs\" ;\n" + + "\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:units = \"dbar\" ;\n" + + "\tbyte Pressure_sigfigs(row) ;\n" + + "\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + + "\tfloat Salinity(row) ;\n" + + "\t\tSalinity:_FillValue = -1.0E10f ;\n" + + "\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag\" ;\n" + + "\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + + "\t\tSalinity:grid_mapping = \"crs\" ;\n" + + "\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + + "\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + + "\tbyte Salinity_sigfigs(row) ;\n" + + "\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + + "\tbyte Salinity_WODflag(row) ;\n" + + "\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Orig_Stat_Num, dataset, Ocean_Vehicle, Temperature_WODprofileflag, Temperature_Instrument, Temperature_uncalibrated, Salinity_WODprofileflag, Salinity_Instrument, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + + + "\t\t:Conventions = \"CF-1.6\" ;\n" + + "\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + + "\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:crs_inverse_flattening = 298.25723f ;\n" + + "\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:crs_semi_major_axis = 6378137.0f ;\n" + + "\t\t:date_created = \"2018-03-24\" ;\n" + + "\t\t:date_modified = \"2018-03-24\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 66.6276f ;\n" + + "\t\t:geospatial_lat_min = -71.2137f ;\n" + + "\t\t:geospatial_lat_resolution = \"point\" ;\n" + + "\t\t:geospatial_lon_max = 8.102386f ;\n" + + "\t\t:geospatial_lon_min = 55.2659f ;\n" + + "\t\t:geospatial_lon_resolution = \"point\" ;\n" + + "\t\t:geospatial_vertical_max = 1975.4133f ;\n" + + "\t\t:geospatial_vertical_min = 0.0f ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"meters\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_apb_2005.nc\" ;\n" + + "\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + + "\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + + "\t\t:project = \"World Ocean Database\" ;\n" + + "\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + + "\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + + "\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + + + "\t\t:source = \"World Ocean Database\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + + "\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + + "\t\t:time_coverage_end = \"2005-12-31\" ;\n" + + "\t\t:time_coverage_start = \"2005-01-01\" ;\n" + + "\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + + "}\n" + + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + + + "UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,0.0,0,1,12.3,3,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,1.0,0,2,12.35,4,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,8.5,0,2,12.35,4,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,22.5,0,3,12.35,4,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033376,2004017,14009590,42.875145,-139.0886,85832.01060199086,20050101,0.2544478,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,12888,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,36.5,0,3,12.35,4,0,-1.0E10,,-1.0E10,,\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 10000000); + results = table.dataToString(5); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + + + "UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,55.0,0,3,8.2,2,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,66.0,0,3,8.1,2,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,77.5,0,3,7.75,3,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,89.5,0,3,7.6,2,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,101.0,0,4,7.35,3,0,-1.0E10,,-1.0E10,,\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 9223380); + results = table.dataToString(); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + + + "UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,550.0,0,4,5.95,3,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,557.5,0,4,5.85,3,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,564.0,0,4,5.85,3,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,570.5,0,4,5.8,2,0,-1.0E10,,-1.0E10,,\n" + + + "UNITED STATES,US033460,2005059,14331034,31.686825,-120.0401,86196.99254602194,20051231,23.821104,77805,TAGGING OF PACIFIC PREDATORS (TOPP),,13046,animal mounted,Elephant Seal,0,ANIMAL MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. DANIEL P.,all_variables,579.0,0,4,5.8,2,0,-1.0E10,,-1.0E10,,\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + // *** just read outer col + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time" }), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = "wod_unique_cast,time\n" + + "14009590,85832.01060199086\n" + + "14009591,85832.03254599497\n" + + "14009592,85832.01828699\n" + + "14009593,85832.0382870026\n" + + "14009594,85832.01134299766\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 346231, ""); + + table.removeRows(0, 346226); + results = table.dataToString(); + expected = "wod_unique_cast,time\n" + + "14331030,86196.96106499434\n" + + "14331031,86196.97773098946\n" + + "14331032,86196.99402803183\n" + + "14331033,86196.97189801931\n" + + "14331034,86196.99254602194\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // just read outer col with constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "14148754" })); + results = table.dataToString(5); + // from above + // "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + // + + // "UNITED + // STATES,US033495,2005057,14148754,48.738785,-133.2403,86025.06550899148,20050713,1.5722158,77805,TAGGING + // OF PACIFIC PREDATORS (TOPP),,2738,animal mounted,Elephant Seal,0,ANIMAL + // MOUNTED: TDR (Time-Depth Recorder) Tag (Wildlife Computers),1,0,,COSTA; DR. + // DANIEL P.,all_variables,55.0,0,3,8.2,2,0,-1.0E10,,-1.0E10,,\n" + + expected = "wod_unique_cast,time\n" + + "14148754,86025.06550899148\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** just read inner col + table.readInvalidCRA(fullName, + new StringArray(new String[] { "z", "Temperature", "Temperature_sigfigs" }), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + // from above + // ...z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + // + + // ...0.0,0,1,12.3,3,0,-1.0E10,,-1.0E10,,\n" + + // ...1.0,0,2,12.35,4,0,-1.0E10,,-1.0E10,,\n" + + // ...8.5,0,2,12.35,4,0,-1.0E10,,-1.0E10,,\n" + + // ...22.5,0,3,12.35,4,0,-1.0E10,,-1.0E10,,\n" + + // ...36.5,0,3,12.35,4,0,-1.0E10,,-1.0E10,,\n" + + expected = "z,Temperature,Temperature_sigfigs\n" + + "0.0,12.3,3\n" + + "1.0,12.35,4\n" + + "8.5,12.35,4\n" + + "22.5,12.35,4\n" + + "36.5,12.35,4\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 19223385, ""); + + table.removeRows(0, 19223380); + results = table.dataToString(); + // from above + // ...z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + // + + // ...550.0,0,4,5.95,3,0,-1.0E10,,-1.0E10,,\n" + + // ...557.5,0,4,5.85,3,0,-1.0E10,,-1.0E10,,\n" + + // ...564.0,0,4,5.85,3,0,-1.0E10,,-1.0E10,,\n" + + // ...570.5,0,4,5.8,2,0,-1.0E10,,-1.0E10,,\n" + + // ...579.0,0,4,5.8,2,0,-1.0E10,,-1.0E10,,\n"; + expected = "z,Temperature,Temperature_sigfigs\n" + + "550.0,5.95,3\n" + + "557.5,5.85,3\n" + + "564.0,5.85,3\n" + + "570.5,5.8,2\n" + + "579.0,5.8,2\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // just read inner col with constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "z", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "570.5", "5.8" })); + results = table.dataToString(5); + expected = "z,Temperature,Temperature_WODflag\n" + + "570.5,5.8,0\n" + + "570.5,5.8,0\n" + + "570.5,5.8,0\n" + + "570.5,5.8,0\n" + + "570.5,5.8,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 22, ""); + + // read outer and inner col with outer constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "14148754" })); + results = table.dataToString(10); + // from above + // ...wod_unique_cast,...z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Pressure,Pressure_sigfigs,Salinity,Salinity_sigfigs,Salinity_WODflag\n" + // + + // ...14148754,... 55.0,0,3,8.2,2,0,-1.0E10,,-1.0E10,,\n" + + // ...14148754,... 66.0,0,3,8.1,2,0,-1.0E10,,-1.0E10,,\n" + + // ...14148754,... 77.5,0,3,7.75,3,0,-1.0E10,,-1.0E10,,\n" + + // ...14148754,... 89.5,0,3,7.6,2,0,-1.0E10,,-1.0E10,,\n" + + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "14148754,86025.06550899148,0.0,13.85,0\n" + + "14148754,86025.06550899148,0.5,13.85,0\n" + + "14148754,86025.06550899148,3.0,13.85,0\n" + + "14148754,86025.06550899148,15.0,13.55,0\n" + + "14148754,86025.06550899148,30.0,10.05,0\n" + + "14148754,86025.06550899148,43.5,8.4,0\n" + + "14148754,86025.06550899148,55.0,8.2,0\n" + + "14148754,86025.06550899148,66.0,8.1,0\n" + + "14148754,86025.06550899148,77.5,7.75,0\n" + + "14148754,86025.06550899148,89.5,7.6,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 90, ""); + + // read outer and inner col with outer and inner constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "14148754", "13.55" })); + results = table.dataToString(5); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "14148754,86025.06550899148,15.0,13.55,0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** list the non-"" PI's + table.readInvalidCRA(fullName, + new StringArray(new String[] { "Primary_Investigator" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "Primary_Investigator" }), + new StringArray(new String[] { "!=" }), + new StringArray(new String[] { "" })); + results = table.dataToString(5); + expected = "Primary_Investigator\n" + + "COSTA; DR. DANIEL P.\n" + + "COSTA; DR. DANIEL P.\n" + + "COSTA; DR. DANIEL P.\n" + + "COSTA; DR. DANIEL P.\n" + + "COSTA; DR. DANIEL P.\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 323499, ""); + + // *** read all ctd !!! This fails with -Xmx6000m of memory. Succeeds with + // -Xmx8000m + fullName = dir + "wod_ctd_2005.nc"; + if (doAll) { + table.readInvalidCRA(fullName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.toString(5); + expected = "{\n" + + "dimensions:\n" + + "\trow = 14843110 ;\n" + + "\tcountry_strlen = 18 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\toriginators_cruise_identifier_strlen = 15 ;\n" + + "\toriginators_station_identifier_strlen = 9 ;\n" + + "\tProject_strlen = 71 ;\n" + + "\tPlatform_strlen = 80 ;\n" + + "\tInstitute_strlen = 80 ;\n" + + "\tCast_Direction_strlen = 4 ;\n" + + "\tWater_Color_strlen = 54 ;\n" + + "\tWave_Direction_strlen = 25 ;\n" + + "\tWave_Height_strlen = 9 ;\n" + + "\tSea_State_strlen = 42 ;\n" + + "\tWave_Period_strlen = 17 ;\n" + + "\tWind_Direction_strlen = 25 ;\n" + + "\tWeather_Condition_strlen = 169 ;\n" + + "\tCloud_Type_strlen = 18 ;\n" + + "\tCloud_Cover_strlen = 65 ;\n" + + "\tdataset_strlen = 4 ;\n" + + "\tRecorder_strlen = 47 ;\n" + + "\tdepth_eq_strlen = 8 ;\n" + + "\tVisibility_strlen = 24 ;\n" + + "\tneeds_z_fix_strlen = 16 ;\n" + + "\treal_time_strlen = 14 ;\n" + + "\tdbase_orig_strlen = 59 ;\n" + + "\torigflagset_strlen = 5 ;\n" + + "\tTemperature_Scale_strlen = 19 ;\n" + + "\tTemperature_Instrument_strlen = 74 ;\n" + + "\tSalinity_Scale_strlen = 15 ;\n" + + "\tSalinity_Instrument_strlen = 74 ;\n" + + "\tOxygen_Instrument_strlen = 103 ;\n" + + "\tOxygen_Method_strlen = 0 ;\n" + + "\tOxygen_Original_units_strlen = 60 ;\n" + + "\tPressure_Instrument_strlen = 65 ;\n" + + "\tChlorophyll_Instrument_strlen = 59 ;\n" + + "\tChlorophyll_Original_units_strlen = 32 ;\n" + + "\tPrimary_Investigator_strlen = 26 ;\n" + + "\tPrimary_Investigator_VAR_strlen = 13 ;\n" + + "variables:\n" + + "\tchar country(row, country_strlen) ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + + "\tchar originators_station_identifier(row, originators_station_identifier_strlen) ;\n" + + "\t\toriginators_station_identifier:long_name = \"originators_station_identifier\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\t\tGMT_time:units = \"hours\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:_FillValue = -99999 ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + + "\tchar Project(row, Project_strlen) ;\n" + + "\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + + "\t\tProject:long_name = \"Project_name\" ;\n" + + "\tchar Platform(row, Platform_strlen) ;\n" + + "\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + + "\t\tPlatform:long_name = \"Platform_name\" ;\n" + + "\tchar Institute(row, Institute_strlen) ;\n" + + "\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + + "\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + + "\tint Cast_Tow_number(row) ;\n" + + "\t\tCast_Tow_number:_FillValue = -99999 ;\n" + + "\t\tCast_Tow_number:comment = \"originator assigned sequential cast or tow_no\" ;\n" + + "\t\tCast_Tow_number:long_name = \"Cast_or_Tow_number\" ;\n" + + "\tint Orig_Stat_Num(row) ;\n" + + "\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + + "\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + + "\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + + "\tfloat Bottom_Depth(row) ;\n" + + "\t\tBottom_Depth:_FillValue = -1.0E10f ;\n" + + "\t\tBottom_Depth:standard_name = \"sea_floor_depth_below_sea_surface\" ;\n" + + "\t\tBottom_Depth:units = \"meters\" ;\n" + + "\tfloat Cast_Duration(row) ;\n" + + "\t\tCast_Duration:_FillValue = -1.0E10f ;\n" + + "\t\tCast_Duration:long_name = \"Cast_Duration\" ;\n" + + "\t\tCast_Duration:units = \"hours\" ;\n" + + "\tchar Cast_Direction(row, Cast_Direction_strlen) ;\n" + + "\t\tCast_Direction:long_name = \"Cast_Direction\" ;\n" + + "\tint High_res_pair(row) ;\n" + + "\t\tHigh_res_pair:_FillValue = -99999 ;\n" + + "\t\tHigh_res_pair:comment = \"WOD unique cast number for bottle/CTD from same rosette\" ;\n" + + "\t\tHigh_res_pair:long_name = \"WOD_high_resolution_pair_number\" ;\n" + + "\tchar Water_Color(row, Water_Color_strlen) ;\n" + + "\t\tWater_Color:long_name = \"Water_Color\" ;\n" + + "\t\tWater_Color:units_wod = \"Forel-Ule scale (00 to 21)\" ;\n" + + "\tfloat Water_Transpar(row) ;\n" + + "\t\tWater_Transpar:_FillValue = -1.0E10f ;\n" + + "\t\tWater_Transpar:comment = \"Secchi disk depth\" ;\n" + + "\t\tWater_Transpar:long_name = \"Water_Transparency\" ;\n" + + "\t\tWater_Transpar:units = \"meters\" ;\n" + + "\tchar Wave_Direction(row, Wave_Direction_strlen) ;\n" + + "\t\tWave_Direction:long_name = \"Wave_Direction\" ;\n" + + "\t\tWave_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + + "\tchar Wave_Height(row, Wave_Height_strlen) ;\n" + + "\t\tWave_Height:long_name = \"Wave_Height\" ;\n" + + "\t\tWave_Height:units_wod = \"WMO 1555 or NODC 0104\" ;\n" + + "\tchar Sea_State(row, Sea_State_strlen) ;\n" + + "\t\tSea_State:long_name = \"Sea_State\" ;\n" + + "\t\tSea_State:units_wod = \"WMO 3700 or NODC 0109\" ;\n" + + "\tchar Wave_Period(row, Wave_Period_strlen) ;\n" + + "\t\tWave_Period:long_name = \"Wave_Period\" ;\n" + + "\t\tWave_Period:units_wod = \"WMO 3155 or NODC 0378\" ;\n" + + "\tchar Wind_Direction(row, Wind_Direction_strlen) ;\n" + + "\t\tWind_Direction:long_name = \"Wind_Direction\" ;\n" + + "\t\tWind_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + + "\tfloat Wind_Speed(row) ;\n" + + "\t\tWind_Speed:_FillValue = -1.0E10f ;\n" + + "\t\tWind_Speed:standard_name = \"wind_speed\" ;\n" + + "\t\tWind_Speed:units = \"knots\" ;\n" + + "\tfloat Barometric_Pres(row) ;\n" + + "\t\tBarometric_Pres:_FillValue = -1.0E10f ;\n" + + "\t\tBarometric_Pres:long_name = \"Barometric_Pressure\" ;\n" + + "\t\tBarometric_Pres:units = \"millibars\" ;\n" + + "\tfloat Dry_Bulb_Temp(row) ;\n" + + "\t\tDry_Bulb_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tDry_Bulb_Temp:long_name = \"Dry_Bulb_Air_Temperature\" ;\n" + + "\t\tDry_Bulb_Temp:units = \"degree_C\" ;\n" + + "\tfloat Wet_Bulb_Temp(row) ;\n" + + "\t\tWet_Bulb_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tWet_Bulb_Temp:long_name = \"Wet_Bulb_Air_Temperature\" ;\n" + + "\t\tWet_Bulb_Temp:units = \"degree_C\" ;\n" + + "\tchar Weather_Condition(row, Weather_Condition_strlen) ;\n" + + "\t\tWeather_Condition:comment = \"Weather conditions at time of measurements\" ;\n" + + "\t\tWeather_Condition:long_name = \"Weather_Condition\" ;\n" + + "\tchar Cloud_Type(row, Cloud_Type_strlen) ;\n" + + "\t\tCloud_Type:long_name = \"Cloud_Type\" ;\n" + + "\t\tCloud_Type:units_wod = \"WMO 0500 or NODC 0053\" ;\n" + + "\tchar Cloud_Cover(row, Cloud_Cover_strlen) ;\n" + + "\t\tCloud_Cover:long_name = \"Cloud_Cover\" ;\n" + + "\t\tCloud_Cover:units_wod = \"WMO 2700 or NODC 0105\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tchar Recorder(row, Recorder_strlen) ;\n" + + "\t\tRecorder:comment = \"Device which recorded measurements\" ;\n" + + "\t\tRecorder:long_name = \"Recorder\" ;\n" + + "\t\tRecorder:units_wod = \"WMO code 4770\" ;\n" + + "\tchar depth_eq(row, depth_eq_strlen) ;\n" + + "\t\tdepth_eq:comment = \"which drop rate equation was used\" ;\n" + + "\t\tdepth_eq:long_name = \"depth_equation_used\" ;\n" + + "\tbyte Bottom_Hit(row) ;\n" + + "\t\tBottom_Hit:_FillValue = -9 ;\n" + + "\t\tBottom_Hit:comment = \"set to one if instrument hit bottom\" ;\n" + + "\t\tBottom_Hit:long_name = \"Bottom_Hit\" ;\n" + + "\tchar Visibility(row, Visibility_strlen) ;\n" + + "\t\tVisibility:long_name = \"Horizontal_visibility\" ;\n" + + "\t\tVisibility:units_wod = \"WMO Code 4300\" ;\n" + + "\tfloat Ref_Surf_Temp(row) ;\n" + + "\t\tRef_Surf_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tRef_Surf_Temp:comment = \"Reference_or_Sea_Surface_Temperature\" ;\n" + + "\t\tRef_Surf_Temp:units = \"degree_C\" ;\n" + + "\tchar needs_z_fix(row, needs_z_fix_strlen) ;\n" + + "\t\tneeds_z_fix:comment = \"instruction for fixing depths\" ;\n" + + "\t\tneeds_z_fix:long_name = \"z_fix_instructions\" ;\n" + + "\t\tneeds_z_fix:units_wod = \"WOD_code\" ;\n" + + "\tchar real_time(row, real_time_strlen) ;\n" + + "\t\treal_time:comment = \"timeliness and quality status\" ;\n" + + "\t\treal_time:long_name = \"real_time_data\" ;\n" + + "\tchar dbase_orig(row, dbase_orig_strlen) ;\n" + + "\t\tdbase_orig:comment = \"Database from which data were extracted\" ;\n" + + "\t\tdbase_orig:long_name = \"database_origin\" ;\n" + + "\tchar origflagset(row, origflagset_strlen) ;\n" + + "\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + + "\tbyte Temperature_WODprofileflag(row) ;\n" + + "\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Temperature_Scale(row, Temperature_Scale_strlen) ;\n" + + "\t\tTemperature_Scale:long_name = \"Scale upon which values were measured\" ;\n" + + "\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + + "\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + + "\tint Temperature_uncalibrated(row) ;\n" + + "\t\tTemperature_uncalibrated:_FillValue = -99999 ;\n" + + "\t\tTemperature_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + + "\tbyte Salinity_WODprofileflag(row) ;\n" + + "\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Salinity_Scale(row, Salinity_Scale_strlen) ;\n" + + "\t\tSalinity_Scale:long_name = \"Scale upon which values were measured\" ;\n" + + "\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + + "\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + + "\tint Salinity_uncalibrated(row) ;\n" + + "\t\tSalinity_uncalibrated:_FillValue = -99999 ;\n" + + "\t\tSalinity_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + + "\tbyte Oxygen_WODprofileflag(row) ;\n" + + "\t\tOxygen_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tOxygen_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tOxygen_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Oxygen_Instrument(row, Oxygen_Instrument_strlen) ;\n" + + "\t\tOxygen_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tOxygen_Instrument:long_name = \"Instrument\" ;\n" + + "\tchar Oxygen_Method(row, Oxygen_Method_strlen) ;\n" + + "\t\tOxygen_Method:comment = \"Method\" ;\n" + + "\tchar Oxygen_Original_units(row, Oxygen_Original_units_strlen) ;\n" + + "\t\tOxygen_Original_units:comment = \"Units originally used: coverted to standard units\" ;\n" + + "\tint Oxygen_uncalibrated(row) ;\n" + + "\t\tOxygen_uncalibrated:_FillValue = -99999 ;\n" + + "\t\tOxygen_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + + "\tchar Pressure_Instrument(row, Pressure_Instrument_strlen) ;\n" + + "\t\tPressure_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tPressure_Instrument:long_name = \"Instrument\" ;\n" + + "\tbyte Chlorophyll_WODprofileflag(row) ;\n" + + "\t\tChlorophyll_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tChlorophyll_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tChlorophyll_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Chlorophyll_Instrument(row, Chlorophyll_Instrument_strlen) ;\n" + + "\t\tChlorophyll_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tChlorophyll_Instrument:long_name = \"Instrument\" ;\n" + + "\tchar Chlorophyll_Original_units(row, Chlorophyll_Original_units_strlen) ;\n" + + "\t\tChlorophyll_Original_units:comment = \"Units originally used: coverted to standard units\" ;\n" + + "\tint Chlorophyll_uncalibrated(row) ;\n" + + "\t\tChlorophyll_uncalibrated:_FillValue = -99999 ;\n" + + "\t\tChlorophyll_uncalibrated:comment = \"set if measurements have not been calibrated\" ;\n" + + "\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + + "\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + + "\tfloat z(row) ;\n" + + "\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + + "\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"depth\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tbyte z_WODflag(row) ;\n" + + "\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + + "\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + + "\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_origflag(row) ;\n" + + "\t\tz_origflag:_FillValue = -9 ;\n" + + "\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + + "\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_sigfigs(row) ;\n" + + "\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\tbyte Temperature_sigfigs(row) ;\n" + + "\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + + "\tbyte Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tbyte Temperature_origflag(row) ;\n" + + "\t\tTemperature_origflag:_FillValue = -9 ;\n" + + "\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tfloat Salinity(row) ;\n" + + "\t\tSalinity:_FillValue = -1.0E10f ;\n" + + "\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag Salinity_origflag\" ;\n" + + + "\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + + "\t\tSalinity:grid_mapping = \"crs\" ;\n" + + "\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + + "\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + + "\tbyte Salinity_sigfigs(row) ;\n" + + "\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + + "\tbyte Salinity_WODflag(row) ;\n" + + "\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tbyte Salinity_origflag(row) ;\n" + + "\t\tSalinity_origflag:_FillValue = -9 ;\n" + + "\t\tSalinity_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tSalinity_origflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tfloat Oxygen(row) ;\n" + + "\t\tOxygen:_FillValue = -1.0E10f ;\n" + + "\t\tOxygen:ancillary_variables = \"Oxygen_sigfigs Oxygen_WODflag Oxygen_WODprofileflag Oxygen_origflag\" ;\n" + + + "\t\tOxygen:coordinates = \"time lat lon z\" ;\n" + + "\t\tOxygen:grid_mapping = \"crs\" ;\n" + + "\t\tOxygen:long_name = \"volume_fraction_of_oxygen_in_sea_water\" ;\n" + + "\t\tOxygen:standard_name = \"volume_fraction_of_oxygen_in_sea_water\" ;\n" + + "\t\tOxygen:units = \"ml/l\" ;\n" + + "\tbyte Oxygen_sigfigs(row) ;\n" + + "\t\tOxygen_sigfigs:long_name = \"volume_fraction_of_oxygen_in_sea_water significant_figures\" ;\n" + + "\tbyte Oxygen_WODflag(row) ;\n" + + "\t\tOxygen_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tOxygen_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tOxygen_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tOxygen_WODflag:standard_name = \"volume_fraction_of_oxygen_in_sea_water status_flag\" ;\n" + + "\tbyte Oxygen_origflag(row) ;\n" + + "\t\tOxygen_origflag:_FillValue = -9 ;\n" + + "\t\tOxygen_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tOxygen_origflag:standard_name = \"volume_fraction_of_oxygen_in_sea_water status_flag\" ;\n" + + "\tfloat Pressure(row) ;\n" + + "\t\tPressure:_FillValue = -1.0E10f ;\n" + + "\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag Pressure_origflag\" ;\n" + + + "\t\tPressure:coordinates = \"time lat lon z\" ;\n" + + "\t\tPressure:grid_mapping = \"crs\" ;\n" + + "\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:units = \"dbar\" ;\n" + + "\tbyte Pressure_sigfigs(row) ;\n" + + "\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + + "\tbyte Pressure_origflag(row) ;\n" + + "\t\tPressure_origflag:_FillValue = -9 ;\n" + + "\t\tPressure_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tPressure_origflag:standard_name = \"sea_water_pressure status_flag\" ;\n" + + "\tfloat Chlorophyll(row) ;\n" + + "\t\tChlorophyll:_FillValue = -1.0E10f ;\n" + + "\t\tChlorophyll:ancillary_variables = \"Chlorophyll_sigfigs Chlorophyll_WODflag Chlorophyll_WODprofileflag Chlorophyll_origflag\" ;\n" + + + "\t\tChlorophyll:coordinates = \"time lat lon z\" ;\n" + + "\t\tChlorophyll:grid_mapping = \"crs\" ;\n" + + "\t\tChlorophyll:long_name = \"mass_concentration_of_chlorophyll_in_sea_water\" ;\n" + + "\t\tChlorophyll:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water\" ;\n" + + "\t\tChlorophyll:units = \"ugram/l\" ;\n" + + "\tbyte Chlorophyll_sigfigs(row) ;\n" + + "\t\tChlorophyll_sigfigs:long_name = \"mass_concentration_of_chlorophyll_in_sea_water significant_figures\" ;\n" + + + "\tbyte Chlorophyll_WODflag(row) ;\n" + + "\t\tChlorophyll_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tChlorophyll_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tChlorophyll_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tChlorophyll_WODflag:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water status_flag\" ;\n" + + "\tbyte Chlorophyll_origflag(row) ;\n" + + "\t\tChlorophyll_origflag:_FillValue = -9 ;\n" + + "\t\tChlorophyll_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tChlorophyll_origflag:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water status_flag\" ;\n" + + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, originators_station_identifier, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Institute, Cast_Tow_number, Orig_Stat_Num, Bottom_Depth, Cast_Duration, Cast_Direction, High_res_pair, Water_Color, Water_Transpar, Wave_Direction, Wave_Height, Sea_State, Wave_Period, Wind_Direction, Wind_Speed, Barometric_Pres, Dry_Bulb_Temp, Wet_Bulb_Temp, Weather_Condition, Cloud_Type, Cloud_Cover, dataset, Recorder, depth_eq, Bottom_Hit, Visibility, Ref_Surf_Temp, needs_z_fix, real_time, dbase_orig, origflagset, Temperature_WODprofileflag, Temperature_Scale, Temperature_Instrument, Temperature_uncalibrated, Salinity_WODprofileflag, Salinity_Scale, Salinity_Instrument, Salinity_uncalibrated, Oxygen_WODprofileflag, Oxygen_Instrument, Oxygen_Method, Oxygen_Original_units, Oxygen_uncalibrated, Pressure_Instrument, Chlorophyll_WODprofileflag, Chlorophyll_Instrument, Chlorophyll_Original_units, Chlorophyll_uncalibrated, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + + + "\t\t:Conventions = \"CF-1.6\" ;\n" + + "\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + + "\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:crs_inverse_flattening = 298.25723f ;\n" + + "\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:crs_semi_major_axis = 6378137.0f ;\n" + + "\t\t:date_created = \"2018-03-24\" ;\n" + + "\t\t:date_modified = \"2018-03-24\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 89.986336f ;\n" + + "\t\t:geospatial_lat_min = -78.579f ;\n" + + "\t\t:geospatial_lat_resolution = \"point\" ;\n" + + "\t\t:geospatial_lon_max = 180.0f ;\n" + + "\t\t:geospatial_lon_min = -180.0f ;\n" + + "\t\t:geospatial_lon_resolution = \"point\" ;\n" + + "\t\t:geospatial_vertical_max = 6473.251f ;\n" + + "\t\t:geospatial_vertical_min = 0.0f ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"meters\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_ctd_2005.nc\" ;\n" + + "\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + + "\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + + "\t\t:project = \"World Ocean Database\" ;\n" + + "\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + + "\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + + "\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + + + "\t\t:source = \"World Ocean Database\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + + "\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + + "\t\t:time_coverage_end = \"2005-12-31\" ;\n" + + "\t\t:time_coverage_start = \"2005-01-01\" ;\n" + + "\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + + "}\n" + + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Cast_Tow_number,Orig_Stat_Num,Bottom_Depth,Cast_Duration,Cast_Direction,High_res_pair,Water_Color,Water_Transpar,Wave_Direction,Wave_Height,Sea_State,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Scale,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Scale,Salinity_Instrument,Salinity_uncalibrated,Oxygen_WODprofileflag,Oxygen_Instrument,Oxygen_Method,Oxygen_Original_units,Oxygen_uncalibrated,Pressure_Instrument,Chlorophyll_WODprofileflag,Chlorophyll_Instrument,Chlorophyll_Original_units,Chlorophyll_uncalibrated,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + + + "NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,0.0,0,-9,1,12.792,5,0,-9,34.702,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,1.0,0,-9,1,13.085,5,0,-9,34.573,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,2.0,0,-9,1,12.729,5,0,-9,34.562,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,3.0,0,-9,1,12.778,5,0,-9,34.585,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "NEW ZEALAND,NZ001156,tan0501,15076949,,-43.427,177.9535,85832.04166666791,20050101,1.0,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,24,332.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,7.0,0,-9,1,12.538,5,0,-9,34.629,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 14843110 - 5); + results = table.dataToString(); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Cast_Tow_number,Orig_Stat_Num,Bottom_Depth,Cast_Duration,Cast_Direction,High_res_pair,Water_Color,Water_Transpar,Wave_Direction,Wave_Height,Sea_State,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Scale,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Scale,Salinity_Instrument,Salinity_uncalibrated,Oxygen_WODprofileflag,Oxygen_Instrument,Oxygen_Method,Oxygen_Original_units,Oxygen_uncalibrated,Pressure_Instrument,Chlorophyll_WODprofileflag,Chlorophyll_Instrument,Chlorophyll_Original_units,Chlorophyll_uncalibrated,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + + + "NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,374.0,0,-9,3,8.695,4,0,-9,34.571,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,375.0,0,-9,3,8.692,4,0,-9,34.571,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,376.0,0,-9,3,8.686,4,0,-9,34.571,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,377.0,0,-9,3,8.682,4,0,-9,34.57,4,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + + + "NEW ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & ATMOSPHERIC RESEARCH LTD (NIWA); AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,378.0,0,-9,3,8.675,4,0,-9,34.57,4,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + // read outer and inner col with outer constraint + // from above + // "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Cast_Tow_number,Orig_Stat_Num,Bottom_Depth,Cast_Duration,Cast_Direction,High_res_pair,Water_Color,Water_Transpar,Wave_Direction,Wave_Height,Sea_State,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Scale,Temperature_Instrument,Temperature_uncalibrated,Salinity_WODprofileflag,Salinity_Scale,Salinity_Instrument,Salinity_uncalibrated,Oxygen_WODprofileflag,Oxygen_Instrument,Oxygen_Method,Oxygen_Original_units,Oxygen_uncalibrated,Pressure_Instrument,Chlorophyll_WODprofileflag,Chlorophyll_Instrument,Chlorophyll_Original_units,Chlorophyll_uncalibrated,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + // + + // "NEW + // ZEALAND,NZ001163,tan0601,15077333,,-43.9471,-179.09016,86196.95902776718,20051231,23.016666,74288,,TANGAROA + // (R/V; call sign ZMFR; built 1991; IMO9011571),NATIONAL INSTITUTE OF WATER & + // ATMOSPHERIC RESEARCH LTD (NIWA); + // AUCKLAND,-99999,25,382.0,-1.0E10,,-99999,,-1.0E10,,,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,CTD,,,-9,,-1.0E10,,,GODAR + // Project,,0,,,-99999,0,,,-99999,0,,,,-99999,,0,,,-99999,,,374.0,0,-9,3,8.695,4,0,-9,34.571,5,0,-9,-1.0E10,,,-9,-1.0E10,,-9,-1.0E10,,,-9\n" + // + + fullName = dir + "wod_ctd_2005.nc"; + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "15077333" })); + results = table.dataToString(5); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "15077333,86196.95902776718,0.0,15.537,0\n" + + "15077333,86196.95902776718,1.0,15.544,0\n" + + "15077333,86196.95902776718,2.0,15.533,0\n" + + "15077333,86196.95902776718,3.0,15.516,0\n" + + "15077333,86196.95902776718,5.0,15.501,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // outer and inner constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "15077333", "15.533" })); + results = table.dataToString(); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "15077333,86196.95902776718,2.0,15.533,0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** read all drb + fullName = dir + "wod_drb_2005.nc"; + if (doAll) { + table.readInvalidCRA(fullName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.toString(5); + expected = "{\n" + + "dimensions:\n" + + "\trow = 846878 ;\n" + + "\tcountry_strlen = 13 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\toriginators_cruise_identifier_strlen = 5 ;\n" + + "\tPlatform_strlen = 17 ;\n" + + "\tInstitute_strlen = 62 ;\n" + + "\tdataset_strlen = 13 ;\n" + + "\tOcean_Vehicle_strlen = 38 ;\n" + + "\tTemperature_Instrument_strlen = 50 ;\n" + + "\tSalinity_Instrument_strlen = 50 ;\n" + + "\tPrimary_Investigator_strlen = 14 ;\n" + + "\tPrimary_Investigator_VAR_strlen = 13 ;\n" + + "variables:\n" + + "\tchar country(row, country_strlen) ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\t\tGMT_time:units = \"hours\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:_FillValue = -99999 ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + + "\tchar Platform(row, Platform_strlen) ;\n" + + "\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + + "\t\tPlatform:long_name = \"Platform_name\" ;\n" + + "\tchar Institute(row, Institute_strlen) ;\n" + + "\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + + "\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + + "\tint Orig_Stat_Num(row) ;\n" + + "\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + + "\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + + "\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tchar Ocean_Vehicle(row, Ocean_Vehicle_strlen) ;\n" + + "\t\tOcean_Vehicle:comment = \"Ocean_vehicle\" ;\n" + + "\tbyte Temperature_WODprofileflag(row) ;\n" + + "\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + + "\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + + "\tbyte Salinity_WODprofileflag(row) ;\n" + + "\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + + "\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + + "\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + + "\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + + "\tfloat z(row) ;\n" + + "\t\tz:ancillary_variables = \"z_sigfigs z_WODflag\" ;\n" + + "\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"depth\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tbyte z_WODflag(row) ;\n" + + "\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + + "\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + + "\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_sigfigs(row) ;\n" + + "\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag\" ;\n" + + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\tbyte Temperature_sigfigs(row) ;\n" + + "\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + + "\tbyte Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tfloat Salinity(row) ;\n" + + "\t\tSalinity:_FillValue = -1.0E10f ;\n" + + "\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag\" ;\n" + + "\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + + "\t\tSalinity:grid_mapping = \"crs\" ;\n" + + "\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + + "\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + + "\tbyte Salinity_sigfigs(row) ;\n" + + "\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + + "\tbyte Salinity_WODflag(row) ;\n" + + "\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tfloat Pressure(row) ;\n" + + "\t\tPressure:_FillValue = -1.0E10f ;\n" + + "\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag\" ;\n" + + "\t\tPressure:coordinates = \"time lat lon z\" ;\n" + + "\t\tPressure:grid_mapping = \"crs\" ;\n" + + "\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:units = \"dbar\" ;\n" + + "\tbyte Pressure_sigfigs(row) ;\n" + + "\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Platform, Institute, Orig_Stat_Num, dataset, Ocean_Vehicle, Temperature_WODprofileflag, Temperature_Instrument, Salinity_WODprofileflag, Salinity_Instrument, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + + + "\t\t:Conventions = \"CF-1.6\" ;\n" + + "\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + + "\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:crs_inverse_flattening = 298.25723f ;\n" + + "\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:crs_semi_major_axis = 6378137.0f ;\n" + + "\t\t:date_created = \"2018-03-25\" ;\n" + + "\t\t:date_modified = \"2018-03-25\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 89.625f ;\n" + + "\t\t:geospatial_lat_min = 76.025f ;\n" + + "\t\t:geospatial_lat_resolution = \"point\" ;\n" + + "\t\t:geospatial_lon_max = 180.0f ;\n" + + "\t\t:geospatial_lon_min = -180.0f ;\n" + + "\t\t:geospatial_lon_resolution = \"point\" ;\n" + + "\t\t:geospatial_vertical_max = 780.2189f ;\n" + + "\t\t:geospatial_vertical_min = 8.113341f ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"meters\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_drb_2005.nc\" ;\n" + + "\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + + "\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + + "\t\t:project = \"World Ocean Database\" ;\n" + + "\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + + "\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + + "\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + + + "\t\t:source = \"World Ocean Database\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + + "\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + + "\t\t:time_coverage_end = \"2005-12-31\" ;\n" + + "\t\t:time_coverage_start = \"2005-01-01\" ;\n" + + "\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + + "}\n" + + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Institute,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Pressure,Pressure_sigfigs\n" + + + "JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,25.348,0,6,-1.738,5,0,31.7095,6,0,-1.0E10,\n" + + + "JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,50.694,0,6,-1.738,5,0,31.7078,6,0,-1.0E10,\n" + + + "JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,81.104,0,6,-1.68,5,0,33.4528,6,0,-1.0E10,\n" + + + "JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,121.808,0,7,-1.286,5,0,34.1678,6,0,-1.0E10,\n" + + + "JAPAN,JP033439,,10899854,88.1995,-15.9725,85832.0,20050101,0.0,14672,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),3006,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,203.193,0,7,0.432,4,0,34.7061,6,0,-1.0E10,\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 846878 - 5); + results = table.dataToString(); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Institute,Orig_Stat_Num,dataset,Ocean_Vehicle,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Pressure,Pressure_sigfigs\n" + + + "JAPAN,JP033440,,10909132,76.025,-11.6514,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504843054,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,106.845,0,7,-1.474,5,0,33.5642,6,0,-1.0E10,\n" + + + "JAPAN,JP033440,,10909132,76.025,-11.6514,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504843054,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,148.032,0,7,-0.74,4,0,34.2258,6,0,-1.0E10,\n" + + + "JAPAN,JP033440,,10909132,76.025,-11.6514,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504843054,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,194.357,0,7,-0.436,4,0,31.0866,6,0,-1.0E10,\n" + + + "JAPAN,JP033441,,10909133,87.4024,-112.5225,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504846154,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,50.447,0,6,-1.6169,5,0,30.988,6,0,-1.0E10,\n" + + + "JAPAN,JP033441,,10909133,87.4024,-112.5225,86196.95833331347,20051231,23.0,-504834352,,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),-504846154,drifting buoy,J-CAD (JAMSTEC Compact Arctic Drifter),0,,0,,,,121.051,0,7,-1.5004,5,0,34.0442,6,0,-1.0E10,\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + // read outer and inner col with outer constraint + fullName = dir + "wod_drb_2005.nc"; + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "10909132" })); + results = table.dataToString(5); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "10909132,86196.95833331347,22.264,-1.818,0\n" + + "10909132,86196.95833331347,44.526,-1.816,0\n" + + "10909132,86196.95833331347,71.236,-1.798,0\n" + + "10909132,86196.95833331347,106.845,-1.474,0\n" + + "10909132,86196.95833331347,148.032,-0.74,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // outer and inner constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "10909132", "-1.798" })); + results = table.dataToString(); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "10909132,86196.95833331347,71.236,-1.798,0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** read all gld + fullName = dir + "wod_gld_2005.nc"; + if (doAll) { + table.readInvalidCRA(fullName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.toString(5); + expected = "{\n" + + "dimensions:\n" + + "\trow = 3398337 ;\n" + + "\tcountry_strlen = 13 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\toriginators_cruise_identifier_strlen = 15 ;\n" + + "\tPlatform_strlen = 80 ;\n" + + "\tInstitute_strlen = 79 ;\n" + + "\tCast_Direction_strlen = 2 ;\n" + + "\tdataset_strlen = 6 ;\n" + + "\tOcean_Vehicle_strlen = 9 ;\n" + + "\torigflagset_strlen = 5 ;\n" + + "\tTemperature_Instrument_strlen = 70 ;\n" + + "\tSalinity_Instrument_strlen = 70 ;\n" + + "\tPrimary_Investigator_strlen = 33 ;\n" + + "\tPrimary_Investigator_VAR_strlen = 27 ;\n" + + "variables:\n" + + "\tchar country(row, country_strlen) ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\t\tGMT_time:units = \"hours\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:_FillValue = -99999 ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + + "\tchar Platform(row, Platform_strlen) ;\n" + + "\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + + "\t\tPlatform:long_name = \"Platform_name\" ;\n" + + "\tchar Institute(row, Institute_strlen) ;\n" + + "\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + + "\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + + "\tint Orig_Stat_Num(row) ;\n" + + "\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + + "\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + + "\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + + "\tchar Cast_Direction(row, Cast_Direction_strlen) ;\n" + + "\t\tCast_Direction:long_name = \"Cast_Direction\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tchar Ocean_Vehicle(row, Ocean_Vehicle_strlen) ;\n" + + "\t\tOcean_Vehicle:comment = \"Ocean_vehicle\" ;\n" + + "\tint WMO_ID(row) ;\n" + + "\t\tWMO_ID:_FillValue = -99999 ;\n" + + "\t\tWMO_ID:long_name = \"WMO_identification_code\" ;\n" + + "\tchar origflagset(row, origflagset_strlen) ;\n" + + "\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + + "\tbyte Temperature_WODprofileflag(row) ;\n" + + "\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + + "\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + + "\tbyte Salinity_WODprofileflag(row) ;\n" + + "\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + + "\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + + "\tbyte Chlorophyll_WODprofileflag(row) ;\n" + + "\t\tChlorophyll_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tChlorophyll_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tChlorophyll_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + + "\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + + "\tfloat z(row) ;\n" + + "\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + + "\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"depth\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tbyte z_WODflag(row) ;\n" + + "\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + + "\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + + "\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_origflag(row) ;\n" + + "\t\tz_origflag:_FillValue = -9 ;\n" + + "\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + + "\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_sigfigs(row) ;\n" + + "\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\tbyte Temperature_sigfigs(row) ;\n" + + "\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + + "\tbyte Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tbyte Temperature_origflag(row) ;\n" + + "\t\tTemperature_origflag:_FillValue = -9 ;\n" + + "\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tfloat Salinity(row) ;\n" + + "\t\tSalinity:_FillValue = -1.0E10f ;\n" + + "\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag Salinity_origflag\" ;\n" + + + "\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + + "\t\tSalinity:grid_mapping = \"crs\" ;\n" + + "\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + + "\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + + "\tbyte Salinity_sigfigs(row) ;\n" + + "\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + + "\tbyte Salinity_WODflag(row) ;\n" + + "\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tbyte Salinity_origflag(row) ;\n" + + "\t\tSalinity_origflag:_FillValue = -9 ;\n" + + "\t\tSalinity_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tSalinity_origflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tfloat Pressure(row) ;\n" + + "\t\tPressure:_FillValue = -1.0E10f ;\n" + + "\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag Pressure_origflag\" ;\n" + + + "\t\tPressure:coordinates = \"time lat lon z\" ;\n" + + "\t\tPressure:grid_mapping = \"crs\" ;\n" + + "\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:units = \"dbar\" ;\n" + + "\tbyte Pressure_sigfigs(row) ;\n" + + "\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + + "\tbyte Pressure_origflag(row) ;\n" + + "\t\tPressure_origflag:_FillValue = -9 ;\n" + + "\t\tPressure_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tPressure_origflag:standard_name = \"sea_water_pressure status_flag\" ;\n" + + "\tfloat Latitude(row) ;\n" + + "\t\tLatitude:_FillValue = -1.0E10f ;\n" + + "\t\tLatitude:ancillary_variables = \"Latitude_sigfigs Latitude_WODflag Latitude_WODprofileflag Latitude_origflag\" ;\n" + + + "\t\tLatitude:coordinates = \"time lat lon z\" ;\n" + + "\t\tLatitude:grid_mapping = \"crs\" ;\n" + + "\t\tLatitude:long_name = \"latitude\" ;\n" + + "\t\tLatitude:standard_name = \"latitude\" ;\n" + + "\t\tLatitude:units = \"degrees_north\" ;\n" + + "\tbyte Latitude_sigfigs(row) ;\n" + + "\t\tLatitude_sigfigs:long_name = \"latitude significant_figures\" ;\n" + + "\tbyte Latitude_WODflag(row) ;\n" + + "\t\tLatitude_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tLatitude_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tLatitude_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tLatitude_WODflag:standard_name = \"latitude status_flag\" ;\n" + + "\tbyte Latitude_origflag(row) ;\n" + + "\t\tLatitude_origflag:_FillValue = -9 ;\n" + + "\t\tLatitude_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tLatitude_origflag:standard_name = \"latitude status_flag\" ;\n" + + "\tfloat Longitude(row) ;\n" + + "\t\tLongitude:_FillValue = -1.0E10f ;\n" + + "\t\tLongitude:ancillary_variables = \"Longitude_sigfigs Longitude_WODflag Longitude_WODprofileflag Longitude_origflag\" ;\n" + + + "\t\tLongitude:coordinates = \"time lat lon z\" ;\n" + + "\t\tLongitude:grid_mapping = \"crs\" ;\n" + + "\t\tLongitude:long_name = \"longitude\" ;\n" + + "\t\tLongitude:standard_name = \"longitude\" ;\n" + + "\t\tLongitude:units = \"degrees_east\" ;\n" + + "\tbyte Longitude_sigfigs(row) ;\n" + + "\t\tLongitude_sigfigs:long_name = \"longitude significant_figures\" ;\n" + + "\tbyte Longitude_WODflag(row) ;\n" + + "\t\tLongitude_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tLongitude_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tLongitude_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tLongitude_WODflag:standard_name = \"longitude status_flag\" ;\n" + + "\tbyte Longitude_origflag(row) ;\n" + + "\t\tLongitude_origflag:_FillValue = -9 ;\n" + + "\t\tLongitude_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tLongitude_origflag:standard_name = \"longitude status_flag\" ;\n" + + "\tfloat JulianDay(row) ;\n" + + "\t\tJulianDay:_FillValue = -1.0E10f ;\n" + + "\t\tJulianDay:ancillary_variables = \"JulianDay_sigfigs JulianDay_WODflag JulianDay_WODprofileflag JulianDay_origflag\" ;\n" + + + "\t\tJulianDay:coordinates = \"time lat lon z\" ;\n" + + "\t\tJulianDay:grid_mapping = \"crs\" ;\n" + + "\t\tJulianDay:long_name = \"JulianDay\" ;\n" + + "\tbyte JulianDay_sigfigs(row) ;\n" + + "\t\tJulianDay_sigfigs:long_name = \"JulianDay significant_figures\" ;\n" + + "\tbyte JulianDay_WODflag(row) ;\n" + + "\t\tJulianDay_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tJulianDay_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tJulianDay_WODflag:long_name = \"JulianDay st\" ;\n" + + "\tbyte JulianDay_origflag(row) ;\n" + + "\t\tJulianDay_origflag:_FillValue = -9 ;\n" + + "\t\tJulianDay_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tJulianDay_origflag:long_name = \"JulianDay st\" ;\n" + + "\tfloat Chlorophyll(row) ;\n" + + "\t\tChlorophyll:_FillValue = -1.0E10f ;\n" + + "\t\tChlorophyll:ancillary_variables = \"Chlorophyll_sigfigs Chlorophyll_WODflag Chlorophyll_WODprofileflag Chlorophyll_origflag\" ;\n" + + + "\t\tChlorophyll:coordinates = \"time lat lon z\" ;\n" + + "\t\tChlorophyll:grid_mapping = \"crs\" ;\n" + + "\t\tChlorophyll:long_name = \"mass_concentration_of_chlorophyll_in_sea_water\" ;\n" + + "\t\tChlorophyll:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water\" ;\n" + + "\t\tChlorophyll:units = \"ugram/l\" ;\n" + + "\tbyte Chlorophyll_sigfigs(row) ;\n" + + "\t\tChlorophyll_sigfigs:long_name = \"mass_concentration_of_chlorophyll_in_sea_water significant_figures\" ;\n" + + + "\tbyte Chlorophyll_WODflag(row) ;\n" + + "\t\tChlorophyll_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tChlorophyll_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tChlorophyll_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tChlorophyll_WODflag:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water status_flag\" ;\n" + + "\tbyte Chlorophyll_origflag(row) ;\n" + + "\t\tChlorophyll_origflag:_FillValue = -9 ;\n" + + "\t\tChlorophyll_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tChlorophyll_origflag:standard_name = \"mass_concentration_of_chlorophyll_in_sea_water status_flag\" ;\n" + + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Platform, Institute, Orig_Stat_Num, Cast_Direction, dataset, Ocean_Vehicle, WMO_ID, origflagset, Temperature_WODprofileflag, Temperature_Instrument, Salinity_WODprofileflag, Salinity_Instrument, Chlorophyll_WODprofileflag, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + + + "\t\t:Conventions = \"CF-1.6\" ;\n" + + "\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + + "\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:crs_inverse_flattening = 298.25723f ;\n" + + "\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:crs_semi_major_axis = 6378137.0f ;\n" + + "\t\t:date_created = \"2018-03-25\" ;\n" + + "\t\t:date_modified = \"2018-03-25\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 63.9972f ;\n" + + "\t\t:geospatial_lat_min = 22.481083f ;\n" + + "\t\t:geospatial_lat_resolution = \"point\" ;\n" + + "\t\t:geospatial_lon_max = 16.887665f ;\n" + + "\t\t:geospatial_lon_min = -158.30486f ;\n" + + "\t\t:geospatial_lon_resolution = \"point\" ;\n" + + "\t\t:geospatial_vertical_max = 1026.7106f ;\n" + + "\t\t:geospatial_vertical_min = -0.29778513f ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"meters\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_gld_2005.nc\" ;\n" + + "\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + + "\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + + "\t\t:project = \"World Ocean Database\" ;\n" + + "\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + + "\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + + "\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + + + "\t\t:source = \"World Ocean Database\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + + "\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + + "\t\t:time_coverage_end = \"2005-12-31\" ;\n" + + "\t\t:time_coverage_start = \"2005-01-01\" ;\n" + + "\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + + "}\n" + + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Institute,Orig_Stat_Num,Cast_Direction,dataset,Ocean_Vehicle,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,Chlorophyll_WODprofileflag,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Latitude,Latitude_sigfigs,Latitude_WODflag,Latitude_origflag,Longitude,Longitude_sigfigs,Longitude_WODflag,Longitude_origflag,JulianDay,JulianDay_sigfigs,JulianDay_WODflag,JulianDay_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + + + "UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,0.89629334,0,1,2,3.2594981,4,0,1,-1.0E10,-127,-127,-9,0.9058805,3,1,56.54242,7,0,1,-55.34162,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + + + "UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,0.8763757,0,1,2,3.5394983,4,0,1,-1.0E10,-127,-127,-9,0.8857498,3,1,56.542416,7,0,1,-55.34162,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + + + "UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,1.1153866,0,1,3,3.6717756,4,0,1,-1.0E10,-127,-127,-9,1.1273179,4,1,56.542416,7,0,1,-55.34162,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + + + "UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,1.4639436,0,1,3,3.678846,4,0,1,34.7831,5,0,1,1.4796048,4,1,56.542416,7,0,1,-55.34162,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + + + "UNITED STATES,US035083,p015,15727905,56.54242,-55.34162,85832.0146483751,20050101,0.351561,111844,SG015 (AUV;Seaglider #015;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),377,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,1.7925826,0,1,3,3.6769755,4,0,1,34.789787,5,0,1,1.811761,4,1,56.542416,7,0,1,-55.341618,7,0,1,0.19433588,5,0,1,-1.0E10,,,-9\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 3398337 - 5); + results = table.dataToString(); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Institute,Orig_Stat_Num,Cast_Direction,dataset,Ocean_Vehicle,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,Chlorophyll_WODprofileflag,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Latitude,Latitude_sigfigs,Latitude_WODflag,Latitude_origflag,Longitude,Longitude_sigfigs,Longitude_WODflag,Longitude_origflag,JulianDay,JulianDay_sigfigs,JulianDay_WODflag,JulianDay_origflag,Chlorophyll,Chlorophyll_sigfigs,Chlorophyll_WODflag,Chlorophyll_origflag\n" + + + "UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,976.9241,0,1,5,3.5159547,4,0,1,34.39147,5,0,1,989.7248,6,1,47.007023,7,0,1,-127.15596,8,0,1,365.91602,8,0,1,-1.0E10,,,-9\n" + + + "UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,980.71027,0,1,5,3.512552,4,0,1,34.39222,5,0,1,993.56976,6,1,47.007023,7,0,1,-127.15583,8,0,1,365.91406,8,0,1,-1.0E10,,,-9\n" + + + "UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,984.67487,0,1,5,3.5072713,4,0,1,-1.0E10,-127,-127,-9,997.5959,6,1,47.00701,7,0,1,-127.15576,8,0,1,365.91406,8,0,1,-1.0E10,,,-9\n" + + + "UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,987.4005,0,1,5,3.5013642,4,0,1,-1.0E10,-127,-127,-9,1000.36383,7,1,47.006985,7,0,1,-127.15577,8,0,1,365.9121,8,0,1,-1.0E10,,,-9\n" + + + "UNITED STATES,US037856,0156003p012,17842328,47.00655,-127.19153,86196.91210919619,20051231,21.890621,156003,SG012 (AUV;Seaglider #012;owned by Applied Phys.Lab.Univ.of Washington),UNIVERSITY OF WASHINGTON; APPLIED PHYSICS LABORATORY (APL),3,UP,glider,Seaglider,-99999,GTSPP,0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,CTD: SBE 41/41CP (Sea-Bird CTD Module for Autonomous Profiling Floats),0,RHINES; PETER B./ERIKSEN; CHARLES,all_variables/all_variables,987.97534,0,1,5,3.5010133,4,0,1,-1.0E10,-127,-127,-9,1000.94763,7,1,47.00696,7,0,1,-127.15578,8,0,1,365.9121,8,0,1,-1.0E10,,,-9\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + // read outer and inner col with outer constraint + fullName = dir + "wod_gld_2005.nc"; + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "17842328" })); + results = table.dataToString(5); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "17842328,86196.91210919619,0.8763757,10.643924,0\n" + + "17842328,86196.91210919619,1.1950568,10.658873,0\n" + + "17842328,86196.91210919619,2.0614686,10.660649,0\n" + + "17842328,86196.91210919619,2.8780832,10.663277,0\n" + + "17842328,86196.91210919619,3.6449013,10.660924,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // outer and inner constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "17842328", "10.660649" })); + results = table.dataToString(); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "17842328,86196.91210919619,2.0614686,10.660649,0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** read all mrb + fullName = dir + "wod_mrb_2005.nc"; + if (doAll) { + table.readInvalidCRA(fullName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.toString(5); + expected = "{\n" + + "dimensions:\n" + + "\trow = 1184438 ;\n" + + "\tcountry_strlen = 13 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\toriginators_cruise_identifier_strlen = 5 ;\n" + + "\tProject_strlen = 80 ;\n" + + "\tPlatform_strlen = 14 ;\n" + + "\tInstitute_strlen = 62 ;\n" + + "\tWind_Direction_strlen = 25 ;\n" + + "\tdataset_strlen = 11 ;\n" + + "\treal_time_strlen = 14 ;\n" + + "\tdbase_orig_strlen = 24 ;\n" + + "\torigflagset_strlen = 24 ;\n" + + "\tTemperature_Instrument_strlen = 52 ;\n" + + "\tSalinity_Instrument_strlen = 52 ;\n" + + "variables:\n" + + "\tchar country(row, country_strlen) ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\t\tGMT_time:units = \"hours\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:_FillValue = -99999 ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + + "\tchar Project(row, Project_strlen) ;\n" + + "\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + + "\t\tProject:long_name = \"Project_name\" ;\n" + + "\tchar Platform(row, Platform_strlen) ;\n" + + "\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + + "\t\tPlatform:long_name = \"Platform_name\" ;\n" + + "\tchar Institute(row, Institute_strlen) ;\n" + + "\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + + "\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + + "\tint Orig_Stat_Num(row) ;\n" + + "\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + + "\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + + "\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + + "\tchar Wind_Direction(row, Wind_Direction_strlen) ;\n" + + "\t\tWind_Direction:long_name = \"Wind_Direction\" ;\n" + + "\t\tWind_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + + "\tfloat Wind_Speed(row) ;\n" + + "\t\tWind_Speed:_FillValue = -1.0E10f ;\n" + + "\t\tWind_Speed:standard_name = \"wind_speed\" ;\n" + + "\t\tWind_Speed:units = \"knots\" ;\n" + + "\tfloat Dry_Bulb_Temp(row) ;\n" + + "\t\tDry_Bulb_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tDry_Bulb_Temp:long_name = \"Dry_Bulb_Air_Temperature\" ;\n" + + "\t\tDry_Bulb_Temp:units = \"degree_C\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tchar real_time(row, real_time_strlen) ;\n" + + "\t\treal_time:comment = \"timeliness and quality status\" ;\n" + + "\t\treal_time:long_name = \"real_time_data\" ;\n" + + "\tchar dbase_orig(row, dbase_orig_strlen) ;\n" + + "\t\tdbase_orig:comment = \"Database from which data were extracted\" ;\n" + + "\t\tdbase_orig:long_name = \"database_origin\" ;\n" + + "\tint WMO_ID(row) ;\n" + + "\t\tWMO_ID:_FillValue = -99999 ;\n" + + "\t\tWMO_ID:long_name = \"WMO_identification_code\" ;\n" + + "\tchar origflagset(row, origflagset_strlen) ;\n" + + "\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + + "\tbyte Temperature_WODprofileflag(row) ;\n" + + "\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + + "\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + + "\tbyte Salinity_WODprofileflag(row) ;\n" + + "\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + + "\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + + "\tfloat z(row) ;\n" + + "\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + + "\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"depth\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tbyte z_WODflag(row) ;\n" + + "\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + + "\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + + "\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_origflag(row) ;\n" + + "\t\tz_origflag:_FillValue = -9 ;\n" + + "\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + + "\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_sigfigs(row) ;\n" + + "\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\tbyte Temperature_sigfigs(row) ;\n" + + "\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + + "\tbyte Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tbyte Temperature_origflag(row) ;\n" + + "\t\tTemperature_origflag:_FillValue = -9 ;\n" + + "\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tfloat Salinity(row) ;\n" + + "\t\tSalinity:_FillValue = -1.0E10f ;\n" + + "\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag Salinity_origflag\" ;\n" + + + "\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + + "\t\tSalinity:grid_mapping = \"crs\" ;\n" + + "\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + + "\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + + "\tbyte Salinity_sigfigs(row) ;\n" + + "\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + + "\tbyte Salinity_WODflag(row) ;\n" + + "\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tbyte Salinity_origflag(row) ;\n" + + "\t\tSalinity_origflag:_FillValue = -9 ;\n" + + "\t\tSalinity_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tSalinity_origflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Institute, Orig_Stat_Num, Wind_Direction, Wind_Speed, Dry_Bulb_Temp, dataset, real_time, dbase_orig, WMO_ID, origflagset, Temperature_WODprofileflag, Temperature_Instrument, Salinity_WODprofileflag, Salinity_Instrument\" ;\n" + + + "\t\t:Conventions = \"CF-1.6\" ;\n" + + "\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + + "\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:crs_inverse_flattening = 298.25723f ;\n" + + "\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:crs_semi_major_axis = 6378137.0f ;\n" + + "\t\t:date_created = \"2018-03-24\" ;\n" + + "\t\t:date_modified = \"2018-03-24\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 80.5578f ;\n" + + "\t\t:geospatial_lat_min = -18.89f ;\n" + + "\t\t:geospatial_lat_resolution = \"point\" ;\n" + + "\t\t:geospatial_lon_max = -0.02999878f ;\n" + + "\t\t:geospatial_lon_min = 80.48f ;\n" + + "\t\t:geospatial_lon_resolution = \"point\" ;\n" + + "\t\t:geospatial_vertical_max = 4309.0f ;\n" + + "\t\t:geospatial_vertical_min = 1.0f ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"meters\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_mrb_2005.nc\" ;\n" + + "\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + + "\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + + "\t\t:project = \"World Ocean Database\" ;\n" + + "\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + + "\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + + "\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + + + "\t\t:source = \"World Ocean Database\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + + "\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + + "\t\t:time_coverage_end = \"2005-12-31\" ;\n" + + "\t\t:time_coverage_start = \"2005-01-01\" ;\n" + + "\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + + "}\n" + + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Wind_Direction,Wind_Speed,Dry_Bulb_Temp,dataset,real_time,dbase_orig,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag\n" + + + "UNITED STATES,US029953,,12631835,80.5578,-68.9076,85832.0,20050101,0.0,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",28.294939,0,-9,5,-1.782,4,0,-9,32.662,5,0,-9\n" + + + "UNITED STATES,US029953,,12631835,80.5578,-68.9076,85832.0,20050101,0.0,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",77.65329,0,-9,5,-1.755,4,0,-9,32.706,5,0,-9\n" + + + "UNITED STATES,US029953,,12631835,80.5578,-68.9076,85832.0,20050101,0.0,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",126.99971,0,-9,6,-1.235,4,0,-9,33.404,5,0,-9\n" + + + "UNITED STATES,US029953,,12631835,80.5578,-68.9076,85832.0,20050101,0.0,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",196.10425,0,-9,6,-0.396,3,0,-9,34.347,5,0,-9\n" + + + "UNITED STATES,US029953,,12631836,80.5578,-68.9076,85832.01000976562,20050101,0.24023438,63240,ARCTIC/SUBARCTIC OCEAN FLUXES (ASOF),,UNIVERSITY OF DELAWARE;SCHOOL OF MARINE SCIENCE AND POLICY,-99999,,-1.0E10,-1.0E10,moored buoy,,,-99999,,0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",0,\"CTD: SBE 37-IM MicroCAT (Sea-Bird Electronics, Inc.)\",27.602451,0,-9,5,-1.782,4,0,-9,32.66,5,0,-9\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 1184438 - 5); + results = table.dataToString(); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Wind_Direction,Wind_Speed,Dry_Bulb_Temp,dataset,real_time,dbase_orig,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Salinity_WODprofileflag,Salinity_Instrument,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag\n" + + + "BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,100.0,0,2,3,26.48,5,0,1,-1.0E10,-127,-127,-9\n" + + + "BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,140.0,0,2,3,15.74,5,0,2,-1.0E10,-127,-127,-9\n" + + + "BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,180.0,0,2,3,13.85,5,0,1,-1.0E10,-127,-127,-9\n" + + + "BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,300.0,0,2,3,11.67,5,0,1,-1.0E10,-127,-127,-9\n" + + + "BRAZIL,BR001182,,10688847,4.09,-37.98,86196.0,20051231,9.96921E36,78936,PIRATA BUOY ARRAY,FIXED PLATFORM,,-99999,85 DEGREES - 94 DEGREES,8.3592005,27.0,moored buoy,,PMEL TAO/PIRATA database,31002,PMEL TAO/PIRATA database,0,,0,,500.0,0,2,3,8.16,4,0,1,-1.0E10,-127,-127,-9\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + // read outer and inner col with outer constraint + fullName = dir + "wod_mrb_2005.nc"; + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "10688847" })); + results = table.dataToString(5); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "10688847,86196.0,1.0,27.98,0\n" + + "10688847,86196.0,20.0,27.98,0\n" + + "10688847,86196.0,40.0,27.99,0\n" + + "10688847,86196.0,60.0,28.0,0\n" + + "10688847,86196.0,80.0,27.97,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // outer and inner constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "10688847", "27.99" })); + results = table.dataToString(); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "10688847,86196.0,40.0,27.99,0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** read all osd -- THIS FILE FAILS BECAUSE IT HAS DataType=Structure! + // fullName = dir + "wod_osd_2005.nc"; + // table.readInvalidCRA(fullName, null, null, null, null); + // results = table.toString(5); + // expected = "zztop\n"; + // Test.ensureEqual(results, expected, "results=\n" + results); + + // table.removeRows(0, 146042 - 5); + // results = table.dataToString(); + // expected = "zztop\n"; + // Test.ensureEqual(results, expected, "results=\n" + results); + + // *** read all + fullName = dir + "wod_pfl_2005.nc"; + if (doAll) { + table.readInvalidCRA(fullName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.toString(5); + expected = "{\n" + + "dimensions:\n" + + "\trow = 4420114 ;\n" + + "\tcountry_strlen = 18 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\toriginators_cruise_identifier_strlen = 8 ;\n" + + "\tProject_strlen = 74 ;\n" + + "\tPlatform_strlen = 15 ;\n" + + "\tInstitute_strlen = 79 ;\n" + + "\tCast_Direction_strlen = 22 ;\n" + + "\tdataset_strlen = 15 ;\n" + + "\tRecorder_strlen = 44 ;\n" + + "\treal_time_strlen = 36 ;\n" + + "\tOcean_Vehicle_strlen = 68 ;\n" + + "\tdbase_orig_strlen = 22 ;\n" + + "\torigflagset_strlen = 21 ;\n" + + "\tTemperature_Instrument_strlen = 40 ;\n" + + "\tSalinity_Instrument_strlen = 40 ;\n" + + "\tSalinity_Method_strlen = 0 ;\n" + + "\tOxygen_Original_units_strlen = 7 ;\n" + + "\tPrimary_Investigator_strlen = 120 ;\n" + + "\tPrimary_Investigator_VAR_strlen = 97 ;\n" + + "variables:\n" + + "\tchar country(row, country_strlen) ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\t\tGMT_time:units = \"hours\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:_FillValue = -99999 ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + + "\tchar Project(row, Project_strlen) ;\n" + + "\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + + "\t\tProject:long_name = \"Project_name\" ;\n" + + "\tchar Platform(row, Platform_strlen) ;\n" + + "\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + + "\t\tPlatform:long_name = \"Platform_name\" ;\n" + + "\tchar Institute(row, Institute_strlen) ;\n" + + "\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + + "\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + + "\tint Orig_Stat_Num(row) ;\n" + + "\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + + "\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + + "\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + + "\tchar Cast_Direction(row, Cast_Direction_strlen) ;\n" + + "\t\tCast_Direction:long_name = \"Cast_Direction\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tchar Recorder(row, Recorder_strlen) ;\n" + + "\t\tRecorder:comment = \"Device which recorded measurements\" ;\n" + + "\t\tRecorder:long_name = \"Recorder\" ;\n" + + "\t\tRecorder:units_wod = \"WMO code 4770\" ;\n" + + "\tchar real_time(row, real_time_strlen) ;\n" + + "\t\treal_time:comment = \"timeliness and quality status\" ;\n" + + "\t\treal_time:long_name = \"real_time_data\" ;\n" + + "\tchar Ocean_Vehicle(row, Ocean_Vehicle_strlen) ;\n" + + "\t\tOcean_Vehicle:comment = \"Ocean_vehicle\" ;\n" + + "\tchar dbase_orig(row, dbase_orig_strlen) ;\n" + + "\t\tdbase_orig:comment = \"Database from which data were extracted\" ;\n" + + "\t\tdbase_orig:long_name = \"database_origin\" ;\n" + + "\tint WMO_ID(row) ;\n" + + "\t\tWMO_ID:_FillValue = -99999 ;\n" + + "\t\tWMO_ID:long_name = \"WMO_identification_code\" ;\n" + + "\tchar origflagset(row, origflagset_strlen) ;\n" + + "\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + + "\tbyte Temperature_WODprofileflag(row) ;\n" + + "\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + + "\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + + "\tfloat Temperature_Adjustment(row) ;\n" + + "\t\tTemperature_Adjustment:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature_Adjustment:comment = \"Adjustment made to original measurement values and measurement units\" ;\n" + + + "\tbyte Salinity_WODprofileflag(row) ;\n" + + "\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Salinity_Instrument(row, Salinity_Instrument_strlen) ;\n" + + "\t\tSalinity_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tSalinity_Instrument:long_name = \"Instrument\" ;\n" + + "\tchar Salinity_Method(row, Salinity_Method_strlen) ;\n" + + "\t\tSalinity_Method:comment = \"Method\" ;\n" + + "\tfloat Salinity_Adjustment(row) ;\n" + + "\t\tSalinity_Adjustment:_FillValue = -1.0E10f ;\n" + + "\t\tSalinity_Adjustment:comment = \"Adjustment made to original measurement values and measurement units\" ;\n" + + + "\tint Salinity_(row) ;\n" + + "\t\tSalinity_:_FillValue = -99999 ;\n" + + "\tfloat Pressure_Adjustment(row) ;\n" + + "\t\tPressure_Adjustment:_FillValue = -1.0E10f ;\n" + + "\t\tPressure_Adjustment:comment = \"Adjustment made to original measurement values and measurement units\" ;\n" + + + "\tbyte Oxygen_WODprofileflag(row) ;\n" + + "\t\tOxygen_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tOxygen_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tOxygen_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Oxygen_Original_units(row, Oxygen_Original_units_strlen) ;\n" + + "\t\tOxygen_Original_units:comment = \"Units originally used: coverted to standard units\" ;\n" + + "\tfloat Oxygen_Adjustment(row) ;\n" + + "\t\tOxygen_Adjustment:_FillValue = -1.0E10f ;\n" + + "\t\tOxygen_Adjustment:comment = \"Adjustment made to original measurement values and measurement units\" ;\n" + + + "\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + + "\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + + "\tfloat z(row) ;\n" + + "\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + + "\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"depth\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tbyte z_WODflag(row) ;\n" + + "\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + + "\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + + "\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_origflag(row) ;\n" + + "\t\tz_origflag:_FillValue = -9 ;\n" + + "\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + + "\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_sigfigs(row) ;\n" + + "\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\tbyte Temperature_sigfigs(row) ;\n" + + "\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + + "\tbyte Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tbyte Temperature_origflag(row) ;\n" + + "\t\tTemperature_origflag:_FillValue = -9 ;\n" + + "\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tfloat Salinity(row) ;\n" + + "\t\tSalinity:_FillValue = -1.0E10f ;\n" + + "\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag Salinity_origflag\" ;\n" + + + "\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + + "\t\tSalinity:grid_mapping = \"crs\" ;\n" + + "\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + + "\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + + "\tbyte Salinity_sigfigs(row) ;\n" + + "\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + + "\tbyte Salinity_WODflag(row) ;\n" + + "\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tbyte Salinity_origflag(row) ;\n" + + "\t\tSalinity_origflag:_FillValue = -9 ;\n" + + "\t\tSalinity_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tSalinity_origflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tfloat Pressure(row) ;\n" + + "\t\tPressure:_FillValue = -1.0E10f ;\n" + + "\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag Pressure_origflag\" ;\n" + + + "\t\tPressure:coordinates = \"time lat lon z\" ;\n" + + "\t\tPressure:grid_mapping = \"crs\" ;\n" + + "\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:units = \"dbar\" ;\n" + + "\tbyte Pressure_sigfigs(row) ;\n" + + "\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + + "\tbyte Pressure_origflag(row) ;\n" + + "\t\tPressure_origflag:_FillValue = -9 ;\n" + + "\t\tPressure_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tPressure_origflag:standard_name = \"sea_water_pressure status_flag\" ;\n" + + "\tfloat Oxygen(row) ;\n" + + "\t\tOxygen:_FillValue = -1.0E10f ;\n" + + "\t\tOxygen:ancillary_variables = \"Oxygen_sigfigs Oxygen_WODflag Oxygen_WODprofileflag Oxygen_origflag\" ;\n" + + + "\t\tOxygen:coordinates = \"time lat lon z\" ;\n" + + "\t\tOxygen:grid_mapping = \"crs\" ;\n" + + "\t\tOxygen:long_name = \"volume_fraction_of_oxygen_in_sea_water\" ;\n" + + "\t\tOxygen:standard_name = \"volume_fraction_of_oxygen_in_sea_water\" ;\n" + + "\t\tOxygen:units = \"ml/l\" ;\n" + + "\tbyte Oxygen_sigfigs(row) ;\n" + + "\t\tOxygen_sigfigs:long_name = \"volume_fraction_of_oxygen_in_sea_water significant_figures\" ;\n" + + "\tbyte Oxygen_WODflag(row) ;\n" + + "\t\tOxygen_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tOxygen_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tOxygen_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tOxygen_WODflag:standard_name = \"volume_fraction_of_oxygen_in_sea_water status_flag\" ;\n" + + "\tbyte Oxygen_origflag(row) ;\n" + + "\t\tOxygen_origflag:_FillValue = -9 ;\n" + + "\t\tOxygen_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tOxygen_origflag:standard_name = \"volume_fraction_of_oxygen_in_sea_water status_flag\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Institute, Orig_Stat_Num, Cast_Direction, dataset, Recorder, real_time, Ocean_Vehicle, dbase_orig, WMO_ID, origflagset, Temperature_WODprofileflag, Temperature_Instrument, Temperature_Adjustment, Salinity_WODprofileflag, Salinity_Instrument, Salinity_Method, Salinity_Adjustment, Salinity_, Pressure_Adjustment, Oxygen_WODprofileflag, Oxygen_Original_units, Oxygen_Adjustment, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + + + "\t\t:Conventions = \"CF-1.6\" ;\n" + + "\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + + "\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:crs_inverse_flattening = 298.25723f ;\n" + + "\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:crs_semi_major_axis = 6378137.0f ;\n" + + "\t\t:date_created = \"2018-03-24\" ;\n" + + "\t\t:date_modified = \"2018-03-24\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 77.427f ;\n" + + "\t\t:geospatial_lat_min = -72.811f ;\n" + + "\t\t:geospatial_lat_resolution = \"point\" ;\n" + + "\t\t:geospatial_lon_max = 180.0f ;\n" + + "\t\t:geospatial_lon_min = -180.0f ;\n" + + "\t\t:geospatial_lon_resolution = \"point\" ;\n" + + "\t\t:geospatial_vertical_max = 6420.1216f ;\n" + + "\t\t:geospatial_vertical_min = -1.0f ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"meters\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_pfl_2005.nc\" ;\n" + + "\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + + "\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + + "\t\t:project = \"World Ocean Database\" ;\n" + + "\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + + "\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + + "\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + + + "\t\t:source = \"World Ocean Database\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + + "\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + + "\t\t:time_coverage_end = \"2005-12-31\" ;\n" + + "\t\t:time_coverage_start = \"2005-01-01\" ;\n" + + "\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + + "}\n" + + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Cast_Direction,dataset,Recorder,real_time,Ocean_Vehicle,dbase_orig,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Temperature_Adjustment,Salinity_WODprofileflag,Salinity_Instrument,Salinity_Method,Salinity_Adjustment,Salinity_,Pressure_Adjustment,Oxygen_WODprofileflag,Oxygen_Original_units,Oxygen_Adjustment,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag\n" + + + "JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,4.4739165,0,1,3,27.817,5,0,1,34.939,5,0,1,4.5,2,1,-1.0E10,,,-9\n" + + + "JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,9.44482,0,1,3,27.745,5,0,1,34.942,5,0,1,9.5,2,1,-1.0E10,,,-9\n" + + + "JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,13.91853,0,1,4,27.408,5,0,1,34.98,5,0,1,14.0,3,1,-1.0E10,,,-9\n" + + + "JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,18.889206,0,1,4,27.286,5,0,1,34.997,5,0,1,19.0,3,1,-1.0E10,,,-9\n" + + + "JAPAN,JP031068,Q1900475,10405561,-13.641,69.829,85832.02929583378,20050101,0.7031,2352,J-ARGO (JAPAN ARGO),,JAPAN AGENCY FOR MARINE-EARTH SCIENCE AND TECHNOLOGY (JAMSTEC),2,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),1900475,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,CTD: TYPE UNKNOWN,,0.0,-99999,0.0,0,,-1.0E10,TAKEUCHI; KENSUKE,all_variables,24.257399,0,1,4,27.233,5,0,1,35.001,5,0,1,24.4,3,1,-1.0E10,,,-9\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 4420114 - 5); + results = table.dataToString(); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Cast_Direction,dataset,Recorder,real_time,Ocean_Vehicle,dbase_orig,WMO_ID,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Temperature_Adjustment,Salinity_WODprofileflag,Salinity_Instrument,Salinity_Method,Salinity_Adjustment,Salinity_,Pressure_Adjustment,Oxygen_WODprofileflag,Oxygen_Original_units,Oxygen_Adjustment,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Salinity_origflag,Pressure,Pressure_sigfigs,Pressure_origflag,Oxygen,Oxygen_sigfigs,Oxygen_WODflag,Oxygen_origflag\n" + + + "UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,613.0759,0,1,5,0.474,3,0,1,34.071,5,0,2,618.7,6,1,-1.0E10,,,-9\n" + + + "UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,632.8637,0,1,5,0.463,3,0,1,34.071,5,0,2,638.7,6,1,-1.0E10,,,-9\n" + + + "UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,652.84753,0,1,5,0.448,3,0,1,34.07,5,0,2,658.9,6,1,-1.0E10,,,-9\n" + + + "UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,672.5326,0,1,5,0.438,3,0,1,34.07,5,0,2,678.8,6,1,-1.0E10,,,-9\n" + + + "UNKNOWN,99005892,2900451,11898775,39.42,132.58,86196.9589958787,20051231,23.015902,42682,,,,45,UP,profiling float,,delayed_mode quality controlled data,\"APEX (Autonomous Profiling Explorer, Webb Research Corporation)\",US GODAE server (Argo),2900451,ARGO profiling floats,0,CTD: TYPE UNKNOWN,0.0,0,\"CTD: Sea-Bird Electronics, MODEL UNKNOWN\",,0.0,-99999,0.0,0,,-1.0E10,SUK; MOON-SIK,all_variables,693.007,0,1,5,0.428,3,0,1,34.07,5,0,2,699.5,6,1,-1.0E10,,,-9\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + // read outer and inner col with outer constraint + fullName = dir + "wod_pfl_2005.nc"; + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "11898775" })); + results = table.dataToString(5); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "11898775,86196.9589958787,4.5649443,7.71,0\n" + + "11898775,86196.9589958787,13.892994,7.696,0\n" + + "11898775,86196.9589958787,24.014437,7.491,0\n" + + "11898775,86196.9589958787,33.83771,7.302,0\n" + + "11898775,86196.9589958787,43.958168,7.241,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // outer and inner constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "11898775", "7.491" })); + results = table.dataToString(); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "11898775,86196.9589958787,24.014437,7.491,0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** read all uor + fullName = dir + "wod_uor_2005.nc"; + if (doAll) { + table.readInvalidCRA(fullName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.toString(5); + expected = "{\n" + + "dimensions:\n" + + "\trow = 1169159 ;\n" + + "\tcountry_strlen = 6 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\toriginators_cruise_identifier_strlen = 9 ;\n" + + "\tPlatform_strlen = 73 ;\n" + + "\tWave_Height_strlen = 10 ;\n" + + "\tWave_Period_strlen = 17 ;\n" + + "\tWind_Direction_strlen = 25 ;\n" + + "\tWeather_Condition_strlen = 169 ;\n" + + "\tCloud_Cover_strlen = 65 ;\n" + + "\tdataset_strlen = 9 ;\n" + + "variables:\n" + + "\tchar country(row, country_strlen) ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\t\tGMT_time:units = \"hours\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:_FillValue = -99999 ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + + "\tchar Platform(row, Platform_strlen) ;\n" + + "\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + + "\t\tPlatform:long_name = \"Platform_name\" ;\n" + + "\tfloat Bottom_Depth(row) ;\n" + + "\t\tBottom_Depth:_FillValue = -1.0E10f ;\n" + + "\t\tBottom_Depth:standard_name = \"sea_floor_depth_below_sea_surface\" ;\n" + + "\t\tBottom_Depth:units = \"meters\" ;\n" + + "\tchar Wave_Height(row, Wave_Height_strlen) ;\n" + + "\t\tWave_Height:long_name = \"Wave_Height\" ;\n" + + "\t\tWave_Height:units_wod = \"WMO 1555 or NODC 0104\" ;\n" + + "\tchar Wave_Period(row, Wave_Period_strlen) ;\n" + + "\t\tWave_Period:long_name = \"Wave_Period\" ;\n" + + "\t\tWave_Period:units_wod = \"WMO 3155 or NODC 0378\" ;\n" + + "\tchar Wind_Direction(row, Wind_Direction_strlen) ;\n" + + "\t\tWind_Direction:long_name = \"Wind_Direction\" ;\n" + + "\t\tWind_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + + "\tfloat Wind_Speed(row) ;\n" + + "\t\tWind_Speed:_FillValue = -1.0E10f ;\n" + + "\t\tWind_Speed:standard_name = \"wind_speed\" ;\n" + + "\t\tWind_Speed:units = \"knots\" ;\n" + + "\tfloat Barometric_Pres(row) ;\n" + + "\t\tBarometric_Pres:_FillValue = -1.0E10f ;\n" + + "\t\tBarometric_Pres:long_name = \"Barometric_Pressure\" ;\n" + + "\t\tBarometric_Pres:units = \"millibars\" ;\n" + + "\tfloat Dry_Bulb_Temp(row) ;\n" + + "\t\tDry_Bulb_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tDry_Bulb_Temp:long_name = \"Dry_Bulb_Air_Temperature\" ;\n" + + "\t\tDry_Bulb_Temp:units = \"degree_C\" ;\n" + + "\tfloat Wet_Bulb_Temp(row) ;\n" + + "\t\tWet_Bulb_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tWet_Bulb_Temp:long_name = \"Wet_Bulb_Air_Temperature\" ;\n" + + "\t\tWet_Bulb_Temp:units = \"degree_C\" ;\n" + + "\tchar Weather_Condition(row, Weather_Condition_strlen) ;\n" + + "\t\tWeather_Condition:comment = \"Weather conditions at time of measurements\" ;\n" + + "\t\tWeather_Condition:long_name = \"Weather_Condition\" ;\n" + + "\tchar Cloud_Cover(row, Cloud_Cover_strlen) ;\n" + + "\t\tCloud_Cover:long_name = \"Cloud_Cover\" ;\n" + + "\t\tCloud_Cover:units_wod = \"WMO 2700 or NODC 0105\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tbyte Temperature_WODprofileflag(row) ;\n" + + "\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tbyte Salinity_WODprofileflag(row) ;\n" + + "\t\tSalinity_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tSalinity_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tfloat z(row) ;\n" + + "\t\tz:ancillary_variables = \"z_sigfigs z_WODflag\" ;\n" + + "\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"depth\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tbyte z_WODflag(row) ;\n" + + "\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + + "\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + + "\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_sigfigs(row) ;\n" + + "\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag\" ;\n" + + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\tbyte Temperature_sigfigs(row) ;\n" + + "\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + + "\tbyte Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tfloat Salinity(row) ;\n" + + "\t\tSalinity:_FillValue = -1.0E10f ;\n" + + "\t\tSalinity:ancillary_variables = \"Salinity_sigfigs Salinity_WODflag Salinity_WODprofileflag\" ;\n" + + "\t\tSalinity:coordinates = \"time lat lon z\" ;\n" + + "\t\tSalinity:grid_mapping = \"crs\" ;\n" + + "\t\tSalinity:long_name = \"sea_water_salinity\" ;\n" + + "\t\tSalinity:standard_name = \"sea_water_salinity\" ;\n" + + "\tbyte Salinity_sigfigs(row) ;\n" + + "\t\tSalinity_sigfigs:long_name = \"sea_water_salinity significant_figures\" ;\n" + + "\tbyte Salinity_WODflag(row) ;\n" + + "\t\tSalinity_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tSalinity_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tSalinity_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tSalinity_WODflag:standard_name = \"sea_water_salinity status_flag\" ;\n" + + "\tfloat Pressure(row) ;\n" + + "\t\tPressure:_FillValue = -1.0E10f ;\n" + + "\t\tPressure:ancillary_variables = \"Pressure_sigfigs Pressure_WODflag Pressure_WODprofileflag\" ;\n" + + "\t\tPressure:coordinates = \"time lat lon z\" ;\n" + + "\t\tPressure:grid_mapping = \"crs\" ;\n" + + "\t\tPressure:long_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:standard_name = \"sea_water_pressure\" ;\n" + + "\t\tPressure:units = \"dbar\" ;\n" + + "\tbyte Pressure_sigfigs(row) ;\n" + + "\t\tPressure_sigfigs:long_name = \"sea_water_pressure significant_figures\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, latitude, longitude, time, date, GMT_time, Access_no, Platform, Bottom_Depth, Wave_Height, Wave_Period, Wind_Direction, Wind_Speed, Barometric_Pres, Dry_Bulb_Temp, Wet_Bulb_Temp, Weather_Condition, Cloud_Cover, dataset, Temperature_WODprofileflag, Salinity_WODprofileflag\" ;\n" + + + "\t\t:Conventions = \"CF-1.6\" ;\n" + + "\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + + "\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:crs_inverse_flattening = 298.25723f ;\n" + + "\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:crs_semi_major_axis = 6378137.0f ;\n" + + "\t\t:date_created = \"2018-03-25\" ;\n" + + "\t\t:date_modified = \"2018-03-25\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 62.485f ;\n" + + "\t\t:geospatial_lat_min = 42.67f ;\n" + + "\t\t:geospatial_lat_resolution = \"point\" ;\n" + + "\t\t:geospatial_lon_max = -46.9317f ;\n" + + "\t\t:geospatial_lon_min = -65.84f ;\n" + + "\t\t:geospatial_lon_resolution = \"point\" ;\n" + + "\t\t:geospatial_vertical_max = 1443.402f ;\n" + + "\t\t:geospatial_vertical_min = 0.0f ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"meters\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_uor_2005.nc\" ;\n" + + "\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + + "\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + + "\t\t:project = \"World Ocean Database\" ;\n" + + "\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + + "\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + + "\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + + + "\t\t:source = \"World Ocean Database\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + + "\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + + "\t\t:time_coverage_end = \"2005-12-17\" ;\n" + + "\t\t:time_coverage_start = \"2005-01-08\" ;\n" + + "\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + + "}\n" + + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Bottom_Depth,Wave_Height,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Cover,dataset,Temperature_WODprofileflag,Salinity_WODprofileflag,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Pressure,Pressure_sigfigs\n" + + + "CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,0.0,0,1,1.321,4,0,33.597,5,0,0.0,1\n" + + + "CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,0.099147804,0,1,1.321,4,0,33.598,5,0,0.1,1\n" + + + "CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,0.19829556,0,1,1.321,4,0,33.601,5,0,0.2,1\n" + + + "CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,0.79318106,0,1,1.321,4,0,33.603,5,0,0.8,1\n" + + + "CANADA,CA155645,18TL05542,10742153,49.435,-50.725,85839.57291668653,20050108,13.75,98794,TELEOST (CGGS;R/V;c.s.CGCB;b.1988;ex.Atlantic Champion 1995;IMO8714346),326.0,2.5 METER,6 OR 7 SECONDS,285 DEGREES - 294 DEGREES,24.8832,1023.0,0.0,-0.1,CLOUDS GENERALLY DISSOLVING OF BECOMING LESS DEVELOPED-CHAR. CHANGE OF STATE OF SKY DURING PAST HR.,6 OKTAS 7/10-8/10,towed CTD,0,0,1.487212,0,2,1.321,4,0,33.604,5,0,1.5,2\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 1169159 - 5); + results = table.dataToString(); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,lat,lon,time,date,GMT_time,Access_no,Platform,Bottom_Depth,Wave_Height,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Cover,dataset,Temperature_WODprofileflag,Salinity_WODprofileflag,z,z_WODflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Salinity,Salinity_sigfigs,Salinity_WODflag,Pressure,Pressure_sigfigs\n" + + + "CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.47443,0,4,2.176,4,0,34.101,5,0,199.3,4\n" + + + "CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.57347,0,4,2.176,4,0,34.101,5,0,199.4,4\n" + + + "CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.6725,0,4,2.174,4,0,34.102,5,0,199.5,4\n" + + + "CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.77153,0,4,2.175,4,0,34.102,5,0,199.6,4\n" + + + "CANADA,CA019465,181C05632,10749307,51.2133,-53.85,86182.78125,20051217,18.75,2026318698,WILFRED TEMPLEMAN (CCGS;F/R/V;call sign CGDV; built 1981;IMO7907099),206.0,1.5 METER,5 SECONDS OR LESS,95 DEGREES - 104 DEGREES,19.8288,1032.0,-1.0E10,-1.0E10,CONTINUOUS FALL OF SNOW FLAKES-MODERATE AT TIME OF OBSERVATION,6 OKTAS 7/10-8/10,towed CTD,0,0,197.87054,0,4,2.178,4,0,34.102,5,0,199.7,4\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + // read outer and inner col with outer constraint + fullName = dir + "wod_uor_2005.nc"; + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "10749307" })); + results = table.dataToString(5); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "10749307,86182.78125,0.0,0.751,0\n" + + "10749307,86182.78125,0.099131815,0.776,0\n" + + "10749307,86182.78125,0.19826359,0.751,0\n" + + "10749307,86182.78125,0.29739532,0.777,0\n" + + "10749307,86182.78125,0.49565855,0.775,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // outer and inner constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "10749307", "0.751" })); + results = table.dataToString(); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "10749307,86182.78125,0.0,0.751,0\n" + + "10749307,86182.78125,0.19826359,0.751,0\n" + + "10749307,86182.78125,2.4782808,0.751,0\n" + + "10749307,86182.78125,4.0643644,0.751,0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** read all xbt + fullName = dir + "wod_xbt_2005.nc"; + if (doAll) { + table.readInvalidCRA(fullName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.toString(5); + expected = "{\n" + + "dimensions:\n" + + "\trow = 25164853 ;\n" + + "\tcountry_strlen = 14 ;\n" + + "\tWOD_cruise_identifier_strlen = 8 ;\n" + + "\toriginators_cruise_identifier_strlen = 15 ;\n" + + "\toriginators_station_identifier_strlen = 10 ;\n" + + "\tProject_strlen = 59 ;\n" + + "\tPlatform_strlen = 80 ;\n" + + "\tInstitute_strlen = 79 ;\n" + + "\tWater_Color_strlen = 37 ;\n" + + "\tWave_Height_strlen = 9 ;\n" + + "\tWave_Period_strlen = 17 ;\n" + + "\tWind_Direction_strlen = 25 ;\n" + + "\tWeather_Condition_strlen = 169 ;\n" + + "\tCloud_Type_strlen = 17 ;\n" + + "\tCloud_Cover_strlen = 65 ;\n" + + "\tdataset_strlen = 3 ;\n" + + "\tRecorder_strlen = 47 ;\n" + + "\tdepth_eq_strlen = 9 ;\n" + + "\tRef_Type_strlen = 6 ;\n" + + "\tVisibility_strlen = 24 ;\n" + + "\tneeds_z_fix_strlen = 39 ;\n" + + "\treal_time_strlen = 14 ;\n" + + "\tdbase_orig_strlen = 13 ;\n" + + "\torigflagset_strlen = 4 ;\n" + + "\tTemperature_Instrument_strlen = 34 ;\n" + + "\tPrimary_Investigator_strlen = 28 ;\n" + + "\tPrimary_Investigator_VAR_strlen = 13 ;\n" + + "variables:\n" + + "\tchar country(row, country_strlen) ;\n" + + "\tchar WOD_cruise_identifier(row, WOD_cruise_identifier_strlen) ;\n" + + "\t\tWOD_cruise_identifier:comment = \"two byte country code + WOD cruise number (unique to country code)\" ;\n" + + + "\t\tWOD_cruise_identifier:long_name = \"WOD_cruise_identifier\" ;\n" + + "\tchar originators_cruise_identifier(row, originators_cruise_identifier_strlen) ;\n" + + "\tint wod_unique_cast(row) ;\n" + + "\t\twod_unique_cast:cf_role = \"profile_id\" ;\n" + + "\tchar originators_station_identifier(row, originators_station_identifier_strlen) ;\n" + + "\t\toriginators_station_identifier:long_name = \"originators_station_identifier\" ;\n" + + "\tfloat lat(row) ;\n" + + "\t\tlat:long_name = \"latitude\" ;\n" + + "\t\tlat:standard_name = \"latitude\" ;\n" + + "\t\tlat:units = \"degrees_north\" ;\n" + + "\tfloat lon(row) ;\n" + + "\t\tlon:long_name = \"longitude\" ;\n" + + "\t\tlon:standard_name = \"longitude\" ;\n" + + "\t\tlon:units = \"degrees_east\" ;\n" + + "\tdouble time(row) ;\n" + + "\t\ttime:long_name = \"time\" ;\n" + + "\t\ttime:standard_name = \"time\" ;\n" + + "\t\ttime:units = \"days since 1770-01-01 00:00:00 UTC\" ;\n" + + "\tint date(row) ;\n" + + "\t\tdate:comment = \"YYYYMMDD\" ;\n" + + "\t\tdate:long_name = \"date\" ;\n" + + "\tfloat GMT_time(row) ;\n" + + "\t\tGMT_time:long_name = \"GMT_time\" ;\n" + + "\t\tGMT_time:units = \"hours\" ;\n" + + "\tint Access_no(row) ;\n" + + "\t\tAccess_no:_FillValue = -99999 ;\n" + + "\t\tAccess_no:comment = \"used to find original data at NODC\" ;\n" + + "\t\tAccess_no:long_name = \"NODC_accession_number\" ;\n" + + "\t\tAccess_no:units_wod = \"NODC_code\" ;\n" + + "\tchar Project(row, Project_strlen) ;\n" + + "\t\tProject:comment = \"name or acronym of project under which data were measured\" ;\n" + + "\t\tProject:long_name = \"Project_name\" ;\n" + + "\tchar Platform(row, Platform_strlen) ;\n" + + "\t\tPlatform:comment = \"name of platform from which measurements were taken\" ;\n" + + "\t\tPlatform:long_name = \"Platform_name\" ;\n" + + "\tchar Institute(row, Institute_strlen) ;\n" + + "\t\tInstitute:comment = \"name of institute which collected data\" ;\n" + + "\t\tInstitute:long_name = \"Responsible_institute\" ;\n" + + "\tint Orig_Stat_Num(row) ;\n" + + "\t\tOrig_Stat_Num:_FillValue = -99999 ;\n" + + "\t\tOrig_Stat_Num:comment = \"number assigned to a given station by data originator\" ;\n" + + "\t\tOrig_Stat_Num:long_name = \"Originators_Station_Number\" ;\n" + + "\tfloat Bottom_Depth(row) ;\n" + + "\t\tBottom_Depth:_FillValue = -1.0E10f ;\n" + + "\t\tBottom_Depth:standard_name = \"sea_floor_depth_below_sea_surface\" ;\n" + + "\t\tBottom_Depth:units = \"meters\" ;\n" + + "\tchar Water_Color(row, Water_Color_strlen) ;\n" + + "\t\tWater_Color:long_name = \"Water_Color\" ;\n" + + "\t\tWater_Color:units_wod = \"Forel-Ule scale (00 to 21)\" ;\n" + + "\tfloat Water_Transpar(row) ;\n" + + "\t\tWater_Transpar:_FillValue = -1.0E10f ;\n" + + "\t\tWater_Transpar:comment = \"Secchi disk depth\" ;\n" + + "\t\tWater_Transpar:long_name = \"Water_Transparency\" ;\n" + + "\t\tWater_Transpar:units = \"meters\" ;\n" + + "\tchar Wave_Height(row, Wave_Height_strlen) ;\n" + + "\t\tWave_Height:long_name = \"Wave_Height\" ;\n" + + "\t\tWave_Height:units_wod = \"WMO 1555 or NODC 0104\" ;\n" + + "\tchar Wave_Period(row, Wave_Period_strlen) ;\n" + + "\t\tWave_Period:long_name = \"Wave_Period\" ;\n" + + "\t\tWave_Period:units_wod = \"WMO 3155 or NODC 0378\" ;\n" + + "\tchar Wind_Direction(row, Wind_Direction_strlen) ;\n" + + "\t\tWind_Direction:long_name = \"Wind_Direction\" ;\n" + + "\t\tWind_Direction:units_wod = \"WMO 0877 or NODC 0110\" ;\n" + + "\tfloat Wind_Speed(row) ;\n" + + "\t\tWind_Speed:_FillValue = -1.0E10f ;\n" + + "\t\tWind_Speed:standard_name = \"wind_speed\" ;\n" + + "\t\tWind_Speed:units = \"knots\" ;\n" + + "\tfloat Barometric_Pres(row) ;\n" + + "\t\tBarometric_Pres:_FillValue = -1.0E10f ;\n" + + "\t\tBarometric_Pres:long_name = \"Barometric_Pressure\" ;\n" + + "\t\tBarometric_Pres:units = \"millibars\" ;\n" + + "\tfloat Dry_Bulb_Temp(row) ;\n" + + "\t\tDry_Bulb_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tDry_Bulb_Temp:long_name = \"Dry_Bulb_Air_Temperature\" ;\n" + + "\t\tDry_Bulb_Temp:units = \"degree_C\" ;\n" + + "\tfloat Wet_Bulb_Temp(row) ;\n" + + "\t\tWet_Bulb_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tWet_Bulb_Temp:long_name = \"Wet_Bulb_Air_Temperature\" ;\n" + + "\t\tWet_Bulb_Temp:units = \"degree_C\" ;\n" + + "\tchar Weather_Condition(row, Weather_Condition_strlen) ;\n" + + "\t\tWeather_Condition:comment = \"Weather conditions at time of measurements\" ;\n" + + "\t\tWeather_Condition:long_name = \"Weather_Condition\" ;\n" + + "\tchar Cloud_Type(row, Cloud_Type_strlen) ;\n" + + "\t\tCloud_Type:long_name = \"Cloud_Type\" ;\n" + + "\t\tCloud_Type:units_wod = \"WMO 0500 or NODC 0053\" ;\n" + + "\tchar Cloud_Cover(row, Cloud_Cover_strlen) ;\n" + + "\t\tCloud_Cover:long_name = \"Cloud_Cover\" ;\n" + + "\t\tCloud_Cover:units_wod = \"WMO 2700 or NODC 0105\" ;\n" + + "\tchar dataset(row, dataset_strlen) ;\n" + + "\t\tdataset:long_name = \"WOD_dataset\" ;\n" + + "\tchar Recorder(row, Recorder_strlen) ;\n" + + "\t\tRecorder:comment = \"Device which recorded measurements\" ;\n" + + "\t\tRecorder:long_name = \"Recorder\" ;\n" + + "\t\tRecorder:units_wod = \"WMO code 4770\" ;\n" + + "\tchar depth_eq(row, depth_eq_strlen) ;\n" + + "\t\tdepth_eq:comment = \"which drop rate equation was used\" ;\n" + + "\t\tdepth_eq:long_name = \"depth_equation_used\" ;\n" + + "\tbyte Bottom_Hit(row) ;\n" + + "\t\tBottom_Hit:_FillValue = -9 ;\n" + + "\t\tBottom_Hit:comment = \"set to one if instrument hit bottom\" ;\n" + + "\t\tBottom_Hit:long_name = \"Bottom_Hit\" ;\n" + + "\tchar Ref_Type(row, Ref_Type_strlen) ;\n" + + "\t\tRef_Type:comment = \"Instrument for reference temperature\" ;\n" + + "\t\tRef_Type:long_name = \"Reference_Instrument\" ;\n" + + "\tchar Visibility(row, Visibility_strlen) ;\n" + + "\t\tVisibility:long_name = \"Horizontal_visibility\" ;\n" + + "\t\tVisibility:units_wod = \"WMO Code 4300\" ;\n" + + "\tfloat Ref_Surf_Temp(row) ;\n" + + "\t\tRef_Surf_Temp:_FillValue = -1.0E10f ;\n" + + "\t\tRef_Surf_Temp:comment = \"Reference_or_Sea_Surface_Temperature\" ;\n" + + "\t\tRef_Surf_Temp:units = \"degree_C\" ;\n" + + "\tchar needs_z_fix(row, needs_z_fix_strlen) ;\n" + + "\t\tneeds_z_fix:comment = \"instruction for fixing depths\" ;\n" + + "\t\tneeds_z_fix:long_name = \"z_fix_instructions\" ;\n" + + "\t\tneeds_z_fix:units_wod = \"WOD_code\" ;\n" + + "\tchar real_time(row, real_time_strlen) ;\n" + + "\t\treal_time:comment = \"timeliness and quality status\" ;\n" + + "\t\treal_time:long_name = \"real_time_data\" ;\n" + + "\tfloat Launch_height(row) ;\n" + + "\t\tLaunch_height:_FillValue = -1.0E10f ;\n" + + "\t\tLaunch_height:long_name = \"Height_of_instrument_launch\" ;\n" + + "\t\tLaunch_height:units = \"meters\" ;\n" + + "\tfloat sensor_depth(row) ;\n" + + "\t\tsensor_depth:_FillValue = -1.0E10f ;\n" + + "\t\tsensor_depth:long_name = \"Depth_of_sea_surface_sensor\" ;\n" + + "\t\tsensor_depth:units = \"meters\" ;\n" + + "\tchar dbase_orig(row, dbase_orig_strlen) ;\n" + + "\t\tdbase_orig:comment = \"Database from which data were extracted\" ;\n" + + "\t\tdbase_orig:long_name = \"database_origin\" ;\n" + + "\tchar origflagset(row, origflagset_strlen) ;\n" + + "\t\torigflagset:comment = \"set of originators flag codes to use\" ;\n" + + "\tbyte Temperature_WODprofileflag(row) ;\n" + + "\t\tTemperature_WODprofileflag:flag_meanings = \"accepted annual_sd_out density_inversion cruise seasonal_sd_out monthly_sd_out annual+seasonal_sd_out anomaly_or_annual+monthly_sd_out seasonal+monthly_sd_out annual+seasonal+monthly_sd_out\" ;\n" + + + "\t\tTemperature_WODprofileflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODprofileflag:long_name = \"WOD_profile_flag\" ;\n" + + "\tchar Temperature_Instrument(row, Temperature_Instrument_strlen) ;\n" + + "\t\tTemperature_Instrument:comment = \"Device used for measurement\" ;\n" + + "\t\tTemperature_Instrument:long_name = \"Instrument\" ;\n" + + "\tchar Primary_Investigator(row, Primary_Investigator_strlen) ;\n" + + "\tchar Primary_Investigator_VAR(row, Primary_Investigator_VAR_strlen) ;\n" + + "\tfloat z(row) ;\n" + + "\t\tz:ancillary_variables = \"z_sigfigs z_WODflag z_origflag\" ;\n" + + "\t\tz:long_name = \"depth_below_sea_surface\" ;\n" + + "\t\tz:positive = \"down\" ;\n" + + "\t\tz:standard_name = \"depth\" ;\n" + + "\t\tz:units = \"m\" ;\n" + + "\tbyte z_WODflag(row) ;\n" + + "\t\tz_WODflag:flag_meanings = \"accepted duplicate_or_inversion density_inversion\" ;\n" + + "\t\tz_WODflag:flag_values = 0, 1, 2 ;\n" + + "\t\tz_WODflag:long_name = \"WOD_depth_level_flag\" ;\n" + + "\t\tz_WODflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_origflag(row) ;\n" + + "\t\tz_origflag:_FillValue = -9 ;\n" + + "\t\tz_origflag:comment = \"Originator flags are dependent on origflagset\" ;\n" + + "\t\tz_origflag:standard_name = \"depth status_flag\" ;\n" + + "\tbyte z_sigfigs(row) ;\n" + + "\t\tz_sigfigs:long_name = \"depth significant figures \" ;\n" + + "\tfloat Temperature(row) ;\n" + + "\t\tTemperature:_FillValue = -1.0E10f ;\n" + + "\t\tTemperature:ancillary_variables = \"Temperature_sigfigs Temperature_WODflag Temperature_WODprofileflag Temperature_origflag\" ;\n" + + + "\t\tTemperature:coordinates = \"time lat lon z\" ;\n" + + "\t\tTemperature:grid_mapping = \"crs\" ;\n" + + "\t\tTemperature:long_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:standard_name = \"sea_water_temperature\" ;\n" + + "\t\tTemperature:units = \"degree_C\" ;\n" + + "\tbyte Temperature_sigfigs(row) ;\n" + + "\t\tTemperature_sigfigs:long_name = \"sea_water_temperature significant_figures\" ;\n" + + "\tbyte Temperature_WODflag(row) ;\n" + + "\t\tTemperature_WODflag:flag_meanings = \"accepted range_out inversion gradient anomaly gradient+inversion range+inversion range+gradient range+anomaly range+inversion+gradient\" ;\n" + + + "\t\tTemperature_WODflag:flag_values = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 ;\n" + + "\t\tTemperature_WODflag:long_name = \"WOD_observation_flag\" ;\n" + + "\t\tTemperature_WODflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\tbyte Temperature_origflag(row) ;\n" + + "\t\tTemperature_origflag:_FillValue = -9 ;\n" + + "\t\tTemperature_origflag:flag_definitions = \"flag definitions dependent on origflagset\" ;\n" + + "\t\tTemperature_origflag:standard_name = \"sea_water_temperature status_flag\" ;\n" + + "\n" + + "// global attributes:\n" + + "\t\t:cdm_data_type = \"Profile\" ;\n" + + "\t\t:cdm_profile_variables = \"country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, originators_station_identifier, latitude, longitude, time, date, GMT_time, Access_no, Project, Platform, Institute, Orig_Stat_Num, Bottom_Depth, Water_Color, Water_Transpar, Wave_Height, Wave_Period, Wind_Direction, Wind_Speed, Barometric_Pres, Dry_Bulb_Temp, Wet_Bulb_Temp, Weather_Condition, Cloud_Type, Cloud_Cover, dataset, Recorder, depth_eq, Bottom_Hit, Ref_Type, Visibility, Ref_Surf_Temp, needs_z_fix, real_time, Launch_height, sensor_depth, dbase_orig, origflagset, Temperature_WODprofileflag, Temperature_Instrument, Primary_Investigator, Primary_Investigator_VAR\" ;\n" + + + "\t\t:Conventions = \"CF-1.6\" ;\n" + + "\t\t:creator_email = \"OCLhelp@noaa.gov\" ;\n" + + "\t\t:creator_name = \"Ocean Climate Lab/NCEI\" ;\n" + + "\t\t:creator_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:crs_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:crs_grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:crs_inverse_flattening = 298.25723f ;\n" + + "\t\t:crs_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:crs_semi_major_axis = 6378137.0f ;\n" + + "\t\t:date_created = \"2018-03-24\" ;\n" + + "\t\t:date_modified = \"2018-03-24\" ;\n" + + "\t\t:featureType = \"Profile\" ;\n" + + "\t\t:geospatial_lat_max = 79.0612f ;\n" + + "\t\t:geospatial_lat_min = -77.556f ;\n" + + "\t\t:geospatial_lat_resolution = \"point\" ;\n" + + "\t\t:geospatial_lon_max = -0.011505127f ;\n" + + "\t\t:geospatial_lon_min = 180.0f ;\n" + + "\t\t:geospatial_lon_resolution = \"point\" ;\n" + + "\t\t:geospatial_vertical_max = 3124.0f ;\n" + + "\t\t:geospatial_vertical_min = 0.0f ;\n" + + "\t\t:geospatial_vertical_positive = \"down\" ;\n" + + "\t\t:geospatial_vertical_units = \"meters\" ;\n" + + "\t\t:grid_mapping_epsg_code = \"EPSG:4326\" ;\n" + + "\t\t:grid_mapping_inverse_flattening = 298.25723f ;\n" + + "\t\t:grid_mapping_longitude_of_prime_meridian = 0.0f ;\n" + + "\t\t:grid_mapping_name = \"latitude_longitude\" ;\n" + + "\t\t:grid_mapping_semi_major_axis = 6378137.0f ;\n" + + "\t\t:id = \"/nodc/data/oc5.clim.0/wod_update_nc/2005/wod_xbt_2005.nc\" ;\n" + + "\t\t:institution = \"National Centers for Environmental Information (NCEI), NOAA\" ;\n" + + "\t\t:naming_authority = \"gov.noaa.nodc\" ;\n" + + "\t\t:project = \"World Ocean Database\" ;\n" + + "\t\t:publisher_email = \"NODC.Services@noaa.gov\" ;\n" + + "\t\t:publisher_name = \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION\" ;\n" + + "\t\t:publisher_url = \"http://www.nodc.noaa.gov\" ;\n" + + "\t\t:references = \"World Ocean Database 2013. URL:http://data.nodc.noaa.gov/woa/WOD/DOC/wod_intro.pdf\" ;\n" + + + "\t\t:source = \"World Ocean Database\" ;\n" + + "\t\t:standard_name_vocabulary = \"CF Standard Name Table v41\" ;\n" + + "\t\t:summary = \"Data for multiple casts from the World Ocean Database\" ;\n" + + "\t\t:time_coverage_end = \"2005-12-31\" ;\n" + + "\t\t:time_coverage_start = \"2005-01-01\" ;\n" + + "\t\t:title = \"World Ocean Database - Multi-cast file\" ;\n" + + "}\n" + + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Bottom_Depth,Water_Color,Water_Transpar,Wave_Height,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Ref_Type,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,Launch_height,sensor_depth,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag\n" + + + "UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,1.0,0,-9,2,5.0,4,0,-9\n" + + + "UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,5.0,0,-9,2,5.0,4,0,-9\n" + + + "UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,73.0,0,-9,3,5.1,4,0,-9\n" + + + "UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,77.0,0,-9,3,4.9,4,0,-9\n" + + + "UNITED STATES,US155628,WCY7054,10216693,,57.51,-147.63,85832.02569444478,20050101,0.6166667,1959,,HMI CAPE LOOKOUT SHOALS (Call Sign WCY7054),,2477204,-1.0E10,,-1.0E10,,,,-1.0E10,-1.0E10,-1.0E10,-1.0E10,,,,XBT,SIPPICAN MK-12,original,-9,,,-1.0E10,needs Hanawa et al.; 1994 applied (XBT),real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: DEEP BLUE (SIPPICAN),,,89.0,0,-9,3,5.0,4,0,-9\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.removeRows(0, 25164853 - 5); + results = table.dataToString(); + expected = "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast,originators_station_identifier,lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Orig_Stat_Num,Bottom_Depth,Water_Color,Water_Transpar,Wave_Height,Wave_Period,Wind_Direction,Wind_Speed,Barometric_Pres,Dry_Bulb_Temp,Wet_Bulb_Temp,Weather_Condition,Cloud_Type,Cloud_Cover,dataset,Recorder,depth_eq,Bottom_Hit,Ref_Type,Visibility,Ref_Surf_Temp,needs_z_fix,real_time,Launch_height,sensor_depth,dbase_orig,origflagset,Temperature_WODprofileflag,Temperature_Instrument,Primary_Investigator,Primary_Investigator_VAR,z,z_WODflag,z_origflag,z_sigfigs,Temperature,Temperature_sigfigs,Temperature_WODflag,Temperature_origflag\n" + + + "UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,88.0,0,-9,3,15.3,5,0,-9\n" + + + "UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,98.0,0,-9,3,15.1,5,0,-9\n" + + + "UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,102.0,0,-9,4,14.7,5,0,-9\n" + + + "UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,167.0,0,-9,4,14.7,5,0,-9\n" + + + "UNKNOWN,,,10731585,,36.55,13.6667,86196.0,20051231,9.96921E36,2516,,,,3028589,-1.0E10,,-1.0E10,,,165 DEGREES - 174 DEGREES,27.216,-1.0E10,-1.0E10,-1.0E10,,,,XBT,,,-9,,,-1.0E10,insufficient information,real-time data,-1.0E10,-1.0E10,GTSP Project,,0,XBT: TYPE UNKNOWN,,,200.0,0,-9,4,14.5,5,0,-9\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } + + // read outer and inner col with outer constraint + fullName = dir + "wod_xbt_2005.nc"; + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast" }), + new StringArray(new String[] { "=" }), + new StringArray(new String[] { "10731585" })); + results = table.dataToString(5); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "10731585,86196.0,0.0,15.8,0\n" + + "10731585,86196.0,23.0,15.7,0\n" + + "10731585,86196.0,47.0,15.3,0\n" + + "10731585,86196.0,50.0,15.4,0\n" + + "10731585,86196.0,65.0,15.2,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // outer and inner constraint + table.readInvalidCRA(fullName, + new StringArray(new String[] { "wod_unique_cast", "time", "z", "Temperature", "Temperature_WODflag" }), + 0, // standardizeWhat=0 + new StringArray(new String[] { "wod_unique_cast", "Temperature" }), + new StringArray(new String[] { "=", "=" }), + new StringArray(new String[] { "10731585", "15.3" })); + results = table.dataToString(); + expected = "wod_unique_cast,time,z,Temperature,Temperature_WODflag\n" + + "10731585,86196.0,47.0,15.3,0\n" + + "10731585,86196.0,88.0,15.3,0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + /* */ + + table.debugMode = false; + } + + /** + * This tests reading an ncCF Contiguous Ragged Array file with 7(!) + * sample_dimension's. + */ + @org.junit.jupiter.api.Test + void testReadNcCF7SampleDims() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCF7SampleDims"); + Table table = new Table(); + String results, expected; + // From Ajay Krishnan, NCEI/NODC, from + // https://data.nodc.noaa.gov/thredds/catalog/testdata/wod_ragged/05052016/catalog.html?dataset=testdata/wod_ragged/05052016/ind199105_ctd.nc + String fileName = TableTests.class.getResource("/nccf/ncei/ind199105_ctd.nc").getPath(); + Attributes gatts; + String scalarVars = ",crs,WODf,WODfd"; + + // String2.log("\n\n** Testing " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + // String2.pressEnterToContinue(NcHelper.ncdump(fileName, "-v crs;WODf;WODfd")); + // String2.pressEnterToContinue(NcHelper.ncdump(fileName, + // "-v + // Temperature_row_size;Salinity_row_size;Oxygen_row_size;Pressure_row_size;Chlorophyll_row_size")); + + // test reading just specified legit "z_obs" outer and inner variables + table.readNcCF(fileName, StringArray.fromCSV( + "zztop,wod_unique_cast,lat,lon,time,z,z_WODflag" + scalarVars), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = + // with netcdf-java 4.6.5 and before, the last 3 vars had 0's. + // with netcdf-java 4.6.6 and after, they are the default cf missing values + // Unidata says it is not a bug. 4.6.6 is correct. see email from Sean Arms June + // 15, 2016 + // I notified source of files: Ajay Krisnan, but he never replied. + // so I'm going with 4.6.6 and odd values + // was + // "wod_unique_cast,lat,lon,time,z,z_WODflag,crs,WODf,WODfd\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,2.9759612,0,0,0,0\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,3.967939,0,0,0,0\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,5.9518795,0,0,0,0\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,7.9358006,0,0,0,0\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,9.919703,0,0,0,0\n" + + // "...\n"; + "wod_unique_cast,lat,lon,time,z,z_WODflag,crs,WODf,WODfd\n" + + "3390296,-43.7802,67.3953,80838.31180554628,2.9759612,0,-2147483647,-32767,-32767\n" + + "3390296,-43.7802,67.3953,80838.31180554628,3.967939,0,-2147483647,-32767,-32767\n" + + "3390296,-43.7802,67.3953,80838.31180554628,5.9518795,0,-2147483647,-32767,-32767\n" + + "3390296,-43.7802,67.3953,80838.31180554628,7.9358006,0,-2147483647,-32767,-32767\n" + + "3390296,-43.7802,67.3953,80838.31180554628,9.919703,0,-2147483647,-32767,-32767\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test reading just specified legit "Temperature_obs" outer and inner variables + table.readNcCF(fileName, StringArray.fromCSV( + "zztop,wod_unique_cast,lat,lon,time,Temperature,Temperature_WODflag" + scalarVars), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = + // was + // "wod_unique_cast,lat,lon,time,Temperature,Temperature_WODflag,crs,WODf,WODfd\n" + // + + // "3390296,-43.7802,67.3953,80838.31180554628,14.519,0,0,0,0\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,14.526,0,0,0,0\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,14.537,0,0,0,0\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,14.533,0,0,0,0\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,14.532,0,0,0,0\n" + + // "...\n"; + "wod_unique_cast,lat,lon,time,Temperature,Temperature_WODflag,crs,WODf,WODfd\n" + + "3390296,-43.7802,67.3953,80838.31180554628,14.519,0,-2147483647,-32767,-32767\n" + + "3390296,-43.7802,67.3953,80838.31180554628,14.526,0,-2147483647,-32767,-32767\n" + + "3390296,-43.7802,67.3953,80838.31180554628,14.537,0,-2147483647,-32767,-32767\n" + + "3390296,-43.7802,67.3953,80838.31180554628,14.533,0,-2147483647,-32767,-32767\n" + + "3390296,-43.7802,67.3953,80838.31180554628,14.532,0,-2147483647,-32767,-32767\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test reading just specified legit outer variables + table.readNcCF(fileName, StringArray.fromCSV( + "zztop,wod_unique_cast,lat,lon,time" + scalarVars), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = + // was + // "wod_unique_cast,lat,lon,time,crs,WODf,WODfd\n" + + // "3390296,-43.7802,67.3953,80838.31180554628,0,0,0\n" + + // "3390301,-44.5177,67.9403,80838.68055558205,0,0,0\n" + + // "3390310,-45.2592,68.3755,80839.08888889104,0,0,0\n" + + // "3390318,-46.0113,68.7568,80839.39652776718,0,0,0\n" + + // "3390328,-47.0115,69.431,80839.87291669846,0,0,0\n" + + // "...\n"; + "wod_unique_cast,lat,lon,time,crs,WODf,WODfd\n" + + "3390296,-43.7802,67.3953,80838.31180554628,-2147483647,-32767,-32767\n" + + "3390301,-44.5177,67.9403,80838.68055558205,-2147483647,-32767,-32767\n" + + "3390310,-45.2592,68.3755,80839.08888889104,-2147483647,-32767,-32767\n" + + "3390318,-46.0113,68.7568,80839.39652776718,-2147483647,-32767,-32767\n" + + "3390328,-47.0115,69.431,80839.87291669846,-2147483647,-32767,-32767\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test reading just specified legit "Temperature_obs" inner variables + table.readNcCF(fileName, StringArray.fromCSV( + "zztop,Temperature,Temperature_WODflag" + scalarVars), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = + // was + // "Temperature,Temperature_WODflag,crs,WODf,WODfd\n" + + // "14.519,0,0,0,0\n" + + // "14.526,0,0,0,0\n" + + // "14.537,0,0,0,0\n" + + // "14.533,0,0,0,0\n" + + // "14.532,0,0,0,0\n" + + // "...\n"; + "Temperature,Temperature_WODflag,crs,WODf,WODfd\n" + + "14.519,0,-2147483647,-32767,-32767\n" + + "14.526,0,-2147483647,-32767,-32767\n" + + "14.537,0,-2147483647,-32767,-32767\n" + + "14.533,0,-2147483647,-32767,-32767\n" + + "14.532,0,-2147483647,-32767,-32767\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test reading just specified legit scalar variables + table.readNcCF(fileName, StringArray.fromCSV( + "zztop,WODf,crs"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = + // was + // "WODf,crs\n" + + // "0,0\n"; + "WODf,crs\n" + + "-32767,-2147483647\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test reading WHOLE file (should just catch z_obs dimension) + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(3); + expected = + // note it catches z_obs dimension (z, z_WODflag, z_sigfig), not others. + // Temperature_row_size, and Temperature_WODprofileflag are [casts], and don't + // use Temperature_obs. + "country,WOD_cruise_identifier,originators_cruise_identifier,wod_unique_cast," + + "lat,lon,time,date,GMT_time,Access_no,Project,Platform,Institute,Cast_Tow_number," + + "Orig_Stat_Num,Bottom_Depth,Cast_Duration,Cast_Direction,High_res_pair,dataset," + + "dbase_orig,origflagset,z,z_WODflag,z_sigfig,Temperature_row_size," + + "Temperature_WODprofileflag,Temperature_Scale,Temperature_Instrument," + + "Salinity_row_size,Salinity_WODprofileflag,Salinity_Scale,Salinity_Instrument," + + "Oxygen_row_size,Oxygen_WODprofileflag,Oxygen_Instrument,Oxygen_Original_units," + + "Pressure_row_size,Chlorophyll_row_size,Chlorophyll_WODprofileflag," + + "Chlorophyll_Instrument,Chlorophyll_uncalibrated,Conductivit_row_size,crs,WODf,WODfp,WODfd\n" + + + "FRANCE,FR008787,35MF68SUZIL,3390296,-43.7802,67.3953,80838.31180554628," + + "19910501,7.483333,841,WORLD OCEAN CIRCULATION EXPERIMENT (WOCE)," + + "MARION DUFRESNE (C.s.FNGB;built 1972;decomm-d 1995;renamed Fres;IMO7208388)," + + "NATIONAL MUSEUM OF NATURAL HISTORY (PARIS),1,37.0,4438.0,9.96921E36,,7498735," + + "CTD,WHO/CCHDO,WOCE,2.9759612,0,3,2204,0,,CTD: NEIL BROWN MARK IIIB,2204,0,," + + "CTD: NEIL BROWN MARK IIIB,2204,5,CTD: NEIL BROWN MARK IIIB,umol/kg,2204,0,0,," + + // was "-2147483647,0,0,0,0,0\n" + + "-2147483647,0,-2147483647,-32767,-32767,-32767\n" + + + "FRANCE,FR008787,35MF68SUZIL,3390296,-43.7802,67.3953,80838.31180554628," + + "19910501,7.483333,841,WORLD OCEAN CIRCULATION EXPERIMENT (WOCE)," + + "MARION DUFRESNE (C.s.FNGB;built 1972;decomm-d 1995;renamed Fres;IMO7208388)," + + "NATIONAL MUSEUM OF NATURAL HISTORY (PARIS),1,37.0,4438.0,9.96921E36,,7498735," + + "CTD,WHO/CCHDO,WOCE,3.967939,0,3,2204,0,,CTD: NEIL BROWN MARK IIIB,2204,0,," + + "CTD: NEIL BROWN MARK IIIB,2204,5,CTD: NEIL BROWN MARK IIIB,umol/kg,2204,0,0,," + + // was "-2147483647,0,0,0,0,0\n" + + "-2147483647,0,-2147483647,-32767,-32767,-32767\n" + + + "FRANCE,FR008787,35MF68SUZIL,3390296,-43.7802,67.3953,80838.31180554628," + + "19910501,7.483333,841,WORLD OCEAN CIRCULATION EXPERIMENT (WOCE)," + + "MARION DUFRESNE (C.s.FNGB;built 1972;decomm-d 1995;renamed Fres;IMO7208388)," + + "NATIONAL MUSEUM OF NATURAL HISTORY (PARIS),1,37.0,4438.0,9.96921E36,,7498735," + + "CTD,WHO/CCHDO,WOCE,5.9518795,0,3,2204,0,,CTD: NEIL BROWN MARK IIIB,2204,0,," + + "CTD: NEIL BROWN MARK IIIB,2204,5,CTD: NEIL BROWN MARK IIIB,umol/kg,2204,0,0,," + + // was "-2147483647,0,0,0,0,0\n" + + "-2147483647,0,-2147483647,-32767,-32767,-32767\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + results = table.globalAttributes().getString("cdm_data_type"); + expected = "Profile"; + Test.ensureEqual(results, expected, "results=\n" + results); + + results = table.globalAttributes().getString("subsetVariables"); + expected = "country, WOD_cruise_identifier, originators_cruise_identifier, wod_unique_cast, " + + "lat, lon, time, date, GMT_time, Access_no, Project, Platform, Institute, " + + "Cast_Tow_number, Orig_Stat_Num, Bottom_Depth, Cast_Duration, Cast_Direction, " + + "High_res_pair, dataset, dbase_orig, origflagset, Temperature_row_size, " + + "Temperature_WODprofileflag, Temperature_Scale, Temperature_Instrument, " + + "Salinity_row_size, Salinity_WODprofileflag, Salinity_Scale, Salinity_Instrument, " + + "Oxygen_row_size, Oxygen_WODprofileflag, Oxygen_Instrument, Oxygen_Original_units, " + + "Pressure_row_size, " + + "Chlorophyll_row_size, Chlorophyll_WODprofileflag, Chlorophyll_Instrument, " + + "Chlorophyll_uncalibrated, Conductivit_row_size, crs, WODf, WODfp, WODfd"; + Test.ensureEqual(results, expected, "results=\n" + results); + + results = table.globalAttributes().getString("cdm_profile_variables"); + // same expected + Test.ensureEqual(results, expected, "results=\n" + results); + + // test reading row_size vars -- are they actually read? + table.readNcCF(fileName, StringArray.fromCSV( + "zztop,z_row_size,Temperature_row_size,Salinity_row_size,Oxygen_row_size," + + "Pressure_row_size,Chlorophyll_row_size,Conductivity_row_size"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(7); + expected = // verified with dumpString above + "Temperature_row_size,Salinity_row_size,Oxygen_row_size,Pressure_row_size,Chlorophyll_row_size\n" + + "2204,2204,2204,2204,0\n" + + "1844,1844,1844,1844,0\n" + + "1684,1684,1684,1684,0\n" + + "1587,1587,1587,1587,0\n" + + "357,357,357,357,0\n" + + "34,34,0,34,34\n" + + "34,34,0,34,34\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test request for vars with 2 different sample_dimensions + // second sample_dim throws error + results = "shouldn't happen"; + try { + table.readNcCF(fileName, StringArray.fromCSV( + "zztop,wod_unique_cast,lat,lon,time,z,z_WODflag,Temperature,Temperature_WODflag" + scalarVars), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + + } catch (Throwable t2) { + results = t2.toString(); + } + expected = "Invalid request: loadVariables includes variables that use two different sample_dimension's (z_obs and Temperature_obs)."; + int po = Math.max(0, results.indexOf(expected)); + Test.ensureEqual(results.substring(po), expected, "results=\n" + results); + // Table.debugMode = oDebug; + } + + /** This tests readNcCF reading point files. */ + @org.junit.jupiter.api.Test + void testReadNcCFPoint() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCFPoint"); + Table table = new Table(); + String results, expected; + String fileName = TableTests.class.getResource("/CFPointConventions/point/point-H.1/point-H.1.nc").getPath(); + Attributes gatts; + + /* */ + // *************** point + // String2.log("\n\n** Testing " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + // String2.log(table.toCSVString()); + results = table.dataToString(5); + expected = "obs,lat,lon,alt,time,temperature,humidity\n" + + "0,41.0,112.0,7.745540487338979,573,26.225288,11.245576\n" + + "1,179.0,68.0,3.0855444414144264,2248,12.695349,67.73824\n" + + "2,10.0,11.0,3.254759157455159,71,21.193731,48.589462\n" + + "3,106.0,22.0,4.549437636401848,1714,35.339344,39.594116\n" + + "4,75.0,16.0,6.061720687265453,1209,22.593496,28.170149\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.readNcCF(fileName, StringArray.fromCSV( + "row,obs,lat,lon,alt,time,temperature,humidity"), + 0, // standardizeWhat=0 + StringArray.fromCSV(""), + StringArray.fromCSV(""), + StringArray.fromCSV("")); + results = table.dataToString(5); + // expected is same + Test.ensureEqual(results, expected, "results=\n" + results); + + results = table.columnAttributes(6).toString(); + expected = " coordinates=time lat lon alt\n" + + " long_name=Humidity\n" + + " missing_value=-999.9f\n" + + " standard_name=specific_humidity\n" + + " units=Percent\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + results = table.globalAttributes().toString(); + expected = " Conventions=CF-1.6\n" + + " featureType=point\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.readNcCF(fileName, StringArray.fromCSV( + "obs,lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("obs"), + StringArray.fromCSV("="), + StringArray.fromCSV("2")); + results = table.dataToString(); + expected = "obs,lat,time,temperature\n" + + "2,10.0,71,21.193731\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.readNcCF(fileName, StringArray.fromCSV( + "obs,lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("71")); + results = table.dataToString(); + expected = "obs,lat,time,temperature\n" + + "2,10.0,71,21.193731\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.readNcCF(fileName, StringArray.fromCSV( + "obs,lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("21.193731")); + results = table.dataToString(); + expected = "obs,lat,time,temperature\n" + + "2,10.0,71,21.193731\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // this is important test of just getting dimension values + // (when there is no corresponding variable) + table.readNcCF(fileName, StringArray.fromCSV( + "obs"), + 0, // standardizeWhat=0 + StringArray.fromCSV("obs"), + StringArray.fromCSV("="), + StringArray.fromCSV("2")); + results = table.dataToString(); + expected = "obs\n" + + "2\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // and test that it gets the global attributes from the file. + results = table.globalAttributes().toString(); + expected = " Conventions=CF-1.6\n" + + " featureType=point\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("21.193731")); + results = table.dataToString(); + expected = "temperature\n" + + "21.193731\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "obs,lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("obs"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "obs,lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "obs,lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("obs"), + 0, // standardizeWhat=0 + StringArray.fromCSV("obs"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + + // String2.log("\n*** Table.testReadNcCFPoint finished successfully"); + // Table.debugMode = oDebug; + } + + /** This tests readNcCF nLevels=1. */ + @org.junit.jupiter.api.Test + @TagLargeFile + void testReadNcCF1() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCF1"); + Table table = new Table(); + String results, expected; + String profileFileName = TableTests.class.getResource("/nccf/Profile.nc").getPath(); + Attributes gatts; + + /* */ + // *************** contiguous profileFileName + // String2.log("\n\n** Testing profile contiguousRagged\n" + + // " " + profileFileName); + // String2.log(NcHelper.ncdump(profileFileName, "-h")); + + // String2.log("\n\n** Test nLevels=1/contiguousRagged no loadVars, no constraints"); + table.readNcCF(profileFileName, null, 0, // standardizeWhat=0 + null, null, null); + // String2.log(table.toCSVString()); + results = table.dataToString(5); + expected = "id,longitude,latitude,time,altitude,chlorophyll,chlorophyll_qc,oxygen,oxygen_qc,pressure,pressure_qc,salinity,salinity_qc,temperature,temperature_qc\n" + + + "465958,163.08,39.0,1.107754559E9,-2.0,,,,,,,,,10.1,0.0\n" + + "465958,163.08,39.0,1.107754559E9,-58.0,,,,,,,,,9.9,0.0\n" + + "465958,163.08,39.0,1.107754559E9,-96.0,,,,,,,,,9.2,0.0\n" + + "465958,163.08,39.0,1.107754559E9,-138.0,,,,,,,,,8.8,0.0\n" + + "465958,163.08,39.0,1.107754559E9,-158.0,,,,,,,,,8.1,0.0\n" + + "...\n"; + Test.ensureEqual(results, expected, ""); + Test.ensureEqual(table.nRows(), 118, table.toString()); + results = table.columnAttributes(0).toString(); + expected = " actual_range=465958i,848984i\n" + + " cf_role=profile_id\n" + + " colorBarMaximum=1000000.0d\n" + + " colorBarMinimum=0.0d\n" + + " ioos_category=Identifier\n" + + " long_name=Sequence ID\n" + + " missing_value=2147483647i\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "id, longitude, latitude, time", gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "id, longitude, latitude, time", gatts.toString()); + + // + // String2.log("\n\n** Test 1 non-existent loadVar test:ncCFcc.set(27)"); + table.readNcCF(profileFileName, StringArray.fromCSV("zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV(""), + StringArray.fromCSV(""), + StringArray.fromCSV("")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + // String2.log("\n\n** Test nLevels=1/contiguousRagged " + + // "many loadVars, constraints, NO_DATA"); + table.readNcCF(profileFileName, StringArray.fromCSV( + "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("id"), + StringArray.fromCSV("="), + StringArray.fromCSV("zztop")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(profileFileName, StringArray.fromCSV( + "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("id"), + StringArray.fromCSV("="), + StringArray.fromCSV("zztop")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(profileFileName, StringArray.fromCSV( + "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("longitude"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(profileFileName, StringArray.fromCSV( + "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(profileFileName, StringArray.fromCSV( + "id,longitude,latitude,time,altitude,salinity,salinity_qc,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + // String2.log("\n\n** Test nLevels=1/contiguousRagged " + + // "just outerTable loadVars, no constraints"); + table.readNcCF(profileFileName, + StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "longitude,latitude,time,id\n" + + "163.08,39.0,1.107754559E9,465958\n" + + "225.84,16.05,1.1077371E9,580888\n" + + "225.4,15.11,1.107751391E9,580889\n" + + "225.0,14.25,1.107764388E9,580890\n" + + "224.49,13.23,1.10778048E9,580891\n" + + "214.66,54.8,1.107759959E9,848984\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "id, longitude, latitude, time", gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "id, longitude, latitude, time", gatts.toString()); + + table.readNcCF(profileFileName, + StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, // standardizeWhat=0 + StringArray.fromCSV("id"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(profileFileName, + StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, // standardizeWhat=0 + StringArray.fromCSV("latitude"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(profileFileName, + StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + // String2.log("\n\n** Test nLevels=1/contiguousRagged " + + // "just outerTable loadVars, constraints"); + table.readNcCF(profileFileName, + StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, // standardizeWhat=0 + + StringArray.fromCSV("id"), + StringArray.fromCSV("="), + StringArray.fromCSV("848984")); + results = table.dataToString(); + expected = "longitude,latitude,time,id\n" + + "214.66,54.8,1.107759959E9,848984\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "id, longitude, latitude, time", gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "id, longitude, latitude, time", gatts.toString()); + + // String2.log("\n\n** Test nLevels=1/contiguousRagged " + + // "just outerTable loadVars, constraints, NO_DATA"); + table.readNcCF(profileFileName, + StringArray.fromCSV("longitude,latitude,time,zztop,id"), 0, // standardizeWhat=0 + StringArray.fromCSV("id"), + StringArray.fromCSV("="), + StringArray.fromCSV("zztop")); + Test.ensureEqual(table.nColumns(), 0, ""); + Test.ensureEqual(table.nRows(), 0, ""); + + // String2.log("\n\n** Test nLevels=1/contiguousRagged, specific loadVars, constraints"); + table.readNcCF(profileFileName, StringArray.fromCSV( + "longitude,latitude,time,altitude,temperature,temperature_qc,zztop,id"), + 0, // standardizeWhat=0 + StringArray.fromCSV("id,temperature"), + StringArray.fromCSV("=,>="), + StringArray.fromCSV("848984,5")); + results = table.dataToString(); + expected = "longitude,latitude,time,altitude,temperature,temperature_qc,id\n" + + "214.66,54.8,1.107759959E9,-2.0,5.8,0.0,848984\n" + + "214.66,54.8,1.107759959E9,-95.0,5.6,0.0,848984\n" + + "214.66,54.8,1.107759959E9,-101.0,5.4,0.0,848984\n" + + "214.66,54.8,1.107759959E9,-107.0,5.0,0.0,848984\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "id, longitude, latitude, time", gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "id, longitude, latitude, time", gatts.toString()); + + // String2.log("\n\n** Test nLevels=1/contiguousRagged just obs loadVars, no constraints"); + table.readNcCF(profileFileName, + StringArray.fromCSV("salinity,temperature,zztop"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "salinity,temperature\n" + + ",10.1\n" + + ",9.9\n" + + ",9.2\n" + + ",8.8\n" + + ",8.1\n" + + ",8.1\n" + + ",7.4\n" + + ",6.7\n" + + ",6.0\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 118, table.dataToString()); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + null, gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + null, gatts.toString()); + + table.readNcCF(profileFileName, + StringArray.fromCSV("salinity"), 0, // standardizeWhat=0 + StringArray.fromCSV("salinity"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + // String2.log("\n\n** Test nLevels=1/contiguousRagged just obs loadVars, constraints"); + table.readNcCF(profileFileName, + StringArray.fromCSV("temperature,zztop"), 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">"), + StringArray.fromCSV("24.5")); + results = table.dataToString(); + expected = "temperature\n" + + "24.8\n" + + "24.7\n" + + "25.0\n" + + "24.9\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "Profile", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + null, gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + null, gatts.toString()); + + // String2.log("\n\n** Test nLevels=1/contiguousRagged " + + // "just obs loadVars, constraints, NO_DATA"); + table.readNcCF(profileFileName, + StringArray.fromCSV("temperature,zztop"), 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-195")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // test quick reject + // if (constraintVar!=NaN or constraintVar=(finite)) and var not in file, + // String2.log("\n\n** Test #1m quick reject var=(nonNumber) if var not in file: NO_DATA"); + table.readNcCF(profileFileName, + StringArray.fromCSV("temperature,zzStation"), 0, // standardizeWhat=0 + StringArray.fromCSV("zzStation"), + StringArray.fromCSV("="), + StringArray.fromCSV("WXURP")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Test #1n quick reject var!=\"\" if var not in file: NO_DATA"); + table.readNcCF(profileFileName, + StringArray.fromCSV("temperature,zzStation"), 0, // standardizeWhat=0 + StringArray.fromCSV("zzStation"), + StringArray.fromCSV("!="), + new StringArray(new String[] { "" })); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // but this can't be quickly rejected + // String2.log("\n\n** Test #1o can't quick reject var=99 if var not in file\n" + + // "(since 99 might be defined as missing_value)"); + table.readNcCF(profileFileName, + StringArray.fromCSV("temperature,zzStation"), 0, // standardizeWhat=0 + StringArray.fromCSV("zzStation"), + StringArray.fromCSV("="), + new StringArray(new String[] { "99" })); + Test.ensureEqual(table.nRows(), 118, ""); + Test.ensureEqual(table.nColumns(), 1, ""); + + /* */ + // *************** nLevels=1 TimeSeries + for (int type = 0; type < 2; type++) { + // ncCF1b and ncCFMA1b have same data, so tests are the same! + String fileType = type == 0 ? "contiguous" : "multidimensional"; + // from EDDTableFromNcFiles.testNcCF1b() and testNcCFMA1b(); + String fileName = TableTests.class.getResource("/nccf/" + (type == 0 ? "ncCF1b.nc" : "ncCFMA1b.nc")).getPath(); + + // String2.log("\n\n** Testing nLevels=1/" + fileType + "\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + + // String2.log("\n\n** Test nLevels=1/" + fileType + " no loadVars, no constraints"); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + // String2.log(table.toString()); + results = table.dataToString(5); + expected = "line_station,longitude,latitude,altitude,time,obsScientific,obsValue,obsUnits\n" + + "076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Argyropelecus sladeni,2,number of larvae\n" + + "076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Chauliodus macouni,3,number of larvae\n" + + "076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Danaphos oculatus,4,number of larvae\n" + + "076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Diogenichthys atlanticus,3,number of larvae\n" + + "076.7_100,-124.32333,33.388332,-214.1,1.10064E9,Idiacanthus antrostomus,3,number of larvae\n" + + "...\n"; + Test.ensureEqual(results, expected, ""); + Test.ensureEqual(table.nRows(), 23, table.toString()); + results = table.columnAttributes(0).toString(); + expected = " cf_role=timeseries_id\n" + + " ioos_category=Identifier\n" + + " long_name=CalCOFI Line + Station\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), + "line_station", gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "line_station", gatts.toString()); + + table.readNcCF(fileName, StringArray.fromCSV(""), 0, // standardizeWhat=0 + StringArray.fromCSV("line_station"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV(""), 0, // standardizeWhat=0 + StringArray.fromCSV("longitude"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV(""), 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV(""), 0, // standardizeWhat=0 + StringArray.fromCSV("obsValue"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + // String2.log("\n\n** Test nLevels=1/" + fileType + " " + + // "just outerTable loadVars, no constraints"); + table.readNcCF(fileName, StringArray.fromCSV( + "line_station,zztop"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "line_station\n" + + "076.7_100\n" + + "080_100\n" + + "083.3_100\n"; // 4 row with all mv was removed + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), + "line_station", gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "line_station", gatts.toString()); + + table.readNcCF(fileName, StringArray.fromCSV("line_station"), + 0, // standardizeWhat=0 + StringArray.fromCSV("line_station"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + // String2.log("\n\n** Test nLevels=1/" + fileType + " " + + // "just outerTable loadVars, constraints"); + table.readNcCF(fileName, StringArray.fromCSV("line_station,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("line_station"), + StringArray.fromCSV("="), + StringArray.fromCSV("083.3_100")); + results = table.dataToString(); + expected = "line_station\n" + + "083.3_100\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), + "line_station", gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "line_station", gatts.toString()); + + // String2.log("\n\n** Test nLevels=1/" + fileType + " " + + // "just outerTable loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, + StringArray.fromCSV("line_station,zztop"), 0, // standardizeWhat=0 + StringArray.fromCSV("line_station"), + StringArray.fromCSV("="), + StringArray.fromCSV("zztop")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Test nLevels=1/" + fileType + ", specific loadVars, constraints"); + table.readNcCF(fileName, StringArray.fromCSV( + "longitude,latitude,altitude,time,line_station,zztop,obsScientific,obsValue,obsUnits"), + 0, // standardizeWhat=0 + StringArray.fromCSV("line_station,obsValue"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("083.3_100,1")); + results = table.dataToString(); + expected = "longitude,latitude,altitude,time,line_station,obsScientific,obsValue,obsUnits\n" + + "-123.49333,32.245,-211.5,1.10027676E9,083.3_100,Argyropelecus sladeni,1,number of larvae\n" + + "-123.49333,32.245,-211.5,1.10027676E9,083.3_100,Diogenichthys atlanticus,1,number of larvae\n" + + "-123.49333,32.245,-211.5,1.10027676E9,083.3_100,Idiacanthus antrostomus,1,number of larvae\n" + + "-123.49333,32.245,-211.5,1.10027676E9,083.3_100,Tetragonurus cuvieri,1,number of larvae\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), + "line_station", gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "line_station", gatts.toString()); + + // String2.log("\n\n** Test nLevels=1/" + fileType + + // ", specific loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, StringArray.fromCSV( + "longitude,latitude,altitude,time,line_station,zztop,obsScientific,obsValue,obsUnits"), + 0, // standardizeWhat=0 + StringArray.fromCSV("line_station,obsValue"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("083.3_100,-9")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Test nLevels=1/" + fileType + " just obs loadVars, no constraints"); + table.readNcCF(fileName, StringArray.fromCSV( + "obsScientific,obsValue,obsUnits,zztop"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "obsScientific,obsValue,obsUnits\n" + + "Argyropelecus sladeni,2,number of larvae\n" + + "Chauliodus macouni,3,number of larvae\n" + + "Danaphos oculatus,4,number of larvae\n" + + "Diogenichthys atlanticus,3,number of larvae\n" + + "Idiacanthus antrostomus,3,number of larvae\n" + + "Lestidiops ringens,1,number of larvae\n" + + "Melamphaes lugubris,1,number of larvae\n" + + "Protomyctophum crockeri,4,number of larvae\n" + + "Stenobrachius leucopsarus,1,number of larvae\n" + + "Total Fish Larvae,22,number of larvae\n" + + "Argyropelecus affinis,1,number of larvae\n" + + "Argyropelecus sladeni,2,number of larvae\n" + + "Danaphos oculatus,1,number of larvae\n" + + "Idiacanthus antrostomus,2,number of larvae\n" + + "Melamphaes parvus,1,number of larvae\n" + + "Nannobrachium spp,2,number of larvae\n" + + "Protomyctophum crockeri,1,number of larvae\n" + + "Total Fish Larvae,10,number of larvae\n" + + "Argyropelecus sladeni,1,number of larvae\n" + + "Diogenichthys atlanticus,1,number of larvae\n" + + "Idiacanthus antrostomus,1,number of larvae\n" + + "Tetragonurus cuvieri,1,number of larvae\n" + + "Total Fish Larvae,4,number of larvae\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), + null, gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + null, gatts.toString()); + + table.readNcCF(fileName, StringArray.fromCSV("obsScientific"), + 0, // standardizeWhat=0 + StringArray.fromCSV("obsScientific"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + // String2.log("\n\n** Test nLevels=1/" + fileType + " just obs loadVars, constraints"); + table.readNcCF(fileName, + StringArray.fromCSV("obsScientific,obsValue,obsUnits,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("obsValue"), + StringArray.fromCSV("="), + StringArray.fromCSV("4")); + results = table.dataToString(); + expected = "obsScientific,obsValue,obsUnits\n" + + "Danaphos oculatus,4,number of larvae\n" + + "Protomyctophum crockeri,4,number of larvae\n" + + "Total Fish Larvae,4,number of larvae\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TimeSeries", gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_timeseries_variables"), + null, gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + null, gatts.toString()); + + // String2.log("\n\n** Test nLevels=1/" + fileType + + // " just obs loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, + StringArray.fromCSV("obsScientific,obsValue,obsUnits,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("obsValue"), + StringArray.fromCSV("="), + StringArray.fromCSV("-99")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + } // end nLevels=1 type loop + + /* */ + // ********* expected errors + // String2.log("\n** Expected errors"); + try { + table.readNcCF(TableTests.class.getResource("/nccf/badIndexed1To6.nc").getPath(), null, + 0, // standardizeWhat=0 + null, null, null); + throw new SimpleException("Shouldn't get here."); + + } catch (Exception e) { + if (e.toString().indexOf( + "Invalid file: The index values must be 0 - 5, but parentIndex[88]=6.") < 0) + throw e; + } + + // ******* another test file, from Kevin O'Brien + try { + table.readNcCF("c:/data/kevin/interpolated_gld.20120620_045152_meta_2.nc", + null, 0, // standardizeWhat=0 + null, null, null); + throw new SimpleException("Shouldn't get here."); + + } catch (Exception e) { + if (e.toString().indexOf( + "Invalid contiguous ragged file: The sum of the values in the rowSizes " + + "variable (rowSize sum=1024368) is greater than the size of the " + + "observationDimension (obs size=1022528).") < 0) + throw e; + } + + /* */ + // Table.debugMode = oDebug; + } + + /** This tests readNcCF nLevels=1. */ + @org.junit.jupiter.api.Test + @TagLargeFile + void testReadNcCF1Kevin() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCF1Kevin"); + Table table = new Table(); + String results, expected; + String fileName = "c:/data/kevin/interpolated_gld.20120620_045152_meta_2.nc"; // from Kevin O'Brien + Attributes gatts; + + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + // String2.log(table.toString()); + // Table.debugMode = oDebug; + } + + /** This tests reading the gocd nccf files. */ + @org.junit.jupiter.api.Test + void testReadGocdNcCF() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadGocdNcCF"); + Table table = new Table(); + String results, expected; + String fileName; + int po; + ByteArrayOutputStream os = new ByteArrayOutputStream(); + + /* + * //*************** non-standard timeSeries file -- TOO WEIRD, don't support it + * //some var var[time=7022][z=1], depth[z=1] + * //and other station vars (latitude, longitude) with no dimensions + * fileName = "/data/gocd/gocdNcCF/gocd_v3_cmetr.nc"; + * String2.log("\n\n** Testing " + fileName); + * String2.log(NcHelper.ncdump(fileName, "-h")); + * // dimensions: + * // z = 1; + * // time = 7022; + * // float sampling_interval; // :_FillValue = 9999.9f; // float + * // float seafloor_depth; + * // float latitude; + * // float longitude; + * // int latitude_quality_flag; + * // int longitude_quality_flag; + * // int crs; + * + * // float depth(z=1); + * // int depth_quality_flag(z=1); + * + * // double time(time=7022); + * // int time_quality_flag(time=7022); + * + * // float u(time=7022, z=1); + * // int u_quality_flag(time=7022, z=1); + * // float v(time=7022, z=1); + * // int v_quality_flag(time=7022, z=1); + * // float current_speed(time=7022, z=1); + * // int current_speed_quality_flag(time=7022, z=1); + * // float current_direction(time=7022, z=1); + * // int current_direction_quality_flag(time=7022, z=1); + * + * // global attributes: + * // :gocd_id = "gocd_a0084999_tr1162.nc"; + * // :id = "0093183"; + * // :featureType = "timeSeries"; + * // :cdm_data_type = "Station"; + * // :instrument_type = ""; + * table.readNcCF(fileName, null, 0, //standardizeWhat=0 + * null, null, null); + * //String2.log(table.toCSVString()); + * results = table.dataToString(5); + * expected = + * "zztop\n"; + * Test.ensureEqual(results, expected, "results=\n" + results); + * /* + */ + + // *************** trajectory profile + // This is important test of Table.readNcCF + // if multidimensional file, 2 levels, and outerDim=ScalarDim + // this tests if var[scalarDim][obs] was read (e.g., depth[obs] + // File dims are outerDim=[scalarDim], inner=[time], obs=[obs] + table = new Table(); + fileName = TableTests.class.getResource("/gocdNcCF/gocd_v3_sadcp.nc").getPath(); + // String2.log("\n\n** Testing " + fileName); + results = NcHelper.ncdump(fileName, "-h"); + // String2.log(results); + // just the structure, rearranged into groups + // dimensions: + // time = 501; + // z = 70; + + // float sampling_interval; + // int crs; + // + // float seafloor_depth(time=501); + // float latitude(time=501); + // float longitude(time=501); + // double time(time=501); + // int latitude_quality_flag(time=501); + // int longitude_quality_flag(time=501); + // int time_quality_flag(time=501); + // + // float depth(z=70); + // int depth_quality_flag(z=70); + // + // float u(time=501, z=70); + // int u_quality_flag(time=501, z=70); + // float v(time=501, z=70); + // int v_quality_flag(time=501, z=70); + // float current_speed(time=501, z=70); + // int current_speed_quality_flag(time=501, z=70); + // float current_direction(time=501, z=70); + // int current_direction_quality_flag(time=501, z=70); + + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + os.reset(); + table.saveAsDAS(os, Table.SEQUENCE_NAME); + results = os.toString(); + expected = "Attributes {\n" + + " s {\n" + + " sampling_interval {\n" + + " Float32 _FillValue 9999.9;\n" + + " String long_name \"Sampling Interval\";\n" + + " String units \"minutes\";\n" + + " }\n" + + " seafloor_depth {\n" + + " Float32 _FillValue 9999.9;\n" + + " String long_name \"Seafloor Depth\";\n" + + " String postive \"down\";\n" + + " String units \"meters\";\n" + + " }\n" + + " latitude {\n" + + " Float32 _FillValue 9999.9;\n" + + " String ancillary_variables \"latitude_quality_flag\";\n" + + " String axis \"Y\";\n" + + " Float64 data_max 21.0958;\n" + + " Float64 data_min -14.3883;\n" + + " String grid_mapping \"crs\";\n" + + " String long_name \"latitude\";\n" + + " String standard_name \"latitude\";\n" + + " String units \"degrees_north\";\n" + + " Float32 valid_max 90.0;\n" + + " Float32 valid_min -90.0;\n" + + " }\n" + + " longitude {\n" + + " Float32 _FillValue 9999.9;\n" + + " String ancillary_variables \"longitude_quality_flag\";\n" + + " String axis \"X\";\n" + + " Float64 data_max -158.3554;\n" + + " Float64 data_min -176.8126;\n" + + " String grid_mapping \"crs\";\n" + + " String long_name \"longitude\";\n" + + " String standard_name \"longitude\";\n" + + " String units \"degrees_east\";\n" + + " Float32 valid_max 180.0;\n" + + " Float32 valid_min -180.0;\n" + + " }\n" + + " latitude_quality_flag {\n" + + " Int32 _FillValue -9;\n" + + " String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + + + " Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + + " String long_name \"Latitude Quality Flag\";\n" + + " }\n" + + " longitude_quality_flag {\n" + + " Int32 _FillValue -9;\n" + + " String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + + + " Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + + " String long_name \"Longitude Quality Flag\";\n" + + " }\n" + + " depth {\n" + + " String C_format \"%7.2f\";\n" + + " Float64 data_max 720.0;\n" + + " Float64 data_min 30.0;\n" + + " String FORTRAN_format \"F7.2\";\n" + + " String long_name \"Depth\";\n" + + " String postive \"down\";\n" + + " String units \"meters\";\n" + + " Float32 valid_max 15000.0;\n" + + " Float32 valid_min 0.0;\n" + + " }\n" + + " depth_quality_flag {\n" + + " Int32 _FillValue -9;\n" + + " String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + + + " Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + + " String long_name \"Depth QC Flags\";\n" + + " }\n" + + " time {\n" + + " String ancillary_variables \"time_quality_flag\";\n" + + " String axis \"T\";\n" + + " String C_format \"%9.4f\";\n" + + " Float64 data_max 38751.8319444442;\n" + + " Float64 data_min 38730.9986111112;\n" + + " String FORTRAN_format \"F9.4\";\n" + + " String long_name \"time\";\n" + + " String standard_name \"time\";\n" + + " String units \"days since 1900-01-01 00:00:00Z\";\n" + + " }\n" + + " time_quality_flag {\n" + + " Int32 _FillValue -9;\n" + + " String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + + + " Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + + " String long_name \"Time Quality Flag\";\n" + + " }\n" + + " u {\n" + + " Float32 _FillValue 9999.9;\n" + + " String ancillary_variables \"u_quality_flag\";\n" + + " String C_format \"%7.4f\";\n" + + " String cell_methods \"time:point z:point\";\n" + + " String coordinates \"time z\";\n" + + " Float64 data_max 0.883000030517578;\n" + + " Float64 data_min -1.25;\n" + + " String FORTRAN_format \"F7.4\";\n" + + " String grid_mapping \"crs\";\n" + + " String long_name \"Eastward Velocity Component\";\n" + + " String standard_name \"eastward_sea_water_velocity\";\n" + + " String units \"m s-1\";\n" + + " Float64 valid_max 5.0;\n" + + " Float64 valid_min -5.0;\n" + + " }\n" + + " u_quality_flag {\n" + + " Int32 _FillValue -9;\n" + + " String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + + + " Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + + " String long_name \"Eastward Velocity component QC Flags\";\n" + + " }\n" + + " v {\n" + + " Float32 _FillValue 9999.9;\n" + + " String ancillary_variables \"v_quality_flag\";\n" + + " String C_format \"%7.4f\";\n" + + " String cell_methods \"time:point z:point\";\n" + + " String coordinates \"time z\";\n" + + " Float64 data_max 0.733;\n" + + " Float64 data_min -0.695;\n" + + " String FORTRAN_format \"F7.4\";\n" + + " String grid_mapping \"crs\";\n" + + " String long_name \"Northward Velocity Component\";\n" + + " String standard_name \"northward_sea_water_velocity\";\n" + + " String units \"m s-1\";\n" + + " Float64 valid_max 5.0;\n" + + " Float64 valid_min -5.0;\n" + + " }\n" + + " v_quality_flag {\n" + + " Int32 _FillValue -9;\n" + + " String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + + + " Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + + " String long_name \"Northward Velocity component QC Flags\";\n" + + " }\n" + + " current_speed {\n" + + " Float32 _FillValue 9999.9;\n" + + " String ancillary_variables \"current_direction_quality_flag\";\n" + + " String C_format \"%7.4f\";\n" + + " String cell_methods \"time:point z:point\";\n" + + " String coordinates \"time z\";\n" + + " Float64 data_max 141.42;\n" + + " Float64 data_min 0.0;\n" + + " String FORTRAN_format \"F7.4\";\n" + + " String grid_mapping \"crs\";\n" + + " String long_name \"Current_Speed\";\n" + + " String units \"m s-1\";\n" + + " Float64 valid_max 7.0711;\n" + + " Float64 valid_min 0.0;\n" + + " }\n" + + " current_speed_quality_flag {\n" + + " String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + + + " Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + + " String long_name \"Current Speed QC Flags\";\n" + + " }\n" + + " current_direction {\n" + + " Float32 _FillValue 9999.9;\n" + + " String ancillary_variables \"current_direction_quality_flag\";\n" + + " String C_format \"%5.1f\";\n" + + " String cell_methods \"time:point z:point\";\n" + + " String comment \"True Direction toward which current is flowing\";\n" + + " String coordinates \"time z\";\n" + + " Float64 data_max 360.0;\n" + + " Float64 data_min 0.3;\n" + + " String FORTRAN_format \"F5.1\";\n" + + " String grid_mapping \"crs\";\n" + + " String long_name \"Current Direction\";\n" + + " String units \"degrees\";\n" + + " Float64 valid_max 360.0;\n" + + " Float64 valid_min 0.0;\n" + + " }\n" + + " current_direction_quality_flag {\n" + + " String flag_meanings \"good_value probably_good probably_bad bad_value modified_value not_used not_used not_used missing_value\";\n" + + + " Int32 flag_values 1, 2, 3, 4, 5, 6, 7, 8, 9;\n" + + " String long_name \"Current Direction QC Flags\";\n" + + " }\n" + + " crs {\n" + + " String epsg_code \"EPSG:4326\";\n" + + " String grid_mapping_name \"latitude_longitude\";\n" + + " String inverse_flattening \"298.257223563\";\n" + + " String long_name \"Coordinate Reference System\";\n" + + " String longitude_of_prime_meridian \"0.0f\";\n" + + " String semi_major_axis \"6378137.0\";\n" + + " }\n" + + " }\n" + + " NC_GLOBAL {\n" + + " String acknowledgment \"These data were acquired from the US NOAA National Centers for Environmental Information (NCEI) on [DATE] from http://www.nodc.noaa.gov/gocd/.\";\n" + + + " String cdm_data_type \"TrajectoryProfile\";\n" + + " String cdm_profile_variables \"seafloor_depth, latitude, longitude, latitude_quality_flag, longitude_quality_flag, time, time_quality_flag\";\n" + + + " String cdm_trajectory_variables \"sampling_interval, crs\";\n" + + " String contributor \"University of Hawaii and NOAA/NMFS\";\n" + + " String Conventions \"CF-1.6\";\n" + + " String creator_email \"Charles.Sun@noaa.gov\";\n" + + " String creator_name \"Charles Sun\";\n" + + " String creator_url \"http://www.nodc.noaa.gov\";\n" + + " String date_created \"2014-12-15T20:20:04Z\";\n" + + " String date_issued \"2016-01-18T04:39:10Z\";\n" + + " String date_modified \"2016-01-18T04:39:10Z\";\n" + + " String featureType \"trajectoryProfile\";\n" + + " Float32 geospatial_lat_max 21.0958;\n" + + " Float32 geospatial_lat_min -14.3883;\n" + + " String geospatial_lat_resolution \"point\";\n" + + " String geospatial_lat_units \"degrees_north\";\n" + + " Float32 geospatial_lon_max -158.3554;\n" + + " Float32 geospatial_lon_min -176.8126;\n" + + " String geospatial_lon_resolution \"point\";\n" + + " String geospatial_lon_units \"degrees_east\";\n" + + " Float32 geospatial_vertical_max 720.0;\n" + + " Float32 geospatial_vertical_min 30.0;\n" + + " String geospatial_vertical_positive \"down\";\n" + + " String geospatial_vertical_resolution \"point\";\n" + + " String geospatial_vertical_units \"meters\";\n" + + " String gocd_format_version \"GOCD-3.0\";\n" + + " String gocd_id \"gocd_a0067774_01192v3.nc\";\n" + + " String grid_mapping_epsg_code \"EPSG:4326\";\n" + + " String grid_mapping_inverse_flattening \"298.257223563\";\n" + + " String grid_mapping_long_name \"Coordinate Reference System\";\n" + + " String grid_mapping_longitude_of_prime_meridian \"0.0f\";\n" + + " String grid_mapping_name \"latitude_longitude\";\n" + + " String grid_mapping_semi_major_axis \"6378137.0\";\n" + + " String history \"Wed Feb 10 18:31:43 2016: ncrename -d depth,z test.nc\n" + + "2016-01-18T04:39:10Z csun updateOCD.R Version 2.0\n" + + "Thu Jan 7 15:59:35 2016: ncatted -a valid_max,seafloor_depth,d,, ../V3/a0067774/gocd_a0067774_01192v3.nc\n" + + "Thu Jan 7 15:59:35 2016: ncatted -a valid_min,seafloor_depth,d,, ../V3/a0067774/gocd_a0067774_01192v3.nc\n" + + "Thu Jan 7 15:59:35 2016: ncatted -a missing_value,seafloor_depth,d,, ../V3/a0067774/gocd_a0067774_01192v3.nc\n" + + + "Thu Jan 7 15:59:35 2016: ncatted -a missing_value,sampling_interval,d,, ../V3/a0067774/gocd_a0067774_01192v3.nc\n" + + + "2016-01-07T14:01:54Z csun updateGOCD.R Version 1.0\n" + + "2014-12-15T20:20:04Z csun convJASADCP.f90 Version 1.0\";\n" + + " String id \"0093183\";\n" + + " String institution \"NOAA National Centers for Environmental Information\";\n" + + " String instrument_type \"Ocean Surveyor OS75\";\n" + + " String keywords \"EARTH SCIENCE,OCEANS,OCEAN CIRCULATION,OCEAN CURRENTS\";\n" + + " String keywords_vocabulary \"GCMD Science Keywords\";\n" + + " String license \"These data are openly available to the public Please acknowledge the use of these data with the text given in the acknowledgment attribute.\";\n" + + + " String Metadata_Conventions \"Unidata Dataset Discovery v1.0\";\n" + + " String naming_authority \"gov.noaa.nodc\";\n" + + " String principal_invesigator \"E.Firing,J.Hummon,R.Brainard\";\n" + + " String project_name \"Coral Reef Ecosystem Investigations\";\n" + + " String publisher_email \"NODC.Services@noaa.gov\";\n" + + " String publisher_name \"US DOC; NESDIS; NATIONAL CENTERS FOR ENVIRONMENTAL INFORMATION - IN295\";\n" + + " String publisher_url \"http://www.nodc.noaa.gov/\";\n" + + " String QC_indicator \"Contact Principle Investigaror(s)\";\n" + // sic + " String QC_Manual \"Contact Principle Investigaror(s)\";\n" + + " String QC_Software \"Contact Principle Investigaror(s)\";\n" + + " String QC_test_codes \"Contact Principle Investigaror(s)\";\n" + + " String QC_test_names \"Contact Principle Investigaror(s)\";\n" + + " String QC_test_results \"Contact Principle Investigaror(s)\";\n" + + " String references \"http://www.nodc.noaa.gov/\";\n" + + " String source \"global ocean currents in the NCEI archive holdings\";\n" + + " String standard_name_vocabulary \"CF-1.6\";\n" + + " String subsetVariables \"sampling_interval, crs, seafloor_depth, latitude, longitude, latitude_quality_flag, longitude_quality_flag, time, time_quality_flag\";\n" + + + " String summary \"global ocean currents in the NCEI archive holdings\";\n" + + " String time_coverage_duration \"P0Y020DT20H00M00S\";\n" + + " String time_coverage_end \"2006-02-05T19:58:00Z\";\n" + + " String time_coverage_resolution \"R000501/2006-01-15T23:58:00Z/P0Y020DT20H00M00\";\n" + + " String time_coverage_start \"2006-01-15T23:58:00Z\";\n" + + " String title \"Global Ocean Currents Database - gocd_a0067774_01192v3.nc\";\n" + + " String uuid \"26f4a163-4c81-437b-9ad7-796822d1ce49\";\n" + + " }\n" + + "}\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + os.reset(); + table.saveAsDDS(os, Table.SEQUENCE_NAME); + results = os.toString(); + expected = "Dataset {\n" + + " Sequence {\n" + + " Float32 sampling_interval;\n" + + " Float32 seafloor_depth;\n" + + " Float32 latitude;\n" + + " Float32 longitude;\n" + + " Int32 latitude_quality_flag;\n" + + " Int32 longitude_quality_flag;\n" + + " Float32 depth;\n" + + " Int32 depth_quality_flag;\n" + + " Float64 time;\n" + + " Int32 time_quality_flag;\n" + + " Float32 u;\n" + + " Int32 u_quality_flag;\n" + + " Float32 v;\n" + + " Int32 v_quality_flag;\n" + + " Float32 current_speed;\n" + + " Int32 current_speed_quality_flag;\n" + + " Float32 current_direction;\n" + + " Int32 current_direction_quality_flag;\n" + + " Int32 crs;\n" + + " } s;\n" + + "} s;\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // String2.log(table.toCSVString()); + results = table.dataToString(5); + expected = "sampling_interval,seafloor_depth,latitude,longitude,latitude_quality_flag,longitude_quality_flag," + + "depth,depth_quality_flag,time,time_quality_flag,u,u_quality_flag,v,v_quality_flag," + + "current_speed,current_speed_quality_flag,current_direction," + + "current_direction_quality_flag,crs\n" + + // sapmInt,sfDpth lat lon depth time u v cspeed cdir crs + "9999.9,9999.9,21.0958,-158.3554,1,1,30.0,1,38730.9986,1,-0.004,1,0.174,1,0.174,1,358.7,1,0\n" + + "9999.9,9999.9,21.0958,-158.3554,1,1,40.0,1,38730.9986,1,-0.008,1,0.169,1,0.1692,1,357.3,1,0\n" + + "9999.9,9999.9,21.0958,-158.3554,1,1,50.0,1,38730.9986,1,-0.01,1,0.165,1,0.1653,1,356.5,1,0\n" + + "9999.9,9999.9,21.0958,-158.3554,1,1,60.0,1,38730.9986,1,-0.009,1,0.163,1,0.1632,1,356.8,1,0\n" + + "9999.9,9999.9,21.0958,-158.3554,1,1,70.0,1,38730.9986,1,-0.012,1,0.173,1,0.1734,1,356.0,1,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + results = table.dataToString(); // no row numbers + expected = // why are cspeed and cdir known, but u,v not? + // sampInt sfDpth lat lon depth time u v cspeed cdir crs + "9999.9,9999.9,-14.2758,-170.6805,1,1,680.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n" + + "9999.9,9999.9,-14.2758,-170.6805,1,1,690.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n" + + "9999.9,9999.9,-14.2758,-170.6805,1,1,700.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n" + + "9999.9,9999.9,-14.2758,-170.6805,1,1,710.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n" + + "9999.9,9999.9,-14.2758,-170.6805,1,1,720.0,1,38751.8319,1,9999.9,-9,9999.9,-9,141.42,1,45.0,1,0\n"; + po = results.indexOf(expected.substring(0, 40)); + Test.ensureEqual(results.substring(po), expected, + "results=\n" + results.substring(po)); + /* */ + + // *************** a similar test + // 2 levels, and outerDim=ScalarDim + // this tests if var[scalarDim][obs] was read (e.g., depth[obs] + // File dims are outerDim=[scalarDim], inner=[time], obs=[obs] + table = new Table(); + fileName = TableTests.class.getResource("/gocd/gocd_v3_madcp.nc").getPath(); + // String2.log("\n\n** Testing " + fileName); + results = NcHelper.ncdump(fileName, "-h"); + // String2.log(results); + // just the structure, rearranged into groups + // z = 14; + // time = 3188; + // int crs; + // float sampling_interval; + // float seafloor_depth; + // float latitude; + // float longitude; + // int latitude_quality_flag; + // int longitude_quality_flag; + + // float depth(z=14); + // int depth_quality_flag(z=14); + + // double time(time=3188); + // int time_quality_flag(time=3188); + + // float u(time=3188, z=14); + // int u_quality_flag(time=3188, z=14); + // float v(time=3188, z=14); + // int v_quality_flag(time=3188, z=14); + // float current_speed(time=3188, z=14); + // int current_speed_quality_flag(time=3188, z=14); + // float current_direction(time=3188, z=14); + // int current_direction_quality_flag(time=3188, z=14); + + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + os.reset(); + table.saveAsDDS(os, Table.SEQUENCE_NAME); + results = os.toString(); + expected = "Dataset {\n" + + " Sequence {\n" + + " Float32 sampling_interval;\n" + + " Float32 seafloor_depth;\n" + + " Float32 latitude;\n" + + " Float32 longitude;\n" + + " Int32 latitude_quality_flag;\n" + + " Int32 longitude_quality_flag;\n" + + " Float32 depth;\n" + + " Int32 depth_quality_flag;\n" + + " Float64 time;\n" + + " Int32 time_quality_flag;\n" + + " Float32 u;\n" + + " Int32 u_quality_flag;\n" + + " Float32 v;\n" + + " Int32 v_quality_flag;\n" + + " Float32 current_speed;\n" + + " Int32 current_speed_quality_flag;\n" + + " Float32 current_direction;\n" + + " Int32 current_direction_quality_flag;\n" + + " Int32 crs;\n" + + " } s;\n" + + "} s;\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // String2.log(table.toCSVString()); + results = table.dataToString(5); + expected = "sampling_interval,seafloor_depth,latitude,longitude," + + "latitude_quality_flag,longitude_quality_flag,depth,depth_quality_flag,time,time_quality_flag,u,u_quality_flag,v,v_quality_flag," + + + "current_speed,current_speed_quality_flag,current_direction," + + "current_direction_quality_flag,crs\n" + + // si sDepth lat lon q q depth q time q u q v q cspeed q cDir q crs + "60.0,32.6386,42.37859,-70.78094,1,1,26.34,1,38621.7448,1,0.0066,1,0.0072,1,0.0111,1,42.8,1,0\n" + + "60.0,32.6386,42.37859,-70.78094,1,1,24.34,1,38621.7448,1,0.0279,1,-0.008,1,0.0292,1,106.0,1,0\n" + + "60.0,32.6386,42.37859,-70.78094,1,1,22.34,1,38621.7448,1,0.0325,1,2.0E-4,1,0.033,1,89.7,1,0\n" + + "60.0,32.6386,42.37859,-70.78094,1,1,20.34,1,38621.7448,1,-0.0094,1,0.0011,1,0.0121,1,277.0,1,0\n" + + "60.0,32.6386,42.37859,-70.78094,1,1,18.34,1,38621.7448,1,-0.0383,1,-0.0367,1,0.0532,1,226.2,1,0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + results = table.dataToString(); // no row numbers + // String2.log(results); + expected = // why are cspeed and cdir known, but u,v not? + // si sDepth lat lon q q depth q time q u q v q cspeed q cDir q crs + "60.0,32.6386,42.37859,-70.78094,1,1,8.34,1,38754.5365,1,-0.0177,1,-0.0152,1,0.0257,1,229.2,1,0\n" + + "60.0,32.6386,42.37859,-70.78094,1,1,6.34,1,38754.5365,1,-0.0186,1,-0.0145,1,0.0251,1,232.0,1,0\n" + + "60.0,32.6386,42.37859,-70.78094,1,1,4.34,1,38754.5365,1,-0.0149,1,-0.0181,1,0.03,1,219.4,1,0\n" + + "60.0,32.6386,42.37859,-70.78094,1,1,2.34,1,38754.5365,1,-0.0026,2,-0.0202,2,0.0293,1,187.4,2,0\n" + + "60.0,32.6386,42.37859,-70.78094,1,1,0.34,1,38754.5365,1,9999.9,9,9999.9,9,9999.9,9,45.0,9,0\n"; + po = results.indexOf(expected.substring(0, 80)); + Test.ensureEqual(results.substring(po), expected, + "results=\n" + results.substring(po)); + /* */ + + // ************* v4 file #1 timeSeries has + // featureType=timeSeriesProfile cdm_data_type=profile + // outerdim=scalar var[time=6952][z=1] time[time=6952] depth[z=1] + table = new Table(); + fileName = TableTests.class.getResource("/gocd/gocd_a0000841_rcm00566_v4.nc").getPath(); + // String2.log("\n\n** Testing " + fileName); + results = NcHelper.ncdump(fileName, "-h"); + // String2.log(results); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + // String2.log(table.dataToString()); + results = table.dataToString(5); + expected = "sampling_interval,seafloor_depth,latitude,longitude,latitude_quality_flag," + + "longitude_quality_flag,depth,depth_quality_flag,time,time_quality_flag," + + "u,u_quality_flag,v,v_quality_flag,current_speed,current_speed_quality_flag," + + "current_direction,current_direction_quality_flag,crs\n" + + // si sd lat lon q q depth q time q u q v q cSpeed p dir q crs + "60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.424999999814,1,0.015,1,0.0865,1,0.0878,1,9.8,1,0\n" + + "60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.46666666679,1,-0.0045,1,0.0933,1,0.0934,1,357.2,1,0\n" + + "60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.508333333302,1,-0.0072,1,0.0856,1,0.0859,1,355.2,1,0\n" + + "60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.549999999814,1,-0.0065999995,1,0.1025,1,0.1027,1,356.3,1,0\n" + + + "60.0,2640.0,62.894997,-35.857998,1,1,1980.0,1,31662.59166666679,1,-0.0036,1,0.11200001,1,0.1121,1,358.2,1,0\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + /* */ + + // ********************* v4 file #2 has + /* + * // featureType=timeSeriesProfile cdm_data_type=profile + * // latitude=scalar var[time=126][z=12] time[time=126] depth[z=12] + * table = new Table(); + * fileName = "/data/gocd/gocd_a0060062_4381adc-a_v4.nc"; + * String2.log("\n\n** Testing " + fileName); + * results = NcHelper.ncdump(fileName, "-h"); + * String2.log(results); + * table.readNcCF(fileName, null, 0, //standardizeWhat=0 + * null, null, null); + * String2.log(table.dataToString()); + * results = table.dataToString(5); + * expected = + * "zz\n"; + * Test.ensureEqual(results, expected, "results=\n" + results); + * /* + */ + + // String2.log("\n*** Table.testReadGocdNcCF finished successfully"); + // Table.debugMode = oDebug; + + } + + /** This tests readNcCF nLevels=2. */ + @org.junit.jupiter.api.Test + void testReadNcCF2() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCF2"); + Table table = new Table(); + String results, expected; + Attributes gatts; + + // *************** nLevels=2 multidimensional + for (int type = 0; type < 2; type++) { + // ncCF2b and ncCFMA2b have same data, so tests are the same! + String fileType = type == 0 ? "ragged" : "multidimensional"; + // from EDDTableFromNcFiles.testNcCF2b() and testNcCFMA2b(); + String fileName = TableTests.class.getResource("/nccf/" + + (type == 0 ? "ncCF2b.nc" : "ncCFMA2b.nc")).getPath(); + String msg = "ERROR when type=" + type + ": "; + + // String2.log("\n\n** Testing type=" + type + " nLevels=2/" + fileType + "\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + /* */ + // String2.log("\n\n** Test nLevels=2/" + fileType + " no loadVars, no constraints"); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + // String2.log(table.toString()); + results = table.dataToString(5); + expected = "platform,cruise,org,type,station_id,longitude,latitude,time,depth,temperature,salinity\n" + + "33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,4.0,-1.84,35.64\n" + + "33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,10.0,-1.84,35.64\n" + + "33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,20.0,-1.83,35.64\n" + + "33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,30.0,-1.83,35.64\n" + + "33P2,Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,49.0,-1.83,35.64\n" + + "...\n"; + Test.ensureEqual(results, expected, msg); + Test.ensureEqual(table.nRows(), 53, msg + table.toString()); + results = table.columnAttributes(0).toString(); + expected = " comment=See the list of platform codes (sorted in various ways) at http://www.nodc.noaa.gov/GTSPP/document/codetbls/calllist.html\n" + + + " ioos_category=Identifier\n" + + " long_name=GTSPP Platform Code\n" + + " references=http://www.nodc.noaa.gov/gtspp/document/codetbls/callist.html\n"; + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "org, type, station_id, longitude, latitude, time", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "platform, cruise, org, type, station_id, longitude, latitude, time", + msg + gatts.toString()); + + // + table.readNcCF(fileName, + StringArray.fromCSV("cruise,latitude,depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("cruise"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, msg); + Test.ensureEqual(table.nColumns(), 0, msg); + + table.readNcCF(fileName, + StringArray.fromCSV("cruise,latitude,depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("latitude"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, msg); + Test.ensureEqual(table.nColumns(), 0, msg); + + table.readNcCF(fileName, + StringArray.fromCSV("cruise,latitude,depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("depth"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, msg); + Test.ensureEqual(table.nColumns(), 0, msg); + + table.readNcCF(fileName, + StringArray.fromCSV("cruise,latitude,depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, msg); + Test.ensureEqual(table.nColumns(), 0, msg); + + // + table.readNcCF(fileName, + StringArray.fromCSV("latitude,depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("latitude"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, msg); + Test.ensureEqual(table.nColumns(), 0, msg); + + table.readNcCF(fileName, + StringArray.fromCSV("latitude,depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("depth"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, msg); + Test.ensureEqual(table.nColumns(), 0, msg); + + table.readNcCF(fileName, + StringArray.fromCSV("latitude,depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, msg); + Test.ensureEqual(table.nColumns(), 0, msg); + + // + table.readNcCF(fileName, StringArray.fromCSV("depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("depth"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, msg); + Test.ensureEqual(table.nColumns(), 0, msg); + + table.readNcCF(fileName, StringArray.fromCSV("depth,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("latitude,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("latitude"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("latitude,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("latitude,cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("latitude"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("latitude,cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("cruise"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("depth,cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("depth"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("depth,cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("cruise"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("temperature,cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("temperature,cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("cruise"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("cruise"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("latitude"), + 0, // standardizeWhat=0 + StringArray.fromCSV("latitude"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("depth"), + 0, // standardizeWhat=0 + StringArray.fromCSV("depth"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just outerTable loadVars, constraints"); + table.readNcCF(fileName, StringArray.fromCSV("platform,cruise,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("platform"), + StringArray.fromCSV("="), + StringArray.fromCSV("33P2")); + results = table.dataToString(); + expected = "platform,cruise\n" + + "33P2,Q990046312\n"; + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), null, + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), "platform, cruise", + msg + gatts.toString()); + + // + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just outerTable loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, StringArray.fromCSV("platform,cruise,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("platform"), + StringArray.fromCSV("="), + StringArray.fromCSV("zztop")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just innerTable loadVars, no constraints"); + // String2.log("ncdump of " + fileName + "\n" + NcHelper.ncdump(fileName, "-v station_id;type")); + table.readNcCF(fileName, + StringArray.fromCSV("station_id,zztop,type"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = + // before: 4th row with mv's is removed + // 2020-08-03 now it isn't removed for type=1 because station_id is int with no + // defined _FillValue or missing_value and [3]=2147483647! + // In other words: this is a flaw in the data file. + // note type0=ragged, type1=multidimensional + "station_id,type\n" + + "13968849,TE\n" + + "13968850,TE\n" + + "13933177,BA\n" + + (type == 0 ? "" : "2147483647,\n"); + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), "type, station_id", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), "type, station_id", + msg + gatts.toString()); + + // + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just innerTable loadVars, constraints"); + table.readNcCF(fileName, StringArray.fromCSV("station_id,zztop,type"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_id"), + StringArray.fromCSV("="), + StringArray.fromCSV("13933177")); + results = table.dataToString(); + expected = "station_id,type\n" + + "13933177,BA\n"; + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), "type, station_id", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), "type, station_id", + msg + gatts.toString()); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just innerTable loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, StringArray.fromCSV("station_id,zztop,type"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_id"), + StringArray.fromCSV("="), + StringArray.fromCSV("zztop")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just outerTable and innerTable loadVars, no constraints"); + table.readNcCF(fileName, StringArray.fromCSV( + "cruise,org,type,station_id,longitude,latitude,time,zztop,platform"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "cruise,org,type,station_id,longitude,latitude,time,platform\n" + + "Q990046312,ME,TE,13968849,176.64,-75.45,1.3351446E9,33P2\n" + + "Q990046312,ME,TE,13968850,176.64,-75.43,1.335216E9,33P2\n" + + "SHIP 12,ME,BA,13933177,173.54,-34.58,1.33514142E9,9999\n" + + (type == 0 ? "" : "SHIP 12,,,2147483647,,,,9999\n"); // 2020-08-03 this also appeared. See 2020-08-03 + // comments above + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "org, type, station_id, longitude, latitude, time", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "platform, cruise, org, type, station_id, longitude, latitude, time", + msg + gatts.toString()); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just outerTable and innerTable loadVars, constraints"); + table.readNcCF(fileName, StringArray.fromCSV( + "row,cruise,org,type,station_id,longitude,latitude,time,zztop,platform"), + 0, // standardizeWhat=0 + StringArray.fromCSV("platform,station_id"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("33P2,13968850")); + results = table.dataToString(); + expected = "cruise,org,type,station_id,longitude,latitude,time,platform\n" + + "Q990046312,ME,TE,13968850,176.64,-75.43,1.335216E9,33P2\n"; + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "org, type, station_id, longitude, latitude, time", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "platform, cruise, org, type, station_id, longitude, latitude, time", + msg + gatts.toString()); + + // + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just outerTable and innerTable loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, StringArray.fromCSV( + "row,cruise,org,type,station_id,longitude,latitude,time,zztop,platform"), + 0, // standardizeWhat=0 + StringArray.fromCSV("platform,station_id"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("33P2,zztop")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just outerTable and obs loadVars, constraints"); + table.readNcCF(fileName, + StringArray.fromCSV("salinity,platform,zztop,cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("platform,salinity"), + StringArray.fromCSV("=,>="), + StringArray.fromCSV("33P2,35.98")); + results = table.dataToString(); + expected = "salinity,platform,cruise\n" + + "35.99,33P2,Q990046312\n" + + "36.0,33P2,Q990046312\n" + + "35.98,33P2,Q990046312\n"; + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), "platform, cruise", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), null, + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), "platform, cruise", + msg + gatts.toString()); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just outerTable and obs loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, + StringArray.fromCSV("salinity,platform,zztop,cruise"), + 0, // standardizeWhat=0 + StringArray.fromCSV("platform,salinity"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("33P2,-100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just innerTable and obs loadVars, no constraints"); + table.readNcCF(fileName, StringArray.fromCSV( + "latitude,longitude,time,zztop,salinity"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "latitude,longitude,time,salinity\n" + + "-75.45,176.64,1.3351446E9,35.64\n" + + "-75.45,176.64,1.3351446E9,35.64\n" + + "-75.45,176.64,1.3351446E9,35.64\n" + + "-75.45,176.64,1.3351446E9,35.64\n" + + "-75.45,176.64,1.3351446E9,35.64\n" + + "-75.45,176.64,1.3351446E9,35.63\n" + + "-75.45,176.64,1.3351446E9,35.59\n" + + "-75.45,176.64,1.3351446E9,35.52\n" + + "-75.45,176.64,1.3351446E9,35.56\n" + + "-75.45,176.64,1.3351446E9,35.77\n" + + "-75.45,176.64,1.3351446E9,35.81\n" + + "-75.45,176.64,1.3351446E9,35.82\n" + + "-75.45,176.64,1.3351446E9,35.88\n" + + "-75.45,176.64,1.3351446E9,35.94\n" + + "-75.45,176.64,1.3351446E9,35.99\n" + + "-75.45,176.64,1.3351446E9,36.0\n" + + "-75.43,176.64,1.335216E9,35.64\n" + + "-75.43,176.64,1.335216E9,35.64\n" + + "-75.43,176.64,1.335216E9,35.64\n" + + "-75.43,176.64,1.335216E9,35.64\n" + + "-75.43,176.64,1.335216E9,35.63\n" + + "-75.43,176.64,1.335216E9,35.63\n" + + "-75.43,176.64,1.335216E9,35.61\n" + + "-75.43,176.64,1.335216E9,35.58\n" + + "-75.43,176.64,1.335216E9,35.5\n" + + "-75.43,176.64,1.335216E9,35.77\n" + + "-75.43,176.64,1.335216E9,35.81\n" + + "-75.43,176.64,1.335216E9,35.86\n" + + "-75.43,176.64,1.335216E9,35.9\n" + + "-75.43,176.64,1.335216E9,35.93\n" + + "-75.43,176.64,1.335216E9,35.96\n" + + "-75.43,176.64,1.335216E9,35.98\n"; + + // multidimensional deletes these rows because all read obs columns have mv's + // This is not ideal, but I don't want to read all obs columns in file to + // determine which rows to delete. + if (fileType.equals("ragged")) + expected += "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n" + + "-34.58,173.54,1.33514142E9,\n"; + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "longitude, latitude, time", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "longitude, latitude, time", + msg + gatts.toString()); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just innerTable and obs loadVars, constraints"); + table.readNcCF(fileName, + StringArray.fromCSV("latitude,longitude,time,zztop,salinity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,salinity"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("1.335216E9,35.77")); + results = table.dataToString(); + expected = "latitude,longitude,time,salinity\n" + + "-75.43,176.64,1.335216E9,35.77\n"; + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), + "longitude, latitude, time", msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), + "longitude, latitude, time", msg + gatts.toString()); + + // + // String2.log("\n\n** Test nLevels=2/" + fileType + " " + + // "just innerTable and obs loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, + StringArray.fromCSV("latitude,longitude,time,zztop,salinity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,salinity"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("1.335216E9,-1000")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Test nLevels=2/" + fileType + " just obs loadVars, constraints"); + table.readNcCF(fileName, StringArray.fromCSV("temperature,salinity,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("salinity"), + StringArray.fromCSV("="), + StringArray.fromCSV("35.77")); + results = table.dataToString(); + expected = "temperature,salinity\n" + + "-1.1,35.77\n" + + "-1.12,35.77\n"; + Test.ensureEqual(results, expected, msg + "results=\n" + results); + gatts = table.globalAttributes(); + Test.ensureEqual(gatts.getString("cdm_data_type"), "TrajectoryProfile", + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_trajectory_variables"), null, + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("cdm_profile_variables"), null, + msg + gatts.toString()); + Test.ensureEqual(gatts.getString("subsetVariables"), null, + msg + gatts.toString()); + + // + // String2.log("\n\n** Test nLevels=2/" + fileType + + // " just obs loadVars, constraints, NO_DATA"); + table.readNcCF(fileName, StringArray.fromCSV("temperature,salinity,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("salinity"), + StringArray.fromCSV("="), + StringArray.fromCSV("-1000")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + } // end nLevels=2 type loop + + // Table.debugMode = oDebug; + } + + /** + * This tests readNcCF profile files from ASA + * via https://github.com/asascience-open/CFPointConventions + * stored in unitTestDataDir/CFPointConventions. + */ + @org.junit.jupiter.api.Test + void testReadNcCFASAProfile() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCFASAProfile"); + Table table = new Table(); + String results, expected, fileName; + + /* */ + // *************** profile contiguous + fileName = TableTests.class.getResource("/CFPointConventions/profile/" + + "profile-Contiguous-Ragged-MultipleProfiles-H.3.4/" + + "profile-Contiguous-Ragged-MultipleProfiles-H.3.4.nc").getPath(); + // String2.log("\n\n** Testing contiguous file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(18); + expected = + /* + * pre 2012-10-02 was + * "lat,lon,profile,time,z,temperature,humidity\n" + + * "137.0,30.0,0,0,8.055641,32.962334,14.262256\n" + + * "137.0,30.0,0,0,8.9350815,25.433783,41.722572\n" + + * "137.0,30.0,0,0,5.1047354,4.0391192,44.34395\n" + + * "137.0,30.0,0,0,4.2890472,6.0850625,13.220096\n" + + * "137.0,30.0,0,0,1.9311341,32.794086,32.313293\n"; + */ + // z seems to be made up numbers. not in order (for a given profile) as one + // would expect. + "lat,lon,profile,time,z,temperature,humidity\n" + + "34.0,115.0,0,0,9.913809,30.592709,32.71529\n" + + "34.0,115.0,0,0,5.699307,17.442251,76.26051\n" + + "34.0,115.0,0,0,0.617254,14.230382,13.789284\n" + + "34.0,115.0,0,0,2.6114788,38.859676,21.792738\n" + + "34.0,115.0,0,0,6.519849,28.003593,33.264217\n" + + "34.0,115.0,0,0,8.975919,10.699942,61.52172\n" + + "34.0,115.0,0,0,9.912431,32.747574,85.96188\n" + + "34.0,115.0,0,0,7.5545244,18.109398,41.733406\n" + + "34.0,115.0,0,0,7.568512,10.165248,84.50128\n" + + "34.0,115.0,0,0,3.376015,0.48572874,5.2108083\n" + + "11.0,95.0,1,3600,0.16332848,1.193263,87.431725\n" + + "11.0,95.0,1,3600,4.9485574,31.53037,65.04175\n" + + "11.0,95.0,1,3600,6.424919,11.956788,54.758873\n" + + "11.0,95.0,1,3600,4.7111635,36.69692,50.6536\n" + + "11.0,95.0,1,3600,6.854408,21.065716,83.941765\n" + + "11.0,95.0,1,3600,9.321201,31.395382,17.139112\n" + + "176.0,17.0,2,7200,7.2918577,17.65049,66.33111\n" + + "176.0,17.0,2,7200,3.270435,35.854877,17.296724\n" + + "...\n"; + + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 58, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("lat,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("lat,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("z,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("z,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("temperature,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("temperature,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV("profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV("z"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // test get outer+obs variables with outer constraint + table.readNcCF(fileName, StringArray.fromCSV("profile,lat,lon,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("11")); + results = table.dataToString(); + expected = "profile,lat,lon,temperature\n" + + "1,11.0,95.0,1.193263\n" + + "1,11.0,95.0,31.53037\n" + + "1,11.0,95.0,11.956788\n" + + "1,11.0,95.0,36.69692\n" + + "1,11.0,95.0,21.065716\n" + + "1,11.0,95.0,31.395382\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test get outer+obs variables with obs constraint + table.readNcCF(fileName, StringArray.fromCSV("profile,lat,lon,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), StringArray.fromCSV("="), StringArray.fromCSV("11.956788")); + results = table.dataToString(); + expected = "profile,lat,lon,temperature\n" + + "1,11.0,95.0,11.956788\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test get obs variables with outer constraint + table.readNcCF(fileName, StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("11")); + results = table.dataToString(); + expected = "lat,temperature\n" + + "11.0,1.193263\n" + + "11.0,31.53037\n" + + "11.0,11.956788\n" + + "11.0,36.69692\n" + + "11.0,21.065716\n" + + "11.0,31.395382\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** profile incomplete multidimensional --- + fileName = TableTests.class.getResource("/CFPointConventions/profile/" + + "profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/" + + "profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.nc").getPath(); + // String2.log("\n\n** Testing incomplete\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(45); + expected = "lat,lon,profile,time,alt,temperature,humidity,wind_speed\n" + + "171.0,119.0,0,0,3.6755686,17.65279,-999.9,51.078896\n" + + "171.0,119.0,0,0,0.26343155,6.2052555,-999.9,64.199974\n" + + "171.0,119.0,0,0,3.175112,12.011641,-999.9,6.9850345\n" + + "171.0,119.0,0,0,4.208357,21.89748,-999.9,58.273148\n" + + "171.0,119.0,0,0,2.6554945,21.416033,-999.9,71.660774\n" + + "171.0,119.0,0,0,4.9972143,1.4952343,-999.9,31.470207\n" + + "171.0,119.0,0,0,1.9827757,21.466,-999.9,11.440447\n" + + "171.0,119.0,0,0,4.1058283,14.191161,-999.9,21.072964\n" + + "171.0,119.0,0,0,5.648934,7.727216,-999.9,20.63561\n" + + "171.0,119.0,0,0,1.2512851,21.434706,-999.9,60.469204\n" + + "171.0,119.0,0,0,9.600934,2.1928697,-999.9,71.77351\n" + + "171.0,119.0,0,0,1.9799258,16.0188,-999.9,55.211063\n" + + "171.0,119.0,0,0,1.2364764,3.242274,-999.9,11.2599\n" + + "171.0,119.0,0,0,2.834809,39.97538,-999.9,84.81159\n" + + "171.0,119.0,0,0,3.950956,19.135057,-999.9,29.651375\n" + + "171.0,119.0,0,0,8.663035,36.685486,-999.9,16.686064\n" + + "171.0,119.0,0,0,1.8081368,31.313751,-999.9,55.862072\n" + + "171.0,119.0,0,0,7.7147174,22.89713,-999.9,55.927597\n" + + "171.0,119.0,0,0,9.629576,18.616583,-999.9,68.66041\n" + + "171.0,119.0,0,0,6.9754705,7.9321976,-999.9,60.648094\n" + + "171.0,119.0,0,0,2.7991323,11.907311,-999.9,67.411575\n" + + "171.0,119.0,0,0,1.5943866,29.448673,-999.9,79.15605\n" + + "171.0,119.0,0,0,0.9762172,3.3020692,-999.9,85.00339\n" + + "171.0,119.0,0,0,5.5088353,12.813819,-999.9,77.104706\n" + + "171.0,119.0,0,0,7.2601357,38.730194,-999.9,18.446539\n" + + "171.0,119.0,0,0,8.384121,19.790619,-999.9,74.80566\n" + + "171.0,119.0,0,0,6.4686337,23.498947,-999.9,76.68345\n" + + "171.0,119.0,0,0,2.0993211,21.344112,-999.9,28.282118\n" + + "171.0,119.0,0,0,0.8403456,17.045395,-999.9,88.80201\n" + + "171.0,119.0,0,0,9.251101,15.639243,-999.9,70.71877\n" + + "171.0,119.0,0,0,1.3482393,9.54115,-999.9,59.91356\n" + + "171.0,119.0,0,0,3.6940877,30.967232,-999.9,35.620453\n" + + "171.0,119.0,0,0,6.3351345,6.0343504,-999.9,44.98056\n" + + "171.0,119.0,0,0,6.3332343,20.940767,-999.9,76.89658\n" + + "171.0,119.0,0,0,0.053762503,20.765089,-999.9,12.856414\n" + + "171.0,119.0,0,0,1.0131614,12.508157,-999.9,69.99224\n" + + "171.0,119.0,0,0,4.424666,37.28969,-999.9,24.69326\n" + + "171.0,119.0,0,0,1.5825375,17.199543,-999.9,63.037647\n" + + "171.0,119.0,0,0,3.072151,13.194056,-999.9,33.561863\n" + + "171.0,119.0,0,0,5.897976,6.350154,-999.9,9.787908\n" + + "171.0,119.0,0,0,1.6135278,22.95996,-999.9,85.10665\n" + + "171.0,119.0,0,0,6.9384937,7.619196,-999.9,33.569344\n" + + "155.0,158.0,1,3600,2.1733663,4.981018,-999.9,41.24567\n" + + "155.0,158.0,1,3600,2.189715,16.313164,-999.9,8.15441\n" + + "155.0,158.0,1,3600,9.445334,18.173727,-999.9,52.259445\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + // 42 * 142 = 5964 obs spaces, so it is incomplete + Test.ensureEqual(table.nRows(), 5754, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("alt,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("alt,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("temperature,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // *************** profile indexed IMPORTANT - I didn't have sample of indexed + try { + fileName = TableTests.class.getResource("/CFPointConventions/profile/" + + "profile-Indexed-Ragged-MultipleProfiles-H.3.5/" + + "profile-Indexed-Ragged-MultipleProfiles-H.3.5.nc").getPath(); + // String2.log("\n\n** Testing indexed file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + // String2.log(table.dataToString()); + results = table.dataToString(20); + expected = "lat,lon,profile,time,z,temperature,humidity\n" + + "93.0,71.0,0,0,0.38200212,23.69535,52.60904\n" + + "93.0,71.0,0,0,1.200709,29.121883,12.060117\n" + + "93.0,71.0,0,0,2.6969194,23.355228,9.943134\n" + + "93.0,71.0,0,0,3.4035592,21.57062,75.10006\n" + + "93.0,71.0,0,0,5.829337,2.9969826,17.760695\n" + + "93.0,71.0,0,0,5.8626857,37.635395,86.32262\n" + + "93.0,71.0,0,0,6.5773344,2.3481517,85.33706\n" + + "93.0,71.0,0,0,7.7204447,5.337912,54.993973\n" + + "93.0,71.0,0,0,8.301987,32.431896,88.71708\n" + + "93.0,71.0,0,0,9.088309,30.518106,44.74581\n" + + "45.0,151.0,1,3600,0.47979552,28.567852,65.933014\n" + + "45.0,151.0,1,3600,0.594338,7.940218,79.38502\n" + + "45.0,151.0,1,3600,4.0314445,20.808128,13.365513\n" + + "45.0,151.0,1,3600,6.101271,4.62561,8.945877\n" + + "45.0,151.0,1,3600,6.1228404,13.251722,50.431633\n" + + "45.0,151.0,1,3600,8.454789,17.803867,4.852586\n" + + "169.0,145.0,2,7200,1.9213479,7.1473145,11.227387\n" + + "169.0,145.0,2,7200,3.328237,27.21546,29.352453\n" + + "112.0,9.0,3,10800,0.009190708,6.3910594,56.909916\n" + + "112.0,9.0,3,10800,0.013856917,13.634793,63.741573\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 100, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // "19,112.0,9.0,3,10800,0.013856917,13.634793,63.741573\n"; + table.readNcCF(fileName, + StringArray.fromCSV("profile,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile,temperature"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("3,13.634793")); + results = table.dataToString(); + expected = "profile,temperature\n" + + "3,13.634793\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("temperature,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // "19,112.0,9.0,3,10800,0.013856917,13.634793,63.741573\n"; + table.readNcCF(fileName, + StringArray.fromCSV("profile,z"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile,z"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("3,0.013856917")); + results = table.dataToString(); + expected = "profile,z\n" + + "3,0.013856917\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // String2.log("\n\n** Testing indexed file NO_DATA - inner"); + table.readNcCF(fileName, + StringArray.fromCSV("lat,lon,profile,time,z,temperature,humidity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-10000")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Testing indexed file NO_DATA - odd combo"); + table.readNcCF(fileName, + StringArray.fromCSV("lat,lon,profile,time,z,temperature,humidity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat,z"), + StringArray.fromCSV("=,="), + StringArray.fromCSV("93,0.594338")); // actual values, but never in this combination + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Testing indexed file NO_DATA - outer"); + table.readNcCF(fileName, + StringArray.fromCSV("lat,lon,profile,time,z,temperature,humidity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("humidity"), + StringArray.fromCSV("="), + StringArray.fromCSV("-10000")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + } catch (Exception e) { + String2.pressEnterToContinue(MustBe.throwableToString(e)); + } + + // *************** profile orthogonal + fileName = TableTests.class.getResource("/CFPointConventions/profile/" + + "profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/" + + "profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.nc").getPath(); + // String2.log("\n\n** Testing orthogonal file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(55); + expected = // z[obs] is in the innerTable + "lat,lon,profile,time,z,temperature,humidity\n" + + "19.0,116.0,0,0,1.6315197,15.477672,45.439682\n" + + "19.0,116.0,0,0,7.0598154,31.758614,35.987625\n" + + "19.0,116.0,0,0,0.36953768,2.4893014,65.79051\n" + + "19.0,116.0,0,0,7.5342026,26.857018,48.042828\n" + + "19.0,116.0,0,0,7.404938,19.151163,35.629215\n" + + "19.0,116.0,0,0,1.4442251,24.565704,37.29833\n" + + "19.0,116.0,0,0,9.80883,15.455084,23.763685\n" + + "19.0,116.0,0,0,8.060886,26.090511,14.579169\n" + + "19.0,116.0,0,0,1.965906,8.010671,69.79476\n" + + "19.0,116.0,0,0,9.60608,26.692741,78.83376\n" + + "19.0,116.0,0,0,9.839138,39.378746,37.22304\n" + + "19.0,116.0,0,0,6.2004266,14.685706,39.81143\n" + + "19.0,116.0,0,0,6.9113455,7.344667,18.64804\n" + + "19.0,116.0,0,0,8.798231,7.1495833,25.831097\n" + + "19.0,116.0,0,0,2.3565977,0.25708458,32.442547\n" + + "19.0,116.0,0,0,8.742956,34.86492,49.41099\n" + + "19.0,116.0,0,0,8.557564,35.413876,66.573906\n" + + "19.0,116.0,0,0,9.6161375,37.28068,4.6605506\n" + + "19.0,116.0,0,0,6.610992,5.4654717,60.635574\n" + + "19.0,116.0,0,0,1.936887,33.513893,82.823166\n" + + "19.0,116.0,0,0,3.0184858,31.41321,75.51568\n" + + "19.0,116.0,0,0,2.5581324,15.092895,79.2067\n" + + "19.0,116.0,0,0,7.1288857,20.573462,27.601343\n" + + "19.0,116.0,0,0,1.5220404,0.5649648,3.6447735\n" + + "19.0,116.0,0,0,3.276416,27.345316,62.10269\n" + + "19.0,116.0,0,0,0.40930283,27.671362,79.762955\n" + + "19.0,116.0,0,0,2.4845016,31.252121,61.57929\n" + + "19.0,116.0,0,0,9.366717,9.342631,78.63049\n" + + "19.0,116.0,0,0,0.3365049,20.81806,29.236477\n" + + "19.0,116.0,0,0,7.646478,3.1961684,7.8138685\n" + + "19.0,116.0,0,0,5.075439,36.427265,20.879707\n" + + "19.0,116.0,0,0,5.1594234,18.314194,6.4109855\n" + + "19.0,116.0,0,0,2.1663764,10.056105,5.798549\n" + + "19.0,116.0,0,0,9.028424,5.7192965,56.243206\n" + + "19.0,116.0,0,0,9.031402,13.884695,36.763905\n" + + "19.0,116.0,0,0,5.26929,3.5693107,84.04594\n" + + "19.0,116.0,0,0,2.6247969,8.933488,28.76576\n" + + "19.0,116.0,0,0,9.745737,24.357897,76.431816\n" + + "19.0,116.0,0,0,3.722143,17.96677,18.759092\n" + + "19.0,116.0,0,0,1.9264901,28.71267,52.148735\n" + + "19.0,116.0,0,0,3.9815784,35.91171,33.082714\n" + + "19.0,116.0,0,0,4.657818,31.10753,65.25383\n" + + "109.0,178.0,1,3600,1.6315197,26.582031,10.312429\n" + + "109.0,178.0,1,3600,7.0598154,4.909754,50.415916\n" + + "109.0,178.0,1,3600,0.36953768,30.069138,36.845417\n" + + "109.0,178.0,1,3600,7.5342026,3.341837,52.53064\n" + + "109.0,178.0,1,3600,7.404938,36.832874,81.62572\n" + + "109.0,178.0,1,3600,1.4442251,21.88992,78.833565\n" + + "109.0,178.0,1,3600,9.80883,25.902088,50.43351\n" + + "109.0,178.0,1,3600,8.060886,30.653927,81.53324\n" + + "109.0,178.0,1,3600,1.965906,0.8834069,86.67266\n" + + "109.0,178.0,1,3600,9.60608,27.2307,74.25348\n" + + "109.0,178.0,1,3600,9.839138,15.706074,86.22133\n" + + "109.0,178.0,1,3600,6.2004266,34.751484,79.71265\n" + + "109.0,178.0,1,3600,6.9113455,16.43026,30.387852\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 5964, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, + StringArray.fromCSV("profile,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("profile,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("profile,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + /* */ + // Table.debugMode = oDebug; + } + + /** + * This tests readNcCF timeseries files from ASA + * via https://github.com/asascience-open/CFPointConventions + * stored in unitTestDataDir/CFPointConventions. + */ + @org.junit.jupiter.api.Test + void testReadNcCFASATimeSeries() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCFASATimeseries"); + Table table = new Table(); + String results, expected, fileName; + + // *************** timeseries orthogonal + fileName = TableTests.class.getResource("/CFPointConventions/timeseries/" + + "timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/" + + "timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.nc").getPath(); + // String2.log("\n\n** Testing orthogonal file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + // !!! obs vars are temperature[time=100][station=10] + // so outer=time and inner is station! + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(12); + expected = "lat,lon,station_name,alt,time,temperature,humidity\n" + + "8.0,146.0,Station-0,0.8488673,0,18.618036,27.177536\n" + + "4.0,53.0,Station-1,1.8478156,0,13.216496,83.71079\n" + + "90.0,159.0,Station-2,3.4614673,0,39.300182,44.69293\n" + + "55.0,25.0,Station-3,4.8902116,0,17.008652,2.3659434\n" + + "115.0,30.0,Station-4,9.45969,0,24.951536,7.1026664\n" + + "165.0,125.0,Station-5,0.17808062,0,35.995247,41.411594\n" + + "143.0,175.0,Station-6,8.85507,0,24.334364,39.776123\n" + + "157.0,175.0,Station-7,0.47320434,0,33.077255,1.1665242\n" + + "101.0,80.0,Station-8,7.470208,0,6.9397545,72.75068\n" + + "167.0,57.0,Station-9,0.6709764,0,28.991974,71.65753\n" + + "8.0,146.0,Station-0,0.8488673,3600,3.0675685,53.43748\n" + + "4.0,53.0,Station-1,1.8478156,3600,37.31892,46.79294\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 1000, ""); + results = table.columnAttributes(5).toString(); // temperature + expected = " coordinates=lat lon alt\n" + // this is what source has. But it should include time. + " long_name=Air Temperature\n" + + " missing_value=-999.9f\n" + + " standard_name=air_temperature\n" + + " units=Celsius\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("alt,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("alt,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // read just inner [station] vars + table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "station_name,lat,lon\n" + + "Station-0,8.0,146.0\n" + + "Station-1,4.0,53.0\n" + + "Station-2,90.0,159.0\n" + + "Station-3,55.0,25.0\n" + + "Station-4,115.0,30.0\n" + + "Station-5,165.0,125.0\n" + + "Station-6,143.0,175.0\n" + + "Station-7,157.0,175.0\n" + + "Station-8,101.0,80.0\n" + + "Station-9,167.0,57.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just inner [station] vars, with constraint + table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), StringArray.fromCSV(">"), StringArray.fromCSV("150")); + results = table.dataToString(); + expected = "station_name,lat,lon\n" + + "Station-5,165.0,125.0\n" + + "Station-7,157.0,175.0\n" + + "Station-9,167.0,57.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just outer [time] vars + table.readNcCF(fileName, StringArray.fromCSV("time"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = "time\n" + + "0\n" + + "3600\n" + + "7200\n" + + "10800\n" + + "14400\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 100, ""); + + // read just outer [time] vars, with constraint + table.readNcCF(fileName, StringArray.fromCSV("time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,time"), StringArray.fromCSV(">,<"), StringArray.fromCSV("7000,11000")); + results = table.dataToString(); + expected = "time\n" + + "7200\n" + + "10800\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just outer+inner [time][station] vars + table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon,time"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "station_name,lat,lon,time\n" + + "Station-0,8.0,146.0,0\n" + + "Station-1,4.0,53.0,0\n" + + "Station-2,90.0,159.0,0\n" + + "Station-3,55.0,25.0,0\n" + + "Station-4,115.0,30.0,0\n" + + "Station-5,165.0,125.0,0\n" + + "Station-6,143.0,175.0,0\n" + + "Station-7,157.0,175.0,0\n" + + "Station-8,101.0,80.0,0\n" + + "Station-9,167.0,57.0,0\n" + + "Station-0,8.0,146.0,3600\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 10 * 100, ""); + + expected = "Station-0,8.0,146.0,345600\n" + + "Station-1,4.0,53.0,345600\n" + + "Station-2,90.0,159.0,345600\n" + + "Station-3,55.0,25.0,345600\n" + + "Station-4,115.0,30.0,345600\n" + + "Station-5,165.0,125.0,345600\n" + + "Station-6,143.0,175.0,345600\n" + + "Station-7,157.0,175.0,345600\n" + + "Station-8,101.0,80.0,345600\n" + + "Station-9,167.0,57.0,345600\n"; + int po = results.indexOf(expected); + Test.ensureTrue(po > 0, "po=" + po); + Test.ensureEqual(results.substring(po, po + expected.length()), expected, "results=\n" + results); + + // read just outer+inner [time][station] vars, with outer [time] constraint + table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), StringArray.fromCSV("="), StringArray.fromCSV("345600")); + results = table.dataToString(); + expected = "station_name,lat,lon,time\n" + + "Station-0,8.0,146.0,345600\n" + + "Station-1,4.0,53.0,345600\n" + + "Station-2,90.0,159.0,345600\n" + + "Station-3,55.0,25.0,345600\n" + + "Station-4,115.0,30.0,345600\n" + + "Station-5,165.0,125.0,345600\n" + + "Station-6,143.0,175.0,345600\n" + + "Station-7,157.0,175.0,345600\n" + + "Station-8,101.0,80.0,345600\n" + + "Station-9,167.0,57.0,345600\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just outer+inner [time][station] vars, with inner [station] constraint + table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("165")); + results = table.dataToString(); + expected = "station_name,lat,lon,time\n" + + "Station-5,165.0,125.0,0\n" + + "Station-5,165.0,125.0,3600\n" + + "Station-5,165.0,125.0,7200\n" + + "Station-5,165.0,125.0,10800\n" + + "Station-5,165.0,125.0,14400\n" + + "Station-5,165.0,125.0,18000\n" + + "Station-5,165.0,125.0,21600\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 100, ""); + + // read just outer+inner [time][station] vars, with outer and inner constraint + table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); + results = table.dataToString(); + expected = "station_name,lat,lon,time\n" + + "Station-5,165.0,125.0,345600\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just outer+inner+obs vars, with outer and inner constraint + table.readNcCF(fileName, StringArray.fromCSV(""), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); + results = table.dataToString(); + expected = "lat,lon,station_name,alt,time,temperature,humidity\n" + + "165.0,125.0,Station-5,0.17808062,345600,38.457962,28.075706\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just outer+obs vars, with outer and inner constraint + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, StringArray.fromCSV("lat,time,temperature,humidity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); + results = table.dataToString(); + expected = "lat,time,temperature,humidity\n" + + "165.0,345600,38.457962,28.075706\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just inner+obs vars, with outer and inner constraint + table.readNcCF(fileName, StringArray.fromCSV("lat,lon,station_name,time,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); + results = table.dataToString(); + expected = "lat,lon,station_name,time,temperature\n" + + "165.0,125.0,Station-5,345600,38.457962\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just obs vars, with outer and inner constraint + table.readNcCF(fileName, StringArray.fromCSV("time,lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,lat"), StringArray.fromCSV("=,="), StringArray.fromCSV("345600,165")); + results = table.dataToString(); + expected = "time,lat,temperature\n" + + "345600,165.0,38.457962\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** timeseries incomplete multidimensional --- + fileName = TableTests.class.getResource("/CFPointConventions/timeseries/" + + "timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/" + + "timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.nc").getPath(); + // String2.log("\n\n** Testing incomplete file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(24); + expected = "lat,lon,station_elevation,station_info,station_name,alt,time,temperature,humidity\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,0,17.0,56.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,3600,7.0,49.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,7200,19.0,86.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,10800,5.0,81.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,14400,0.0,55.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,18000,10.0,9.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,21600,32.0,57.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,25200,39.0,39.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,28800,39.0,68.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,32400,29.0,6.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,36000,26.0,12.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,39600,24.0,72.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,43200,14.0,80.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,46800,38.0,52.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,50400,35.0,46.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,54000,33.0,48.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,57600,34.0,85.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,61200,27.0,3.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,64800,37.0,61.0\n" + + "121.0,81.0,4.859895,0,Station-0,1.9358816,68400,0.0,0.0\n" + + "150.0,73.0,2.6002314,1,Station-1,4.052759,0,25.0,73.0\n" + + "150.0,73.0,2.6002314,1,Station-1,4.052759,3600,29.0,74.0\n" + + "150.0,73.0,2.6002314,1,Station-1,4.052759,7200,33.0,88.0\n" + + "150.0,73.0,2.6002314,1,Station-1,4.052759,10800,25.0,3.0\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 200, ""); + results = table.columnAttributes(7).toString(); // temperature + expected = " coordinates=time lat lon alt\n" + + " long_name=Air Temperature\n" + + " missing_value=-999.9f\n" + + " standard_name=air_temperature\n" + + " units=Celsius\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // read just outer [station] vars + table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon"), 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "station_name,lat,lon\n" + + "Station-0,121.0,81.0\n" + + "Station-1,150.0,73.0\n" + + "Station-2,107.0,152.0\n" + + "Station-3,117.0,143.0\n" + + "Station-4,107.0,11.0\n" + + "Station-5,161.0,100.0\n" + + "Station-6,150.0,169.0\n" + + "Station-7,176.0,85.0\n" + + "Station-8,83.0,126.0\n" + + "Station-9,84.0,170.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just outer [station] vars, with constraint + table.readNcCF(fileName, StringArray.fromCSV("station_name,lat,lon"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), StringArray.fromCSV(">"), StringArray.fromCSV("155")); + results = table.dataToString(); + expected = "station_name,lat,lon\n" + + "Station-5,161.0,100.0\n" + + "Station-7,176.0,85.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // There are no just inner[obs] variables + + // read just outer+obs vars, with outer constraint + table.readNcCF(fileName, StringArray.fromCSV("lat,time,temperature,humidity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), StringArray.fromCSV("="), StringArray.fromCSV("150")); + results = table.dataToString(); + expected = + // metadata mv=-999.9 for temp and humidity, so 9e36 below are "valid" values + "lat,time,temperature,humidity\n" + + "150.0,0,25.0,73.0\n" + + "150.0,3600,29.0,74.0\n" + + "150.0,7200,33.0,88.0\n" + + "150.0,10800,25.0,3.0\n" + + "150.0,14400,2.0,70.0\n" + + "150.0,18000,9.0,37.0\n" + + "150.0,21600,10.0,45.0\n" + + "150.0,25200,33.0,24.0\n" + + "150.0,28800,1.0,43.0\n" + + "150.0,32400,26.0,0.0\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,-2147483647,9.96921E36,9.96921E36\n" + + "150.0,0,18.0,4.0\n" + + "150.0,3600,18.0,83.0\n" + + "150.0,7200,27.0,10.0\n" + + "150.0,10800,33.0,43.0\n" + + "150.0,14400,34.0,31.0\n" + + "150.0,18000,0.0,69.0\n" + + "150.0,21600,27.0,34.0\n" + + "150.0,25200,3.0,41.0\n" + + "150.0,28800,38.0,14.0\n" + + "150.0,32400,20.0,5.0\n" + + "150.0,36000,26.0,48.0\n" + + "150.0,39600,11.0,29.0\n" + + "150.0,43200,22.0,60.0\n" + + "150.0,46800,39.0,63.0\n" + + "150.0,50400,27.0,18.0\n" + + "150.0,54000,26.0,84.0\n" + + "150.0,57600,26.0,71.0\n" + + "150.0,61200,33.0,25.0\n" + + "150.0,64800,27.0,17.0\n" + + "150.0,68400,17.0,79.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just outer+obs vars, with outer + obs constraint + table.readNcCF(fileName, StringArray.fromCSV("lat,time,temperature,humidity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat,humidity"), StringArray.fromCSV("=,="), StringArray.fromCSV("150,43")); + results = table.dataToString(); + expected = "lat,time,temperature,humidity\n" + + "150.0,28800,1.0,43.0\n" + + "150.0,10800,33.0,43.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just outer+obs vars, + table.readNcCF(fileName, StringArray.fromCSV("time,temperature,humidity"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,temperature"), StringArray.fromCSV("=,="), StringArray.fromCSV("7200,33")); + results = table.dataToString(); + expected = + // "22,150.0,73.0,2.6002314,1,Station-1,4.052759,7200,33.0,88.0\n" + from above + "time,temperature,humidity\n" + + "7200,33.0,88.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just obs vars, with outer and obs constraint + table.readNcCF(fileName, StringArray.fromCSV("time,lon,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,lon"), StringArray.fromCSV("=,="), StringArray.fromCSV("7200,73")); + results = table.dataToString(); + expected = "time,lon,alt,temperature\n" + + "7200,73.0,4.052759,33.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + /* */ + // read just obs vars, with outer and obs constraint + table.readNcCF(fileName, StringArray.fromCSV("time,lon,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lon,temperature"), StringArray.fromCSV("=,="), StringArray.fromCSV("73,33")); + results = table.dataToString(); + expected = "time,lon,alt,temperature\n" + + "7200,73.0,4.052759,33.0\n" + + "25200,73.0,4.052759,33.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // read just obs vars, with outer and obs constraint + table.readNcCF(fileName, StringArray.fromCSV("time,lon,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time,temperature"), StringArray.fromCSV("=,="), StringArray.fromCSV("7200,33")); + results = table.dataToString(); + expected = "time,lon,alt,temperature\n" + + "7200,73.0,4.052759,33.0\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // Table.debugMode = oDebug; + } + + /** + * This tests readNcCF trajectory files from ASA + * via https://github.com/asascience-open/CFPointConventions + * stored in unitTestDataDir/CFPointConventions. + */ + @org.junit.jupiter.api.Test + void testReadNcCFASATrajectory() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCFASATrajectory"); + Table table = new Table(); + String results, expected, fileName; + + /* */ + // *************** trajectory contiguous + fileName = TableTests.class.getResource("/CFPointConventions/trajectory/" + + "trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/" + + "trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.nc").getPath(); + // String2.log("\n\n** Testing contiguous file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(20); + expected = "lat,lon,trajectory_info,trajectory_name,time,z,temperature,humidity\n" + + "16.937433,-35.901237,0,Trajectory0,0,0.0,18.559397,46.487503\n" + + "32.011345,-8.81588,0,Trajectory0,3600,1.0,34.649773,16.22458\n" + + "3.137092,-64.15942,0,Trajectory0,7200,2.0,35.318504,77.41457\n" + + "10.783036,-11.503419,0,Trajectory0,10800,3.0,19.39111,56.601\n" + + "4.6016994,-6.416601,0,Trajectory0,14400,4.0,5.4162874,62.606712\n" + + "25.337688,-69.37197,0,Trajectory0,18000,5.0,2.604784,16.390015\n" + + "30.219189,-71.78619,0,Trajectory0,21600,6.0,22.968603,62.276855\n" + + "5.3421707,-29.245968,0,Trajectory0,25200,7.0,8.609019,14.976101\n" + + "25.687958,-57.089973,0,Trajectory0,28800,8.0,9.202528,79.17113\n" + + "31.82367,-58.56237,0,Trajectory0,32400,9.0,1.5670301,26.49425\n" + + "23.310976,-3.997997,0,Trajectory0,36000,10.0,23.187065,64.34719\n" + + "43.486816,-62.39688,0,Trajectory0,39600,11.0,37.44155,29.570276\n" + + "44.56024,-54.139122,0,Trajectory0,43200,12.0,11.75348,72.36402\n" + + "42.48622,-42.518707,1,Trajectory1,0,0.0,20.665886,67.27393\n" + + "32.187572,-73.20317,1,Trajectory1,3600,1.0,26.498121,79.754486\n" + + "6.4802227,-72.74957,1,Trajectory1,7200,2.0,17.64227,70.126625\n" + + "38.596996,-67.64374,1,Trajectory1,10800,3.0,23.615097,59.626125\n" + + "24.085066,-63.833694,1,Trajectory1,14400,4.0,30.743101,35.862038\n" + + "24.221394,-57.373817,1,Trajectory1,18000,5.0,39.391495,28.661589\n" + + "22.637892,-47.858807,1,Trajectory1,21600,6.0,1.2310536,55.708595\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 163, ""); + results = table.columnAttributes(5).toString(); // temperature + expected = " axis=Z\n" + + " long_name=height above mean sea level\n" + + " missing_value=-999.0f\n" + + " positive=up\n" + + " standard_name=altitude\n" + + " units=m\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("temperature,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // *************** trajectory single multidimensional --- + fileName = TableTests.class.getResource("/CFPointConventions/trajectory/" + + "trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/" + + "trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.nc").getPath(); + // String2.log("\n\n** Testing single multidimensional file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = "lat,lon,trajectory_info,trajectory_name,time,z,temperature,humidity\n" + + "42.003387,-7.9335957,0,Trajectory1,0,0.0,12.522581,35.668747\n" + + "8.972063,-46.335754,0,Trajectory1,3600,1.0,25.658121,1.0647067\n" + + "25.841967,-49.1959,0,Trajectory1,7200,2.0,35.43442,13.059927\n" + + "35.699753,-40.790943,0,Trajectory1,10800,3.0,35.752117,48.576355\n" + + "11.132234,-25.553247,0,Trajectory1,14400,4.0,6.082586,64.91749\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 100, ""); + results = table.columnAttributes(table.findColumnNumber("temperature")).toString(); + expected = " coordinates=time lat lon z\n" + + " long_name=Air Temperature\n" + + " missing_value=-999.9f\n" + + " standard_name=air_temperature\n" + + " units=Celsius\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("temperature,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // *************** trajectory indexed --- + fileName = TableTests.class.getResource("/CFPointConventions/trajectory/" + + "trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/" + + "trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.nc").getPath(); + // String2.log("\n\n** Testing indexed file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = "lat,lon,trajectory_info,trajectory_name,time,z,temperature,humidity\n" + + "11.256147,-5.989336,8,Trajectory8,72000,12.518082,14.902713,37.237553\n" + + "26.104128,-2.6626983,3,Trajectory3,111600,7.372036,24.243849,12.862466\n" + + "22.414213,-23.53803,4,Trajectory4,68400,5.7999315,1.4940661,20.668322\n" + + "22.181162,-34.355854,4,Trajectory4,122400,20.127024,6.8310843,55.93755\n" + + "2.177301,-58.388607,5,Trajectory5,162000,1.764841,27.893003,28.2276\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 213, ""); + results = table.columnAttributes(6).toString(); // temperature + expected = " coordinates=time lat lon z\n" + + " long_name=Air Temperature\n" + + " missing_value=-999.9f\n" + + " standard_name=air_temperature\n" + + " units=Celsius\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("lat,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("z,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("temperature,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature,trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, + StringArray.fromCSV("trajectory_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, + StringArray.fromCSV("z"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + /* */ + // Table.debugMode = oDebug; + } + + /** + * This tests readNcCF timeSeriesProfile files from ASA + * via https://github.com/asascience-open/CFPointConventions + * stored in unitTestDataDir/CFPointConventions. + */ + @org.junit.jupiter.api.Test + void testReadNcCFASATimeSeriesProfile() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCFASATimeSeriesProfile"); + Table table = new Table(); + String results, expected, fileName; + String orthoMultiDimH51FileName = TableTests.class.getResource("/CFPointConventions/timeSeriesProfile/" + + "timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/" + + "timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.nc").getPath(); + String raggedSingleStationFileName = TableTests.class.getResource("/CFPointConventions/timeSeriesProfile/" + + "timeSeriesProfile-Ragged-SingleStation-H.5.3/" + + "timeSeriesProfile-Ragged-SingleStation-H.5.3.nc").getPath(); + + // *************** timeSeriesProfile multidimensional --- + fileName = TableTests.class.getResource("/CFPointConventions/timeSeriesProfile/" + + "timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/" + + "timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.nc").getPath(); + // String2.log("\n\n** Testing incomplete file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(5); + expected = "lat,lon,station_info,station_name,alt,time,temperature\n" + + "37.5,-76.5,0,Station1,0.0,0,0.0\n" + + "37.5,-76.5,0,Station1,2.5,0,0.1\n" + + "37.5,-76.5,0,Station1,5.0,0,0.2\n" + + "37.5,-76.5,0,Station1,7.5,0,0.3\n" + + "37.5,-76.5,0,Station1,10.0,0,0.4\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 240, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // *************** timeSeriesProfile multidimensional single station + fileName = TableTests.class.getResource("/CFPointConventions/timeSeriesProfile/" + + "timeSeriesProfile-Multidimensional-SingleStation-H.5.2/" + + "timeSeriesProfile-Multidimensional-SingleStation-H.5.2.nc").getPath(); + // String2.log("\n\n** Testing contiguous file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "lat,lon,station_info,station_name,alt,time,temperature\n" + + "37.5,-76.5,0,Station1,0.0,0,0.0\n" + + "37.5,-76.5,0,Station1,2.5,0,0.1\n" + + "37.5,-76.5,0,Station1,5.0,0,0.2\n" + + "37.5,-76.5,0,Station1,7.5,0,0.3\n" + + "37.5,-76.5,0,Station1,10.0,0,0.4\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + expected = "37.5,-76.5,0,Station1,287.5,10800,11.5\n" + + "37.5,-76.5,0,Station1,290.0,10800,11.6\n" + + "37.5,-76.5,0,Station1,292.5,10800,11.7\n" + + "37.5,-76.5,0,Station1,295.0,10800,11.8\n" + + "37.5,-76.5,0,Station1,297.5,10800,11.9\n"; + Test.ensureEqual(results.substring(results.length() - expected.length()), + expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 120, ""); + results = table.columnAttributes(table.findColumnNumber("alt")).toString(); + expected = " axis=Z\n" + + " positive=up\n" + + " units=m\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + results = table.columnAttributes(table.findColumnNumber("temperature")).toString(); + expected = " coordinates=time lat lon alt\n" + + " long_name=Water Temperature\n" + + " missing_value=-999.9f\n" + + " units=Celsius\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // *************** timeSeriesProfile orthogonal multidimensional --- + // !!! IMPORTANT/ONLY test of file with variable[innerDim] for innerTable + // and variable[time][z][station] which is allowed, ordering + fileName = orthoMultiDimH51FileName; + // String2.log("\n\n** Testing incomplete file\n" + " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(12); + expected = "lat,lon,alt,station_info,station_name,time,temperature,humidity\n" + + "37.5,-76.5,0.0,0,Station1,0,15.698009,89.70879\n" + + "32.5,-78.3,0.0,1,Station2,0,8.11997,33.637585\n" + + "37.5,-76.5,10.0,0,Station1,0,10.9166565,55.78947\n" + + "32.5,-78.3,10.0,1,Station2,0,39.356647,65.43795\n" + + "37.5,-76.5,20.0,0,Station1,0,15.666663,50.176994\n" + + "32.5,-78.3,20.0,1,Station2,0,33.733116,58.14976\n" + + "37.5,-76.5,30.0,0,Station1,0,1.1587523,36.855045\n" + + "32.5,-78.3,30.0,1,Station2,0,4.65479,63.862186\n" + + "37.5,-76.5,0.0,0,Station1,3600,31.059647,65.01694\n" + + "32.5,-78.3,0.0,1,Station2,3600,33.374344,22.771135\n" + + "37.5,-76.5,10.0,0,Station1,3600,5.680936,35.675472\n" + + "32.5,-78.3,10.0,1,Station2,3600,17.763374,38.54674\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 800, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + fileName = orthoMultiDimH51FileName; + // String2.log("\n\n** Testing incomplete file with constraints\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(orthoMultiDimH51FileName, "-h")); + table.readNcCF(fileName, null, + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("Station1")); + results = table.dataToString(12); + expected = "lat,lon,alt,station_info,station_name,time,temperature,humidity\n" + + "37.5,-76.5,0.0,0,Station1,0,15.698009,89.70879\n" + + "37.5,-76.5,10.0,0,Station1,0,10.9166565,55.78947\n" + + "37.5,-76.5,20.0,0,Station1,0,15.666663,50.176994\n" + + "37.5,-76.5,30.0,0,Station1,0,1.1587523,36.855045\n" + + "37.5,-76.5,0.0,0,Station1,3600,31.059647,65.01694\n" + + "37.5,-76.5,10.0,0,Station1,3600,5.680936,35.675472\n" + + "37.5,-76.5,20.0,0,Station1,3600,24.156359,45.77856\n" + + "37.5,-76.5,30.0,0,Station1,3600,25.934822,35.178967\n" + + "37.5,-76.5,0.0,0,Station1,7200,6.518481,12.735875\n" + + "37.5,-76.5,10.0,0,Station1,7200,4.463567,47.44697\n" + + "37.5,-76.5,20.0,0,Station1,7200,29.448772,20.438272\n" + + "37.5,-76.5,30.0,0,Station1,7200,37.245636,62.655357\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 400, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // test just variable[obs] (interiorTable) + // String2.log("\n\n** Testing incomplete file\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, StringArray.fromCSV("lat,lon,station_name,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("Station1")); + results = table.dataToString(); + expected = "lat,lon,station_name\n" + + "37.5,-76.5,Station1\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 1, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // ********** NO_DATA + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, + // outer/inner/obsVar + // String2.log("\n\n** Testing orthoMultiDimH51FileName just outer/inner/obsVar, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("time,zztop,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // outerVar + // String2.log("\n\n** Testing orthoMultiDimH51FileName just outerVar, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("zztop,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // innerVar + // String2.log("\n\n** Testing orthoMultiDimH51FileName just innerVar, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("alt,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("10000")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // obsVar + // String2.log("\n\n** Testing orthoMultiDimH51File just obsVar, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("zztop,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // outerVar* and innerVar + // String2.log("\n\n** Testing orthoMultiDimH51File just outer*/innerVar, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("zztop,time,alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // outerVar and innerVar* + // String2.log("\n\n** Testing orthoMultiDimH51File just outer/innerVar*, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("zztop,time,alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("10000")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // outerVar* and obsVar + // String2.log("\n\n** Testing orthoMultiDimH51File just outer*/obsVar, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("time,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // outerVar and obsVar* + // String2.log("\n\n** Testing orthoMultiDimH51File just outer/obsVar*, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("time,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // innerVar* and obsVar + // String2.log("\n\n** Testing orthoMultiDimH51File just inner*/obsVar, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("alt,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("10000")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile orthoMultiDimH51FileName --- NO_DATA, just + // innerVar and obsVar* + // String2.log("\n\n** Testing orthoMultiDimH51File just inner/obsVar*, NO_DATA\n" + + // " " + orthoMultiDimH51FileName); + table.readNcCF(orthoMultiDimH51FileName, + StringArray.fromCSV("alt,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ******* + // *************** timeSeriesProfile ragged --- + fileName = TableTests.class.getResource("/CFPointConventions/timeSeriesProfile/" + + "timeSeriesProfile-Ragged-MultipeStations-H.5.3/" + + "timeSeriesProfile-Ragged-MultipeStations-H.5.3.nc").getPath(); + // String2.log("\n\n** Testing timeSeriesProfile ragged file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = + // file has: + // lat, lon, station_info, station_name, profile, time, station_index, row_size, + // height, temperature + "lat,lon,station_info,station_name,profile,time,height,temperature\n" + + "37.5,-76.5,0,Station1,0,0,0.5,6.7\n" + + "37.5,-76.5,0,Station1,0,0,1.5,6.9\n" + + "32.5,-78.3,1,Station2,1,3600,0.8,7.6\n" + + "32.5,-78.3,1,Station2,1,3600,1.8,7.7\n" + + "32.5,-78.3,1,Station2,1,3600,2.8,7.9\n" + + "32.5,-78.3,1,Station2,1,3600,3.8,8.0\n" + + "37.5,-76.5,0,Station1,2,7200,0.5,6.7\n" + + "37.5,-76.5,0,Station1,2,7200,1.5,7.0\n" + + "32.5,-78.3,1,Station2,3,10800,0.8,8.2\n" + + "32.5,-78.3,1,Station2,3,10800,1.8,7.7\n" + + "32.5,-78.3,1,Station2,3,10800,2.8,7.8\n" + + "32.5,-78.3,1,Station2,3,10800,3.8,9.1\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 12, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "height,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "height,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "height,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "height,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "height"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // *************** timeSeriesProfile ragged single station --- + // This is ONLY TEST FILE of nLevels=2 single station (outerTable are scalar + // vars)!!!!!!!! + // Note also the lack of a stationIndex var with + // instance_dimension="someDimension" + // since there is no instance_dimension + fileName = raggedSingleStationFileName; + // String2.log("\n\n** Testing raggedSingleStationFile\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "lat,lon,station_info,station_name,profile,time,height,temperature\n" + + "37.5,-76.5,0,Station1,0,0,0.5,6.7\n" + + "37.5,-76.5,0,Station1,0,0,1.5,6.9\n" + + "37.5,-76.5,0,Station1,1,3600,0.5,6.8\n" + + "37.5,-76.5,0,Station1,1,3600,1.5,7.9\n" + + "37.5,-76.5,0,Station1,2,7200,0.5,6.8\n" + + "37.5,-76.5,0,Station1,2,7200,1.5,7.9\n" + + "37.5,-76.5,0,Station1,2,7200,2.5,8.4\n" + + "37.5,-76.5,0,Station1,3,10800,0.5,5.7\n" + + "37.5,-76.5,0,Station1,3,10800,1.5,9.2\n" + + "37.5,-76.5,0,Station1,3,10800,2.5,8.3\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 10, ""); + results = table.columnAttributes(table.findColumnNumber("profile")).toString(); + expected = " cf_role=profile_id\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "station_name,lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "height,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "height,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "height,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "height,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "height,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "station_name"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_name"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "height"), + 0, // standardizeWhat=0 + StringArray.fromCSV("height"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // *************** timeSeriesProfile ragged single station --- just outerVar + // String2.log("\n\n** Testing raggedSingleStationFile just outerVar\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("zztop,lat,lon,station_info,station_name"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "lat,lon,station_info,station_name\n" + + "37.5,-76.5,0,Station1\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 1, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station latitude\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** timeSeriesProfile ragged single station --- just innerVar + // String2.log("\n\n** Testing raggedSingleStationFile just innerVar\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("time,zztop,profile"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "time,profile\n" + + "0,0\n" + + "3600,1\n" + + "7200,2\n" + + "10800,3\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 4, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=time\n" + + " missing_value=-999i\n" + + " standard_name=time\n" + + " units=seconds since 1990-01-01 00:00:00\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** timeSeriesProfile ragged single station --- just outerVar and + // innerVar + // String2.log("\n\n** Testing raggedSingleStationFile just outerVar and innerVar\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("station_info,station_name,lon,lat,time,profile,"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "station_info,station_name,lon,lat,time,profile\n" + + "0,Station1,-76.5,37.5,0,0\n" + + "0,Station1,-76.5,37.5,3600,1\n" + + "0,Station1,-76.5,37.5,7200,2\n" + + "0,Station1,-76.5,37.5,10800,3\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 4, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station info\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** timeSeriesProfile ragged single station --- just outerVar and + // obsVar + // String2.log("\n\n** Testing raggedSingleStationFile just outerVar and obsVar\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("station_info,temperature,zztop,station_name,"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("8")); + results = table.dataToString(); + expected = "station_info,temperature,station_name\n" + + "0,8.4,Station1\n" + + "0,9.2,Station1\n" + + "0,8.3,Station1\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 3, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station info\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** timeSeriesProfile ragged single station --- just innerVar and + // obsVar + // String2.log("\n\n** Testing raggedSingleStationFile just innerVar and obsVar\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("temperature,zztop,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("8")); + results = table.dataToString(); + expected = "temperature,time\n" + + "8.4,7200\n" + + "9.2,10800\n" + + "8.3,10800\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 3, ""); + results = table.columnAttributes(0).toString(); + expected = " coordinates=time lat lon height\n" + + " long_name=Water Temperature\n" + + " missing_value=-999.9f\n" + + " standard_name=sea_water_temperature\n" + + " units=Celsius\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // ********** NO_DATA + // ********** timeSeriesProfile ragged single station --- NO_DATA, + // outer/inner/obsVar + // String2.log("\n\n** Testing raggedSingleStationFile just outer/inner/obsVar, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("station_info,zztop,profile,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just outerVar + // String2.log("\n\n** Testing raggedSingleStationFile just outerVar, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("zztop,station_info"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_info"), + StringArray.fromCSV("="), + StringArray.fromCSV("10")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just innerVar + // String2.log("\n\n** Testing raggedSingleStationFile just innerVar, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("profile,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just obsVar + // String2.log("\n\n** Testing raggedSingleStationFile just obsVar, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("zztop,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just + // outerVar* and innerVar + // String2.log("\n\n** Testing raggedSingleStationFile just outer*/innerVar, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("zztop,station_info,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_info"), + StringArray.fromCSV("="), + StringArray.fromCSV("10")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just outerVar + // and innerVar* + // String2.log("\n\n** Testing raggedSingleStationFile just outer/innerVar*, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("zztop,station_info,profile"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just + // outerVar* and obsVar + // String2.log("\n\n** Testing raggedSingleStationFile just outer*/obsVar, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("temperature,station_info,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("station_info"), + StringArray.fromCSV("="), + StringArray.fromCSV("10")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just outerVar + // and obsVar* + // String2.log("\n\n** Testing raggedSingleStationFile just outer/obsVar*, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("temperature,station_info,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just + // innerVar* and obsVar + // String2.log("\n\n** Testing raggedSingleStationFile just inner*/obsVar, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("temperature,profile,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("profile"), + StringArray.fromCSV("="), + StringArray.fromCSV("-1")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** timeSeriesProfile ragged single station --- NO_DATA, just innerVar + // and obsVar* + // String2.log("\n\n** Testing raggedSingleStationFile just inner/obsVar*, NO_DATA\n" + + // " " + raggedSingleStationFileName); + table.readNcCF(raggedSingleStationFileName, + StringArray.fromCSV("temperature,profile,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + /* */ + // Table.debugMode = oDebug; + } + + /** + * This tests readNcCF trajectoryProfile files from ASA + * via https://github.com/asascience-open/CFPointConventions + * stored in unitTestDataDir/CFPointConventions. + */ + @org.junit.jupiter.api.Test + void testReadNcCFASATrajectoryProfile() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + boolean oDebug = Table.debugMode; + // Table.debugMode = true; + // String2.log("\n*** Table.testReadNcCFASATrajectoryProfile"); + Table table = new Table(); + String results, expected, fileName; + String orthoMultiDimH61FileName = TableTests.class.getResource("/CFPointConventions/trajectoryProfile/" + + "trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/" + + "trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.nc").getPath(); + String raggedMultipleStationFileName = TableTests.class.getResource("/CFPointConventions/trajectoryProfile/" + + "trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/" + + "trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.nc").getPath(); + + /* */ + // *************** trajectoryProfile multidimensional single station + try { + fileName = TableTests.class.getResource("/CFPointConventions/trajectoryProfile/" + + "trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/" + + "trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.nc").getPath(); + // String2.log("\n\n** Testing contiguous file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "-h")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "lat,lon,trajectory,alt,time,temperature,salinity\n" + + "4.9986253,-35.718536,0,0.0,0,3.2502668,79.006065\n" + + "4.9986253,-35.718536,0,1.0,0,30.566391,37.089394\n" + + "4.9986253,-35.718536,0,2.0,0,0.8428718,20.478456\n" + + "1.4658529,-25.19569,0,0.0,3600,27.982288,17.57356\n" + + "1.4658529,-25.19569,0,1.0,3600,15.750698,11.152985\n" + + "1.4658529,-25.19569,0,2.0,3600,39.36954,31.84863\n" + + "1.4658529,-25.19569,0,3.0,3600,8.506618,77.88138\n" + + "1.4658529,-25.19569,0,4.0,3600,39.580475,77.575645\n" + + "38.299484,-55.72639,0,0.0,7200,36.646107,77.1104\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 20, ""); + results = table.columnAttributes(table.findColumnNumber("lat")).toString(); + expected = " long_name=Latitude\n" + + " missing_value=-999.9f\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + results = table.columnAttributes(table.findColumnNumber("alt")).toString(); + expected = " axis=Z\n" + + " long_name=height below mean sea level\n" + + " missing_value=-999.9f\n" + + " positive=down\n" + + " standard_name=altitude\n" + + " units=m\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + } catch (Exception e) { + String2.pressEnterToContinue(MustBe.throwableToString(e)); + } + + // *************** trajectoryProfile orthogonal multidimensional --- + try { + fileName = orthoMultiDimH61FileName; + // String2.log("\n\n** Testing orthogonal multidim file\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(14); + expected = "lat,lon,trajectory,alt,time,temperature,salinity\n" + + "18.736742,-28.520071,0,0.0,0,8.067447,62.835354\n" + + "18.736742,-28.520071,0,1.0,0,15.871663,27.454027\n" + + "18.736742,-28.520071,0,2.0,0,32.306496,61.80094\n" + + "18.736742,-28.520071,0,3.0,0,27.631369,74.84051\n" + + "18.736742,-28.520071,0,4.0,0,22.757963,73.378914\n" + + "39.43245,-57.711514,1,0.0,0,36.39878,77.23479\n" + + "39.43245,-57.711514,1,1.0,0,14.957566,7.621207\n" + + "39.43245,-57.711514,1,2.0,0,5.405648,56.557266\n" + + "39.43245,-57.711514,1,3.0,0,4.9267964,75.427795\n" + + "39.43245,-57.711514,1,4.0,0,7.806849,42.65483\n" + + "39.43245,-57.711514,1,5.0,0,28.784224,13.940006\n" + + "39.43245,-57.711514,1,6.0,0,19.139135,53.46242\n" + + "25.034857,-62.39183,1,0.0,3600,24.302265,62.551056\n" + + "25.034857,-62.39183,1,1.0,3600,11.195762,4.3670874\n" + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 65, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=Latitude\n" + + " missing_value=-999.9f\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "alt,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "alt"), + 0, // standardizeWhat=0 + StringArray.fromCSV("alt"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // String2.log("\n\n** Testing incomplete file with constraints\n" + + // " " + orthoMultiDimH61FileName); + // String2.log(NcHelper.ncdump(orthoMultiDimH61FileName, "-h")); + table.readNcCF(orthoMultiDimH61FileName, null, + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("1")); + results = table.dataToString(); + expected = "lat,lon,trajectory,alt,time,temperature,salinity\n" + + "39.43245,-57.711514,1,0.0,0,36.39878,77.23479\n" + + "39.43245,-57.711514,1,1.0,0,14.957566,7.621207\n" + + "39.43245,-57.711514,1,2.0,0,5.405648,56.557266\n" + + "39.43245,-57.711514,1,3.0,0,4.9267964,75.427795\n" + + "39.43245,-57.711514,1,4.0,0,7.806849,42.65483\n" + + "39.43245,-57.711514,1,5.0,0,28.784224,13.940006\n" + + "39.43245,-57.711514,1,6.0,0,19.139135,53.46242\n" + + "25.034857,-62.39183,1,0.0,3600,24.302265,62.551056\n" + + "25.034857,-62.39183,1,1.0,3600,11.195762,4.3670874\n" + + "25.034857,-62.39183,1,2.0,3600,20.055767,62.966892\n" + + "25.034857,-62.39183,1,3.0,3600,38.838474,49.101334\n" + + "25.034857,-62.39183,1,4.0,3600,16.995031,19.580278\n" + + "25.034857,-62.39183,1,5.0,3600,5.6433516,62.23398\n" + + "25.034857,-62.39183,1,6.0,3600,3.8319156,3.1172054\n" + + "27.619982,-46.87254,1,0.0,7200,26.57189,22.247057\n" + + "27.619982,-46.87254,1,1.0,7200,6.7928324,61.507736\n" + + "27.619982,-46.87254,1,2.0,7200,37.85058,49.765\n" + + "27.619982,-46.87254,1,3.0,7200,31.926285,65.68376\n" + + "27.619982,-46.87254,1,4.0,7200,36.00912,39.43354\n" + + "27.619982,-46.87254,1,5.0,7200,1.9108725,22.057114\n" + + "27.619982,-46.87254,1,6.0,7200,23.234598,62.765938\n" + + "16.401363,-38.747154,1,0.0,10800,39.38336,41.227074\n" + + "16.401363,-38.747154,1,1.0,10800,22.487091,60.7646\n" + + "16.401363,-38.747154,1,2.0,10800,16.574474,5.8886514\n" + + "16.401363,-38.747154,1,3.0,10800,3.2033331,48.783085\n" + + "16.401363,-38.747154,1,4.0,10800,32.13747,12.481885\n" + + "16.401363,-38.747154,1,5.0,10800,5.927774,46.63955\n" + + "16.401363,-38.747154,1,6.0,10800,9.936579,44.746056\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 28, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=Latitude\n" + + " missing_value=-999.9f\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // test just variable[obs] (interiorTable) + // String2.log("\n\n** Testing incomplete file\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, StringArray.fromCSV("lat,lon,trajectory,time,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("2")); + results = table.dataToString(); + expected = "lat,lon,trajectory,time\n" + + "22.20038,-74.5625,2,0\n" + + "39.905518,-15.35749,2,3600\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + results = table.columnAttributes(0).toString(); + expected = " long_name=Latitude\n" + + " missing_value=-999.9f\n" + + " standard_name=latitude\n" + + " units=degrees_north\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + } catch (Exception e) { + String2.pressEnterToContinue(MustBe.throwableToString(e)); + } + + // ********** NO_DATA + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, + // outer/inner/obsVar + // String2.log("\n\n** Testing orthoMultiDimH61FileName just outer/inner/obsVar, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("trajectory,lat,zztop,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // outerVar + // String2.log("\n\n** Testing orthoMultiDimH61FileName just outerVar, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("zztop,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // innerVar + // String2.log("\n\n** Testing orthoMultiDimH61FileName just innerVar, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("lat,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // obsVar + // String2.log("\n\n** Testing orthoMultiDimH51File just obsVar, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("zztop,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // outerVar* and innerVar + // String2.log("\n\n** Testing orthoMultiDimH51File just outer* /innerVar, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("zztop,trajectory,lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // outerVar and innerVar* + // String2.log("\n\n** Testing orthoMultiDimH51File just outer/innerVar*, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("zztop,trajectory,lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // outerVar* and obsVar + // String2.log("\n\n** Testing orthoMultiDimH51File just outer* /obsVar, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("trajectory,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // outerVar and obsVar* + // String2.log("\n\n** Testing orthoMultiDimH51File just outer/obsVar*, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("trajectory,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // innerVar* and obsVar + // String2.log("\n\n** Testing orthoMultiDimH51File just inner* /obsVar, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("lat,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile orthoMultiDimH61FileName --- NO_DATA, just + // innerVar and obsVar* + // String2.log("\n\n** Testing orthoMultiDimH51File just inner/obsVar*, NO_DATA\n" + + // " " + orthoMultiDimH61FileName); + table.readNcCF(orthoMultiDimH61FileName, + StringArray.fromCSV("lat,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ******* + // *************** trajectoryProfile ragged multiple station --- + try { + fileName = raggedMultipleStationFileName; + // String2.log("\n\n** Testing raggedMultipleStationFile\n" + + // " " + fileName); + // String2.log(NcHelper.ncdump(fileName, "")); + table.readNcCF(fileName, null, 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "trajectory,lat,lon,time,z,temperature,humidity\n" + + "0,49.0,-60.0,176400,0.0,39.174652,78.30777\n" + + "0,49.0,-60.0,176400,1.0,30.924078,58.185684\n" + + "0,49.0,-60.0,176400,2.0,19.258087,47.014008\n" + + "0,49.0,-60.0,176400,3.0,33.512325,77.832664\n" + + "0,49.0,-60.0,176400,4.0,35.435345,55.649605\n" + + "0,49.0,-60.0,176400,5.0,17.33441,60.725643\n" + + "0,49.0,-60.0,176400,6.0,6.3611813,40.747665\n" + + "0,49.0,-60.0,176400,7.0,37.18272,32.312344\n" + + "0,49.0,-60.0,176400,8.0,31.59126,30.934\n" + + "0,49.0,-60.0,176400,9.0,36.08196,48.639427\n" + + "0,49.0,-60.0,176400,10.0,22.3596,16.427603\n" + + "0,49.0,-60.0,176400,11.0,6.2299767,16.590557\n" + + "0,53.0,-60.0,104400,0.0,13.244916,28.135975\n" + + "0,53.0,-60.0,104400,1.0,17.160164,41.951385\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, + "results=\n" + results); + expected = "4,47.0,-44.0,136800,33.0,8.7725,74.930565\n" + + "4,47.0,-44.0,136800,34.0,29.10568,31.136621\n" + + "4,47.0,-44.0,136800,35.0,4.7999196,18.904522\n" + + "4,47.0,-44.0,136800,36.0,1.4633778,47.546745\n" + + "4,47.0,-44.0,136800,37.0,24.846626,77.9313\n" + + "4,47.0,-44.0,136800,38.0,16.368006,8.343946\n"; + Test.ensureEqual( + results.substring(results.length() - expected.length(), results.length()), + expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 594, ""); + results = table.columnAttributes(0).toString(); + expected = " cf_role=trajectory_id\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory,lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "z,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "lat,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "z,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "z,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "z,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "z,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // + table.readNcCF(fileName, StringArray.fromCSV( + "trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "lat"), + 0, // standardizeWhat=0 + StringArray.fromCSV("lat"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + table.readNcCF(fileName, StringArray.fromCSV( + "z"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-12345")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // *************** trajectoryProfile ragged multiple station --- just outerVar + // String2.log("\n\n** Testing raggedMultipleStationFile just outerVar\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("zztop,trajectory"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(20); + expected = "trajectory\n" + + "0\n" + + "1\n" + + "2\n" + + "3\n" + + "4\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 5, ""); + results = table.columnAttributes(0).toString(); + expected = " cf_role=trajectory_id\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** trajectoryProfile ragged multiple station --- just innerVar + // String2.log("\n\n** Testing raggedMultipleStationFile just innerVar\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("time,zztop,trajectory"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "time,trajectory\n" + + "176400,0\n" + + "104400,0\n" + + "140400,0\n" + + "151200,0\n" + + "111600,1\n" + + "36000,1\n" + + "64800,1\n" + + "46800,1\n" + + "0,2\n" + + "162000,2\n" + + "180000,2\n" + + "129600,2\n" + + "154800,3\n" + + "3600,3\n" + + "122400,3\n" + + "32400,3\n" + + "136800,4\n" + + "140400,4\n" + + "140400,4\n" + + "136800,4\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 20, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=time of measurement\n" + + " missing_value=-999i\n" + + " standard_name=time\n" + + " units=seconds since 1990-01-01 00:00:00\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** trajectoryProfile ragged multiple station --- just outerVar + // and innerVar + // String2.log("\n\n** Testing raggedMultipleStationFile just outerVar and innerVar\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("lon,lat,time,trajectory,"), + 0, // standardizeWhat=0 + null, null, null); + results = table.dataToString(); + expected = "lon,lat,time,trajectory\n" + + "-60.0,49.0,176400,0\n" + + "-60.0,53.0,104400,0\n" + + "-63.0,45.0,140400,0\n" + + "-62.0,45.0,151200,0\n" + + "-56.0,54.0,111600,1\n" + + "-68.0,53.0,36000,1\n" + + "-66.0,43.0,64800,1\n" + + "-47.0,58.0,46800,1\n" + + "-52.0,47.0,0,2\n" + + "-50.0,48.0,162000,2\n" + + "-60.0,59.0,180000,2\n" + + "-71.0,42.0,129600,2\n" + + "-66.0,53.0,154800,3\n" + + "-53.0,50.0,3600,3\n" + + "-67.0,56.0,122400,3\n" + + "-73.0,48.0,32400,3\n" + + "-67.0,47.0,136800,4\n" + + "-45.0,43.0,140400,4\n" + + "-40.0,54.0,140400,4\n" + + "-44.0,47.0,136800,4\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 20, ""); + results = table.columnAttributes(0).toString(); + expected = " long_name=station longitude\n" + + " standard_name=longitude\n" + + " units=degrees_east\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** trajectoryProfile ragged multiple station --- just outerVar + // and obsVar + // String2.log("\n\n** Testing raggedMultipleStationFile just outerVar and obsVar\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("trajectory,temperature,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("39")); + results = table.dataToString(); + expected = "trajectory,temperature\n" + + "0,39.174652\n" + + "0,39.157566\n" + + "0,39.915646\n" + + "0,39.041203\n" + + "1,39.104313\n" + + "1,39.74818\n" + + "1,39.077923\n" + + "1,39.406986\n" + + "2,39.85588\n" + + "2,39.213017\n" + + "2,39.89851\n" + + "2,39.404697\n" + + "2,39.012913\n" + + "3,39.276768\n" + + "3,39.832867\n" + + "3,39.119217\n" + + "3,39.335064\n" + + "3,39.261826\n" + + "3,39.501484\n" + + "4,39.015987\n" + + "4,39.5769\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 21, ""); + results = table.columnAttributes(0).toString(); + expected = " cf_role=trajectory_id\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *************** trajectoryProfile ragged multiple station --- just innerVar + // and obsVar + // String2.log("\n\n** Testing raggedMultipleStationFile just innerVar and obsVar\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("temperature,zztop,time"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("39")); + results = table.dataToString(); + expected = "temperature,time\n" + + "39.174652,176400\n" + + "39.157566,104400\n" + + "39.915646,104400\n" + + "39.041203,104400\n" + + "39.104313,111600\n" + + "39.74818,36000\n" + + "39.077923,64800\n" + + "39.406986,64800\n" + + "39.85588,0\n" + + "39.213017,180000\n" + + "39.89851,180000\n" + + "39.404697,180000\n" + + "39.012913,180000\n" + + "39.276768,154800\n" + + "39.832867,3600\n" + + "39.119217,122400\n" + + "39.335064,122400\n" + + "39.261826,122400\n" + + "39.501484,122400\n" + + "39.015987,140400\n" + + "39.5769,136800\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + Test.ensureEqual(table.nRows(), 21, ""); + results = table.columnAttributes(0).toString(); + expected = " coordinates=time lat lon z\n" + + " long_name=Air Temperature\n" + + " missing_value=-999.9f\n" + + " standard_name=air_temperature\n" + + " units=Celsius\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // ********** NO_DATA + // ********** trajectoryProfile ragged multiple station --- NO_DATA, + // outer/inner/obsVar + // String2.log("\n\n** Testing raggedMultipleStationFile just outer/inner/obsVar, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("trajectory,zztop,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just + // outerVar + // String2.log("\n\n** Testing raggedMultipleStationFile just outerVar, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("zztop,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("10")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just + // innerVar + // String2.log("\n\n** Testing raggedMultipleStationFile just innerVar, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("time,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("time"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just obsVar + // String2.log("\n\n** Testing raggedMultipleStationFile just obsVar, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("zztop,temperature"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just + // outerVar* and innerVar + // String2.log("\n\n** Testing raggedMultipleStationFile just outer*/innerVar, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("zztop,z,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just + // outerVar and innerVar* + // String2.log("\n\n** Testing raggedMultipleStationFile just outer/innerVar*, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("zztop,z,trajectory"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-5")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just + // outerVar* and obsVar + // String2.log("\n\n** Testing raggedMultipleStationFile just outer*/obsVar, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("temperature,trajectory,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("trajectory"), + StringArray.fromCSV("="), + StringArray.fromCSV("-10")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just + // outerVar and obsVar* + // String2.log("\n\n** Testing raggedMultipleStationFile just outer/obsVar*, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("temperature,trajectory,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just + // innerVar* and obsVar + // String2.log("\n\n** Testing raggedMultipleStationFile just inner*/obsVar, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("temperature,z,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("z"), + StringArray.fromCSV("="), + StringArray.fromCSV("-1")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + + // ********** trajectoryProfile ragged multiple station --- NO_DATA, just + // innerVar and obsVar* + // String2.log("\n\n** Testing raggedMultipleStationFile just inner/obsVar*, NO_DATA\n" + + // " " + raggedMultipleStationFileName); + table.readNcCF(raggedMultipleStationFileName, + StringArray.fromCSV("temperature,z,zztop"), + 0, // standardizeWhat=0 + StringArray.fromCSV("temperature"), + StringArray.fromCSV(">="), + StringArray.fromCSV("100")); + Test.ensureEqual(table.nRows(), 0, ""); + Test.ensureEqual(table.nColumns(), 0, ""); + } catch (Exception e) { + String2.pressEnterToContinue(MustBe.throwableToString(e)); + } + /* */ + // Table.debugMode = oDebug; + } + + /** + * This tests reading a very large TSV file: 764MB before .gz, 52MB after .gz, + * 33 columns, 3503266 rows. + * I switched to StringHolder in StringArray after complaints this file took + * ~10GB to load. + * I also made several other significant memory saving changes. + * Now, reading the file into StringArray ~1600MB is the high point. + * While parsing the lines, it shrinks to ~671MB (lots of small strings). + * After convert to binary data types: ~420MB. + * Total time to read and ingest=~33s from gz file (was ~420s before). + */ + @org.junit.jupiter.api.Test + @TagLargeFile + void testBigAscii() throws Exception { + // PrimitiveArray.reallyVerbose = true; + Math2.gcAndWait("Table (between tests)"); + Math2.gcAndWait("Table (between tests)"); // in a test + // String2.log("\n*** Table.testBigAscii(): " + Math2.memoryString()); + + Table table = new Table(); + long time = System.currentTimeMillis(); + table.readASCII("/data/biddle/3937_v1_CTD_Profiles.tsv.gz"); + time = System.currentTimeMillis() - time; + Math2.gcAndWait("Table (between tests)"); + Math2.gcAndWait("Table (between tests)"); // in a test + // String2.log(" done. " + Math2.memoryString() + "\n" + + // String2.canonicalStatistics()); // in a test + String results = table.dataToString(4); + // String2.log(results); + String expected = "cruise_name,station,cast,ISO_DateTime,Year,Month,Day,timeutc,lon,lat,depth_max,pres_max,Date,timecode,HOT_summary_file_name,parameters,num_bottles,section,nav_code,depth_hgt,EXPOCODE,Ship,comments,CTDPRS,CTDTMP,CTDSAL,CTDOXY,XMISS,CHLPIG,NUMBER,NITRATE,FLUOR,QUALT1\n" + + + "001,2,1,1988-10-30T21:34:00,1988,10,30,2134,-157.9967,22.7483,4750,238,103088,BE,cruise.summaries/hot1.sum,NaN,11,PRS2,GPS,4514,32MW001_1,32MW001/1,NaN,0.0,26.2412,35.2615,183.2,4.99,-0.0126,0,,,666666\n" + + + "001,2,1,1988-10-30T21:34:00,1988,10,30,2134,-157.9967,22.7483,4750,238,103088,BE,cruise.summaries/hot1.sum,NaN,11,PRS2,GPS,4514,32MW001_1,32MW001/1,NaN,2.0,26.2412,35.2615,183.2,4.99,-0.0126,36,,,222322\n" + + + "001,2,1,1988-10-30T21:34:00,1988,10,30,2134,-157.9967,22.7483,4750,238,103088,BE,cruise.summaries/hot1.sum,NaN,11,PRS2,GPS,4514,32MW001_1,32MW001/1,NaN,4.0,26.2554,35.2530,185.5,4.08,0.0026,72,,,223322\n" + + + "001,2,1,1988-10-30T21:34:00,1988,10,30,2134,-157.9967,22.7483,4750,238,103088,BE,cruise.summaries/hot1.sum,NaN,11,PRS2,GPS,4514,32MW001_1,32MW001/1,NaN,6.0,26.2377,35.2455,204.8,3.05,0.0167,108,,,222122\n" + + + "...\n"; + try { + Test.ensureEqual(results, expected, ""); + } catch (Exception e) { + String2.pressEnterToContinue(MustBe.throwableToString(e)); + } + + Test.ensureEqual(table.nRows(), 3503266, ""); + Test.ensureEqual(table.nColumns(), 33, ""); + + table.removeRows(0, 3503261); + results = table.saveAsNccsv(false, true, 0, Integer.MAX_VALUE); // catchScalars, writeMetadata, firstDataRow, + // lastDataRow + + expected = // many vars are scalar because they're constant in last 6 rows + "*GLOBAL*,Conventions,\"COARDS, CF-1.10, ACDD-1.3, NCCSV-1.2\"\n" + + "cruise_name,*DATA_TYPE*,String\n" + + "station,*DATA_TYPE*,byte\n" + + "cast,*DATA_TYPE*,byte\n" + + "ISO_DateTime,*DATA_TYPE*,String\n" + + "Year,*DATA_TYPE*,short\n" + + "Month,*DATA_TYPE*,byte\n" + + "Day,*DATA_TYPE*,String\n" + + "timeutc,*DATA_TYPE*,String\n" + + "lon,*DATA_TYPE*,float\n" + + "lat,*DATA_TYPE*,float\n" + + "depth_max,*DATA_TYPE*,short\n" + + "pres_max,*DATA_TYPE*,short\n" + + "Date,*DATA_TYPE*,String\n" + + "timecode,*DATA_TYPE*,String\n" + + "HOT_summary_file_name,*DATA_TYPE*,String\n" + + "parameters,*DATA_TYPE*,String\n" + + "num_bottles,*DATA_TYPE*,byte\n" + + "section,*DATA_TYPE*,String\n" + + "nav_code,*DATA_TYPE*,String\n" + + "depth_hgt,*DATA_TYPE*,short\n" + + "EXPOCODE,*DATA_TYPE*,String\n" + + "Ship,*DATA_TYPE*,String\n" + + "comments,*DATA_TYPE*,String\n" + + "CTDPRS,*DATA_TYPE*,float\n" + + "CTDTMP,*DATA_TYPE*,float\n" + + "CTDSAL,*DATA_TYPE*,String\n" + + "CTDOXY,*DATA_TYPE*,String\n" + + "XMISS,*DATA_TYPE*,float\n" + + "CHLPIG,*DATA_TYPE*,String\n" + + "NUMBER,*DATA_TYPE*,String\n" + + "NITRATE,*DATA_TYPE*,float\n" + + "FLUOR,*DATA_TYPE*,double\n" + + "QUALT1,*DATA_TYPE*,String\n" + + "\n" + + "*END_METADATA*\n" + + "cruise_name,station,cast,ISO_DateTime,Year,Month,Day,timeutc,lon,lat,depth_max,pres_max,Date,timecode,HOT_summary_file_name,parameters,num_bottles,section,nav_code,depth_hgt,EXPOCODE,Ship,comments,CTDPRS,CTDTMP,CTDSAL,CTDOXY,XMISS,CHLPIG,NUMBER,NITRATE,FLUOR,QUALT1\n" + + + "288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,194.0,18.2746,34.9098,203.9,,0.0254,144,,,222192\n" + + + "288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,196.0,18.159,34.9027,203.8,,0.0257,108,,,222192\n" + + + "288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,198.0,17.9686,34.8727,203.8,,0.0257,156,,,222192\n" + + + "288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,200.0,17.8751,34.8506,201.8,,0.0248,108,,,222192\n" + + + "288,50,1,2016-11-28T17:51:00,2016,11,28,1751,-157.9373,22.7703,4705,202,112816,BE,cruise.summaries/hot288.sum,NaN,22,PRS2,GPS,4504,33KB288_1,33KB288/1,Dual T; C sensors,202.0,17.7435,34.8246,202.1,,0.0248,60,,,222192\n" + + + "*END_DATA*\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + Math2.gcAndWait("Table (between tests)"); // in a test + String msg = Math2.memoryString() + "\n" + + String2.canonicalStatistics() + "\n" + + "testBigAscii time=" + time + + "ms. file read time should be ~60 - 90s in java 17 (but I think it should be faster -- too much gc) (but longer when computer is busy) (Java 8 was 45s. was 36s before v2.10)"; + // String2.log(msg); + Test.ensureTrue(time < 60000, "Too slow! " + msg); + } + + /** + * This tests if nc files are closed when "try with resources" approach is + * taken. + * 2022-09-09 With tryWithResources, ERDDAP crashes every 2 days (like THREDDS)! + * So go back to: finally {nc.close()} + */ + @org.junit.jupiter.api.Test + @TagIncompleteTest // The test fails on CJohn's machine because FileVisitorDNLS doesn't handle + // paths with drive letters for local files. + void testNcCloseTryWithResources() throws Throwable { + // String2.log("\n*** Table.testNcCloseTryWithResources()"); + + long time = System.currentTimeMillis(); + String fileName = TableTests.class.getResource("/points/erdCalcofiSubsurface/1950/subsurface_19500106_69_144.nc") + .getPath(); + int n = 100000; + for (int i = 0; i < n; i++) { + try (NetcdfFile ncfile = NcHelper.openFile(fileName)) { + if (i % 10000 == 0) + String2.log("" + i); + // } catch (Exception e) { + // String2.log("i=" + i + " " + e.toString()); + } + } + String2.log("Opened the same file " + n + " times and auto-closed them. time=" + (System.currentTimeMillis() - time) + + " (exp=35534ms)"); + + // open all of the 10,000 scripps glider files in batch14 after manually: gunzip + // *.gz + time = System.currentTimeMillis(); + Table table = FileVisitorDNLS.oneStep(TableTests.class.getResource("/points/scrippsGliders/batch14/").getPath(), + ".*\\.nc", true, "", false); + PrimitiveArray dirs = table.getColumn(0); + PrimitiveArray names = table.getColumn(1); + n = dirs.size(); + // String2.log("nFiles found=" + n); + for (int i = 0; i < n; i++) { + try (NetcdfFile ncfile = NcHelper.openFile(dirs.getString(i) + names.getString(i))) { + if (i % 1000 == 0) + String2.log("" + i); + } + } + String2.log( + "Opened " + n + " files and auto-closed them. time=" + (System.currentTimeMillis() - time) + " (exp=4530ms)"); + } + + /** + * This tests readXml. + */ + @org.junit.jupiter.api.Test + @TagMissingFile + void testXml() throws Exception { + // String2.log("\n*** Table.testXml()"); + // Table.verbose = true; + // Table.reallyVerbose = true; + // TableXmlHandler.verbose = true; + Table table = null; + String xml, results, expected; + + // *** WFS + table = new Table(); + BufferedReader reader = File2.getDecompressedBufferedFileReaderUtf8( + "c:/programs/mapserver/WVBoreholeResponse.xml"); + try { + table.readXml(reader, + false, // no validate since no .dtd + "/wfs:FeatureCollection/wfs:member", // default tRowElementXPath, + // was "/wfs:FeatureCollection/gml:featureMember", + null, false); // row attributes, simplify + } finally { + reader.close(); + } + results = table.dataToString(3); + expected = "aasg:BoreholeTemperature/aasg:ObservationURI,aasg:BoreholeTemperature/aasg:WellName,aasg:BoreholeTemperature/aasg:APINo,aasg:BoreholeTemperature/aasg:HeaderURI,aasg:BoreholeTemperature/aasg:OtherName,aasg:BoreholeTemperature/aasg:Label,aasg:BoreholeTemperature/aasg:Operator,aasg:BoreholeTemperature/aasg:SpudDate,aasg:BoreholeTemperature/aasg:EndedDrillingDate,aasg:BoreholeTemperature/aasg:WellType,aasg:BoreholeTemperature/aasg:StatusDate,aasg:BoreholeTemperature/aasg:ReleaseDate,aasg:BoreholeTemperature/aasg:Field,aasg:BoreholeTemperature/aasg:County,aasg:BoreholeTemperature/aasg:State,aasg:BoreholeTemperature/aasg:UTM_E,aasg:BoreholeTemperature/aasg:UTM_N,aasg:BoreholeTemperature/aasg:LatDegree,aasg:BoreholeTemperature/aasg:LongDegree,aasg:BoreholeTemperature/aasg:SRS,aasg:BoreholeTemperature/aasg:LocationUncertaintyStatement,aasg:BoreholeTemperature/aasg:LocationUncertaintyRadius,aasg:BoreholeTemperature/aasg:DrillerTotalDepth,aasg:BoreholeTemperature/aasg:DepthReferencePoint,aasg:BoreholeTemperature/aasg:LengthUnits,aasg:BoreholeTemperature/aasg:WellBoreShape,aasg:BoreholeTemperature/aasg:TrueVerticalDepth,aasg:BoreholeTemperature/aasg:ElevationKB,aasg:BoreholeTemperature/aasg:ElevationDF,aasg:BoreholeTemperature/aasg:ElevationGL,aasg:BoreholeTemperature/aasg:FormationTD,aasg:BoreholeTemperature/aasg:BitDiameterTD,aasg:BoreholeTemperature/aasg:MaximumRecordedTemperature,aasg:BoreholeTemperature/aasg:MeasuredTemperature,aasg:BoreholeTemperature/aasg:CorrectedTemperature,aasg:BoreholeTemperature/aasg:TemperatureUnits,aasg:BoreholeTemperature/aasg:CirculationDuration,aasg:BoreholeTemperature/aasg:MeasurementProcedure,aasg:BoreholeTemperature/aasg:DepthOfMeasurement,aasg:BoreholeTemperature/aasg:MeasurementDateTime,aasg:BoreholeTemperature/aasg:MeasurementFormation,aasg:BoreholeTemperature/aasg:MeasurementSource,aasg:BoreholeTemperature/aasg:RelatedResource,aasg:BoreholeTemperature/aasg:CasingBottomDepthDriller,aasg:BoreholeTemperature/aasg:CasingTopDepth,aasg:BoreholeTemperature/aasg:CasingPipeDiameter,aasg:BoreholeTemperature/aasg:CasingWeight,aasg:BoreholeTemperature/aasg:CasingThickness,aasg:BoreholeTemperature/aasg:pH,aasg:BoreholeTemperature/aasg:InformationSource,aasg:BoreholeTemperature/aasg:Shape/gml:Point/latitude,aasg:BoreholeTemperature/aasg:Shape/gml:Point/longitude,aasg:BoreholeTemperature/aasg:LeaseName,aasg:BoreholeTemperature/aasg:LeaseOwner,aasg:BoreholeTemperature/aasg:LeaseNo,aasg:BoreholeTemperature/aasg:TimeSinceCirculation,aasg:BoreholeTemperature/aasg:Status,aasg:BoreholeTemperature/aasg:CommodityOfInterest,aasg:BoreholeTemperature/aasg:Function,aasg:BoreholeTemperature/aasg:Production,aasg:BoreholeTemperature/aasg:ProducingInterval,aasg:BoreholeTemperature/aasg:Notes\n" + + + "http://resources.usgin.org/uri-gin/wvges/bhtemp/4705500185/,Dominion Appalachian Development Co. Gilbert Bailey 1,4705500185,http://resources.usgin.org/uri-gin/wvges/well/api:4705500185/,Gilbert Bailey,4705500185,Dominion Appalachian Development Co.,1998-04-02T00:00:00,1998-04-13T00:00:00,Gas,1900-01-01T00:00:00,1900-01-01T00:00:00,Stovall Ridge,Mercer,West Virginia,0.0,0.0,37.4834349990001,-81.1519399999999,EPSG:4326,Location recorded as received from official permit application converted to NAD83 if required,0.0,4854,G.L.,ft,vertical,4854,0.0,0.0,2563,Up Devonian undiff:Berea to Lo Huron,0.0,0.0,87.8,0.0,F,0.0,Temperature log evaluated by WVGES staff for deepest stable log segment to extract data otherwise used given bottom hole temperature on log header if available,3550,1900-01-01T00:00:00,Big Lime,Well Temperature Log,TL | GR | DEN | NEL | IL | CAL | SL,0.0,0.0,0.0,0.0,0.0,0.0,West Virginia Geological and Economic Survey 2013,37.48343499900005,-81.15193999999991,,,,,,,,,,\n" + + + "http://resources.usgin.org/uri-gin/wvges/bhtemp/4705500113/,\"Stonewall Gas Co., Inc. State Conserv Comm 2\",4705500113,http://resources.usgin.org/uri-gin/wvges/well/api:4705500113/,Blue Jay Lumber Co,4705500113,\"Stonewall Gas Co., Inc.\",1991-09-20T00:00:00,1991-09-27T00:00:00,Gas,1900-01-01T00:00:00,1900-01-01T00:00:00,Rhodell,Mercer,West Virginia,0.0,0.0,37.530177999,-81.1708569999999,EPSG:4326,Location recorded as received from official permit application converted to NAD83 if required,0.0,4100,G.L.,ft,vertical,4100,0.0,0.0,2442,Price Fm & equivs,0.0,0.0,90,0.0,F,0.0,Temperature log evaluated by WVGES staff for deepest stable log segment to extract data otherwise used given bottom hole temperature on log header if available,3940,1900-01-01T00:00:00,,Well Temperature Log,TL | GR | DEN | NEL | IL | CAL | SL,0.0,0.0,0.0,0.0,0.0,0.0,West Virginia Geological and Economic Survey 2013,37.53017799900005,-81.1708569999999,,,,,,,,,,\n" + + + "http://resources.usgin.org/uri-gin/wvges/bhtemp/4705500115/,\"Stonewall Gas Co., Inc. State Conserv Comm 4\",4705500115,http://resources.usgin.org/uri-gin/wvges/well/api:4705500115/,Blue Jay Lumber Co 4,4705500115,\"Stonewall Gas Co., Inc.\",1992-12-01T00:00:00,1992-12-08T00:00:00,Gas,1900-01-01T00:00:00,1900-01-01T00:00:00,Rhodell,Mercer,West Virginia,0.0,0.0,37.533804999,-81.1585159999999,EPSG:4326,Location recorded as received from official permit application converted to NAD83 if required,0.0,4097,G.L.,ft,vertical,4097,0.0,0.0,2463,Price Fm & equivs,0.0,0.0,98,0.0,F,0.0,Temperature log evaluated by WVGES staff for deepest stable log segment to extract data otherwise used given bottom hole temperature on log header if available,3920,1900-01-01T00:00:00,,Well Temperature Log,TL | GR | DEN | NEL | IL | CAL | SL,0.0,0.0,0.0,0.0,0.0,0.0,West Virginia Geological and Economic Survey 2013,37.53380499900004,-81.15851599999991,,,,,,,,,,\n" + + + "...\n"; + Test.ensureEqual(results, expected, "results=\n" + results); + + // *** darwin core + // Lines are commented out to test some aspects of readXml. + xml = "\n" + + "\n" + + "
\n" + + "$Revision: 1.12 $\n" + + "
\n" + + "\n" + + // "Marine Fish Division, Fisheries and Oceans + // Canada\n" + + "Gwaii Haanas Marine Algae\n" + + "100-MACRINT\n" + + "Macrocystis integrifolia\n" + + "sciName2\n" + + "52.65172\n" + + "-131.66368\n" + + "\n" + + "\n" + + " child1data\n" + + " child2data\n" + + " child22data\n" + + "\n" + + "BIO\n" + + "GHMP\n" + + "100-MACRINT\n" + + "Macrocystis integrifolia\n" + + "52.65172\n" + + "-131.66368\n" + + "\n" + + "\n" + + // "Marine Fish Division, Fisheries and Oceans + // Canada\n" + + "Gwaii Haanas Marine Algae\n" + + "10036-MACRINT\n" + + "Macrocystis integrifolia\n" + + "53.292\n" + + "-132.4223\n" + + "\n" + + "\n" + + "\n" + + "\n"; + + // this doesn't test heirarchical elements + table = new Table(); + reader = new BufferedReader(new StringReader(xml)); + try { + table.readXml(reader, + false, // no validate since no .dtd + "/response/content/record", null, true); + } finally { + reader.close(); + } + table.ensureValid(); // throws Exception if not + Test.ensureEqual(table.nRows(), 3, ""); + Test.ensureEqual(table.nColumns(), 10, ""); + Test.ensureEqual(table.getColumnName(0), "darwin:CollectionCode", ""); + Test.ensureEqual(table.getColumnName(1), "darwin:CatalogNumber", ""); + Test.ensureEqual(table.getColumnName(2), "darwin:ScientificName", ""); + Test.ensureEqual(table.getColumnName(3), "darwin:ScientificName2", ""); + Test.ensureEqual(table.getColumnName(4), "darwin:Latitude", ""); + Test.ensureEqual(table.getColumnName(5), "darwin:Longitude", ""); + // Test.ensureEqual(table.getColumnName(5), "obis:Temperature", ""); //no data, + // so no column + Test.ensureEqual(table.getColumnName(6), "parent/child1", ""); + Test.ensureEqual(table.getColumnName(7), "parent/child2", ""); + Test.ensureEqual(table.getColumnName(8), "parent/child22", ""); + Test.ensureEqual(table.getColumnName(9), "darwin:InstitutionCode", ""); + Test.ensureEqual(table.getColumn(0).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(1).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(2).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(3).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(4).elementTypeString(), "float", ""); + Test.ensureEqual(table.getColumn(5).elementTypeString(), "double", ""); + Test.ensureEqual(table.getColumn(6).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(7).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(8).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(9).elementTypeString(), "String", ""); + Test.ensureEqual(table.getStringData(0, 2), "Gwaii Haanas Marine Algae", ""); + Test.ensureEqual(table.getStringData(1, 2), "10036-MACRINT", ""); + Test.ensureEqual(table.getStringData(2, 2), "Macrocystis integrifolia", ""); + Test.ensureEqual(table.getStringData(3, 0), "sciName2", ""); + Test.ensureEqual(table.getFloatData(4, 2), 53.292f, ""); + Test.ensureEqual(table.getFloatData(5, 2), -132.4223f, ""); + Test.ensureEqual(table.getStringData(6, 0), "child1data", ""); + Test.ensureEqual(table.getStringData(7, 0), "child2data", ""); + Test.ensureEqual(table.getStringData(8, 0), "child22data", ""); + Test.ensureEqual(table.getStringData(9, 0), "", ""); + Test.ensureEqual(table.getStringData(9, 1), "BIO", ""); + Test.ensureEqual(table.getStringData(9, 2), "", ""); + + // a subset of https://opendap.co-ops.nos.noaa.gov/stations/stationsXML.jsp + String stationsXml = "\n" + + " \n" + + "\n" + + "\n" + + "\n" + + " 48 28.7 N \n" + + " 129 21.5 W \n" + + " \n" + + "\n" + + " 2003-01-01 \n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + " 57 29.9 N \n" + + " 144 0.06 W \n" + + " \n" + + "\n" + + " 2001-01-01 \n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + " 17 58.3 N \n" + + " 67 2.8 W \n" + + " PR \n" + + "\n" + + " 1954-12-01 \n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n" + + "\n"; + table.clear(); + reader = new BufferedReader(new StringReader(stationsXml)); + try { + table.readXml(reader, + false, // no validate since no .dtd + "/stations/station", new String[] { "name", "ID" }, true); + } finally { + reader.close(); + } + table.ensureValid(); // throws Exception if not + // String2.log(table.toString()); + // Row name ID metadata/locat metadata/locat metadata/date_ metadata/locat + // 0 DART BUOY 4641 1600013 48 28.7 N 129 21.5 W 2003-01-01 + // 1 DART BUOY 4641 1600014 57 29.9 N 144 0.06 W 2001-01-01 + // 2 Magueyes Islan 9759110 17 58.3 N 67 2.8 W 1954-12-01 PR + Test.ensureEqual(table.nRows(), 3, ""); + Test.ensureEqual(table.nColumns(), 6, ""); + Test.ensureEqual(table.getColumnName(0), "name", ""); + Test.ensureEqual(table.getColumnName(1), "ID", ""); + Test.ensureEqual(table.getColumnName(2), "metadata/location/lat", ""); + Test.ensureEqual(table.getColumnName(3), "metadata/location/long", ""); + Test.ensureEqual(table.getColumnName(4), "metadata/date_established", ""); + Test.ensureEqual(table.getColumnName(5), "metadata/location/state", ""); + Test.ensureEqual(table.getColumn(0).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(1).elementTypeString(), "int", ""); + Test.ensureEqual(table.getColumn(2).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(3).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(4).elementTypeString(), "String", ""); + Test.ensureEqual(table.getColumn(5).elementTypeString(), "String", ""); + Test.ensureEqual(table.getStringData(0, 0), "DART BUOY 46419", ""); + Test.ensureEqual(table.getStringData(1, 0), "1600013", ""); + Test.ensureEqual(table.getStringData(2, 0), "48 28.7 N", ""); + Test.ensureEqual(table.getStringData(3, 0), "129 21.5 W", ""); + Test.ensureEqual(table.getStringData(4, 0), "2003-01-01", ""); + Test.ensureEqual(table.getStringData(5, 0), "", ""); + Test.ensureEqual(table.getStringData(0, 2), "Magueyes Island", ""); + Test.ensureEqual(table.getStringData(1, 2), "9759110", ""); + Test.ensureEqual(table.getStringData(2, 2), "17 58.3 N", ""); + Test.ensureEqual(table.getStringData(3, 2), "67 2.8 W", ""); + Test.ensureEqual(table.getStringData(4, 2), "1954-12-01", ""); + Test.ensureEqual(table.getStringData(5, 2), "PR", ""); + + TableXmlHandler.verbose = false; + + } + + /** + * This tests the readSql and saveAsSql methods. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + @TagPassword + void testSql() throws Exception { + // String2.log("\n*** Table.testSql"); + // Table.verbose = true; + // Table.reallyVerbose = true; + + // load the sql driver (the actual driver .jar must be in the classpath) + Class.forName("org.postgresql.Driver"); + + // set up connection and query + String url = "jdbc:postgresql://otter.pfeg.noaa.gov/posttest"; // database name + String user = "postadmin"; + String password = String2.getPasswordFromSystemIn("Password for '" + user + "'? "); + if (password.length() == 0) { + String2.log("No password, so skipping the test."); + return; + } + long tTime = System.currentTimeMillis(); + Connection con = DriverManager.getConnection(url, user, password); + // String2.log("getConnection time=" + (System.currentTimeMillis() - tTime) + "ms"); // often 9s ! + + DatabaseMetaData dm = con.getMetaData(); + // String2.log("getMaxRowSize=" + dm.getMaxRowSize()); // 1GB + + // get catalog info -- has one col with name(s) of databases for this user + // ... + + // test getSqlSchemas + StringArray schemas = Table.getSqlSchemas(con); + Test.ensureTrue(schemas.indexOf("public") >= 0, "schemas=" + schemas.toString()); + + // sometimes: make names table + if (false) { + Table namesTable = new Table(); + namesTable.addColumn("id", PrimitiveArray.factory(new int[] { 1, 2, 3 })); + namesTable.addColumn("first_name", PrimitiveArray.factory(new String[] { "Bob", "Nate", "Nancy" })); + namesTable.addColumn("last_name", PrimitiveArray.factory(new String[] { "Smith", "Smith", "Jones" })); + namesTable.saveAsSql( + con, true, // 'true' tests dropSqlTable, too + "names", 0, null, null, null, 2); + } + + // test getSqlTableNames + StringArray tableNames = Table.getSqlTableNames(con, "public", new String[] { "TABLE" }); + // String2.log("tableNames=" + tableNames); + Test.ensureTrue(tableNames.indexOf("names") >= 0, "tableNames=" + tableNames.toString()); + Test.ensureTrue(tableNames.indexOf("zztop") < 0, "tableNames=" + tableNames.toString()); // doesn't exist + + // test getSqlTableType + Test.ensureEqual(Table.getSqlTableType(con, "public", "names"), "TABLE", ""); + Test.ensureEqual(Table.getSqlTableType(con, "public", "zztop"), null, ""); // doesn't exist + + // *** test saveAsSql (create a table) (this tests dropSqlTable, too) + if (true) { + String tempTableName = "TempTest"; + String dates[] = { "1960-01-02", "1971-01-02", null, "2020-12-31" }; + double dateDoubles[] = new double[4]; + String timestamps[] = { "1960-01-02 01:02:03", "1971-01-02 07:08:09", null, "2020-12-31 23:59:59" }; + double timestampDoubles[] = new double[4]; + String times[] = { "01:02:03", "07:08:09", null, "23:59:59" }; + for (int i = 0; i < 4; i++) { + dateDoubles[i] = dates[i] == null ? Double.NaN : Calendar2.isoStringToEpochSeconds(dates[i]); + timestampDoubles[i] = timestamps[i] == null ? Double.NaN : Calendar2.isoStringToEpochSeconds(timestamps[i]); + } + Table tempTable = new Table(); + tempTable.addColumn("uid", PrimitiveArray.factory(new int[] { 1, 2, 3, 4 })); + tempTable.addColumn("short", PrimitiveArray.factory(new short[] { -10, 0, Short.MAX_VALUE, 10 })); + // Math2.random makes this test different every time. ensures old table is + // dropped and new one created. + tempTable.addColumn("int", PrimitiveArray.factory(new int[] { Math2.random(1000), 0, Integer.MAX_VALUE, 20 })); + tempTable.addColumn("long", PrimitiveArray.factory(new long[] { -30, 0, Long.MAX_VALUE, 30 })); + tempTable.addColumn("float", PrimitiveArray.factory(new float[] { -44.4f, 0f, Float.NaN, 44.4f })); + tempTable.addColumn("double", PrimitiveArray.factory(new double[] { -55.5, 0, Double.NaN, 55.5 })); + tempTable.addColumn("string", PrimitiveArray.factory(new String[] { "ab", "", null, "longer" })); + tempTable.addColumn("date", PrimitiveArray.factory(dateDoubles)); + tempTable.addColumn("timestamp", PrimitiveArray.factory(timestampDoubles)); + tempTable.addColumn("time", PrimitiveArray.factory(times)); + tempTable.saveAsSql( + con, true, // 'true' tests dropSqlTable, too + tempTableName, 0, new int[] { 7 }, new int[] { 8 }, new int[] { 9 }, 1.5); + + // test readSql (read a table) + Table tempTable2 = new Table(); + tempTable2.readSql(con, "SELECT * FROM " + tempTableName); + Test.ensureEqual(tempTable, tempTable2, ""); + + // *** test rollback: add data that causes database to throw exception + tempTable2.setIntData(0, 0, 5); // ok + tempTable2.setIntData(0, 1, 6); // ok + tempTable2.setIntData(0, 2, 7); // ok + tempTable2.setIntData(0, 3, 1); // not ok because not unique + try { // try to add new tempTable2 to database table + tempTable2.saveAsSql( + con, false, // false, so added to previous data + tempTableName, 0, new int[] { 7 }, new int[] { 8 }, new int[] { 9 }, 1.5); + String2.log("Shouldn't get here."); + Math2.sleep(60000); + } catch (Exception e) { + // this error is expected + // make sure it has both parts of the error message + String2.log("\nEXPECTED " + String2.ERROR + ":\n" + MustBe.throwableToString(e)); + Test.ensureTrue(e.toString().indexOf( + "PSQLException: " + String2.ERROR + + ": duplicate key violates unique constraint \"temptest_pkey\"") >= 0, + "(A) The error was: " + e.toString()); + Test.ensureTrue(e.toString().indexOf( + "java.sql.BatchUpdateException: Batch entry 3 INSERT INTO TempTest (") >= 0, + "(B)The error was: " + e.toString()); + } + + // and ensure database was rolled back to previous state + tempTable2.readSql(con, "SELECT * FROM " + tempTableName); + Test.ensureEqual(tempTable, tempTable2, ""); + + // *** test pre-execute errors: add data that causes saveAsSql to throw + // exception + tempTable2.setIntData(0, 0, 5); // ok, so new rows can be added + tempTable2.setIntData(0, 1, 6); // ok + tempTable2.setIntData(0, 2, 7); // ok + tempTable2.setIntData(0, 3, 8); // ok + int timeCol = tempTable2.findColumnNumber("time"); + // invalid date will be caught before statement is fully prepared + tempTable2.setStringData(timeCol, 3, "20.1/30"); // first 3 rows succeed, this should fail + try { // try to add new tempTable2 to database table + tempTable2.saveAsSql( + con, false, // false, so added to previous data + tempTableName, 0, new int[] { 7 }, new int[] { 8 }, new int[] { 9 }, 1.5); + String2.log("Shouldn't get here."); + Math2.sleep(60000); + } catch (Exception e) { + // this error is expected + // make sure it is the right error + String2.log("\nEXPECTED " + String2.ERROR + ":\n" + MustBe.throwableToString(e)); + Test.ensureTrue(e.toString().indexOf( + "java.lang.RuntimeException: ERROR in Table.saveAsSql(TempTest):\n" + + "Time format must be " + + "HH:MM:SS. Bad value=20.1/30 in row=3 col=9") >= 0, + "error=" + e.toString()); + } + + // and ensure it rolls back to previous state + tempTable2.readSql(con, "SELECT * FROM " + tempTableName); + Test.ensureEqual(tempTable, tempTable2, ""); + + // *** test successfully add data (and ensure previous rollbacks worked + // assign row numbers so new rows can be added (and so different from possibly + // added 5,6,7,8) + tempTable2.setIntData(0, 0, 9); // ok, + tempTable2.setIntData(0, 1, 10); // ok + tempTable2.setIntData(0, 2, 11); // ok + tempTable2.setIntData(0, 3, 12); // ok + tempTable2.saveAsSql( + con, false, // false, so added to previous data + tempTableName, 0, new int[] { 7 }, new int[] { 8 }, new int[] { 9 }, 1.5); + + // and ensure result has 8 rows + tempTable2.readSql(con, "SELECT uid, string FROM " + tempTableName); + Test.ensureEqual(tempTable2.getColumn(0).toString(), "1, 2, 3, 4, 9, 10, 11, 12", ""); + Test.ensureEqual(tempTable2.getColumn(1).toString(), "ab, , [null], longer, ab, , [null], longer", ""); + } + + // don't drop the table, so I can view it in phpPgAdmin + + // how read just column names and types? query that returns no rows??? + + } + + /** + * This tests readIObis. + */ + @org.junit.jupiter.api.Test + @TagIncompleteTest + void testIobis() throws Exception { + // Table.verbose = true; + // Table.reallyVerbose = true; + // String2.log("\n*** Table.testIobis"); + String testName = "c:/programs/digir/Macrocyctis.nc"; + Table table = new Table(); + if (true) { + table.readIobis(Table.IOBIS_URL, "Macrocystis", "", // String genus, String species, + "", "", "53", "54", // String west, String east, String south, String north, + "", "", // String minDepth, String maxDepth, + "1970-01-01", "", // String iso startDate, String iso endDate, + new String[] { "Institutioncode", "Collectioncode", "Scientificname", "Temperature" }); // String + // loadColumns[]) + + // table.saveAsFlatNc(testName, "row"); + } else { + table.readFlatNc(testName, null, 1); // standardizeWhat + } + // String2.log(table.toString()); + table.testObis5354Table(); + + } + + @org.junit.jupiter.api.Test + @TagIncompleteTest + // This test relies on setting bits on a static member during all of the + // existing tests. + // We can probably use normal coverage tooling instead of properly implemnting + // this test. + void testReadNcCFCodeCoverage() { + Table.ncCFcc.flip(0, 100); // there are currently 99 code coverage tests + Test.ensureEqual(Table.ncCFcc.toString(), "{}", "Table.readNcCF code coverage"); + Table.ncCFcc = null; // turn off test of readNcCF code coverage + } + + /** + * Make a test Table. + * + * @param includeLongs set this to true if you want a column with longs + * @param includeStrings set this to true if you want a column with Strings + * @return Table + */ + private static Table getTestTable(boolean includeLongs, boolean includeStrings) { + + String testTimes[] = { "1970-01-01T00:00:00", "2005-08-31T16:01:02", "2005-11-02T18:04:09", "" }; + Table table = new Table(); + int nRows = testTimes.length; + + // global attributes + table.globalAttributes().set("global_att1", "a string"); + table.globalAttributes().set("global_att2", new IntArray(new int[] { 1, 100 })); + + // add the data variables (and their attributes) + + // 0=seconds + double[] ad = new double[nRows]; + for (int i = 0; i < nRows; i++) + ad[i] = Calendar2.safeIsoStringToEpochSeconds(testTimes[i]); + int col = table.addColumn("Time", new DoubleArray(ad)); + table.columnAttributes(col).set("units", Calendar2.SECONDS_SINCE_1970); + table.columnAttributes(col).set("time_att2", new DoubleArray(new double[] { -1e300, 1e300 })); + + // 1=lon + int[] ai = { -3, -2, -1, Integer.MAX_VALUE }; + col = table.addColumn("Longitude", new IntArray(ai).setMaxIsMV(true)); + table.columnAttributes(col).set("units", "degrees_east"); + table.columnAttributes(col).set("lon_att2", new IntArray(new int[] { -2000000000, 2000000000 })); + + // 2=lat + float[] af = { 1, 1.5f, 2, Float.NaN }; + col = table.addColumn("Latitude", new FloatArray(af)); + table.columnAttributes(col).set("units", "degrees_north"); + table.columnAttributes(col).set("lat_att2", new FloatArray(new float[] { -1e30f, 1e30f })); + + // 3=double + ad = new double[] { -1e300, 3.123, 1e300, Double.NaN }; + col = table.addColumn("Double Data", new DoubleArray(ad)); + table.columnAttributes(col).set("units", "doubles"); + table.columnAttributes(col).set("double_att2", new DoubleArray(new double[] { -1e300, 1e300 })); + + // 4=long + if (includeLongs) { + long[] al = { -2000000000000000L, 2, 2000000000000000L, Long.MAX_VALUE }; + col = table.addColumn("Long Data", new LongArray(al).setMaxIsMV(true)); + table.columnAttributes(col).set("units", new StringArray(new String[] { "longs" })); + table.columnAttributes(col).set("long_att2", new LongArray(new long[] { -2000000000000000L, 2000000000000000L })); + } + + // 5=int + ai = new int[] { -2000000000, 2, 2000000000, Integer.MAX_VALUE }; + col = table.addColumn("Int Data", new IntArray(ai).setMaxIsMV(true)); + table.columnAttributes(col).set("units", new StringArray(new String[] { "ints" })); + table.columnAttributes(col).set("int_att2", new IntArray(new int[] { -2000000000, 2000000000 })); + + // 6=short + short[] as = { (short) -32000, (short) 7, (short) 32000, Short.MAX_VALUE }; + col = table.addColumn("Short Data", new ShortArray(as).setMaxIsMV(true)); + table.columnAttributes(col).set("units", new StringArray(new String[] { "shorts" })); + table.columnAttributes(col).set("short_att2", new ShortArray(new short[] { (short) -30000, (short) 30000 })); + + // 7=byte + byte[] ab = { (byte) -120, (byte) 8, (byte) 120, Byte.MAX_VALUE }; + col = table.addColumn("Byte Data", new ByteArray(ab).setMaxIsMV(true)); + table.columnAttributes(col).set("units", "bytes"); + table.columnAttributes(col).set("byte_att2", new ByteArray(new byte[] { (byte) -120, (byte) 120 })); + + // 8=String + if (includeStrings) { + char[] ac = { ',', '"', '\u20ac', '\uffff' }; + col = table.addColumn("Char Data", new CharArray(ac).setMaxIsMV(true)); + table.columnAttributes(col).set("units", "chars"); + table.columnAttributes(col).set("char_att2", new CharArray(new char[] { ',', '"', '\u00fc', '\u20ac' })); + + String[] aS = { "a", "bb", "ccc", "" }; + col = table.addColumn("String Data", new StringArray(aS)); + table.columnAttributes(col).set("units", "Strings"); + table.columnAttributes(col).set("String_att2", new StringArray(new String[] { "a string" })); + } + + table.ensureValid(); // throws Exception if not + return table; + } + + /** + * This makes a tough test table. + */ + private static Table makeToughTestTable() { + + Table table = new Table(); + + Attributes gatts = table.globalAttributes(); + gatts.add("tests", "a\u00fcb\nc\td\u20acz"); + gatts.add("testc", '\u00fc'); + gatts.add("testub", UByteArray.fromCSV("0, 255")); + gatts.add("testus", UShortArray.fromCSV("0, 65535")); + gatts.add("testui", UIntArray.fromCSV("0, 4294967295")); + gatts.add("testl", new LongArray(new long[] { Long.MIN_VALUE, Long.MAX_VALUE })); + gatts.add("testul", ULongArray.fromCSV("0, 9223372036854775807, 18446744073709551615")); + gatts.add("testi", new IntArray(new int[] { Integer.MIN_VALUE, Integer.MAX_VALUE })); + + table.addColumn(0, "aString", + new StringArray(new String[] { "a\u00fcb\nc\td\u20ace", "ab", "", "cd", "" }), + (new Attributes()).add("test", "a\u00fcb\nc\td\u20ace")); + + table.addColumn(1, "aChar", + new CharArray(new char[] { '\u00fc', (char) 0, 'A', '\t', '\u20ac' }), + (new Attributes()).add("test", '\u00fc')); + + table.addColumn(2, "aByte", // min, med, fv, max-1, max + new ByteArray(new byte[] { Byte.MIN_VALUE, 0, 99, 126, Byte.MAX_VALUE }).setMaxIsMV(true), + (new Attributes()).add("_FillValue", ByteArray.fromCSV("99")) + .add("test", ByteArray.fromCSV("-128, 127"))); + table.addColumn(3, "aUByte", + new UByteArray(new short[] { 0, 127, 99, 254, 255 }).setMaxIsMV(true), + (new Attributes()).add("_FillValue", UByteArray.fromCSV("99")) + .add("test", UByteArray.fromCSV("0, 255"))); + table.addColumn(4, "aShort", + new ShortArray(new short[] { Short.MIN_VALUE, 0, 9999, 32766, Short.MAX_VALUE }).setMaxIsMV(true), + (new Attributes()).add("_FillValue", ShortArray.fromCSV("9999")) + .add("test", ShortArray.fromCSV("-32768, 32767"))); + table.addColumn(5, "aUShort", + UShortArray.fromCSV("0, 32767, 9999, 65534, 65535").setMaxIsMV(true), + (new Attributes()).add("_FillValue", UShortArray.fromCSV("9999")) + .add("test", UShortArray.fromCSV("0, 65535"))); + table.addColumn(6, "anInt", + new IntArray(new int[] { Integer.MIN_VALUE, 0, 999999999, Integer.MAX_VALUE - 1, Integer.MAX_VALUE }) + .setMaxIsMV(true), + (new Attributes()).add("_FillValue", IntArray.fromCSV("999999999")) + .add("test", IntArray.fromCSV("-2147483648, 2147483647"))); + table.addColumn(7, "aUInt", + new UIntArray(new long[] { 0, 7, Integer.MAX_VALUE, Math2.UINT_MAX_VALUE - 1, Math2.UINT_MAX_VALUE }) + .setMaxIsMV(true), + (new Attributes()).add("_FillValue", UIntArray.fromCSV("999999999")) + .add("test", UIntArray.fromCSV("0, 4294967295"))); + table.addColumn(8, "aLong", + new LongArray(new long[] { Long.MIN_VALUE, 0, 8, Long.MAX_VALUE - 1, Long.MAX_VALUE }).setMaxIsMV(true), + (new Attributes()).add("_FillValue", LongArray.fromCSV("999999999999")) + .add("test", LongArray.fromCSV("-9223372036854775808, 9223372036854775807"))); + table.addColumn(9, "aULong", + ULongArray.fromCSV("0, 1, 9223372036854775807, 18446744073709551614, 18446744073709551615").setMaxIsMV(true), + (new Attributes()).add("_FillValue", ULongArray.fromCSV("999999999999")) + .add("test", ULongArray.fromCSV("0, 18446744073709551615"))); + table.addColumn(10, "aFloat", + new FloatArray(new float[] { -Float.MAX_VALUE, 2.2f, Float.MIN_VALUE, Float.MAX_VALUE, Float.NaN }), + (new Attributes()).add("_FillValue", 1e36f) + .add("test", new FloatArray(new float[] { -Float.MAX_VALUE, Float.NaN }))); + table.addColumn(11, "aDouble", + new DoubleArray(new double[] { -Double.MAX_VALUE, 3.3, Double.MIN_VALUE, Double.MAX_VALUE, Double.NaN }), + (new Attributes()).add("_FillValue", 1e300) + .add("test", new DoubleArray(new double[] { -Double.MAX_VALUE, Double.NaN }))); + return table; + } +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/util/RegexFilenameFilterTests.java b/src/test/java/gov/noaa/pfel/coastwatch/util/RegexFilenameFilterTests.java new file mode 100644 index 000000000..a66dc8af0 --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/util/RegexFilenameFilterTests.java @@ -0,0 +1,104 @@ +package gov.noaa.pfel.coastwatch.util; + +import com.cohort.array.PrimitiveArray; +import com.cohort.array.StringArray; +import com.cohort.util.Calendar2; +import com.cohort.util.File2; +import com.cohort.util.String2; +import com.cohort.util.Test; + +class RegexFilenameFilterTests { + + /** + * This tests the methods of RegexFilenameFilter. + * + * @throws Exception if trouble + */ + @org.junit.jupiter.api.Test + void basicTest() throws Exception { + String2.log("\n* RegexFilenameFilter.basicTest ..."); + String coastwatchDir = File2.getClassPath() // with / separator and / at the end + + "gov/noaa/pfel/coastwatch/"; + + // test list + String[] sar = RegexFilenameFilter.list(coastwatchDir, "S.+\\.java"); + String[] shouldBe = { + "Screen.java", + "Shared.java" }; + Test.ensureEqual(sar, shouldBe, "RegexFilenameFilter.list"); + + // test fullNameList + sar = RegexFilenameFilter.fullNameList(coastwatchDir, "S.+\\.java"); + shouldBe = new String[] { + coastwatchDir + "Screen.java", + coastwatchDir + "Shared.java" + }; + Test.ensureEqual(sar, shouldBe, "RegexFilenameFilter.fullNameList"); + + // test recursiveList + sar = RegexFilenameFilter.recursiveFullNameList(coastwatchDir, "S.+\\.java", true); + shouldBe = new String[] { + coastwatchDir + "Screen.java", + coastwatchDir + "Shared.java", + coastwatchDir + "griddata/", + coastwatchDir + "griddata/SaveOpendap.java", + coastwatchDir + "hdf/", + coastwatchDir + "hdf/SdsReader.java", + coastwatchDir + "hdf/SdsWriter.java", + coastwatchDir + "netcheck/", + coastwatchDir + "pointdata/", + coastwatchDir + "pointdata/ScriptRow.java", + coastwatchDir + "pointdata/StationVariableNc4D.java", + coastwatchDir + "pointdata/StoredIndex.java", + coastwatchDir + "sgt/", + coastwatchDir + "sgt/SGTPointsVector.java", + coastwatchDir + "sgt/SgtGraph.java", + coastwatchDir + "sgt/SgtMap.java", + coastwatchDir + "sgt/SgtUtil.java", + coastwatchDir + "util/", + coastwatchDir + "util/SSR.java", + coastwatchDir + "util/SimpleXMLReader.java", + coastwatchDir + "util/StringObject.java" + }; + Test.ensureEqual(sar, shouldBe, "RegexFilenameFilter.recursiveFullNameList"); + + // test recursiveList no directories + sar = RegexFilenameFilter.recursiveFullNameList(coastwatchDir, "S.+\\.java", false); + shouldBe = new String[] { + coastwatchDir + "Screen.java", + coastwatchDir + "Shared.java", + coastwatchDir + "griddata/SaveOpendap.java", + coastwatchDir + "hdf/SdsReader.java", + coastwatchDir + "hdf/SdsWriter.java", + coastwatchDir + "pointdata/ScriptRow.java", + coastwatchDir + "pointdata/StationVariableNc4D.java", + coastwatchDir + "pointdata/StoredIndex.java", + coastwatchDir + "sgt/SGTPointsVector.java", + coastwatchDir + "sgt/SgtGraph.java", + coastwatchDir + "sgt/SgtMap.java", + coastwatchDir + "sgt/SgtUtil.java", + coastwatchDir + "util/SSR.java", + coastwatchDir + "util/SimpleXMLReader.java", + coastwatchDir + "util/StringObject.java" + }; + Test.ensureEqual(sar, shouldBe, "RegexFilenameFilter.recursiveFullNameList"); + + // gatherInfo + PrimitiveArray info[] = RegexFilenameFilter.gatherInfo(coastwatchDir, "Browser.*"); + int tn = info[1].size(); + StringArray lastMod = new StringArray(); + for (int i = 0; i < tn; i++) + lastMod.add(Calendar2.safeEpochSecondsToIsoStringTZ(info[2].getLong(i) / 1000.0, "ERROR")); + Test.ensureEqual(info[0].toString(), + "griddata, hdf, netcheck, pointdata, sgt, util", ""); + Test.ensureEqual(info[1].toString(), + "Browser.class, Browser.java, BrowserDefault.properties", ""); + // The below is flaky. Consider using a dedicated test resource directory instead of a code directory + // and turn these back on. + // Test.ensureEqual(lastMod.toString(), "2007-04-23T18:24:38Z, + // 2007-05-02T19:18:32Z", ""); + // Test.ensureEqual(info[3].toString(), + // "155937, 359559, 89254", ""); + } + +} diff --git a/src/test/java/gov/noaa/pfel/coastwatch/util/TestSSR.java b/src/test/java/gov/noaa/pfel/coastwatch/util/TestSSR.java new file mode 100644 index 000000000..5027bf9b8 --- /dev/null +++ b/src/test/java/gov/noaa/pfel/coastwatch/util/TestSSR.java @@ -0,0 +1,705 @@ +/* + * TestSSR Copyright 2005, NOAA. + * See the LICENSE.txt file in this file's directory. + */ +package gov.noaa.pfel.coastwatch.util; + +import com.cohort.util.File2; +import com.cohort.util.Math2; +import com.cohort.util.MustBe; +import com.cohort.util.String2; +import com.cohort.util.Test; + +import tags.TagAWS; +import tags.TagLocalERDDAP; +import tags.TagPassword; + +import java.io.BufferedInputStream; +import java.io.BufferedOutputStream; +import java.io.FileOutputStream; + +/** + * This is a Java program to test all of the methods in SSR. + * + * @author Robert Simons was bob.simons@noaa.gov, now BobSimons2.00@gmail.com + * January 2005 + */ +public class TestSSR { + + static String classPath = File2.getClassPath(); // with / separator and / at the end + + /** + * Run all of the tests which are operating system independent. + */ + @org.junit.jupiter.api.Test + @TagPassword + void runNonUnixTests() throws Throwable { + String sar[]; + + String2.log("\n*** TestSSR"); + String2.log("This must be run in a command line window so passwords can be entered!"); + + /* + * //sendSoap + * String soap = SSR.sendSoap( + * "http://services.xmethods.net:80/soap/servlet/rpcrouter", + * " \n" + * + + * " 93950\n" + + * " \n", + * ""); + * String2.log(soap); + * System.exit(0); + */ + + // percentDecode(String query) + String s = "~`!@#$%^&*()_-+=|\\{[}]:;\"'<,>.?/ a\nA°1"; // after A is degree #176/B0 + Test.ensureEqual(SSR.percentEncode(s), // it is utf-8'd then % encoded + // note that I modified Java code so ' ' becomes %20, not + + "%7E%60%21%40%23%24%25%5E%26*%28%29_-%2B%3D%7C%5C%7B%5B%7D%5D%3A%3B%22%27%3C%2C%3E.%3F%2F%20a%0AA%C2%B01", + ""); // It encodes ~!*()' + Test.ensureEqual(SSR.minimalPercentEncode(s), // + "~%60!%40%23%24%25%5E%26*()_-%2B%3D%7C%5C%7B%5B%7D%5D%3A%3B%22%27%3C%2C%3E.%3F%2F%20a%0AA%C2%B01", ""); + Test.ensureEqual(SSR.percentDecode("%2B%20%3Aq*~%3F%3D%26%25"), "+ :q*~?=&%", ""); + + s = "AZaz09 \t\r\n`"; + Test.ensureEqual(SSR.minimalPercentEncode(s), + "AZaz09%20%09%0D%0A%60", ""); + Test.ensureEqual(SSR.percentEncode(s), + "AZaz09%20%09%0D%0A%60", ""); + Test.ensureEqual(SSR.percentDecode("AZaz09%20%09%0D%0A%60"), s, ""); + + s = "~!@#$%^&*()"; + Test.ensureEqual(SSR.minimalPercentEncode(s), + "~!%40%23%24%25%5E%26*()", ""); + Test.ensureEqual(SSR.percentEncode(s), + "%7E%21%40%23%24%25%5E%26*%28%29", ""); + Test.ensureEqual(SSR.percentDecode("%7E%21%40%23%24%25%5E%26*%28%29"), s, ""); + + s = "-_=+\\|[{]};"; + Test.ensureEqual(SSR.minimalPercentEncode(s), + "-_%3D%2B%5C%7C%5B%7B%5D%7D%3B", ""); + Test.ensureEqual(SSR.percentEncode(s), + "-_%3D%2B%5C%7C%5B%7B%5D%7D%3B", ""); + Test.ensureEqual(SSR.percentDecode("-_%3D%2B%5C%7C%5B%7B%5D%7D%3B"), s, ""); + + s = ":'\",<.>/?"; + Test.ensureEqual(SSR.minimalPercentEncode(s), + "%3A%27%22%2C%3C.%3E%2F%3F", ""); + Test.ensureEqual(SSR.percentEncode(s), + "%3A%27%22%2C%3C.%3E%2F%3F", ""); + Test.ensureEqual(SSR.percentDecode("%3A%27%22%2C%3C.%3E%2F%3F"), s, ""); + + /* + * 2014-08-05 DEACTIVATED BECAUSE NOT USED. IF NEEDED, SWITCH TO Apache + * commons-net??? + * //sftp + * String2.log("test sftp"); + * String password = String2.getPasswordFromSystemIn(//String2.beep(1) + + * "cwatch password for coastwatch computer (enter \"\" to skip the test)? "); + * if (password.length() > 0) { + * String fileName = "Rainbow.cpt"; + * StringBuilder cmds = new StringBuilder( + * "lcd " + SSR.getTempDirectory() + "\n" + + * "cd /u00/cwatch/bobtemp\n" + //on coastwatch computer; don't use + * String2.testU00Dir + * "get " + fileName); + * File2.delete(SSR.getTempDirectory() + fileName); + * SSR.sftp("coastwatch.pfeg.noaa.gov", "cwatch", password, cmds.toString()); + * Test.ensureEqual(File2.length(SSR.getTempDirectory() + fileName), 214, "a"); + * File2.delete(SSR.getTempDirectory() + fileName); + * } + * Math2.sleep(3000); //allow j2ssh to finish closing and writing messages + */ + + // SSR.windowsSftp never worked (authentication trouble) and SSR.sftp is + // better anyway because it is Java-based and therefore platform independent. + // SSR.windowsSftp("coastwatch.pfeg.noaa.gov", "cwatch", password, + // "\\temp\\", + // "/usr/local/jakarta-tomcat-5.5.4/webapps/cwexperimental/WEB-INF/secure/", + // new String[]{"btemplate.xml"}, //send + // new String[]{}, 10); //receive + + // dosShell + String2.log("test dosShell"); + String tempGif = File2.webInfParentDirectory() + // with / separator and / at the end + "images/temp.gif"; + File2.delete(tempGif); + try { + Test.ensureEqual( + String2.toNewlineString(SSR.dosShell( + "\"C:\\Program Files (x86)\\ImageMagick-6.8.0-Q16\\convert\" " + + File2.webInfParentDirectory() + // with / separator and / at the end + "images/subtitle.jpg " + + tempGif, + 10).toArray()), + "", "dosShell a"); + Test.ensureTrue(File2.isFile(tempGif), "dosShell b"); + } catch (Exception e) { + Test.knownProblem( + "IMAGEMAGICK NOT SET UP ON BOB'S DELL M4700 or Lenovo.", + MustBe.throwableToString(e)); + } + File2.delete(tempGif); + + // cutChar + String2.log("test cutChar"); + Test.ensureEqual(SSR.cutChar("abcd", 2, 3), "bc", "a"); + Test.ensureEqual(SSR.cutChar("abcd", 1, 4), "abcd", "b"); + Test.ensureEqual(SSR.cutChar("abcd", 0, 4), "abcd", "c"); + Test.ensureEqual(SSR.cutChar("abcd", 1, 5), "abcd", "d"); + Test.ensureEqual(SSR.cutChar("abcd", 3, 3), "c", "e"); + Test.ensureEqual(SSR.cutChar("abcd", 4, 1), "", "f"); + Test.ensureEqual(SSR.cutChar("abcd", -2, 0), "", "g"); + + Test.ensureEqual(SSR.cutChar("abcd", 1), "abcd", "a"); + Test.ensureEqual(SSR.cutChar("abcd", 0), "abcd", "b"); + Test.ensureEqual(SSR.cutChar("abcd", -1), "abcd", "c"); + Test.ensureEqual(SSR.cutChar("abcd", 2), "bcd", "d"); + Test.ensureEqual(SSR.cutChar("abcd", 4), "d", "e"); + Test.ensureEqual(SSR.cutChar("abcd", 5), "", "f"); + + // make a big chunk of text + StringBuilder sb = new StringBuilder(); + for (int i = 0; i < 1000000; i++) + sb.append("This is a really, really, long line of text to text compression speed.\n"); + String longText = sb.toString(); + sb = null; + String testMB = " " + (longText.length() / Math2.BytesPerMB) + " MB"; + + // zip without directory info + String2.log("\n* test zip without dir info" + testMB); + String middleDir = "gov/noaa/pfel/coastwatch/"; + String zipDir = classPath + middleDir; + String zipName = "TestSSR.zip"; + String fileName = "TestSSR.txt"; + // write a longText file + Test.ensureEqual(File2.writeToFile88591(zipDir + fileName, longText), "", "SSR.zip a"); + // make the zip file + File2.delete(zipDir + zipName); + long time1 = System.currentTimeMillis(); + SSR.zip(zipDir + zipName, new String[] { zipDir + fileName }, 10); + time1 = System.currentTimeMillis() - time1; + File2.delete(zipDir + fileName); + // unzip the zip file + long time2 = System.currentTimeMillis(); + SSR.unzip(zipDir + zipName, zipDir, // note: extract to zipDir, since it doesn't include dir + false, 10, null); // false 'ignoreDirectoryInfo', but there is none + time2 = System.currentTimeMillis() - time2; + // ensure results are as expected + String[] results = File2.readFromFile88591(zipDir + fileName); + Test.ensureEqual(results[0], "", "SSR.zip b"); + Test.ensureEqual(results[1], longText, "SSR.zip c"); + String2.log("zip+unzip time=" + (time1 + time2) + "ms (Java 1.7M4700 967ms, 1.6 4000-11000ms)"); + File2.delete(zipDir + zipName); + File2.delete(zipDir + fileName); + + // zip with directory info + String2.log("\n* test zip with dir info" + testMB); + // write a longText file + Test.ensureEqual(File2.writeToFile88591(zipDir + fileName, longText), "", "SSR.zip a"); + // make the zip file + File2.delete(zipDir + zipName); + time1 = System.currentTimeMillis(); + SSR.zip(zipDir + zipName, new String[] { zipDir + fileName }, 10, classPath); + time1 = System.currentTimeMillis() - time1; + File2.delete(zipDir + fileName); + // unzip the zip file + time2 = System.currentTimeMillis(); + SSR.unzip(zipDir + zipName, classPath, // note: extract to classPath, since includes dir + false, 10, null); // false 'ignoreDirectoryInfo' + time2 = System.currentTimeMillis() - time2; + // ensure results are as expected + results = File2.readFromFile88591(zipDir + fileName); + Test.ensureEqual(results[0], "", "SSR.zip b"); + Test.ensureEqual(results[1], longText, "SSR.zip c"); + String2.log("zip+unzip (w directory info) time=" + (time1 + time2) + + "ms (Java 1.7M4700 937, 1.6 ~4000-11000ms)"); + File2.delete(zipDir + zipName); + File2.delete(zipDir + fileName); + + // gzip without directory info + for (int rep = 0; rep < 2; rep++) { + String2.log("\n* test gzip without dir info" + testMB); + middleDir = "gov/noaa/pfel/coastwatch/"; + String gzipDir = classPath + middleDir; + String gzipName = "TestSSRG.txt.gz"; + fileName = "TestSSRG.txt"; + // write a longText file + Test.ensureEqual(File2.writeToFile88591(gzipDir + fileName, longText), "", "SSR.gz a"); + // make the gzip file + File2.delete(gzipDir + gzipName); + time1 = System.currentTimeMillis(); + SSR.gzip(gzipDir + gzipName, new String[] { gzipDir + fileName }, 10); // don't include dir info + time1 = System.currentTimeMillis() - time1; + File2.delete(gzipDir + fileName); + // unzip the gzip file + time2 = System.currentTimeMillis(); + SSR.unGzip(gzipDir + gzipName, gzipDir, // note: extract to classPath, since doesn't include dir + true, 10); // false 'ignoreDirectoryInfo' + time2 = System.currentTimeMillis() - time2; + // ensure results are as expected + results = File2.readFromFile88591(gzipDir + fileName); + Test.ensureEqual(results[0], "", "SSR.gz b"); + Test.ensureEqual(results[1], longText, "SSR.z c"); + String2.log("gzip+ungzip time=" + (time1 + time2) + + "ms (Java 1.7M4700 780-880ms, 1.6 ~4000-11000ms)"); + File2.delete(gzipDir + gzipName); + File2.delete(gzipDir + fileName); + } + + // getURLResponse (which uses getURLInputStream) + // FUTURE: test various compressed url's + String2.log("test getURLResponse"); + try { + sar = SSR.getUrlResponseLines("https://coastwatch.pfeg.noaa.gov/erddap/index.html"); + Test.ensureEqual( + String2.lineContaining(sar, + "ERDDAP is a data server that gives you a simple, consistent way") == -1, + false, "Response=" + String2.toNewlineString(sar)); + } catch (Exception e) { + String2.log(MustBe.throwableToString(e)); + String2.pressEnterToContinue("\nRecover from failure?"); + } + + // test non-existent file + long rTime = System.currentTimeMillis(); + try { + sar = SSR.getUrlResponseLines("https://coastwatch.pfeg.noaa.gov/zzz.html"); + throw new Throwable("shouldn't get here."); + } catch (Exception e) { // not throwable + String2.log("SSR.getUrlResponse for non existent url time=" + (System.currentTimeMillis() - rTime) + "ms"); + // String2.pressEnterToContinue(); + } catch (Throwable t) { + Test.error(t.toString()); // converts it to Exception and stops the testing + } + + // note there is no continuity (session cookie isn't being sent) + // but you can put as many params on one line as needed (from any screen) + // and put edit=... to determine which screen gets returned + sar = SSR.getUrlResponseLines("https://coastwatch.pfeg.noaa.gov/coastwatch/CWBrowser.jsp?edit=Grid+Data"); + String2.log("****beginResponse\n" + String2.toNewlineString(sar) + "\n****endResponse"); + Test.ensureNotEqual(String2.lineContaining(sar, "Download the grid data:"), -1, "e"); + + // postHTMLForm (always right after contact the website above) + // I NEVER GOT THIS WORKING. JUST USE 'GET' TESTS ABOVE + // String2.log("test postHTMLForm"); + + // for apache commons version + // sar = SSR.postHTMLForm("https://coastwatch.pfeg.noaa.gov/cwexperimental/", + // "CWBrowser.jsp", + // new String[]{"edit", "Bathymetry"}); + + // for devx version + // sar = + // SSR.postHTMLForm("https://coastwatch.pfeg.noaa.gov/cwexperimental/CWBrowser.jsp", + // new Object[]{"bathymetry", "false", "edit", "Bathymetry"}); + + // for java almanac version + // sar = SSR.postHTMLForm("coastwatch.pfeg.noaa.gov", + // "/cwexperimental/CWBrowser.jsp", + // "edit=Bathymetry"); + + // String2.log("****beginResponse\n" + String2.toNewlineString(sar) + + // "\n****endResponse"); + // Test.ensureNotEqual(String2.lineContaining(sar, "1) Draw bathymetry lines:"), + // -1, "a"); + + // getFirstLineStartsWith + String2.log("test getFirstLineStartsWith"); + String tFileName = classPath + "testSSR.txt"; + File2.writeToFile88591(tFileName, "This is\na file\nwith a few lines."); + Test.ensureEqual(SSR.getFirstLineStartsWith(tFileName, File2.ISO_8859_1, "with "), "with a few lines.", "a"); + Test.ensureEqual(SSR.getFirstLineStartsWith(tFileName, File2.ISO_8859_1, "hi "), null, "b"); + + // getFirstLineMatching + String2.log("test getFirstLineMatching"); + Test.ensureEqual(SSR.getFirstLineMatching(tFileName, File2.ISO_8859_1, ".*?i.*"), "This is", "a"); // find first + // of many + // matches + Test.ensureEqual(SSR.getFirstLineMatching(tFileName, File2.ISO_8859_1, "^a.*"), "a file", "b"); // start of line + Test.ensureEqual(SSR.getFirstLineMatching(tFileName, File2.ISO_8859_1, ".*?\\sfew\\s.*"), "with a few lines.", + "c"); // containing + Test.ensureEqual(SSR.getFirstLineMatching(tFileName, File2.ISO_8859_1, "q"), null, "d"); // no match + + Test.ensureTrue(File2.delete(tFileName), "delete " + tFileName); + + // getContextDirectory + String2.log("test getContextDirectory current=" + + File2.webInfParentDirectory()); // with / separator and / at the end + // there is no way to test this and have it work with different installations + // test for my computer (comment out on other computers): + // ensureEqual(String2.getContextDirectory(), //with / separator and / at the + // end + // "C:/programs/_tomcat/webapps/cwexperimental/", "a"); + // wimpy test, but works on all computers + Test.ensureNotNull(File2.webInfParentDirectory(), // with / separator and / at the end + "contextDirectory"); + + // getTempDirectory + String2.log("test getTempDirectory current=" + SSR.getTempDirectory()); + // wimpy test + Test.ensureEqual(SSR.getTempDirectory(), File2.webInfParentDirectory() + "WEB-INF/temp/", "a"); + + // done + String2.log("\nDone. All non-Unix tests passed!"); + + } + + /** + * If this fails with "Connection refused" error, make sure McAffee "Virus Scan + * Console : + * Access Protection Properties : Anti Virus Standard Protections : + * Prevent mass mailing worms from sending mail" is un-checked. + */ + @org.junit.jupiter.api.Test + @TagPassword + void testEmail() throws Exception { + + String emailServer, emailPort, emailProperties, emailUser, + emailPassword, emailReplyToAddress, emailToAddresses; + SSR.debugMode = true; + + // *** sendEmail via Google uses starttls authentication + emailServer = String2.getStringFromSystemIn( + "\n\n***gmail email server (e.g., smtp.gmail.com)? "); + if (emailServer.length() == 0) + emailServer = "smtp.gmail.com"; + + emailPort = String2.getStringFromSystemIn( + "gmail email port (e.g., 465 or 587 (default))? "); + if (emailPort.length() == 0) + emailPort = "587"; + + emailUser = String2.getStringFromSystemIn( + "gmail email user (e.g., erd.data@noaa.gov)? "); + if (emailUser.length() == 0) + emailUser = "erd.data@noaa.gov"; + + emailPassword = String2.getPasswordFromSystemIn( + "gmail email password\n" + + "(e.g., password (or \"\" to skip this test. Bob: use 'application specific password')? "); + + if (emailPassword.length() > 0) { + emailReplyToAddress = String2.getStringFromSystemIn( + "gmail email Reply To address (e.g., erd.data@noaa.gov)? "); + if (emailReplyToAddress.length() == 0) + emailReplyToAddress = "erd.data@noaa.gov"; + + emailToAddresses = String2.getStringFromSystemIn( + "1+ email To addresses (e.g., BobSimons2.00@gmail.com,CoHortSoftware@gmail.com)? "); + if (emailToAddresses.length() == 0) + emailToAddresses = "BobSimons2.00@gmail.com,CoHortSoftware@gmail.com"; + + try { + String2.log("test gmail email " + emailToAddresses); + SSR.sendEmail(emailServer, String2.parseInt(emailPort), emailUser, emailPassword, + "mail.smtp.starttls.enable|true", + emailReplyToAddress, emailToAddresses, + "gmail email test", // Euro + "This is a gmail email test from TestSSR with embedded special characters < > & û \u20ac .\nSecond line."); + } catch (Exception e) { + String2.pressEnterToContinue(MustBe.throwableToString(e)); + } + } + SSR.debugMode = false; + } + + /** + * Test email. + * If this fails with "Connection refused" error, make sure McAffee "Virus Scan + * Console : + * Access Protection Properties : Anti Virus Standard Protections : + * Prevent mass mailing worms from sending mail" is un-checked. + * + */ + public static void testEmail(String emailUser, String password) throws Exception { + + String title = "Email Test from TestSSR"; + String content = "This is an email test (local) from user=" + emailUser + " in TestSSR."; + String2.log("\n*** " + content); + SSR.debugMode = true; + if (true) { + String emailServer = "smtp.gmail.com"; + // Thunderbird used 465. 587 is what we're supposed to use. Dave Nordello opened + // it up. + int emailPort = 587; + SSR.sendEmail(emailServer, emailPort, emailUser, password, + "mail.smtp.starttls.enable|true", + emailUser, "erd.data@noaa.gov,CoHortSoftware@gmail.com,null", title, content); + } + SSR.debugMode = false; + } + + /** + * Test posting info and getting response. + */ + @org.junit.jupiter.api.Test + @TagLocalERDDAP + void testPostFormGetResponseString() throws Exception { + for (int i = 0; i < 2; i++) { + try { + String s = SSR.postFormGetResponseString( + "https://coastwatch.pfeg.noaa.gov/erddap/search/index.html?page=1&itemsPerPage=1000&searchFor=jplmursst41"); + String2.log("\nSSR.testPostFormGetResponseString() result:\n" + s); + Test.ensureTrue(s.indexOf("Do a Full Text Search for Datasets:") >= 0, ""); + Test.ensureTrue(s.indexOf("Multi-scale Ultra-high Resolution (MUR) SST Analysis fv04.1, Global") >= 0, + ""); + Test.ensureTrue(s.indexOf("ERDDAP, Version") >= 0, ""); + + // 2018-10-24 I verified that + // * This request appears as a POST (not GET) in tomcat's + // localhost_access_lot[date].txt + // * The parameters don't appear in that file (whereas they do for GET requests) + // * The parameters don't appear in ERDDAP log (whereas they do for GET + // requests), + // * and it is labelled as a POST request. + s = SSR.postFormGetResponseString( + "http://localhost:8080/cwexperimental/search/index.html?page=1&itemsPerPage=1000&searchFor=jplmursst41"); + String2.log("\nSSR.testPostFormGetResponseString() result:\n" + s); + Test.ensureTrue(s.indexOf("Do a Full Text Search for Datasets:") >= 0, ""); + Test.ensureTrue(s.indexOf("Multi-scale Ultra-high Resolution (MUR) SST Analysis fv04.1, Global") >= 0, + "This test requires MUR 4.1 in the local host ERDDAP."); + Test.ensureTrue(s.indexOf("ERDDAP, Version") >= 0, ""); + break; // if successful, don't do i=1 loop + } catch (Exception e) { + String2.pressEnterToContinue(MustBe.throwableToString(e) + + "This requires localhost ERDDAP.\nPress Enter to " + + (i == 0 ? "try again." : "skip this test.")); + } + } + } + + /** + * Run all of the tests which are dependent on Unix. + */ + @org.junit.jupiter.api.Test + void runUnixTests() throws Exception { + // cShell + String2.log("test cShell"); + // Test.ensureEqual(toNewlineString(SSR.cShell("")), "", "a"); + + String2.log("Done. All Unix tests passed!"); + } + + /** + * Runs some AWS S3-related tests. + */ + @org.junit.jupiter.api.Test + @TagAWS + void testAwsS3() throws Exception { + + String2.log("\n*** TestSSR.testAwsS3() -- THIS TEST REQUIRES testPrivateAwsS3MediaFiles in localhost erddap."); + String localFile20 = "/u00/data/points/testMediaFiles/ShouldWork/noaa20.gif"; + String privateAwsSource20 = "https://bobsimonsdata.s3.us-east-1.amazonaws.com/testMediaFiles/noaa20.gif"; + String privateErddapSource20 = "http://localhost:8080/cwexperimental/files/testPrivateAwsS3MediaFiles/noaa20.gif"; + BufferedInputStream bis; + BufferedOutputStream bos; + String dest = File2.getSystemTempDirectory() + "testS3"; + String results, expected; + + // String2.isRemote() and String2.isTrulyRemote() + Test.ensureEqual(String2.isRemote(localFile20), false, ""); + Test.ensureEqual(String2.isTrulyRemote(localFile20), false, ""); + Test.ensureEqual(String2.isRemote(privateAwsSource20), true, ""); + Test.ensureEqual(String2.isTrulyRemote(privateAwsSource20), false, ""); + Test.ensureEqual(String2.isRemote(privateErddapSource20), true, ""); + Test.ensureEqual(String2.isTrulyRemote(privateErddapSource20), true, ""); + + String bro[] = String2.parseAwsS3Url(privateAwsSource20); + Test.ensureEqual(bro[0], "bobsimonsdata", ""); + Test.ensureEqual(bro[1], "us-east-1", ""); + Test.ensureEqual(bro[2], "testMediaFiles/noaa20.gif", ""); + + bro = String2.parseAwsS3Url("http://some.bucket.s3-website-us-east-1.amazonaws.com/some/object.gif"); + Test.ensureEqual(bro[0], "some.bucket", ""); + Test.ensureEqual(bro[1], "us-east-1", ""); + Test.ensureEqual(bro[2], "some/object.gif", ""); + + // private file length + Test.ensureEqual(File2.length(localFile20), 1043, ""); + Test.ensureEqual(File2.length(privateAwsSource20), 1043, ""); + + // private file lastModified + Test.ensureEqual(File2.getLastModified(localFile20), 1302534310000L, ""); + Test.ensureEqual(File2.getLastModified(privateAwsSource20), 1620243246000L, ""); // the instant I put it in S3 + + // a public bucket/file should allow access via a simple https request + results = "okay"; + try { + SSR.touchUrl("https://nasanex.s3.us-west-2.amazonaws.com/NEX-DCP30/doi.txt", 5000, false); // handleS3ViaSDK=false + } catch (Exception e) { + results = e.toString(); + } + Test.ensureEqual(results, "okay", + "A public S3 file should be accessible (e.g., touchUrl) via a simple URL."); + + // a private bucket/file shouldn't allow access via a simple https request + results = "shouldn't happen"; + try { + SSR.touchUrl(privateAwsSource20, 5000, false); // handleS3ViaSDK=false + } catch (Exception e) { + results = e.toString(); + } + expected = "java.io.IOException: HTTP status code=403 for URL: https://bobsimonsdata.s3.us-east-1.amazonaws.com/testMediaFiles/noaa20.gif\n"; + Test.ensureEqual(results.substring(0, expected.length()), expected, + "A private S3 file shouldn't be accessible (e.g., touchUrl) via a simple URL (even with credentials on this computer). results=" + + results); + + // byte range private + Test.ensureTrue(File2.copy(privateAwsSource20, dest + "1a"), ""); + results = File2.hexDump(dest + "1a", 96); + String expected1 = "47 49 46 38 39 61 14 00 14 00 f7 00 00 14 3a 8c GIF89a : |\n" + + "2c a2 d4 94 d2 ec 4c 6e a4 8c a2 c4 04 86 d4 34 , Ln 4 |\n" + + "56 9c cc ea f4 6c 86 b4 64 ba e4 84 c6 e4 24 4a V l d $J |\n" + + "94 44 aa dc 14 96 d4 e4 f6 fc ac ba d4 cc d2 e4 D |\n" + + "64 7e ac 44 62 9c 34 a6 dc 7c 92 bc bc ca dc 14 d~ Db 4 | |\n" + + "42 8c 5c 76 ac 9c ae cc 74 c2 e4 14 96 dc fc fe B \\v t |\n"; + Test.ensureEqual(results, expected1, "results=\n" + results); + + // range request + Test.ensureTrue(File2.copy(privateAwsSource20, dest + "2a", 16, 95), ""); + results = File2.hexDump(dest + "2a", 1000); // read all + String expected2 = // same but without 1st row (16 bytes) + "2c a2 d4 94 d2 ec 4c 6e a4 8c a2 c4 04 86 d4 34 , Ln 4 |\n" + + "56 9c cc ea f4 6c 86 b4 64 ba e4 84 c6 e4 24 4a V l d $J |\n" + + "94 44 aa dc 14 96 d4 e4 f6 fc ac ba d4 cc d2 e4 D |\n" + + "64 7e ac 44 62 9c 34 a6 dc 7c 92 bc bc ca dc 14 d~ Db 4 | |\n" + + "42 8c 5c 76 ac 9c ae cc 74 c2 e4 14 96 dc fc fe B \\v t |\n"; + Test.ensureEqual(results, expected2, "results=\n" + results); + + // byte range private + bis = (BufferedInputStream) SSR.getUrlConnBufferedInputStream(privateErddapSource20, + 30000, false, false, 0, -1, false)[1]; + bos = new BufferedOutputStream(new FileOutputStream(dest + "1b")); + File2.copy(bis, bos, 0, -1); + bis.close(); + bos.close(); + results = File2.hexDump(dest + "1b", 96); + Test.ensureEqual(results, expected1, "results=\n" + results); + + // range request + bis = (BufferedInputStream) SSR.getUrlConnBufferedInputStream(privateErddapSource20, + 30000, false, false, 16, 95, false)[1]; // 16 to 95 + bos = new BufferedOutputStream(new FileOutputStream(dest + "2b")); + File2.copy(bis, bos, 0, -1); + bis.close(); + bos.close(); + results = File2.hexDump(dest + "2b", 1000); // all + Test.ensureEqual(results, expected2, "results=\n" + results); + + // range request + bis = (BufferedInputStream) SSR.getUrlConnBufferedInputStream(privateErddapSource20, + 30000, false, false, 16, -1, false)[1]; // 16 to end + bos = new BufferedOutputStream(new FileOutputStream(dest + "2b2")); + File2.copy(bis, bos, 0, -1); + bis.close(); + bos.close(); + results = File2.hexDump(dest + "2b2", 80); + Test.ensureEqual(results, expected2, "results=\n" + results); + } + + /** + * Tests Aws TransferManager. + */ + @org.junit.jupiter.api.Test + @TagAWS + void testAwsTransferManager() throws Exception { + + // *** test a lot of AWS S3 actions on a private AWS bucket + // delete a file on S3 to ensure it doesn't exist (ignore result) + String origLocal = String2.unitTestDataDir + "ascii/standardizeWhat1.csv"; + String tempLocal = File2.getSystemTempDirectory() + "testAwsS3.csv"; + String awsUrl = "https://bobsimonsdata.s3.us-east-1.amazonaws.com/testMediaFiles/testAwsS3.csv"; + // bucket is publicly readible in a browser via http but not https + String awsUrl2 = "http://bob.simons.public.output.s3-website-us-east-1.amazonaws.com/testAwsS3.csv"; + String content; + + // delete files I will create + File2.deleteAwsS3File(awsUrl); + File2.delete(tempLocal); + + // isAwsS3File + Test.ensureEqual(File2.isAwsS3File(awsUrl), false, ""); + + // upload a file to S3 + SSR.uploadFileToAwsS3(null, origLocal, awsUrl, "text/csv"); + + // length of Aws S3 file + Test.ensureEqual(File2.length(awsUrl), 44, ""); + + // isAwsS3File + Test.ensureEqual(File2.isAwsS3File(awsUrl), true, ""); + + // download a file from S3 + SSR.downloadFile(awsUrl, tempLocal, false); // tryToUseCompression is ignored + + // read local file + content = File2.directReadFrom88591File(tempLocal); + Test.ensureEqual(content, + "date,data\n" + + "20100101000000,1\n" + + "20100102000000,2\n", + "content=" + String2.annotatedString(content)); + + // delete files I created + File2.deleteAwsS3File(awsUrl); + File2.delete(tempLocal); + + // isAwsS3File + Test.ensureEqual(File2.isAwsS3File(awsUrl), false, ""); + + // ************** again but with awsUrl2 + // delete files I will create + File2.deleteAwsS3File(awsUrl2); + File2.delete(tempLocal); + + // isAwsS3File + Test.ensureEqual(File2.isAwsS3File(awsUrl2), false, ""); + + // upload a file to S3 + // fails here. + // "software.amazon.awssdk.crt.s3.CrtS3RuntimeException: Retry cannot be + // attempted + // because the maximum number of retries has been exceeded. + // AWS_IO_MAX_RETRIES_EXCEEDED(1069) + // at com.amazonaws.s3.S3NativeClient$3.onFinished(S3NativeClient.java:313)" + // a permissions problem? + SSR.uploadFileToAwsS3(null, origLocal, awsUrl2, "text/csv"); + + // length of Aws S3 file + Test.ensureEqual(File2.length(awsUrl2), 44, ""); + + // isAwsS3File + Test.ensureEqual(File2.isAwsS3File(awsUrl2), true, ""); + + // download a file from S3 + SSR.downloadFile(awsUrl2, tempLocal, false); // tryToUseCompression is ignored + + // read local file + content = File2.directReadFrom88591File(tempLocal); + Test.ensureEqual(content, + "date,data\n" + + "20100101000000,1\n" + + "20100102000000,2\n", + "content=" + String2.annotatedString(content)); + + // delete files I created + File2.deleteAwsS3File(awsUrl2); + File2.delete(tempLocal); + + // isAwsS3File + Test.ensureEqual(File2.isAwsS3File(awsUrl2), false, ""); + } + + /** + * Run all of the tests + */ + public static void main(String args[]) throws Throwable { + SSR.verbose = true; + + // runUnixTests(); + } + +} diff --git a/src/test/java/tags/TagAWS.java b/src/test/java/tags/TagAWS.java new file mode 100644 index 000000000..98fe57d2e --- /dev/null +++ b/src/test/java/tags/TagAWS.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("AWS") +public @interface TagAWS { +} \ No newline at end of file diff --git a/src/test/java/tags/TagExternalERDDAP.java b/src/test/java/tags/TagExternalERDDAP.java new file mode 100644 index 000000000..47117baf9 --- /dev/null +++ b/src/test/java/tags/TagExternalERDDAP.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("ExternalERDDAP") +public @interface TagExternalERDDAP { +} diff --git a/src/test/java/tags/TagExternalOther.java b/src/test/java/tags/TagExternalOther.java new file mode 100644 index 000000000..adbafb548 --- /dev/null +++ b/src/test/java/tags/TagExternalOther.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("ExternalOther") +public @interface TagExternalOther { +} \ No newline at end of file diff --git a/src/test/java/tags/TagIncompleteTest.java b/src/test/java/tags/TagIncompleteTest.java new file mode 100644 index 000000000..55ad90c1f --- /dev/null +++ b/src/test/java/tags/TagIncompleteTest.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("IncompleteTest") +public @interface TagIncompleteTest { +} \ No newline at end of file diff --git a/src/test/java/tags/TagLargeFile.java b/src/test/java/tags/TagLargeFile.java new file mode 100644 index 000000000..55f8a8654 --- /dev/null +++ b/src/test/java/tags/TagLargeFile.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("LargeFile") +public @interface TagLargeFile { +} \ No newline at end of file diff --git a/src/test/java/tags/TagLocalERDDAP.java b/src/test/java/tags/TagLocalERDDAP.java new file mode 100644 index 000000000..43354d8f3 --- /dev/null +++ b/src/test/java/tags/TagLocalERDDAP.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("LocalERDDAP") +public @interface TagLocalERDDAP { +} \ No newline at end of file diff --git a/src/test/java/tags/TagMissingFile.java b/src/test/java/tags/TagMissingFile.java new file mode 100644 index 000000000..620cd15b1 --- /dev/null +++ b/src/test/java/tags/TagMissingFile.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("MissingFile") +public @interface TagMissingFile { +} \ No newline at end of file diff --git a/src/test/java/tags/TagPassword.java b/src/test/java/tags/TagPassword.java new file mode 100644 index 000000000..d3775870f --- /dev/null +++ b/src/test/java/tags/TagPassword.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("Password") +public @interface TagPassword { +} \ No newline at end of file diff --git a/src/test/java/tags/TagThredds.java b/src/test/java/tags/TagThredds.java new file mode 100644 index 000000000..a313b81f1 --- /dev/null +++ b/src/test/java/tags/TagThredds.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("Thredds") +public @interface TagThredds { +} diff --git a/src/test/java/tags/TagWebInfStructureDependency.java b/src/test/java/tags/TagWebInfStructureDependency.java new file mode 100644 index 000000000..133ea5b5d --- /dev/null +++ b/src/test/java/tags/TagWebInfStructureDependency.java @@ -0,0 +1,17 @@ +package tags; + +import org.junit.jupiter.api.Tag; + +import java.lang.annotation.Documented; +import java.lang.annotation.ElementType; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; +import java.lang.annotation.Target; + +/** TODO: Make tests with this tag runnable. */ +@Target({ ElementType.TYPE, ElementType.METHOD }) +@Retention(RetentionPolicy.RUNTIME) +@Documented +@Tag("WebInfStructureDependency") +public @interface TagWebInfStructureDependency { +} diff --git a/src/test/resources/CFPointConventions/.gitignore b/src/test/resources/CFPointConventions/.gitignore new file mode 100644 index 000000000..b25c15b81 --- /dev/null +++ b/src/test/resources/CFPointConventions/.gitignore @@ -0,0 +1 @@ +*~ diff --git a/src/test/resources/CFPointConventions/INSTALL_NETCDF b/src/test/resources/CFPointConventions/INSTALL_NETCDF new file mode 100644 index 000000000..b3e3b8717 --- /dev/null +++ b/src/test/resources/CFPointConventions/INSTALL_NETCDF @@ -0,0 +1,134 @@ +INSTALL_PATH=/usr/local +mkdir -p $INSTALL_PATH/src + +# ANTLR2 +APP=antlr-2.7.7 +ANTLR_PATH=/usr +cd $INSTALL_PATH/src + +rm -rf antlr-2.7.7* +wget http://www.antlr2.org/download/antlr-2.7.7.tar.gz +tar xzf antlr-2.7.7.tar.gz ; cd antlr-2.7.7 + +# Bug in antlr-2.7.7 +sed -i "13a #include " lib/cpp/antlr/CharScanner.hpp +sed -i "14a #include " lib/cpp/antlr/CharScanner.hpp + +CC=gcc CXX='' ./configure \ +--prefix=$ANTLR_PATH \ +--disable-csharp \ +--disable-java \ +--disable-python 2>&1 | tee $APP.config +make 2>&1 | tee $APP.make +make install 2>&1 | tee $APP.install + +# UDUNITS +APP=udunits-2.1.24 +UDUNITS_PATH=$INSTALL_PATH/$APP +rm -rf $UDUNITS_PATH +cd $INSTALL_PATH/src + +rm -rf udunits-2.1.24* +wget ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.1.24.tar.gz +tar xzf udunits-2.1.24.tar.gz ; cd udunits-2.1.24 + +CC=gcc CXX='' F77=gfortran ./configure \ +--prefix=$UDUNITS_PATH 2>&1 | tee $APP.config +make 2>&1 | tee $APP.make +make install 2>&1 | tee $APP.install + +# ZLIB +APP=zlib-1.2.5 +ZLIB_PATH=$INSTALL_PATH/$APP +rm -rf $ZLIB_PATH +cd $INSTALL_PATH/src + +rm -rf zlib-1.2.5* +wget http://zlib.net/zlib-1.2.5.tar.gz +tar zxf zlib-1.2.5.tar.gz ; cd zlib-1.2.5 + +CC=gcc FC=gfortran CXX='' ./configure \ +--prefix=$ZLIB_PATH | tee $APP.config +make 2>&1 | tee $APP.make +make install 2>&1 | tee $APP.install + +# HDF4 +APP=hdf-4.2.6 +HDF4_PATH=$INSTALL_PATH/$APP +rm -rf $HDF4_PATH +cd $INSTALL_PATH/src + +rm -rf hdf-4.2.6* +wget http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/hdf-4.2.6.tar.gz +tar xzf hdf-4.2.6.tar.gz ; cd hdf-4.2.6 + +# Bug in configure script, need to define EGREP variable here +EGREP=egrep CC=gcc FC=gfortran F77=gfortran ./configure \ +--prefix=$HDF4_PATH \ +--disable-netcdf \ +--enable-fortran \ +--with-zlib=$ZLIB_PATH \ +--with-pic 2>&1 | tee $APP.config +make 2>&1 | tee $APP.make +make install 2>&1 | tee $APP.install + +# HDF5 +APP=hdf5-1.8.8 +HDF5_PATH=$INSTALL_PATH/$APP +rm -rf $HDF5_PATH +cd $INSTALL_PATH/src + +rm -rf hdf5-1.8.8* +wget http://www.hdfgroup.org/ftp/HDF5/prev-releases/hdf5-1.8.8/src/hdf5-1.8.8.tar.gz +tar xzf hdf5-1.8.8.tar.gz ; cd hdf5-1.8.8 + +CC=gcc FC=gfortran CXX='' ./configure \ +--prefix=$HDF5_PATH \ +--enable-fortran \ +--with-zlib=$ZLIB_PATH \ +--with-pic 2>&1 | tee $APP.config +make 2>&1 | tee $APP.make +make install 2>&1 | tee $APP.install + +export LD_LIBRARY_PATH=$HDF4_PATH/lib:$LD_LIBRARY_PATH +export PATH=$HDF4_PATH/bin:$PATH +export LD_LIBRARY_PATH=$HDF5_PATH/lib:$LD_LIBRARY_PATH +export PATH=$HDF5_PATH/bin:$PATH +export LD_LIBRARY_PATH=$ANTLR_PATH/lib:$LD_LIBRARY_PATH +export PATH=$ANTLR_PATH/bin:$PATH +export LD_LIBRARY_PATH=$UDUNITS_PATH/lib:$LD_LIBRARY_PATH +export PATH=$UDUNITS_PATH/bin:$PATH +export LD_LIBRARY_PATH=$ZLIB_PATH/lib:$LD_LIBRARY_PATH +export PATH=$ZLIB_PATH/bin:$PATH + +# NetCDF4 +APP=netcdf-4.1.3 +NETCDF4_PATH=$INSTALL_PATH/$APP +rm -rf $NETCDF4_PATH +cd $INSTALL_PATH/src + +rm -rf netcdf-4.1.3* +wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz +tar xzf netcdf-4.1.3.tar.gz ; cd netcdf-4.1.3 + +CPPFLAGS="-I$HDF5_PATH/include -I$ZLIB_PATH/include -I$HDF4_PATH/include" \ +LDFLAGS="-L$HDF5_PATH/lib -L$ZLIB_PATH/lib -L$HDF4_PATH/lib" \ +LIBS="-lmfhdf -lhdf5_hl -lhdf5 -lantlr -ldf -ljpeg -lz" \ +CXX=g++ CC=gcc FC=gfortran F77=gfortran ./configure \ +--prefix=$NETCDF4_PATH \ +--with-hdf5=$HDF5_PATH \ +--with-hdf4=$HDF4_PATH \ +--enable-fortran \ +--enable-static \ +--enable-shared \ +--enable-f77 \ +--enable-f90 \ +--enable-netcdf4 \ +--enable-hdf4 \ +--enable-cxx-4 \ +--with-pic 2>&1 | tee $APP.config +make 2>&1 | tee $APP.make +make install 2>&1 | tee $APP.install + +export LD_LIBRARY_PATH=$NETCDF4_PATH/lib:$LD_LIBRARY_PATH +export PATH=$NETCDF4_PATH/bin:$PATH \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/README b/src/test/resources/CFPointConventions/README new file mode 100644 index 000000000..9941f67cb --- /dev/null +++ b/src/test/resources/CFPointConventions/README @@ -0,0 +1,47 @@ +Templates of the CF PointObservationConventions + +Outputs in NetCDF, CDL, and NcML + +See: http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#appendix-examples-discrete-geometries + +To get started: + +* Install the NetCDF C libraries: + - Most linux distros will have a package: + - YUM (cent/rh/fedora) - netcdf-devel + - APT (debian) - netcdf-bin + - If not, see the INSTALL_NETCDF file for a helper script to install from source. + +* Install Ruby >= 1.9.1 + - Most distros will have this as a package. Make sure you are using Ruby >= 1.9.1. + +* Download and Install narray: + - wget https://github.com/masa16/narray/tarball/0.6.0.1 + - tar zxvf 0.6.0.1 + - cd masa16-narray-4429bdf + - ruby extconf.rb + - make + - make install + +* Download and Install narray_miss + - wget http://ruby.gfd-dennou.org/products/narray_miss/narray_miss-1.2.2.tar.gz + - tar zxvf narray_miss-1.2.2.tar.gz + - cd narray_miss-1.2.2 + - ruby setup.rb + +* Download and Install Ruby-NetCDF + - wget http://ruby.gfd-dennou.org/products/ruby-netcdf/ruby-netcdf-0.6.5.tar.gz + - tar zxvf ruby-netcdf-0.6.5.tar.gz + - cd ruby-netcdf-0.6.5 + - ruby extconf.rb + + You may get some errors and need to point Ruby to the NArray and/or Netcdf headers + The instructions are provided if it fails. + + - make + - make install + + +* Run the generators + - ./runScripts + diff --git a/src/test/resources/CFPointConventions/point/point-H.1.rb b/src/test/resources/CFPointConventions/point/point-H.1.rb new file mode 100644 index 000000000..4eb3e08b5 --- /dev/null +++ b/src/test/resources/CFPointConventions/point/point-H.1.rb @@ -0,0 +1,70 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","point") + +o = 100 +obs_dim = file.def_dim("obs",o) + +lat = file.def_var("lat","float",[obs_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","latitude of the observation") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","float",[obs_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","longitude of the observation") +lon.put_att("standard_name","longitude") + +alt = file.def_var("alt","float",[obs_dim]) +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("standard_name","height") + +time = file.def_var("time","int",[obs_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +temp = file.def_var("temperature","sfloat",[obs_dim]) +temp.put_att("long_name","Water Temperature") +temp.put_att("standard_name","sea_water_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[obs_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon alt") +humi.put_att("missing_value",-999.9,"sfloat") + + +# Stop the definitions, lets write some data +file.enddef + +# lat/lon/time/alt do not have to be increasing, +# since each observation is not related to any other +lat.put(NArray.int(o).random!(180)) +lon.put(NArray.int(o).random!(180)) +time.put(NArray.int(o).random!(3600)) +alt.put(NArray.float(o).random!(10)) +temp.put(NArray.float(o).random!(40)) +humi.put(NArray.float(o).random!(90)) + + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/point/point-H.1/README b/src/test/resources/CFPointConventions/point/point-H.1/README new file mode 100644 index 000000000..18db378b4 --- /dev/null +++ b/src/test/resources/CFPointConventions/point/point-H.1/README @@ -0,0 +1,5 @@ +** point-H.1 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.cdl b/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.cdl new file mode 100644 index 000000000..d3ada0804 --- /dev/null +++ b/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.cdl @@ -0,0 +1,39 @@ +netcdf point-H.1 { +dimensions: + obs = 100 ; +variables: + double lat(obs) ; + lat:units = "degrees_north" ; + lat:long_name = "latitude of the observation" ; + lat:standard_name = "latitude" ; + double lon(obs) ; + lon:units = "degrees_east" ; + lon:long_name = "longitude of the observation" ; + lon:standard_name = "longitude" ; + double alt(obs) ; + alt:units = "m" ; + alt:positive = "up" ; + alt:axis = "Z" ; + alt:standard_name = "height" ; + int time(obs) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float temperature(obs) ; + temperature:long_name = "Water Temperature" ; + temperature:standard_name = "sea_water_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon alt" ; + temperature:missing_value = -999.9f ; + float humidity(obs) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon alt" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "point" ; +} diff --git a/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.nc b/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.nc new file mode 100644 index 000000000..f1b8c8241 Binary files /dev/null and b/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.nc differ diff --git a/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.ncml b/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.ncml new file mode 100644 index 000000000..552a5b8c9 --- /dev/null +++ b/src/test/resources/CFPointConventions/point/point-H.1/point-H.1.ncml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.rb b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.rb new file mode 100644 index 000000000..340ae869d --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.rb @@ -0,0 +1,99 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","profile") + +p = 4 +o = 0 #UNLIMITED + +obs_dim = file.def_dim("obs",o) +profile_dim = file.def_dim("profile",p) + +lat = file.def_var("lat","sfloat",[profile_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[profile_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +profile = file.def_var("profile","int",[profile_dim]) +profile.put_att("cf_role", "profile_id") + +rowsize = file.def_var("rowSize","int",[profile_dim]) +rowsize.put_att("long_name", "number of obs for this profile") +rowsize.put_att("sample_dimension", "obs") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("z","sfloat",[obs_dim]) +alt.put_att("long_name","height above mean sea level") +alt.put_att("standard_name","altitude") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +temp = file.def_var("temperature","sfloat",[obs_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[obs_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +# Uniquely identifiying values for each profile. +# Just iterates by 1 (0,1,2,3, ... ,p) +profile.put(NArray.int(p).indgen!) + +lat.put(NArray.int(p).random!(180)) +lon.put(NArray.int(p).random!(180)) + +#time.put(NArray.int(100).random!(3600), "start" => [0], "end" => [99]) +time.put(NArray.int(p).indgen!*3600) + +# We define the row_sizes here. Four profiles. +# 1: 10 obs +# 2: 6 obs +# 3: 2 obs +# 4: 40 obs +# total: 58 obs +rowsize.put([10,6,2,40]) + +#alt.put(NArray.float(58).random!(40)) +alt.put(NArray.float(10).random!(10), "start" => [0], "end" => [9]) +alt.put(NArray.float(6).random!(10), "start" => [10], "end" => [15]) +alt.put(NArray.float(2).random!(10), "start" => [16], "end" => [17]) +alt.put(NArray.float(40).random!(10), "start" => [18], "end" => [57]) + +temp.put(NArray.float(58).random!(40)) +humi.put(NArray.float(58).random!(90)) + + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/README b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/README new file mode 100644 index 000000000..47199ebe6 --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/README @@ -0,0 +1,5 @@ +** profile-Contiguous-Ragged-MultipleProfiles-H.3.4 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.cdl b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.cdl new file mode 100644 index 000000000..5b1211d6e --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.cdl @@ -0,0 +1,47 @@ +netcdf profile-Contiguous-Ragged-MultipleProfiles-H.3.4 { +dimensions: + obs = UNLIMITED ; // (58 currently) + profile = 4 ; +variables: + float lat(profile) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(profile) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int profile(profile) ; + profile:cf_role = "profile_id" ; + int rowSize(profile) ; + rowSize:long_name = "number of obs for this profile" ; + rowSize:sample_dimension = "obs" ; + int time(profile) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float z(obs) ; + z:long_name = "height above mean sea level" ; + z:standard_name = "altitude" ; + z:units = "m" ; + z:positive = "up" ; + z:axis = "Z" ; + z:missing_value = -999.9f ; + float temperature(obs) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(obs) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "profile" ; +} diff --git a/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.nc b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.nc new file mode 100644 index 000000000..7d1ff5d58 Binary files /dev/null and b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.nc differ diff --git a/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.ncml b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.ncml new file mode 100644 index 000000000..61f4b1d9b --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Contiguous-Ragged-MultipleProfiles-H.3.4/profile-Contiguous-Ragged-MultipleProfiles-H.3.4.ncml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.rb b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.rb new file mode 100644 index 000000000..46450ddfd --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.rb @@ -0,0 +1,108 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8360656 + +There is no wind data for the last 100 profiles + +There is no humidity data for the first 3 profiles + +There is no temperature data for profiles 50-52 and 100-102 + +There is no data for profiles 20-24 +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","profile") + +p = 142 +z = 42 + +profile_dim = file.def_dim("profile",p) +z_dim = file.def_dim("alt",z) + +lat = file.def_var("lat","sfloat",[profile_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[profile_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +profile = file.def_var("profile","int",[profile_dim]) +profile.put_att("cf_role", "profile_id") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("alt","sfloat",[z_dim, profile_dim]) +alt.put_att("units","m") +alt.put_att("standard_name","altitude") +alt.put_att("long_name","height above mean sea level") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +temp = file.def_var("temperature","sfloat",[z_dim, profile_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[z_dim, profile_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon alt") +humi.put_att("missing_value",-999.9,"sfloat") + +wind = file.def_var("wind_speed","sfloat",[z_dim, profile_dim]) +wind.put_att("long_name","Wind Speed") +wind.put_att("standard_name","wind_speed") +wind.put_att("units","m/s") +wind.put_att("coordinates", "time lat lon alt") +wind.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +# Uniquely identifiying values for each profile. +# Just iterates by 1 (0,1,2,3, ... ,p) +profile.put(NArray.int(p).indgen!) + +lat.put(NArray.int(p).random!(180)) +lon.put(NArray.int(p).random!(180)) +time.put(NArray.int(p).indgen!*3600) + +alt.put(NArray.float(p,z).random!(10)) +alt.put(NArray.float(z,5).fill!(-999.9), "start" => [0,20], "end" => [z-1,24]) + +temp.put(NArray.float(p,z).random!(40)) +temp.put(NArray.float(z,3).fill!(-999.9), "start" => [0,50], "end" => [z-1,52]) +temp.put(NArray.float(z,3).fill!(-999.9), "start" => [0,100], "end" => [z-1,102]) +temp.put(NArray.float(z,5).fill!(-999.9), "start" => [0,20], "end" => [z-1,24]) + +humi.put(NArray.float(p,z).random!(90)) +humi.put(NArray.float(z,3).fill!(-999.9), "start" => [0,0], "end" => [z-1,2]) +humi.put(NArray.float(z,5).fill!(-999.9), "start" => [0,20], "end" => [z-1,24]) + +first = p - 100 +second = p - first +wind.put(NArray.float(z,first).random!(90), "start" => [0,0], "end" => [z-1,first-1]) +wind.put(NArray.float(z,second).fill!(-999.9), "start" => [0,first], "end" => [z-1,p-1]) +wind.put(NArray.float(z,5).fill!(-999.9), "start" => [0,20], "end" => [z-1,24]) + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/README b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/README new file mode 100644 index 000000000..67dad10fc --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/README @@ -0,0 +1,14 @@ +** profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2 ** + + +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8360656 + +There is no wind data for the last 100 profiles + +There is no humidity data for the first 3 profiles + +There is no temperature data for profiles 50-52 and 100-102 + +There is no data for profiles 20-24 + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.cdl b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.cdl new file mode 100644 index 000000000..7d7865bad --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.cdl @@ -0,0 +1,49 @@ +netcdf profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2 { +dimensions: + profile = 142 ; + alt = 42 ; +variables: + float lat(profile) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(profile) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int profile(profile) ; + profile:cf_role = "profile_id" ; + int time(profile) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float alt(profile, alt) ; + alt:units = "m" ; + alt:standard_name = "altitude" ; + alt:long_name = "height above mean sea level" ; + alt:positive = "up" ; + alt:axis = "Z" ; + alt:missing_value = -999.9f ; + float temperature(profile, alt) ; + temperature:long_name = "Air Temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon alt" ; + temperature:missing_value = -999.9f ; + float humidity(profile, alt) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon alt" ; + humidity:missing_value = -999.9f ; + float wind_speed(profile, alt) ; + wind_speed:long_name = "Wind Speed" ; + wind_speed:standard_name = "wind_speed" ; + wind_speed:units = "m/s" ; + wind_speed:coordinates = "time lat lon alt" ; + wind_speed:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "profile" ; +} diff --git a/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.nc b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.nc new file mode 100644 index 000000000..213f541ff Binary files /dev/null and b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.nc differ diff --git a/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.ncml b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.ncml new file mode 100644 index 000000000..03e1425a3 --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2/profile-Incomplete-MultiDimensional-MultipleProfiles-H.3.2.ncml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5.rb b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5.rb new file mode 100644 index 000000000..7fc91f3bf --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5.rb @@ -0,0 +1,113 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","profile") + +p = 6 +o = 0 #UNLIMITED + +obs_dim = file.def_dim("obs",o) +profile_dim = file.def_dim("profile",p) + +lat = file.def_var("lat","sfloat",[profile_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[profile_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +profile = file.def_var("profile","int",[profile_dim]) +profile.put_att("cf_role", "profile_id") + +parent = file.def_var("parentIndex","int",[obs_dim]) +parent.put_att("long_name", "index of profile") +parent.put_att("instance_dimension", "profile") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("z","sfloat",[obs_dim]) +alt.put_att("long_name","height above mean sea level") +alt.put_att("standard_name","altitude") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +temp = file.def_var("temperature","sfloat",[obs_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[obs_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + + +# Stop the definitions, lets write some data +file.enddef + +# Uniquely identifiying values for each profile. +# Just iterates by 1 (0,1,2,3, ... ,p) +profile.put(NArray.int(p).indgen!) + +lat.put(NArray.int(p).random!(180)) +lon.put(NArray.int(p).random!(180)) + +#time.put(NArray.int(100).random!(3600), "start" => [0], "end" => [99]) +time.put(NArray.int(p).indgen!*3600) + +# We define the parent indexes here. Six profiles, and a total of with 100 observations. +# This maps the observations to the profile (which has a lat/lon/time) +# 1: 10 obs +# 2: 6 obs +# 3: 2 obs +# 4: 40 obs +# 5: 30 obs +# 6: 12 obs +# total: 100 obs +first = NArray.int(10).fill!(0).to_a +second = NArray.int(6).fill!(1).to_a +third = NArray.int(2).fill!(2).to_a +fourth = NArray.int(40).fill!(3).to_a +fifth = NArray.int(30).fill!(4).to_a +sixth = NArray.int(12).fill!(5).to_a + +parent.put(first + second + third + fourth + fifth + sixth, "start" => [0], "end" => [99]) + +# could do it this way, but be more verbose so it is more easily understood what is happening. +#alt.put(NArray.float(100).random!(40)) +alt.put(NArray.float(10).random!(10).sort, "start" => [0], "end" => [9]) +alt.put(NArray.float(6).random!(10).sort, "start" => [10], "end" => [15]) +alt.put(NArray.float(2).random!(10).sort, "start" => [16], "end" => [17]) +alt.put(NArray.float(40).random!(10).sort, "start" => [18], "end" => [57]) +alt.put(NArray.float(30).random!(10).sort, "start" => [58], "end" => [87]) +alt.put(NArray.float(12).random!(10).sort, "start" => [88], "end" => [99]) + +temp.put(NArray.float(100).random!(40)) +humi.put(NArray.float(100).random!(90)) + + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/README b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/README new file mode 100644 index 000000000..23cb3304d --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/README @@ -0,0 +1,5 @@ +** profile-Indexed-Ragged-MultipleProfiles-H.3.5 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.cdl b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.cdl new file mode 100644 index 000000000..fbb308bbb --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.cdl @@ -0,0 +1,47 @@ +netcdf profile-Indexed-Ragged-MultipleProfiles-H.3.5 { +dimensions: + obs = UNLIMITED ; // (100 currently) + profile = 6 ; +variables: + float lat(profile) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(profile) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int profile(profile) ; + profile:cf_role = "profile_id" ; + int parentIndex(obs) ; + parentIndex:long_name = "index of profile" ; + parentIndex:instance_dimension = "profile" ; + int time(profile) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float z(obs) ; + z:long_name = "height above mean sea level" ; + z:standard_name = "altitude" ; + z:units = "m" ; + z:positive = "up" ; + z:axis = "Z" ; + z:missing_value = -999.9f ; + float temperature(obs) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(obs) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "profile" ; +} diff --git a/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.nc b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.nc new file mode 100644 index 000000000..311a17b56 Binary files /dev/null and b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.nc differ diff --git a/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.ncml b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.ncml new file mode 100644 index 000000000..0173c1d98 --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Indexed-Ragged-MultipleProfiles-H.3.5/profile-Indexed-Ragged-MultipleProfiles-H.3.5.ncml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.rb b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.rb new file mode 100644 index 000000000..e657a0b4b --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.rb @@ -0,0 +1,78 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","profile") + +p = 142 +z = 42 + +profile_dim = file.def_dim("profile",p) +z_dim = file.def_dim("z",z) + +lat = file.def_var("lat","sfloat",[profile_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[profile_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +profile = file.def_var("profile","int",[profile_dim]) +profile.put_att("cf_role", "profile_id") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("z","sfloat",[z_dim]) +alt.put_att("units","m") +alt.put_att("standard_name","altitude") +alt.put_att("long_name","height above mean sea level") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +temp = file.def_var("temperature","sfloat",[z_dim, profile_dim]) +temp.put_att("long_name","Water Temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[z_dim, profile_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +# Uniquely identifiying values for each profile. +# Just iterates by 1 (0,1,2,3, ... ,p) +profile.put(NArray.int(p).indgen!) + +lat.put(NArray.int(p).random!(180)) +lon.put(NArray.int(p).random!(180)) +time.put(NArray.int(p).indgen!*3600) +alt.put(NArray.float(z).random!(10)) + +temp.put(NArray.float(p,z).random!(40)) +humi.put(NArray.float(p,z).random!(90)) + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/README b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/README new file mode 100644 index 000000000..064ad5afb --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/README @@ -0,0 +1,5 @@ +** profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.cdl b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.cdl new file mode 100644 index 000000000..fe0983102 --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.cdl @@ -0,0 +1,43 @@ +netcdf profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1 { +dimensions: + profile = 142 ; + z = 42 ; +variables: + float lat(profile) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(profile) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int profile(profile) ; + profile:cf_role = "profile_id" ; + int time(profile) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float z(z) ; + z:units = "m" ; + z:standard_name = "altitude" ; + z:long_name = "height above mean sea level" ; + z:positive = "up" ; + z:axis = "Z" ; + z:missing_value = -999.9f ; + float temperature(profile, z) ; + temperature:long_name = "Water Temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(profile, z) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "profile" ; +} diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.nc b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.nc new file mode 100644 index 000000000..add97686c Binary files /dev/null and b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.nc differ diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.ncml b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.ncml new file mode 100644 index 000000000..2ba0ae1cd --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1/profile-Orthogonal-MultiDimensional-MultipleProfiles-H.3.1.ncml @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.rb b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.rb new file mode 100644 index 000000000..0a5e6160b --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.rb @@ -0,0 +1,73 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","profile") + +z = 42 + +z_dim = file.def_dim("z",z) + +lat = file.def_var("lat","sfloat",[]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +profile = file.def_var("profile","int",[]) +profile.put_att("cf_role", "profile_id") + +time = file.def_var("time","int",[]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") + +alt = file.def_var("z","sfloat",[z_dim]) +alt.put_att("units","m") +alt.put_att("standard_name","altitude") +alt.put_att("long_name","height above mean sea level") +alt.put_att("positive","up") +alt.put_att("axis","Z") + +temp = file.def_var("temperature","sfloat",[z_dim]) +temp.put_att("long_name","Water Temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[z_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +# Uniquely identifiying value for this profile. +profile.put(0) + +lat.put([37.5]) +lon.put([-76.5]) +time.put(NArray.int(1).indgen!*3600) + +alt.put(NArray.float(z).random!(10)) +temp.put(NArray.float(z).random!(40)) +humi.put(NArray.float(z).random!(90)) + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/README b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/README new file mode 100644 index 000000000..0a211844b --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/README @@ -0,0 +1,5 @@ +** profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.cdl b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.cdl new file mode 100644 index 000000000..f166472a9 --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.cdl @@ -0,0 +1,40 @@ +netcdf profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3 { +dimensions: + z = 42 ; +variables: + float lat ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int profile ; + profile:cf_role = "profile_id" ; + int time ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + float z(z) ; + z:units = "m" ; + z:standard_name = "altitude" ; + z:long_name = "height above mean sea level" ; + z:positive = "up" ; + z:axis = "Z" ; + float temperature(z) ; + temperature:long_name = "Water Temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(z) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "profile" ; +} diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.nc b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.nc new file mode 100644 index 000000000..f3ffb399f Binary files /dev/null and b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.nc differ diff --git a/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.ncml b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.ncml new file mode 100644 index 000000000..b4d283040 --- /dev/null +++ b/src/test/resources/CFPointConventions/profile/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3/profile-Orthogonal-SingleDimensional-SingleProfile-H.3.3.ncml @@ -0,0 +1,44 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/runScripts b/src/test/resources/CFPointConventions/runScripts new file mode 100644 index 000000000..9fc8b4b0c --- /dev/null +++ b/src/test/resources/CFPointConventions/runScripts @@ -0,0 +1,7 @@ +#!/bin/bash + +find . -name "*.rb" -not -name "utils.rb" | while read f; +do + ruby $f +done + diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.rb b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.rb new file mode 100644 index 000000000..b71d2da56 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.rb @@ -0,0 +1,127 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","timeSeries") + +s = 0 #UNLIMITED +o = 20 +name = 50 + +station_dim = file.def_dim("station",s) +obs_dim = file.def_dim("obs",o) +name_dim = file.def_dim("name_strlen",name) + + +lat = file.def_var("lat","sfloat",[station_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[station_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +stationelev = file.def_var("station_elevation","sfloat",[station_dim]) +stationelev.put_att("long_name","height above the geoid") +stationelev.put_att("standard_name","surface_altitude") +stationelev.put_att("units","m") + +stationinfo = file.def_var("station_info","int",[station_dim]) +stationinfo.put_att("long_name","station info") + +stationname = file.def_var("station_name","char",[name_dim, station_dim]) +stationname.put_att("cf_role", "timeseries_id") +stationname.put_att("long_name", "station name") + +alt = file.def_var("alt","sfloat",[station_dim]) +alt.put_att("long_name","vertical disance above the surface") +alt.put_att("standard_name","height") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") + +time = file.def_var("time","int",[obs_dim, station_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value", -999.9,"int") + +temp = file.def_var("temperature","sfloat",[obs_dim, station_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[obs_dim, station_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon alt") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +s = 10 + +alt.put(NArray.float(s).random!(10), "start" => [0], "end" => [s-1]) + +lat.put(NArray.int(s).random!(180), "start" => [0], "end" => [s-1]) +lon.put(NArray.int(s).random!(180), "start" => [0], "end" => [s-1]) + +blank = Array.new(name) +stats = (0..s-1).map{|n| ("Station-#{n}".split(//).map!{|d|d.ord} + blank)[0..name-1] } +stationname.put(stats, "start" => [0,0], "end" => [name-1,s-1]) + +stationinfo.put((0..s-1).map{|d|d}) + +stationelev.put(NArray.float(s).random!(5), "start" => [0], "end" => [s-1]) + +time.put(NArray.int(o).indgen!*3600, "start" => [0,0], "end" => [-1,0]) +time.put(NArray.int(o-10).indgen!*3600, "start" => [0,1], "end" => [o-11,1]) +time.put(NArray.int(o-5).indgen!*3600, "start" => [0,2], "end" => [o-6,2]) +time.put(NArray.int(o-3).indgen!*3600, "start" => [0,3], "end" => [o-4,3]) +time.put(NArray.int(o-16).indgen!*3600, "start" => [0,4], "end" => [o-17,4]) +time.put(NArray.int(o).indgen!*3600, "start" => [0,5], "end" => [-1,5]) +time.put(NArray.int(o).indgen!*3600, "start" => [0,6], "end" => [-1,6]) +time.put(NArray.int(o-4).indgen!*3600, "start" => [0,7], "end" => [o-5,7]) +time.put(NArray.int(o-10).indgen!*3600, "start" => [0,8], "end" => [o-11,8]) +time.put(NArray.int(o-8).indgen!*3600, "start" => [0,9], "end" => [o-9,9]) + +temp.put(NArray.int(o).random!(40), "start" => [0,0], "end" => [-1,0]) +temp.put(NArray.int(o-10).random!(40), "start" => [0,1], "end" => [o-11,1]) +temp.put(NArray.int(o-5).random!(40), "start" => [0,2], "end" => [o-6,2]) +temp.put(NArray.int(o-3).random!(40), "start" => [0,3], "end" => [o-4,3]) +temp.put(NArray.int(o-16).random!(40), "start" => [0,4], "end" => [o-17,4]) +temp.put(NArray.int(o).random!(40), "start" => [0,5], "end" => [-1,5]) +temp.put(NArray.int(o).random!(40), "start" => [0,6], "end" => [-1,6]) +temp.put(NArray.int(o-4).random!(40), "start" => [0,7], "end" => [o-5,7]) +temp.put(NArray.int(o-10).random!(40), "start" => [0,8], "end" => [o-11,8]) +temp.put(NArray.int(o-8).random!(40), "start" => [0,9], "end" => [o-9,9]) + +humi.put(NArray.int(o).random!(90), "start" => [0,0], "end" => [-1,0]) +humi.put(NArray.int(o-10).random!(90), "start" => [0,1], "end" => [o-11,1]) +humi.put(NArray.int(o-5).random!(90), "start" => [0,2], "end" => [o-6,2]) +humi.put(NArray.int(o-3).random!(90), "start" => [0,3], "end" => [o-4,3]) +humi.put(NArray.int(o-16).random!(90), "start" => [0,4], "end" => [o-17,4]) +humi.put(NArray.int(o).random!(90), "start" => [0,5], "end" => [-1,5]) +humi.put(NArray.int(o).random!(90), "start" => [0,6], "end" => [-1,6]) +humi.put(NArray.int(o-4).random!(90), "start" => [0,7], "end" => [o-5,7]) +humi.put(NArray.int(o-10).random!(90), "start" => [0,8], "end" => [o-11,8]) +humi.put(NArray.int(o-8).random!(90), "start" => [0,9], "end" => [o-9,9]) + + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/README b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/README new file mode 100644 index 000000000..7e4c75b40 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/README @@ -0,0 +1,5 @@ +** timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.cdl b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.cdl new file mode 100644 index 000000000..5b1d78139 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.cdl @@ -0,0 +1,51 @@ +netcdf timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2 { +dimensions: + station = UNLIMITED ; // (10 currently) + obs = 20 ; + name_strlen = 50 ; +variables: + float lat(station) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(station) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + float station_elevation(station) ; + station_elevation:long_name = "height above the geoid" ; + station_elevation:standard_name = "surface_altitude" ; + station_elevation:units = "m" ; + int station_info(station) ; + station_info:long_name = "station info" ; + char station_name(station, name_strlen) ; + station_name:cf_role = "timeseries_id" ; + station_name:long_name = "station name" ; + float alt(station) ; + alt:long_name = "vertical disance above the surface" ; + alt:standard_name = "height" ; + alt:units = "m" ; + alt:positive = "up" ; + alt:axis = "Z" ; + int time(station, obs) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float temperature(station, obs) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon alt" ; + temperature:missing_value = -999.9f ; + float humidity(station, obs) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon alt" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "timeSeries" ; +} diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.nc b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.nc new file mode 100644 index 000000000..8c3885df7 Binary files /dev/null and b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.nc differ diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.ncml b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.ncml new file mode 100644 index 000000000..73e7c3c97 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2/timeSeries-Incomplete-MultiDimensional-MultipleStations-H.2.2.ncml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.rb b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.rb new file mode 100644 index 000000000..bcdf936c0 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.rb @@ -0,0 +1,94 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8307552 + +All of the 'stations' in this file need to have the same 'time' values (they share the 'time' +variable as a dimension). This means that each of the wind sensors would need to be taking +measurements at exactly the same time. While rather unlikely, some post-processing of data +will normalize measurements to the even minute and this format might be useful. +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","timeSeries") + +s = 10 +t = 0 #UNLIMITED +name = 50 + +station_dim = file.def_dim("station",s) +time_dim = file.def_dim("time",t) +name_dim = file.def_dim("name_strlen",name) + + +lat = file.def_var("lat","sfloat",[station_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[station_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +stationname = file.def_var("station_name","char",[name_dim, station_dim]) +stationname.put_att("cf_role", "timeseries_id") +stationname.put_att("long_name", "station name") + +alt = file.def_var("alt","sfloat",[station_dim]) +alt.put_att("long_name","vertical disance above the surface") +alt.put_att("standard_name","height") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") + +time = file.def_var("time","int",[time_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +temp = file.def_var("temperature","sfloat",[station_dim, time_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[station_dim, time_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "lat lon alt") +humi.put_att("missing_value",-999.9,"sfloat") + + + +# Stop the definitions, lets write some data +file.enddef + +lat.put(NArray.int(s).random!(180)) +lon.put(NArray.int(s).random!(180)) + +blank = Array.new(name) + +stats = (0..s-1).map{|n| ("Station-#{n}".split(//).map!{|d|d.ord} + blank)[0..name-1] } +stationname.put(stats) + +#time.put(NArray.int(100).random!(3600), "start" => [0], "end" => [99]) +time.put(NArray.int(100).indgen!*3600, "start" => [0], "end" => [99]) +alt.put(NArray.float(s).random!(10)) + +temp.put(NArray.float(s,100).random!(40)) +humi.put(NArray.float(s,100).random!(90)) + + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/README b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/README new file mode 100644 index 000000000..fb677e45a --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/README @@ -0,0 +1,11 @@ +** timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1 ** + + +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8307552 + +All of the 'stations' in this file need to have the same 'time' values (they share the 'time' +variable as a dimension). This means that each of the wind sensors would need to be taking +measurements at exactly the same time. While rather unlikely, some post-processing of data +will normalize measurements to the even minute and this format might be useful. + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.cdl b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.cdl new file mode 100644 index 000000000..bd612b88a --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.cdl @@ -0,0 +1,45 @@ +netcdf timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1 { +dimensions: + station = 10 ; + time = UNLIMITED ; // (100 currently) + name_strlen = 50 ; +variables: + float lat(station) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(station) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + char station_name(station, name_strlen) ; + station_name:cf_role = "timeseries_id" ; + station_name:long_name = "station name" ; + float alt(station) ; + alt:long_name = "vertical disance above the surface" ; + alt:standard_name = "height" ; + alt:units = "m" ; + alt:positive = "up" ; + alt:axis = "Z" ; + int time(time) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float temperature(time, station) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "lat lon alt" ; + temperature:missing_value = -999.9f ; + float humidity(time, station) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "lat lon alt" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "timeSeries" ; +} diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.nc b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.nc new file mode 100644 index 000000000..11653f974 Binary files /dev/null and b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.nc differ diff --git a/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.ncml b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.ncml new file mode 100644 index 000000000..72daf0ece --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeries/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1/timeSeries-Orthogonal-Multidimenstional-MultipleStations-H.2.1.ncml @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.rb b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.rb new file mode 100644 index 000000000..726be2de6 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.rb @@ -0,0 +1,84 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","timeSeriesProfile") + +s = 2 +p = 4 +z = 30 +name = 50 +station_dim = file.def_dim("station",s) +profile_dim = file.def_dim("profile",p) +z_dim = file.def_dim("z",z) +name_dim = file.def_dim("name_strlen",name) + +lat = file.def_var("lat","float",[station_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","float",[station_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +stationinfo = file.def_var("station_info","int",[station_dim]) +stationinfo.put_att("long_name","station info") + +stationname = file.def_var("station_name","char",[name_dim, station_dim]) +stationname.put_att("cf_role", "timeseries_id") +stationname.put_att("long_name", "station name") + +alt = file.def_var("alt","float",[z_dim, profile_dim, station_dim]) +alt.put_att("standard_name","altitude") +alt.put_att("long_name", "height above mean sea level") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") + +time = file.def_var("time","int",[profile_dim, station_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +temp = file.def_var("temperature","sfloat",[z_dim, profile_dim, station_dim]) +temp.put_att("long_name","Water Temperature") +temp.put_att("standard_name","sea_water_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +lat.put([37.5, 32.5]) +lon.put([-76.5, -78.3]) +stationinfo.put([0,1]) + +blank = Array.new(name) +name1 = ("Station1".split(//).map!{|d|d.ord} + blank)[0..name-1] +name2 = ("Station2".split(//).map!{|d|d.ord} + blank)[0..name-1] + +stationname.put([[name1],[name2]]) + +time.put( NArray.int(s*p).indgen!*3600) + +alt.put(NArray.float(s*p*z).indgen!*2.5) + +data = NArray.float(s,p,z).indgen!*0.1 +temp.put(data) + + +file.close +nc.create_output \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/README b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/README new file mode 100644 index 000000000..e002464c7 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/README @@ -0,0 +1,5 @@ +** timeSeriesProfile-Multidimensional-MultipeStations-H.5.1 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.cdl b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.cdl new file mode 100644 index 000000000..55a7c59bd --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.cdl @@ -0,0 +1,42 @@ +netcdf timeSeriesProfile-Multidimensional-MultipeStations-H.5.1 { +dimensions: + station = 2 ; + profile = 4 ; + z = 30 ; + name_strlen = 50 ; +variables: + double lat(station) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + double lon(station) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int station_info(station) ; + station_info:long_name = "station info" ; + char station_name(station, name_strlen) ; + station_name:cf_role = "timeseries_id" ; + station_name:long_name = "station name" ; + double alt(station, profile, z) ; + alt:standard_name = "altitude" ; + alt:long_name = "height above mean sea level" ; + alt:units = "m" ; + alt:positive = "up" ; + alt:axis = "Z" ; + int time(station, profile) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float temperature(station, profile, z) ; + temperature:long_name = "Water Temperature" ; + temperature:standard_name = "sea_water_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon alt" ; + temperature:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "timeSeriesProfile" ; +} diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.nc b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.nc new file mode 100644 index 000000000..eda1d3494 Binary files /dev/null and b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.nc differ diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.ncml b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.ncml new file mode 100644 index 000000000..e8c117aa0 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Multidimensional-MultipeStations-H.5.1.ncml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.rb b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.rb new file mode 100644 index 000000000..d75cc1701 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.rb @@ -0,0 +1,78 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","timeSeriesProfile") + +p = 4 +z = 30 +name = 50 +profile_dim = file.def_dim("profile",p) +z_dim = file.def_dim("z",z) +name_dim = file.def_dim("name_strlen",name) + +lat = file.def_var("lat","float",[]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","float",[]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +stationinfo = file.def_var("station_info","int",[]) +stationinfo.put_att("long_name","station info") + +stationname = file.def_var("station_name","char",[name_dim]) +stationname.put_att("cf_role", "timeseries_id") +stationname.put_att("long_name", "station name") + +alt = file.def_var("alt","float",[z_dim, profile_dim]) +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +temp = file.def_var("temperature","sfloat",[z_dim, profile_dim]) +temp.put_att("long_name","Water Temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +lat.put([37.5]) +lon.put([-76.5]) +stationinfo.put([0]) + +blank = Array.new(name) +name1 = ("Station1".split(//).map!{|d|d.ord} + blank)[0..name-1] + +stationname.put([name1]) + +time.put( NArray.int(p).indgen!*3600) + +alt.put(NArray.float(p*z).indgen!*2.5) + +data = NArray.float(p,z).indgen!*0.1 +temp.put(data ) + + +file.close +nc.create_output \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/README b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/README new file mode 100644 index 000000000..f6db5f37a --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/README @@ -0,0 +1,5 @@ +** timeSeriesProfile-Multidimensional-SingleStation-H.5.2 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.cdl b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.cdl new file mode 100644 index 000000000..3a6140385 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.cdl @@ -0,0 +1,38 @@ +netcdf timeSeriesProfile-Multidimensional-SingleStation-H.5.2 { +dimensions: + profile = 4 ; + z = 30 ; + name_strlen = 50 ; +variables: + double lat ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + double lon ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int station_info ; + station_info:long_name = "station info" ; + char station_name(name_strlen) ; + station_name:cf_role = "timeseries_id" ; + station_name:long_name = "station name" ; + double alt(profile, z) ; + alt:units = "m" ; + alt:positive = "up" ; + alt:axis = "Z" ; + int time(profile) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float temperature(profile, z) ; + temperature:long_name = "Water Temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon alt" ; + temperature:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "timeSeriesProfile" ; +} diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.nc b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.nc new file mode 100644 index 000000000..81cf2cb7e Binary files /dev/null and b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.nc differ diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.ncml b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.ncml new file mode 100644 index 000000000..28c60e548 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Multidimensional-SingleStation-H.5.2/timeSeriesProfile-Multidimensional-SingleStation-H.5.2.ncml @@ -0,0 +1,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.rb b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.rb new file mode 100644 index 000000000..689e7f6df --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.rb @@ -0,0 +1,91 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","timeSeriesProfile") + +s = 2 +z = 4 +t = 0 # UNLIMITED +name = 50 + +station_dim = file.def_dim("station",s) +z_dim = file.def_dim("z",z) +name_dim = file.def_dim("name_strlen",name) +time_dim = file.def_dim("time",t) + +lat = file.def_var("lat","sfloat",[station_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[station_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +alt = file.def_var("alt","sfloat",[z_dim]) +alt.put_att("units","m") +alt.put_att("standard_name","altitude") +alt.put_att("long_name","height below mean sea level") +alt.put_att("positive","down") +alt.put_att("axis","Z") + +stationinfo = file.def_var("station_info","int",[station_dim]) +stationinfo.put_att("long_name","station info") + +stationname = file.def_var("station_name","char",[name_dim, station_dim]) +stationname.put_att("cf_role", "timeseries_id") +stationname.put_att("long_name", "station name") + +time = file.def_var("time","int",[time_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +temp = file.def_var("temperature","sfloat",[station_dim, z_dim, time_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[station_dim, z_dim, time_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon alt") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +lat.put([37.5, 32.5]) +lon.put([-76.5, -78.3]) +stationinfo.put([0,1]) + +blank = Array.new(name) +name1 = ("Station1".split(//).map!{|d|d.ord} + blank)[0..name-1] +name2 = ("Station2".split(//).map!{|d|d.ord} + blank)[0..name-1] + +stationname.put([[name1],[name2]]) + +time.put(NArray.int(100).indgen!*3600, "start" => [0], "end" => [99]) +alt.put(NArray.float(z).indgen!*10) + +temp.put(NArray.float(s,z,100).random!(40)) +humi.put(NArray.float(s,z,100).random!(90)) + + +file.close +nc.create_output \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/README b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/README new file mode 100644 index 000000000..ddb3c8294 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/README @@ -0,0 +1,5 @@ +** timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.cdl b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.cdl new file mode 100644 index 000000000..4d3798532 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.cdl @@ -0,0 +1,48 @@ +netcdf timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1 { +dimensions: + station = 2 ; + z = 4 ; + name_strlen = 50 ; + time = UNLIMITED ; // (100 currently) +variables: + float lat(station) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(station) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + float alt(z) ; + alt:units = "m" ; + alt:standard_name = "altitude" ; + alt:long_name = "height below mean sea level" ; + alt:positive = "down" ; + alt:axis = "Z" ; + int station_info(station) ; + station_info:long_name = "station info" ; + char station_name(station, name_strlen) ; + station_name:cf_role = "timeseries_id" ; + station_name:long_name = "station name" ; + int time(time) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float temperature(time, z, station) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon alt" ; + temperature:missing_value = -999.9f ; + float humidity(time, z, station) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon alt" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "timeSeriesProfile" ; +} diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.nc b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.nc new file mode 100644 index 000000000..c64ef971d Binary files /dev/null and b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.nc differ diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.ncml b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.ncml new file mode 100644 index 000000000..c84ded2dc --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1/timeSeriesProfile-Orthogonal-Multidimensional-MultipeStations-H.5.1.ncml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3.rb b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3.rb new file mode 100644 index 000000000..a20914128 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3.rb @@ -0,0 +1,101 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","timeSeriesProfile") + +s = 2 +p = 4 +o = 12 #UNLIMITED +name = 50 + +station_dim = file.def_dim("station",s) +profile_dim = file.def_dim("profile",p) +obs_dim = file.def_dim("obs",o) +name_dim = file.def_dim("name_strlen",name) + +lat = file.def_var("lat","float",[station_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","float",[station_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +stationinfo = file.def_var("station_info","int",[station_dim]) +stationinfo.put_att("long_name","station info") + +stationname = file.def_var("station_name","char",[name_dim, station_dim]) +stationname.put_att("cf_role", "timeseries_id") +stationname.put_att("long_name", "station name") + +profile = file.def_var("profile","int",[profile_dim]) +profile.put_att("cf_role", "profile_id") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +stationindex = file.def_var("station_index","int",[profile_dim]) +stationindex.put_att("long_name", "the station this profile is associated with") +stationindex.put_att("instance_dimension", "station") + +rowsize = file.def_var("row_size","int",[profile_dim]) +rowsize.put_att("long_name", "number of obs in this profile") +rowsize.put_att("sample_dimension", "obs") + +height = file.def_var("height","float",[obs_dim]) +height.put_att("long_name","height above sea surface") +height.put_att("standard_name","height") +height.put_att("units","meters") +height.put_att("axis","Z") +height.put_att("positive","up") + +temp = file.def_var("temperature","sfloat",[obs_dim]) +temp.put_att("standard_name","sea_water_temperature") +temp.put_att("long_name","Water Temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon height") +temp.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +lat.put([37.5, 32.5]) +lon.put([-76.5, -78.3]) +stationinfo.put([0,1]) +profile.put([0,1,2,3]) +stationindex.put([0,1,0,1]) +rowsize.put([2,4,2,4]) + +blank = Array.new(name) +name1 = ("Station1".split(//).map!{|d|d.ord} + blank)[0..name-1] +name2 = ("Station2".split(//).map!{|d|d.ord} + blank)[0..name-1] + +stationname.put([[name1],[name2]]) + +time.put( NArray.int(p).indgen!*3600) + +# row_size is 2,4,2,4 +# station_index is 0,1,0,1 +heights = [0.5,1.5] + [0.8,1.8,2.8,3.8] + [0.5,1.5] + [0.8,1.8,2.8,3.8] +temp_data = [6.7,6.9] + [7.6,7.7,7.9,8.0] + [6.7,7.0] + [8.2,7.7,7.8,9.1] +height.put(heights) +temp.put(temp_data) + + +file.close +nc.create_output \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/README b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/README new file mode 100644 index 000000000..edaefa3ee --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/README @@ -0,0 +1,5 @@ +** timeSeriesProfile-Ragged-MultipeStations-H.5.3 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.cdl b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.cdl new file mode 100644 index 000000000..0d881b79d --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.cdl @@ -0,0 +1,50 @@ +netcdf timeSeriesProfile-Ragged-MultipeStations-H.5.3 { +dimensions: + station = 2 ; + profile = 4 ; + obs = 12 ; + name_strlen = 50 ; +variables: + double lat(station) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + double lon(station) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int station_info(station) ; + station_info:long_name = "station info" ; + char station_name(station, name_strlen) ; + station_name:cf_role = "timeseries_id" ; + station_name:long_name = "station name" ; + int profile(profile) ; + profile:cf_role = "profile_id" ; + int time(profile) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + int station_index(profile) ; + station_index:long_name = "the station this profile is associated with" ; + station_index:instance_dimension = "station" ; + int row_size(profile) ; + row_size:long_name = "number of obs in this profile" ; + row_size:sample_dimension = "obs" ; + double height(obs) ; + height:long_name = "height above sea surface" ; + height:standard_name = "height" ; + height:units = "meters" ; + height:axis = "Z" ; + height:positive = "up" ; + float temperature(obs) ; + temperature:standard_name = "sea_water_temperature" ; + temperature:long_name = "Water Temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon height" ; + temperature:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "timeSeriesProfile" ; +} diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.nc b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.nc new file mode 100644 index 000000000..56db76f3a Binary files /dev/null and b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.nc differ diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.ncml b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.ncml new file mode 100644 index 000000000..0a3cd8303 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-MultipeStations-H.5.3/timeSeriesProfile-Ragged-MultipeStations-H.5.3.ncml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3.rb b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3.rb new file mode 100644 index 000000000..b79ccbdc8 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3.rb @@ -0,0 +1,91 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","timeSeriesProfile") + +p = 4 +o = 10 #UNLIMITED +name = 50 + +profile_dim = file.def_dim("profile",p) +obs_dim = file.def_dim("obs",o) +name_dim = file.def_dim("name_strlen",name) + +lat = file.def_var("lat","float",[]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","float",[]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +stationinfo = file.def_var("station_info","int",[]) +stationinfo.put_att("long_name","station info") + +stationname = file.def_var("station_name","char",[name_dim]) +stationname.put_att("cf_role", "timeseries_id") +stationname.put_att("long_name", "station name") + +profile = file.def_var("profile","int",[profile_dim]) +profile.put_att("cf_role", "profile_id") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +rowsize = file.def_var("row_size","int",[profile_dim]) +rowsize.put_att("long_name", "number of obs in this profile") +rowsize.put_att("sample_dimension", "obs") + +height = file.def_var("height","sfloat",[obs_dim]) +height.put_att("long_name","height above sea surface") +height.put_att("standard_name","height") +height.put_att("units","meters") +height.put_att("axis","Z") +height.put_att("positive","up") + +temp = file.def_var("temperature","sfloat",[obs_dim]) +temp.put_att("standard_name","sea_water_temperature") +temp.put_att("long_name","Water Temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon height") +temp.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +lat.put([37.5]) +lon.put([-76.5]) +stationinfo.put([0]) +profile.put([0,1,2,3]) +rowsize.put([2,2,3,3]) + +blank = Array.new(name) +name1 = ("Station1".split(//).map!{|d|d.ord} + blank)[0..name-1] +stationname.put([name1]) + +time.put( NArray.int(p).indgen!*3600) + +# row_size is 2,2,3,3 +heights = [0.5,1.5] + [0.5,1.5] + [0.5,1.5,2.5] + [0.5,1.5,2.5] +temp_data = [6.7,6.9] + [6.8,7.9] + [6.8,7.9,8.4] + [5.7,9.2,8.3] +height.put(heights) +temp.put(temp_data) + + +file.close +nc.create_output \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/README b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/README new file mode 100644 index 000000000..929519707 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/README @@ -0,0 +1,5 @@ +** timeSeriesProfile-Ragged-SingleStation-H.5.3 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.cdl b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.cdl new file mode 100644 index 000000000..41e8340ce --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.cdl @@ -0,0 +1,46 @@ +netcdf timeSeriesProfile-Ragged-SingleStation-H.5.3 { +dimensions: + profile = 4 ; + obs = 10 ; + name_strlen = 50 ; +variables: + double lat ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + double lon ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int station_info ; + station_info:long_name = "station info" ; + char station_name(name_strlen) ; + station_name:cf_role = "timeseries_id" ; + station_name:long_name = "station name" ; + int profile(profile) ; + profile:cf_role = "profile_id" ; + int time(profile) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + int row_size(profile) ; + row_size:long_name = "number of obs in this profile" ; + row_size:sample_dimension = "obs" ; + float height(obs) ; + height:long_name = "height above sea surface" ; + height:standard_name = "height" ; + height:units = "meters" ; + height:axis = "Z" ; + height:positive = "up" ; + float temperature(obs) ; + temperature:standard_name = "sea_water_temperature" ; + temperature:long_name = "Water Temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon height" ; + temperature:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "timeSeriesProfile" ; +} diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.nc b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.nc new file mode 100644 index 000000000..da8d74d96 Binary files /dev/null and b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.nc differ diff --git a/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.ncml b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.ncml new file mode 100644 index 000000000..f960edec9 --- /dev/null +++ b/src/test/resources/CFPointConventions/timeSeriesProfile/timeSeriesProfile-Ragged-SingleStation-H.5.3/timeSeriesProfile-Ragged-SingleStation-H.5.3.ncml @@ -0,0 +1,52 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.rb b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.rb new file mode 100644 index 000000000..9a5cfc4aa --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.rb @@ -0,0 +1,115 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8393872 +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","trajectory") + +t = 6 +o = 0 # UNLIMITED +name = 50 + +obs_dim = file.def_dim("obs",o) +trajectory_dim = file.def_dim("trajectory",t) +name_dim = file.def_dim("name_strlen",name) + +lat = file.def_var("lat","sfloat",[obs_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[obs_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +trajectory_info = file.def_var("trajectory_info","int",[trajectory_dim]) +trajectory_info.put_att("long_name", "trajectory info") +trajectory_info.put_att("missing_value",-999,"int") + +trajectory_name = file.def_var("trajectory_name","char",[name_dim, trajectory_dim]) +trajectory_name.put_att("cf_role", "trajectory_id") +trajectory_name.put_att("long_name", "trajectory name") + +rowsize = file.def_var("rowSize","int",[trajectory_dim]) +rowsize.put_att("long_name", "number of obs for this trajectory") +rowsize.put_att("sample_dimension", "obs") + +time = file.def_var("time","int",[obs_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("z","sfloat",[obs_dim]) +alt.put_att("long_name","height above mean sea level") +alt.put_att("standard_name","altitude") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999,"sfloat") + +temp = file.def_var("temperature","sfloat",[obs_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[obs_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +blank = Array.new(name) +traj_name_data = [] +(0..t-1).each do |i| + traj_name_data << [("Trajectory#{i}".split(//).map!{|d|d.ord} + blank)[0..name-1]] +end +trajectory_name.put(traj_name_data) + +# Fill the trajectory_info variable with increasing integers +trajectory_info.put(NArray.int(t).indgen!) + +random = Random.new + +# Stores the Row Sizes of each trajectory +sizes = [] + +# Iterate over each trajectory and generates random position and values +(0..t-1).each do |traj| + obs_so_far = sizes.inject(0,&:+) + os = random.rand(10..50) + sizes << os + + lat.put(NArray.float(os).random!(45), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + lon.put(NArray.float(os).random!(-76), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + time.put(NArray.int(os).indgen!*3600, "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + alt.put(NArray.float(os).indgen!, "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + temp.put(NArray.float(os).random!(40), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + humi.put(NArray.float(os).random!(80), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) +end + +rowsize.put([sizes]) + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/README b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/README new file mode 100644 index 000000000..a4950dc24 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/README @@ -0,0 +1,6 @@ +** trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3 ** + + +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8393872 + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.cdl b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.cdl new file mode 100644 index 000000000..2f57812ec --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.cdl @@ -0,0 +1,52 @@ +netcdf trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3 { +dimensions: + obs = UNLIMITED ; // (163 currently) + trajectory = 6 ; + name_strlen = 50 ; +variables: + float lat(obs) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(obs) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int trajectory_info(trajectory) ; + trajectory_info:long_name = "trajectory info" ; + trajectory_info:missing_value = -999 ; + char trajectory_name(trajectory, name_strlen) ; + trajectory_name:cf_role = "trajectory_id" ; + trajectory_name:long_name = "trajectory name" ; + int rowSize(trajectory) ; + rowSize:long_name = "number of obs for this trajectory" ; + rowSize:sample_dimension = "obs" ; + int time(obs) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float z(obs) ; + z:long_name = "height above mean sea level" ; + z:standard_name = "altitude" ; + z:units = "m" ; + z:positive = "up" ; + z:axis = "Z" ; + z:missing_value = -999.f ; + float temperature(obs) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(obs) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "trajectory" ; +} diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.nc b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.nc new file mode 100644 index 000000000..79def9185 Binary files /dev/null and b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.nc differ diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.ncml b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.ncml new file mode 100644 index 000000000..bff87d186 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3/trajectory-Contiguous-Ragged-MultipleTrajectories-H.4.3.ncml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.rb b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.rb new file mode 100644 index 000000000..99b93731d --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.rb @@ -0,0 +1,106 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8382496 +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","trajectory") + +t = 4 +o = 50 +name = 50 + +obs_dim = file.def_dim("obs",o) +trajectory_dim = file.def_dim("trajectory",t) +name_dim = file.def_dim("name_strlen",name) + +lat = file.def_var("lat","sfloat",[obs_dim, trajectory_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[obs_dim, trajectory_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +trajectory_info = file.def_var("trajectory_info","int",[trajectory_dim]) +trajectory_info.put_att("long_name", "trajectory info") +trajectory_info.put_att("missing_value",-999,"int") + +trajectory_name = file.def_var("trajectory_name","char",[name_dim, trajectory_dim]) +trajectory_name.put_att("cf_role", "trajectory_id") +trajectory_name.put_att("long_name", "trajectory name") + +time = file.def_var("time","int",[obs_dim, trajectory_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("z","sfloat",[obs_dim, trajectory_dim]) +alt.put_att("long_name","height above mean sea level") +alt.put_att("standard_name","altitude") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +temp = file.def_var("temperature","sfloat",[obs_dim, trajectory_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[obs_dim, trajectory_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +blank = Array.new(name) +traj_name_data = [] +(0..t-1).each do |i| + traj_name_data << [("Trajectory#{i}".split(//).map!{|d|d.ord} + blank)[0..name-1]] +end +trajectory_name.put(traj_name_data) + +# Fill the trajectory_info variable with increasing integers +trajectory_info.put(NArray.int(t).indgen!) + +# Iterate over each trajectory and generates random position and values +(0..t-1).each do |traj| + os = Random.rand(o-1) + 1 + + lat.put(NArray.float(os).random!(45), "start" => [0,traj], "end" => [os-1,traj]) + lat.put(NArray.float(o-os).fill(-999.9), "start" => [os,traj], "end" => [o-1,traj]) + + lon.put(NArray.float(os).random!(-76), "start" => [0,traj], "end" => [os-1,traj]) + lon.put(NArray.float(o-os).fill(-999.9), "start" => [os,traj], "end" => [o-1,traj]) + + time.put(NArray.int(os).indgen!*3600, "start" => [0,traj], "end" => [os-1,traj]) + time.put(NArray.int(o-os).fill(-999), "start" => [os,traj], "end" => [o-1,traj]) + + alt.put(NArray.float(os).indgen!, "start" => [0,traj], "end" => [os-1,traj]) + alt.put(NArray.float(o-os).fill(-999.9), "start" => [os,traj], "end" => [o-1,traj]) + temp.put(NArray.float(os).random!(40), "start" => [0,traj], "end" => [os-1,traj]) + temp.put(NArray.float(o-os).fill(-999.9), "start" => [os,traj], "end" => [o-1,traj]) + humi.put(NArray.float(os).random!(80), "start" => [0,traj], "end" => [os-1,traj]) + humi.put(NArray.float(o-os).fill(-999.9), "start" => [os,traj], "end" => [o-1,traj]) +end + +file.close +nc.create_output \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/README b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/README new file mode 100644 index 000000000..1eed3c667 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/README @@ -0,0 +1,6 @@ +** trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1 ** + + +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8382496 + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.cdl b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.cdl new file mode 100644 index 000000000..5294c8c71 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.cdl @@ -0,0 +1,49 @@ +netcdf trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1 { +dimensions: + obs = 50 ; + trajectory = 4 ; + name_strlen = 50 ; +variables: + float lat(trajectory, obs) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(trajectory, obs) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int trajectory_info(trajectory) ; + trajectory_info:long_name = "trajectory info" ; + trajectory_info:missing_value = -999 ; + char trajectory_name(trajectory, name_strlen) ; + trajectory_name:cf_role = "trajectory_id" ; + trajectory_name:long_name = "trajectory name" ; + int time(trajectory, obs) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float z(trajectory, obs) ; + z:long_name = "height above mean sea level" ; + z:standard_name = "altitude" ; + z:units = "m" ; + z:positive = "up" ; + z:axis = "Z" ; + z:missing_value = -999.9f ; + float temperature(trajectory, obs) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(trajectory, obs) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "trajectory" ; +} diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.nc b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.nc new file mode 100644 index 000000000..16b7d73f5 Binary files /dev/null and b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.nc differ diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.ncml b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.ncml new file mode 100644 index 000000000..72ae7fde5 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1/trajectory-Incomplete-Multidimensional-MultipleTrajectories-H.4.1.ncml @@ -0,0 +1,54 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.rb b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.rb new file mode 100644 index 000000000..977888621 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.rb @@ -0,0 +1,88 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8388800 +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","trajectory") + +tm = 100 +name = 50 + +time_dim = file.def_dim("time",tm) +name_dim = file.def_dim("name_strlen",name) + +lat = file.def_var("lat","sfloat",[time_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[time_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +trajectory_info = file.def_var("trajectory_info","int",[]) +trajectory_info.put_att("long_name", "trajectory info") +trajectory_info.put_att("missing_value",-999,"int") + +trajectory_name = file.def_var("trajectory_name","char",[name_dim]) +trajectory_name.put_att("cf_role", "trajectory_id") +trajectory_name.put_att("long_name", "trajectory name") + +time = file.def_var("time","int",[time_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("z","sfloat",[time_dim]) +alt.put_att("long_name","height above mean sea level") +alt.put_att("standard_name","altitude") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +temp = file.def_var("temperature","sfloat",[time_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[time_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +blank = Array.new(name) +name1 = [("Trajectory1".split(//).map!{|d|d.ord} + blank)[0..name-1]] +trajectory_name.put([name1]) + +# Fill the trajectory_info variable with increasing integers +trajectory_info.put(0) + +lat.put(NArray.float(tm).random!(45)) +lon.put(NArray.float(tm).random!(-76)) +time.put(NArray.int(tm).indgen!*3600) +alt.put(NArray.float(tm).indgen!) +temp.put(NArray.float(tm).random!(40)) +humi.put(NArray.float(tm).random!(80)) + + +file.close +nc.create_output \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/README b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/README new file mode 100644 index 000000000..66dd59909 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/README @@ -0,0 +1,6 @@ +** trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2 ** + + +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8388800 + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.cdl b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.cdl new file mode 100644 index 000000000..dd34e4c4f --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.cdl @@ -0,0 +1,48 @@ +netcdf trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2 { +dimensions: + time = 100 ; + name_strlen = 50 ; +variables: + float lat(time) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(time) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int trajectory_info ; + trajectory_info:long_name = "trajectory info" ; + trajectory_info:missing_value = -999 ; + char trajectory_name(name_strlen) ; + trajectory_name:cf_role = "trajectory_id" ; + trajectory_name:long_name = "trajectory name" ; + int time(time) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float z(time) ; + z:long_name = "height above mean sea level" ; + z:standard_name = "altitude" ; + z:units = "m" ; + z:positive = "up" ; + z:axis = "Z" ; + z:missing_value = -999.9f ; + float temperature(time) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(time) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "trajectory" ; +} diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.nc b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.nc new file mode 100644 index 000000000..5a982081e Binary files /dev/null and b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.nc differ diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.ncml b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.ncml new file mode 100644 index 000000000..d26ab25d7 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2/trajectory-Incomplete-Multidimensional-SingleTrajectory-H.4.2.ncml @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.rb b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.rb new file mode 100644 index 000000000..5c853d6e8 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.rb @@ -0,0 +1,117 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8399648 +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","trajectory") + +t = 10 +o = 0 # UNLIMITED +name = 50 + +obs_dim = file.def_dim("obs",o) +trajectory_dim = file.def_dim("trajectory",t) +name_dim = file.def_dim("name_strlen",name) + +lat = file.def_var("lat","sfloat",[obs_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[obs_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +trajectory_info = file.def_var("trajectory_info","int",[trajectory_dim]) +trajectory_info.put_att("long_name", "trajectory info") +trajectory_info.put_att("missing_value",-999,"int") + +trajectory_name = file.def_var("trajectory_name","char",[name_dim, trajectory_dim]) +trajectory_name.put_att("cf_role", "trajectory_id") +trajectory_name.put_att("long_name", "trajectory name") + +trajectory_index = file.def_var("trajectory_index","int",[obs_dim]) +trajectory_index.put_att("long_name", "index of trajectory this obs belongs to") +trajectory_index.put_att("instance_dimension", "trajectory") + +time = file.def_var("time","int",[obs_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("z","sfloat",[obs_dim]) +alt.put_att("long_name","height above mean sea level") +alt.put_att("standard_name","altitude") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +temp = file.def_var("temperature","sfloat",[obs_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[obs_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +blank = Array.new(name) +traj_name_data = [] +(0..t-1).each do |i| + traj_name_data << [("Trajectory#{i}".split(//).map!{|d|d.ord} + blank)[0..name-1]] +end +trajectory_name.put(traj_name_data) + +# Fill the trajectory_info variable with increasing integers +trajectory_info.put(NArray.int(t).indgen!) + +random = Random.new + +# Stores the Row Sizes of each trajectory +sizes = [] + +# Iterate over each trajectory and generates random position and values +(0..t-1).each do |traj| + obs_so_far = sizes.inject(0,&:+) + os = random.rand(10..30) + sizes << os + + trajectory_index.put(NArray.int(os).random!(t), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + lat.put(NArray.float(os).random!(45), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + lon.put(NArray.float(os).random!(-76), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + timedata = NArray.int(os).random!(50) + multdata = NArray.int(os).fill!(3600) + time.put(timedata * multdata, "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + alt.put(NArray.float(os).random!(30), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + temp.put(NArray.float(os).random!(40), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + + humi.put(NArray.float(os).random!(80), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) +end + +file.close +nc.create_output \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/README b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/README new file mode 100644 index 000000000..d5e9dae9e --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/README @@ -0,0 +1,6 @@ +** trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4 ** + + +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8399648 + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.cdl b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.cdl new file mode 100644 index 000000000..dbf9f43ce --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.cdl @@ -0,0 +1,52 @@ +netcdf trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4 { +dimensions: + obs = UNLIMITED ; // (213 currently) + trajectory = 10 ; + name_strlen = 50 ; +variables: + float lat(obs) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(obs) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int trajectory_info(trajectory) ; + trajectory_info:long_name = "trajectory info" ; + trajectory_info:missing_value = -999 ; + char trajectory_name(trajectory, name_strlen) ; + trajectory_name:cf_role = "trajectory_id" ; + trajectory_name:long_name = "trajectory name" ; + int trajectory_index(obs) ; + trajectory_index:long_name = "index of trajectory this obs belongs to" ; + trajectory_index:instance_dimension = "trajectory" ; + int time(obs) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float z(obs) ; + z:long_name = "height above mean sea level" ; + z:standard_name = "altitude" ; + z:units = "m" ; + z:positive = "up" ; + z:axis = "Z" ; + z:missing_value = -999.9f ; + float temperature(obs) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(obs) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "trajectory" ; +} diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.nc b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.nc new file mode 100644 index 000000000..a3d7e8ee4 Binary files /dev/null and b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.nc differ diff --git a/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.ncml b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.ncml new file mode 100644 index 000000000..5d67a6acb --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectory/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4/trajectory-Indexed-Ragged-MultipleTrajectories-H.4.4.ncml @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.rb b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.rb new file mode 100644 index 000000000..c53a5f0b9 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.rb @@ -0,0 +1,112 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +"http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8443504 * + +This assumes that there are the same number of profiles for all +trajectories, and the same number of vertical level for every profile. + +Use case: + +Unlimited Dimension: + Any of the three dimensions (profile, trajectory, or z) can be the + NetCDF unlimited dimension if it might be useful to enlarge it. + One must know the maximum size of the non-unlimited dimensions before file creation. +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","trajectoryProfile") + +t = 0 # UNLIMITED +p = 10 +z = 8 + +trajectory_dim = file.def_dim("trajectory",t) +profile_dim = file.def_dim("profile",p) +z_dim = file.def_dim("z",z) + +lat = file.def_var("lat","sfloat",[profile_dim, trajectory_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","Latitude") +lat.put_att("standard_name","latitude") +lat.put_att("missing_value",-999.9,"sfloat") + +lon = file.def_var("lon","sfloat",[profile_dim, trajectory_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","Longitude") +lon.put_att("standard_name","longitude") +lon.put_att("missing_value",-999.9,"sfloat") + +trajectory = file.def_var("trajectory","int",[trajectory_dim]) +trajectory.put_att("cf_role","trajectory_id") + +alt = file.def_var("alt","sfloat",[z_dim, profile_dim, trajectory_dim]) +alt.put_att("standard_name","altitude") +alt.put_att("long_name", "height below mean sea level") +alt.put_att("units","m") +alt.put_att("positive","down") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +time = file.def_var("time","int",[profile_dim, trajectory_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +temp = file.def_var("temperature","sfloat",[z_dim, profile_dim, trajectory_dim]) +temp.put_att("long_name","Water Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +salt = file.def_var("salinity","sfloat",[z_dim, profile_dim, trajectory_dim]) +salt.put_att("long_name","Sea Water Salinity") +salt.put_att("standard_name","sea_water_salinity") +salt.put_att("units","PSU") +salt.put_att("coordinates", "time lat lon alt") +salt.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +num_t = 6 + +trajectory.put( NArray.int(num_t).indgen!, "start" => [0], "end" => [num_t - 1]) + +random = Random.new + +# Iterate over each trajectory and generate a random number of profiles and depths +# for each +(0..num_t-1).each do |traj| + ps = Random.rand(p-1) + 1 + dep = Random.rand(z-1) + 1 + + lat.put(NArray.float(ps).random!(45), "start" => [0,traj], "end" => [ps-1,traj]) + lat.put(NArray.float(p-ps).fill(-999.9), "start" => [ps,traj], "end" => [p-1,traj]) + + lon.put(NArray.float(ps).random!(-76), "start" => [0,traj], "end" => [ps-1,traj]) + lon.put(NArray.float(p-ps).fill(-999.9), "start" => [ps,traj], "end" => [p-1,traj]) + + time.put(NArray.float(ps).indgen!*3600, "start" => [0,traj], "end" => [ps-1,traj]) + time.put(NArray.int(p-ps).fill(-999), "start" => [ps,traj], "end" => [p-1,traj]) + + (0..ps-1).each do |set| + alt.put(NArray.float(dep).indgen!, "start" => [0,set,traj], "end" => [dep-1,set,traj]) + alt.put(NArray.float(z-dep).fill(-999.9), "start" => [dep,set,traj], "end" => [z-1,set,traj]) + temp.put(NArray.float(dep).random!(40), "start" => [0,set,traj], "end" => [dep-1,set,traj]) + temp.put(NArray.float(z-dep).fill(-999.9), "start" => [dep,set,traj], "end" => [z-1,set,traj]) + salt.put(NArray.float(dep).random!(80), "start" => [0,set,traj], "end" => [dep-1,set,traj]) + salt.put(NArray.float(z-dep).fill(-999.9), "start" => [dep,set,traj], "end" => [z-1,set,traj]) + end +end + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/README b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/README new file mode 100644 index 000000000..e76ec06d4 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/README @@ -0,0 +1,15 @@ +** trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1 ** + + http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8443504 * + +This assumes that there are the same number of profiles for all +trajectories, and the same number of vertical level for every profile. + +Use case: + +Unlimited Dimension: + Any of the three dimensions (profile, trajectory, or z) can be the + NetCDF unlimited dimension if it might be useful to enlarge it. + One must know the maximum size of the non-unlimited dimensions before file creation. + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.cdl b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.cdl new file mode 100644 index 000000000..789e3cd06 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.cdl @@ -0,0 +1,47 @@ +netcdf trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1 { +dimensions: + trajectory = UNLIMITED ; // (6 currently) + profile = 10 ; + z = 8 ; +variables: + float lat(trajectory, profile) ; + lat:units = "degrees_north" ; + lat:long_name = "Latitude" ; + lat:standard_name = "latitude" ; + lat:missing_value = -999.9f ; + float lon(trajectory, profile) ; + lon:units = "degrees_east" ; + lon:long_name = "Longitude" ; + lon:standard_name = "longitude" ; + lon:missing_value = -999.9f ; + int trajectory(trajectory) ; + trajectory:cf_role = "trajectory_id" ; + float alt(trajectory, profile, z) ; + alt:standard_name = "altitude" ; + alt:long_name = "height below mean sea level" ; + alt:units = "m" ; + alt:positive = "down" ; + alt:axis = "Z" ; + alt:missing_value = -999.9f ; + int time(trajectory, profile) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float temperature(trajectory, profile, z) ; + temperature:long_name = "Water Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon alt" ; + temperature:missing_value = -999.9f ; + float salinity(trajectory, profile, z) ; + salinity:long_name = "Sea Water Salinity" ; + salinity:standard_name = "sea_water_salinity" ; + salinity:units = "PSU" ; + salinity:coordinates = "time lat lon alt" ; + salinity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "trajectoryProfile" ; +} diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.nc b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.nc new file mode 100644 index 000000000..a7439fb73 Binary files /dev/null and b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.nc differ diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.ncml b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.ncml new file mode 100644 index 000000000..0d5dea5ef --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1/trajectoryProfile-Multidimensional-MultipleTrajectories-H.6.1.ncml @@ -0,0 +1,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.rb b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.rb new file mode 100644 index 000000000..b8521a55f --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.rb @@ -0,0 +1,92 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8451344 +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","trajectoryProfile") + +p = 0 # UNLIMITED +z = 8 + +profile_dim = file.def_dim("profile",p) +z_dim = file.def_dim("z",z) + +lat = file.def_var("lat","sfloat",[profile_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","Latitude") +lat.put_att("standard_name","latitude") +lat.put_att("missing_value",-999.9,"sfloat") + +lon = file.def_var("lon","sfloat",[profile_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","Longitude") +lon.put_att("standard_name","longitude") +lon.put_att("missing_value",-999.9,"sfloat") + +trajectory = file.def_var("trajectory","int",[]) +trajectory.put_att("cf_role","trajectory_id") + +alt = file.def_var("alt","sfloat",[z_dim, profile_dim]) +alt.put_att("standard_name","altitude") +alt.put_att("long_name", "height below mean sea level") +alt.put_att("units","m") +alt.put_att("positive","down") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999.9,"sfloat") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +temp = file.def_var("temperature","sfloat",[z_dim, profile_dim]) +temp.put_att("long_name","Water Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon alt") +temp.put_att("missing_value",-999.9,"sfloat") + +salt = file.def_var("salinity","sfloat",[z_dim, profile_dim]) +salt.put_att("long_name","Sea Water Salinity") +salt.put_att("standard_name","sea_water_salinity") +salt.put_att("units","PSU") +salt.put_att("coordinates", "time lat lon alt") +salt.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +num_p = 6 + +trajectory.put([0]) + +random = Random.new + +time.put(NArray.float(num_p).indgen!*3600, "start" => [0], "end" => [num_p-1]) +lat.put(NArray.float(num_p).random!(45), "start" => [0], "end" => [num_p-1]) +lon.put(NArray.float(num_p).random!(-76), "start" => [0], "end" => [num_p-1]) + +# Iterate over each profile and generate a random number of depths for each +(0..num_p-1).each do |set| + ps = Random.rand(num_p-1) + 1 + dep = Random.rand(z-1) + 1 + alt.put(NArray.float(dep).indgen!, "start" => [0,set], "end" => [dep-1,set]) + alt.put(NArray.float(z-dep).fill(-999.9), "start" => [dep,set], "end" => [z-1,set]) + temp.put(NArray.float(dep).random!(40), "start" => [0,set], "end" => [dep-1,set]) + temp.put(NArray.float(z-dep).fill(-999.9), "start" => [dep,set], "end" => [z-1,set]) + salt.put(NArray.float(dep).random!(80), "start" => [0,set], "end" => [dep-1,set]) + salt.put(NArray.float(z-dep).fill(-999.9), "start" => [dep,set], "end" => [z-1,set]) +end + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/README b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/README new file mode 100644 index 000000000..dc1277bb0 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/README @@ -0,0 +1,6 @@ +** trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2 ** + + +http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#idp8451344 + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.cdl b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.cdl new file mode 100644 index 000000000..80e4b37c1 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.cdl @@ -0,0 +1,46 @@ +netcdf trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2 { +dimensions: + profile = UNLIMITED ; // (6 currently) + z = 8 ; +variables: + float lat(profile) ; + lat:units = "degrees_north" ; + lat:long_name = "Latitude" ; + lat:standard_name = "latitude" ; + lat:missing_value = -999.9f ; + float lon(profile) ; + lon:units = "degrees_east" ; + lon:long_name = "Longitude" ; + lon:standard_name = "longitude" ; + lon:missing_value = -999.9f ; + int trajectory ; + trajectory:cf_role = "trajectory_id" ; + float alt(profile, z) ; + alt:standard_name = "altitude" ; + alt:long_name = "height below mean sea level" ; + alt:units = "m" ; + alt:positive = "down" ; + alt:axis = "Z" ; + alt:missing_value = -999.9f ; + int time(profile) ; + time:long_name = "time" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float temperature(profile, z) ; + temperature:long_name = "Water Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon alt" ; + temperature:missing_value = -999.9f ; + float salinity(profile, z) ; + salinity:long_name = "Sea Water Salinity" ; + salinity:standard_name = "sea_water_salinity" ; + salinity:units = "PSU" ; + salinity:coordinates = "time lat lon alt" ; + salinity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "trajectoryProfile" ; +} diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.nc b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.nc new file mode 100644 index 000000000..618fc3cc6 Binary files /dev/null and b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.nc differ diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.ncml b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.ncml new file mode 100644 index 000000000..80abab5d1 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2/trajectoryProfile-Multidimensional-SingleTrajectory-H.6.2.ncml @@ -0,0 +1,50 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.rb b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.rb new file mode 100644 index 000000000..11c07690c --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.rb @@ -0,0 +1,117 @@ +#! ruby + +require 'numru/netcdf' +require_relative '../utils' + +include NumRu + +readme = \ +" +" + +nc = CFNetCDF.new(__FILE__, readme) +file = nc.netcdf_file +file.put_att("featureType","trajectoryProfile") + +o = 0 # UNLIMITED +p = 20 +t = 5 + +obs_dim = file.def_dim("obs",o) +profile_dim = file.def_dim("profile",p) +trajectory_dim = file.def_dim("trajectory",t) + +trajectory = file.def_var("trajectory","int",[trajectory_dim]) +trajectory.put_att("cf_role", "trajectory_id") + +lat = file.def_var("lat","sfloat",[profile_dim]) +lat.put_att("units","degrees_north") +lat.put_att("long_name","station latitude") +lat.put_att("standard_name","latitude") + +lon = file.def_var("lon","sfloat",[profile_dim]) +lon.put_att("units","degrees_east") +lon.put_att("long_name","station longitude") +lon.put_att("standard_name","longitude") + +rowsize = file.def_var("rowSize","int",[profile_dim]) +rowsize.put_att("long_name", "number of obs for this trajectory") +rowsize.put_att("sample_dimension", "obs") + +trajectory_index = file.def_var("trajectory_index","int",[profile_dim]) +trajectory_index.put_att("long_name", "which trajectory this profile is for") +trajectory_index.put_att("instance_dimension", "trajectory") + +time = file.def_var("time","int",[profile_dim]) +time.put_att("long_name","time of measurement") +time.put_att("standard_name","time") +time.put_att("units","seconds since 1990-01-01 00:00:00") +time.put_att("missing_value",-999,"int") + +alt = file.def_var("z","sfloat",[obs_dim]) +alt.put_att("long_name","height above mean sea level") +alt.put_att("standard_name","altitude") +alt.put_att("units","m") +alt.put_att("positive","up") +alt.put_att("axis","Z") +alt.put_att("missing_value",-999,"sfloat") + +temp = file.def_var("temperature","sfloat",[obs_dim]) +temp.put_att("long_name","Air Temperature") +temp.put_att("standard_name","air_temperature") +temp.put_att("units","Celsius") +temp.put_att("coordinates", "time lat lon z") +temp.put_att("missing_value",-999.9,"sfloat") + +humi = file.def_var("humidity","sfloat",[obs_dim]) +humi.put_att("long_name","Humidity") +humi.put_att("standard_name","specific_humidity") +humi.put_att("units","Percent") +humi.put_att("coordinates", "time lat lon z") +humi.put_att("missing_value",-999.9,"sfloat") + +# Stop the definitions, lets write some data +file.enddef + +random = Random.new + +# Profiles per trajectory +ppj = (p/t).floor + +# Stores the Row Sizes of each trajectory +sizes = [] +# Stores the # of profiles +psizes = [] + +trajectory.put(NArray.int(t).indgen!) + +# Iterate over each trajectory and generates random profiles and values +(0..t-1).each do |traj| + ps_so_far = psizes.inject(0,&:+) + psizes << ppj + + (0..ppj-1).each do |prof| + obs_so_far = sizes.inject(0,&:+) + os = random.rand(10..50) + sizes << os + + # Indexes + trajectory_index.put([traj], "start" => [ps_so_far + prof], "end" => [ps_so_far + prof]) + rowsize.put(os, "start" => [ps_so_far + prof], "end" => [ps_so_far + prof]) + timedata = random.rand(0..50) + multdata = 3600 + time.put(timedata * multdata, "start" => [ps_so_far + prof], "end" => [ps_so_far + prof]) + # Lat/lon + lat.put(random.rand(40..60), "start" => [ps_so_far + prof], "end" => [ps_so_far + prof]) + lon.put(random.rand(-76..-40), "start" => [ps_so_far + prof], "end" => [ps_so_far + prof]) + + # Data vars (obs) + alt.put(NArray.float(os).indgen!, "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + temp.put(NArray.float(os).random!(40), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + humi.put(NArray.float(os).random!(80), "start" => [obs_so_far], "end" => [obs_so_far + os - 1]) + end + +end + +file.close +nc.create_output diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/README b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/README new file mode 100644 index 000000000..9e5678479 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/README @@ -0,0 +1,5 @@ +** trajectoryProfile-Ragged-MultipleTrajectories-H.6.3 ** + + + + \ No newline at end of file diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.cdl b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.cdl new file mode 100644 index 000000000..af39302a8 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.cdl @@ -0,0 +1,51 @@ +netcdf trajectoryProfile-Ragged-MultipleTrajectories-H.6.3 { +dimensions: + obs = UNLIMITED ; // (594 currently) + profile = 20 ; + trajectory = 5 ; +variables: + int trajectory(trajectory) ; + trajectory:cf_role = "trajectory_id" ; + float lat(profile) ; + lat:units = "degrees_north" ; + lat:long_name = "station latitude" ; + lat:standard_name = "latitude" ; + float lon(profile) ; + lon:units = "degrees_east" ; + lon:long_name = "station longitude" ; + lon:standard_name = "longitude" ; + int rowSize(profile) ; + rowSize:long_name = "number of obs for this trajectory" ; + rowSize:sample_dimension = "obs" ; + int trajectory_index(profile) ; + trajectory_index:long_name = "which trajectory this profile is for" ; + trajectory_index:instance_dimension = "trajectory" ; + int time(profile) ; + time:long_name = "time of measurement" ; + time:standard_name = "time" ; + time:units = "seconds since 1990-01-01 00:00:00" ; + time:missing_value = -999 ; + float z(obs) ; + z:long_name = "height above mean sea level" ; + z:standard_name = "altitude" ; + z:units = "m" ; + z:positive = "up" ; + z:axis = "Z" ; + z:missing_value = -999.f ; + float temperature(obs) ; + temperature:long_name = "Air Temperature" ; + temperature:standard_name = "air_temperature" ; + temperature:units = "Celsius" ; + temperature:coordinates = "time lat lon z" ; + temperature:missing_value = -999.9f ; + float humidity(obs) ; + humidity:long_name = "Humidity" ; + humidity:standard_name = "specific_humidity" ; + humidity:units = "Percent" ; + humidity:coordinates = "time lat lon z" ; + humidity:missing_value = -999.9f ; + +// global attributes: + :Conventions = "CF-1.6" ; + :featureType = "trajectoryProfile" ; +} diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.nc b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.nc new file mode 100644 index 000000000..fb3655b56 Binary files /dev/null and b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.nc differ diff --git a/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.ncml b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.ncml new file mode 100644 index 000000000..e0101b042 --- /dev/null +++ b/src/test/resources/CFPointConventions/trajectoryProfile/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3/trajectoryProfile-Ragged-MultipleTrajectories-H.6.3.ncml @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/test/resources/CFPointConventions/utils.rb b/src/test/resources/CFPointConventions/utils.rb new file mode 100644 index 000000000..01054a5ae --- /dev/null +++ b/src/test/resources/CFPointConventions/utils.rb @@ -0,0 +1,32 @@ +require 'fileutils' + +class CFNetCDF + + attr_accessor :netcdf_file + + def initialize(file_name,readme) + @base_name = File.basename(file_name).gsub(".rb","") + root_path = File.dirname(file_name) + "/" + @base_name + @netcdf_path = root_path + "/" + @base_name + ".nc" + @ncml_path = root_path + "/" + @base_name + ".ncml" + @cdl_path = root_path + "/" + @base_name + ".cdl" + @readme_path = root_path + "/README" + FileUtils.mkdir(root_path) unless File.exists?(root_path) + + @netcdf_file = NetCDF.create(@netcdf_path) + @netcdf_file.put_att("Conventions","CF-1.6") + + @readme = \ + "** #{@base_name} ** + + #{readme} + " + end + + def create_output + `ncdump -h #{@netcdf_path} > #{@cdl_path}` + `ncdump -x -h #{@netcdf_path} > #{@ncml_path}` + open(@readme_path,"w"){|f| f.write(@readme)} + end + +end \ No newline at end of file diff --git a/src/test/resources/LICENSE.txt b/src/test/resources/LICENSE.txt new file mode 100644 index 000000000..0968e26ac --- /dev/null +++ b/src/test/resources/LICENSE.txt @@ -0,0 +1,23 @@ +All of the computer files distributed as part of the EMA project (notably, +the files in the com.cohort.array, com.cohort.util and com.cohort.ema +packages) are Copyright (c) 2005 Robert Alten Simons (info@cohort.com). + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is furnished +to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. + +(This is license is like the MIT/X License.) diff --git a/src/test/resources/aws/xml/SNFLS-2012-11-03T20_30_01Z.xml b/src/test/resources/aws/xml/SNFLS-2012-11-03T20_30_01Z.xml new file mode 100644 index 000000000..4603e94cf --- /dev/null +++ b/src/test/resources/aws/xml/SNFLS-2012-11-03T20_30_01Z.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + SNFLS + Exploratorium + San Francisco, CA + + 32 + 0 + 54 + 0 + 67 + + + + + + + + + + + E + 8 + 63 + 100 + 63 + -6 + 90 + +4.6 + 67.9 + -0.3 + 82 + 30.1 + 30.14 + 30.06 + -0.01 + 0.21 + 0 + 0 + 0 + 1.76 + 66.9 + 67 + 52 + 3.8 + + + + + + + + + + + + + + + + + + + + + 59.162 + 0 + 2 + ENE + E + + \ No newline at end of file diff --git a/src/test/resources/aws/xml/SNFLS-2012-11-03T20_30_01Z.xmlNotPretty b/src/test/resources/aws/xml/SNFLS-2012-11-03T20_30_01Z.xmlNotPretty new file mode 100644 index 000000000..b118a6dc0 --- /dev/null +++ b/src/test/resources/aws/xml/SNFLS-2012-11-03T20_30_01Z.xmlNotPretty @@ -0,0 +1 @@ +SNFLSExploratoriumSan Francisco, CA32054067E86310063-690+4.667.9-0.38230.130.1430.06-0.010.210001.7666.967523.859.16202ENEE \ No newline at end of file diff --git a/src/test/resources/cPostDet3.files.json.gz b/src/test/resources/cPostDet3.files.json.gz new file mode 100644 index 000000000..c5737d67f Binary files /dev/null and b/src/test/resources/cPostDet3.files.json.gz differ diff --git a/src/test/resources/columnarAsciiWithComments.txt b/src/test/resources/columnarAsciiWithComments.txt new file mode 100644 index 000000000..6d0086d01 --- /dev/null +++ b/src/test/resources/columnarAsciiWithComments.txt @@ -0,0 +1,27 @@ +This is a header line. +END OF HEADER +% a comment line +Will be skipped because dataStartsLine=3: 0-length lines at the end of the file are intentional +012345678911234567892123456789312345678941234567895123456789612345678971234567898123456 +% a comment line will all kinds of text to muck up the column detector algorithm +aString aChar aBoolean aByte aShort anInt aLong aFloat aDouble +% a comment line will all kinds of text to muck up the column detector algorithm +abcdef Ab t 24 24000 240000002400000000002.4 2.412345678987654 +short: +fg F true 11 12001 1200000 12000000000 1.21 1e200 +%fg F true 11 12001 1200000 12000000000 1.21 1e200 +%h H 1 12 12002 120000 1200000000 1.22 2e200 +h H 1 12 12002 120000 1200000000 1.22 2e200 +i I TRUE 13 12003 12000 120000000 1.23 3e200 +j J f 14 12004 1200 12000000 1.24 4e200 +k K false 15 12005 120 1200000 1.25 5e200 +l L 0 16 12006 12 120000 1.26 6e200 +m M FALSE 17 12007 121 12000 1.27 7e200 +n N 8 18 12008 122 1200 1.28 8e200 + + + + + + + diff --git a/src/test/resources/csvAscii.txt b/src/test/resources/csvAscii.txt new file mode 100644 index 000000000..3deff9394 --- /dev/null +++ b/src/test/resources/csvAscii.txt @@ -0,0 +1,29 @@ +this is a header line +# this is another header line +*** END OF HEADER +# this is a comment +aString, aChar, aBoolean, aByte, aShort, anInt, aLong, aFloat, aDouble +# this is a comment +" b,d ", Ab, t, 24, 24000, 24000000,240000000000,2.4, 2.412345678987654 +# this is a comment +needs,1comma: +# this is a comment +fg,F,true, 11, 12001, 1200000, 12000000000, 1.21, 1e200 +# this is a comment +# this is a comment +h, H, 1, 12, 12002, 120000 , 1200000000, 1.22, 2e200 +i, I, TRUE, 13, 12003, 12000 , 120000000 , 1.23, 3e200 +j, J, f, 14, 12004, 1200 , 12000000 , 1.24, 4e200 +k, K, false, 15, 12005, 120 , 1200000 , 1.25, 5e200 +"BAD LINE: UNCLOSED QUOTE,K,false,15,12005,120,1200000,1.25, 5.5e200 +l, L, 0, 16, 12006, 12 , 120000 , 1.26, 6e200 +m, M, FALSE, 17, 12007, 121 , 12000 , 1.27, 7e200 +n, N, 8, 18, 12008, 122 , 1200 , 1.28, 8e200 +# this is a comment + + + + + + + diff --git a/src/test/resources/gocd/gocd_a0000841_rcm00566_v4.nc b/src/test/resources/gocd/gocd_a0000841_rcm00566_v4.nc new file mode 100644 index 000000000..20ae42759 Binary files /dev/null and b/src/test/resources/gocd/gocd_a0000841_rcm00566_v4.nc differ diff --git a/src/test/resources/gocd/gocd_v3_madcp.nc b/src/test/resources/gocd/gocd_v3_madcp.nc new file mode 100644 index 000000000..b22a59b97 Binary files /dev/null and b/src/test/resources/gocd/gocd_v3_madcp.nc differ diff --git a/src/test/resources/gocdNcCF/gocd_v3_sadcp.nc b/src/test/resources/gocdNcCF/gocd_v3_sadcp.nc new file mode 100644 index 000000000..bb1dd6497 Binary files /dev/null and b/src/test/resources/gocdNcCF/gocd_v3_sadcp.nc differ diff --git a/src/test/resources/httpGet/46088/46088_1980-01.jsonl b/src/test/resources/httpGet/46088/46088_1980-01.jsonl new file mode 100644 index 000000000..1e4186af4 --- /dev/null +++ b/src/test/resources/httpGet/46088/46088_1980-01.jsonl @@ -0,0 +1,7 @@ +["stationID","time","aByte","aChar","aShort","anInt","aFloat","aDouble","aString","timestamp","author","command"] +["46088",3.3,17,"g",30000,2,1.23,1.2345678901234,"abcdefghijkl",1.677103573093E9,"bsimons",0] +["46088",4.4,18,"\u20ac",30002,3,1.45,1.3," s\n\t\u00c3\u20ac123",1.67710357411E9,"bsimons",0] +["46088",5.5,19," ",30003,3,1.67,1.4," \n\u20ac ",1.67710357411E9,"bsimons",0] +["46088",3.3,20,"\u00bc",30010,9,1.99,1.999,"",1.677103574116E9,"bsimons",0] +["46088",3.3,30," ",null,null,null,null,"",1.677103574122E9,"bsimons",0] +["46088",3.3,null,null,null,null,null,null,"",1.677103574128E9,"bsimons",1] diff --git a/src/test/resources/images/testImagesIdentical_1.png b/src/test/resources/images/testImagesIdentical_1.png new file mode 100644 index 000000000..335174f9c Binary files /dev/null and b/src/test/resources/images/testImagesIdentical_1.png differ diff --git a/src/test/resources/images/testImagesIdentical_2.png b/src/test/resources/images/testImagesIdentical_2.png new file mode 100644 index 000000000..d8fb5b791 Binary files /dev/null and b/src/test/resources/images/testImagesIdentical_2.png differ diff --git a/WEB-INF/classes/com/cohort/util/testmap.gif b/src/test/resources/images/testmap.gif similarity index 100% rename from WEB-INF/classes/com/cohort/util/testmap.gif rename to src/test/resources/images/testmap.gif diff --git a/src/test/resources/jsonl/sampleCSV.jsonl b/src/test/resources/jsonl/sampleCSV.jsonl new file mode 100644 index 000000000..9557695db --- /dev/null +++ b/src/test/resources/jsonl/sampleCSV.jsonl @@ -0,0 +1,10 @@ +["ship","time","lat","lon","status","testLong","sst"] +["Bell M. Shimada","2017-03-23T00:45:00Z",28.0002,-130.2576,"A",-9223372036854775808,10.9] +["Bell M. Shimada","2017-03-23T01:45:00Z",28.0003,-130.3472,"\u20AC",-1234567890123456,null] +["Bell M. Shimada","2017-03-23T02:45:00Z",28.0001,-130.4305,"\t",0,10.7] +["This is a FLAWED ROW with only 1 column"] +This is a FLAWED ROW: not a json array. +["Bell M. Shimada","2017-03-23T12:45:00Z",27.9998,-131.5578,"\"",1234567890123456,99] +[" a\t~\u00fc,\n'z\"\u20ac","2017-03-23T21:45:00Z",28.0003,-132.0014,"\u00fc",9223372036854775806,10.0] +[null,null,null,null,null,null,null] + \ No newline at end of file diff --git a/src/test/resources/nc/2901175_prof.nc b/src/test/resources/nc/2901175_prof.nc new file mode 100644 index 000000000..9465fd9e8 Binary files /dev/null and b/src/test/resources/nc/2901175_prof.nc differ diff --git a/src/test/resources/nc/GLsubdir/GL_201207_TS_DB_44761.nc b/src/test/resources/nc/GLsubdir/GL_201207_TS_DB_44761.nc new file mode 100644 index 000000000..1e0c8885e Binary files /dev/null and b/src/test/resources/nc/GLsubdir/GL_201207_TS_DB_44761.nc differ diff --git a/src/test/resources/nc/GLsubdir/GL_201207_TS_DB_44761.nc.txt b/src/test/resources/nc/GLsubdir/GL_201207_TS_DB_44761.nc.txt new file mode 100644 index 000000000..c296aeb19 --- /dev/null +++ b/src/test/resources/nc/GLsubdir/GL_201207_TS_DB_44761.nc.txt @@ -0,0 +1,211 @@ +netcdf GL_201207_TS_DB_44761.nc { + dimensions: + TIME = UNLIMITED; // (491 currently) + DEPTH = 1; + LATITUDE = 491; + LONGITUDE = 491; + POSITION = 491; + variables: + double TIME(TIME=491); + :long_name = "time"; + :standard_name = "time"; + :units = "days since 1950-01-01T00:00:00Z"; + :valid_min = 0.0; // double + :valid_max = 90000.0; // double + :QC_indicator = 1; // int + :QC_procedure = 1; // int + :uncertainty = " "; + :comment = " "; + :axis = "T"; + + byte TIME_QC(TIME=491); + :long_name = "quality flag"; + :conventions = "OceanSites reference table 2"; + :_FillValue = -128B; // byte + :valid_min = 0B; // byte + :valid_max = 9B; // byte + :flag_values = 0B, 1B, 2B, 3B, 4B, 5B, 6B, 7B, 8B, 9B; // byte + :flag_meanings = "no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable +bad_data value_changed not_used nominal_value interpolated_value missing_value"; + + float DEPTH(DEPTH=1); + :long_name = "Depth of each measurement"; + :standard_name = "depth"; + :units = "meter"; + :positive = "down"; + :_FillValue = -99999.0f; // float + :valid_min = 0.0; // double + :valid_max = 12000.0; // double + :QC_indicator = 1; // int + :QC_procedure = 1; // int + :uncertainty = " "; + :comment = " "; + :axis = "Z"; + :reference = "sea_level"; + :coordinate_reference_frame = "urn:ogc:crs:EPSG::5113"; + + byte DEPTH_QC(DEPTH=1); + :long_name = "quality flag"; + :conventions = "OceanSites reference table 2"; + :_FillValue = -128B; // byte + :valid_min = 0B; // byte + :valid_max = 9B; // byte + :flag_values = 0B, 1B, 2B, 3B, 4B, 5B, 6B, 7B, 8B, 9B; // byte + :flag_meanings = "no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable +bad_data value_changed not_used nominal_value interpolated_value missing_value"; + + float LATITUDE(LATITUDE=491); + :long_name = "Latitude of each location"; + :standard_name = "latitude"; + :units = "degrees_north"; + :valid_min = -90.0; // double + :valid_max = 90.0; // double + :QC_indicator = 1; // int + :QC_procedure = 1; // int + :uncertainty = " "; + :comment = " "; + :axis = "Y"; + + float LONGITUDE(LONGITUDE=491); + :long_name = "Longitude of each location"; + :standard_name = "longitude"; + :units = "degrees_east"; + :valid_min = -180.0; // double + :valid_max = 180.0; // double + :QC_indicator = 1; // int + :QC_procedure = 1; // int + :uncertainty = " "; + :comment = " "; + :axis = "X"; + + byte POSITION_QC(POSITION=491); + :long_name = "quality flag"; + :conventions = "OceanSites reference table 2"; + :_FillValue = -128B; // byte + :valid_min = 0B; // byte + :valid_max = 9B; // byte + :flag_values = 0B, 1B, 2B, 3B, 4B, 5B, 6B, 7B, 8B, 9B; // byte + :flag_meanings = "no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable +bad_data value_changed not_used nominal_value interpolated_value missing_value"; + + char POSITIONING_SYSTEM(POSITION=491); + :long_name = "Positioning system"; + :_FillValue = " "; + :flag_values = "A, G, L, N, U"; + :flag_meanings = "Argos, GPS, Loran, Nominal, Unknown"; + + float TEMP(TIME=491, DEPTH=1); + :long_name = "Sea temperature"; + :standard_name = "sea_water_temperature"; + :units = "degree_Celsius"; + :_FillValue = 9.96921E36f; // float + + byte TEMP_QC(TIME=491, DEPTH=1); + :long_name = "quality flag"; + :conventions = "OceanSites reference table 2"; + :_FillValue = -128B; // byte + :valid_min = 0B; // byte + :valid_max = 9B; // byte + :flag_values = 0B, 1B, 2B, 3B, 4B, 5B, 6B, 7B, 8B, 9B; // byte + :flag_meanings = "no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable +bad_data value_changed not_used nominal_value interpolated_value missing_value"; + + char TEMP_DM(TIME=491, DEPTH=1); + :long_name = "method of data processing"; + :conventions = "OceanSITES reference table 5"; + :flag_values = "R, P, D, M"; + :flag_meanings = "realtime post-recovery delayed-mode mixed"; + :_FillValue = " "; + + float ATPT(TIME=491, DEPTH=1); + :long_name = "Atmospheric pressure hourly tendency"; + :standard_name = "tendency_of_air_pressure"; + :units = "hectopascal/hour"; + :_FillValue = 9.96921E36f; // float + + byte ATPT_QC(TIME=491, DEPTH=1); + :long_name = "quality flag"; + :conventions = "OceanSites reference table 2"; + :_FillValue = -128B; // byte + :valid_min = 0B; // byte + :valid_max = 9B; // byte + :flag_values = 0B, 1B, 2B, 3B, 4B, 5B, 6B, 7B, 8B, 9B; // byte + :flag_meanings = "no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable +bad_data value_changed not_used nominal_value interpolated_value missing_value"; + + char ATPT_DM(TIME=491, DEPTH=1); + :long_name = "method of data processing"; + :conventions = "OceanSITES reference table 5"; + :flag_values = "R, P, D, M"; + :flag_meanings = "realtime post-recovery delayed-mode mixed"; + :_FillValue = " "; + + float ATMS(TIME=491, DEPTH=1); + :long_name = "Atmospheric pressure at sea level"; + :standard_name = "air_pressure_at_sea_level"; + :units = "hectopascal"; + :_FillValue = 9.96921E36f; // float + + byte ATMS_QC(TIME=491, DEPTH=1); + :long_name = "quality flag"; + :conventions = "OceanSites reference table 2"; + :_FillValue = -128B; // byte + :valid_min = 0B; // byte + :valid_max = 9B; // byte + :flag_values = 0B, 1B, 2B, 3B, 4B, 5B, 6B, 7B, 8B, 9B; // byte + :flag_meanings = "no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable +bad_data value_changed not_used nominal_value interpolated_value missing_value"; + + char ATMS_DM(TIME=491, DEPTH=1); + :long_name = "method of data processing"; + :conventions = "OceanSITES reference table 5"; + :flag_values = "R, P, D, M"; + :flag_meanings = "realtime post-recovery delayed-mode mixed"; + :_FillValue = " "; + + // global attributes: + :data_type = "OceanSITES time-series data"; + :format_version = "1.1"; + :platform_code = "44761"; + :date_update = "2012-08-06T22:07:01Z"; + :institution = "Unknown institution"; + :site_code = " "; + :wmo_platform_code = "44761"; + :platform_name = " "; + :source = "BUOY/MOORING: SURFACE, DRIFTING : observation"; + :history = "2012-08-06T22:07:01Z : Creation"; + :data_mode = "R"; + :quality_control_indicator = "6"; + :quality_index = "A"; + :references = "http://www.myocean.eu.org,http://www.coriolis.eu.org"; + :comment = " "; + :conventions = "OceanSITES Manual 1.1, CF-1.1"; + :netcdf_version = "3.5"; + :title = " "; + :summary = " "; + :naming_authority = "OceanSITES"; + :id = "GL_201207_TS_DB_44761"; + :cdm_data_type = "Time-series"; + :area = "Global Ocean"; + :geospatial_lat_min = "47.763"; + :geospatial_lat_max = "51.078"; + :geospatial_lon_min = "-44.112"; + :geospatial_lon_max = "-39.878"; + :geospatial_vertical_min = " "; + :geospatial_vertical_max = " "; + :time_coverage_start = "2012-07-11T13:00:00Z"; + :time_coverage_end = "2012-07-31T23:00:00Z"; + :institution_references = "http://www.coriolis.eu.org"; + :contact = "codac@ifremer.fr"; + :author = "Coriolis and MyOcean data provider"; + :data_assembly_center = "Coriolis"; + :pi_name = ""; + :distribution_statement = "These data follow MyOcean standards; they are public and free of charge. User assu +mes all risk for use of data. User must display citation in any publication or product using data. User must co +ntact PI prior to any commercial use of data. More on: http://www.myocean.eu/data_policy"; + :citation = "These data were collected and made freely available by the MyOcean project and the programs that + contribute to it"; + :update_interval = "daily"; + :qc_manual = "OceanSITES User's Manual v1.1"; + data: +} \ No newline at end of file diff --git a/src/test/resources/nc/SDScompound.h5 b/src/test/resources/nc/SDScompound.h5 new file mode 100644 index 000000000..68230e383 Binary files /dev/null and b/src/test/resources/nc/SDScompound.h5 differ diff --git a/src/test/resources/nccf/Profile.nc b/src/test/resources/nccf/Profile.nc new file mode 100644 index 000000000..bbab93c76 Binary files /dev/null and b/src/test/resources/nccf/Profile.nc differ diff --git a/src/test/resources/nccf/badIndexed1To6.nc b/src/test/resources/nccf/badIndexed1To6.nc new file mode 100644 index 000000000..301c75d7c Binary files /dev/null and b/src/test/resources/nccf/badIndexed1To6.nc differ diff --git a/src/test/resources/nccf/ncCF1b.nc b/src/test/resources/nccf/ncCF1b.nc new file mode 100644 index 000000000..680572e3c Binary files /dev/null and b/src/test/resources/nccf/ncCF1b.nc differ diff --git a/src/test/resources/nccf/ncCF2b.nc b/src/test/resources/nccf/ncCF2b.nc new file mode 100644 index 000000000..856359726 Binary files /dev/null and b/src/test/resources/nccf/ncCF2b.nc differ diff --git a/src/test/resources/nccf/ncCFMA1b.nc b/src/test/resources/nccf/ncCFMA1b.nc new file mode 100644 index 000000000..029918f3c Binary files /dev/null and b/src/test/resources/nccf/ncCFMA1b.nc differ diff --git a/src/test/resources/nccf/ncCFMA2b.nc b/src/test/resources/nccf/ncCFMA2b.nc new file mode 100644 index 000000000..17ec9b9c2 Binary files /dev/null and b/src/test/resources/nccf/ncCFMA2b.nc differ diff --git a/src/test/resources/nccf/ncei/biology_JP14323.nc b/src/test/resources/nccf/ncei/biology_JP14323.nc new file mode 100644 index 000000000..4648bfeb6 Binary files /dev/null and b/src/test/resources/nccf/ncei/biology_JP14323.nc differ diff --git a/src/test/resources/nccf/ncei/ind199105_ctd.nc b/src/test/resources/nccf/ncei/ind199105_ctd.nc new file mode 100644 index 000000000..77b216d85 Binary files /dev/null and b/src/test/resources/nccf/ncei/ind199105_ctd.nc differ diff --git a/src/test/resources/nccsv/sample.csv b/src/test/resources/nccsv/sample.csv new file mode 100644 index 000000000..0b603a273 --- /dev/null +++ b/src/test/resources/nccsv/sample.csv @@ -0,0 +1,61 @@ +*GLOBAL*,Conventions,"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.1" +*GLOBAL*,cdm_trajectory_variables,"ship" +*GLOBAL*,creator_email,bob.simons@noaa.gov +*GLOBAL*,creator_name,Bob Simons +*GLOBAL*,creator_type,person +*GLOBAL*,creator_url,https://www.pfeg.noaa.gov +*GLOBAL*,featureType,trajectory +*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html +*GLOBAL*,institution,"NOAA NMFS SWFSC ERD, NOAA PMEL" +*GLOBAL*,license,"""NCCSV Demonstration"" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ ." +*GLOBAL*,keywords,"NOAA, sea, ship, sst, surface, temperature, trajectory" +*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55 +*GLOBAL*,subsetVariables,"ship" +*GLOBAL*,summary,"This is a paragraph or two describing the dataset." +*GLOBAL*,title,NCCSV Demonstration +ship,*DATA_TYPE*,String +ship,cf_role,trajectory_id +time,*DATA_TYPE*,String +time,standard_name,time +time,units,"yyyy-MM-dd'T'HH:mm:ssZ" +lat,*DATA_TYPE*,double +lat,units,degrees_north +lon,*DATA_TYPE*,double +"lon","units","degrees_east" +status,*DATA_TYPE*,char +status,comment,"From http://some.url.gov/someProjectDocument , Table C" +testByte,*DATA_TYPE*,byte +testByte,units,1 +testUByte,*DATA_TYPE*,ubyte +testUByte,units,1 +testLong,*DATA_TYPE*,long +testLong,units,1 +testULong,*DATA_TYPE*,ulong +testULong,units,1 +sst,*DATA_TYPE*,float +sst,standard_name,sea_surface_temperature +sst,actual_range,0.17f,23.58f +sst,units,degree_C +sst,missing_value,99f +sst,testBytes,-128b,0b,127b +sst,testShorts,-32768s,0s,32767s +sst,testInts,-2147483648i,0i,2147483647i +sst,testLongs,-9223372036854775808L,0L,9223372036854775807L +sst,testFloats,-3.40282347e38f,0f,3.40282347E+38f +sst,testDoubles,-1.79769313486231570e308d,0d,1.79769313486231570E+308d +sst,testChars,"','","'""'","'\u20AC'" +sst,testStrings," a\t~\u00fc,\n'z""\u20AC" +sst,testUBytes,0ub,127ub,255ub +sst,testUInts,0ui,2147483647ui,4294967295ui +sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL +sst,testUShorts,0us,32767us,65535us + +*END_METADATA* +ship,time,lat,lon,status,testByte,testUByte,testLong,testULong,sst +Bell M. Shimada,2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128, 0,-9223372036854775808L,0uL,10.9 +Bell M. Shimada,2017-03-23T01:45:00Z,28.0003,-130.3472,\u20AC,0,127,-9007199254740992L,9223372036854775807uL,10.0 +"Bell M. Shimada","2017-03-23T02:45:00Z",28.0001,-130.4305,"'\t'",126,254,9223372036854775806L,18446744073709551614uL,99 +Bell M. Shimada,2017-03-23T12:45:00Z,27.9998,-131.5578,"'""'",127,255,9223372036854775807L,18446744073709551615uL,NaN +Bell M. Shimada,2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,128,256,9223372036854775808L,18446744073709551616uL,1e309 +Bell M. Shimada,2017-03-23T23:45:00Z,28.0002,-132.1591,,,,,, +*END_DATA* diff --git a/src/test/resources/nccsv/sampleExcel.csv b/src/test/resources/nccsv/sampleExcel.csv new file mode 100644 index 000000000..dc734e15f --- /dev/null +++ b/src/test/resources/nccsv/sampleExcel.csv @@ -0,0 +1,62 @@ +*GLOBAL*,Conventions,"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.1" +*GLOBAL*,cdm_trajectory_variables,"ship" +*GLOBAL*,creator_email,bob.simons@noaa.gov +*GLOBAL*,creator_name,Bob Simons +*GLOBAL*,creator_type,person +*GLOBAL*,creator_url,https://www.pfeg.noaa.gov +*GLOBAL*,featureType,trajectory +*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html +*GLOBAL*,institution,"NOAA NMFS SWFSC ERD, NOAA PMEL" +*GLOBAL*,license,"""NCCSV Demonstration"" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ ." +*GLOBAL*,keywords,"NOAA, sea, ship, sst, surface, temperature, trajectory" +*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55 +*GLOBAL*,subsetVariables,"ship" +*GLOBAL*,summary,"This is a paragraph or two describing the dataset." +*GLOBAL*,title,NCCSV Demonstration +ship,*SCALAR*," a\t~\u00fc,\n'z""\u20AC" +ship,cf_role,trajectory_id +time,*DATA_TYPE*,String +time,standard_name,time +time,units,"yyyy-MM-dd'T'HH:mm:ssZ" +lat,*DATA_TYPE*,double +lat,units,degrees_north +lon,*DATA_TYPE*,double +"lon","units","degrees_east" +status,*DATA_TYPE*,char +status,comment,"From http://some.url.gov/someProjectDocument , Table C" +testByte,*DATA_TYPE*,byte +testByte,units,1 +testUByte,*DATA_TYPE*,ubyte +testUByte,units,1 +testLong,*DATA_TYPE*,long +testLong,units,1 +testULong,*DATA_TYPE*,ulong +testULong,units,1 +sst,*DATA_TYPE*,float +sst,standard_name,sea_surface_temperature +sst,actual_range,0.17f,23.58f +sst,units,degree_C +sst,missing_value,99f +sst,testBytes,-128b,0b,127b +sst,testShorts,-32768s,0s,32767s +sst,testInts,-2147483648i,0i,2147483647i +sst,testLongs,-9223372036854775808L,-9007199254740992L,9007199254740992L,9223372036854775806L,9223372036854775807L +sst,testFloats,-3.40282347e38f,0f,3.40282347E+38f +sst,testDoubles,-1.79769313486231570e308d,0d,1.79769313486231570E+308d +sst,testChars,"','","'""'","'\u20AC'" +sst,testStrings," a\t~\u00fc,\n'z""\u20AC" +sst,testUBytes,0ub,127ub,255ub +sst,testUInts,0ui,2147483647ui,4294967295ui +sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL +sst,testUShorts,0us,32767us,65535us + +*END_METADATA* +time,lat,lon,status,testByte,testUByte,testLong,testULong,sst +2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128, 0,-9223372036854775808L,0uL,10.9 +2017-03-23T01:45:00Z,28.0003,-130.3472,\u20AC,0,127,-9007199254740992L,9223372036854775807uL,10.0 +"2017-03-23T02:45:00Z",28.0001,-130.4305,"'\t'",126,254,9223372036854775806L,18446744073709551614uL,99 +2017-03-23T12:45:00Z,27.9998,-131.5578,"'""'",127,255,9223372036854775807L,18446744073709551615uL,NaN +BAD ROW: TOO FEW ITEMS +2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,128,256,9223372036854775808L,18446744073709551616uL,1e309 +2017-03-23T23:45:00Z,28.0002,-132.1591,,,,,, +*END_DATA* diff --git a/src/test/resources/nccsv/sampleExcel.png b/src/test/resources/nccsv/sampleExcel.png new file mode 100644 index 000000000..4905ba92d Binary files /dev/null and b/src/test/resources/nccsv/sampleExcel.png differ diff --git a/src/test/resources/nccsv/sampleMetadata.csv b/src/test/resources/nccsv/sampleMetadata.csv new file mode 100644 index 000000000..2fb714590 --- /dev/null +++ b/src/test/resources/nccsv/sampleMetadata.csv @@ -0,0 +1,47 @@ +*GLOBAL*,Conventions,"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.1" +*GLOBAL*,cdm_trajectory_variables,"ship" +*GLOBAL*,creator_email,bob.simons@noaa.gov +*GLOBAL*,creator_name,Bob Simons +*GLOBAL*,creator_type,person +*GLOBAL*,creator_url,https://www.pfeg.noaa.gov +*GLOBAL*,featureType,trajectory +*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html +*GLOBAL*,institution,"NOAA NMFS SWFSC ERD, NOAA PMEL" +*GLOBAL*,license,"""NCCSV Demonstration"" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ ." +*GLOBAL*,keywords,"NOAA, sea, ship, sst, surface, temperature, trajectory" +*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55 +*GLOBAL*,subsetVariables,"ship" +*GLOBAL*,summary,"This is a paragraph or two describing the dataset." +*GLOBAL*,title,NCCSV Demonstration +ship,*SCALAR*,Bell M. Shimada +ship,cf_role,trajectory_id +time,*DATA_TYPE*,String +time,standard_name,time +time,units,"yyyy-MM-dd'T'HH:mm:ssZ" +lat,*DATA_TYPE*,double +lat,units,degrees_north +lon,*DATA_TYPE*,double +"lon","units","degrees_east" +status,*DATA_TYPE*,char +status,comment,"From http://some.url.gov/someProjectDocument , Table C" +testLong,*DATA_TYPE*,long +testLong,units,1 +sst,*DATA_TYPE*,float +sst,standard_name,sea_surface_temperature +sst,actual_range,0.17f,23.58f +sst,units,degree_C +sst,missing_value,99f +sst,testBytes,-128b,0b,127b +sst,testShorts,-32768s,0s,32767s +sst,testInts,-2147483648i,0i,2147483647i +sst,testLongs,-9223372036854775808L,0L,9223372036854775807L +sst,testFloats,-3.40282347e38f,0f,3.40282347E+38f +sst,testDoubles,-1.79769313486231570e308d,0d,1.79769313486231570E+308d +sst,testChars,"','","'""'","'\u20AC'" +sst,testStrings," a\t~\u00fc,\n'z""\u20AC" +sst,testUBytes,0ub,127ub,255ub +sst,testUInts,0ui,2147483647ui,4294967295ui +sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL +sst,testUShorts,0us,32767us,65535us + +*END_METADATA* diff --git a/src/test/resources/nccsv/sampleScalar.csv b/src/test/resources/nccsv/sampleScalar.csv new file mode 100644 index 000000000..92e4ed27a --- /dev/null +++ b/src/test/resources/nccsv/sampleScalar.csv @@ -0,0 +1,62 @@ +*GLOBAL*,Conventions,"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.1" +*GLOBAL*,cdm_trajectory_variables,"ship" +*GLOBAL*,creator_email,bob.simons@noaa.gov +*GLOBAL*,creator_name,Bob Simons +*GLOBAL*,creator_type,person +*GLOBAL*,creator_url,https://www.pfeg.noaa.gov +*GLOBAL*,featureType,trajectory +*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html +*GLOBAL*,institution,"NOAA NMFS SWFSC ERD, NOAA PMEL" +*GLOBAL*,license,"""NCCSV Demonstration"" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ ." +*GLOBAL*,keywords,"NOAA, sea, ship, sst, surface, temperature, trajectory" +*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55 +*GLOBAL*,subsetVariables,"ship" +*GLOBAL*,summary,"This is a paragraph or two describing the dataset." +*GLOBAL*,title,NCCSV Demonstration +ship,*SCALAR*,Bell M. Shimada +ship,cf_role,trajectory_id +time,*DATA_TYPE*,String +time,standard_name,time +time,units,"yyyy-MM-dd'T'HH:mm:ssZ" +lat,*DATA_TYPE*,double +lat,units,degrees_north +lon,*DATA_TYPE*,double +"lon","units","degrees_east" +status,*DATA_TYPE*,char +status,comment,"From http://some.url.gov/someProjectDocument , Table C" +testByte,*DATA_TYPE*,byte +testByte,units,1 +testUByte,*DATA_TYPE*,ubyte +testUByte,units,1 +testLong,*DATA_TYPE*,long +testLong,units,1 +testULong,*DATA_TYPE*,ulong +testULong,units,1 +sst,*DATA_TYPE*,float +sst,standard_name,sea_surface_temperature +sst,actual_range,0.17f,23.58f +sst,units,degree_C +sst,missing_value,99f +sst,testBytes,-128b,0b,127b +sst,testShorts,-32768s,0s,32767s +sst,testInts,-2147483648i,0i,2147483647i +sst,testLongs,-9223372036854775808L,0L,9223372036854775807L +sst,testFloats,-3.40282347e38f,0f,3.40282347E+38f +sst,testDoubles,-1.79769313486231570e308d,0d,1.79769313486231570E+308d +sst,testChars,"','","'""'","'\u20AC'" +sst,testStrings," a\t~\u00fc,\n'z""\u20AC" +sst,testUBytes,0ub,127ub,255ub +sst,testUInts,0ui,2147483647ui,4294967295ui +sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL +sst,testUShorts,0us,32767us,65535us + +*END_METADATA* +time,lat,lon,status,testByte,testUByte,testLong,testULong,sst +2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128, 0,-9223372036854775808L,0uL,10.9 +2017-03-23T01:45:00Z,28.0003,-130.3472,\u20AC,0,127,-9007199254740992L,9223372036854775807uL,10.0 +"2017-03-23T02:45:00Z",28.0001,-130.4305,"'\t'",126,254,9223372036854775806L,18446744073709551614uL,99 +2017-03-23T12:45:00Z,27.9998,-131.5578,"'""'",127,255,9223372036854775807L,18446744073709551615uL,NaN +2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,128,256,9223372036854775808L,18446744073709551616uL,1e309 +2017-03-23T23:45:00Z,28.0002,-132.1591,,,,,, + +*END_DATA* diff --git a/src/test/resources/nccsv/testScalar.csv b/src/test/resources/nccsv/testScalar.csv new file mode 100644 index 000000000..dc734e15f --- /dev/null +++ b/src/test/resources/nccsv/testScalar.csv @@ -0,0 +1,62 @@ +*GLOBAL*,Conventions,"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.1" +*GLOBAL*,cdm_trajectory_variables,"ship" +*GLOBAL*,creator_email,bob.simons@noaa.gov +*GLOBAL*,creator_name,Bob Simons +*GLOBAL*,creator_type,person +*GLOBAL*,creator_url,https://www.pfeg.noaa.gov +*GLOBAL*,featureType,trajectory +*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html +*GLOBAL*,institution,"NOAA NMFS SWFSC ERD, NOAA PMEL" +*GLOBAL*,license,"""NCCSV Demonstration"" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ ." +*GLOBAL*,keywords,"NOAA, sea, ship, sst, surface, temperature, trajectory" +*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55 +*GLOBAL*,subsetVariables,"ship" +*GLOBAL*,summary,"This is a paragraph or two describing the dataset." +*GLOBAL*,title,NCCSV Demonstration +ship,*SCALAR*," a\t~\u00fc,\n'z""\u20AC" +ship,cf_role,trajectory_id +time,*DATA_TYPE*,String +time,standard_name,time +time,units,"yyyy-MM-dd'T'HH:mm:ssZ" +lat,*DATA_TYPE*,double +lat,units,degrees_north +lon,*DATA_TYPE*,double +"lon","units","degrees_east" +status,*DATA_TYPE*,char +status,comment,"From http://some.url.gov/someProjectDocument , Table C" +testByte,*DATA_TYPE*,byte +testByte,units,1 +testUByte,*DATA_TYPE*,ubyte +testUByte,units,1 +testLong,*DATA_TYPE*,long +testLong,units,1 +testULong,*DATA_TYPE*,ulong +testULong,units,1 +sst,*DATA_TYPE*,float +sst,standard_name,sea_surface_temperature +sst,actual_range,0.17f,23.58f +sst,units,degree_C +sst,missing_value,99f +sst,testBytes,-128b,0b,127b +sst,testShorts,-32768s,0s,32767s +sst,testInts,-2147483648i,0i,2147483647i +sst,testLongs,-9223372036854775808L,-9007199254740992L,9007199254740992L,9223372036854775806L,9223372036854775807L +sst,testFloats,-3.40282347e38f,0f,3.40282347E+38f +sst,testDoubles,-1.79769313486231570e308d,0d,1.79769313486231570E+308d +sst,testChars,"','","'""'","'\u20AC'" +sst,testStrings," a\t~\u00fc,\n'z""\u20AC" +sst,testUBytes,0ub,127ub,255ub +sst,testUInts,0ui,2147483647ui,4294967295ui +sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL +sst,testUShorts,0us,32767us,65535us + +*END_METADATA* +time,lat,lon,status,testByte,testUByte,testLong,testULong,sst +2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128, 0,-9223372036854775808L,0uL,10.9 +2017-03-23T01:45:00Z,28.0003,-130.3472,\u20AC,0,127,-9007199254740992L,9223372036854775807uL,10.0 +"2017-03-23T02:45:00Z",28.0001,-130.4305,"'\t'",126,254,9223372036854775806L,18446744073709551614uL,99 +2017-03-23T12:45:00Z,27.9998,-131.5578,"'""'",127,255,9223372036854775807L,18446744073709551615uL,NaN +BAD ROW: TOO FEW ITEMS +2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,128,256,9223372036854775808L,18446744073709551616uL,1e309 +2017-03-23T23:45:00Z,28.0002,-132.1591,,,,,, +*END_DATA* diff --git a/src/test/resources/nccsv/testScalar_1.1.csv b/src/test/resources/nccsv/testScalar_1.1.csv new file mode 100644 index 000000000..dc734e15f --- /dev/null +++ b/src/test/resources/nccsv/testScalar_1.1.csv @@ -0,0 +1,62 @@ +*GLOBAL*,Conventions,"COARDS, CF-1.6, ACDD-1.3, NCCSV-1.1" +*GLOBAL*,cdm_trajectory_variables,"ship" +*GLOBAL*,creator_email,bob.simons@noaa.gov +*GLOBAL*,creator_name,Bob Simons +*GLOBAL*,creator_type,person +*GLOBAL*,creator_url,https://www.pfeg.noaa.gov +*GLOBAL*,featureType,trajectory +*GLOBAL*,infoUrl,https://coastwatch.pfeg.noaa.gov/erddap/download/NCCSV.html +*GLOBAL*,institution,"NOAA NMFS SWFSC ERD, NOAA PMEL" +*GLOBAL*,license,"""NCCSV Demonstration"" by Bob Simons and Steve Hankin is licensed under CC BY 4.0, https://creativecommons.org/licenses/by/4.0/ ." +*GLOBAL*,keywords,"NOAA, sea, ship, sst, surface, temperature, trajectory" +*GLOBAL*,standard_name_vocabulary,CF Standard Name Table v55 +*GLOBAL*,subsetVariables,"ship" +*GLOBAL*,summary,"This is a paragraph or two describing the dataset." +*GLOBAL*,title,NCCSV Demonstration +ship,*SCALAR*," a\t~\u00fc,\n'z""\u20AC" +ship,cf_role,trajectory_id +time,*DATA_TYPE*,String +time,standard_name,time +time,units,"yyyy-MM-dd'T'HH:mm:ssZ" +lat,*DATA_TYPE*,double +lat,units,degrees_north +lon,*DATA_TYPE*,double +"lon","units","degrees_east" +status,*DATA_TYPE*,char +status,comment,"From http://some.url.gov/someProjectDocument , Table C" +testByte,*DATA_TYPE*,byte +testByte,units,1 +testUByte,*DATA_TYPE*,ubyte +testUByte,units,1 +testLong,*DATA_TYPE*,long +testLong,units,1 +testULong,*DATA_TYPE*,ulong +testULong,units,1 +sst,*DATA_TYPE*,float +sst,standard_name,sea_surface_temperature +sst,actual_range,0.17f,23.58f +sst,units,degree_C +sst,missing_value,99f +sst,testBytes,-128b,0b,127b +sst,testShorts,-32768s,0s,32767s +sst,testInts,-2147483648i,0i,2147483647i +sst,testLongs,-9223372036854775808L,-9007199254740992L,9007199254740992L,9223372036854775806L,9223372036854775807L +sst,testFloats,-3.40282347e38f,0f,3.40282347E+38f +sst,testDoubles,-1.79769313486231570e308d,0d,1.79769313486231570E+308d +sst,testChars,"','","'""'","'\u20AC'" +sst,testStrings," a\t~\u00fc,\n'z""\u20AC" +sst,testUBytes,0ub,127ub,255ub +sst,testUInts,0ui,2147483647ui,4294967295ui +sst,testULongs,0uL,9223372036854775807uL,18446744073709551615uL +sst,testUShorts,0us,32767us,65535us + +*END_METADATA* +time,lat,lon,status,testByte,testUByte,testLong,testULong,sst +2017-03-23T00:45:00Z,28.0002,-130.2576,A,-128, 0,-9223372036854775808L,0uL,10.9 +2017-03-23T01:45:00Z,28.0003,-130.3472,\u20AC,0,127,-9007199254740992L,9223372036854775807uL,10.0 +"2017-03-23T02:45:00Z",28.0001,-130.4305,"'\t'",126,254,9223372036854775806L,18446744073709551614uL,99 +2017-03-23T12:45:00Z,27.9998,-131.5578,"'""'",127,255,9223372036854775807L,18446744073709551615uL,NaN +BAD ROW: TOO FEW ITEMS +2017-03-23T21:45:00Z,28.0003,-132.0014,\u00fc,128,256,9223372036854775808L,18446744073709551616uL,1e309 +2017-03-23T23:45:00Z,28.0002,-132.1591,,,,,, +*END_DATA* diff --git a/src/test/resources/nodcTemplates/ncCFMA2a.nc b/src/test/resources/nodcTemplates/ncCFMA2a.nc new file mode 100644 index 000000000..4cf9722d2 Binary files /dev/null and b/src/test/resources/nodcTemplates/ncCFMA2a.nc differ diff --git a/src/test/resources/nodcTemplates/pointKachemakBay.nc b/src/test/resources/nodcTemplates/pointKachemakBay.nc new file mode 100644 index 000000000..d22a98a0b Binary files /dev/null and b/src/test/resources/nodcTemplates/pointKachemakBay.nc differ diff --git a/src/test/resources/nodcTemplates/timeSeriesBodegaMarineLabBuoy.nc b/src/test/resources/nodcTemplates/timeSeriesBodegaMarineLabBuoy.nc new file mode 100644 index 000000000..3296a2311 Binary files /dev/null and b/src/test/resources/nodcTemplates/timeSeriesBodegaMarineLabBuoy.nc differ diff --git a/src/test/resources/nodcTemplates/timeSeriesProfileUsgs_internal_wave_timeSeries.nc b/src/test/resources/nodcTemplates/timeSeriesProfileUsgs_internal_wave_timeSeries.nc new file mode 100644 index 000000000..9fba734a0 Binary files /dev/null and b/src/test/resources/nodcTemplates/timeSeriesProfileUsgs_internal_wave_timeSeries.nc differ diff --git a/src/test/resources/nodcTemplates/trajectoryAoml_tsg.nc b/src/test/resources/nodcTemplates/trajectoryAoml_tsg.nc new file mode 100644 index 000000000..3968e6b91 Binary files /dev/null and b/src/test/resources/nodcTemplates/trajectoryAoml_tsg.nc differ diff --git a/src/test/resources/nodcTemplates/trajectoryJason2_satelliteAltimeter.nc b/src/test/resources/nodcTemplates/trajectoryJason2_satelliteAltimeter.nc new file mode 100644 index 000000000..a31b4bedc Binary files /dev/null and b/src/test/resources/nodcTemplates/trajectoryJason2_satelliteAltimeter.nc differ diff --git a/src/test/resources/points/erdCalcofiSubsurface/1950/subsurface_19500106_69_144.nc b/src/test/resources/points/erdCalcofiSubsurface/1950/subsurface_19500106_69_144.nc new file mode 100644 index 000000000..14687e748 Binary files /dev/null and b/src/test/resources/points/erdCalcofiSubsurface/1950/subsurface_19500106_69_144.nc differ diff --git a/src/test/resources/points/ndbcMet2HistoricalTxt/41009h1990.txt b/src/test/resources/points/ndbcMet2HistoricalTxt/41009h1990.txt new file mode 100644 index 000000000..87d1cb3e9 --- /dev/null +++ b/src/test/resources/points/ndbcMet2HistoricalTxt/41009h1990.txt @@ -0,0 +1,17118 @@ +YY MM DD hh WD WSPD GST WVHT DPD APD MWD BAR ATMP WTMP DEWP VIS +90 01 01 00 161 08.6 10.7 01.50 05.00 04.80 999 1017.2 22.7 22.0 999.0 99.0 +90 01 01 01 163 09.3 11.3 01.50 05.00 04.90 999 1017.3 22.7 22.0 999.0 99.0 +90 01 01 01 164 09.2 10.6 01.60 04.80 04.90 999 1017.3 22.7 22.0 999.0 99.0 +90 01 01 02 167 08.7 10.7 01.60 05.00 04.80 999 1017.5 22.7 22.0 999.0 99.0 +90 01 01 02 168 08.2 09.5 01.50 04.50 04.70 999 1017.8 22.7 21.9 999.0 99.0 +90 01 01 03 175 08.1 09.6 01.50 04.80 04.80 999 1017.9 22.7 21.9 999.0 99.0 +90 01 01 03 183 07.6 09.3 01.50 08.30 05.00 999 1017.9 22.2 21.9 999.0 99.0 +90 01 01 04 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