Allow http file to be closed early

Signed-off-by: Tom Sellman <[email protected]>

modules/nf-commons/src/main/nextflow/extension/FilesEx.groovy

@@ -16,6 +16,11 @@
 
 package nextflow.extension
 
+import groovy.transform.stc.SimpleType
+import org.codehaus.groovy.runtime.IOGroovyMethods
+
+import java.nio.file.OpenOption
+
 import static java.nio.file.StandardCopyOption.*
 
 import java.nio.ByteBuffer
@@ -617,6 +622,14 @@ class FilesEx {
         renameTo( self, FileHelper.asPath(target) )
     }
 
+    static <T> T withInputStream(Path self, OpenOption option, @ClosureParams(value = SimpleType.class, options = "java.io.InputStream") Closure<T> closure) throws IOException {
+        return IOGroovyMethods.withStream(newInputStream(self, option), closure)
+    }
+
+    static InputStream newInputStream(Path self, OpenOption... options) {
+        return Files.newInputStream(self, options)
+    }
+
     /**
      * List the content of a given path folder. The method is semantically
      * equivalent to {@code File#list()}

modules/nf-httpfs/src/main/nextflow/file/http/HttpOpenOption.groovy

@@ -0,0 +1,16 @@
+package nextflow.file.http
+
+import java.nio.file.OpenOption
+
+/**
+ * Options which can be used to modify how an HTTP resource is opened as a file.
+ */
+enum HttpOpenOption implements OpenOption {
+    /**
+     * If this option is supplied when opening an HTTP file, no exception will be thrown if the stream is
+     * closed before all data has been received.
+     *
+     * This can be useful, for example, to read just the first line without downloading the whole file.
+     */
+    ALLOW_EARLY_CLOSE
+}

modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy

@@ -341,18 +341,21 @@ abstract class XFileSystemProvider extends FileSystemProvider {
         if (path.class != XPath)
             throw new ProviderMismatchException()
 
+        boolean allowEarlyClose = false
         if (options.length > 0) {
             for (OpenOption opt: options) {
                 // All OpenOption values except for APPEND and WRITE are allowed
-                if (opt == StandardOpenOption.APPEND ||
-                        opt == StandardOpenOption.WRITE)
-                    throw new UnsupportedOperationException("'$opt' not allowed");
+                if (opt == StandardOpenOption.APPEND || opt == StandardOpenOption.WRITE)
+                    throw new UnsupportedOperationException("'$opt' not allowed")
+
+                if (opt == HttpOpenOption.ALLOW_EARLY_CLOSE)
+                    allowEarlyClose = true
             }
         }
 
         final conn = toConnection(path)
         final length = conn.getContentLengthLong()
-        return length>0
+        return length>0 && !allowEarlyClose
             ? new FixedInputStream(conn.getInputStream(), length)
             : conn.getInputStream()
     }