Fix Error while publishing S3 file with blanks

This error is reported when publishing a S3 file that container one or more blanks *and* trace logging is enabled. The issue is caused by the use of the Path.toUri method that tries to convert the S3 path to a URI object which does not support the blank chars. The method toUriString should be used instead which is safer to render cloud paths to fully qualified path string Signed-off-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Mar 9, 2024 · b74c022 · b74c022
1 parent bb5c4f9
commit b74c022
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Showing 4 changed files with 6 additions and 4 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/file/FilePorter.groovy b/modules/nextflow/src/main/groovy/nextflow/file/FilePorter.groovy
@@ -333,7 +333,7 @@ class FilePorter {
         }
 
         private String fmtError(Path filePath, Exception e) {
-            def message = "Can't stage file ${filePath.toUri().toString()}"
+            def message = "Can't stage file ${FilesEx.toUriString(filePath)}"
             if( e instanceof NoSuchFileException )
                 message += " -- file does not exist"
             else if( e.message )

diff --git a/modules/nf-commons/src/main/nextflow/file/CopyMoveHelper.java b/modules/nf-commons/src/main/nextflow/file/CopyMoveHelper.java
@@ -32,6 +32,7 @@
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.EnumSet;
 
+import nextflow.extension.FilesEx;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -130,7 +131,7 @@ public FileVisitResult visitFile(Path current, BasicFileAttributes attr)
                 String delta = rel != null ? rel.toString() : null;
                 Path newFile = delta != null ? target.resolve(delta) : target;
                 if( log.isTraceEnabled())
-                    log.trace("Copy file: " + current + " -> "+newFile.toUri());
+                    log.trace("Copy file: " + current + " -> "+ FilesEx.toUriString(newFile));
                 copyFile(current, newFile, foreign, options);
                 return FileVisitResult.CONTINUE;
             }

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java
@@ -78,6 +78,7 @@
 import com.amazonaws.services.s3.transfer.UploadContext;
 import nextflow.cloud.aws.nio.util.S3MultipartOptions;
 import nextflow.cloud.aws.util.AwsHelper;
+import nextflow.extension.FilesEx;
 import nextflow.util.Duration;
 import nextflow.util.ThreadPoolHelper;
 import nextflow.util.ThreadPoolManager;
@@ -551,7 +552,7 @@ public FileVisitResult visitFile(Path current, BasicFileAttributes attr) {
 				String delta = rel != null ? rel.toString() : null;
 				Path newFile = delta != null ? target.resolve(delta) : target;
 				if( log.isTraceEnabled())
-					log.trace("Copy file: " + current + " -> "+newFile.toUri());
+					log.trace("Copy file: " + current + " -> "+ FilesEx.toUriString(newFile));
 
 				String sourceKey = ((S3Path) current).getKey();
 				Download it = transferManager() .download(source.getBucket(), sourceKey, newFile.toFile());

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
@@ -666,7 +666,7 @@ public <V extends FileAttributeView> V getFileAttributeView(Path path, Class<V>
 				return (V) new S3FileAttributesView(readAttr0(s3Path));
 			}
 			catch (IOException e) {
-				throw new RuntimeException("Unable read attributes for file: " + s3Path.toUri(), e);
+				throw new RuntimeException("Unable read attributes for file: " + FilesEx.toUriString(s3Path), e);
 			}
 		}
 		throw new UnsupportedOperationException("Not a valid S3 file system provider file attribute view: " + type.getName());