Fix http files stream (nextflow-io#5405) [e2e stage]

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

modules/nf-commons/src/main/nextflow/file/CopyMoveHelper.java

@@ -41,6 +41,10 @@
  * Helper class to handle copy/move files and directories
  */
 public class CopyMoveHelper {
+    /**
+     * True if currently performing a copy of a foreign file.
+     */
+    public static final ThreadLocal<Boolean> IN_FOREIGN_COPY = new ThreadLocal<>();
 
     private static Logger log = LoggerFactory.getLogger(CopyMoveHelper.class);
 
@@ -81,14 +85,16 @@ private static CopyOption[] convertMoveToCopyOptions(CopyOption... options)
     private static void copyFile(Path source, Path target, boolean foreign, CopyOption... options)
             throws IOException
     {
-
         if( !foreign ) {
             source.getFileSystem().provider().copy(source, target, options);
             return;
         }
 
+        IN_FOREIGN_COPY.set(true);
         try (InputStream in = Files.newInputStream(source)) {
             Files.copy(in, target);
+        } finally {
+            IN_FOREIGN_COPY.set(false);
         }
     }
 

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

@@ -16,6 +16,8 @@
 
 package nextflow.file.http
 
+import nextflow.file.CopyMoveHelper
+
 import static nextflow.file.http.XFileSystemConfig.*
 
 import java.nio.ByteBuffer
@@ -352,7 +354,8 @@ abstract class XFileSystemProvider extends FileSystemProvider {
 
         final conn = toConnection(path)
         final length = conn.getContentLengthLong()
-        return length>0
+        // only apply the FixedInputStream check if staging files
+        return length>0 && CopyMoveHelper.IN_FOREIGN_COPY.get()
             ? new FixedInputStream(conn.getInputStream(), length)
             : conn.getInputStream()
     }