Fixed issue #65 An input file that is staged from a foreign file syst…

…em lost it's original name
nextflow-io · Aug 14, 2015 · b8907b5 · b8907b5
1 parent 4159a72
commit b8907b5
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1146,9 +1146,10 @@ abstract class TaskProcessor {
          * when it is a file stored in a "foreign" storage, copy
          * to a local file and return a reference holder to the local file
          */
-        def result = Nextflow.tempFile(altName)
+
         if( input instanceof Path ) {
             log.debug "Copying to process workdir foreign file: ${input.toUri().toString()}"
+            def result = Nextflow.tempFile(input.getFileName().toString())
             Files.copy(Files.newInputStream(input), result)
             return new FileHolder(input, result)
         }
@@ -1158,6 +1159,7 @@ abstract class TaskProcessor {
          * to a local file
          */
         def source = input?.toString() ?: ''
+        def result = Nextflow.tempFile(altName)
         result.text = source
         return new FileHolder(source, result)
     }

diff --git a/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -338,7 +338,7 @@ class TaskProcessorTest extends Specification {
 
         /*
          * when the input file is on the local file system
-         * simple return a refernce to it in the holder object
+         * simple return a reference to it in the holder object
          */
         when:
         holder = processor.normalizeInputToFile(localFile,null)
@@ -354,12 +354,12 @@ class TaskProcessorTest extends Specification {
         when:
         def remoteFile = TestHelper.createInMemTempFile('remote_file.txt')
         remoteFile.text = 'alpha beta gamma delta'
-        holder = processor.normalizeInputToFile(remoteFile,'local_copy.txt')
+        holder = processor.normalizeInputToFile(remoteFile,'input.1')
         then:
         holder.sourceObj == remoteFile
         holder.storePath.fileSystem == FileSystems.default
         holder.storePath.text == 'alpha beta gamma delta'
-        holder.stageName == 'local_copy.txt'
+        holder.stageName == remoteFile.getName()
 
         /*
          * any generic input that is not a file is converted to a string