13976: Filter out keep references with secondaryFiles from list of files to upload

[arvados.git] / sdk / cwl / arvados_cwl / runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 3ad1aa6a704632a945b2ed059c10f40a87cdb578..79be881912eba88100b75423715869128ceb6c1c 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -168,8 +168,13 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 
-    for d in discovered:
-        sc.extend(discovered[d])
+    for d in list(discovered.keys()):
+        # Only interested in discovered secondaryFiles which are local
+        # files that need to be uploaded.
+        if d.startswith("file:"):
+            sc.extend(discovered[d])
+        else:
+            del discovered[d]
 
     mapper = ArvPathMapper(arvrunner, sc, "",
                            "keep:%s",