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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 a0617e1df68e8955ef71a33952c1afe9498ac58c..79be881912eba88100b75423715869128ceb6c1c 100644
(file)
--- a/
sdk/cwl/arvados_cwl/runner.py
+++ b/
sdk/cwl/arvados_cwl/runner.py
@@
-129,8
+129,7
@@
def upload_dependencies(arvrunner, name, document_loader,
sc = []
def only_real(obj):
sc = []
def only_real(obj):
- loc = obj.get("location", "")
- if loc.startswith("file:") or loc.startswith("keep:"):
+ if obj.get("location", "").startswith("file:"):
sc.append(obj)
visit_class(sc_result, ("File", "Directory"), only_real)
sc.append(obj)
visit_class(sc_result, ("File", "Directory"), only_real)
@@
-169,8
+168,13
@@
def upload_dependencies(arvrunner, name, document_loader,
visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
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",
mapper = ArvPathMapper(arvrunner, sc, "",
"keep:%s",