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Merge branch '10081-cwl-run-same-job' into 9988-cwl-arv-hints
[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 155c6a05039ec65649975d038073185fbc5c4338..cf2f1db997b9db9688b52258994bc6179863783d 100644
(file)
--- a/
sdk/cwl/arvados_cwl/runner.py
+++ b/
sdk/cwl/arvados_cwl/runner.py
@@
-69,25
+69,19
@@
def upload_dependencies(arvrunner, name, document_loader,
set(("$include", "$schemas", "location")),
loadref)
set(("$include", "$schemas", "location")),
loadref)
- files = []
- def visitFiles(path):
- files.append(path)
-
- adjustFileObjs(sc, visitFiles)
- adjustDirObjs(sc, visitFiles)
-
- normalizeFilesDirs(files)
+ normalizeFilesDirs(sc)
if "id" in workflowobj:
if "id" in workflowobj:
-
files
.append({"class": "File", "location": workflowobj["id"]})
+
sc
.append({"class": "File", "location": workflowobj["id"]})
- mapper = ArvPathMapper(arvrunner,
files
, "",
+ mapper = ArvPathMapper(arvrunner,
sc
, "",
"keep:%s",
"keep:%s/%s",
name=name)
def setloc(p):
"keep:%s",
"keep:%s/%s",
name=name)
def setloc(p):
- p["location"] = mapper.mapper(p["location"]).target
+ if not p["location"].startswith("_:") and not p["location"].startswith("keep:"):
+ p["location"] = mapper.mapper(p["location"]).target
adjustFileObjs(workflowobj, setloc)
adjustDirObjs(workflowobj, setloc)
adjustFileObjs(workflowobj, setloc)
adjustDirObjs(workflowobj, setloc)