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Merge branch '10081-cwl-run-same-job' into 9988-cwl-arv-hints
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
arvworkflow.py
diff --git
a/sdk/cwl/arvados_cwl/arvworkflow.py
b/sdk/cwl/arvados_cwl/arvworkflow.py
index 6087648a45e42e516d85eb00776d560a2c2a49ee..ab8ad035fd6c8d13d14b3d226135993e6c0792ce 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/
sdk/cwl/arvados_cwl/arvworkflow.py
@@
-6,7
+6,7
@@
import logging
from cwltool.pack import pack
from cwltool.load_tool import fetch_document
from cwltool.process import shortname
from cwltool.pack import pack
from cwltool.load_tool import fetch_document
from cwltool.process import shortname
-from cwltool.workflow import Workflow
+from cwltool.workflow import Workflow
, WorkflowException
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
import ruamel.yaml as yaml
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
import ruamel.yaml as yaml
@@
-83,8
+83,10
@@
class ArvadosWorkflow(Workflow):
def keepmount(obj):
if obj["location"].startswith("keep:"):
obj["location"] = "/keep/" + obj["location"][5:]
def keepmount(obj):
if obj["location"].startswith("keep:"):
obj["location"] = "/keep/" + obj["location"][5:]
+ elif obj["location"].startswith("_:"):
+ pass
else:
else:
- raise
Exception("Uh oh %s
" % obj["location"])
+ raise
WorkflowException("Location is not a keep reference or a literal: '%s'
" % obj["location"])
if "listing" in obj:
del obj["listing"]
adjustFileObjs(joborder_keepmount, keepmount)
if "listing" in obj:
del obj["listing"]
adjustFileObjs(joborder_keepmount, keepmount)