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Bug #17300
openarray of array of File causes 'NoneType' object has no attribute 'resolved'
Status:
New
Priority:
High
Assigned To:
-
Category:
-
Target version:
-
Start date:
Due date:
% Done:
0%
Estimated time:
Story points:
-
Release:
Release relationship:
Auto
Description
When running an ExpressionTool which has an output of the following type:
outputs: subject_images: type: type: array # subjects items: type: array # timepoints items: File
I receive the following error:
ERROR Unhandled error: 'NoneType' object has no attribute 'resolved' Traceback (most recent call last): File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/main.py", line 833, in main logger=_logger) File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/executor.py", line 767, in arv_executor self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes, self.output_tags, self.final_output) File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/executor.py", line 467, in make_output_collection adjustFileObjs(outputObj, rewrite) File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/pathmapper.py", line 48, in adjustFileObjs visit_class(rec, ("File",), op) File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/utils.py", line 221, in visit_class visit_class(rec[d], cls, op) File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/utils.py", line 224, in visit_class visit_class(d, cls, op) File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/utils.py", line 224, in visit_class visit_class(d, cls, op) File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/cwltool/utils.py", line 219, in visit_class op(rec) File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/executor.py", line 461, in rewrite fileobj["location"] = generatemapper.mapper(fileobj["location"]).target File "/usr/share/python2.7/dist/python-arvados-cwl-runner/lib/python2.7/site-packages/arvados_cwl/pathmapper.py", line 332, in mapper return MapperEnt(v.resolved, v.target + src[i:], v.type, v.staged) AttributeError: 'NoneType' object has no attribute 'resolved'
If I replace type: File with type: string and store locations instead of File objects the request finishes successfully and returns the expected list of locations.
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