Add check for Arvados when an optional output for a step is missing #58
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Please see Issue #57
In get_output_task in arvados_platform.py if an output is missing for e.g. it could be an optional output from an optional step of the pipeline we get an error:
File "/scratch/mount1/06-RNA-Seq-pipeline-solve-issues/RNA-Seq-Launcher/launcher/src/launcher.py", line 507, in do_work
outputs = construct_output_list(platform, args.reference_model, merge_task)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/scratch/mount1/06-RNA-Seq-pipeline-solve-issues/RNA-Seq-Launcher/launcher/src/launcher.py", line 34, in construct_output_list
source_file = platform.get_task_output(merge_task, output_field)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ec2-user/.pyenv/versions/RNASeq_pipeline_solve_issues_py3.11.0/lib/python3.11/site-packages/cwl_platform/arvados_platform.py", line 434, in get_task_output
if 'location' in output_field:
^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: argument of type 'NoneType' is not iterable
Therefore, we need to add a check in get_output_task if the output_field is None we return None.
In SevenBridges, if the file is missing it is already returned as None.