Skip to content

Pre-create expected output file on disk#1276

Merged
mvdbeek merged 1 commit intogalaxyproject:masterfrom
mvdbeek:output_collect_robustness
Oct 19, 2022
Merged

Pre-create expected output file on disk#1276
mvdbeek merged 1 commit intogalaxyproject:masterfrom
mvdbeek:output_collect_robustness

Conversation

@mvdbeek
Copy link
Member

@mvdbeek mvdbeek commented Oct 6, 2022

Should "fix"

There were problems with 1 test(s) - out of 1 test(s) executed. See /home/runner/work/iwc/iwc/tool_test_output.html for detailed breakdown.
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.7.14/x64/lib/python3.7/site-packages/planemo/galaxy/activity.py", line 53, in execute
    return _execute(ctx, config, runnable, job_path, **kwds)
  File "/opt/hostedtoolcache/Python/3.7.14/x64/lib/python3.7/site-packages/planemo/galaxy/activity.py", line 227, in _execute
    run_response.collect_outputs(ctx, output_directory)
  File "/opt/hostedtoolcache/Python/3.7.14/x64/lib/python3.7/site-packages/planemo/galaxy/activity.py", line 429, in collect_outputs
    pseduo_location=True,
  File "/opt/hostedtoolcache/Python/3.7.14/x64/lib/python3.7/site-packages/galaxy/tool_util/cwl/util.py", line 456, in output_to_cwl_json
    properties = output_properties(pseduo_location=pseduo_location, **dataset_dict)
  File "/opt/hostedtoolcache/Python/3.7.14/x64/lib/python3.7/site-packages/galaxy/tool_util/cwl/util.py", line 35, in output_properties
    f = open(path, "rb")
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp_yvc0mvo/full contaminant + mito scaffold list'
VGP-Decontamination-pipeline---Db-not-included.ga_0: failed

In @Delphine-L's https://github.com/galaxyproject/iwc/actions/runs/3176857778/jobs/5176648484

@mvdbeek mvdbeek requested review from jmchilton and nsoranzo October 6, 2022 12:26
@jmchilton
Copy link
Member

An empty file is better than no file? I'm confused by this but I trust you.

@mvdbeek
Copy link
Member Author

mvdbeek commented Oct 10, 2022

This became necessary when we started downloading all workflow outputs and then comparing the outputs to expectations... i don't think this is actually the proper fix, I'm not sure what the right fix is. Maybe we shouldn't be downloading all outputs in test mode and instead follow the verify pattern from galaxy-tool-util more closely?

@mvdbeek mvdbeek merged commit d791736 into galaxyproject:master Oct 19, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants