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Description
Has #846 come back?
I see the same reported behaviour with a fresh Galaxy dev checkout and planemo 0.72.0.dev0
When I remove a test output and run test --update_test_data, planemo does correctly recreate the missing output but the test fails with:
Test file (outfile_sample) is missing. If you use planemo try --update_test_data to generate one.
It is indeed not really passing the test if there's a missing output so this needs some thought.
Perhaps planemo should have an unforgiving "test" that does exactly that and fails if it fails....as distinct from a different command to execute the specified test and generate fresh appropriate outputs, then test properly? Once generated, those fresh outputs are then ideal for the real pass/fail test. In generating them there has certainly been a test, but it seems odd to report that process as successful - I think I'll want to re-test with the generated output before declaring victory.
Here's the traceback:
`
FAIL: ( pyrevargparse ) > Test-1
Traceback (most recent call last):
File "/home/ross/galaxy/test/functional/test_toolbox.py", line 99, in test_tool
self.do_it(tool_version=tool_version, test_index=test_index)
File "/home/ross/galaxy/test/functional/test_toolbox.py", line 36, in do_it
verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data)
File "/home/ross/galaxy/lib/galaxy/tool_util/verify/interactor.py", line 834, in verify_tool
raise e
File "/home/ross/galaxy/lib/galaxy/tool_util/verify/interactor.py", line 830, in verify_tool
job_stdio = _verify_outputs(testdef, test_history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=quiet)
File "/home/ross/galaxy/lib/galaxy/tool_util/verify/interactor.py", line 1005, in _verify_outputs
raise JobOutputsError(found_exceptions, job_stdio)
galaxy.tool_util.verify.interactor.JobOutputsError: Test file (outfile_sample) is missing. If you use planemo try --update_test_data to generate one.
`