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Tool test that is expected to fail does not get the exit code #14206

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bernt-matthias opened this issue Jun 27, 2022 · 0 comments
Closed

Tool test that is expected to fail does not get the exit code #14206

bernt-matthias opened this issue Jun 27, 2022 · 0 comments
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@bernt-matthias
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kind/bug
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23.0

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@bernt-matthias
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Describe the bug

This test currently fails IUC weekly CI with:

galaxy.tool_util.verify.interactor.JobOutputsError: Expected job to complete with exit code 1, found None

Log also shows:

2022-06-27 17:46:36,665 INFO  [galaxy.tool_util.output_checker] Job error detected, failing job. Reasons are [{'type': 'exit_code', 'desc': 'Fatal error: Exit code 1 ()', 'exit_code': 1, 'code_desc': '', 'error_level': 3}]
2022-06-27 17:46:36,794 ERROR [galaxy.jobs] fail(): Missing output file in working directory: [Errno 2] No such file or directory: '/tmp/tmpv0bf6i9k/job_working_directory/000/18/outputs/galaxy_dataset_e186ea7c-1414-4db6-bdc9-c3a477607611.dat'
2022-06-27 17:46:36,795 ERROR [galaxy.jobs] fail(): Missing output file in working directory: [Errno 2] No such file or directory: '/tmp/tmpv0bf6i9k/job_working_directory/000/18/outputs/galaxy_dataset_479a87b7-8403-4217-95e7-90e57789621a.dat'

Galaxy Version and/or server at which you observed the bug

Should be 582a7b9 (todays master branch)

To Reproduce

GALAXY_SLOTS=2 planemo test --biocontainers --no_dependency_resolution --no_conda_auto_init --galaxy_python_version 3.7 dada2_filterAndTrim.xml

Expected behavior

Test should be successful.
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jun 28, 2022
@bernt-matthias
JobWrapper: use correct fail method
6803572 
if the JobWrapper.fail method is called directly exit code (etc)
are lost.

fixes galaxyproject#14206

not sure why this error popped up now, probably a change in
tool verification ..?
@bernt-matthias bernt-matthias mentioned this issue Jun 28, 2022
Closed
5 tasks
@mvdbeek mvdbeek added this to the 22.05 milestone Jun 28, 2022
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jun 30, 2022
@bernt-matthias
add a test tool deleting output
5c0450e 
which should fail (galaxyproject#14206)
@bernt-matthias bernt-matthias mentioned this issue Jun 30, 2022
Draft
5 tasks
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jun 30, 2022
@bernt-matthias
add a test tool deleting output
cf618e6 
which should fail (galaxyproject#14206)
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 1, 2022
@bernt-matthias
JobWrapper: use correct fail method
361c9ad 
if the JobWrapper.fail method is called directly exit code (etc)
are lost.

fixes galaxyproject#14206

not sure why this error popped up now, probably a change in
tool verification ..?
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 4, 2022
@bernt-matthias
add a test tool deleting output
37b3225 
which should fail (galaxyproject#14206)
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Jul 4, 2022
@bernt-matthias
JobWrapper: use correct fail method
23b8cc2 
if the JobWrapper.fail method is called directly exit code (etc)
are lost.

fixes galaxyproject#14206

not sure why this error popped up now, probably a change in
tool verification ..?
@mvdbeek mvdbeek modified the milestones: 22.05, 22.09 Aug 22, 2022
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Aug 29, 2022
@bernt-matthias
JobWrapper: use correct fail method
c2566ec 
if the JobWrapper.fail method is called directly exit code (etc)
are lost.

fixes galaxyproject#14206

not sure why this error popped up now, probably a change in
tool verification ..?
bernt-matthias added a commit to bernt-matthias/galaxy that referenced this issue Sep 14, 2022
@bernt-matthias
JobWrapper: use correct fail method
8623e27 
if the JobWrapper.fail method is called directly exit code (etc)
are lost.

fixes galaxyproject#14206

not sure why this error popped up now, probably a change in
tool verification ..?
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JobWrapper: use correct fail method bernt-matthias/galaxy
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@mvdbeek @bernt-matthias