JobWrapper: use correct fail method #14210
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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 ..?
planemo started using outputs_to_working_directory with your PR (galaxyproject/planemo#1199), and we only recently cut a new release. Maybe backport to 21.09, then we (almost) cover the whole year of supported releases. Any chance you could add test tool for this and add it to https://github.com/galaxyproject/galaxy/blob/dev/test/integration/test_job_outputs_to_working_directory.py#L20 ? |
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Will add a test |
should be covered by a small change to strict_shell_profile.xml (added analogous changes to strict_shell_*.xml)
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If the test passes I will revert 6803572 .. to see if it works as desired...
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This reverts commit 6803572.
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@mvdbeek any idea why the test tool isn't failing after reverting the fix? Is the tool / the test environment missing something? |
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Galaxy seems to create the output files (empty) in the jwd before the job .. so it appears that the failing dada2 tool calls an Will adapt the test tool accordingly (or better create a new one). I think I will create a new PR targeting 21.09. |
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superseded by #14235 |
if the JobWrapper.fail method is called directly exit code (etc)
are lost.
fixes #14206
not sure why this error popped up now, probably a change in
tool verification ..?
For fixing the IUC CI job we probably need to backport this .. is 22.01 sufficient?
How to test the changes?
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