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[24.0] Don't set dataset peek for errored jobs #18231

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mvdbeek
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@mvdbeek mvdbeek commented May 27, 2024

This is consistent with the extended metadata logic, and prevents:

Message
Job wrapper finish method failed
Stack Trace

Newest

IndexError
list index out of range

which only makes it harder to diagnose the actual error, which in the
case of https://sentry.galaxyproject.org/share/issue/831261683ce642a4976efa20a9a0e55c/
is \nslurmstepd: error: *** JOB 1910486 ON js2-gpu-small0 CANCELLED AT 2024-05-26T23:30:00 DUE TO TIME LIMIT ***\n

Also merges line_count handling to common method, never fail further processing of the job if set_peek fails and fix gro set_peek method to produce a blurb indicating that the file is likely not a valid GRO file.

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

mvdbeek added 3 commits May 27, 2024 10:06
This is consistent with the extended metadata logic, and prevents:
```
Message
Job wrapper finish method failed
Stack Trace

Newest

IndexError
list index out of range
```
which only makes it harder to diagnose the actual error, which in the
case of https://sentry.galaxyproject.org/share/issue/831261683ce642a4976efa20a9a0e55c/
is `\nslurmstepd: error: *** JOB 1910486 ON js2-gpu-small0 CANCELLED AT 2024-05-26T23:30:00 DUE TO TIME LIMIT ***\n`
@jmchilton jmchilton merged commit 62b53c5 into galaxyproject:release_24.0 May 27, 2024
50 checks passed
@jdavcs jdavcs added this to the 24.1 milestone Jun 19, 2024
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3 participants