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Fix setting env and tags on resubmission #19753

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Fix setting env and tags on resubmission #19753

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bernt-matthias
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supersedes #9747

Targeting 24.1 because that's the version I'm using ... will deploy this fix now on my test instance

How to test the changes?

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  • 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]

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

@github-actions github-actions bot changed the title [24.1] Fix setting env and tags on resubmission Fix setting env and tags on resubmission Mar 6, 2025
@github-actions github-actions bot added this to the 25.0 milestone Mar 6, 2025
@nsoranzo nsoranzo changed the base branch from dev to release_24.1 March 6, 2025 14:05
@github-actions github-actions bot changed the title Fix setting env and tags on resubmission [24.1] Fix setting env and tags on resubmission Mar 6, 2025
@nsoranzo
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nsoranzo commented Mar 6, 2025

Targeting 24.1 because that's the version I'm using

I've changed the target branch accordingly.

@mvdbeek mvdbeek requested a review from a team March 25, 2025 15:11
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mvdbeek commented Mar 26, 2025

I am a little worried about this kind of change with not a lot of test coverage targeting releases that are not even the last stable version.

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mvdbeek commented Mar 26, 2025

test/integration/test_job_resubmission.py::TestJobResubmissionToolDetectedErrorResubmitsIntegration::test_dynamic_resubmission - galaxy.tool_util.verify.interactor.JobOutputsError: Expected job to fail but Galaxy indicated the job successfully completed.

looks relevant ?

@bernt-matthias
fix resubmission integration test
70bfcc4 
the test `test/integration/test_job_resubmission.py::TestJobResubmissionToolDetectedErrorResubmitsIntegration`
resubmits with:

```
        <destination id="local_resubmit" runner="local">
            <env id="GX_TARGET_EXIT_CODE">4</env>
            <resubmit condition="tool_detected_failure" destination="local_good" />
        </destination>

        <destination id="local_good" runner="local">
            <env id="GX_TARGET_EXIT_CODE">0</env>
        </destination>
```

since env variables are lost on resubmission the current test
was still evaluated successful (because `${GX_TARGET_EXIT_CODE:-0}`).
Now the test fails if `GX_TARGET_EXIT_CODE` is not set.
@bernt-matthias
set env and tags on resubmission
8165b9e 
supersedes galaxyproject#9747
@bernt-matthias
fix test tool test
0247be1
@bernt-matthias
fix test
5b017b2 
tool fails with no env var set
failing tool tests allow no output
@bernt-matthias bernt-matthias changed the base branch from release_24.1 to dev March 26, 2025 12:53
@bernt-matthias bernt-matthias changed the title [24.1] Fix setting env and tags on resubmission Fix setting env and tags on resubmission Mar 26, 2025
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I am a little worried about this kind of change with not a lot of test coverage targeting releases that are not even the last stable version.

Agreed. Lets go for dev.

looks relevant ?

Will have a look.

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@bernt-matthias @nsoranzo @mvdbeek