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Move and re-use persist_extra_files #16955

Merged
merged 4 commits into from
Nov 1, 2023
Merged

Move and re-use persist_extra_files #16955

merged 4 commits into from
Nov 1, 2023

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mvdbeek
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@mvdbeek mvdbeek commented Nov 1, 2023 •
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This is in preparation of improving the directory datatype.

#BIOHACKEU23

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 mvdbeek added kind/refactoring cleanup or refactoring of existing code, no functional changes area/objectstore labels Nov 1, 2023
@github-actions github-actions bot added this to the 23.2 milestone Nov 1, 2023
@jmchilton
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What an obviously solid and useful fix. I really love this.

@mvdbeek
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mvdbeek commented Nov 1, 2023

just a sec though, the integration test failure is real.

@mvdbeek mvdbeek marked this pull request as draft November 1, 2023 15:40
nsoranzo
nsoranzo reviewed Nov 1, 2023
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lib/galaxy/job_execution/output_collect.py Outdated Show resolved Hide resolved
lib/galaxy/objectstore/__init__.py Outdated Show resolved Hide resolved
@mvdbeek mvdbeek force-pushed the unify_extra_files_path_persistence branch 2 times, most recently from 274b720 to e6f3169 Compare November 1, 2023 17:59
@mvdbeek
Move and re-use persist_extra_files
f0dd85c
@mvdbeek
Fix wrong relpath calculation if object store cache is used
3776f9c
@mvdbeek
Fix typo-ish bug with persisting collection element extra files
3f3e451 
I suppose we have no way to express in tools that we are discovering
collection elements with extra files, and that's why that hasn't caused
any problems ? Caught by 🦅👀!
@mvdbeek mvdbeek force-pushed the unify_extra_files_path_persistence branch from 7ad16a1 to 3f3e451 Compare November 1, 2023 18:24
@mvdbeek mvdbeek marked this pull request as ready for review November 1, 2023 20:40
nsoranzo
nsoranzo approved these changes Nov 1, 2023
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lib/galaxy/objectstore/__init__.py Outdated Show resolved Hide resolved
lib/galaxy/job_execution/output_collect.py Outdated Show resolved Hide resolved
@mvdbeek @nsoranzo
Add return type annotation for collect_extra_files
dbca442 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
@mvdbeek mvdbeek merged commit 8dad464 into galaxyproject:dev Nov 1, 2023
38 of 42 checks passed
@nsoranzo nsoranzo deleted the unify_extra_files_path_persistence branch November 2, 2023 17:47
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@jmchilton jmchilton jmchilton approved these changes

@nsoranzo nsoranzo nsoranzo approved these changes

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@mvdbeek @jmchilton @nsoranzo