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[24.0] Fix various invocation export issues #19215

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mvdbeek
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@mvdbeek mvdbeek commented Nov 27, 2024

Fixes #18927 and #18995:

  • Make sure datasets and collections that are referenced multiple times are exported just once
  • Fix non-job invocation steps not being persisted
  • Break copied_from chain if copied_from source is not part of export
  • Don't store from_path on imported workflow, which prevents editing the associated workflow
  • Fix up action_arguments for workflows imported via gxformat2 (independent gxformat2 fix in Fix gxformat2 to .ga conversion if hide: true specified on output gxformat2#106)

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.

if the step is not a job step. This broke in galaxyproject@ab2f76c
where
```
                # Safeguard: imported_invocation_step was implicitly merged into this Session prior to SQLAlchemy 2.0.
                self.sa_session.add(imported_invocation_step)
```
was replaced with
```
ensure_object_added_to_session(imported_invocation, session=self.sa_session)
```
which seems like a small typo-like bug.
Without this change jobs like `__EXTRACT_DATASET__` would not be
included in a history or invocation export`.
It's a temporary path and probably doesn't make much sense in the
context of an imported invocation.
@mvdbeek mvdbeek force-pushed the 24_0_fix_various_invocation_export_issues branch from 6bccf37 to 91fc1d8 Compare November 27, 2024 18:04
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mvdbeek commented Nov 28, 2024

Test failures should all be unrelated.

@mvdbeek mvdbeek force-pushed the 24_0_fix_various_invocation_export_issues branch from 1503622 to e301ec9 Compare November 28, 2024 14:16
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mvdbeek commented Nov 29, 2024

Still all unrelated if someone wants to merge

@jmchilton jmchilton merged commit 1e6a5c0 into galaxyproject:release_24.0 Nov 29, 2024
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2 participants