[26.0] Fix AttributeError serializing implicit output collections during job prep#22034
Merged
mvdbeek merged 2 commits intogalaxyproject:release_26.0from Mar 10, 2026
Conversation
… prep For map-over jobs, `io_dicts(exclude_implicit_outputs=True)` unconditionally included `output_dataset_collections` (JobToImplicitOutputDatasetCollectionAssociation). These are shared DatasetCollections with N precreated elements where only the current job's element has its HDA set. Serializing the full collection during metadata setup crashes on the N-1 unpopulated elements. Exclude these implicit output collections when `exclude_implicit_outputs=True`, consistent with the existing exclusion of output_dataset_collection_instances. Fixes galaxyproject#22015
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
For map-over jobs,
io_dicts(exclude_implicit_outputs=True)unconditionally includedoutput_dataset_collections(JobToImplicitOutputDatasetCollectionAssociation). These are shared DatasetCollections with N precreated elements where only the current job's element has its HDA set. Serializing the full collection during metadata setup crashes on the N-1 unpopulated elements.Exclude these implicit output collections when
exclude_implicit_outputs=True, consistent with the existing exclusion of output_dataset_collection_instances.Fixes #22015
Don't love the test but it's tricky to test in a real workflow, I think you'd have to be able to have discovered outputs be ready at different points. The unit test though make it really clear that we're dealing with an implicit output collection and that the change is correct.
How to test the changes?
(Select all options that apply)
License