Fix bug when providing subactions in provenance #116
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If subactions are provided in the initial provenance or via set_provenance, they may be duplicated in the stored provenance if a module in the subaction list is run by the callback server. This fix processes initial subactions correctly.
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Pull Request Overview
This PR fixes a bug where subactions were being duplicated in provenance when they were provided in initial provenance and then executed by the callback server. The fix ensures subactions are processed correctly through the existing add_subaction method rather than being added directly to avoid duplication.
- Modified provenance initialization to use
add_subactionmethod for processing initial subactions - Updated test to use double quotes instead of single quotes for consistency
- Added comprehensive test case to verify subaction deduplication behavior
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| JobRunner/provenance.py | Fixed subaction initialization to prevent duplication by using add_subaction method |
| test/test_callback_server_integration.py | Updated quote style and added test case for subaction deduplication |
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bio-boris
approved these changes
Aug 18, 2025
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Seems like codecov has been having issues recently |
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If subactions are provided in the initial provenance or via set_provenance, they may be duplicated in the stored provenance if a module in the subaction list is run by the callback server. This fix processes initial subactions correctly.