fix: Remove incomplete marker for job finished only after metadata is written #3197
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🧹 Outside diff range and nitpick comments (1)
snakemake/persistence.py (1)
355-355: Consider adding error handling around metadata operations.While the change fixes the immediate issue, consider these improvements:
- Wrap metadata operations in try-except to ensure incomplete marker is only removed if metadata is successfully written
- Consider making file operations async for better performance
Example implementation:
async def finished(self, job): if not self.dag.workflow.execution_settings.keep_metadata: # do not store metadata if not requested return + try: code = self._code(job.rule) # ... existing code ... for f in job.output: # ... existing code ... self._record( self._metadata_path, { # ... existing metadata ... }, f, ) + self._remove_incomplete_marker(job) + except Exception as e: + logger.error(f"Failed to write metadata: {e}") + raise - self._remove_incomplete_marker(job)
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🔇 Additional comments (1)
snakemake/persistence.py (1)
355-355: LGTM! This change fixes the metadata recording issue.
Moving the _remove_incomplete_marker call after metadata is written ensures that the job"s start time is properly preserved in the metadata. This is crucial for accurate runtime reporting in plots.
johanneskoester
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Nov 12, 2024
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Nov 21, 2024
Fix: This PR adds back the removal of the incomplete marker file also when keep_metadata is False (i.e. --drop-metadata is active). The removal calls were merged and put at the start of the function in #3162, but this caused loss of starttime info in the metadata record. In #3197 this was fixed, but by moving the removal call to the end of the function, the incomplete tracker file was not removed anymore when --drop-metadata was active. This PR adds the call to the removal function back also for that case, and adds a note to inform why the code is structured this way. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Bug Fixes** - Improved handling of job metadata by ensuring the incomplete marker is removed only after successful metadata record creation, preserving job start time. - **Documentation** - Added clarifying comments to explain changes regarding the incomplete marker removal. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: Johannes Köster <[email protected]>
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🤖 I have created a release *beep* *boop* --- ## [8.25.4](v8.25.3...v8.25.4) (2024-11-27) ### Bug Fixes * clean env vars in apptainer ([#3199](#3199)) ([76d5329](76d5329)) * ensure that intermediate files in job groups do not cause spurious mtime errors when checking for consistency with output files ([#3220](#3220)) ([4ba2bdf](4ba2bdf)) * Remove incomplete marker also when drop-metadata is active ([#3215](#3215)) ([a4f2e5c](a4f2e5c)) * Remove incomplete marker for job finished only after metadata is written ([#3197](#3197)) ([6567e5f](6567e5f)) * Support versioned URLs in Asset class and fix missing versions in Snakemake report ([#3203](#3203)) ([f086f6c](f086f6c)) * update rust-script usage to recent version (v0.35.0) [#3183](#3183) ([#3208](#3208)) ([43885d7](43885d7)) ### Documentation * clarify continuously updated input section ([#3219](#3219)) ([72a6994](72a6994)) * Fix typo in CHANGELOG.md ([#3198](#3198)) ([0e445ed](0e445ed)) * refer to Merkle trees instead of "blockchain" in caching.rst ([#3216](#3216)) ([282e5d9](282e5d9)) * remove twitter in favor of bluesky and mastodon ([#3217](#3217)) ([231c6df](231c6df)) * use "dictionary" not "array" wording in config docs ([#3156](#3156)) ([17aed41](17aed41)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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This PR makes Snakemake remove the incomplete marker for a job thats finished only after the metadata is written. Otherwise the jobs starttime for the report was missing in the metadata and caused problems in the plot for the runtimes of individual jobs.
Summary by CodeRabbit
Bug Fixes
Refactor
finishedmethod for better clarity and maintainability while retaining existing functionality.