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Separate unread and read stats and logging files and avoid a circular rename #5141

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merged 13 commits into from
Nov 20, 2024

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This might fix #1727 by definitively moving stats and logging files from a stats/inbox directory to a stats/archive directory when the leader processes them. It no longer renames them back to the .new suffix they had when they were being written, which avoids trying to directly undo a rename that just happened from another node, which is a thing that a very broken filesystem might find confusing.

This also means we don't need to scan through all previously-processed stats and logging files to find new ones; we only have to scan stats/inbox.

Changelog Entry

To be copied to the draft changelog by merger:

  • Organize stats and logging files into stats/inbox and stats/archive and avoid a circular rename.

Reviewer Checklist

  • Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
    • If it is coming from an external repo, make sure to pull it in for CI with:
      contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
      
    • If there is no associated issue, create one.
  • Read through the code changes. Make sure that it doesn't have:
    • Addition of trailing whitespace.
    • New variable or member names in camelCase that want to be in snake_case.
    • New functions without type hints.
    • New functions or classes without informative docstrings.
    • Changes to semantics not reflected in the relevant docstrings.
    • New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
    • New features without tests.
  • Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
  • Finish the review with an overall description of your opinion.

Merger Checklist

  • Make sure the PR passes tests.
  • Make sure the PR has been reviewed since its last modification. If not, review it.
  • Merge with the Github "Squash and merge" feature.
    • If there are multiple authors' commits, add Co-authored-by to give credit to all contributing authors.
  • Copy its recommended changelog entry to the Draft Changelog.
  • Append the issue number in parentheses to the changelog entry.

@adamnovak adamnovak requested a review from stxue1 November 6, 2024 18:17
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Looks pretty good to me

@adamnovak adamnovak merged commit a5657cf into master Nov 20, 2024
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@adamnovak adamnovak deleted the issues/1727-avoid-circular-rename branch November 20, 2024 16:33
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cwltoil managing LSF will occasionally print dead jobs logging info repetitively in DEBUG mode
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