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Make promises harder to break#5457

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adamnovak wants to merge 2 commits intomasterfrom
issues/5456-broken-promises
Open

Make promises harder to break#5457
adamnovak wants to merge 2 commits intomasterfrom
issues/5456-broken-promises

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@adamnovak
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This should help with #5456 by making sure the update_file_stream() function can never result in an empty file if the writer crashes.

Previously, with the FileJobStore, we would truncate the old value before writing anything form the new stream. If the writer failed in the middle, the old value would be lost.

Now, all the job store implementations detect failure of the stream-writing context manager scope, and only commit the update if it succeeded.

I'm also making promise fulfillment log more, to see if we can catch #5456 again.

Changelog Entry

To be copied to the draft changelog by merger:

  • Updating files in the job store by stream is now atomic: either the stream writer succeeds and the new content is visible, or something goes wrong and the old content is visible

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 passed tests, including the Gitlab tests, for the most recent commit in its branch.
  • Make sure the PR has been reviewed. If not, review it. If it has been reviewed and any requested changes seem to have been addressed, proceed.
  • 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.

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