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Implement removing leading whitespace from un-evaluated String expressions #4891

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This should fix #4854 by implementing the spec behavior of removing common leading whitespace before substituting in the values in the expressions.

It still can't handle a line that begins with a placeholder or an expression that has whitespace within placeholders; it will find the common leading whitespace of other lines and remove that.

This will break some workflows that expect to be able to dedent beyond where the command string starts. I have an argument to the function for this but it's not bound out to the command line.

This should have tests, but currently doesn't, beyond the conformance tests.

Changelog Entry

To be copied to the draft changelog by merger:

  • toil-wdl-runner now removes whitespace before evaluating command strings.

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 and others added 30 commits April 29, 2024 11:58
…tespace' into issues/4854-common-leading-whitespace
…tespace' into issues/4854-common-leading-whitespace
…tespace' into issues/4854-common-leading-whitespace
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Successfully merging this pull request may close these issues.

Handle leading whitespace in WDL command blocks more correctly
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