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Anonymous access to Google Storage #4518

Merged
merged 14 commits into from
Jul 18, 2023
Merged

Anonymous access to Google Storage #4518

merged 14 commits into from
Jul 18, 2023

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adamnovak
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@adamnovak adamnovak commented Jun 29, 2023

This fixes #4517.

Changelog Entry

To be copied to the draft changelog by merger:

  • Toil can now read gs:// URIs without a Google account and Google Cloud billing project
  • WDL tests can now run with Singularity or Docker
  • Stopped WDL input polling from failing before polling all the places by fixing import file existence sniffing

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 mr-c June 29, 2023 17:17
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@mr-c mr-c left a comment

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LGTM, except for one small typo

src/toil/jobStores/abstractJobStore.py Outdated Show resolved Hide resolved
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@DailyDreaming DailyDreaming left a comment

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LGTM.

@mr-c mr-c force-pushed the issues/4517-anonymous-gs branch from 574445c to ae44b4f Compare July 18, 2023 08:12
@mr-c mr-c enabled auto-merge (squash) July 18, 2023 08:12
@mr-c mr-c merged commit aaa451b into master Jul 18, 2023
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Enable anonymous access to public Google Storage URIs
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