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Allow importing on workers #5098

Merged
merged 7 commits into from
Sep 26, 2024
Merged

Allow importing on workers #5098

merged 7 commits into from
Sep 26, 2024

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stxue1
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@stxue1 stxue1 commented Sep 19, 2024

#5025

Changelog Entry

To be copied to the draft changelog by merger:

  • Added support to import files on workers for toil-cwl-runner
    • --runImportsOnWorkers to enable importing files on workers
    • --importWorkersDisk to control how much disk space the import worker will use

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.

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  • 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.

DailyDreaming
DailyDreaming previously requested changes Sep 19, 2024
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Looks good so far, but really needs a test.

src/toil/cwl/cwltoil.py Outdated
@@ -3143,7 +3177,7 @@ def __init__(
self.cwlwf = cwlwf
self.cwljob = cwljob
self.runtime_context = runtime_context
self.cwlwf = remove_pickle_problems(self.cwlwf)
self.cwlwf = self.cwlwf
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No-op.

src/toil/cwl/cwltoil.py
@@ -3111,7 +3141,11 @@ def hasChild(self, c: Job) -> Any:


def remove_pickle_problems(obj: ProcessType) -> ProcessType:
"""Doc_loader does not pickle correctly, causing Toil errors, remove from objects."""
"""
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This function is only called in one place now, other than itself. Is it safe to remove and was the issue resolved?

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I think it's still needed as I ran into this issue while creating the CWLImportJob. Something internal in the CWL tool object is unpickleable and must be removed. Before it was being called in every Job initialization, but now I moved it to be ran only once on the leader.

src/toil/cwl/cwltoil.py Outdated
@@ -1,4 +1,5 @@
"""Implemented support for Common Workflow Language (CWL) for Toil."""
import argparse
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Unused import?

src/toil/options/cwl.py
@@ -281,6 +282,21 @@ def add_cwl_options(parser: ArgumentParser, suppress: bool = True) -> None:
help=suppress_help or "Disable file streaming for files that have 'streamable' flag True",
dest="disable_streaming",
)
parser.add_argument(
"--runImportsOnWorkers", "--run-imports-on-workers",
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Can we add a test for this?

@adamnovak
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You have to say the magic word "Fixes #5025" or Github won't auto-link the PR to the issue.

@adamnovak adamnovak linked an issue Sep 24, 2024 that may be closed by this pull request
S3, Add runImportsOnWorkers parameter to execute imports from Worker #5025
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I'm not sure why https://ucsc-ci.com/databiosphere/toil/-/jobs/78630 timed out. The main Gitlab server did not drop off the network, and the newly added test runs to completion quickly on my machine.

@adamnovak adamnovak dismissed DailyDreaming’s stale review September 24, 2024 17:51

Looks like the requested changes have been made.

@adamnovak adamnovak merged commit 716eb1b into master Sep 26, 2024
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@adamnovak adamnovak deleted the issues/5025-import-on-workers branch September 26, 2024 16:30
@adamnovak adamnovak mentioned this pull request Oct 2, 2024
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@stxue1 stxue1 mentioned this pull request Oct 24, 2024
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@adamnovak adamnovak adamnovak approved these changes

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S3, Add runImportsOnWorkers parameter to execute imports from Worker
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@stxue1 @adamnovak @DailyDreaming