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Add leader fallback for worker file imports #5189

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@stxue1 stxue1 commented Dec 18, 2024

Resolves #5135

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To be copied to the draft changelog by merger:

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This looks pretty good, but I think one of the new functions is missing a docstring, and I'm not sure about the clarity of some of the variable/function names.

src/toil/cwl/cwltoil.py Outdated Show resolved Hide resolved
)

# files with a associated filesize that are valid to be imported on workers
valid_files_to_data = dict()
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This isn't really mapping to file data (bits in the file), right? This is metadata consisting of file size and... something.

Maybe this should be renamed and have a comment explaining what's actually in the values? Or an inline type hint and not just auto-typing?

basedir: str,
skip_remote: bool,
bypass_file_store: bool,
) -> tuple[Process, CWLObjectType]:
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I think this is missing a docstring.

It also might need a better name. It sounds like it is going to e.g. convert files from DOC to PDF or something, and really it is going to fill in Toil file IDs and replace URLs with other URLs.

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Add leader import fallback to running imports on workers
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