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refactor: simplify default resolvers and local storage data #241

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merged 1 commit into from
Apr 15, 2024

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mmalenic
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Closes #239, there's no need for the defaults to be any more complicated than a 1-1 mapping.

Changes

  • Change default resolvers to .* and $0, and default local storage locations to the current directory.
    • When running with default settings, data can still be fetched from data/.../<id>.
    • Docker examples also work with a 1-1 mapping between the mount point and url paths.

@mmalenic mmalenic self-assigned this Apr 15, 2024
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@brainstorm brainstorm left a comment

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Thanks @mmalenic!

So if I understand the description of changes correctly hartwigmedical/hmftools#541 (and other third parties like GA4GH and NBIS) don't need to change their docker run nor client invocations because data/ is greedily matched now via .* (instead of (data)/(.*)).

Great!

@mmalenic
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So if I understand the description of changes correctly hartwigmedical/hmftools#541 (and other third parties like GA4GH and NBIS) don't need to change their docker run nor client invocations because data/ is greedily matched now via .* (instead of (data)/(.*)).

Yep, basically, data is now matched like any other path component. If it's present in the directory htsget is launched from (or mounted in the docker container), it can used as a file source, and so can any other directory.

@mmalenic mmalenic added this pull request to the merge queue Apr 15, 2024
Merged via the queue into main with commit c84be9a Apr 15, 2024
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@mmalenic mmalenic deleted the refactor/default-resolvers branch September 24, 2024 01:30
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Simplify resolver match logic
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