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429 implement tool to fix mal-formed urls #430

Merged
merged 3 commits into from
Mar 18, 2025
Merged

429 implement tool to fix mal-formed urls #430

merged 3 commits into from
Mar 18, 2025

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mbthornton-lbl
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@mbthornton-lbl mbthornton-lbl commented Mar 14, 2025 •
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This PR provides a command fix-data-object-urls that:

  • Finds DataObjects with mal-formed URLS - in this case including the incorrect path with /ficus/ in the path and:
    • Updates the URL in the DataObject to the correct URL if the data_object_type is not raw sequencing
    • Deletes the URL if the DataObject is raw sequencing
  • validates the updated data_object_set
  • if selected, submit the updated data object set to the metadata:submit endpoint

Successfully tested in the dev environment - verified that the corrected URLs were resolvable

@mbthornton-lbl mbthornton-lbl linked an issue Mar 14, 2025 that may be closed by this pull request
Implement tool to fix mal-formed URLs #429
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@mbthornton-lbl mbthornton-lbl mentioned this pull request Mar 14, 2025
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@mbthornton-lbl mbthornton-lbl linked an issue Mar 14, 2025 that may be closed by this pull request
raw fastq data object files have a url that doesn't resolve #422
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bioscales_urls_no_update.log

@kaijli
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kaijli commented Mar 17, 2025

@mbthornton-lbl can this be merged?

@kaijli kaijli mentioned this pull request Mar 17, 2025
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@mbthornton-lbl mbthornton-lbl merged commit bf9d226 into main Mar 18, 2025
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@aclum aclum aclum approved these changes

@kaijli kaijli Awaiting requested review from kaijli

@AmitBinf AmitBinf Awaiting requested review from AmitBinf

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Implement tool to fix mal-formed URLs raw fastq data object files have a url that doesn't resolve
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