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[21.01] Use keep_original in pysam.tabix_index to not remove original data #11913

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mvdbeek
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@mvdbeek mvdbeek commented Apr 29, 2021

What did you do?

  • Use keep_original in pysam.tabix_index to not remove original data

Without this you can take a VCF dataset, switch it to VcfGz, and then see that the source dataset is gone (it's now compressed at source_dataset_path.gz).

Why did you make this change?

Had an odd case of a disappearing dataset from a data library reported.

How to test the changes?

(select the most appropriate option; if the latter, provide steps for testing below)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    take a VCF dataset, switch it to VcfGz, and then see that the source dataset is not gone

License

For UI Components

  • I've included a screenshot of the changes

@github-actions github-actions bot added this to the 21.05 milestone Apr 29, 2021
@mvdbeek mvdbeek merged commit 26049fa into galaxyproject:release_21.01 May 3, 2021
@galaxyproject galaxyproject deleted a comment from github-actions bot May 3, 2021
@nsoranzo nsoranzo deleted the keep_original_keep_data branch May 3, 2021 15:39
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3 participants