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Patched cleanup_archer_fastqs(), added test generation script #5

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merged 1 commit into from
May 3, 2024

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@g-pyxl g-pyxl commented May 3, 2024

  1. Patch applied to cleanup_archer_fastqs(). In multiple project_id (e.g., ADX12345: 1001, 1002, 1003) runs, the first iteration of the main loop deletes fastqs for all projects linked to the same ADX number. Sequential loops then return an error and break the loop due to absence of these files this this stage.

cleanup_archer_fastqs() will now return True when project_id specific fastqs are not present, and simply log a warning rather than an error. This allows final stages for each sequential loop (update_list_archived_projects(), cleanup_genomics_server()) to safely complete as data must successfully uploaded to DNAnexus before loop can reach this stage.

  1. Added generate_test_data.py script. Allows user to generate/teardown a structured series of blank tar.gz, fastq.gz and symlinks within the test directories on the Archer server to facilitate safer end-to-end testing of main scripts. Instructions added to README.md within the testing section.

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Reviewed 3 of 3 files at r1, all commit messages.
Reviewable status: :shipit: complete! all files reviewed, all discussions resolved (waiting on @g-pyxl)

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Reviewable status: :shipit: complete! all files reviewed, all discussions resolved (waiting on @g-pyxl)

@rebeccahaines1 rebeccahaines1 merged commit 6423931 into main May 3, 2024
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@rebeccahaines1 rebeccahaines1 deleted the cleanup_patch branch May 3, 2024 15:45
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2 participants