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Add fallback protection to Rosetta pipeline #375

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alex-l-kong opened this issue May 18, 2023 · 1 comment
Open

Add fallback protection to Rosetta pipeline #375

alex-l-kong opened this issue May 18, 2023 · 1 comment
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enhancement New feature or request

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@alex-l-kong
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Is your feature request related to a problem? Please describe.

If the Rosetta pipeline crashes in the middle of a process, there isn't a recovery scheme in place to prevent needing to re-run it in its entirety. The functions where this has been problematic:

  • copy_image_files
  • generate_rosetta_test_imgs
  • create_tiled_comparison
  • add_source_channel_to_tiled_image
  • compensate_image_data

Even over Ethernet connection to the NAS, certain processes can still take several hours.

Describe the solution you'd like

These functions, and the notebook itself, need to bypass files and directories that have already been created. This involves adding additional checks similar to what we do in the Pixie pipeline.

@alex-l-kong alex-l-kong added the enhancement New feature or request label May 18, 2023
@ngreenwald
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I think #403 should help to speed up the testing workflow. This would still be worth doing for the actual compensation step though, since is run across the entire cohort.

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