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Rework PRP inputs and add upload #109

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Rework PRP inputs and add upload #109

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mhkc
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@mhkc mhkc commented Jan 13, 2025

This PR makes some major revision to PRP.

  1. It replaces the create-bonsai-input command with parse.
  2. Uses a config file with paths to all relevant files as input instead of the old json blob.
  3. It adds a command to upload samples to bonsai.

@mhkc mhkc linked an issue Jan 13, 2025 that may be closed by this pull request
Use config with file paths as input #95
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So we are removing rerun_bonsai_input()? We should also remove create_cdm_input() becasue it is not processing results, it's calculating qc information.

@mhkc mhkc force-pushed the 95-use-config-with-file-paths-as-input branch from 24fc788 to 0aad7c3 Compare January 14, 2025 15:00
@mhkc mhkc requested a review from ryanjameskennedy January 14, 2025 15:04
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mhkc commented Jan 14, 2025 •
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So we are removing rerun_bonsai_input()? We should also remove create_cdm_input() becasue it is not processing results, it's calculating qc information.

It has been renamed and reworked to be more clear and easier to read. The create_cdm_input has been renamed to cdm and tweaked to take the sample config as input.

I think we should keep cdm in PRP. Its one of those vital things for processing the JASEN output.

@mhkc mhkc force-pushed the 95-use-config-with-file-paths-as-input branch from 60e00cb to 99e2a72 Compare January 14, 2025 15:18
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Use config with file paths as input
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@mhkc @ryanjameskennedy