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CIDC-1713 CIDC-1714 add serum, dna qc text #579

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merged 3 commits into from
May 2, 2023
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scvannost
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What

  1. Allow type string for DNA QC markers in normal blood/tissue and tumor tissue DNA manifests
  2. Add Serum as valid processed_sample_type

Why

  1. For 10057 / TCR, DNA QC were not recorded, want to use a string N/A value to correct represent
  2. For 2017-0349 / olink, were submitted as first batch of serum samples

How

  1. Update schemas/sample.json
  2. Regenerate all shipping manifests (since they use processed_sample_type)

Remarks

Didn't add any tests for the new values.

Checklist

Please include and complete the following checklist. You can mark an item as complete with the - [x] prefix:

  • Tests - Added unit tests for new code, regression tests for bugs and updated the integration tests if required
  • Formatting & Linting - black and flake8 have been used to ensure styling guidelines are met
  • Type Annotations - All new code has been type annotated in the function signatures using type hints
  • Docstrings - Docstrings have been provided for functions
  • Documentation - Documentation in docs/ has be regenerated and README and CHANGELOG have been updated to explain major changes & new features
  • Package version - Manually bumped the Schemas package version in cidc_schemas/__init__.py

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@crouchcd crouchcd left a comment

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@scvannost Looks good to me. We were definitely on the same page which is reassuring. The only thing I noticed is the "Legend" for the DNA QC columns is still showing "Number" not "Number, String".

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codeclimate bot commented Apr 27, 2023

Code Climate has analyzed commit bfaea02 and detected 0 issues on this pull request.

The test coverage on the diff in this pull request is 100.0% (50% is the threshold).

This pull request will bring the total coverage in the repository to 94.4% (0.0% change).

View more on Code Climate.

@scvannost scvannost merged commit be412fb into master May 2, 2023
@scvannost scvannost deleted the manifest-tweaks branch May 2, 2023 14:38
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2 participants