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Changes reflecting ClinVar API updates and improvements

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@northwestwitch northwestwitch released this 28 Nov 13:57

[2.0]

Added

  • A new tsv_2_json endpoint to convert TSV files in json submission objects
  • Keep a Changelog GitHub action
  • Black GitHub action
  • Flake8 Lint GitHub action
  • Vulture GitHub action
  • Woke GitHub action
  • Badges showing the status of GitHub actions on README page
  • File conversion endpoints accept optional parameters to set the following key/values: submissionName, clinvarSubmissionReleaseStatus, assertionCriteria

Changed

  • New API schema introduced on 2022-11-21
  • Modified file parsing code to create submission jsons compliant with the new API
  • Renamed the old demo CSV files to FILENAME_before_221121.csv
  • Demo json submission file to include submissionName and clinvarSubmissionReleaseStatus key/values

Fixed

  • Do not crash when parsing Variant CSV files with no assertion criteria
  • Simplify and fix CSV and TSV files parsing