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feat!: update models to ga4gh gks nov 2024 ballot releases #420

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merged 19 commits into from
Feb 14, 2025

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korikuzma
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@korikuzma korikuzma commented Jan 21, 2025

Marking this as medium priority, since I can work locally for now. But this is required for VarCat MVP / ClinVar submission.

close #415

Changes:

  • Update vicc normalizers and ga4gh gks versions to point to latest ballot releases
    • This also updates transformers to use correct representations with these new models
  • Therapeutic Procedure / Agent --> Therapy rename to align with GKS

Comments:

  • In a previous version, we created Proposition nodes in the database. Since we need to get something out ASAP, I did not create these. If needed in the future, we can create a new issue.
  • CIViC was generated used the cache here

Still todo before opening/merging:

  • Use VA Spec pypi package (once made)

@korikuzma korikuzma added enhancement New feature or request priority:medium Medium priority labels Jan 21, 2025
@korikuzma korikuzma self-assigned this Jan 21, 2025
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@katiestahl @mcannon068nw This is ready for review. Keeping as draft so I don't forget to change deps to use VA Spec pypi package

@korikuzma korikuzma changed the base branch from staging to resolve-ruff January 24, 2025 15:50
Base automatically changed from resolve-ruff to staging January 24, 2025 16:21
mcannon068nw
mcannon068nw previously approved these changes Jan 28, 2025
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looks good to me!

katiestahl
katiestahl previously approved these changes Feb 4, 2025
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so sorry, thought I had approved this a while ago. I think I forgot to hit submit. Looks good to me!

@korikuzma korikuzma dismissed stale reviews from katiestahl and mcannon068nw via 79afbe6 February 13, 2025 23:56
@korikuzma korikuzma marked this pull request as ready for review February 14, 2025 14:56
@korikuzma korikuzma merged commit c36a564 into staging Feb 14, 2025
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@korikuzma korikuzma deleted the issue-415 branch February 14, 2025 14:58
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Update transformers to use the Nov 2024 ballot releases
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