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use cat-vrs-python and va-spec-python #388

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korikuzma opened this issue Jul 16, 2024 · 2 comments · Fixed by #404
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use cat-vrs-python and va-spec-python #388

korikuzma opened this issue Jul 16, 2024 · 2 comments · Fixed by #404
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enhancement New feature or request priority:high High priority

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We currently store Cat VRS + VA-Spec Pydantic models in https://github.com/cancervariants/metakb/tree/staging/src/metakb/schemas. However, we are now separating these out into their respective Python packages. There have also been many breaking changes in these models which are updated in cat-vrs-python and va-spec-python. We should remove the current schemas and leverage these python packages for the Pydantic models.
@korikuzma korikuzma added enhancement New feature or request priority:high High priority labels Jul 16, 2024
@korikuzma korikuzma self-assigned this Jul 16, 2024
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Will also update VRS-Python version

@korikuzma korikuzma mentioned this issue Oct 30, 2024
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@korikuzma korikuzma linked a pull request Nov 14, 2024 that will close this issue
feat!: use cat-vrs-python + va-spec-python #404
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korikuzma added a commit that referenced this issue Nov 20, 2024
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feat!: use cat-vrs-python + va-spec-python (#404)
261c065 
close #388 , #395, #309

* Breaking changes
  * Update/add ga4gh packages
    * Add `ga4gh.cat_vrs` + `ga4gh.va_spec` packages 
* The Pydantic models in these packages replace the manually created
models in `metakb/schemas/annotation.py`,
`metakb/schemas/categorical_variation.py`, and
`metakb/schemas/variation_statement.py`. (#388)
    * `ga4gh.vrs` version bumped
* The models in all ga4gh packages caused breaking changes (mainly
renaming) to the evidence models (such as #395)
* Represent categorical variation members and constraints properly
(#309)
  * Standardize representing normalizer data in extensions
* The `extension.name` will always be `vicc_normalizer_data` and value
will contain `id`, `label`, and optional `mondo_id` (for disease)
* Simplify assertion checks in tests
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Closed by #404.

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feat!: use cat-vrs-python + va-spec-python cancervariants/metakb
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