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feat(gks)!: add constraints to categorical variants#233

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issue-217-add-oncofrom
issue-209
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feat(gks)!: add constraints to categorical variants#233
korikuzma wants to merge 1 commit into
issue-217-add-oncofrom
issue-209

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@korikuzma

@korikuzma korikuzma commented Jun 5, 2026

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close #209

  • Migrate work from metakb (@jsstevenson helped write this code)
  • Adds Variation Normalizer REST Data Proxy to retrieve normalized VRS variations (only supports Allele and CopyNumberChange)
  • Require that Molecular Profiles represented as Categorical Variants use constraints
  • Add identifiers to mappings in Categorical Variant

@korikuzma korikuzma self-assigned this Jun 5, 2026

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Would love to eventually split out the current test_exports.py module

molecular_profile, expressions, variation_normalizer
)

super().__init__(

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Open question: Should we be returning the recipes, such as PSC, CategoricalCNV, etc? Or have downstream users validate these constraints?

@korikuzma korikuzma changed the base branch from issue-217 to issue-217-add-onco June 24, 2026 14:28
close #209

* Migrate work from metakb (@jsstevenson helped write this code)
* Adds Variation Normalizer REST Data Proxy to retrieve normalized VRS variations (only supports Allele and CopyNumberChange)
* Require that Molecular Profiles represented as Categorical Variants use constraints

Co-authored-by: James Stevenson <james.stevenson@nationwidechildrens.org>
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