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feat!: store allele origin as mapping, not extension #236

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feat!: store allele origin as mapping, not extension #236

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feat!: store allele origin as mapping, not extension
korikuzma Jun 23, 2026
6b48250
dont hardcode + apply aw suggestions
korikuzma Jun 25, 2026
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7 changes: 6 additions & 1 deletion civicpy/exports/civic_gks_record.py
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Expand Up @@ -634,7 +634,12 @@ def get_allele_origin_qualifier(record: Evidence | Assertion) -> MappableConcept

return MappableConcept(
name=VARIANT_ORIGIN_TO_ALLELE_ORIGIN[variant_origin],
extensions=[Extension(name="civic_variant_origin", value=variant_origin)],
mappings=[
ConceptMapping(
coding=Coding(code="SOMATIC", system="https://civicdb.org"),
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relation=Relation.EXACT_MATCH,
)
],
)

@staticmethod
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7 changes: 6 additions & 1 deletion civicpy/tests/test_exports.py
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Expand Up @@ -368,7 +368,12 @@ def gks_therapeutic_proposition(gks_mpid33, gks_gid19, gks_tid146, gks_did8):
"geneContextQualifier": gks_gid19,
"alleleOriginQualifier": {
"name": "somatic",
"extensions": [{"name": "civic_variant_origin", "value": "SOMATIC"}],
"mappings": [
{
"coding": {"code": "SOMATIC", "system": "https://civicdb.org"},
"relation": "exactMatch",
}
],
},
"predicate": "predictsSensitivityTo",
"objectTherapeutic": gks_tid146,
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