From b21606d0eab6113d1b102600b1ea1ab72d893dc8 Mon Sep 17 00:00:00 2001 From: Kori Kuzma Date: Wed, 30 Sep 2026 10:27:21 -0400 Subject: [PATCH] feat!: update submodules for gks -> gkm term change ga4gh-gks-term -> ga4gh-gkm-term --- src/ga4gh/cat_vrs/relations.py | 2 +- submodules/cat_vrs | 2 +- tests/validation/test_cat_vrs_models.py | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/ga4gh/cat_vrs/relations.py b/src/ga4gh/cat_vrs/relations.py index 6a7f3b6..7edeb52 100644 --- a/src/ga4gh/cat_vrs/relations.py +++ b/src/ga4gh/cat_vrs/relations.py @@ -19,7 +19,7 @@ class SystemUri(str, Enum): """Define constraints for systems used in relations""" SEQUENCE_ONTOLOGY = "http://www.sequenceontology.org" - GKS_ALLELE_RELATION = "ga4gh-gks-term:allele-relation" + GKS_ALLELE_RELATION = "ga4gh-gkm-term:allele-relation" def _build_relation_concept(relation: Relation, system: SystemUri) -> MappableConcept: diff --git a/submodules/cat_vrs b/submodules/cat_vrs index 4083598..6b467bf 160000 --- a/submodules/cat_vrs +++ b/submodules/cat_vrs @@ -1 +1 @@ -Subproject commit 408359835d13077feeb303d914d148b4b7868ac4 +Subproject commit 6b467bfafc9646ea84eb148ee580b83817505291 diff --git a/tests/validation/test_cat_vrs_models.py b/tests/validation/test_cat_vrs_models.py index da40408..38ca96f 100644 --- a/tests/validation/test_cat_vrs_models.py +++ b/tests/validation/test_cat_vrs_models.py @@ -331,7 +331,7 @@ def test_categorical_cnv( ] with pytest.raises( ValueError, - match="`DefiningLocationConstraint` found, but must contain at least one relation where `primaryCoding.code` is 'liftover_to' and `primaryCoding.system` is 'ga4gh-gks-term:allele-relation'.", + match="`DefiningLocationConstraint` found, but must contain at least one relation where `primaryCoding.code` is 'liftover_to' and `primaryCoding.system` is 'ga4gh-gkm-term:allele-relation'.", ): recipes.CategoricalCnv(**invalid_params) @@ -354,7 +354,7 @@ def test_categorical_cnv( MappableConcept( primaryCoding=Coding( code=code("transcribed_to"), - system="ga4gh-gks-term:allele-relation", + system="ga4gh-gkm-term:allele-relation", ) ) ] @@ -364,7 +364,7 @@ def test_categorical_cnv( ] with pytest.raises( ValueError, - match="`DefiningLocationConstraint` found, but must contain at least one relation where `primaryCoding.code` is 'liftover_to' and `primaryCoding.system` is 'ga4gh-gks-term:allele-relation'.", + match="`DefiningLocationConstraint` found, but must contain at least one relation where `primaryCoding.code` is 'liftover_to' and `primaryCoding.system` is 'ga4gh-gkm-term:allele-relation'.", ): recipes.CategoricalCnv(**invalid_params)