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feat!: update submodules for gks -> gkm term change #52

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Merged
korikuzma merged 1 commit into from
Sep 30, 2026
Merged

feat!: update submodules for gks -> gkm term change #52

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2 changes: 1 addition & 1 deletion src/ga4gh/cat_vrs/relations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion submodules/cat_vrs
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Submodule cat_vrs updated 37 files
+1 −1 README.md
+1 −1 docs/source/_includes/_guidance_ga4gh_gkm_term_warning.rst
+2 −2 docs/source/_includes/_guidance_match_characteristic_sequence_location.rst
+4 −4 docs/source/appendices/design_decisions.rst
+9 −9 docs/source/concepts/Constraints/DefiningAlleleConstraint.rst
+4 −4 docs/source/concepts/Constraints/DefiningLocationConstraint.rst
+2 −2 docs/source/concepts/Recipes/CanonicalAllele.rst
+2 −2 docs/source/concepts/Recipes/CategoricalCnv.rst
+1 −1 docs/source/concepts/Recipes/ProteinSequenceConsequence.rst
+1 −1 docs/source/conf.py
+4 −5 docs/source/getting_involved.rst
+1 −1 docs/source/quickstart.rst
+4 −3 docs/source/rst_epilog
+1 −1 examples/json/braf-v600.annotated.json
+1 −1 examples/json/braf-v600.json
+1 −1 examples/json/canonicalAllele-ex1.json
+1 −1 examples/json/canonicalAllele-ex2.json
+2 −2 examples/json/categoricalCnv-ex1.json
+2 −2 examples/json/categoricalCnv-ex2.json
+2 −2 examples/json/categoricalCnv-ex3.json
+2 −2 examples/json/tp53-copy-loss.annotated.json
+2 −2 examples/json/tp53-copy-loss.json
+1 −1 examples/yaml/braf-v600.annotated.yaml
+1 −1 examples/yaml/braf-v600.yaml
+1 −1 examples/yaml/canonicalAllele-ex1.yaml
+1 −1 examples/yaml/canonicalAllele-ex2.yaml
+2 −2 examples/yaml/categoricalCnv-ex1.yaml
+2 −2 examples/yaml/categoricalCnv-ex2.yaml
+2 −2 examples/yaml/categoricalCnv-ex3.yaml
+2 −2 examples/yaml/tp53-copy-loss.annotated.yaml
+2 −2 examples/yaml/tp53-copy-loss.yaml
+1 −1 schema/cat-vrs/def/ConceptSet.rst
+1 −1 schema/cat-vrs/def/iriReference.rst
+1 −1 schema/cat-vrs/json/CanonicalAllele
+1 −1 schema/cat-vrs/json/CategoricalCnv
+2 −2 schema/cat-vrs/recipes-source.yaml
+1 −1 submodules/vrs
6 changes: 3 additions & 3 deletions tests/validation/test_cat_vrs_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand All @@ -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",
)
)
]
Expand All @@ -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)

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