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feat: update models to gkm-core 1.2.0 and vrs 2.1.0 #652

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

feat: update models to gkm-core 1.2.0 and vrs 2.1.0 #652

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2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
[submodule "submodules/vrs"]
path = submodules/vrs
url = https://github.com/ga4gh/vrs.git
branch = 2.1.0-snapshot.2026-02
branch = 2.1
12 changes: 8 additions & 4 deletions src/ga4gh/core/models.py
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Expand Up @@ -22,9 +22,9 @@


class GKSCoreMetadataMixin(GKSMetadataMixin):
"""Provide GKS-Core model metadata."""
"""Provide gkm-core model metadata."""

_product_name = "gks-core"
_product_name = "gkm-core"
_product_version = CORE_VERSION


Expand Down Expand Up @@ -220,7 +220,7 @@ class ConceptMapping(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
)


class ConceptSet(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
class ConceptSet(GKSCoreMetadataMixin, Entity, BaseModelForbidExtra):
"""A set of concepts that may be considered as dependent (occurring together), or
independent (existing separately) in the context of some knowledge reported about
them, as indicated by a set membership operator. e.g. a set of independent molecular
Expand Down Expand Up @@ -271,11 +271,15 @@ class Extension(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
)


class MappableConcept(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
class MappableConcept(GKSCoreMetadataMixin, Entity, BaseModelForbidExtra):
"""A concept based on a primaryCoding and/or name that may be mapped to one or more other `Codings`."""

_maturity: ClassVar[Maturity] = Maturity.TRIAL_USE

type: Literal["MappableConcept"] = Field(
default="MappableConcept",
description='MUST be "MappableConcept".',
)
conceptType: str | None = Field( # noqa: N815
default=None,
description="A term indicating the type of concept being represented by the MappableConcept.",
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4 changes: 2 additions & 2 deletions src/ga4gh/core/version.py
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@@ -1,3 +1,3 @@
"""Define GKS-Core version"""
"""Define GKM-Core version"""

CORE_VERSION = "1.1.0"
CORE_VERSION = "1.2.0"
2 changes: 1 addition & 1 deletion src/ga4gh/vrs/version.py
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@@ -1,3 +1,3 @@
"""Define VRS version"""

VRS_VERSION = "2.1.0-snapshot.2026-02.2"
VRS_VERSION = "2.1.0"
2 changes: 1 addition & 1 deletion submodules/vrs
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Submodule vrs updated 82 files
+75 −0 .claude/CLAUDE.md
+2 −0 .gitignore
+4 −4 .gitmodules
+14 −1 .pre-commit-config.yaml
+92 −0 CITATION.cff
+1 −1 README.md
+0 −5 TODO
+5 −5 docs/source/appendices/design_decisions.rst
+145 −47 docs/source/appendices/maturity_model.rst
+11 −11 docs/source/concepts/AdditionalDataTypes/index.rst
+2 −2 docs/source/concepts/LocationAndReference/SequenceReference.rst
+52 −0 docs/source/concepts/MolecularVariation/RelativeAllele.rst
+1 −1 docs/source/conventions/computed_identifiers.rst
+43 −16 docs/source/conventions/normalization.rst
+1 −0 docs/source/def/gkm-core
+0 −1 docs/source/def/gks-core
+2 −0 docs/source/examples/SpliceVariants/index.rst
+20 −0 docs/source/getting_involved.rst
+12 −12 docs/source/images/schema-current.drawio.svg
+1 −0 docs/source/index.rst
+12 −2 docs/source/quickstart.rst
+64 −0 docs/source/releases/2.1.rst
+4 −1 docs/source/releases/index.rst
+1 −1 docs/source/rst_epilog
+34 −0 examples/Makefile
+19 −0 examples/README.md
+81 −0 examples/generate_readme.py
+25 −0 examples/json/SPDI_contraction.json
+25 −0 examples/json/SPDI_expansion.json
+30 −0 examples/json/ambiguous_linker.json
+27 −0 examples/json/invalid_adjacency.json
+30 −0 examples/json/precise_linker.json
+26 −0 examples/json/revcomp_breakpoint.json
+32 −0 examples/json/sequence_homology.json
+26 −0 examples/json/simple_breakpoint.json
+36 −0 examples/json/simple_haplotype.json
+116 −0 examples/json/sv_derivative_molecule.json
+14 −0 examples/json/terminal_breakend.json
+32 −39 notebooks/referencing.ipynb
+17 −0 pre-commit-hooks/update-examples.sh
+17 −0 pre-commit-hooks/update-validation.sh
+1 −0 schema/gkm-core
+0 −1 schema/gks-core
+1 −1 schema/vrs/def/Expression.rst
+1 −1 schema/vrs/def/Ga4ghIdentifiableObject.rst
+1 −1 schema/vrs/def/SequenceExpression.rst
+1 −1 schema/vrs/def/SequenceOffsetLocation.rst
+1 −1 schema/vrs/def/SequenceReference.rst
+1 −1 schema/vrs/def/TraversalBlock.rst
+9 −9 schema/vrs/json/Adjacency
+8 −8 schema/vrs/json/Allele
+6 −6 schema/vrs/json/CisPhasedBlock
+5 −5 schema/vrs/json/CopyNumberChange
+6 −6 schema/vrs/json/CopyNumberCount
+8 −8 schema/vrs/json/DerivativeMolecule
+2 −2 schema/vrs/json/Expression
+3 −3 schema/vrs/json/LengthExpression
+3 −3 schema/vrs/json/LiteralSequenceExpression
+3 −3 schema/vrs/json/Location
+7 −7 schema/vrs/json/MolecularVariation
+1 −1 schema/vrs/json/Range
+4 −4 schema/vrs/json/ReferenceLengthExpression
+11 −11 schema/vrs/json/RelativeAllele
+6 −6 schema/vrs/json/RelativeSequenceLocation
+4 −4 schema/vrs/json/SequenceExpression
+7 −7 schema/vrs/json/SequenceLocation
+6 −6 schema/vrs/json/SequenceOffsetLocation
+3 −3 schema/vrs/json/SequenceReference
+3 −3 schema/vrs/json/SystemicVariation
+6 −6 schema/vrs/json/Terminus
+3 −3 schema/vrs/json/TraversalBlock
+9 −9 schema/vrs/json/Variation
+1 −1 schema/vrs/json/residue
+1 −1 schema/vrs/json/sequenceString
+21 −21 schema/vrs/vrs-source.yaml
+1 −0 submodules/gkm-core
+0 −1 submodules/gks-core
+67 −1 tests/test_basic.py
+29 −0 validation/Makefile
+16 −0 validation/json/functions.json
+576 −0 validation/json/models.json
+93 −0 validation/models.yaml
8 changes: 4 additions & 4 deletions tests/validation/test_model_metadata.py
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Expand Up @@ -16,11 +16,11 @@
core_models,
SUBMODULES_DIR
/ "submodules"
/ "gks-core"
/ "gkm-core"
/ "schema"
/ "gks-core"
/ "gks-core-source.yaml",
SUBMODULES_DIR / "submodules" / "gks-core" / "schema" / "gks-core" / "json",
/ "gkm-core"
/ "gkm-core-source.yaml",
SUBMODULES_DIR / "submodules" / "gkm-core" / "schema" / "gkm-core" / "json",
),
(
vrs_models,
Expand Down
2 changes: 1 addition & 1 deletion tests/validation/test_schemas.py
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Expand Up @@ -61,7 +61,7 @@ def _update_gks_schema_mapping(
# Get core classes
core_mapping = GKS_SCHEMA_MAPPING[GKSSchema.CORE]
for f in (
SUBMODULES_DIR / "submodules" / "gks-core" / "schema" / "gks-core" / "json"
SUBMODULES_DIR / "submodules" / "gkm-core" / "schema" / "gkm-core" / "json"
).glob("*"):
_update_gks_schema_mapping(f, core_mapping)

Expand Down
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