repoint 1.x to 2.0.0-snapshot.2025-02 vrs branch

ga4gh · Feb 11, 2025 · 11848ce · 11848ce
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Showing 14 changed files with 32 additions and 27 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,4 +1,4 @@
 [submodule "submodules/vrs"]
 	path = submodules/vrs
 	url = https://github.com/ga4gh/vrs.git
-	branch = 2.x
+	branch = 2.0.0-snapshot.2025-02
diff --git a/docs/source/concepts/imported/Element.rst b/docs/source/concepts/imported/Element.rst
@@ -1,4 +1,5 @@
 .. _Element:
+.. _gks-core:Element:
 
 Element
 !!!!!!!

diff --git a/docs/source/concepts/imported/Entity.rst b/docs/source/concepts/imported/Entity.rst
@@ -1,4 +1,5 @@
 .. _Entity:
+.. _gks-core:Entity:
 
 Entity
 !!!!!!

diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml
@@ -9,8 +9,8 @@ imports:
   vrs: ../vrs/vrs-source.yaml
 
 namespaces:
-  gks.core: /ga4gh/schema/gks-core/1.x/json/
-  vrs: /ga4gh/schema/vrs/2.x/json/
+  gks.core: /ga4gh/schema/gks-core/1.0.0-snapshot.2025-02/json/
+  vrs: /ga4gh/schema/vrs/2.0.0-snapshot.2025-02/json/
 
 $defs:
 

diff --git a/schema/cat-vrs/def/CanonicalAllele.rst b/schema/cat-vrs/def/CanonicalAllele.rst
@@ -4,7 +4,7 @@
 
 **Computational Definition**
 
-A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#>`_ that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.
+A canonical allele is defined by an :ref:`Allele` that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.
 
 **Information Model**
 

diff --git a/schema/cat-vrs/def/ProteinSequenceConsequence.rst b/schema/cat-vrs/def/ProteinSequenceConsequence.rst
@@ -4,7 +4,7 @@
 
 **Computational Definition**
 
-A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a :ref:`CanonicalAllele`, is defined by an `Allele <https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#>`_ that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).
+A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a :ref:`CanonicalAllele`, is defined by an :ref:`Allele` that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).
 
 **Information Model**
 

diff --git a/schema/cat-vrs/json/CanonicalAllele b/schema/cat-vrs/json/CanonicalAllele
@@ -4,7 +4,7 @@
    "title": "CanonicalAllele",
    "type": "object",
    "maturity": "trial use",
-   "description": "A canonical allele is defined by an [Allele](https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#) that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.",
+   "description": "A canonical allele is defined by an Allele that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.",
    "allOf": [
       {
          "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant"

diff --git a/schema/cat-vrs/json/CategoricalVariant b/schema/cat-vrs/json/CategoricalVariant
@@ -31,7 +31,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
@@ -50,10 +50,10 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+                  "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference"
                },
                {
-                  "$ref": "/ga4gh/schema/vrs/2.x/json/Variation"
+                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Variation"
                }
             ]
          }
@@ -82,7 +82,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.x/json/ConceptMapping"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/ConceptMapping"
          },
          "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation."
       }

diff --git a/schema/cat-vrs/json/CopyCountConstraint b/schema/cat-vrs/json/CopyCountConstraint
@@ -16,7 +16,7 @@
          "description": "The precise value or range of copies members of this categorical variant must satisfy.",
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.x/json/Range"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Range"
             },
             {
                "type": "integer"

diff --git a/schema/cat-vrs/json/DefiningAlleleConstraint b/schema/cat-vrs/json/DefiningAlleleConstraint
@@ -15,18 +15,18 @@
       "allele": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+               "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.x/json/Allele"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Allele"
             }
          ]
       },
       "relations": {
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/MappableConcept"
          },
          "description": "Defined relationships from which members relate to the defining allele."
       }

diff --git a/schema/cat-vrs/json/DefiningLocationConstraint b/schema/cat-vrs/json/DefiningLocationConstraint
@@ -15,24 +15,24 @@
       "location": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
+               "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/SequenceLocation"
             }
          ]
       },
       "relations": {
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/MappableConcept"
          },
          "description": "Defined relationships from which members relate to the defining location."
       },
       "matchCharacteristic": {
          "description": "A characteristic of the location that is used to match the defining location to member locations.",
-         "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept"
+         "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/MappableConcept"
       }
    },
    "required": [

diff --git a/schema/cat-vrs/json/ProteinSequenceConsequence b/schema/cat-vrs/json/ProteinSequenceConsequence
@@ -4,7 +4,7 @@
    "title": "ProteinSequenceConsequence",
    "type": "object",
    "maturity": "trial use",
-   "description": "A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a CanonicalAllele, is defined by an [Allele](https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#) that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).",
+   "description": "A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a CanonicalAllele, is defined by an Allele that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).",
    "allOf": [
       {
          "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant"

diff --git a/schema/cat-vrs/recipes-source.yaml b/schema/cat-vrs/recipes-source.yaml
@@ -4,19 +4,22 @@ title: GA4GH-Cat-VRS-Recipe-Definitions
 type: object
 
 imports:
-  gks.core-im: ../gks-core/gks-core-source.yaml
+  gks.core: ../gks-core/gks-core-source.yaml
   vrs: ../vrs/vrs-source.yaml
   cat-vrs: ./cat-vrs-source.yaml
 
+namespaces:
+  gks.core: /ga4gh/schema/gks-core/1.0.0-snapshot.2025-02/json/
+  vrs: /ga4gh/schema/vrs/2.0.0-snapshot.2025-02/json/
+
 $defs:
   ProteinSequenceConsequence:
     maturity: trial use
     description: >-
       A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature
       of the genetic code, there are often several genomic changes that can cause a protein sequence consequence.
       The protein sequence consequence, like a :ref:`CanonicalAllele`, is defined by an
-      `Allele <https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#>`_
-      that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).
+      :ref:`Allele` that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).
     allOf:
       - $ref: CategoricalVariant
       - properties:
@@ -38,10 +41,10 @@ $defs:
   CanonicalAllele:
     maturity: trial use
     description: >-
-      A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#>`_
-      that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid
-      change on different underlying reference sequences. Congruent representations of an Allele often exist
-      across different genome assemblies and associated cDNA transcript representations.
+      A canonical allele is defined by an :ref:`Allele` that is representative of a collection of congruent
+      Alleles, each of which depict the same nucleic acid different underlying reference sequences.
+      Congruent representations of an Allele often exist across different genome assemblies and associated
+      cDNA transcript representations.
     allOf:
       - $ref: CategoricalVariant
       - properties:

diff --git a/submodules/vrs b/submodules/vrs
+1 −0		.gitmodules
+1 −1		docs/source/requirements.txt
+8 −8		schema/vrs/json/Adjacency
+8 −8		schema/vrs/json/Allele
+6 −6		schema/vrs/json/CisPhasedBlock
+6 −6		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
+2 −2		schema/vrs/json/Location
+6 −6		schema/vrs/json/MolecularVariation
+1 −1		schema/vrs/json/Range
+4 −4		schema/vrs/json/ReferenceLengthExpression
+4 −4		schema/vrs/json/SequenceExpression
+7 −7		schema/vrs/json/SequenceLocation
+3 −3		schema/vrs/json/SequenceReference
+3 −3		schema/vrs/json/SystemicVariation
+5 −5		schema/vrs/json/Terminus
+3 −3		schema/vrs/json/TraversalBlock
+8 −8		schema/vrs/json/Variation
+1 −1		schema/vrs/json/residue
+1 −1		schema/vrs/json/sequenceString
+2 −2		schema/vrs/vrs-source.yaml
+1 −1		submodules/gks-core