From 470b600b781d5c7692b04c62d6a1b2a2cdb7eae2 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Tue, 26 Nov 2024 20:40:12 -0500 Subject: [PATCH] update versions --- schema/cat-vrs/cat-vrs-source.yaml | 6 +++--- schema/cat-vrs/json/CanonicalAllele | 6 +++--- schema/cat-vrs/json/CategoricalCnv | 10 +++++----- schema/cat-vrs/json/CategoricalVariant | 18 +++++++++--------- schema/cat-vrs/json/Constraint | 10 +++++----- schema/cat-vrs/json/CopyChangeConstraint | 2 +- schema/cat-vrs/json/CopyCountConstraint | 4 ++-- schema/cat-vrs/json/DefiningAlleleConstraint | 8 ++++---- schema/cat-vrs/json/DefiningLocationConstraint | 10 +++++----- schema/cat-vrs/json/ProteinSequenceConsequence | 6 +++--- schema/cat-vrs/recipes-source.yaml | 2 +- submodules/vrs | 2 +- 12 files changed, 42 insertions(+), 42 deletions(-) diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml index 81f1dac..617b14c 100644 --- a/schema/cat-vrs/cat-vrs-source.yaml +++ b/schema/cat-vrs/cat-vrs-source.yaml @@ -1,5 +1,5 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/cat-vrs-source.yaml" +$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/cat-vrs-source.yaml" title: GA4GH-Cat-VRS-Definitions type: object strict: true @@ -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.2024-11.2/json/ + vrs: /ga4gh/schema/vrs/1.0.0-ballot.2024-11.1/json/ $defs: diff --git a/schema/cat-vrs/json/CanonicalAllele b/schema/cat-vrs/json/CanonicalAllele index b225449..ba90880 100644 --- a/schema/cat-vrs/json/CanonicalAllele +++ b/schema/cat-vrs/json/CanonicalAllele @@ -1,13 +1,13 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CanonicalAllele", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CanonicalAllele", "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.", "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CategoricalVariant" }, { "properties": { @@ -17,7 +17,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningAlleleConstraint" }, { "type": "object", diff --git a/schema/cat-vrs/json/CategoricalCnv b/schema/cat-vrs/json/CategoricalCnv index 1b9c9c1..29c6d1d 100644 --- a/schema/cat-vrs/json/CategoricalCnv +++ b/schema/cat-vrs/json/CategoricalCnv @@ -1,13 +1,13 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalCnv", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CategoricalCnv", "title": "CategoricalCnv", "type": "object", "maturity": "draft", "description": "A representation of the constraints for matching knowledge about CNVs.", "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CategoricalVariant" }, { "properties": { @@ -20,7 +20,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningLocationConstraint" }, { "properties": { @@ -42,10 +42,10 @@ "contains": { "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CopyChangeConstraint" } ] } diff --git a/schema/cat-vrs/json/CategoricalVariant b/schema/cat-vrs/json/CategoricalVariant index 72c38e7..746c5b8 100644 --- a/schema/cat-vrs/json/CategoricalVariant +++ b/schema/cat-vrs/json/CategoricalVariant @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CategoricalVariant", "title": "CategoricalVariant", "type": "object", "maturity": "trial use", @@ -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.2024-11.1/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" + "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2024-11.1/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-11.1/json/Variation" } ] } @@ -64,16 +64,16 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CopyChangeConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningAlleleConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningLocationConstraint" } ] } @@ -82,7 +82,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2024-11.1/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." } diff --git a/schema/cat-vrs/json/Constraint b/schema/cat-vrs/json/Constraint index 471f900..81108cb 100644 --- a/schema/cat-vrs/json/Constraint +++ b/schema/cat-vrs/json/Constraint @@ -1,22 +1,22 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/Constraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/Constraint", "title": "Constraint", "type": "object", "maturity": "trial use", "description": "Constraints are used to construct an intensional semantics of categorical variant types.", "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CopyChangeConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningAlleleConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningLocationConstraint" } ] } \ No newline at end of file diff --git a/schema/cat-vrs/json/CopyChangeConstraint b/schema/cat-vrs/json/CopyChangeConstraint index 4d50814..c6f89ec 100644 --- a/schema/cat-vrs/json/CopyChangeConstraint +++ b/schema/cat-vrs/json/CopyChangeConstraint @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CopyChangeConstraint", "title": "CopyChangeConstraint", "type": "object", "maturity": "draft", diff --git a/schema/cat-vrs/json/CopyCountConstraint b/schema/cat-vrs/json/CopyCountConstraint index a3ef9a1..ffb5b56 100644 --- a/schema/cat-vrs/json/CopyCountConstraint +++ b/schema/cat-vrs/json/CopyCountConstraint @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CopyCountConstraint", "title": "CopyCountConstraint", "type": "object", "maturity": "trial use", @@ -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-ballot.2024-11.1/json/Range" }, { "type": "integer" diff --git a/schema/cat-vrs/json/DefiningAlleleConstraint b/schema/cat-vrs/json/DefiningAlleleConstraint index c233adc..af709a1 100644 --- a/schema/cat-vrs/json/DefiningAlleleConstraint +++ b/schema/cat-vrs/json/DefiningAlleleConstraint @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningAlleleConstraint", "title": "DefiningAlleleConstraint", "type": "object", "maturity": "trial use", @@ -15,10 +15,10 @@ "allele": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2024-11.1/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-11.1/json/Allele" } ] }, @@ -26,7 +26,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2024-11.1/json/MappableConcept" }, "description": "Defined relationships from which members relate to the defining allele." } diff --git a/schema/cat-vrs/json/DefiningLocationConstraint b/schema/cat-vrs/json/DefiningLocationConstraint index 3f0f8e4..87d5f9f 100644 --- a/schema/cat-vrs/json/DefiningLocationConstraint +++ b/schema/cat-vrs/json/DefiningLocationConstraint @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningLocationConstraint", "title": "DefiningLocationConstraint", "type": "object", "maturity": "trial use", @@ -15,10 +15,10 @@ "location": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2024-11.1/json/iriReference" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-11.1/json/SequenceLocation" } ] }, @@ -26,13 +26,13 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" + "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2024-11.1/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.2024-11.1/json/MappableConcept" } }, "required": [ diff --git a/schema/cat-vrs/json/ProteinSequenceConsequence b/schema/cat-vrs/json/ProteinSequenceConsequence index 655b421..13684d9 100644 --- a/schema/cat-vrs/json/ProteinSequenceConsequence +++ b/schema/cat-vrs/json/ProteinSequenceConsequence @@ -1,13 +1,13 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/ProteinSequenceConsequence", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/ProteinSequenceConsequence", "title": "ProteinSequenceConsequence", "type": "object", "maturity": "trial use", "description": "A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a CanonicalAllele, is defined by an [Allele](https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#) that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).", "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/CategoricalVariant" }, { "properties": { @@ -15,7 +15,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/json/DefiningAlleleConstraint" }, { "type": "object", diff --git a/schema/cat-vrs/recipes-source.yaml b/schema/cat-vrs/recipes-source.yaml index d2470f2..83ae052 100644 --- a/schema/cat-vrs/recipes-source.yaml +++ b/schema/cat-vrs/recipes-source.yaml @@ -1,5 +1,5 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/recipes-source.yaml" +$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-ballot.2024-11.1/recipes-source.yaml" title: GA4GH-Cat-VRS-Recipe-Definitions type: object diff --git a/submodules/vrs b/submodules/vrs index 0106b48..58374b2 160000 --- a/submodules/vrs +++ b/submodules/vrs @@ -1 +1 @@ -Subproject commit 0106b48c1db0b420efd787cc769e4b35f415068e +Subproject commit 58374b2d810f619bd523e3800bc09729b9bbd036