From ff3f62bd9db1f4493899b7c62dd3511444412d11 Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Tue, 11 Feb 2025 13:39:51 -0500 Subject: [PATCH] prepare a 1.0.0-snapshot.2025-02 pre-release --- 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 | 10 +++++----- schema/cat-vrs/json/Constraint | 10 +++++----- schema/cat-vrs/json/CopyChangeConstraint | 2 +- schema/cat-vrs/json/CopyCountConstraint | 2 +- schema/cat-vrs/json/DefiningAlleleConstraint | 2 +- schema/cat-vrs/json/DefiningLocationConstraint | 2 +- schema/cat-vrs/json/ProteinSequenceConsequence | 6 +++--- schema/cat-vrs/recipes-source.yaml | 8 +------- 11 files changed, 29 insertions(+), 35 deletions(-) diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml index 6988d62..52dc6dd 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-snapshot.2025-02.1/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/1.0.0-snapshot.2025-02/json/ - vrs: /ga4gh/schema/vrs/2.0.0-snapshot.2025-02/json/ + gks.core: /ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/ + vrs: /ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/ $defs: diff --git a/schema/cat-vrs/json/CanonicalAllele b/schema/cat-vrs/json/CanonicalAllele index a13aa0d..9dae17f 100644 --- a/schema/cat-vrs/json/CanonicalAllele +++ b/schema/cat-vrs/json/CanonicalAllele @@ -1,13 +1,13 @@ { "$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-snapshot.2025-02.1/json/CanonicalAllele", "title": "CanonicalAllele", "type": "object", "maturity": "trial use", "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": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/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-snapshot.2025-02.1/json/DefiningAlleleConstraint" }, { "type": "object", diff --git a/schema/cat-vrs/json/CategoricalCnv b/schema/cat-vrs/json/CategoricalCnv index 2c432c6..f098132 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", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CategoricalCnv", "title": "CategoricalCnv", "type": "object", "maturity": "draft", "description": "A representation of the constraints for matching knowledge about CNVs.", "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CategoricalVariant" }, { "properties": { @@ -20,7 +20,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/DefiningLocationConstraint" }, { "properties": { @@ -42,10 +42,10 @@ "contains": { "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CopyChangeConstraint" } ] } diff --git a/schema/cat-vrs/json/CategoricalVariant b/schema/cat-vrs/json/CategoricalVariant index 229124b..dd11203 100644 --- a/schema/cat-vrs/json/CategoricalVariant +++ b/schema/cat-vrs/json/CategoricalVariant @@ -1,6 +1,6 @@ { "$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-snapshot.2025-02.1/json/CategoricalVariant", "title": "CategoricalVariant", "type": "object", "maturity": "trial use", @@ -64,16 +64,16 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CopyChangeConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/DefiningAlleleConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/DefiningLocationConstraint" } ] } diff --git a/schema/cat-vrs/json/Constraint b/schema/cat-vrs/json/Constraint index 3ac239d..3636aea 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", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/Constraint", "title": "Constraint", "type": "object", "maturity": "trial use", "description": "Constraints are used to construct an intensional semantics of categorical variant types.", "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CopyChangeConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningAlleleConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/DefiningAlleleConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningLocationConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/DefiningLocationConstraint" } ] } diff --git a/schema/cat-vrs/json/CopyChangeConstraint b/schema/cat-vrs/json/CopyChangeConstraint index b2904de..5c7206f 100644 --- a/schema/cat-vrs/json/CopyChangeConstraint +++ b/schema/cat-vrs/json/CopyChangeConstraint @@ -1,6 +1,6 @@ { "$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-snapshot.2025-02.1/json/CopyChangeConstraint", "title": "CopyChangeConstraint", "type": "object", "maturity": "draft", diff --git a/schema/cat-vrs/json/CopyCountConstraint b/schema/cat-vrs/json/CopyCountConstraint index 2a57771..b232642 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", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/CopyCountConstraint", "title": "CopyCountConstraint", "type": "object", "maturity": "trial use", diff --git a/schema/cat-vrs/json/DefiningAlleleConstraint b/schema/cat-vrs/json/DefiningAlleleConstraint index debd337..98bf1bd 100644 --- a/schema/cat-vrs/json/DefiningAlleleConstraint +++ b/schema/cat-vrs/json/DefiningAlleleConstraint @@ -1,6 +1,6 @@ { "$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-snapshot.2025-02.1/json/DefiningAlleleConstraint", "title": "DefiningAlleleConstraint", "type": "object", "maturity": "trial use", diff --git a/schema/cat-vrs/json/DefiningLocationConstraint b/schema/cat-vrs/json/DefiningLocationConstraint index 3f989e1..380e427 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", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/json/DefiningLocationConstraint", "title": "DefiningLocationConstraint", "type": "object", "maturity": "trial use", diff --git a/schema/cat-vrs/json/ProteinSequenceConsequence b/schema/cat-vrs/json/ProteinSequenceConsequence index bf3d0de..6430f5b 100644 --- a/schema/cat-vrs/json/ProteinSequenceConsequence +++ b/schema/cat-vrs/json/ProteinSequenceConsequence @@ -1,13 +1,13 @@ { "$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-snapshot.2025-02.1/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 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-snapshot.2025-02.1/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-snapshot.2025-02.1/json/DefiningAlleleConstraint" }, { "type": "object", diff --git a/schema/cat-vrs/recipes-source.yaml b/schema/cat-vrs/recipes-source.yaml index 6f996d2..7472587 100644 --- a/schema/cat-vrs/recipes-source.yaml +++ b/schema/cat-vrs/recipes-source.yaml @@ -1,17 +1,11 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/recipes-source.yaml" +$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-snapshot.2025-02.1/recipes-source.yaml" title: GA4GH-Cat-VRS-Recipe-Definitions type: object imports: - 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