diff --git a/schema/vrs/json/Adjacency b/schema/vrs/json/Adjacency index f139f3e1..47f4c916 100644 --- a/schema/vrs/json/Adjacency +++ b/schema/vrs/json/Adjacency @@ -39,7 +39,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -72,7 +72,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], "not": { diff --git a/schema/vrs/json/Allele b/schema/vrs/json/Allele index 0637db1d..279f580d 100644 --- a/schema/vrs/json/Allele +++ b/schema/vrs/json/Allele @@ -39,7 +39,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -68,7 +68,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], "description": "The location of the Allele" diff --git a/schema/vrs/json/CisPhasedBlock b/schema/vrs/json/CisPhasedBlock index ec9d07e8..483747e3 100644 --- a/schema/vrs/json/CisPhasedBlock +++ b/schema/vrs/json/CisPhasedBlock @@ -38,7 +38,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -72,7 +72,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" }, { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ] }, diff --git a/schema/vrs/json/CopyNumberChange b/schema/vrs/json/CopyNumberChange index 2a8f03c1..7809d238 100644 --- a/schema/vrs/json/CopyNumberChange +++ b/schema/vrs/json/CopyNumberChange @@ -39,7 +39,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -68,14 +68,14 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], "description": "The location of the subject of the copy change." }, "copyChange": { "description": "MUST use a `primaryCode` representing one of \"EFO:0030069\" (complete genomic loss), \"EFO:0020073\" (high-level loss), \"EFO:0030068\" (low-level loss), \"EFO:0030067\" (loss), \"EFO:0030064\" (regional base ploidy), \"EFO:0030070\" (gain), \"EFO:0030071\" (low-level gain), \"EFO:0030072\" (high-level gain).", - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/MappableConcept" + "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept" } }, "required": [ diff --git a/schema/vrs/json/CopyNumberCount b/schema/vrs/json/CopyNumberCount index b1baeef5..2f95d7bc 100644 --- a/schema/vrs/json/CopyNumberCount +++ b/schema/vrs/json/CopyNumberCount @@ -39,7 +39,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -68,7 +68,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], "description": "The location of the subject of the copy count." diff --git a/schema/vrs/json/DerivativeMolecule b/schema/vrs/json/DerivativeMolecule index a5c47e99..c7aa3c3d 100644 --- a/schema/vrs/json/DerivativeMolecule +++ b/schema/vrs/json/DerivativeMolecule @@ -38,7 +38,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -80,7 +80,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/TraversalBlock" }, { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ] }, diff --git a/schema/vrs/json/Expression b/schema/vrs/json/Expression index aab152d1..9404a2c0 100644 --- a/schema/vrs/json/Expression +++ b/schema/vrs/json/Expression @@ -14,7 +14,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." diff --git a/schema/vrs/json/LengthExpression b/schema/vrs/json/LengthExpression index c96b6c45..24d0fe37 100644 --- a/schema/vrs/json/LengthExpression +++ b/schema/vrs/json/LengthExpression @@ -37,7 +37,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" }, "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." diff --git a/schema/vrs/json/LiteralSequenceExpression b/schema/vrs/json/LiteralSequenceExpression index 9744de30..126621f7 100644 --- a/schema/vrs/json/LiteralSequenceExpression +++ b/schema/vrs/json/LiteralSequenceExpression @@ -37,7 +37,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." diff --git a/schema/vrs/json/ReferenceLengthExpression b/schema/vrs/json/ReferenceLengthExpression index ec8bbaf1..b803e12b 100644 --- a/schema/vrs/json/ReferenceLengthExpression +++ b/schema/vrs/json/ReferenceLengthExpression @@ -38,7 +38,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" }, "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." diff --git a/schema/vrs/json/SequenceLocation b/schema/vrs/json/SequenceLocation index 9d347b3f..305f3483 100644 --- a/schema/vrs/json/SequenceLocation +++ b/schema/vrs/json/SequenceLocation @@ -40,7 +40,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -62,7 +62,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceReference" }, { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], "description": "A reference to a SequenceReference on which the location is defined." diff --git a/schema/vrs/json/SequenceReference b/schema/vrs/json/SequenceReference index 0043ca70..9cfc2c04 100644 --- a/schema/vrs/json/SequenceReference +++ b/schema/vrs/json/SequenceReference @@ -37,7 +37,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." diff --git a/schema/vrs/json/Terminus b/schema/vrs/json/Terminus index 1d2936f6..e7f6df7c 100644 --- a/schema/vrs/json/Terminus +++ b/schema/vrs/json/Terminus @@ -38,7 +38,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" }, "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." @@ -67,7 +67,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference" + "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference" } ], "description": "The location of the terminus." diff --git a/schema/vrs/json/TraversalBlock b/schema/vrs/json/TraversalBlock index 72f91819..075dfa0d 100644 --- a/schema/vrs/json/TraversalBlock +++ b/schema/vrs/json/TraversalBlock @@ -38,7 +38,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension" }, "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." diff --git a/schema/vrs/vrs-source.yaml b/schema/vrs/vrs-source.yaml index 3d6d9cb8..002129ad 100644 --- a/schema/vrs/vrs-source.yaml +++ b/schema/vrs/vrs-source.yaml @@ -18,7 +18,7 @@ imports: gks-core: ../gks-core/gks-core-source.yaml namespaces: - gks.core: /ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/ + gks.core: /ga4gh/schema/gks-core/1.x/json/ $defs: # VRS definitions are presented top-down. Everything rolls up to diff --git a/submodules/gks-core b/submodules/gks-core index 58bd904d..a4b4f816 160000 --- a/submodules/gks-core +++ b/submodules/gks-core @@ -1 +1 @@ -Subproject commit 58bd904d3b9122c16aecdbef00e0ea4ac2d53ab0 +Subproject commit a4b4f816742185671d22d1e253007a4155f25ed3