repoint 2.0.0-snapshot.2025-02 pre-release to 1.0.0-snapshot.2025-02 …

…gks-core branch
ga4gh · Feb 11, 2025 · 15989fe · 15989fe
1 parent a6c429c
commit 15989fe
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Showing 25 changed files with 102 additions and 101 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,4 @@
 [submodule "submodules/gks-core"]
 	path = submodules/gks-core
 	url = https://github.com/ga4gh/gks-core.git
+	branch = 1.0.0-snapshot.2025-02
diff --git a/schema/vrs/json/Adjacency b/schema/vrs/json/Adjacency
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Adjacency",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Adjacency",
    "title": "Adjacency",
    "type": "object",
    "maturity": "trial use",
@@ -39,7 +39,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
@@ -53,7 +53,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Expression"
          }
       },
       "type": {
@@ -69,10 +69,10 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/SequenceLocation"
+                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/SequenceLocation"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference"
+                  "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference"
                }
             ],
             "not": {
@@ -90,13 +90,13 @@
          "description": "The sequence found between adjoined sequences.",
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/LengthExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/LengthExpression"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/LiteralSequenceExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/LiteralSequenceExpression"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/ReferenceLengthExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/ReferenceLengthExpression"
             }
          ]
       },

diff --git a/schema/vrs/json/Allele b/schema/vrs/json/Allele
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Allele",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Allele",
    "title": "Allele",
    "type": "object",
    "maturity": "trial use",
@@ -39,7 +39,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
@@ -53,7 +53,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Expression"
          }
       },
       "type": {
@@ -65,10 +65,10 @@
       "location": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/SequenceLocation"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference"
+               "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference"
             }
          ],
          "description": "The location of the Allele"
@@ -77,13 +77,13 @@
          "description": "An expression of the sequence state",
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/LengthExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/LengthExpression"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/LiteralSequenceExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/LiteralSequenceExpression"
             },
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/ReferenceLengthExpression"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/ReferenceLengthExpression"
             }
          ]
       }

diff --git a/schema/vrs/json/CisPhasedBlock b/schema/vrs/json/CisPhasedBlock
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/CisPhasedBlock",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/CisPhasedBlock",
    "title": "CisPhasedBlock",
    "type": "object",
    "maturity": "trial use",
@@ -38,7 +38,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
@@ -52,7 +52,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Expression"
          }
       },
       "type": {
@@ -69,17 +69,17 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Allele"
+                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Allele"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference"
+                  "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference"
                }
             ]
          },
          "description": "A list of Alleles that are found in-cis on a shared molecule."
       },
       "sequenceReference": {
-         "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/SequenceReference",
+         "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/SequenceReference",
          "description": "An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the `sequenceReference` attribute for each of the CisPhasedBlock member Alleles."
       }
    },

diff --git a/schema/vrs/json/CopyNumberChange b/schema/vrs/json/CopyNumberChange
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/CopyNumberChange",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/CopyNumberChange",
    "title": "CopyNumberChange",
    "type": "object",
    "maturity": "draft",
@@ -39,7 +39,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
@@ -53,7 +53,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Expression"
          }
       },
       "type": {
@@ -65,17 +65,17 @@
       "location": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/SequenceLocation"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference"
+               "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/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/1.0.0-snapshot.2025-02.2/json/MappableConcept"
       }
    },
    "required": [

diff --git a/schema/vrs/json/CopyNumberCount b/schema/vrs/json/CopyNumberCount
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/CopyNumberCount",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/CopyNumberCount",
    "title": "CopyNumberCount",
    "type": "object",
    "maturity": "trial use",
@@ -39,7 +39,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
@@ -53,7 +53,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Expression"
          }
       },
       "type": {
@@ -65,18 +65,18 @@
       "location": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/SequenceLocation"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference"
+               "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference"
             }
          ],
          "description": "The location of the subject of the copy count."
       },
       "copies": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Range"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Range"
             },
             {
                "type": "integer"

diff --git a/schema/vrs/json/DerivativeMolecule b/schema/vrs/json/DerivativeMolecule
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/DerivativeMolecule",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/DerivativeMolecule",
    "title": "DerivativeMolecule",
    "type": "object",
    "maturity": "draft",
@@ -38,7 +38,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
@@ -52,7 +52,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Expression"
+            "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Expression"
          }
       },
       "type": {
@@ -68,19 +68,19 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Allele"
+                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Allele"
                },
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/CisPhasedBlock"
+                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/CisPhasedBlock"
                },
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Terminus"
+                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Terminus"
                },
                {
-                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/TraversalBlock"
+                  "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/TraversalBlock"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/iriReference"
+                  "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference"
                }
             ]
          },

diff --git a/schema/vrs/json/Expression b/schema/vrs/json/Expression
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Expression",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Expression",
    "title": "Expression",
    "type": "object",
    "maturity": "trial use",
@@ -14,7 +14,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."

diff --git a/schema/vrs/json/LengthExpression b/schema/vrs/json/LengthExpression
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/LengthExpression",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/LengthExpression",
    "title": "LengthExpression",
    "type": "object",
    "maturity": "draft",
@@ -37,7 +37,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
@@ -53,7 +53,7 @@
          "description": "The length of the sequence.",
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Range"
+               "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Range"
             },
             {
                "type": "integer"

diff --git a/schema/vrs/json/LiteralSequenceExpression b/schema/vrs/json/LiteralSequenceExpression
@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/LiteralSequenceExpression",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/LiteralSequenceExpression",
    "title": "LiteralSequenceExpression",
    "type": "object",
    "maturity": "trial use",
@@ -37,7 +37,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.1/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
@@ -50,7 +50,7 @@
          "default": "LiteralSequenceExpression"
       },
       "sequence": {
-         "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/sequenceString",
+         "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/sequenceString",
          "description": "the literal sequence"
       }
    },

diff --git a/schema/vrs/json/Location b/schema/vrs/json/Location
@@ -1,13 +1,13 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/Location",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/Location",
    "title": "Location",
    "type": "object",
    "maturity": "trial use",
    "description": "A contiguous segment of a biological sequence.",
    "oneOf": [
       {
-         "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.1/json/SequenceLocation"
+         "$ref": "/ga4gh/schema/vrs/2.0.0-snapshot.2025-02.2/json/SequenceLocation"
       }
    ],
    "discriminator": {