align 2.x dev branch with gks-core 1.x dev branch

ga4gh · Feb 11, 2025 · aef9596 · aef9596
1 parent 61911d4
commit aef9596
Show file tree

Hide file tree

Showing 16 changed files with 25 additions and 25 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
+1 −1		.requirements.txt
+0 −15		schema/gks-core/def/MappableConcept.rst
+1 −1		schema/gks-core/gks-core-source.yaml
+1 −1		schema/gks-core/json/Code
+3 −3		schema/gks-core/json/Coding
+3 −3		schema/gks-core/json/ConceptMapping
+2 −2		schema/gks-core/json/Extension
+4 −4		schema/gks-core/json/MappableConcept
+1 −1		schema/gks-core/json/date
+1 −1		schema/gks-core/json/datetime
+1 −1		schema/gks-core/json/iriReference