SMU datatype merge to core-im

ga4gh · Oct 10, 2024 · ddbed32 · ddbed32
1 parent 93bcd9d
commit ddbed32
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Showing 16 changed files with 32 additions and 38 deletions.
diff --git a/schema/data-types b/schema/data-types
diff --git a/schema/vrs/json/Adjacency b/schema/vrs/json/Adjacency
@@ -39,7 +39,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
                }
             ]
          },

diff --git a/schema/vrs/json/Allele b/schema/vrs/json/Allele
@@ -39,7 +39,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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"
             },
             {
-               "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+               "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
             }
          ],
          "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": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
                }
             ]
          },

diff --git a/schema/vrs/json/CopyNumberChange b/schema/vrs/json/CopyNumberChange
@@ -39,7 +39,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+               "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
             }
          ],
          "description": "A location for which the number of systemic copies is described."
@@ -74,8 +74,8 @@
          "description": "MUST be \"CopyNumberChange\""
       },
       "copyChange": {
-         "description": "MUST be a Coding 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).",
-         "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding"
+         "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding",
+         "description": "MUST be a Coding 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)."
       }
    },
    "required": [

diff --git a/schema/vrs/json/CopyNumberCount b/schema/vrs/json/CopyNumberCount
@@ -39,7 +39,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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/SequenceLocation"
             },
             {
-               "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+               "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
             }
          ],
          "description": "A location for which the number of systemic copies is described."

diff --git a/schema/vrs/json/DerivativeMolecule b/schema/vrs/json/DerivativeMolecule
@@ -38,7 +38,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
@@ -71,7 +71,7 @@
                   "$ref": "/ga4gh/schema/vrs/2.x/json/TraversalBlock"
                },
                {
-                  "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
                }
             ]
          },

diff --git a/schema/vrs/json/LengthExpression b/schema/vrs/json/LengthExpression
@@ -37,7 +37,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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"
             },
             {
-               "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+               "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
             }
          ],
          "description": "A reference to a Sequence 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": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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"
             },
             {
-               "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+               "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
             }
          ],
          "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": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/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
@@ -16,11 +16,6 @@ strict: true
 
 imports:
   gks.core-im: ../core-im/core-im-source.yaml
-  gks.data-types: ../data-types/data-types-source.yaml
-
-namespaces:
-  gks.core-im: ../core-im/core-im-source.json#/$defs/
-  gks.data-types: ../data-types/data-types-source.json#/$defs/
 
 $defs:
   # VRS definitions are presented top-down.  Everything rolls up to
@@ -143,7 +138,7 @@ $defs:
           MUST be "Allele"
       location:
         oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
           - $ref: "#/$defs/Location"
         description: >-
           The location of the Allele
@@ -178,7 +173,7 @@ $defs:
         items:
           oneOf:
             - $ref: "#/$defs/Allele"
-            - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" 
+            - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" 
         description: >-
           A list of :ref:`Alleles <Allele>` that are found in-cis on a shared molecule.
       sequenceReference:
@@ -203,7 +198,7 @@ $defs:
     heritableProperties:
       location:
         oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
           - $ref: "#/$defs/Location"
         description: >-
           A location for which the number of systemic copies is described.
@@ -254,7 +249,7 @@ $defs:
         description: >-
           MUST be "CopyNumberChange"
       copyChange:
-        $refCurie: gks.data-types:Coding
+        $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/Coding"
         description: >-
           MUST be a :ref:`Coding` 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),
@@ -292,7 +287,7 @@ $defs:
         description: MUST be "SequenceLocation"
       sequenceReference:
         oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
           - $ref: "#/$defs/SequenceReference"
         description: A reference to a :ref:`Sequence` on which the location is defined.
       start:
@@ -519,7 +514,7 @@ $defs:
         ordered: true
         items:
           oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
           - $ref: "#/$defs/Location"
         description: The terminal sequence or pair of adjoined sequences that defines in the adjacency.
         minItems: 2
@@ -556,7 +551,7 @@ $defs:
         description: MUST be "Terminus".
       location:
         oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
           - $ref: "#/$defs/Location"
         description: The location of the terminus.
     required:
@@ -585,7 +580,7 @@ $defs:
         ordered: true
         items:
           oneOf:
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
           - $ref: "#/$defs/TraversalBlock"
         description: >-
           The molecular components that constitute the derivative molecule.

diff --git a/submodules/gks-common b/submodules/gks-common