added Element PR from gks-core to add Extensions

ga4gh · Oct 31, 2024 · 0587e0c · 0587e0c
1 parent 7c28ba3
commit 0587e0c
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Showing 12 changed files with 20 additions and 9 deletions.
diff --git a/docs/source/concepts/AdditionalDataTypes/Code.rst b/docs/source/concepts/AdditionalDataTypes/Code.rst
@@ -3,4 +3,4 @@
 Code
 !!!!
 
-.. include::  ../../def/gks.common/core-im/Code.rst
+.. include::  ../../def/gks-core/Code.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/Coding.rst b/docs/source/concepts/AdditionalDataTypes/Coding.rst
@@ -3,4 +3,4 @@
 Coding
 !!!!!!
 
-.. include::  ../../def/gks.common/core-im/Coding.rst
+.. include::  ../../def/gks-core/Coding.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/Entity.rst b/docs/source/concepts/AdditionalDataTypes/Entity.rst
@@ -3,4 +3,4 @@
 Entity
 !!!!!!
 
-.. include::  ../../def/gks.common/core-im/Entity.rst
+.. include::  ../../def/gks-core/Entity.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/Extension.rst b/docs/source/concepts/AdditionalDataTypes/Extension.rst
@@ -3,4 +3,4 @@
 Extension
 !!!!!!!!!
 
-.. include::  ../../def/gks.common/core-im/Extension.rst
+.. include::  ../../def/gks-core/Extension.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/IRI.rst b/docs/source/concepts/AdditionalDataTypes/IRI.rst
@@ -3,4 +3,4 @@
 IRI
 !!!
 
-.. include::  ../../def/gks.common/core-im/IRI.rst
+.. include::  ../../def/gks-core/IRI.rst
diff --git a/docs/source/def/gks-core b/docs/source/def/gks-core
@@ -0,0 +1 @@
+../../../schema/gks-core/def
diff --git a/docs/source/def/gks.common/core-im b/docs/source/def/gks.common/core-im
diff --git a/docs/source/def/gks.common/data-types b/docs/source/def/gks.common/data-types
diff --git a/schema/vrs/def/Expression.rst b/schema/vrs/def/Expression.rst
@@ -25,6 +25,10 @@ Some Expression attributes are inherited from :ref:`gks-core:Element`.
       - string
       - 0..1
       - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :ref:`Extension`
+      - 0..m
+      - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - syntax
       - string
       - 1..1

diff --git a/schema/vrs/json/Expression b/schema/vrs/json/Expression
@@ -10,6 +10,15 @@
          "type": "string",
          "description": "The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another."
       },
+      "extensions": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.x/json/Extension"
+         },
+         "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
+         "$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."
+      },
       "syntax": {
          "type": "string",
          "enum": [

diff --git a/schema/vrs/vrs-source.yaml b/schema/vrs/vrs-source.yaml
@@ -456,7 +456,6 @@ $defs:
   # Numerics, Comparators, and Ranges
 
   Range:
-    inherits: gks-core:Element
     maturity: trial use
     description: An inclusive range of values bounded by one or more integers.
     type: array

diff --git a/submodules/gks-core b/submodules/gks-core
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,4 +3,4 @@ @@
     Code
     !!!!
-    .. include::  ../../def/gks.common/core-im/Code.rst
+    .. include::  ../../def/gks-core/Code.rst
+4 −1		examples/mappable-concept-gene.yaml
+4 −0		schema/gks-core/def/Characteristic.rst
+4 −0		schema/gks-core/def/Coding.rst
+4 −0		schema/gks-core/def/ConceptMapping.rst
+4 −0		schema/gks-core/def/Element.rst
+4 −0		schema/gks-core/def/Extension.rst
+4 −0		schema/gks-core/def/MappableConcept.rst
+4 −0		schema/gks-core/def/RecordMetadata.rst
+12 −0		schema/gks-core/gks-core-source.yaml
+9 −0		schema/gks-core/json/Characteristic
+9 −0		schema/gks-core/json/Coding
+9 −0		schema/gks-core/json/ConceptMapping
+9 −0		schema/gks-core/json/Extension
+9 −0		schema/gks-core/json/MappableConcept
+9 −0		schema/gks-core/json/RecordMetadata