update submodule

ga4gh · Jul 9, 2024 · 6a3922d · 6a3922d
1 parent 5d65e54
commit 6a3922d
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Showing 14 changed files with 90 additions and 91 deletions.
diff --git a/schema/catvrs/catvrs-source.yaml b/schema/catvrs/catvrs-source.yaml
@@ -5,12 +5,12 @@ type: object
 strict: true
 
 imports:
-  gks.core: ../gks-core-im/core-im-source.yaml
+  gks.common: ../gks-common/common-source.yaml
   vrs: ../vrs/vrs-source.yaml
 
 namespaces:
   vrs: ../vrs/vrs.yaml#/$defs/
-  gks.core: ../gks-core-im/core-im.yaml#/$defs/
+  gks.common: ../gks-common/common.yaml#/$defs/
 
 $defs:
   # Categorical Variation are presented top-down. Everything rolls up to
@@ -22,7 +22,7 @@ $defs:
   # =============================================================================
 
   CategoricalVariation:
-    inherits: gks.core:DomainEntity
+    inherits: gks.common:DomainEntity
     description: >-
       A representation of a categorically-defined domain for variation, in which individual 
       contextual variation instances may be members of the domain.
@@ -41,7 +41,7 @@ $defs:
         items:
           oneOf:
             - $refCurie: vrs:Variation
-            - $refCurie: gks.core:IRI
+            - $refCurie: gks.common:IRI
 
   ProteinSequenceConsequence:
     maturity: draft
@@ -55,14 +55,14 @@ $defs:
       of congruent Protein Alleles that share the same altered codon(s).
     properties:
       type:
-        type: string
+        extends: type
         const: ProteinSequenceConsequence
         default: ProteinSequenceConsequence
         description: 'MUST be "ProteinSequenceConsequence"'
       definingContext:
         oneOf:
           - $refCurie: vrs:Allele
-          - $refCurie: gks.core:IRI
+          - $refCurie: gks.common:IRI
         description: >-
           The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_
           object that is congruent with (projects to the same codons) as alleles on other protein reference 
@@ -81,14 +81,14 @@ $defs:
     type: object
     properties:
       type:
-        type: string
+        extends: type
         const: CanonicalAllele
         default: CanonicalAllele
         description: 'MUST be "CanonicalAllele"'
       definingContext:
         oneOf:
           - $refCurie: vrs:Allele
-          - $refCurie: gks.core:IRI
+          - $refCurie: gks.common:IRI
         description: >-
           The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_
           object that is congruent with variants on alternate reference sequences.
@@ -108,7 +108,7 @@ $defs:
       member CNVs.
     properties:
       type:
-        type: string
+        extends: type
         const: CategoricalCnv
         default: CategoricalCnv
         description: 'MUST be "CategoricalCnv"'
@@ -157,7 +157,7 @@ $defs:
       to indicate how a categorical variation concept should be evaluated for matching variants.
     properties:
       type:
-        type: string
+        extends: type
         const: DescribedVariation
         default: DescribedVariation
         description: 'MUST be "DescribedVariation"'
@@ -342,7 +342,7 @@ $defs:
   # =============================================================================
 
   CategoricalVariant:
-    inherits: gks.core:DomainEntity
+    inherits: gks.common:DomainEntity
     description: >-
       A top-level representation of a categorically-defined domain for variation across one or multiple biological levels in which individual contextual variants may be members of the domain.
     # type: object
@@ -363,7 +363,7 @@ $defs:
     #     type: array
     #     ordered: true
     #     items:
-    #       - $refExtension: gks.core:Extension
+    #       - $refExtension: gks.common:Extension
 
 
 

diff --git a/schema/catvrs/def/CanonicalAllele.rst b/schema/catvrs/def/CanonicalAllele.rst
@@ -33,22 +33,22 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`.
           - 0..m
           - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
-       *  - type
-          - string
-          - 1..1
-          - MUST be "CanonicalAllele"
        *  - mappings
-          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
+          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
           - 0..m
           - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
+       *  - type
+          - string
+          - 1..1
+          - MUST be "CanonicalAllele"
        *  - definingContext
-          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
+          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 1..1
           - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with variants on alternate reference sequences.
diff --git a/schema/catvrs/def/CategoricalCnv.rst b/schema/catvrs/def/CategoricalCnv.rst
@@ -33,21 +33,21 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
           - 0..m
           - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
-       *  - type
-          - string
-          - 1..1
-          - MUST be "CategoricalCnv"
        *  - mappings
-          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
+          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
           - 0..m
           - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
+       *  - type
+          - string
+          - 1..1
+          - MUST be "CategoricalCnv"
        *  - location
           - {'$ref': '../vrs/vrs.yaml#/$defs/Location'}
           - 1..1

diff --git a/schema/catvrs/def/CategoricalVariation.rst b/schema/catvrs/def/CategoricalVariation.rst
@@ -4,7 +4,7 @@ A representation of a categorically-defined domain for variation, in which indiv
 
     **Information Model**
 
-Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEntity`.
+Some CategoricalVariation attributes are inherited from :ref:`gks.common:DomainEntity`.
 
     .. list-table::
        :class: clean-wrap
@@ -20,6 +20,10 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEnt
           - string
           - 0..1
           - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
+       *  - type
+          - string
+          - 1..1
+          - 
        *  - label
           - string
           - 0..1
@@ -33,18 +37,14 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEnt
           - 0..m
           - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
-       *  - type
-          - string
-          - 1..1
-          - 
        *  - mappings
-          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
+          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
           - 0..m
           - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
diff --git a/schema/catvrs/def/DescribedVariation.rst b/schema/catvrs/def/DescribedVariation.rst
@@ -25,21 +25,21 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation
           - 0..m
           - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
-       *  - type
-          - string
-          - 1..1
-          - MUST be "DescribedVariation"
        *  - mappings
-          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
+          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
           - 0..m
           - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
+       *  - type
+          - string
+          - 1..1
+          - MUST be "DescribedVariation"
        *  - label
           - string
           - 1..1

diff --git a/schema/catvrs/def/ProteinSequenceConsequence.rst b/schema/catvrs/def/ProteinSequenceConsequence.rst
@@ -33,22 +33,22 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV
           - 0..m
           - Alternative name(s) for the Entity.
        *  - extensions
-          - `Extension <../gks-core-im/core.json#/$defs/Extension>`_
+          - `Extension <../gks-common/common.json#/$defs/Extension>`_
           - 0..m
           - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
-       *  - type
-          - string
-          - 1..1
-          - MUST be "ProteinSequenceConsequence"
        *  - mappings
-          - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_
+          - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_
           - 0..m
           - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
        *  - members
-          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
+          - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 0..m
           - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
+       *  - type
+          - string
+          - 1..1
+          - MUST be "ProteinSequenceConsequence"
        *  - definingContext
-          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_
+          - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_
           - 1..1
           - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with (projects to the same codons) as alleles on other protein reference  sequences.
diff --git a/schema/catvrs/json/CanonicalAllele b/schema/catvrs/json/CanonicalAllele
@@ -30,21 +30,15 @@
          "type": "array",
          "ordered": true,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core-im/1.x/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension"
          },
          "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
       },
-      "type": {
-         "type": "string",
-         "const": "CanonicalAllele",
-         "default": "CanonicalAllele",
-         "description": "MUST be \"CanonicalAllele\""
-      },
       "mappings": {
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core-im/1.x/json/ConceptMapping"
+            "$ref": "/ga4gh/schema/gks-common/1.x/json/ConceptMapping"
          },
          "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation."
       },
@@ -55,18 +49,24 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI"
                },
                {
                   "$ref": "/ga4gh/schema/vrs/2.x/json/Variation"
                }
             ]
          }
       },
+      "type": {
+         "type": "string",
+         "const": "CanonicalAllele",
+         "default": "CanonicalAllele",
+         "description": "MUST be \"CanonicalAllele\""
+      },
       "definingContext": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI"
+               "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI"
             },
             {
                "$ref": "/ga4gh/schema/vrs/2.x/json/Allele"

diff --git a/schema/catvrs/json/CategoricalCnv b/schema/catvrs/json/CategoricalCnv
@@ -30,21 +30,15 @@
          "type": "array",
          "ordered": true,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core-im/1.x/json/Extension"
+            "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension"
          },
          "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
       },
-      "type": {
-         "type": "string",
-         "const": "CategoricalCnv",
-         "default": "CategoricalCnv",
-         "description": "MUST be \"CategoricalCnv\""
-      },
       "mappings": {
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core-im/1.x/json/ConceptMapping"
+            "$ref": "/ga4gh/schema/gks-common/1.x/json/ConceptMapping"
          },
          "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation."
       },
@@ -55,14 +49,20 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI"
                },
                {
                   "$ref": "/ga4gh/schema/vrs/2.x/json/Variation"
                }
             ]
          }
       },
+      "type": {
+         "type": "string",
+         "const": "CategoricalCnv",
+         "default": "CategoricalCnv",
+         "description": "MUST be \"CategoricalCnv\""
+      },
       "location": {
          "type": {
             "$ref": "/ga4gh/schema/vrs/2.x/json/Location"