SMU, datatype merge, doc fixes

ga4gh · Oct 10, 2024 · 4d1e6df · 4d1e6df
1 parent 1458c87
commit 4d1e6df
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Showing 11 changed files with 19 additions and 28 deletions.
diff --git a/docs/source/def b/docs/source/def
diff --git a/docs/source/def-core b/docs/source/def-core
@@ -0,0 +1 @@
+../../schema/cat-vrs/core/def
diff --git a/docs/source/def-profiles b/docs/source/def-profiles
@@ -0,0 +1 @@
+../../schema/cat-vrs/profiles/def
diff --git a/docs/source/schema.rst b/docs/source/schema.rst
@@ -19,11 +19,11 @@ JSON files for each class in the schema (|vrs_json|).
 Contributions to the schema MUST be written in the YAML document.
 
 
-.. _CategoricalVariationSchemata:
-.. _CategoricalVariation:
+.. _CategoricalVariantSchemata:
+.. _CategoricalVariant:
 
-Categorical Variation Schemata
-@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+Categorical Variant Schemata
+@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 
 THIS SECTION WILL GET UPDATEED WHEN I HAVE SCHEMATA READY
 PLEASE CHECK BACK IN THE FUTURE!
@@ -33,32 +33,25 @@ PLEASE CHECK BACK IN THE FUTURE!
     :alt: An irresistably cute kittynaut beckoning you to enter the Cat-VRS.
     :align: center
 
-.. include:: def/CategoricalVariation.rst
+.. include:: def-core/CategoricalVariant.rst
 
 .. _CanonicalAllele:
 
 Canonical Allele
 ################
 
-.. include:: def/CanonicalAllele.rst
-
-.. _DescribedVariation:
-
-Described Variation
-###################
-
-.. include:: def/DescribedVariation.rst
+.. include:: def-profiles/CanonicalAllele.rst
 
 .. _CategoricalCnv:
 
 Categorical Copy Number
 #######################
 
-.. include:: def/CategoricalCnv.rst
+.. include:: def-profiles/CategoricalCnv.rst
 
 .. _ProteinSequenceConsequence:
 
 Protein Sequence Consequence
 ############################
 
-.. include:: def/ProteinSequenceConsequence.rst
+.. include:: def-profiles/ProteinSequenceConsequence.rst
diff --git a/schema/cat-vrs/core/cat-vrs-core-source.yaml b/schema/cat-vrs/core/cat-vrs-core-source.yaml
@@ -6,7 +6,6 @@ strict: true
 
 imports:
   gks.core-im: ../../core-im/core-im-source.yaml
-  gks.data-types: ../../data-types/data-types-source.yaml
   vrs: ../../vrs/vrs-source.yaml
 
 $defs:
@@ -37,7 +36,7 @@ $defs:
         items:
           oneOf:
             - $ref: /ga4gh/schema/vrs/2.x/json/Variation
-            - $ref: /ga4gh/schema/gks-common/1.x/data-types/json/IRI
+            - $ref: /ga4gh/schema/gks-common/1.x/core-im/json/IRI
       constraints:
         type: array
         ordered: false
@@ -79,7 +78,7 @@ $defs:
         oneOf:
           - $ref: /ga4gh/schema/vrs/2.x/json/Variation
           - $ref: /ga4gh/schema/vrs/2.x/json/Location
-          - $ref: /ga4gh/schema/gks-common/1.x/data-types/json/IRI
+          - $ref: /ga4gh/schema/gks-common/1.x/core-im/json/IRI
       relations:
         type: array
         ordered: false
@@ -129,7 +128,7 @@ $defs:
         default: CopyChangeConstraint
         description: 'MUST be "CopyChangeConstraint"'
       copyChange:
-        $ref: /ga4gh/schema/gks-common/1.x/data-types/json/Coding
+        $ref: /ga4gh/schema/gks-common/1.x/core-im/json/Coding
         items:
           properties:
             code:

diff --git a/schema/cat-vrs/core/json/CategoricalVariant b/schema/cat-vrs/core/json/CategoricalVariant
@@ -31,7 +31,7 @@
          "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.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
@@ -40,7 +40,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping"
+            "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/ConceptMapping"
          },
          "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation."
       },
@@ -58,7 +58,7 @@
          "items": {
             "oneOf": [
                {
-                  "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+                  "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
                },
                {
                   "$ref": "/ga4gh/schema/vrs/2.x/json/Variation"

diff --git a/schema/cat-vrs/core/json/CopyChangeConstraint b/schema/cat-vrs/core/json/CopyChangeConstraint
@@ -13,7 +13,7 @@
          "description": "MUST be \"CopyChangeConstraint\""
       },
       "copyChange": {
-         "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding",
+         "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding",
          "items": {
             "properties": {
                "code": {

diff --git a/schema/cat-vrs/core/json/DefiningContextConstraint b/schema/cat-vrs/core/json/DefiningContextConstraint
@@ -15,7 +15,7 @@
       "definingContext": {
          "oneOf": [
             {
-               "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+               "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
             },
             {
                "$ref": "/ga4gh/schema/vrs/2.x/json/Location"

diff --git a/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml b/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml
@@ -5,7 +5,6 @@ type: object
 
 imports:
   gks.core-im: ../../core-im/core-im-source.yaml
-  gks.data-types: ../../data-types/data-types-source.yaml
   vrs: ../../vrs/vrs-source.yaml
   cat.core: ../core/cat-vrs-core-source.yaml
 

diff --git a/schema/data-types b/schema/data-types
diff --git a/submodules/vrs b/submodules/vrs