create JSON for single-ref abstract classes

src/ga4gh/gks/metaschema/tools/source_proc.py

@@ -63,10 +63,14 @@ def build_inheritance_dicts(self):
         #   If it inherits from a class, register the inheritance
         for cls, cls_def in self.raw_defs.items():
             cls_url = f'#/{self.schema_def_keyword}/{cls}'
-            if self.class_is_abstract(cls) and 'oneOf' in cls_def:
+            if self.class_is_abstract(cls) and ('oneOf' in cls_def or '$ref' in cls_def):
                 maps_to_urls = self.has_children_urls.get(cls_url, set())
                 maps_to = self.has_children.get(cls, set())
-                for record in cls_def['oneOf']:
+                if 'oneOf' in cls_def:
+                    records = cls_def['oneOf']
+                else:
+                    records = [{'$ref': cls_def['$ref']}]
+                for record in records:
                     if not isinstance(record, dict):
                         continue
                     assert len(record) == 1
@@ -440,7 +444,7 @@ def clean_for_js(self):
                 schema_definition.pop('ga4ghDigest', None)
                 schema_definition.pop('header_level', None)
                 self.concretize_js_object(schema_definition)
-                if 'oneOf' not in schema_definition and 'allOf' not in schema_definition:
+                if 'oneOf' not in schema_definition and 'allOf' not in schema_definition and '$ref' not in schema_definition:
                     abstract_class_removals.append(schema_class)
             if 'description' in schema_definition:
                 schema_definition['description'] = \

tests/data/gnomAD/json/GnomadCAF

@@ -4,32 +4,6 @@
    "title": "GnomadCAF",
    "type": "object",
    "$defs": {
-      "GrpMaxFAF95": {
-         "description": "The group maximum filtering allele frequency at 95% CI",
-         "protectedClassOf": "GnomadCAF",
-         "type": "object",
-         "maturity": "draft",
-         "properties": {
-            "frequency": {
-               "type": "number"
-            },
-            "confidenceInterval": {
-               "type": "number",
-               "const": 0.95,
-               "default": 0.95
-            },
-            "groupId": {
-               "type": "string",
-               "description": "The genetic ancestry group from which the max frequency was calculated."
-            }
-         },
-         "required": [
-            "confidenceInterval",
-            "frequency",
-            "groupId"
-         ],
-         "additionalProperties": false
-      },
       "GnomadCafProperties": {
          "description": "Additional properties specific to the gnomAD CAF model.",
          "protectedClassOf": "GnomadCAF",
@@ -101,6 +75,32 @@
             }
          },
          "required": []
+      },
+      "GrpMaxFAF95": {
+         "description": "The group maximum filtering allele frequency at 95% CI",
+         "protectedClassOf": "GnomadCAF",
+         "type": "object",
+         "maturity": "draft",
+         "properties": {
+            "frequency": {
+               "type": "number"
+            },
+            "confidenceInterval": {
+               "type": "number",
+               "const": 0.95,
+               "default": 0.95
+            },
+            "groupId": {
+               "type": "string",
+               "description": "The genetic ancestry group from which the max frequency was calculated."
+            }
+         },
+         "required": [
+            "confidenceInterval",
+            "frequency",
+            "groupId"
+         ],
+         "additionalProperties": false
       }
    },
    "maturity": "draft",

tests/data/vrs/def/Adjacency.rst

@@ -29,7 +29,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type
@@ -45,7 +45,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
       - 0..m
       - 
    *  - adjoinedSequences
-      - `IRI <../gks-common/$defs/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..2
       - The terminal sequence or pair of adjoined sequences that defines in the adjacency.
    *  - linker

tests/data/vrs/def/Allele.rst

@@ -29,7 +29,7 @@ Some Allele attributes are inherited from :ref:`Variation`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type
@@ -45,7 +45,7 @@ Some Allele attributes are inherited from :ref:`Variation`.
       - 0..m
       - 
    *  - location
-      - `IRI <../gks-common/$defs/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - The location of the Allele
    *  - state

tests/data/vrs/def/CopyNumber.rst

@@ -29,7 +29,7 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type
@@ -45,6 +45,6 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
       - 0..m
       - 
    *  - location
-      - `IRI <../gks-common/$defs/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.

tests/data/vrs/def/CopyNumberChange.rst

@@ -29,7 +29,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type
@@ -45,7 +45,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
       - 0..m
       - 
    *  - location
-      - `IRI <../gks-common/$defs/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.
    *  - copyChange

tests/data/vrs/def/CopyNumberCount.rst

@@ -29,7 +29,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type
@@ -45,7 +45,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
       - 0..m
       - 
    *  - location
-      - `IRI <../gks-common/$defs/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.
    *  - copies

tests/data/vrs/def/Ga4ghIdentifiableObject.rst

@@ -29,7 +29,7 @@ Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core:Entity
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type

tests/data/vrs/def/Haplotype.rst

@@ -29,7 +29,7 @@ Some Haplotype attributes are inherited from :ref:`Variation`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type
@@ -45,6 +45,6 @@ Some Haplotype attributes are inherited from :ref:`Variation`.
       - 0..m
       - 
    *  - members
-      - :ref:`Adjacency` | :ref:`Allele` | `IRI <../gks-common/$defs/IRI>`_
+      - :ref:`Adjacency` | :ref:`Allele` | :ref:`IRI`
       - 2..m
       - A list of :ref:`Alleles <Allele>` and :ref:`Adjacencies <Adjacency>` that comprise a Haplotype.  Members must share the same reference sequence as adjacent members. Alleles should not have overlapping or adjacent coordinates with neighboring Alleles. Neighboring alleles should be ordered  by ascending coordinates, unless represented on a DNA inversion (following an Adjacency with  end-defined adjoinedSequences), in which case they should be ordered in descending coordinates.  Sequence references MUST be consistent for all members between and including the end of one  Adjacency and the beginning of another.

tests/data/vrs/def/LengthExpression.rst

@@ -29,7 +29,7 @@ Some LengthExpression attributes are inherited from :ref:`SequenceExpression`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type

tests/data/vrs/def/LiteralSequenceExpression.rst

@@ -29,7 +29,7 @@ Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpre
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type

tests/data/vrs/def/ReferenceLengthExpression.rst

@@ -29,7 +29,7 @@ Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpre
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type

tests/data/vrs/def/SequenceExpression.rst

@@ -29,7 +29,7 @@ Some SequenceExpression attributes are inherited from :ref:`gks.core:Entity`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type

tests/data/vrs/def/SequenceLocation.rst

@@ -29,7 +29,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type
@@ -41,7 +41,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
       - 0..1
       - A sha512t24u digest created using the VRS Computed Identifier algorithm.
    *  - sequenceReference
-      - `IRI <../gks-common/$defs/IRI>`_ | :ref:`SequenceReference`
+      - :ref:`IRI` | :ref:`SequenceReference`
       - 0..1
       - A :ref:`SequenceReference`.
    *  - start

tests/data/vrs/def/SequenceReference.rst

@@ -29,7 +29,7 @@ Some SequenceReference attributes are inherited from :ref:`gks.core:Entity`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type

tests/data/vrs/def/Variation.rst

@@ -29,7 +29,7 @@ Some Variation attributes are inherited from :ref:`Ga4ghIdentifiableObject`.
       - 0..1
       - A free-text description of the entity.
    *  - extensions
-      - `Extension <../gks-common/core.json#/$defs/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - 
    *  - type

tests/data/vrs/json/Location

@@ -0,0 +1,11 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/Location",
+   "title": "Location",
+   "type": "object",
+   "description": "A contiguous segment of a biological sequence.",
+   "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation",
+   "discriminator": {
+      "propertyName": "type"
+   }
+}

tests/data/vrs/vrs.yaml

@@ -303,6 +303,11 @@ $defs:
     - copyChange
     - location
     additionalProperties: false
+  Location:
+    description: A contiguous segment of a biological sequence.
+    $ref: '#/$defs/SequenceLocation'
+    discriminator:
+      propertyName: type
   SequenceLocation:
     maturity: draft
     ga4ghDigest: