Add SV Genotype Example

README.md

@@ -89,7 +89,7 @@ those implementing tools with VRS.
 
 ## Using smoketests
 
-The smoketests require python 3.8+. This is the recommended setup:
+The smoketests require python 3.9+. This is the recommended setup:
 
 ```
 $ python3 -m venv venv

examples/sv_genotype.yaml

@@ -0,0 +1,44 @@
+id: sv_genotype
+type: Genotype
+count: 2
+members:
+- id: genotype_member1
+  count: 1
+  variation:
+    id: haplotype1
+    type: Haplotype
+    members:
+    - id: ga4gh:AJ.WSHvYBlk-fTVCyCYeDeGuhK6z61cQfB4
+      type: Adjacency
+      adjoinedSequences:
+        - type: SequenceLocation
+          sequenceReference:
+            refgetAccession: SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU
+            residueAlphabet: na
+            id: NC_000001.10
+          end: 2000
+        - type: SequenceLocation
+          start: 1000
+    - id: ga4gh:VA.-tOc0wAbtHAU8uIK3t9OQzm95aTD7yOx
+      type: Allele
+      location:
+        type: SequenceLocation
+        start: 1500
+        end: 1501
+      state:
+        type: LiteralSequenceExpression
+        sequence: C
+- id: genotype_member2
+  count: 1
+  variation:
+    id: ga4gh:AJ.kfptigQUh7Gj7IIYtXiA1talIvXu9w6x
+    type: Adjacency
+    adjoinedSequences:
+      - type: SequenceLocation
+        sequenceReference:
+          refgetAccession: SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU
+          residueAlphabet: na
+          id: NC_000001.10
+        end: 850
+      - type: SequenceLocation
+        start: 950

schema/merged.yaml

@@ -44,6 +44,7 @@ $defs:
   MolecularVariation:
     description: A variation on a contiguous molecule.
     oneOf:
+    - $ref: '#/$defs/Adjacency'
     - $ref: '#/$defs/Allele'
     - $ref: '#/$defs/Haplotype'
     discriminator:
@@ -661,6 +662,7 @@ $defs:
         description: The number of copies of the `variation` at a Genotype locus.
       variation:
         oneOf:
+        - $ref: '#/$defs/Adjacency'
         - $ref: '#/$defs/Allele'
         - $ref: '#/$defs/Haplotype'
         description: A MolecularVariation at a Genotype locus.

schema/vrs-source.yaml

@@ -94,6 +94,7 @@ $defs:
     oneOf:
       - $ref: "#/$defs/Allele"
       - $ref: "#/$defs/Haplotype"
+      - $ref: "#/$defs/Adjacency"
     discriminator:
       propertyName: type
 
@@ -506,6 +507,7 @@ $defs:
         oneOf:
           - $ref: "#/$defs/Allele"
           - $ref: "#/$defs/Haplotype"
+          - $ref: "#/$defs/Adjacency"
         description: >-
           A :ref:`MolecularVariation` at a :ref:`Genotype` locus.
     required: [ "count", "variation" ]

schema/vrs.json

@@ -65,6 +65,9 @@
       "MolecularVariation": {
          "description": "A variation on a contiguous molecule.",
          "oneOf": [
+            {
+               "$ref": "#/$defs/Adjacency"
+            },
             {
                "$ref": "#/$defs/Allele"
             },
@@ -865,6 +868,9 @@
             },
             "variation": {
                "oneOf": [
+                  {
+                     "$ref": "#/$defs/Adjacency"
+                  },
                   {
                      "$ref": "#/$defs/Allele"
                   },

schema/vrs.yaml

@@ -44,6 +44,7 @@ $defs:
   MolecularVariation:
     description: A variation on a contiguous molecule.
     oneOf:
+    - $ref: '#/$defs/Adjacency'
     - $ref: '#/$defs/Allele'
     - $ref: '#/$defs/Haplotype'
     discriminator:
@@ -661,6 +662,7 @@ $defs:
         description: The number of copies of the `variation` at a Genotype locus.
       variation:
         oneOf:
+        - $ref: '#/$defs/Adjacency'
         - $ref: '#/$defs/Allele'
         - $ref: '#/$defs/Haplotype'
         description: A MolecularVariation at a Genotype locus.

tests/test_definitions.yaml

@@ -1,39 +1,44 @@
 tests:
   - test_file: simple_breakpoint.yaml
     description: An adjacency between two sequence locations.
-    image: ../../docs/images/ex_simple_breakpoint.png
+    image: ../docs/source/images/tests/ex_simple_breakpoint.png
     schema: vrs
     definition: Adjacency
   - test_file: revcomp_breakpoint.yaml
     description: An adjacency between two sequence locations, the 2nd of which is in reverse orientation.
-    image: ../../docs/images/ex_revcomp_breakpoint.png
+    image: ../docs/source/images/tests/ex_revcomp_breakpoint.png
     schema: vrs
     definition: Adjacency
   - test_file: terminal_breakend.yaml
     description: An adjacency with only the starting sequence location. defining the break at which the adjacency ends or terminates.
-    image: ../../docs/images/ex_terminal_breakend.png
+    image: ../docs/source/images/tests/ex_terminal_breakend.png
     schema: vrs
     definition: Adjacency
   - test_file: sequence_homology.yaml
     description: An adjacency in which the two sequence locations have a homologous overlapping adjoined sequences.
-    image: ../../docs/images/ex_sequence_homology.png
+    image: ../docs/source/images/tests/ex_sequence_homology.png
     schema: vrs
     definition: Adjacency
   - test_file: precise_linker.yaml
     description: An adjacency with a literal sequence linking the two sequence locations that make up the adjoined sequences.
-    image: ../../docs/images/ex_precise_linker.png
+    image: ../docs/source/images/tests/ex_precise_linker.png
     schema: vrs
     definition: Adjacency
   - test_file: ambiguous_linker.yaml
     description: An adjacency with a length expression linking the two sequence locations that make up the adjoined sequences.
-    image: ../../docs/images/ex_ambiguous_linker.png
+    image: ../docs/source/images/tests/ex_ambiguous_linker.png
     schema: vrs
     definition: Adjacency
   - test_file: sv_haplotype.yaml
     description: A haplotype of 3 members. First an adjacency with a litereal sequence linker followed by an SNV on the 2nd sequence and ending with a simple breakpoint adjacency that ends with the 1st sequence in the haplotype.
-    image: ../../docs/images/ex_sv_haplotype.png
+    image: ../docs/source/images/tests/ex_sv_haplotype.png
     schema: vrs
     definition: Haplotype
+  - test_file: sv_genotype.yaml
+    description: A genotype consisting of 2 members. The first member has a tandem duplication with a SNV on the second copy of the duplicated region. The second member has a deletion.
+    image: ../docs/source/images/tests/ex_sv_genotype.png
+    schema: vrs
+    definition: Genotype
   - test_file: simple_haplotype.yaml
     description: A haplotype of two alleles on a shared chromosome reference sequence.
     schema: vrs

tests/test_examples.py

@@ -1,6 +1,6 @@
 from config import test_dir, schema_dir, examples_dir
 import yaml
-from jsonschema import validate
+from jsonschema import validate, ValidationError
 
 
 def get_schema(schema_file, schema_class, kw="$defs"):
@@ -22,5 +22,5 @@ def test_examples():
         )
         try:
             assert validate(data, schema) is None
-        except AssertionError as e:
-            raise AssertionError(f"AssertionError in {test['test_file']}: {e}")
+        except ValidationError as e:
+            raise ValidationError(f"AssertionError in {test['test_file']}: {e}")