Add constraint to items in adjoinedSequences (#556)

* Add constraint to items in adjoinedSequences

* Add unit test for invalid adjoinedSequence

examples/invalid_adjacency.yaml

@@ -0,0 +1,18 @@
+id: simple_breakpoint
+type: Adjacency
+adjoinedSequences:
+  - type: SequenceLocation
+    sequenceReference:
+      type: SequenceReference
+      refgetAccession: SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU
+      residueAlphabet: na
+      id: NC_000001.10
+    start: 100
+    end: 200
+  - type: SequenceLocation
+    sequenceReference:
+      type: SequenceReference
+      refgetAccession: SQ.9KdcA9ZpY1Cpvxvg8bMSLYDUpsX6GDLO
+      residueAlphabet: na
+      id: NC_000002.11
+    start: 456

schema/vrs/json/Adjacency

@@ -74,7 +74,13 @@
                {
                   "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
                }
-            ]
+            ],
+            "not": {
+               "required": [
+                  "start",
+                  "end"
+               ]
+            }
          },
          "description": "The terminal sequence or pair of adjoined sequences that defines in the adjacency.",
          "minItems": 2,

schema/vrs/vrs-source.yaml

@@ -516,6 +516,8 @@ $defs:
           oneOf:
           - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
           - $ref: "#/$defs/Location"
+          not:
+            required: ["start", "end"]
         description: The terminal sequence or pair of adjoined sequences that defines in the adjacency.
         minItems: 2
         maxItems: 2

tests/test_definitions.yaml

@@ -46,3 +46,8 @@ tests:
     description: A simple RLE expansion from SPDI representation
     schema: vrs
     definition: Allele
+  - test_file: invalid_adjacency.yaml
+    description: An adjacency with an adjoinedSequence incorrectly containing both a start and end
+    schema: vrs
+    definition: Adjacency
+    shouldValidationFail: true

tests/test_examples.py

@@ -1,7 +1,9 @@
 from config import test_path, examples_path
 import yaml
 from config import validator
-
+from pytest import raises
+from jsonschema.exceptions import ValidationError
+from contextlib import nullcontext
 
 def test_examples():
     with open(test_path / 'test_definitions.yaml') as def_file:
@@ -10,7 +12,9 @@ def test_examples():
         with open(examples_path / test['test_file']) as datafile:
             data = yaml.safe_load(datafile)
         class_validator = validator[test['definition']]
+
         try:
-            assert class_validator.validate(data) is None
+            with raises(ValidationError) if test.get("shouldValidationFail") else nullcontext():
+                assert class_validator.validate(data) is None
         except AssertionError as e:
             raise AssertionError(f"AssertionError in {test['test_file']}: {e}")