Merge pull request #387 from sierra-moxon/mkg_qualifiers

Adding qualifiers to MetaEdge fixes #342

TranslatorReasonerAPI.yaml

@@ -22,7 +22,7 @@ info:
       url: https://github.com/NCATSTranslator/translator_extensions/blob/\
         production/x-translator/
   x-trapi:
-    version: 1.3.0
+    version: 1.4.0-dev
     asyncquery: REPLACE-WITH-true-IF-/asyncquery-IS-IMPLEMENTED-ELSE-false
     operations:
       - LIST-ALL-SUPPORTED-OPERATION-IDS-HERE-OR-REMOVE-THIS-SECTION
@@ -1273,11 +1273,50 @@ components:
           items:
             $ref: '#/components/schemas/MetaAttribute'
           nullable: true
+        qualifiers:
+          description: >-
+            Qualifiers that are possible to be found on this edge type.
+          items:
+            $ref: '#/components/schemas/MetaQualifier'
+          nullable: true
+          type: array
+        association:
+          type: object
+          $ref: '#/components/schemas/BiolinkEntity'
+          description: >-
+            The Biolink association type (entity) that this edge represents.
+            Associations are classes in Biolink
+            that represent a relationship between two entities.
+            For example, the association 'gene interacts with gene'
+            is represented by the Biolink class,
+            'biolink:GeneToGeneAssociation'.  If association
+            is filled out, then the testing harness can
+            help validate that the qualifiers are being used
+            correctly.
+          example: biolink:ChemicalToGeneAssociation
       required:
         - subject
         - predicate
         - object
       additionalProperties: false
+    MetaQualifier:
+      type: object
+      properties:
+        qualifier_type_id:
+          $ref: '#/components/schemas/CURIE'
+          description: >-
+            The CURIE of the qualifier type.
+          example: biolink:subject_aspect_qualifier
+          nullable: false
+        applicable_values:
+          type: array
+          description: >-
+                The list of values that are possible for this qualifier.
+          items:
+            type: string
+            example: [expression, activity, abundance, degradation]
+      required:
+        - qualifier_type_id
     MetaAttribute:
       type: object
       properties:

examples/MetaKnowledgeGraph/metaedge_with_qualifiers.json

@@ -0,0 +1,61 @@
+{
+  "nodes": {
+    "biolink:MolecularActivity": {
+      "id_prefixes": [
+        "RHEA",
+        "REACT",
+        "GO",
+        "UMLS"
+      ]
+    },
+    "biolink:SmallMolecule": {
+      "id_prefixes": [
+        "CHEBI",
+        "CHEMBL.COMPOUND",
+        "UMLS",
+        "UNII",
+        "PUBCHEM.COMPOUND",
+        "DRUGBANK",
+        "MESH",
+        "KEGG.COMPOUND",
+        "HMDB",
+        "CAS",
+        "KEGG.DRUG"
+      ]
+    }
+  },
+  "edges": [
+    {
+      "subject": "biolink:ChemicalEntity",
+      "predicate": "biolink:affects",
+      "object": "biolink:Gene",
+      "knowledge_types": [
+        "lookup"
+      ],
+      "association": "biolink:ChemicalToGeneAssociation",
+      "qualifiers": [
+        {
+          "qualifier_type_id": "biolink:subject_aspect_qualifier",
+          "applicable_values": [
+            "expression",
+            "abundance"
+          ]
+        },
+        {
+          "qualifier_type_id": "biolink:subject_aspect_qualifier",
+          "applicable_values": [
+            "expression",
+            "abundance",
+            "activity"
+          ]
+        },
+        {
+          "qualifier_type_id": "biolink:qualified_predicate",
+          "applicable_values": [
+            "biolink:causes"
+          ]
+        }
+      ]
+    }
+  ]
+}

tests/test_valid.py

@@ -22,10 +22,11 @@ def test_valid():
     jsonschema.validate(spec, openapi_schema)
 
 
-def test_examples():
+def test_message_examples():
     dir_path = os.path.dirname(os.path.realpath(__file__))
     with open(os.path.join(dir_path, '..', 'TranslatorReasonerAPI.yaml')) as f:
         spec = yaml.load(f, Loader=yaml.SafeLoader)
+        print(spec)
     dir_path_json = os.path.join(dir_path, '../examples/Message')
     for filename in os.listdir(dir_path_json):
         full_path = os.path.join(dir_path_json, filename)
@@ -36,6 +37,7 @@ def test_examples():
                 example = json.load(f)
                 trapi_version_locally = spec['info']['x-trapi']['version']
                 validator = TRAPISchemaValidator(trapi_version=trapi_version_locally)
+                print(validator.trapi_version)
                 try:
                     validator.validate(
                         instance=example,
@@ -45,3 +47,30 @@ def test_examples():
                     print(validator.to_dict(), file=stderr)
                     raise ValueError('TRAPI example is not valid against the trapi_version specified!')
 
+
+def metakg_examples():  # def test_metakg_examples():
+    mtest_directory('../examples/MetaKnowledgeGraph', 'MetaKnowledgeGraph')
+    mtest_directory('../examples/Message', 'Message')
+
+
+def mtest_directory(json_path, object_to_validate):
+    dir_path = os.path.dirname(os.path.realpath(__file__))
+    with open(os.path.join(dir_path, '..', 'TranslatorReasonerAPI.yaml')) as f:
+        spec = yaml.load(f, Loader=yaml.SafeLoader)
+    dir_path_json = os.path.join(dir_path, json_path)
+    for filename in os.listdir(dir_path_json):
+        full_path = os.path.join(dir_path_json, filename)
+        file_extension = pathlib.Path(full_path).suffix
+        if file_extension == '.json':
+            with open(full_path) as f:
+                example = json.load(f)
+                trapi_version_locally = spec['info']['x-trapi']['version']
+                validator = TRAPISchemaValidator(trapi_version=trapi_version_locally)
+                try:
+                    validator.validate(
+                        instance=example,
+                        component=object_to_validate
+                    )
+                except ValidationError:
+                    print(validator.to_dict(), file=stderr)
+                    raise ValueError('TRAPI example is not valid against the trapi_version specified!')