Split the qualifier validation reporting into distinct codes for the …

…qualifier_type_id ("qualifier.type_id.unknown") versus qualifier_value ("qualifier.value.unresolved")
NCATSTranslator · Mar 16, 2023 · 8dec02c · 8dec02c
1 parent d824426
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diff --git a/docs/validation_codes_dictionary.md b/docs/validation_codes_dictionary.md
@@ -510,11 +510,17 @@
 
 **Description:** Value of a 'qualifier_constraints.qualifier_set' property in a Query Graph must not be non-empty array!
 
-### error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.invalid
+### error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.type_id.unknown
 
-**Message:** Edge '{identifier}' qualifier entry is invalid!
+**Message:** Edge '{identifier}' qualifier type_id '{qualifier_type_id}' is unknown!
 
-**Description:** A 'qualifier' entry must be a valid JSON object with valid 'qualifier_type_id' and corresponding 'qualifier_value'!
+**Description:** A qualifier qualifier_type_id must be defined in the specified version of Biolink!
+
+### error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.value.unresolved
+
+**Message:** Edge '{identifier}' qualifier_value '{qualifier_value}' for '{qualifier_type_id}' cannot be resolved!
+
+**Description:** A 'qualifier_value' for the specified 'qualifier_type_id' of a qualifier likely could not be resolved without knowledge of the edge category!
 
 ### error.knowledge_graph.nodes.empty
 
@@ -750,9 +756,15 @@
 
 **Description:** Value of a 'qualifiers' property in a Knowledge Graph must not be non-empty array!
 
-### error.knowledge_graph.edge.qualifiers.qualifier.invalid
+### error.knowledge_graph.edge.qualifiers.qualifier.type_id.unknown
+
+**Message:** Edge '{identifier}' qualifier type_id '{qualifier_type_id}' is unknown!
+
+**Description:** A qualifier qualifier_type_id must be defined in the specified version of Biolink!
+
+### error.knowledge_graph.edge.qualifiers.qualifier.value.unresolved
 
-**Message:** Edge '{identifier}' qualifier entry is invalid!
+**Message:** Edge '{identifier}' qualifier_value '{qualifier_value}' for '{qualifier_type_id}' cannot be resolved!
 
-**Description:** A 'qualifier' entry must be a valid JSON object with valid 'qualifier_type_id' and corresponding 'qualifier_value'!
+**Description:** A 'qualifier_value' for the specified 'qualifier_type_id' of a qualifier likely could not be resolved without knowledge of the edge category!
 
diff --git a/reasoner_validator/biolink/__init__.py b/reasoner_validator/biolink/__init__.py
@@ -466,13 +466,19 @@ def validate_qualifier_entry(self, context: str, edge_id: str, qualifiers: List[
             qualifier_type_id: str = qualifier['qualifier_type_id']
             qualifier_value: str = qualifier['qualifier_value']
             try:
-                if not self.bmt.validate_qualifier(
+                if not self.bmt.is_qualifier(name=qualifier_type_id):
+                    self.report(
+                        code=f"error.{context}.qualifier.type_id.unknown",
+                        identifier=edge_id,
+                        qualifier_type_id=qualifier_type_id
+                    )
+                elif not self.bmt.validate_qualifier(
                         # TODO: temporary workaround, parse 'qualifier_type_id' to core name
                         qualifier_type_id=parse_name(qualifier_type_id),
                         qualifier_value=qualifier_value
                 ):
                     self.report(
-                        code=f"error.{context}.qualifier.invalid",
+                        code=f"error.{context}.qualifier.value.unresolved",
                         identifier=edge_id,
                         qualifier_type_id=qualifier_type_id,
                         qualifier_value=qualifier_value

diff --git a/reasoner_validator/codes.yaml b/reasoner_validator/codes.yaml
@@ -334,9 +334,14 @@ error:
               $message: "Edge '{identifier}' qualifier_set property value is empty!"
               $description: "Value of a 'qualifier_constraints.qualifier_set' property in a Query Graph must not be non-empty array!"
           qualifier:
-            invalid:
-              $message: "Edge '{identifier}' qualifier entry is invalid!"
-              $description: "A 'qualifier' entry must be a valid JSON object with valid 'qualifier_type_id' and corresponding 'qualifier_value'!"
+            type_id:
+              unknown:
+                $message: "Edge '{identifier}' qualifier type_id '{qualifier_type_id}' is unknown!"
+                $description: "A qualifier qualifier_type_id must be defined in the specified version of Biolink!"
+            value:
+              unresolved:
+                $message: "Edge '{identifier}' qualifier_value '{qualifier_value}' for '{qualifier_type_id}' cannot be resolved!"
+                $description: "A 'qualifier_value' for the specified 'qualifier_type_id' of a qualifier likely could not be resolved without knowledge of the edge category!"
   knowledge_graph:
     nodes:
       empty:
@@ -474,6 +479,11 @@ error:
           $message: "Edge '{identifier}' qualifiers property value is empty!"
           $description: "Value of a 'qualifiers' property in a Knowledge Graph must not be non-empty array!"
         qualifier:
-          invalid:
-            $message: "Edge '{identifier}' qualifier entry is invalid!"
-            $description: "A 'qualifier' entry must be a valid JSON object with valid 'qualifier_type_id' and corresponding 'qualifier_value'!"
+          type_id:
+            unknown:
+              $message: "Edge '{identifier}' qualifier type_id '{qualifier_type_id}' is unknown!"
+              $description: "A qualifier qualifier_type_id must be defined in the specified version of Biolink!"
+          value:
+            unresolved:
+              $message: "Edge '{identifier}' qualifier_value '{qualifier_value}' for '{qualifier_type_id}' cannot be resolved!"
+              $description: "A 'qualifier_value' for the specified 'qualifier_type_id' of a qualifier likely could not be resolved without knowledge of the edge category!"
diff --git a/tests/test_biolink_compliance_validation.py b/tests/test_biolink_compliance_validation.py
@@ -1202,7 +1202,7 @@ def qualifier_validator(tested_method, edge_model: str, query: Tuple[Dict, str])
                     }
                 ]
             },
-            "error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.invalid"
+            "error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.type_id.unknown"
         ),
         (  # Query 13 - 'qualifier_type_id' property value is unknown
             {
@@ -1217,7 +1217,7 @@ def qualifier_validator(tested_method, edge_model: str, query: Tuple[Dict, str])
                     }
                 ]
             },
-            "error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.invalid"
+            "error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.type_id.unknown"
         ),
         (  # Query 14 - 'qualifier_type_id' property value is valid but abstract
             {
@@ -1233,7 +1233,7 @@ def qualifier_validator(tested_method, edge_model: str, query: Tuple[Dict, str])
                 ]
             },
             # "info.query_graph.edge.qualifier.abstract"
-            "error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.invalid"
+            "error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.value.unresolved"
         ),
         (  # Query 15 - 'qualifier_type_id' property value is not a Biolink qualifier term
             {
@@ -1248,7 +1248,7 @@ def qualifier_validator(tested_method, edge_model: str, query: Tuple[Dict, str])
                     }
                 ]
             },
-            "error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.invalid"
+            "error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.type_id.unknown"
         ),
         (  # Query 16 - 'qualifier' entry is missing its 'qualifier_value' property - invalidated by TRAPI schema
             {
@@ -1380,7 +1380,7 @@ def test_validate_qualifier_constraints(query: Tuple[Dict, str]):
                     }
                 ]
             },
-            "error.knowledge_graph.edge.qualifiers.qualifier.invalid"
+            "error.knowledge_graph.edge.qualifiers.qualifier.type_id.unknown"
         ),
         (  # Query 8 - 'qualifier_type_id' property value is unknown
             {
@@ -1391,7 +1391,7 @@ def test_validate_qualifier_constraints(query: Tuple[Dict, str]):
                     }
                 ]
             },
-            "error.knowledge_graph.edge.qualifiers.qualifier.invalid"
+            "error.knowledge_graph.edge.qualifiers.qualifier.type_id.unknown"
         ),
         (  # Query 9 - 'qualifier_type_id' property value is valid but abstract
             {
@@ -1403,7 +1403,7 @@ def test_validate_qualifier_constraints(query: Tuple[Dict, str]):
                 ]
             },
             # "info.query_graph.edge.qualifier.abstract"
-            "error.knowledge_graph.edge.qualifiers.qualifier.invalid"
+            "error.knowledge_graph.edge.qualifiers.qualifier.value.unresolved"
         ),
         (  # Query 10 - 'qualifier_type_id' property value is not a Biolink qualifier term
             {
@@ -1414,7 +1414,7 @@ def test_validate_qualifier_constraints(query: Tuple[Dict, str]):
                     }
                 ]
             },
-            "error.knowledge_graph.edge.qualifiers.qualifier.invalid"
+            "error.knowledge_graph.edge.qualifiers.qualifier.type_id.unknown"
         ),
         (  # Query 11 - 'qualifier' entry is missing its 'qualifier_value' property - invalidated by TRAPI schema
             {