Renamed a few more validation codes then fixed code and unit tests ac…

…cordingly
NCATSTranslator · May 10, 2024 · 74e4efb · 74e4efb
1 parent 44d705a
commit 74e4efb
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Showing 4 changed files with 18 additions and 17 deletions.
diff --git a/docs/validation_codes_dictionary.md b/docs/validation_codes_dictionary.md
@@ -896,13 +896,13 @@
 
 **Description:** The TRAPI Response should specify its Biolink Model version compliance.
 
-### warning.trapi.response.knowledge_graph.empty
+### warning.trapi.response.message.knowledge_graph.empty
 
 **Message:** Response returned an empty Message Knowledge Graph?
 
 **Description:** An empty Knowledge Graph is allowed but merits a boundary response warning?
 
-### warning.trapi.response.results.empty
+### warning.trapi.response.message.results.empty
 
 **Message:** Response returned empty Message.results?
 

diff --git a/reasoner_validator/codes.yaml b/reasoner_validator/codes.yaml
@@ -689,14 +689,15 @@ warning:
         missing:
           $message: "TRAPI Response is missing its Biolink Model version"
           $description:  "The TRAPI Response should specify its Biolink Model version compliance."
-      knowledge_graph:
-        empty:
-          $message: "Response returned an empty Message Knowledge Graph?"
-          $description: "An empty Knowledge Graph is allowed but merits a boundary response warning?"
-      results:
-        empty:
-          $message: "Response returned empty Message.results?"
-          $description: "Empty Results is allowed but merits a boundary response warning?"
+      message:
+        knowledge_graph:
+          empty:
+            $message: "Response returned an empty Message Knowledge Graph?"
+            $description: "An empty Knowledge Graph is allowed but merits a boundary response warning?"
+        results:
+          empty:
+            $message: "Response returned empty Message.results?"
+            $description: "Empty Results is allowed but merits a boundary response warning?"
       workflow:
         runner_parameters:
           missing:

diff --git a/reasoner_validator/validator.py b/reasoner_validator/validator.py
@@ -311,7 +311,7 @@ def has_valid_knowledge_graph(
                 # An empty knowledge graph (warning) does not generally invalidate
                 # the whole Message, but no more validation tests are needed
                 if not self.suppress_empty_data_warnings:
-                    self.report(code="warning.trapi.response.knowledge_graph.empty")
+                    self.report(code="warning.trapi.response.message.knowledge_graph.empty")
             else:
                 mapping_validator: MappingValidator = check_node_edge_mappings(knowledge_graph)
                 if mapping_validator.has_messages():
@@ -360,7 +360,7 @@ def has_valid_results(self, message: Dict, sample_size: int = 0) -> bool:
 
             if not (results and len(results) > 0):
                 if not self.suppress_empty_data_warnings:
-                    self.report(code="warning.trapi.response.results.empty")
+                    self.report(code="warning.trapi.response.message.results.empty")
                     # An empty result (warning) does not generally invalidate
                     # the whole Message, but no more validation tests are needed
 

diff --git a/tests/test_response_validator.py b/tests/test_response_validator.py
@@ -450,7 +450,7 @@ def test_sample_graph(edges_limit: int, number_of_nodes_returned: int, number_of
 
 
 @pytest.mark.parametrize(
-    "response,trapi_version,biolink_version,target_provenance,strict_validation,message",
+    "response,trapi_version,biolink_version,target_provenance,strict_validation,code",
     [
         (   # Query 0 - Completely empty Response.Message
             {
@@ -526,7 +526,7 @@ def test_sample_graph(edges_limit: int, number_of_nodes_returned: int, number_of
             None,
             False,
             # "Validate TRAPI Response: WARNING - Response returned an empty Message Knowledge Graph?"
-            "warning.trapi.response.knowledge_graph.empty"
+            "warning.trapi.response.message.knowledge_graph.empty"
         ),
         (
             # Query 5 - Partly empty Response.Message with a modest but workable
@@ -560,7 +560,7 @@ def test_sample_graph(edges_limit: int, number_of_nodes_returned: int, number_of
             None,
             False,
             # "Validate TRAPI Response: WARNING -Response returned empty Message.results?"
-            "warning.trapi.response.results.empty"
+            "warning.trapi.response.message.results.empty"
         ),
         (
             # Query 7 - Partly empty Response.Message with a modest but workable
@@ -999,7 +999,7 @@ def test_check_biolink_model_compliance_of_trapi_response(
         biolink_version: str,
         target_provenance: Dict,
         strict_validation: bool,
-        message: str
+        code
 ):
     validator: TRAPIResponseValidator = TRAPIResponseValidator(
         trapi_version=trapi_version,
@@ -1008,7 +1008,7 @@ def test_check_biolink_model_compliance_of_trapi_response(
         target_provenance=target_provenance
     )
     validator.check_compliance_of_trapi_response(response=response)
-    check_messages(validator, message, no_errors=True)
+    check_messages(validator, code, no_errors=True)
 
 
 @pytest.mark.parametrize(