diff --git a/tests/test_biolink_compliance_validation.py b/tests/test_biolink_compliance_validation.py index f85795b..7ea13a4 100644 --- a/tests/test_biolink_compliance_validation.py +++ b/tests/test_biolink_compliance_validation.py @@ -64,6 +64,7 @@ def test_is_curie(identifier: str, outcome: bool): def test_get_reference(identifier: str, reference: str): assert get_reference(identifier) == reference + pp = PrettyPrinter(indent=4) # January 25, 2023 - as of reasoner-validator 3.1.0, @@ -122,6 +123,12 @@ def test_message(): assert not reporter.has_messages() reporter.report("info.compliant") assert reporter.has_messages() + reporter.report( + code="warning.knowledge_graph.edge.qualifiers.qualifier.value.unresolved", + edge_id="test_message edge", + identifier="activity_or_abundance", + qualifier_type_id="subject aspect qualifier" + ) reporter.dump() @@ -266,7 +273,7 @@ def test_inverse_predicate(): "info.input_edge.predicate.abstract" ), ( # Query 10 - Predicate is a mixin; default 'strict_validation' == False for input_edge - LATEST_BIOLINK_MODEL_VERSION, + "4.1.7", # LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:Drug', 'object_category': 'biolink:BiologicalProcess', @@ -372,7 +379,7 @@ def test_inverse_predicate(): }, "" ), - # ( # Query xx - Deprecated node category - no example of this in BIolink 3.1.1 + # ( # Query xx - Deprecated node category - no example of this in Biolink 3.1.1 # LATEST_BIOLINK_MODEL, # { # 'subject_category': 'biolink:Nutrient', @@ -1169,7 +1176,7 @@ def test_check_biolink_model_default_compliance_of_query_graph( "biolink_version,query_graph,validation_code", [ ( - LATEST_BIOLINK_MODEL_VERSION, + "4.1.7", # LATEST_BIOLINK_MODEL_VERSION, # Query 0: Query edge predicate is a mixin - non-strict validation { "nodes": { @@ -1719,7 +1726,7 @@ def qualifier_validator( tested_method, edge_model: str, edge: Dict, - message: str, + validation_code: str, trapi_version: Optional[str] = None, biolink_version: Optional[str] = LATEST_BIOLINK_MODEL_VERSION, associations: Optional[List[str]] = None, @@ -1790,13 +1797,13 @@ def qualifier_validator( check_messages( validator, - message, + validation_code, source_trail=source_trail ) @pytest.mark.parametrize( - "edge,message", + "edge,validation_code", [ ( # Query 0 - no 'qualifier_constraints' key - since nullable: true, this should pass {}, @@ -2027,13 +2034,13 @@ def qualifier_validator( ) ] ) -def test_validate_qualifier_constraints(edge: Dict, message: str): +def test_validate_qualifier_constraints(edge: Dict, validation_code: str): # TODO: to review: which of the validation tests that may be overridden by earlier TRAPI validation qualifier_validator( tested_method=BiolinkValidator.validate_qualifier_constraints, edge_model="QEdge", edge=edge, - message=message + validation_code=validation_code ) @@ -2083,7 +2090,7 @@ def test_validate_infores(identifier: str, validation_code: str): @pytest.mark.parametrize( - "edge,message", + "edge,validation_code", [ ( # Query 0 - 'qualifier_type_id' is the special qualifier case 'biolink:qualified_predicate' # an incorrect value, which is not a Biolink predicate, but... @@ -2122,12 +2129,12 @@ def test_validate_infores(identifier: str, validation_code: str): ) ] ) -def test_biolink_validation_suppressed_validate_qualifier_constraints(edge: Dict, message: str): +def test_biolink_validation_suppressed_validate_qualifier_constraints(edge: Dict, validation_code: str): qualifier_validator( tested_method=BiolinkValidator.validate_qualifier_constraints, edge_model="QEdge", edge=edge, - message=message, + validation_code=validation_code, biolink_version="suppress" ) @@ -2147,7 +2154,7 @@ def test_biolink_validation_suppressed_validate_qualifier_constraints(edge: Dict @pytest.mark.parametrize( - "trapi_version,edge,message", + "trapi_version,edge,validation_code", [ ( # Query 0 - 'qualifier_type_id' value not a Biolink CURIE - seen as 'unknown' in TRAPI < 1.4.0-beta TRAPI_1_3_0, @@ -2161,18 +2168,18 @@ def test_biolink_validation_suppressed_validate_qualifier_constraints(edge: Dict ) ] ) -def test_validate_biolink_curie_in_qualifier_constraints(trapi_version: str, edge: Dict, message: str): +def test_validate_biolink_curie_in_qualifier_constraints(trapi_version: str, edge: Dict, validation_code: str): qualifier_validator( tested_method=BiolinkValidator.validate_qualifier_constraints, edge_model="QEdge", edge=edge, - message=message, + validation_code=validation_code, trapi_version=trapi_version ) @pytest.mark.parametrize( - "edge,message,source_trail", + "edge,validation_code,source_trail", [ ( # Query 0 - no 'qualifiers' key - since nullable: true, this should pass {}, @@ -2306,12 +2313,12 @@ def test_validate_biolink_curie_in_qualifier_constraints(trapi_version: str, edg # ) ] ) -def test_validate_qualifiers(edge: Dict, message: str, source_trail: str): +def test_validate_qualifiers(edge: Dict, validation_code: str, source_trail: str): qualifier_validator( tested_method=BiolinkValidator.validate_qualifiers, edge_model="Edge", edge=edge, - message=message, + validation_code=validation_code, source_trail=source_trail ) @@ -2449,7 +2456,7 @@ def test_validate_qualifiers_with_association( tested_method=BiolinkValidator.validate_qualifiers, edge_model="Edge", edge=edge, - message=message, + validation_code=message, associations=associations, source_trail=source_trail ) @@ -2489,7 +2496,7 @@ def test_validate_biolink_curie_in_qualifiers( tested_method=BiolinkValidator.validate_qualifiers, edge_model="Edge", edge=edge, - message=message, + validation_code=message, trapi_version=trapi_version ) @@ -3265,7 +3272,7 @@ def test_validate_agent_type(value: Optional[str], code: str): "info.knowledge_graph.edge.predicate.mixin" ), ( - LATEST_BIOLINK_MODEL_VERSION, + "4.1.7", # LATEST_BIOLINK_MODEL_VERSION, # Query 22: 'biolink:treats' is a beast with special behaviours to be vetted { "nodes": {