diff --git a/CHANGELOG.md b/CHANGELOG.md index cfad7b7..72a233f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,9 @@ The Reasoner Validator package is evolving along with progress in TRAPI and Biolink Model standards within the NCATS Biomedical Knowledge Translator. +## v3.5.7 +- patch to fix a previously unnoticed bug in SRI Testing related 'input edge' validation method (wouldn't affect non-SRI Testing related code usage of reasoner-validator) + ## v3.5.6 - **ars_uuid_result_test_runner.py** renamed to **trapi_response_validator.py** and generalized to accept a local TRAPI Response or possibly, an explicit endpoint URL and the TRAPI Request JSON with which to query, whose TRAPI Response is then validated. diff --git a/poetry.lock b/poetry.lock index 6aba51e..0152c80 100644 --- a/poetry.lock +++ b/poetry.lock @@ -648,61 +648,61 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] [[package]] name = "markupsafe" -version = "2.1.2" +version = "2.1.3" 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else None predicate = edge['predicate'] if 'predicate' in edge else None - subject_curie = edge['subject'] if 'subject' in edge else None - object_curie = edge['object'] if 'object' in edge else None + + if 'subject_id' in edge: + subject_curie = edge['subject_id'] + elif 'subject' in edge: + subject_curie = edge['subject'] + else: + subject_curie = None + + if 'object_id' in edge: + object_curie = edge['object_id'] + elif 'object' in edge: + object_curie = edge['object'] + else: + object_curie = None edge_id = f"{str(subject_curie)}--{predicate}->{str(object_curie)}" diff --git a/tests/test_biolink_compliance_validation.py b/tests/test_biolink_compliance_validation.py index d92a708..6205724 100644 --- a/tests/test_biolink_compliance_validation.py +++ b/tests/test_biolink_compliance_validation.py @@ -98,209 +98,220 @@ def test_inverse_predicate(): 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:subclass_of', - 'subject': 'UBERON:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' }, "" ), - ( # Query 1 - Missing subject category - LATEST_BIOLINK_MODEL_VERSION, + ( # Query 1 - Valid edge object, using original 'subject' and 'object' JSON tags + LATEST_BIOLINK_MODEL_VERSION, # Biolink Model Version { + 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:subclass_of', 'subject': 'UBERON:0005453', 'object': 'UBERON:0035769' }, + "" # should still no generate an error message + ), + ( # Query 2 - Missing subject category + LATEST_BIOLINK_MODEL_VERSION, + { + 'object_category': 'biolink:AnatomicalEntity', + 'predicate': 'biolink:subclass_of', + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' + }, # f"{INPUT_EDGE_PREFIX}: ERROR - Subject has a missing Biolink category!" "error.input_edge.node.category.missing" ), - ( # Query 2 - Invalid subject category + ( # Query 3 - Invalid subject category LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:NotACategory', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:subclass_of', - 'subject': 'UBERON:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: ERROR - Subject element 'biolink:NotACategory' is unknown!" "error.input_edge.node.category.unknown" ), - ( # Query 3 - Missing object category + ( # Query 4 - Missing object category LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:subclass_of', - 'subject': 'UBERON:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: ERROR - Object has a missing Biolink category!" "error.input_edge.node.category.missing" ), - ( # Query 4 - Invalid object category + ( # Query 5 - Invalid object category LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:NotACategory', 'predicate': 'biolink:subclass_of', - 'subject': 'UBERON:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: ERROR - Object element 'biolink:NotACategory' is unknown!" "error.input_edge.node.category.unknown" ), - ( # Query 5 - Missing predicate + ( # Query 6 - Missing predicate LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', - 'subject': 'UBERON:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: ERROR - Predicate is missing or empty!" "error.input_edge.predicate.missing" ), - ( # Query 6 - Empty predicate + ( # Query 7- Empty predicate LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': '', - 'subject': 'UBERON:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: ERROR - Predicate is missing or empty!" "error.input_edge.predicate.missing" ), - ( # Query 7 - Predicate is deprecated + ( # Query 8 - Predicate is deprecated LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:Drug', 'object_category': 'biolink:Protein', 'predicate': 'biolink:increases_amount_or_activity_of', - 'subject': 'NDC:0002-8215-01', # a form of insulin - 'object': 'MONDO:0005148' # type 2 diabetes? + 'subject_id': 'NDC:0002-8215-01', # a form of insulin + 'object_id': 'MONDO:0005148' # type 2 diabetes? }, # f"{INPUT_EDGE_PREFIX}: WARNING - Predicate element " + # "'binds' is deprecated?" # in Biolink 3.1.1 "warning.input_edge.predicate.deprecated" ), - ( # Query 8 - Predicate is abstract + ( # Query 9 - Predicate is abstract LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:InformationContentEntity', 'object_category': 'biolink:Agent', 'predicate': 'biolink:contributor', - 'subject': 'PMID:1234', - 'object': 'ORCID:56789' + 'subject_id': 'PMID:1234', + 'object_id': 'ORCID:56789' }, # f"{INPUT_EDGE_PREFIX}: INFO - Predicate element 'biolink:contributor' is abstract." "info.input_edge.predicate.abstract" ), - ( # Query 9 - Predicate is a mixin + ( # Query 10 - Predicate is a mixin LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:Drug', 'object_category': 'biolink:BiologicalProcess', 'predicate': 'biolink:decreases_amount_or_activity_of', - 'subject': 'NDC:50090‑0766', # Metformin - 'object': 'GO:0006094' # Gluconeogenesis + 'subject_id': 'NDC:50090‑0766', # Metformin + 'object_id': 'GO:0006094' # Gluconeogenesis }, # f"{INPUT_EDGE_PREFIX}: INFO - Predicate element 'biolink:decreases_amount_or_activity_of' is a mixin." "info.input_edge.predicate.mixin" ), - ( # Query 10 - Unknown predicate element + ( # Query 11 - Unknown predicate element LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:not_a_predicate', - 'subject': 'UBERON:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: ERROR - Predicate element 'biolink:not_a_predicate' is unknown!" "error.input_edge.predicate.unknown" ), - ( # Query 11 - Invalid or unknown predicate + ( # Query 12 - Invalid or unknown predicate LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:has_unit', - 'subject': 'UBERON:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: ERROR - Predicate element 'biolink:has_unit' is invalid!" "error.input_edge.predicate.invalid" ), - ( # Query 12 - Non-canonical directed predicate + ( # Query 13 - Non-canonical directed predicate LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:SmallMolecule', 'object_category': 'biolink:Disease', 'predicate': 'biolink:affected_by', - 'subject': 'DRUGBANK:DB00331', - 'object': 'MONDO:0005148' + 'subject_id': 'DRUGBANK:DB00331', + 'object_id': 'MONDO:0005148' }, # f"{INPUT_EDGE_PREFIX}: WARNING - Edge predicate 'biolink:affected_by' is non-canonical?" "warning.input_edge.predicate.non_canonical" ), - ( # Query 13 - Missing subject + ( # Query 14 - Missing subject LATEST_BIOLINK_MODEL_VERSION, # Biolink Model Version { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:subclass_of', - 'object': 'UBERON:0035769' + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: ERROR - Subject node identifier is missing!" "error.input_edge.node.id.missing" ), - ( # Query 14 - Unmappable subject namespace + ( # Query 15 - Unmappable subject namespace LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:subclass_of', - 'subject': 'FOO:0005453', - 'object': 'UBERON:0035769' + 'subject_id': 'FOO:0005453', + 'object_id': 'UBERON:0035769' }, # f"{INPUT_EDGE_PREFIX}: WARNING - Subject node identifier 'FOO:0005453' " + # "is unmapped to 'biolink:AnatomicalEntity'?" "warning.input_edge.node.id.unmapped_to_category" ), - ( # Query 15 - missing object + ( # Query 16 - missing object LATEST_BIOLINK_MODEL_VERSION, # Biolink Model Version { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:subclass_of', - 'subject': "UBERON:0005453" + 'subject_id': "UBERON:0005453" }, # f"{INPUT_EDGE_PREFIX}: ERROR - Object node identifier is missing!" "error.input_edge.node.id.missing" ), - ( # Query 16 - Unmappable object namespace + ( # Query 17 - Unmappable object namespace LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AnatomicalEntity', 'object_category': 'biolink:AnatomicalEntity', 'predicate': 'biolink:subclass_of', - 'subject': 'UBERON:0005453', - 'object': 'BAR:0035769' + 'subject_id': 'UBERON:0005453', + 'object_id': 'BAR:0035769' }, # f"{INPUT_EDGE_PREFIX}: WARNING - Object node identifier 'BAR:0035769' " + # "is unmapped to 'biolink:AnatomicalEntity'?" "warning.input_edge.node.id.unmapped_to_category" ), - ( # Query 17 - Valid other model + ( # Query 18 - Valid other model "1.8.2", { 'subject_category': 'biolink:ChemicalSubstance', 'object_category': 'biolink:Protein', 'predicate': 'biolink:entity_negatively_regulates_entity', - 'subject': 'DRUGBANK:DB00945', - 'object': 'UniProtKB:P23219' + 'subject_id': 'DRUGBANK:DB00945', + 'object_id': 'UniProtKB:P23219' }, "" ), @@ -316,25 +327,25 @@ def test_inverse_predicate(): # # f"{INPUT_EDGE_PREFIX}: WARNING - Subject 'biolink:Nutrient' is deprecated?" # "warning.input_edge.node.category.deprecated" # ), - ( # Query 18 - Issue a warning for input_edge data with a category that is a mixin? + ( # Query 19 - Issue a warning for input_edge data with a category that is a mixin? LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:GeneOrGeneProduct', 'object_category': 'biolink:Protein', 'predicate': 'biolink:related_to', - 'subject': 'HGNC:9604', - 'object': 'UniProtKB:P23219' + 'subject_id': 'HGNC:9604', + 'object_id': 'UniProtKB:P23219' }, "warning.input_edge.node.category.not_concrete" ), - ( # Query 19 - Issue a warning for input_edge data with a category that is abstract? + ( # Query 20 - Issue a warning for input_edge data with a category that is abstract? LATEST_BIOLINK_MODEL_VERSION, { 'subject_category': 'biolink:AdministrativeEntity', 'object_category': 'biolink:Agent', 'predicate': 'biolink:related_to', - 'subject': 'isbn:1234', - 'object': 'ORCID:1234' + 'subject_id': 'isbn:1234', + 'object_id': 'ORCID:1234' }, "warning.input_edge.node.category.not_concrete" )