diff --git a/kazu/tests/test_ontology_parser.py b/kazu/tests/test_ontology_parser.py index 6a75e5cc..ecab4935 100644 --- a/kazu/tests/test_ontology_parser.py +++ b/kazu/tests/test_ontology_parser.py @@ -44,7 +44,7 @@ pytestmark = pytest.mark.usefixtures("mock_kazu_disk_cache_on_parsers") -def parser_data_with_target_synonym(): +def parser_data_with_target_synonym() -> dict[str, list[str]]: parser_data = deepcopy(DummyParser.DEFAULT_DUMMY_DATA) parser_data[IDX].append(TARGET_SYNONYM) parser_data[DEFAULT_LABEL].append(TARGET_SYNONYM) @@ -53,7 +53,7 @@ def parser_data_with_target_synonym(): return parser_data -def parser_data_with_split_equiv_id_set(): +def parser_data_with_split_equiv_id_set() -> dict[str, list[str]]: parser_data = deepcopy(DummyParser.DEFAULT_DUMMY_DATA) parser_data[IDX].append(TARGET_SYNONYM) parser_data[DEFAULT_LABEL].append(TARGET_SYNONYM) @@ -103,9 +103,9 @@ def setup_databases( data=parser_data, entity_class=ENTITY_CLASS, curations_path=str(curations_path) if curations_path is not None else None, - global_actions=load_global_actions(global_actions_path) - if global_actions_path is not None - else None, + global_actions=( + load_global_actions(global_actions_path) if global_actions_path is not None else None + ), ) noop_curations_path_str: Optional[str] if noop_parser_curations_style == "empty": @@ -132,7 +132,7 @@ def setup_databases( return SynonymDatabase() -def test_should_add_resource_to_parser(tmp_path): +def test_should_add_resource_to_parser(tmp_path) -> None: resource = OntologyStringResource( original_synonyms=frozenset( [ @@ -165,7 +165,7 @@ def test_should_add_resource_to_parser(tmp_path): assert len(syn_db.get_all(PARSER_1_NAME)) == len(syn_db.get_all(NOOP_PARSER_NAME)) + 1 -def test_should_drop_from_parser_via_general_rule(tmp_path): +def test_should_drop_from_parser_via_general_rule(tmp_path) -> None: global_actions = GlobalParserActions( actions=[ ParserAction( @@ -187,7 +187,7 @@ def test_should_drop_from_parser_via_general_rule(tmp_path): assert len(syn_db.get_all(PARSER_1_NAME)) + 2 == len(syn_db.get_all(NOOP_PARSER_NAME)) -def test_should_modify_resource_from_parser_via_general_rule(tmp_path): +def test_should_modify_resource_from_parser_via_general_rule(tmp_path) -> None: # note, this test is similar to test_should_drop_from_parser_via_general_rule, # although it tests that a OntologyStringResource is also affected by a general rule global_actions = GlobalParserActions( @@ -249,7 +249,7 @@ def test_should_modify_resource_from_parser_via_general_rule(tmp_path): assert len(syn_db.get_syns_for_id(PARSER_1_NAME, "first")) == 0 -def test_should_not_add_a_resource_as_id_nonexistant(tmp_path): +def test_should_not_add_a_resource_as_id_nonexistant(tmp_path) -> None: override_id = "I do not exist" resource = OntologyStringResource( original_synonyms=frozenset( @@ -291,7 +291,7 @@ def test_should_not_add_a_resource_as_id_nonexistant(tmp_path): assert override_id not in modified_equivalent_ids -def test_should_override_id_set(tmp_path): +def test_should_override_id_set(tmp_path) -> None: resource = OntologyStringResource( original_synonyms=frozenset( [ @@ -332,7 +332,7 @@ def test_should_override_id_set(tmp_path): assert "second" in equiv_id_set.ids -def test_should_not_add_a_resource_to_db_as_one_already_exists(tmp_path): +def test_should_not_add_a_resource_to_db_as_one_already_exists(tmp_path) -> None: resource = OntologyStringResource( original_synonyms=frozenset( [ @@ -369,7 +369,7 @@ def test_should_not_add_a_resource_to_db_as_one_already_exists(tmp_path): assert len(syn_db.get_all(PARSER_1_NAME)) == len(syn_db.get_all(NOOP_PARSER_NAME)) -def test_should_not_add_a_resource_as_can_infer_associated_id_sets(tmp_path): +def test_should_not_add_a_resource_as_can_infer_associated_id_sets(tmp_path) -> None: resource = OntologyStringResource( original_synonyms=frozenset( [ @@ -392,7 +392,7 @@ def test_should_not_add_a_resource_as_can_infer_associated_id_sets(tmp_path): assert len(syn_db.get_all(PARSER_1_NAME)) == len(syn_db.get_all(NOOP_PARSER_NAME)) -def test_conflicting_overrides_in_associated_id_sets(tmp_path): +def test_conflicting_overrides_in_associated_id_sets(tmp_path) -> None: resource1 = OntologyStringResource( original_synonyms=frozenset( [ @@ -453,7 +453,7 @@ def test_conflicting_overrides_in_associated_id_sets(tmp_path): ) -def test_gene_ontology_caching(tmp_path): +def test_gene_ontology_caching(tmp_path) -> None: micro_graph = """ @prefix : . @prefix owl: .