def test_gorule57(): assoc = make_annotation(db="HELLO", db_id="123", qualifier="contributes_to", goid="GO:0003674", evidence="ECO:0000501", taxon="taxon:2", from_gaf=False).associations[0] # Look at evidence_code, reference, annotation_properties config = assocparser.AssocParserConfig(group_metadata={ "id": "mgi", "label": "Mouse Genome Informatics", "filter_out": { "evidence": ["ECO:0000501"], "evidence_reference": [ { "evidence": "ECO:0000320", "reference": "PMID:21873635" } ], "annotation_properties": ["noctua-model-id"] } }) test_result = qc.GoRule57().test(assoc, config) assert test_result.result_type == qc.ResultType.ERROR assoc.evidence.type = Curie.from_str("ECO:0000320") assoc.evidence.has_supporting_reference = [Curie.from_str("PMID:21873635")] test_result = qc.GoRule57().test(assoc, config) assert test_result.result_type == qc.ResultType.ERROR assoc.evidence.type = Curie.from_str("ECO:some_garbage") assoc.evidence.has_supporting_reference = [Curie.from_str("PMID:some_garbage")] assoc.properties = {"noctua-model-id": "some_garbage"} test_result = qc.GoRule57().test(assoc, config) assert test_result.result_type == qc.ResultType.ERROR assoc.properties = {} test_result = qc.GoRule57().test(assoc, config) assert test_result.result_type == qc.ResultType.PASS
def test_gorule57(): a = ["blah"] * 12 a[0] = "HELLO" a[1] = "123" a[2] = "contributes_to" a[3] = "GO:0003674" a[4] = "PMID:12345" a[5] = "ECO:0000501" a[7] = "taxon:2" a[8] = "20200303" a[9] = "MGI" a[10] = "" a[11] = "" res = gpadparser.to_association(a) assoc = gpadparser.to_association(a).associations[0] # Look at evidence_code, reference, annotation_properties config = assocparser.AssocParserConfig(group_metadata={ "id": "mgi", "label": "Mouse Genome Informatics", "filter_out": { "evidence": ["ECO:0000501"], "evidence_reference": [ { "evidence": "ECO:0000320", "reference": "PMID:21873635" } ], "annotation_properties": ["noctua-model-id"] } }) test_result = qc.GoRule57().test(assoc, config) assert test_result.result_type == qc.ResultType.ERROR assoc.evidence.type = "ECO:0000320" assoc.evidence.has_supporting_reference = "PMID:21873635" test_result = qc.GoRule57().test(assoc, config) assert test_result.result_type == qc.ResultType.ERROR assoc.evidence.type = "ECO:some_garbage" assoc.evidence.has_supporting_reference = "PMID:some_garbage" assoc.properties = {"noctua-model-id": "some_garbage"} test_result = qc.GoRule57().test(assoc, config) assert test_result.result_type == qc.ResultType.ERROR assoc.properties = {} test_result = qc.GoRule57().test(assoc, config) assert test_result.result_type == qc.ResultType.PASS