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