def test_go_rule08():
a = ["blah"] * 16
a[4] = "GO:0006810" # do not annotate
a[6] = "IEA"
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
a[6] = "IC"
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
a[4] = "GO:0007049" # do not manually annotate
# evidence is IC, non IEA
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
a[6] = "IEA"
# IEA, but on not manual, so should pass
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
a[4] = "GO:0034655" # neither
a[6] = "IC"
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule08():
assoc = make_annotation(goid="GO:0006810", evidence="IEA").associations[0]
test_result = qc.GoRule08().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.type = Curie.from_str("ECO:0000305")
test_result = qc.GoRule08().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = Curie.from_str("GO:0007049") # do not manually annotate
# evidence is IC, non IEA
test_result = qc.GoRule08().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.type = Curie.from_str("ECO:0000501") #IEA
# IEA, but on not manual, so should pass
test_result = qc.GoRule08().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = Curie.from_str("GO:0034655") # neither
assoc.evidence.type = Curie.from_str("ECO:0000305")
test_result = qc.GoRule08().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule08():
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0006810" # do not annotate
a[6] = "IEA"
a[8] = "P"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.type = "ECO:0000305"
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = "GO:0007049" # do not manually annotate
# evidence is IC, non IEA
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.type = "ECO:0000501" #IEA
# IEA, but on not manual, so should pass
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = "GO:0034655" # neither
assoc.evidence.type = "ECO:0000305"
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS