def test_go_rule_16():
# No GO term w/ID
assoc = make_annotation(evidence="IC",
withfrom="BLAH:12345").associations[0]
test_result = qc.GoRule16().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.ERROR
# withfrom has GO term
assoc.evidence.with_support_from = association.ConjunctiveSet.str_to_conjunctions(
"GO:0023456")
test_result = qc.GoRule16().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.PASS
# Pipe
assoc.evidence.with_support_from = association.ConjunctiveSet.str_to_conjunctions(
"GO:0012345|BLAH:54321")
test_result = qc.GoRule16().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.PASS
# Empty withfrom
assoc.evidence.with_support_from = []
test_result = qc.GoRule16().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.ERROR
# Not IC
assoc.evidence.type = Curie.from_str("ECO:0000501")
assoc.evidence.with_support_from = association.ConjunctiveSet.str_to_conjunctions(
"BLAH:5555555|FOO:999999")
test_result = qc.GoRule16().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule_16_list_terms():
gr16 = qc.GoRule16()
withfrom = "GO:12345"
assert gr16._list_terms(withfrom) == ["GO:12345"]
withfrom = ""
assert gr16._list_terms(withfrom) == []
withfrom = "GO:12345|GO:2223334"
assert gr16._list_terms(withfrom) == ["GO:12345", "GO:2223334"]
def test_go_rule_16():
# No GO term w/ID
a = ["blah"] * 16
a[6] = "IC"
a[7] = "BLAH:12345"
test_result = qc.GoRule16().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
# withfrom has GO term
a = ["blah"] * 16
a[6] = "IC"
a[7] = "GO:12345"
test_result = qc.GoRule16().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
# Pipe
a = ["blah"] * 16
a[6] = "IC"
a[7] = "GO:12345|BLAH:54321"
test_result = qc.GoRule16().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
# Empty withfrom
a = ["blah"] * 16
a[6] = "IC"
a[7] = ""
test_result = qc.GoRule16().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
# Not IC
a = ["blah"] * 16
a[6] = "GOT"
a[7] = "BLAH:5555555|FOO:999999"
test_result = qc.GoRule16().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule_16():
# No GO term w/ID
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:1234567"
a[6] = "IC"
a[7] = "BLAH:12345"
a[8] = "P"
a[13] = "20200303"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
# withfrom has GO term
assoc.evidence.with_support_from = [association.ConjunctiveSet(["GO:0023456"])]
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
# Pipe
assoc.evidence.with_support_from = [association.ConjunctiveSet(["GO:0012345"]), association.ConjunctiveSet(["BLAH:54321"])]
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
# Empty withfrom
assoc.evidence.with_support_from = []
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
# Not IC
assoc.evidence.type = "ECO:0000501"
assoc.evidence.with_support_from = [association.ConjunctiveSet(["BLAH:5555555"]), association.ConjunctiveSet(["FOO:999999"])]
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS