def test_gorule30():
assoc = make_annotation(references="GO_REF:0000033").associations[0]
config = assocparser.AssocParserConfig(goref_metadata={
"goref-0000033": {
"authors":
"Pascale Gaudet, Michael Livstone, Paul Thomas, The Reference Genome Project",
"id": "GO_REF:0000033",
"is_obsolete": True
}
},
rule_set=assocparser.RuleSet.ALL)
test_result = qc.GoRule30().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.has_supporting_reference = [
Curie.from_str("GO_PAINT:0000000")
]
test_result = qc.GoRule30().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.has_supporting_reference = [
Curie.from_str("FOO:123"),
Curie.from_str("GO_REF:0000033")
]
test_result = qc.GoRule30().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.has_supporting_reference = [Curie.from_str("FOO:123")]
test_result = qc.GoRule30().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
def test_gorule30():
a = ["blah"] * 15
a[3] = ""
a[5] = "GO_REF:0000033"
a[8] = "P"
assoc = gafparser.to_association(a).associations[0]
config = assocparser.AssocParserConfig(
goref_metadata={
"goref-0000033": {
"authors":
"Pascale Gaudet, Michael Livstone, Paul Thomas, The Reference Genome Project",
"id": "GO_REF:0000033",
"is_obsolete": True
}
})
test_result = qc.GoRule30().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.has_supporting_reference = ["GO_PAINT:0000000"]
test_result = qc.GoRule30().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.has_supporting_reference = ["FOO:123", "GO_REF:0000033"]
test_result = qc.GoRule30().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.has_supporting_reference = ["FOO:123"]
test_result = qc.GoRule30().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
def test_gorule30():
a = ["blah"] * 16
a[5] = "GO_REF:0000033"
config = assocparser.AssocParserConfig(
goref_metadata={
"goref-0000033": {
"authors":
"Pascale Gaudet, Michael Livstone, Paul Thomas, The Reference Genome Project",
"id": "GO_REF:0000033",
"is_obsolete": True
}
})
test_result = qc.GoRule30().test(a, config)
assert test_result.result_type == qc.ResultType.ERROR
a[5] = "GO_PAINT:0000000"
test_result = qc.GoRule30().test(a, config)
assert test_result.result_type == qc.ResultType.ERROR
a[5] = "FOO:123|GO_REF:0000033"
test_result = qc.GoRule30().test(a, config)
assert test_result.result_type == qc.ResultType.ERROR
a[5] = "FOO:123"
test_result = qc.GoRule30().test(a, config)
assert test_result.result_type == qc.ResultType.PASS
def test_gorule30():
a = ["blah"] * 16
a[5] = "GO_REF:0000033"
test_result = qc.GoRule30().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
a[5] = "GO_PAINT:0000000"
test_result = qc.GoRule30().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
a[5] = "FOO:123|GO_REF:0000033"
test_result = qc.GoRule30().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
a[5] = "FOO:123"
test_result = qc.GoRule30().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS