def parse_with(f, p):
p.config.ecomap = EcoMap()
is_gaf = f == POMBASE
ont = OntologyFactory().create(ONT)
if is_gaf:
# only do ontology checking on GAF parse;
# this is because ontology is made from GAF
p.config.ontology = ont
else:
p.config.ontology = None
results = p.parse(open(f, "r"), skipheader=True)
print(p.report.to_markdown())
r1 = results[0]
# TODO: test datafile does not have ECOs yet!!
assert ecomap.ecoclass_to_coderef(str(
r1.evidence.type))[0] == 'ISO' or str(
r1.evidence.type) == 'ECO:0000201'
assert r1.evidence.with_support_from == [
association.ConjunctiveSet(
[association.Curie.from_str('SGD:S000001583')])
]
assert r1.evidence.has_supporting_reference == [
association.Curie.from_str('GO_REF:0000024')
]
if is_gaf:
assert r1.subject.label == 'ypf1'
assert association.ymd_str(r1.date, "") == '20150305'
for r in results:
#print(str(r))
sid = r.subject.id
prov = r.provided_by
assert prov == 'PomBase' or prov == 'UniProt'
assert r.object.id.namespace == "GO"
assert sid.namespace == 'PomBase' or (not is_gaf
and sid.namespace == 'PR')
if is_gaf:
assert str(r.subject.taxon) == 'NCBITaxon:4896'
# for m in p.report.messages:
# print("MESSAGE: {}".format(m))
print("MESSAGES (sample): {}".format(p.report.messages[0:5]))
# Messages that aren't about upgrading qualifiers in rule 59 should be 0
assert len([
msg for msg in p.report.messages
if msg["rule"] != 59 and msg["rule"] != 27
]) == 0
def test_date():
date_str = "20210105"
date = association.Date(date_str[0:4], date_str[4:6], date_str[6:8], "")
assert association.ymd_str(date, "-") == "2021-01-05"