def test_rdfgen_includes_taxon_in_gp_class():
assoc = association.GoAssociation(
source_line=
"PomBase\tSPAC25B8.17\typf1\t\tGO:1990578\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20150305\tPomBase\t\t",
subject=association.Subject(
id=association.Curie("PomBase", "SPAC25B8.17"),
label="ypf1",
type="protein",
fullname=
"intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)",
synonyms=["ppp81"],
taxon=association.Curie("NCBITaxon", "4896")),
object=association.Term(id=association.Curie("GO", "0000006"),
taxon=association.Curie("NCBITaxon", "4896")),
negated=False,
qualifiers=[],
aspect=association.Aspect("C"),
relation=association.Curie("BFO", "0000050"),
interacting_taxon=association.Curie("NCBITaxon", "555"),
evidence=association.Evidence(
type=association.Curie("ECO", "0000266"),
has_supporting_reference=[association.Curie("GO_REF", "0000024")],
with_support_from=[
association.ConjunctiveSet(
elements=[association.Curie("SGD", "S000001583")])
]),
provided_by=association.Provider("PomBase"),
date=association.Date("20150305"),
subject_extensions=[
association.ExtensionUnit(
relation=association.Curie("rdfs", "subClassOf"),
term=association.Curie("UniProtKB", "P12345"))
],
object_extensions=[
association.ConjunctiveSet(elements=[
association.ExtensionUnit(relation=association.Curie(
"BFO", "0000050"),
term=association.Curie("X", "1")),
association.ExtensionUnit(
relation=association.Curie("BFO", "0000066"),
term=association.Curie("GO", "0016020"))
]),
association.ConjunctiveSet(elements=[
association.ExtensionUnit(
relation=association.Curie("RO", "0002233"),
term=association.Curie("PomBase", "12345"))
])
],
properties=dict())
rdfWriter = TurtleRdfWriter(label="pombase_single.ttl")
gaf_transformer = CamRdfTransform(writer=rdfWriter)
gaf_transformer.translate(assoc)
gaf_transformer.provenance()
gp_res = rdfWriter.graph.query(gene_product_class_query())
for row in gp_res:
assert str(row["cls"]) == "http://identifiers.org/pombase/SPAC25B8.17"
assert str(
row["taxon"]) == "http://purl.obolibrary.org/obo/NCBITaxon_4896"
def parse_date(date: str, report: Report,
line: List) -> Optional[association.Date]:
if date == "":
report.error(line,
Report.INVALID_DATE,
"\'\'",
"GORULE:0000001: empty",
rule=1)
return None
d = None
if len(date) == 8 and date.isdigit():
# For GAF date, should be YYYYMMDD all as digits and
# a well formed date string here will be exactly 8 characters long
d = association.Date(year=date[0:4],
month=date[4:6],
day=date[6:8],
time="")
else:
report.warning(
line,
report.INVALID_DATE,
date,
"GORULE:0000001: Date field must be YYYYMMDD, got: {}".format(
date),
rule=1)
parsed = None
try:
parsed = dateutil.parser.parse(date)
except:
report.error(
line,
Report.INVALID_DATE,
date,
"GORULE:0000001: Could not parse date '{}' at all".format(
date),
rule=1)
return None
d = association.Date(year="{:02d}".format(parsed.year),
month="{:02d}".format(parsed.month),
day="{:02d}".format(parsed.day),
time="")
return d
def test_go_rule29():
# Nov 11, 1990, more than a year old
assoc = make_annotation(evidence="IEA", date="19901111").associations[0]
## Base test: old IEA.
test_result = qc.GoRule29().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.ERROR
## Pass if not IEA
assoc.evidence.type = Curie.from_str(ic_eco) # Not IEA
test_result = qc.GoRule29().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.PASS
## Pass if only a half year old.
now = datetime.datetime.now()
six_months_ago = now - datetime.timedelta(days=180)
assoc.date = association.Date(six_months_ago.year, six_months_ago.month,
six_months_ago.day, "")
assoc.evidence.type = Curie.from_str(iea_eco)
test_result = qc.GoRule29().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.PASS
## Warning if a year and a half year old.
eighteen_months_ago = now - datetime.timedelta(days=(30 * 18))
assoc.date = association.Date(eighteen_months_ago.year,
eighteen_months_ago.month,
eighteen_months_ago.day, "")
test_result = qc.GoRule29().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.WARNING
## Confirm the test can parse a YYYY-MM-DD date format from GPAD 2.0
gpad_2_0_vals = assoc.to_gpad_2_0_tsv(
) # Cheat to shortcut DB and DB_Object_ID concatenation
gpad_2_0_vals[5] = iea_eco
gpad_2_0_vals[8] = "1990-11-11"
assoc = gpadparser.to_association(gpad_2_0_vals,
version="2.0").associations[0]
test_result = qc.GoRule29().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.ERROR
def parse_with_dateutil(date: str, repot: Report, line: List) -> Optional[association.Date]:
parsed = None
try:
parsed = dateutil.parser.parse(date)
except:
report.error(line, Report.INVALID_DATE, date, "GORULE:0000001: Could not parse date '{}' at all".format(date), rule=1)
return None
return association.Date(
year="{:02d}".format(parsed.year),
month="{:02d}".format(parsed.month),
day="{:02d}".format(parsed.day),
time=parsed.time().isoformat())
def parse_iso_date(date: str, report: Report, line: List) -> Optional[association.Date]:
def parse_with_dateutil(date: str, repot: Report, line: List) -> Optional[association.Date]:
parsed = None
try:
parsed = dateutil.parser.parse(date)
except:
report.error(line, Report.INVALID_DATE, date, "GORULE:0000001: Could not parse date '{}' at all".format(date), rule=1)
return None
return association.Date(
year="{:02d}".format(parsed.year),
month="{:02d}".format(parsed.month),
day="{:02d}".format(parsed.day),
time=parsed.time().isoformat())
if date == "":
report.error(line, Report.INVALID_DATE, "\'\'", "GORULE:0000001: empty", rule=1)
return None
d = None
if len(date) >= 10:
# For ISO style date, should be YYYY-MM-DD all as digits and
# a well formed date string here will be at least 10 characters long.
# Optionally, there could be an appended THH:MM
year = date[0:4]
month = date[5:7]
day = date[8:10]
time = date[11:]
if year.isdigit() and month.isdigit() and day.isdigit():
d = association.Date(year=year, month=month, day=day, time=time)
else:
# If any of year, month, day are not made of digits, then try to parse with dateutil
report.warning(line, report.INVALID_DATE, date, "GORULE:0000001: Date field must be YYYY-MM-DD, got: {}".format(date), rule=1)
d = parse_with_dateutil(date, report, line)
else:
# If we got the wrong number characters in the date, then fallback to dateutil
report.warning(line, report.INVALID_DATE, date, "GORULE:0000001: Date field must be YYYY-MM-DD, got: {}".format(date), rule=1)
d = parse_with_dateutil(date, report, line)
return d
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"