def test_model_dates():
model_associations = []
version = "2.0"
report = assocparser.Report(group="unknown", dataset="unknown")
vals = [
"MGI:MGI:1915834", "", "RO:0002327", "GO:0003674",
"MGI:MGI:2156816|GO_REF:0000015", "ECO:0000307", "", "", "2020-10-09",
"MGI", "",
"creation-date=2020-09-17|modification-date=2020-10-09|contributor-id=http://orcid.org/0000-0003-2689-5511"
]
model_associations = model_associations + to_association(
list(vals), report=report, version=version).associations
# Different term, earlier creation-date
vals[3], vals[11] = "GO:0016301", "creation-date=2011-12-13"
model_associations = model_associations + to_association(
list(vals), report=report, version=version).associations
# Different term, no annotation properties
vals[3], vals[11] = "GO:0001962", ""
model_associations = model_associations + to_association(
list(vals), report=report, version=version).associations
builder = gocam_builder.GoCamBuilder(parser_config=PARSER_CONFIG,
modelstate="test")
model = builder.translate_to_model(gene="MGI:MGI:1915834",
assocs=model_associations)
assert model.date == "2020-10-09"
assert model.creation_date == "2011-12-13"
assert model.import_date == datetime.date.today().isoformat()
def make_annotation(db="blah",
db_id="blah12345",
db_obj_symb="blah",
qualifier="",
negated=False,
goid="GO:1234567",
references="BLAH:54321",
evidence="IDA",
withfrom="BLAH:12345",
aspect="C",
db_obj_name="",
db_obj_syn="",
db_obj_type="blah",
taxon="taxon:12345",
date="20200330",
assigned_by="blah",
extension="",
gene_form_id="",
properties="",
version=None,
from_gaf=True):
if from_gaf:
qual_parse = assocparser.Qualifier2_1()
if version == "2.2":
qual_parse = assocparser.Qualifier2_2()
annotation = [
db, db_id, db_obj_symb, qualifier, goid, references, evidence,
withfrom, aspect, db_obj_name, db_obj_syn, db_obj_type, taxon,
date, assigned_by, extension, gene_form_id
]
return gafparser.to_association(annotation,
qualifier_parser=qual_parse)
else:
if version != "2.0":
# Default to 1.2 if we're anything but 2.0
annotation = [
db, db_id, qualifier, goid, references, evidence, withfrom,
taxon, date, assigned_by, extension, properties
]
return gpadparser.to_association(annotation, version="1.2")
else:
annotation = [
"{}:{}".format(db, db_id), "NOT" if negated else "", qualifier,
goid, references, evidence, withfrom, taxon, date, assigned_by,
extension, properties
]
return gpadparser.to_association(annotation, version="2.0")
def test_get_with_froms():
gpi_ents = gocam_builder.GoCamBuilder.parse_gpi(
gpi_file="tests/resources/mgi2.test_entities.gpi")
report = assocparser.Report(group="unknown", dataset="unknown")
vals = [
"MGI:MGI:1929608",
"",
"RO:0001025",
"GO:0005515",
"MGI:MGI:3028747|PMID:14627703",
"ECO:0000353",
"MGI:MGI:1915834", # with/from
"",
"2004-04-30",
"MGI",
"",
"creation-date=2004-04-30|modification-date=2004-04-30|contributor-id=http://orcid.org/0000-0002-9796-7693"
]
result = to_association(list(vals), report=report, version="2.0")
go_assoc = result.associations[0]
ca_set = collapsed_assoc.CollapsedAssociationSet(GO_ONTO, gpi_ents)
with_froms = ca_set.get_with_froms(go_assoc)
assert len(with_froms) == 1 and \
with_froms[0].header == ["MGI:MGI:1915834"] and \
with_froms[0].line == ["MGI:MGI:1915834"]
vals[6] = "MGI:MGI:1915834|FAKE:12345"
result = to_association(list(vals), report=report, version="2.0")
go_assoc = result.associations[0]
ca_set = collapsed_assoc.CollapsedAssociationSet(GO_ONTO, gpi_ents)
with_froms = ca_set.get_with_froms(go_assoc)
# FAKE:12345 should be on line since not in GPI nor does it have same taxon as subject MGI:MGI:1929608
assert len(with_froms) == 2 and \
with_froms[0].header == ["MGI:MGI:1915834"] and \
with_froms[0].line == ["MGI:MGI:1915834"] and \
with_froms[1].header == [] and \
with_froms[1].line == ["FAKE:12345"]
# Test merging of same-header with/from values in different order
ca_set = collapsed_assoc.CollapsedAssociationSet(GO_ONTO, gpi_ents)
header1 = collapsed_assoc.GoAssocWithFrom(
header=["MGI:MGI:1915834", "FAKE:12345"])
header2 = collapsed_assoc.GoAssocWithFrom(
header=["FAKE:12345", "MGI:MGI:1915834"])
ca_set.find_or_create_collapsed_association(go_assoc, with_from=header1)
ca_set.find_or_create_collapsed_association(go_assoc, with_from=header2)
assert len(ca_set.collapsed_associations
) == 1 and ca_set.collapsed_associations[0].with_froms == [
"FAKE:12345", "MGI:MGI:1915834"
]
def test_gorule57():
a = ["blah"] * 12
a[0] = "HELLO"
a[1] = "123"
a[2] = "contributes_to"
a[3] = "GO:0003674"
a[4] = "PMID:12345"
a[5] = "ECO:0000501"
a[7] = "taxon:2"
a[8] = "20200303"
a[9] = "MGI"
a[10] = ""
a[11] = ""
res = gpadparser.to_association(a)
assoc = gpadparser.to_association(a).associations[0]
# Look at evidence_code, reference, annotation_properties
config = assocparser.AssocParserConfig(group_metadata={
"id": "mgi",
"label": "Mouse Genome Informatics",
"filter_out": {
"evidence": ["ECO:0000501"],
"evidence_reference": [
{
"evidence": "ECO:0000320",
"reference": "PMID:21873635"
}
],
"annotation_properties": ["noctua-model-id"]
}
})
test_result = qc.GoRule57().test(assoc, config)
assert test_result.result_type == qc.ResultType.ERROR
assoc.evidence.type = "ECO:0000320"
assoc.evidence.has_supporting_reference = "PMID:21873635"
test_result = qc.GoRule57().test(assoc, config)
assert test_result.result_type == qc.ResultType.ERROR
assoc.evidence.type = "ECO:some_garbage"
assoc.evidence.has_supporting_reference = "PMID:some_garbage"
assoc.properties = {"noctua-model-id": "some_garbage"}
test_result = qc.GoRule57().test(assoc, config)
assert test_result.result_type == qc.ResultType.ERROR
assoc.properties = {}
test_result = qc.GoRule57().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
def make_annotation(db="blah",
db_id="blah12345",
db_obj_symb="blah",
qualifier="",
goid="GO:1234567",
references="BLAH:54321",
evidence="IDA",
withfrom="BLAH:12345",
aspect="C",
db_obj_name="",
db_obj_syn="",
db_obj_type="blah",
taxon="taxon:12345",
date="20200330",
assigned_by="blah",
extension="",
gene_form_id="",
properties="",
from_gaf=True):
if from_gaf:
annotation = [db, db_id, db_obj_symb, qualifier, goid, references, evidence, withfrom, aspect, db_obj_name, db_obj_syn, db_obj_type, taxon, date, assigned_by, extension, gene_form_id]
return gafparser.to_association(annotation)
else:
annotation = [db, db_id, qualifier, goid, references, evidence, withfrom, taxon, date, assigned_by, extension, properties]
return gpadparser.to_association(annotation)
def test_parse_interacting_taxon():
report = assocparser.Report(group="unknown", dataset="unknown")
vals = [
"MGI", "MGI:1918911", "enables", "GO:0003674",
"MGI:MGI:2156816|GO_REF:0000015", "ECO:0000307", "", "taxon:5678",
"20100209", "MGI", "",
"creation-date=2020-09-17|modification-date=2020-09-17|contributor-id=http://orcid.org/0000-0003-2689-5511"
]
result = to_association(list(vals), report=report, version="1.2")
assert result.associations[0].interacting_taxon == Curie(
namespace="NCBITaxon", identity="5678")
def test_parse_1_2():
report = assocparser.Report(group="unknown", dataset="unknown")
vals = [
"MGI", "MGI:1918911", "enables", "GO:0003674",
"MGI:MGI:2156816|GO_REF:0000015", "ECO:0000307", "", "", "20100209",
"MGI", "",
"creation-date=2020-09-17|modification-date=2020-09-17|contributor-id=http://orcid.org/0000-0003-2689-5511"
]
result = to_association(list(vals), report=report, version="1.2")
assert result.skipped == 0
assert len([m for m in result.report.messages
if m["level"] == "ERROR"]) == 0
assert len(result.associations) == 1
def test_parse_2_0():
version = "2.0"
report = assocparser.Report(group="unknown", dataset="unknown")
vals = [
"MGI:MGI:1918911",
"",
"RO:0002327",
"GO:0003674",
"MGI:MGI:2156816|GO_REF:0000015",
"ECO:0000307",
"",
"",
"2020-09-17",
"MGI",
"",
"creation-date=2020-09-17|modification-date=2020-09-17|contributor-id=http://orcid.org/0000-0003-2689-5511"
]
result = to_association(list(vals), report=report, version=version)
assert result.skipped == 0
assert len([m for m in result.report.messages if m["level"] == "ERROR"]) == 0
assert len(result.associations) == 1
# Annotation_Extensions
vals[10] = "BFO:0000066(CL:0000010),GOREL:0001004(CL:0000010)"
result = to_association(list(vals), report=report, version=version)
assert result.associations[0].object_extensions == [ConjunctiveSet([
ExtensionUnit(Curie("BFO", "0000066"), Curie("CL", "0000010")),
ExtensionUnit(Curie("GOREL", "0001004"), Curie("CL", "0000010"))
])]
# With_or_From
vals[6] = "PR:Q505B8|PR:Q8CHK4"
result = to_association(list(vals), report=report, version=version)
assert result.associations[0].evidence.with_support_from == [
ConjunctiveSet([Curie("PR", "Q505B8")]),
ConjunctiveSet([Curie("PR", "Q8CHK4")])
]
# Interacting taxon - this example should fail
vals[7] = "Staphylococcus aureus ; NCBITaxon:1280"
result = to_association(list(vals), report=report, version=version)
assert len([m for m in result.report.messages if m["level"] == "ERROR"]) > 0
assert len(result.associations) == 0
# Now test valid interacting taxon value
vals[7] = "NCBITaxon:1280"
result = to_association(list(vals), report=report, version=version)
assert result.associations[0].interacting_taxon == Curie("NCBITaxon", "1280")
# Confirm non-"MGI:MGI:" IDs will parse
vals[0] = "WB:WBGene00001189"
result = to_association(list(vals), report=report, version=version)
assert result.associations[0].subject.id == Curie("WB", "WBGene00001189")
# Test annotation property retrieval
contributors = result.associations[0].annotation_property_values(property_key="contributor-id")
assert set(contributors) == {"http://orcid.org/0000-0003-2689-5511"}
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
