def test_go_rule08():
assoc = make_annotation(goid="GO:0006810", evidence="IEA").associations[0]
test_result = qc.GoRule08().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.type = Curie.from_str("ECO:0000305")
test_result = qc.GoRule08().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = Curie.from_str("GO:0007049") # do not manually annotate
# evidence is IC, non IEA
test_result = qc.GoRule08().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.type = Curie.from_str("ECO:0000501") #IEA
# IEA, but on not manual, so should pass
test_result = qc.GoRule08().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = Curie.from_str("GO:0034655") # neither
assoc.evidence.type = Curie.from_str("ECO:0000305")
test_result = qc.GoRule08().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def produce_ttl(dataset, target_dir, gaf_path, ontology_graph):
gafparser = GafParser()
gafparser.config = assocparser.AssocParserConfig(ontology=ontology_graph)
with open(gaf_path) as sg:
lines = sum(1 for line in sg)
ttl_path = os.path.join(
os.path.split(gaf_path)[0], "{}_cam.ttl".format(dataset))
click.echo("Producing ttl: {}".format(ttl_path))
rdf_writer = assoc_rdfgen.TurtleRdfWriter()
transformer = assoc_rdfgen.CamRdfTransform(writer=rdf_writer)
parser_config = assocparser.AssocParserConfig(ontology=ontology_graph)
with open(gaf_path) as gf:
with click.progressbar(
iterable=gafparser.association_generator(file=gf),
length=lines) as associations:
for association in associations:
if "header" not in association or not association["header"]:
transformer.provenance()
transformer.translate(association)
with open(ttl_path, "wb") as ttl:
click.echo("Writing ttl to disk")
rdf_writer.serialize(destination=ttl)
return ttl_path
def test_go_rule29():
a = ["blah"] * 15
a[3] = ""
a[6] = "IEA"
a[8] = "P"
a[13] = "19901111" # Nov 11, 1990, more than a year old
assoc = gafparser.to_association(a).associations[0]
## Base test: old IEA.
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
## Pass if not IEA
assoc.evidence.type = "ECO:0000305" #Not IEA
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
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 = six_months_ago.strftime("%Y%m%d")
assoc.evidence.type = "ECO:0000501"
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
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 = eighteen_months_ago.strftime("%Y%m%d")
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
def test_gorule55():
a = ["blah"] * 15
a[0] = "HELLO"
a[1] = "123"
a[3] = ""
a[5] = "GO:0012345|PMID:1234567"
a[6] = "ISS"
a[7] = "HELLO:123"
a[8] = "P"
a[12] = "taxon:12345"
a[13] = "20200303"
assoc = make_annotation(db="HELLO",
db_id="123",
references="GO:0012345|PMID:1234567",
evidence="ISS",
withfrom="HELLO:123").associations[0]
test_result = qc.GoRule55().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.has_supporting_reference = [
association.Curie.from_str("GO:0001234"),
association.Curie.from_str("GO:123456")
]
test_result = qc.GoRule55().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
def test_go_rule26():
config = assocparser.AssocParserConfig(ontology=ontology, paint=True)
a = make_annotation("GO:BLAHBLAH", "IBA")
a[8] = "P"
a[3] = ""
assoc = gafparser.to_association(a).associations[0]
# Pass due to IBA in paint
test_result = qc.GoRule26().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
config = assocparser.AssocParserConfig(ontology=ontology, paint=False)
a = make_annotation("GO:BLAHBLAH", "IPI")
a[8] = "P"
a[3] = ""
assoc = gafparser.to_association(a).associations[0]
# Pass due to non IBA
test_result = qc.GoRule26().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
config = assocparser.AssocParserConfig(ontology=ontology, paint=False)
a = make_annotation("GO:BLAHBLAH", "IBA")
a[8] = "P"
a[3] = ""
assoc = gafparser.to_association(a).associations[0]
# Pass due to non IBA
test_result = qc.GoRule26().test(assoc, config)
assert test_result.result_type == qc.ResultType.ERROR
def test_go_rules_15():
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0044419"
a[6] = "IEA"
a[8] = "P"
a[12] = "taxon:123|taxon:456"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule15().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = "GO:1234567"
test_result = qc.GoRule15().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = "GO:0044215"
assoc.object.id = "NCBITaxon:123"
assoc.interacting_taxon = None # This is the important part, no interacting taxon
test_result = qc.GoRule15().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_gorule46():
config = assocparser.AssocParserConfig(ontology=ontology)
# Self-binding, yes
assoc = make_annotation(db="PomBase", db_id="SPAC25B8.17", goid="GO:0051260", withfrom="PomBase:SPAC25B8.17").associations[0]
test_result = qc.GoRule46().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.with_support_from = association.ConjunctiveSet.str_to_conjunctions("PomBase:BLAH123")
test_result = qc.GoRule46().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.with_support_from = association.ConjunctiveSet.str_to_conjunctions("PomBase:SPAC25B8.17|PomBase:BLAH123")
test_result = qc.GoRule46().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = Curie.from_str("GO:0000123")
# Not in a self-binding mode
test_result = qc.GoRule46().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
# Test no ontology should just pass
assoc.object.id = Curie.from_str("GO:0051260")
test_result = qc.GoRule46().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_gorule37():
a = ["blah"] * 15
a[3] = ""
a[6] = "IBA"
a[5] = "PMID:21873635"
a[8] = "P"
a[14] = "GO_Central"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule37().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.type = "ECO:0000305" # Rule doesn't apply, not IBA
test_result = qc.GoRule37().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.type = "ECO:0000318"
assoc.evidence.has_supporting_reference = ["GO_REF:123"
] # IBA, but wrong ref
test_result = qc.GoRule37().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
assoc.evidence.has_supporting_reference = ["PMID:21873635"]
assoc.provided_by = "Pascale" # IBA, but wrong assigned_by
test_result = qc.GoRule37().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
def test_go_rule08():
a = ["blah"] * 16
a[4] = "GO:0006810" # do not annotate
a[6] = "IEA"
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
a[6] = "IC"
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
a[4] = "GO:0007049" # do not manually annotate
# evidence is IC, non IEA
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
a[6] = "IEA"
# IEA, but on not manual, so should pass
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
a[4] = "GO:0034655" # neither
a[6] = "IC"
test_result = qc.GoRule08().test(
a, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_gorule46():
config = assocparser.AssocParserConfig(ontology=ontology)
a = ["blah"] * 15
a[0] = "PomBase"
a[1] = "SPAC25B8.17"
a[3] = ""
a[4] = "GO:0051260" # Self-binding, yes
a[7] = "PomBase:SPAC25B8.17"
a[8] = "P"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule46().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.with_support_from = ["PomBase:BLAH123"]
test_result = qc.GoRule46().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.with_support_from = [
"PomBase:SPAC25B8.17", "PomBase:BLAH123"
]
test_result = qc.GoRule46().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = "GO:0000123"
# Not in a self-binding mode
test_result = qc.GoRule46().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
# Test no ontology should just pass
assoc.object.id = "GO:0051260"
test_result = qc.GoRule46().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule26():
config = assocparser.AssocParserConfig(ontology=ontology,
paint=True,
rule_set=assocparser.RuleSet.ALL)
assoc = make_annotation(goid="GO:1234567", evidence="IBA").associations[0]
# Pass due to IBA in paint
test_result = qc.GoRule26().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
config = assocparser.AssocParserConfig(ontology=ontology,
paint=False,
rule_set=assocparser.RuleSet.ALL)
assoc = make_annotation(goid="GO:1234567", evidence="IPI").associations[0]
# Pass due to non IBA
test_result = qc.GoRule26().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
config = assocparser.AssocParserConfig(ontology=ontology,
paint=False,
rule_set=assocparser.RuleSet.ALL)
assoc = make_annotation(goid="GO:1234567", evidence="IBA").associations[0]
# Fail due to non paint
test_result = qc.GoRule26().test(assoc, config)
assert test_result.result_type == qc.ResultType.ERROR
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, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
## Pass if not IEA
assoc.evidence.type = Curie.from_str("ECO:0000305") # Not IEA
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
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 = six_months_ago.strftime("%Y%m%d")
assoc.evidence.type = Curie.from_str("ECO:0000501")
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
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 = eighteen_months_ago.strftime("%Y%m%d")
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
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, assocparser.AssocParserConfig())
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, assocparser.AssocParserConfig())
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, 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 = 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, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_go_rules_13():
a = ["PomBase", "SPBC11B10.09", "cdc2", "", "GO:0007275", "PMID:21873635", "IBA", "PANTHER:PTN000623979|TAIR:locus:2099478", "P", "Cyclin-dependent kinase 1", "UniProtKB:P04551|PTN000624043", "protein", "taxon:284812", "20170228", "GO_Central", "", ""]
assoc = gafparser.to_association(a).associations[0]
gaferences = gaference.load_gaferencer_inferences_from_file("tests/resources/test.inferences.json")
test_result = qc.GoRule13().test(assoc, assocparser.AssocParserConfig(annotation_inferences=gaferences))
assert test_result.result_type == qc.ResultType.ERROR
a = ["PomBase", "SPBC11B10.09", "cdc2", "", "GO:0007275", "PMID:21873635", "EXP", "PANTHER:PTN000623979|TAIR:locus:2099478", "P", "Cyclin-dependent kinase 1", "UniProtKB:P04551|PTN000624043", "protein", "taxon:284812", "20170228", "GO_Central", "", ""]
assoc = gafparser.to_association(a).associations[0]
gaferences = gaference.load_gaferencer_inferences_from_file("tests/resources/test.inferences.json")
test_result = qc.GoRule13().test(assoc, assocparser.AssocParserConfig(annotation_inferences=gaferences))
assert test_result.result_type == qc.ResultType.WARNING
a = ["PomBase", "SPBC11B10.09", "cdc2", "NOT", "GO:0007275", "PMID:21873635", "EXP", "PANTHER:PTN000623979|TAIR:locus:2099478", "P", "Cyclin-dependent kinase 1", "UniProtKB:P04551|PTN000624043", "protein", "taxon:284812", "20170228", "GO_Central", "", ""]
assoc = gafparser.to_association(a).associations[0]
gaferences = gaference.load_gaferencer_inferences_from_file("tests/resources/test.inferences.json")
test_result = qc.GoRule13().test(assoc, assocparser.AssocParserConfig(annotation_inferences=gaferences))
assert test_result.result_type == qc.ResultType.PASS
a = ["AspGD", "ASPL0000059928", "AN0127", "", "GO:0032258", "AspGD_REF:ASPL0000000005", "IEA", "SGD:S000001917", "P", "", "AN0127|ANID_00127|ANIA_00127", "gene_product", "taxon:227321", "20200201", "AspGD", "", ""]
assoc = gafparser.to_association(a).associations[0]
gaferences = gaference.load_gaferencer_inferences_from_file("tests/resources/test.inferences.json")
test_result = qc.GoRule13().test(assoc, assocparser.AssocParserConfig(annotation_inferences=gaferences))
assert test_result.result_type == qc.ResultType.ERROR
def test_gaf_2_1_simple_terms():
line = ["SGD", "S000000819", "AFG3", "", "GO:0006259", "PMID:8681382|SGD_REF:S000055187", "IMP", "", "P", "Mitochondrial inner membrane m-AAA protease component", "YER017C|AAA family ATPase AFG3|YTA10", "gene", "taxon:559292", "20170428", "SGD"]
ontology = OntologyFactory().create("tests/resources/goslim_generic.json")
p = GafParser(config=assocparser.AssocParserConfig(ontology=ontology))
p.make_internal_cell_component_closure()
parsed = gafparser.to_association(line)
assoc = p.upgrade_empty_qualifier(parsed.associations[0])
assert assoc.qualifiers[0] == association.Curie(namespace="RO", identity="0002264")
line = ["SGD", "S000000819", "AFG3", "", "GO:0042393", "PMID:8681382|SGD_REF:S000055187", "IMP", "", "P",
"Mitochondrial inner membrane m-AAA protease component", "YER017C|AAA family ATPase AFG3|YTA10", "gene",
"taxon:559292", "20170428", "SGD"]
ontology = OntologyFactory().create("tests/resources/goslim_generic.json")
p = GafParser(config=assocparser.AssocParserConfig(ontology=ontology))
p.make_internal_cell_component_closure()
parsed = gafparser.to_association(line)
assoc = p.upgrade_empty_qualifier(parsed.associations[0])
assert assoc.qualifiers[0] == association.Curie(namespace="RO", identity="0002327")
line = ["SGD", "S000000819", "AFG3", "", "GO:0005773", "PMID:8681382|SGD_REF:S000055187", "IMP", "", "P",
"Mitochondrial inner membrane m-AAA protease component", "YER017C|AAA family ATPase AFG3|YTA10", "gene",
"taxon:559292", "20170428", "SGD"]
ontology = OntologyFactory().create("tests/resources/goslim_generic.json")
p = GafParser(config=assocparser.AssocParserConfig(ontology=ontology))
p.make_internal_cell_component_closure()
parsed = gafparser.to_association(line)
assoc = p.upgrade_empty_qualifier(parsed.associations[0])
assert assoc.qualifiers[0] == association.Curie(namespace="RO", identity="0001025")
def test_go_rule08():
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0006810" # do not annotate
a[6] = "IEA"
a[8] = "P"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.type = "ECO:0000305"
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = "GO:0007049" # do not manually annotate
# evidence is IC, non IEA
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.type = "ECO:0000501" #IEA
# IEA, but on not manual, so should pass
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = "GO:0034655" # neither
assoc.evidence.type = "ECO:0000305"
test_result = qc.GoRule08().test(
assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule11():
a = ["blah"] * 16
a[4] = "GO:0003674"
a[6] = "ND"
test_result = qc.GoRule11().test(a, assocparser.AssocParserConfig())
print("first test, we have {}".format(test_result))
assert test_result.result_type == qc.ResultType.PASS
# Bad GO ID
a = ["blah"] * 16
a[4] = "GO:1234567"
a[6] = "ND"
test_result = qc.GoRule11().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
# Not ND and not Root
a = ["blah"] * 16
a[4] = "GO:1234567"
a[6] = "FOO"
test_result = qc.GoRule11().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
# Root, but not ND
a = ["blah"] * 16
a[4] = "GO:0003674"
a[6] = "FOO"
test_result = qc.GoRule11().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
def test_create_parser_gpad():
parser = collections.create_parser_from_header(
"!gpa-version: 1.2", assocparser.AssocParserConfig())
assert isinstance(parser, gpadparser.GpadParser)
assert parser.version == "1.2"
parser = collections.create_parser_from_header(
"!gpad-version: 2.0", assocparser.AssocParserConfig())
assert isinstance(parser, gpadparser.GpadParser)
assert parser.version == "2.0"
def test_create_parser_gaf():
parser = collections.create_parser_from_header(
"!gaf-version: 2.1", assocparser.AssocParserConfig())
assert isinstance(parser, gafparser.GafParser)
assert parser.version == "2.1"
parser = collections.create_parser_from_header(
"!gaf-version: 2.2", assocparser.AssocParserConfig())
assert isinstance(parser, gafparser.GafParser)
assert parser.version == "2.2"
def test_go_rule_17():
# IDA with anything in withfrom
assoc = make_annotation(evidence="IDA", withfrom="BLAH:12345").associations[0]
test_result = qc.GoRule17().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
# Nothing in withfrom, passes
assoc.evidence.with_support_from = []
test_result = qc.GoRule17().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def make_products(dataset, target_dir, gaf_path, products, ontology_graph):
gafparser = GafParser()
gafparser.config = assocparser.AssocParserConfig(
ontology=ontology_graph,
paint=True
)
with open(gaf_path) as sg:
lines = sum(1 for line in sg)
product_files = {
"gpad": open(os.path.join(os.path.split(gaf_path)[0], "{}.gpad".format(dataset)), "w"),
"ttl": open(os.path.join(os.path.split(gaf_path)[0], "{}_cam.ttl".format(dataset)), "wb")
}
if not products["gpad"] and not products["ttl"]:
# Bail if we have no products
return []
# def write_gpi_entity(association, bridge, gpiwriter):
with open(gaf_path) as gf:
# gpi info:
click.echo("Using {} as the gaf to build data products with".format(gaf_path))
if products["ttl"]:
click.echo("Setting up {}".format(product_files["ttl"].name))
rdf_writer = assoc_rdfgen.TurtleRdfWriter(label=os.path.split(product_files["ttl"].name)[1] )
transformer = assoc_rdfgen.CamRdfTransform(writer=rdf_writer)
parser_config = assocparser.AssocParserConfig(ontology=ontology_graph)
if products["gpad"]:
click.echo("Setting up {}".format(product_files["gpad"].name))
gpadwriter = GpadWriter(file=product_files["gpad"])
click.echo("Making products...")
with click.progressbar(iterable=gafparser.association_generator(file=gf), length=lines) as associations:
for association in associations:
if products["ttl"]:
if "header" not in association or not association["header"]:
transformer.provenance()
transformer.translate(association)
if products["gpad"]:
gpadwriter.write_assoc(association)
# post ttl steps
if products["ttl"]:
click.echo("Writing ttl to disk")
rdf_writer.serialize(destination=product_files["ttl"])
# After we run through associations
for f in product_files.values():
f.close()
return [product_files[prod].name for prod in sorted(product_files.keys()) if products[prod]]
def test_go_rule_18():
# IDA with nothing in withfrom
a = ["blah"] * 16
a[6] = "IPI"
a[7] = ""
test_result = qc.GoRule18().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
# Something in withfrom, passes
a[7] = "BLAH:12345"
test_result = qc.GoRule18().test(a, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_gorule39():
assoc = make_annotation(db="ComplexPortal", goid="GO:0032991").associations[0]
test_result = qc.GoRule39().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
assoc.subject.id = association.Curie("FB", "1234")
test_result = qc.GoRule39().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.subject.id = association.Curie("ComplexPortal", "12345")
assoc.object.id = association.Curie("GO", "0000023")
test_result = qc.GoRule39().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_gorule42():
assoc = make_annotation(qualifier="NOT", evidence="IKR").associations[0]
test_result = qc.GoRule42().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.type = "ECO:0000305" # Not IKR so this rule is fine
test_result = qc.GoRule42().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.type = "ECO:0000320"
assoc.negated = False # Not negated, so wrong
test_result = qc.GoRule42().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
def test_go_rule02():
assoc = make_annotation(qualifier="NOT", goid="GO:0005515").associations[0]
test_result = qc.GoRule02().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
assoc.negated = False
test_result = qc.GoRule02().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.negated = True
assoc.object.id = Curie.from_str("GO:0003674")
test_result = qc.GoRule02().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule_06():
assoc = make_annotation(goid="GO:0005575", evidence="HEP", aspect="C").associations[0]
test_result = qc.GoRule06().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.ERROR
assoc.aspect = "P"
assoc.object.id = Curie.from_str("GO:0008150")
test_result = qc.GoRule06().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.type = Curie.from_str("ECO:0000501")
test_result = qc.GoRule06().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule_07():
assoc = make_annotation(goid="GO:0003824", evidence="IPI").associations[0]
test_result = qc.GoRule07().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = Curie.from_str("GO:1234567")
test_result = qc.GoRule07().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = Curie.from_str("GO:0003824")
assoc.evidence.type = "ECO:0000501" # Not IPI
test_result = qc.GoRule07().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def produce_gpi(dataset, target_dir, gaf_path, ontology_graph):
gafparser = GafParser()
gafparser.config = assocparser.AssocParserConfig(ontology=ontology_graph)
with open(gaf_path) as sg:
lines = sum(1 for line in sg)
gpi_path = os.path.join(
os.path.split(gaf_path)[0], "{}.gpi".format(dataset))
with open(gaf_path) as gf, open(gpi_path, "w") as gpi:
click.echo("Using {} as the gaf to build gpi with".format(gaf_path))
bridge = gafgpibridge.GafGpiBridge()
gpiwriter = entitywriter.GpiWriter(file=gpi)
gpi_cache = set()
with click.progressbar(
iterable=gafparser.association_generator(file=gf),
length=lines) as associations:
for association in associations:
entity = bridge.convert_association(association)
if entity not in gpi_cache and entity is not None:
# If the entity is not in the cache, add it and write it out
gpi_cache.add(entity)
gpiwriter.write_entity(entity)
return gpi_path
def __init__(self, config=None, group="unknown", dataset="unknown"):
"""
Arguments:
---------
config : a AssocParserConfig object
"""
if config is None:
config = assocparser.AssocParserConfig()
self.config = config
self.report = assocparser.Report(group=group, dataset=dataset)
self.gpi = None
if self.config.gpi_authority_path is not None:
self.gpi = dict()
parser = entityparser.GpiParser()
with open(self.config.gpi_authority_path) as gpi_f:
entities = parser.parse(file=gpi_f)
for entity in entities:
self.gpi[entity["id"]] = {
"symbol": entity["label"],
"name": entity["full_name"],
"synonyms": entitywriter.stringify(entity["synonyms"]),
"type": entity["type"]
}
print("Loaded {} entities from {}".format(len(self.gpi.keys()), self.config.gpi_authority_path))
def test_errors_gaf():
config = assocparser.AssocParserConfig(ecomap=EcoMap())
p = GafParser(config=config)
assocs = p.parse(open("tests/resources/errors.gaf", "r"), skipheader=True)
msgs = p.report.messages
print(json.dumps(p.report.to_report_json(), indent=4))
# print("MESSAGES: {}".format(len(msgs)))
n_invalid_idspace = 0
for m in msgs:
print("MESSAGE: {}".format(m))
if m['type'] == assocparser.Report.INVALID_IDSPACE:
n_invalid_idspace += 1
assert len(msgs) == 13
assert n_invalid_idspace == 1
assert len(assocs) == 2
w = GafWriter()
w.write(assocs)
for a in assocs:
if a.object_extensions != []:
# our test file has no ORs, so in DNF this is always the first
xs = a.object_extensions[0].elements
print(xs)
for x in xs:
print('X: {}'.format(x))
# ensure that invalid expressions have been eliminated
assert x.relation == association.Curie("BFO", "0000050")
assert x.term == association.Curie.from_str('X:1')
assert len(xs) == 1
