def test_unmapped_eco_to_gaf_codes():
# By default, ECO codes in GPAD need to be convertible to an ECO GAF code (e.g. IDA, ISO)
vals = [
"MGI",
"MGI:88276",
"is_active_in",
"GO:0098831",
"PMID:8909549",
"ECO:0000164",
"",
"",
"20180711",
"SynGO",
"part_of(UBERON:0000956)",
""
]
parser = GpadParser(config=assocparser.AssocParserConfig())
result = parser.parse_line("\t".join(vals))
assert len(result.associations) == 0
messages = parser.report.messages
assert messages[0]["type"] == parser.report.UNKNOWN_EVIDENCE_CLASS
parser.config.allow_unmapped_eco = True
result = parser.parse_line("\t".join(vals))
assert len(result.associations) == 1
parser.config.allow_unmapped_eco = False
vals[5] = "ECO:0000314" # maps to IDA
result = parser.parse_line("\t".join(vals))
assert len(result.associations) == 1
vals[5] = "ECO:0006003" # indirectly maps to IDA via gaf-eco-mapping-derived.txt
result = parser.parse_line("\t".join(vals))
assert len(result.associations) == 1
def test_obsolete_term_repair_withfrom():
vals = ["ZFIN",
"ZFIN:ZDB-GENE-980526-362",
"acts_upstream_of_or_within",
"GO:0007155",
"PMID:15494018",
"ECO:0000305",
"GO:0005913|GO:1,GO:4|ZFIN:ZDB-MRPHLNO-010101-1,MGI:1232453",
"",
"20041026",
"ZFIN",
"",
"contributor=GOC:zfin_curators|model-state=production|noctua-model-id=gomodel:ZFIN_ZDB-GENE-980526-362"
]
ont = OntologyFactory().create(ALT_ID_ONT)
config = assocparser.AssocParserConfig(ontology=ont, rule_set=assocparser.RuleSet.ALL)
parser = GpadParser(config=config)
result = parser.parse_line("\t".join(vals))
assoc = result.associations[0]
# GO:0005913 should be repaired to its replacement term, GO:00005912
assert [ConjunctiveSet(elements=[Curie(namespace='GO', identity='0005912')]),
# repaired test GO elements
ConjunctiveSet(elements=[Curie(namespace='GO', identity='2'), Curie(namespace='GO', identity='3')]),
# non GO elements stay the same, could be obsolete or not
ConjunctiveSet(elements=[Curie(namespace='ZFIN', identity='ZDB-MRPHLNO-010101-1'),
Curie(namespace='MGI', identity='1232453')])] == assoc.evidence.with_support_from
def test_aspect_fill_for_obsolete_terms():
# Test null aspect on an obsolete term
# GO:4 is obsolete and has no aspect (hasOBONamespace) in obsolete.json ontology
# GO:3 is it's replacement term
# Note that GPAD lines contain no aspect data
vals = [
"MGI",
"MGI:105128",
"involved_in",
"GO:4",
"PMID:25901318",
"ECO:0000314",
"",
"",
"20190517",
"MGI",
"",
"contributor=http://orcid.org/0000-0002-9796-7693|model-state=production|noctua-model-id=gomodel:5c4605cc00004132"
]
ont = OntologyFactory().create(ALT_ID_ONT)
config = assocparser.AssocParserConfig(ontology=ont, rule_set=assocparser.RuleSet.ALL)
parser = GpadParser(config=config)
result = parser.parse_line("\t".join(vals))
assoc = result.associations[0]
assert assoc.object.id == Curie("GO", "3") # GO:4 should be repaired to its replacement term, GO:3
assert assoc.aspect == 'P' # Aspect should not be empty
def filter_rule_validate_lines(annots, assoc_filter):
filtered = []
# Converts split GPAD line into ontobio assoc obj for passing into standard FilterRule validation
gpad_parser = GpadParser()
for a in annots:
parse_result = gpad_parser.parse_line("\t".join(a))
if len(parse_result.associations) > 0:
# Right now, GpadParser only returns 0 or 1 associations
assoc = parse_result.associations[0]
assoc = extract_properties(assoc)
if "annotation_properties" in assoc:
a.append(assoc["annotation_properties"])
if assoc_filter.validate_line(assoc):
filtered.append(a)
return filtered
