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For #346 #662

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Dec 1, 2023
Merged

For #346 #662

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11 changes: 10 additions & 1 deletion ontobio/io/gpadparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,8 +157,17 @@ def parse_line(self, line):

split_line = assocparser.SplitLine(line=line, values=vals, taxon="")

#With/From
for wf in assoc.evidence.with_support_from:
validated = self.validate_curie_ids(wf.elements, split_line)
if validated is None:
return assocparser.ParseResult(line, [], True)

# repair any GO terms in the with/from field that may be obsolete
assoc.evidence.with_support_from = self._unroll_withfrom_and_replair_obsoletes(split_line, 'gpad')
with_support_from = self._unroll_withfrom_and_replair_obsoletes(split_line, 'gpad')
if with_support_from is None:
return assocparser.ParseResult(line, [], True)
assoc.evidence.with_support_from = with_support_from

# repair, if possible any GO terms in the extensions that may be obsolete
if (0 < len(assoc.object_extensions)):
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19 changes: 19 additions & 0 deletions tests/test_gpad_parser.py
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Expand Up @@ -41,6 +41,25 @@ def test_obsolete_term_repair_withfrom():
Curie(namespace='MGI', identity='1232453')])] == assoc.evidence.with_support_from


obsolete_go_with_from_no_replacement = ["ZFIN",
"ZFIN:ZDB-GENE-980526-362",
"acts_upstream_of_or_within",
"GO:0007155",
"PMID:15494018",
"ECO:0000305",
"GO:0016458|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(obsolete_go_with_from_no_replacement))
assert result.associations == []

def test_obsolete_term_repair_extensions():

vals = ["ZFIN",
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6 changes: 1 addition & 5 deletions tests/test_qc.py
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Expand Up @@ -254,7 +254,6 @@ def test_go_rule_16():
# GO term same as with/ID
assoc = make_annotation(goid="GO:0044419", evidence="IC", withfrom="GO:0044419").associations[0]

#GO term same as withfrom
test_result = qc.GoRule16().test(assoc, all_rules_config())
assert test_result.result_type == qc.ResultType.WARNING

Expand All @@ -268,10 +267,7 @@ def test_go_rule_16():
parser = GpadParser(obs_config)
gpadLine = "MGI\tMGI:1916040\tlocated_in\tGO:0005634\tPMID:23369715\tECO:0000305\tGO:0016458\t\t20200518\tMGI\t\tcontributor=https://orcid.org/0000-0001-7476-6306|noctua-model-id=gomodel:MGI_MGI_1916040|contributor=https://orcid.org/0000-0003-2689-5511|model-state=production"
result = parser.parse_line(gpadLine)
assoc = result.associations[0]
test_result = qc.GoRule16().test(assoc, obs_config)
assert test_result.result_type == qc.ResultType.WARNING

assert result.associations == []

# No GO term w/ID
assoc = make_annotation(evidence="IC", withfrom="BLAH:12345").associations[0]
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