For #2175 validate go id

biolink · Nov 10, 2023 · ba4eded · ba4eded
1 parent 625ee02
commit ba4eded
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Showing 4 changed files with 67 additions and 2 deletions.
diff --git a/ontobio/io/gafparser.py b/ontobio/io/gafparser.py
@@ -435,8 +435,15 @@ def to_association(gaf_line: List[str], report=None, group="unknown", dataset="u
     qualifiers = [association.Curie.from_str(curie_util.contract_uri(relations.lookup_label(q), strict=False)[0]) for q in qualifiers]
 
     object = association.Term(association.Curie.from_str(gaf_line[4]), taxon)
-    if isinstance(object, association.Error):
+    if isinstance(object, association.Error) or isinstance(object.id, association.Error):
         report.error(source_line, Report.INVALID_SYMBOL, gaf_line[4], "Problem parsing GO Term", taxon=gaf_line[TAXON_INDEX], rule=1)
+        return assocparser.ParseResult(source_line, [], True, report=report)         
+
+    # Check GO Term namespace and identifier
+    go_term = object.id
+    if go_term.namespace != "GO" or go_term.identity.isnumeric == False:
+        report.error(source_line, Report.INVALID_SYMBOL, gaf_line[4], "Namespace should be \"GO\" and identity a numeric value greater than \"0\"", taxon=gaf_line[TAXON_INDEX], rule=1)
+        return assocparser.ParseResult(source_line, [], True, report=report)      
 
     # References
     references = [association.Curie.from_str(e) for e in gaf_line[5].split("|") if e]

diff --git a/ontobio/io/gpadparser.py b/ontobio/io/gpadparser.py
@@ -305,6 +305,10 @@ def from_1_2(gpad_line: List[str], report=None, group="unknown", dataset="unknow
     if go_term.is_error():
         report.error(source_line, Report.INVALID_SYMBOL, gpad_line[3], "Problem parsing GO Term", taxon=str(taxon), rule=1)
         return assocparser.ParseResult(source_line, [], True, report=report)
+
+    if go_term.namespace != "GO" or go_term.identity.isnumeric == False:
+        report.error(source_line, Report.INVALID_SYMBOL, gpad_line[3], "Namespace should be \"GO\" and identity a numeric value greater than \"0\"", taxon=str(taxon), rule=1)
+        return assocparser.ParseResult(source_line, [], True, report=report)    
 
     object = association.Term(go_term, taxon)
 
@@ -449,7 +453,11 @@ def from_2_0(gpad_line: List[str], report=None, group="unknown", dataset="unknow
     if go_term.is_error():
         report.error(source_line, Report.INVALID_SYMBOL, gpad_line[ONTOLOGY_CLASS_INDEX], "Problem parsing GO Term", taxon=str(taxon), rule=1)
         return assocparser.ParseResult(source_line, [], True, report=report)
-
+
+    if go_term.namespace != "GO" or go_term.identity.isnumeric == False:
+        report.error(source_line, Report.INVALID_SYMBOL, gpad_line[ONTOLOGY_CLASS_INDEX], "Namespace should be \"GO\" and identity a numeric value greater than \"0\"", taxon=str(taxon), rule=1)
+        return assocparser.ParseResult(source_line, [], True, report=report)
+
     object = association.Term(go_term, taxon)
 
     evidence_type = association.Curie.from_str(gpad_line[EVIDENCE_INDEX])

diff --git a/tests/test_gafparser.py b/tests/test_gafparser.py
@@ -420,6 +420,12 @@ def test_bad_date():
     assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\tTODAY\tPomBase\tfoo(X:1)")
     assert assoc_result.skipped == True
     assert assoc_result.associations == []
+
+def test_bad_go_id():
+    p = GafParser()
+    assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tINVALID:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20231110\tPomBase\tfoo(X:1)")
+    assert assoc_result.skipped == True
+    assert assoc_result.associations == []    
 
 def test_bad_taxon():
     p = GafParser()

diff --git a/tests/test_gpad_parser.py b/tests/test_gpad_parser.py
@@ -124,6 +124,27 @@ def test_parse_interacting_taxon():
     ]
     result = to_association(list(vals), report=report, version="1.2")
     assert result.associations[0].interacting_taxon == Curie(namespace="NCBITaxon", identity="5678")
+
+def test_parse_go_id_1_2():
+    report = assocparser.Report(group="unknown", dataset="unknown")
+    vals = [
+        "MGI",
+        "MGI:1918911",
+        "enables",
+        "UBERON:1234",
+        "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 == 1
+    assert len([m for m in result.report.messages if m["level"] == "ERROR"]) == 1
+    assert len(result.associations) == 0    
 
 
 def test_duplicate_key_annot_properties():
@@ -189,6 +210,29 @@ def test_parse_2_0():
     # 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_parse_go_id_2_0():
+    version = "2.0"
+    report = assocparser.Report(group="unknown", dataset="unknown")
+    vals = [
+        "MGI:MGI:1918911",
+        "",
+        "RO:0002327",
+        "UBERON:5678",
+        "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 == 1
+    assert len([m for m in result.report.messages if m["level"] == "ERROR"]) == 1
+    assert len(result.associations) == 0    
 
 
 def test_aspect_fill_for_obsolete_terms():