From 79e31fa121061592a5e0276df83434d206b077ae Mon Sep 17 00:00:00 2001
From: Anushya Muruganujan <muruganu@usc.edu>
Date: Thu, 30 Nov 2023 15:12:25 -0800
Subject: [PATCH] For #346

---
 ontobio/io/gpadparser.py  | 11 ++++++++++-
 tests/test_gpad_parser.py | 19 +++++++++++++++++++
 tests/test_qc.py          |  6 +-----
 3 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/ontobio/io/gpadparser.py b/ontobio/io/gpadparser.py
index 0c5259a9..4876fa88 100644
--- a/ontobio/io/gpadparser.py
+++ b/ontobio/io/gpadparser.py
@@ -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)):
diff --git a/tests/test_gpad_parser.py b/tests/test_gpad_parser.py
index 2628795a..b07beaba 100644
--- a/tests/test_gpad_parser.py
+++ b/tests/test_gpad_parser.py
@@ -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",
diff --git a/tests/test_qc.py b/tests/test_qc.py
index bd72ec59..a5016483 100644
--- a/tests/test_qc.py
+++ b/tests/test_qc.py
@@ -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
     
@@ -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]