Merge pull request #633 from biolink/go-site-844-gorule-0000020-error…

…s-before-warnings For #844
biolink · May 12, 2023 · c5f06bc · c5f06bc
2 parents 5d4eee5 + cfb179e
commit c5f06bc
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/ontobio/io/assocparser.py b/ontobio/io/assocparser.py
@@ -421,10 +421,11 @@ def to_report_json(self):
     def sort_messages(self, r, messages):
         if len(messages) > 0:
             # Messages for GORULE:0000020 are sorted by level (Error before Warning), then by GO id 
-            if r != "GORULE:0000020":
+            if r != "gorule-0000020":
                 return None
-            messages.sort(key=lambda x: x.get('level'))
             messages.sort(key=lambda x: x.get('obj'))
+            messages.sort(key=lambda x: x.get('level'))
+
 
     def to_markdown(self):
         """

diff --git a/tests/test_gafparser.py b/tests/test_gafparser.py
@@ -508,8 +508,8 @@ def test_obsolete_replair_of_extensions():
     assoc_result = p.parse_line("ZFIN\tZDB-GENE-980526-362\tctnnb1\t\tGO:0007155\tPMID:15494018\tIC\tGO:0005912\tP\tcatenin (cadherin-associated protein), beta 1\tctnnb|id:ibd2058|wu:fb73e10|wu:fi81c06|wu:fk25h01\tprotein_coding_gene\ttaxon:7955\t20041026\tZFIN\tpart_of(GO:0005913)|part_of(GO:0016458)\tUniProtKB:P12345")
     print(p.report.to_markdown())
     assert assoc_result.associations == []
-    assert p.report.to_report_json()["messages"]["gorule-0000020"][0]["obj"] == "GO:0005913"    
-    assert p.report.to_report_json()["messages"]["gorule-0000020"][1]["obj"] == "GO:0016458"          
+    assert p.report.to_report_json()["messages"]["gorule-0000020"][0]["obj"] == "GO:0016458"    
+    assert p.report.to_report_json()["messages"]["gorule-0000020"][1]["obj"] == "GO:0005913"
 
     #Reset the report
     p = GafParser(config=assocparser.AssocParserConfig(