Fix failing test

biopragmatics · Feb 1, 2021 · 1246a5d · 1246a5d
1 parent 5f67c77
commit 1246a5d
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/src/pyobo/struct/struct.py b/src/pyobo/struct/struct.py
@@ -689,11 +689,11 @@ def from_obonet(cls, graph: nx.MultiDiGraph) -> 'Obo':
                 e.reference = reference
                 raise e
             xrefs, provenance = [], []
-            for reference in node_xrefs:
-                if reference.prefix in PROVENANCE_PREFIXES:
-                    provenance.append(reference)
+            for node_xref in node_xrefs:
+                if node_xref.prefix in PROVENANCE_PREFIXES:
+                    provenance.append(node_xref)
                 else:
-                    xrefs.append(reference)
+                    xrefs.append(node_xref)
 
             try:
                 alt_ids = list(iterate_node_alt_ids(data))

diff --git a/tests/test_get.py b/tests/test_get.py
@@ -174,5 +174,6 @@ def test_get_id_alts_mapping(self):
             alt_id: CHEBI:14384
         """
         id_alts_mapping = self.obo.get_id_alts_mapping()
-        self.assertIn('16042', id_alts_mapping)
+        self.assertNotIn('C00462', id_alts_mapping)
+        self.assertIn('16042', id_alts_mapping, msg='halide anion alt_id fields not parsed')
         self.assertEqual({'5605', '14384'}, set(id_alts_mapping['16042']))