term lookup fixes

bel/db/arangodb.py

@@ -211,6 +211,7 @@ def get_resources_handles(client, username=None, password=None):
             IndexDefinition(
                 type="persistent", fields=["obsolete_keys[*]"], unique=False, sparse=True
             ),
+            IndexDefinition(type="persistent", fields=["synonyms[*]"], unique=False, sparse=True),
         ],
     )
     update_index_state(

bel/terms/terms.py

@@ -60,11 +60,14 @@ def get_terms(term_key: Key) -> List[Term]:
     results = list(resources_db.aql.execute(query))
 
     if len(results) == 0:
+        if namespace == "EG":
+            return []
+
         (namespace, label) = term_key.split(":")
         query = f"""
         for doc in {terms_coll_name}
             filter doc.namespace == "{namespace}"
-            filter "{label}" in doc.synonyms
+            filter '{label}' in doc.synonyms
             return doc
         """
         results = list(resources_db.aql.execute(query))

tests/lang/test_ast.py

@@ -64,6 +64,24 @@ def test_ast_orthologization():
         assert False, "Not orthologizable"
 
 
+def test_ast_nested_orthologization():
+
+    assertion = AssertionStr(entire="p(HGNC:AKT1) increases (p(HGNC:AKT1) increases p(HGNC:EGF))")
+    ast = bel.lang.ast.BELAst(assertion=assertion)
+
+    orthologizable = ast.orthologizable("TAX:10090")
+    print("Orthologizable", orthologizable)
+
+    ast.orthologize("TAX:10090").decanonicalize()
+
+    expected = ""
+
+    result = ast.to_string()
+    print("Result", result)
+
+    assert result == expected
+
+
 def test_ast_orthologizable():
     """Test AST orthologization"""