Fixed: newick to tree improper closing of ''

Author: kayjan

bigtree/tree/construct.py

@@ -1182,10 +1182,14 @@ def _raise_value_error(tree_idx: int) -> None:
                 NewickState.PARSE_STRING,
                 NewickState.PARSE_ATTRIBUTE_NAME,
             ]:
+                if cumulative_string:
+                    _raise_value_error(tree_string_idx)
                 cumulative_string = tree_string[
                     tree_string_idx + 1 : quote_end_idx  # noqa: E203
                 ]
             else:
+                if cumulative_string_value:
+                    _raise_value_error(tree_string_idx)
                 cumulative_string_value = tree_string[
                     tree_string_idx + 1 : quote_end_idx  # noqa: E203
                 ]

tests/tree/test_construct.py

@@ -2554,6 +2554,24 @@ def test_newick_to_tree_node_type(self):
         )
         assert_tree_structure_node_root(root)
 
+    def test_newick_to_tree_invalid_character_error(self):
+        newick_strs_error = [
+            (
+                """((d,(g,h)e)b,(f)c)"'a'\"""",
+                19,
+            ),  # NewickCharacter.ATTR_QUOTE, wrong order of bracket (name)
+            (
+                """((d,(g,h)e)b,(f[age="'38'"])c)a""",
+                21,
+            ),  # NewickCharacter.ATTR_QUOTE, wrong order of bracket (attr value)
+        ]
+        for newick_str, error_idx in newick_strs_error:
+            with pytest.raises(ValueError) as exc_info:
+                newick_to_tree(newick_str)
+            assert str(exc_info.value) == Constants.ERROR_NODE_NEWICK_NOT_CLOSED.format(
+                index=error_idx
+            )
+
 
 def assert_tree_structure_phylogenetic(root):
     assert root.max_depth == 4, f"Expected max_depth 4, received {root.max_depth}"