Merge pull request #1439 from datajoint/fix/simplify-indexes-and-warn-mariadb

refactor: simplify index query, warn on MariaDB connections

Author: dimitri-yatsenko

CONTRIBUTING.md

@@ -56,7 +56,7 @@ export DOCKER_HOST=unix://$HOME/.docker/run/docker.sock
 
 ### PostgreSQL Backend
 
-DataJoint supports PostgreSQL 15+ as an alternative to MySQL 8+. To install the PostgreSQL driver:
+DataJoint supports MySQL 8.0.13+ and PostgreSQL 15+ as production database backends. To install the PostgreSQL driver:
 
 ```bash
 pip install -e ".[postgres]"    # Installs psycopg2-binary

src/datajoint/adapters/mysql.py

@@ -423,7 +423,7 @@ def create_table_sql(
             fk_cols = ", ".join(self.quote_identifier(col) for col in fk["columns"])
             ref_cols = ", ".join(self.quote_identifier(col) for col in fk["ref_columns"])
             lines.append(
-                f"FOREIGN KEY ({fk_cols}) REFERENCES {fk['ref_table']} ({ref_cols}) " f"ON UPDATE CASCADE ON DELETE RESTRICT"
+                f"FOREIGN KEY ({fk_cols}) REFERENCES {fk['ref_table']} ({ref_cols}) ON UPDATE CASCADE ON DELETE RESTRICT"
             )
 
         # Indexes
@@ -735,26 +735,7 @@ def parse_foreign_key_error(self, error_message: str) -> dict[str, str | list[st
         return result
 
     def get_indexes_sql(self, schema_name: str, table_name: str) -> str:
-        """Query to get index definitions.
-
-        Note: For MySQL 8.0.13+, EXPRESSION column contains the expression for
-        functional indexes. COLUMN_NAME is NULL for such indexes.
-        On MySQL < 8.0.13 and MariaDB, the EXPRESSION column does not exist;
-        heading.py falls back to get_indexes_sql_fallback() in that case.
-        """
-        return (
-            f"SELECT INDEX_NAME as index_name, "
-            f"COALESCE(COLUMN_NAME, CONCAT('(', EXPRESSION, ')')) as column_name, "
-            f"NON_UNIQUE as non_unique, SEQ_IN_INDEX as seq_in_index "
-            f"FROM information_schema.statistics "
-            f"WHERE table_schema = {self.quote_string(schema_name)} "
-            f"AND table_name = {self.quote_string(table_name)} "
-            f"AND index_name != 'PRIMARY' "
-            f"ORDER BY index_name, seq_in_index"
-        )
-
-    def get_indexes_sql_fallback(self, schema_name: str, table_name: str) -> str:
-        """Fallback index query for MySQL < 8.0.13 and MariaDB (no EXPRESSION column)."""
+        """Query to get index definitions. Functional indexes (NULL COLUMN_NAME) are skipped downstream."""
         return (
             f"SELECT INDEX_NAME as index_name, "
             f"COLUMN_NAME as column_name, "

src/datajoint/connection.py

@@ -108,6 +108,18 @@ def conn(
     return conn.connection
 
 
+def _warn_if_mariadb(version_str: str) -> None:
+    """Emit a UserWarning if `version_str` looks like MariaDB. No-op for MySQL."""
+    if "MariaDB" in version_str:
+        warnings.warn(
+            f"MariaDB is not officially supported by DataJoint 2.x "
+            f"(server reports {version_str}). Compatibility is best-effort "
+            f"and may break in future releases.",
+            UserWarning,
+            stacklevel=3,
+        )
+
+
 class EmulatedCursor:
     """acts like a cursor"""
 
@@ -221,6 +233,8 @@ def __init__(
                 f"{self.conn_info['user']}@{self.conn_info['host']}:{self.conn_info['port']}{db_str}"
             )
             self.connection_id = self.adapter.get_connection_id(self._conn)
+            if self.adapter.backend == "mysql":
+                _warn_if_mariadb(self.query("SELECT @@version").fetchone()[0])
         else:
             raise errors.LostConnectionError(
                 f"Connection failed {self.conn_info['user']}@{self.conn_info['host']}:{self.conn_info['port']}"

src/datajoint/heading.py

@@ -551,30 +551,13 @@ def _init_from_database(self) -> None:
 
         # Read and tabulate secondary indexes
         keys = defaultdict(dict)
-        try:
-            index_rows = conn.query(
-                adapter.get_indexes_sql(database, table_name),
-                as_dict=True,
-            )
-        except Exception:
-            # Fall back for MySQL < 8.0.13 / MariaDB (no EXPRESSION column)
-            index_rows = (
-                conn.query(
-                    adapter.get_indexes_sql_fallback(database, table_name),
-                    as_dict=True,
-                )
-                if hasattr(adapter, "get_indexes_sql_fallback")
-                else []
-            )
-        for item in index_rows:
-            # Note: adapter.get_indexes_sql() already filters out PRIMARY key
-            # MySQL/PostgreSQL adapters return: index_name, column_name, non_unique
+        for item in conn.query(
+            adapter.get_indexes_sql(database, table_name),
+            as_dict=True,
+        ):
             index_name = item.get("index_name") or item.get("Key_name")
             seq = item.get("seq_in_index") or item.get("Seq_in_index") or len(keys[index_name]) + 1
             column = item.get("column_name") or item.get("Column_name")
-            # MySQL EXPRESSION column stores escaped single quotes - unescape them
-            if column:
-                column = column.replace("\\'", "'")
             non_unique = item.get("non_unique") or item.get("Non_unique")
             nullable = item.get("nullable") or (item.get("Null", "NO").lower() == "yes")
 

tests/integration/test_json.py

@@ -119,6 +119,10 @@ def test_insert_update(schema_json):
     assert not q
 
 
+@pytest.mark.skip(
+    reason="Functional indexes are not currently round-tripped through Heading.indexes; "
+    "describe() drops them. Re-enable when functional-index introspection is restored."
+)
 def test_describe(schema_json):
     rel = Team()
     context = inspect.currentframe().f_globals

tests/unit/test_connection_warning.py

@@ -0,0 +1,42 @@
+"""Unit tests for the MariaDB compatibility warning emitted at connect time."""
+
+import warnings
+
+import pytest
+
+from datajoint.connection import _warn_if_mariadb
+
+
+@pytest.mark.parametrize(
+    "version_str",
+    [
+        "10.11.5-MariaDB",
+        "10.5.5-MariaDB-1~bionic",
+        "5.5.68-MariaDB",
+    ],
+)
+def test_warn_on_mariadb(version_str):
+    with warnings.catch_warnings(record=True) as caught:
+        warnings.simplefilter("always")
+        _warn_if_mariadb(version_str)
+    assert len(caught) == 1
+    assert issubclass(caught[0].category, UserWarning)
+    assert "MariaDB is not officially supported" in str(caught[0].message)
+    assert version_str in str(caught[0].message)
+
+
+@pytest.mark.parametrize(
+    "version_str",
+    [
+        "8.0.40",
+        "8.0.13",
+        "8.0.40-0ubuntu0.22.04.1",
+        "8.4.2-log",
+        "9.0.0",
+    ],
+)
+def test_no_warn_on_mysql(version_str):
+    with warnings.catch_warnings(record=True) as caught:
+        warnings.simplefilter("always")
+        _warn_if_mariadb(version_str)
+    assert caught == []