bug: Incorrect UTC time zone with mySQL backend triggers OperationalError #7918
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bug
Incorrect behavior inside of ibis
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cpcloud
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Jan 8, 2024
## Description of changes When trying to connect to a mySQL backend, the following error can appear: ``` OperationalError: (pymysql.err.OperationalError) (1298, "Unknown or incorrect time zone: 'UTC'") (Background on this error at: https://sqlalche.me/e/20/e3q8) ``` This is due to an exception generated by PyMySQL. The exception, formerly generated by SQLAlchemy was already caught by Ibis since #6010, this PR adds a catching of the PyMySQL exception. ## Issues closed Resolves #7918
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What happened?
When trying to connect to a mySQL backend, I get the following error:
This error has been already report in #6010 , but still seems to be present in Ibis 7.2.0.
Seems to be related to this issue from the PyMySQL repo #624
What version of ibis are you using?
7.2.0
What backend(s) are you using, if any?
mySQL 5.5.5
mariaDB 10.3.38
Relevant log output
connection = ibis.mysql.connect( host=server, user=user, password=pwd, port=3306, database='db_name', ) connection.list_tables() --------------------------------------------------------------------------- OperationalError Traceback (most recent call last) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/base.py:145, in Connection.__init__(self, engine, connection, _has_events, _allow_revalidate, _allow_autobegin) 144 try: --> 145 self._dbapi_connection = engine.raw_connection() 146 except dialect.loaded_dbapi.Error as err: File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/base.py:3292, in Engine.raw_connection(self) 3271 """Return a "raw" DBAPI connection from the connection pool. 3272 3273 The returned object is a proxied version of the DBAPI (...) 3290 3291 """ -> 3292 return self.pool.connect() File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:452, in Pool.connect(self) 445 """Return a DBAPI connection from the pool. 446 447 The connection is instrumented such that when its (...) 450 451 """ --> 452 return _ConnectionFairy._checkout(self) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:1269, in _ConnectionFairy._checkout(cls, pool, threadconns, fairy) 1268 if not fairy: -> 1269 fairy = _ConnectionRecord.checkout(pool) 1271 if threadconns is not None: File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:716, in _ConnectionRecord.checkout(cls, pool) 715 else: --> 716 rec = pool._do_get() 718 try: File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/impl.py:480, in StaticPool._do_get(self) 479 def _do_get(self) -> ConnectionPoolEntry: --> 480 rec = self.connection 481 if rec._is_hard_or_soft_invalidated(): File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py:1146, in _memoized_property.__get__(self, obj, cls) 1145 return self -> 1146 obj.__dict__[self.__name__] = result = self.fget(obj) 1147 return result File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/impl.py:437, in StaticPool.connection(self) 435 @util.memoized_property 436 def connection(self) -> _ConnectionRecord: --> 437 return _ConnectionRecord(self) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:678, in _ConnectionRecord.__init__(self, pool, connect) 677 if connect: --> 678 self.__connect() 679 self.finalize_callback = deque() File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:916, in _ConnectionRecord.__connect(self) 912 # init of the dialect now takes place within the connect 913 # event, so ensure a mutex is used on the first run 914 pool.dispatch.connect.for_modify( 915 pool.dispatch --> 916 )._exec_w_sync_on_first_run(self.dbapi_connection, self) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/event/attr.py:473, in _CompoundListener._exec_w_sync_on_first_run(self, *args, **kw) 472 try: --> 473 self(*args, **kw) 474 except: File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/event/attr.py:487, in _CompoundListener.__call__(self, *args, **kw) 486 for fn in self.listeners: --> 487 fn(*args, **kw) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/ibis/backends/mysql/__init__.py:114, in Backend.do_connect.<locals>.connect(dbapi_connection, connection_record) 113 try: --> 114 cur.execute("SET @@session.time_zone = 'UTC'") 115 except sa.exc.OperationalError: File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/cursors.py:153, in Cursor.execute(self, query, args) 151 query = self.mogrify(query, args) --> 153 result = self._query(query) 154 self._executed = query File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/cursors.py:322, in Cursor._query(self, q) 321 self._clear_result() --> 322 conn.query(q) 323 self._do_get_result() File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/connections.py:558, in Connection.query(self, sql, unbuffered) 557 self._execute_command(COMMAND.COM_QUERY, sql) --> 558 self._affected_rows = self._read_query_result(unbuffered=unbuffered) 559 return self._affected_rows File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/connections.py:822, in Connection._read_query_result(self, unbuffered) 821 result = MySQLResult(self) --> 822 result.read() 823 self._result = result File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/connections.py:1200, in MySQLResult.read(self) 1199 try: -> 1200 first_packet = self.connection._read_packet() 1202 if first_packet.is_ok_packet(): File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/connections.py:772, in Connection._read_packet(self, packet_type) 771 self._result.unbuffered_active = False --> 772 packet.raise_for_error() 773 return packet File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/protocol.py:221, in MysqlPacket.raise_for_error(self) 220 print("errno =", errno) --> 221 err.raise_mysql_exception(self._data) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/err.py:143, in raise_mysql_exception(data) 142 errorclass = InternalError if errno < 1000 else OperationalError --> 143 raise errorclass(errno, errval) OperationalError: (1298, "Unknown or incorrect time zone: 'UTC'") The above exception was the direct cause of the following exception: OperationalError Traceback (most recent call last) Cell In[48], line 1 ----> 1 connection.list_tables() File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/ibis/backends/base/sql/alchemy/__init__.py:170, in BaseAlchemyBackend.list_tables(self, like, database) 169 def list_tables(self, like=None, database=None): --> 170 tables = self.inspector.get_table_names(schema=database) 171 views = self.inspector.get_view_names(schema=database) 172 return self._filter_with_like(tables + views, like) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/ibis/backends/base/sql/alchemy/__init__.py:177, in BaseAlchemyBackend.inspector(self) 174 @property 175 def inspector(self): 176 if self._inspector is None: --> 177 self._inspector = sa.inspect(self.con) 178 else: 179 self._inspector.info_cache.clear() File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/inspection.py:145, in inspect(subject, raiseerr) 143 elif reg is True: 144 return subject --> 145 ret = reg(subject) 146 if ret is not None: 147 return ret File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/reflection.py:303, in Inspector._engine_insp(bind) 301 @inspection._inspects(Engine) 302 def _engine_insp(bind: Engine) -> Inspector: # type: ignore[misc] --> 303 return Inspector._construct(Inspector._init_engine, bind) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/reflection.py:236, in Inspector._construct(cls, init, bind) 233 cls = bind.dialect.inspector 235 self = cls.__new__(cls) --> 236 init(self, bind) 237 return self File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/reflection.py:247, in Inspector._init_engine(self, engine) 245 def _init_engine(self, engine: Engine) -> None: 246 self.bind = self.engine = engine --> 247 engine.connect().close() 248 self._op_context_requires_connect = True 249 self.dialect = self.engine.dialect File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/base.py:3268, in Engine.connect(self) 3245 def connect(self) -> Connection: 3246 """Return a new :class:`_engine.Connection` object. 3247 3248 The :class:`_engine.Connection` acts as a Python context manager, so (...) 3265 3266 """ -> 3268 return self._connection_cls(self) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/base.py:147, in Connection.__init__(self, engine, connection, _has_events, _allow_revalidate, _allow_autobegin) 145 self._dbapi_connection = engine.raw_connection() 146 except dialect.loaded_dbapi.Error as err: --> 147 Connection._handle_dbapi_exception_noconnection( 148 err, dialect, engine 149 ) 150 raise 151 else: File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/base.py:2430, in Connection._handle_dbapi_exception_noconnection(cls, e, dialect, engine, is_disconnect, invalidate_pool_on_disconnect, is_pre_ping) 2428 elif should_wrap: 2429 assert sqlalchemy_exception is not None -> 2430 raise sqlalchemy_exception.with_traceback(exc_info[2]) from e 2431 else: 2432 assert exc_info[1] is not None File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/base.py:145, in Connection.__init__(self, engine, connection, _has_events, _allow_revalidate, _allow_autobegin) 143 if connection is None: 144 try: --> 145 self._dbapi_connection = engine.raw_connection() 146 except dialect.loaded_dbapi.Error as err: 147 Connection._handle_dbapi_exception_noconnection( 148 err, dialect, engine 149 ) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/engine/base.py:3292, in Engine.raw_connection(self) 3270 def raw_connection(self) -> PoolProxiedConnection: 3271 """Return a "raw" DBAPI connection from the connection pool. 3272 3273 The returned object is a proxied version of the DBAPI (...) 3290 3291 """ -> 3292 return self.pool.connect() File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:452, in Pool.connect(self) 444 def connect(self) -> PoolProxiedConnection: 445 """Return a DBAPI connection from the pool. 446 447 The connection is instrumented such that when its (...) 450 451 """ --> 452 return _ConnectionFairy._checkout(self) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:1269, in _ConnectionFairy._checkout(cls, pool, threadconns, fairy) 1261 @classmethod 1262 def _checkout( 1263 cls, (...) 1266 fairy: Optional[_ConnectionFairy] = None, 1267 ) -> _ConnectionFairy: 1268 if not fairy: -> 1269 fairy = _ConnectionRecord.checkout(pool) 1271 if threadconns is not None: 1272 threadconns.current = weakref.ref(fairy) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:716, in _ConnectionRecord.checkout(cls, pool) 714 rec = cast(_ConnectionRecord, pool._do_get()) 715 else: --> 716 rec = pool._do_get() 718 try: 719 dbapi_connection = rec.get_connection() File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/impl.py:480, in StaticPool._do_get(self) 479 def _do_get(self) -> ConnectionPoolEntry: --> 480 rec = self.connection 481 if rec._is_hard_or_soft_invalidated(): 482 del self.__dict__["connection"] File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py:1146, in _memoized_property.__get__(self, obj, cls) 1144 if obj is None: 1145 return self -> 1146 obj.__dict__[self.__name__] = result = self.fget(obj) 1147 return result File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/impl.py:437, in StaticPool.connection(self) 435 @util.memoized_property 436 def connection(self) -> _ConnectionRecord: --> 437 return _ConnectionRecord(self) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:678, in _ConnectionRecord.__init__(self, pool, connect) 676 self.__pool = pool 677 if connect: --> 678 self.__connect() 679 self.finalize_callback = deque() File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/pool/base.py:916, in _ConnectionRecord.__connect(self) 908 pool.dispatch.first_connect.for_modify( 909 pool.dispatch 910 ).exec_once_unless_exception(self.dbapi_connection, self) 912 # init of the dialect now takes place within the connect 913 # event, so ensure a mutex is used on the first run 914 pool.dispatch.connect.for_modify( 915 pool.dispatch --> 916 )._exec_w_sync_on_first_run(self.dbapi_connection, self) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/event/attr.py:473, in _CompoundListener._exec_w_sync_on_first_run(self, *args, **kw) 471 with self._exec_once_mutex: 472 try: --> 473 self(*args, **kw) 474 except: 475 raise File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/sqlalchemy/event/attr.py:487, in _CompoundListener.__call__(self, *args, **kw) 485 fn(*args, **kw) 486 for fn in self.listeners: --> 487 fn(*args, **kw) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/ibis/backends/mysql/__init__.py:114, in Backend.do_connect.<locals>.connect(dbapi_connection, connection_record) 112 with dbapi_connection.cursor() as cur: 113 try: --> 114 cur.execute("SET @@session.time_zone = 'UTC'") 115 except sa.exc.OperationalError: 116 warnings.warn("Unable to set session timezone to UTC.") File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/cursors.py:153, in Cursor.execute(self, query, args) 149 pass 151 query = self.mogrify(query, args) --> 153 result = self._query(query) 154 self._executed = query 155 return result File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/cursors.py:322, in Cursor._query(self, q) 320 conn = self._get_db() 321 self._clear_result() --> 322 conn.query(q) 323 self._do_get_result() 324 return self.rowcount File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/connections.py:558, in Connection.query(self, sql, unbuffered) 556 sql = sql.encode(self.encoding, "surrogateescape") 557 self._execute_command(COMMAND.COM_QUERY, sql) --> 558 self._affected_rows = self._read_query_result(unbuffered=unbuffered) 559 return self._affected_rows File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/connections.py:822, in Connection._read_query_result(self, unbuffered) 820 else: 821 result = MySQLResult(self) --> 822 result.read() 823 self._result = result 824 if result.server_status is not None: File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/connections.py:1200, in MySQLResult.read(self) 1198 def read(self): 1199 try: -> 1200 first_packet = self.connection._read_packet() 1202 if first_packet.is_ok_packet(): 1203 self._read_ok_packet(first_packet) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/connections.py:772, in Connection._read_packet(self, packet_type) 770 if self._result is not None and self._result.unbuffered_active is True: 771 self._result.unbuffered_active = False --> 772 packet.raise_for_error() 773 return packet File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/protocol.py:221, in MysqlPacket.raise_for_error(self) 219 if DEBUG: 220 print("errno =", errno) --> 221 err.raise_mysql_exception(self._data) File /r1/people/maxime_borry/miniforge3/envs/speleothem/lib/python3.11/site-packages/pymysql/err.py:143, in raise_mysql_exception(data) 141 if errorclass is None: 142 errorclass = InternalError if errno < 1000 else OperationalError --> 143 raise errorclass(errno, errval) OperationalError: (pymysql.err.OperationalError) (1298, "Unknown or incorrect time zone: 'UTC'") (Background on this error at: https://sqlalche.me/e/20/e3q8)Code of Conduct
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