Question

在尝试从表中删除时，有时会出现Lock wait timeout exceeded错误。当许多.populate命令（带有reserve_jobs=True）并行运行时，似乎会发生这种情况。删除这些作业（中止其执行）并重新启动并不能立即生效，而是需要几分钟的时间。有什么想法吗？ delete命令本身不应接触当前正在处理的数据集。

InternalError                             Traceback (most recent call last)
<ipython-input-16-c52a52b02f79> in <module>()
----> 1 MakeDatasetsSessions.populate()

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\datajoint\autopopulate.py in populate(self, suppress_errors, reserve_jobs, order, limit, max_calls, display_progress, *restrictions)
    135                     call_count += 1
    136                     try:
--> 137                         make(dict(key))
    138                     except (KeyboardInterrupt, SystemExit, Exception) as error:
    139                         try:

c:\work\python\dj-moser-imaging\dj_schemas\preprocess.py in make(self, key)
    470                                     dataset_to_delete = (Dataset * Session.Data & 'session_name="{}"'.format(session_dict['session_name'])\
    471                                                          & 'datasettype="{}"'.format(datasettype)).fetch1('dataset_name')
--> 472                                     (Dataset & 'dataset_name = "{}"'.format(dataset_to_delete)).delete()
    473                             except dj.DataJointError:
    474                                  logger.error('Session {} for animal {}: Tried to delete datasets after mismatch was detected, but could not proceed. '.format(\

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\datajoint\base_relation.py in delete(self, verbose)
    358         try:
    359             for r in reversed(list(delete_list.values())):
--> 360                 count = r.delete_quick(get_count=True)
    361                 total += count
    362                 if (verbose or safe) and count:

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\datajoint\base_relation.py in delete_quick(self, get_count)
    296         """
    297         query = 'DELETE FROM ' + self.full_table_name + self.where_clause
--> 298         self.connection.query(query)
    299         count = self.connection.query("SELECT ROW_COUNT()").fetchone()[0] if get_count else None
    300         self._log(query[:255])

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\datajoint\connection.py in query(self, query, args, as_dict, suppress_warnings)
    131                     # suppress all warnings arising from underlying SQL library
    132                     warnings.simplefilter("ignore")
--> 133                 cur.execute(query, args)
    134 
    135         except err.OperationalError as e:

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\pymysql\cursors.py in execute(self, query, args)
    168         query = self.mogrify(query, args)
    169 
--> 170         result = self._query(query)
    171         self._executed = query
    172         return result

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\pymysql\cursors.py in _query(self, q)
    326         self._last_executed = q
    327         self._clear_result()
--> 328         conn.query(q)
    329         self._do_get_result()
    330         return self.rowcount

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\pymysql\connections.py in query(self, sql, unbuffered)
    514                 sql = sql.encode(self.encoding, 'surrogateescape')
    515         self._execute_command(COMMAND.COM_QUERY, sql)
--> 516         self._affected_rows = self._read_query_result(unbuffered=unbuffered)
    517         return self._affected_rows
    518 

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\pymysql\connections.py in _read_query_result(self, unbuffered)
    725         else:
    726             result = MySQLResult(self)
--> 727             result.read()
    728         self._result = result
    729         if result.server_status is not None:

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\pymysql\connections.py in read(self)
   1064     def read(self):
   1065         try:
-> 1066             first_packet = self.connection._read_packet()
   1067 
   1068             if first_packet.is_ok_packet():

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\pymysql\connections.py in _read_packet(self, packet_type)
    681 
    682         packet = packet_type(buff, self.encoding)
--> 683         packet.check_error()
    684         return packet
    685 

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\pymysql\protocol.py in check_error(self)
    218             errno = self.read_uint16()
    219             if DEBUG: print("errno =", errno)
--> 220             err.raise_mysql_exception(self._data)
    221 
    222     def dump(self):

~\AppData\Local\conda\conda\envs\analysis\lib\site-packages\pymysql\err.py in raise_mysql_exception(data)
    107         errval = data[3:].decode('utf-8', 'replace')
    108     errorclass = error_map.get(errno, InternalError)
--> 109     raise errorclass(errno, errval)

InternalError: (1205, 'Lock wait timeout exceeded; try restarting transaction')

Answer 1

在常规的DataJoint使用中，超时很少会发生。如果发生这种情况，我们需要彻底理解问题并提出建议以帮助避免它们。

在您的示例中，看起来好像MakeDatasetsSessions的make方法试图删除某些内容。填充调用中的删除操作不是标准做法，我们需要了解（a）为什么需要删除，以及（b）为什么此特定删除导致超时。

要了解这一点，请发布包含MakeDataSetsSessions以及从中删除的表的make方法和ERD的代码？

数据联接：锁定等待超时超出错误

1 个答案: