Python.Dataframe to MySql: MySQL server has gone away

Question

I am trying to write several dataframes in mysql. I use mysql.connector for the connection and sqlalchemy to create an engine.

Most dataframes are written correctly to the database. Unfortunately the application stops with the following error:

sqlalchemy.exc.DatabaseError: (mysql.connector.errors.DatabaseError) 2006 (HY000): MySQL server has gone away
...
During handling of the above exception, another exception occurred:
...
_mysql_connector.MySQLInterfaceError: MySQL server has gone away

Since the dataframe that breaks the connection is also the largest one (pickle file: 198MB) I assumed that it is due to the MySql-Server setting max_allowed_packet or timeout. (As described here)

So I have extended the config file within my SQLConnector (see below) by 'connect_timeout': 900. Unfortunately without result. I have also read that you should adjust the my.cnf of the MySql server. Unfortunately I did not know exactly where to find them. After a long search I found the following order. C:\Program Files\MySQL\MySQL Server 8.0\etc with the file mysqlrouter.conf.sample. Here I have downloaded a my.cnf file and put it into the folder. Unfortunately without result, because I did not know how to set up MySql so that the server uses this file.

Does anyone know how I can fix this error? Or how I can configure the MySql Server preference settings max_allowed_packet or timeout?

Main:

   mysqlConnector = MySQLConnector()
   dbConnection = mysqlConnector.init_engine()
   for df_tuple in df_all_tuple:
       df_name = df_tuple[0]
       df = pd.DataFrame(df_tuple[1])
       df.to_sql(con=mydb, name=df_name, if_exists='fail', chunksize=20000)

SQLConnector:

import mysql.connector
from mysql.connector import errorcode
import sqlalchemy as db

config = {
    'user': 'root',
    'password': '',
    'host': '127.0.0.1',
    'database': 'test',
    'raise_on_warnings': True,
    'use_pure': False,
    'autocommit': True,
    'connect_timeout': 900
}


class MySQLConnector:
    def __init__(self):
        connectTest = self.connect()
        print("Connection to database: " + str(connectTest))

    def init_engine(self):
        try:
            connect_string = 'mysql+mysqlconnector://{}:{}@{}/{}?charset=utf8mb4'.format(config.get("user"),
                                                                                         config.get("password"),
                                                                                         config.get("host"),
                                                                                         config.get("database"),
                                                                                         pool_pre_ping=True)
            print("Engine: " + connect_string)
            sqlengine = db.create_engine(connect_string)
        except:
            print("SQLConnector: Sqlalchemy error. Can't create engine....")
        else:
            dbConnection = sqlengine.connect()
            return dbConnection

    def connect(self):
        try:
            con = mysql.connector.connect(**config)
        except mysql.connector.Error as err:
            if err.errno == errorcode.ER_ACCESS_DENIED_ERROR:
                print("Something is wrong with your user name or password")
            elif err.errno == errorcode.ER_BAD_DB_ERROR:
                print("Database does not exist")
                if self.createDB() is True:
                    return self.connect()
            elif err.errno == errorcode.CR_SERVER_GONE_ERROR:
                print("The client couldn't send a question to the server.")
                print("err: " + err)
            elif err.errno == errorcode.CR_SERVER_LOST:
                print(
                    "The client didn't get an error when writing to the server, but it didn't get a full answer (or any answer) to the question.")
                print("err: " + err)
            else:
                print(err)
            return None
        else:
            if con.is_connected():
                db_Info = con.get_server_info()
                print("Connected to MySQL Server version ", db_Info)
            sqlcursor = con.cursor()
            return con

    def createDB(self):
        try:
            mydb = mysql.connector.connect(
                host=config.get("host"),
                user=config.get("user"),
                passwd=config.get("password")
            )
        except mysql.connector.Error as err:
            print(err)
        else:
            sqlcursor = mydb.cursor()
        try:
            sqlcursor.execute('CREATE DATABASE {}'.format(config.get("database")))
        except mysql.connector.Error as err:
            print(err)
            return False
        else:
            print("Database created!")
            return True

Python.Dataframe to MySql: MySQL server has gone away

0 Answers0