Let this application decide if you want queries logged and log queries on MySQLs side if you want all queries logged.
Doctrine has a builtin logger interface and a demo logger in the package. From http://docs.doctrine-project.org/en/2.0.x/reference/configuration.html#sql-logger-optional :
setSQLLogger($logger);
$config->getSQLLogger();
Gets or sets the logger to use for logging all SQL statements executed by Doctrine. The logger class must implement the Doctrine\DBAL\Logging\SQLLogger interface. A simple default implementation that logs to the standard output using echo and var_dump can be found at Doctrine\DBAL\Logging\EchoSQLLogger.`
