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You can either set a global query timeout for your connection using set @@max_statement_time=XX (be carefull, value for MariaDB are in seconds, and MySQL in milliseconds)
if you are using MariaDB, you can set that per command, prefixing commands with SET STATEMENT max_statement_time=XX FOR <command>.
JDBC implementation:
schedule a timer thread to send "KILL QUERY" command to mysql server when the statement executed over a timeout
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