Java JDBC Communication Link Failure

Hi,
I have a Java application which utilizes the JDBC mysql connector 5.1.6. It works great, and I am able to connect to my MySQL database just fine and execute queries perfectly.
However, it seems that if my server idles for certain periods of time without issuing a command to the MySQL server (and this idle period seems to be variant; sometimes if it sites just 5 minutes I get this error, other times it has to idle for close to 25 minutes before it gives me this error):
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
Last packet sent to the server was 1493610 ms ago.Obviously the "... ms ago" part varies based on how long the server was idling.
This is a particular problem for me because the purpose of my application is to be one part in more of an enterprise information system. So this connection to the database is intended to make an update every 25 minutes to update a user's session data in my database. Unfortunately, when idling for this long it will just error out.
My temporary solution has been to catch this exception, reconnect, and re-issue the query which is working, but that's like putting a band-aid on a wound that needs stitches. The real problem is I have so many areas in my code where I execute commands that it would make it difficult to maintain if I had to use this Try-Catch method of reconnecting in each spot.
Is there some timeout setting I need to set in MySQL or in the JDBC to stopt his error from happening? I have read the MySQL documentation and its timeout is already set to an hour so that shouldn't be the problem...
Thanks!

I searched for this on google:
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications
and here is a link that might help:
http://forums.mysql.com/read.php?39,199085,204628#msg-204628
I think the key to your problem is the last line in that link. In connection pooling, you should get a connection, use it, then close it as quickly as possible (ideally, all in the same function within try/catch/finally block) for each time you need to use a connection (hundreds of times within your application). I suspect you open a connection and keep it open with the anticipation that there is a performance penalty in alternatively opening and closing it hundreds of times. There is none. The act of getting and closing a connection from a connection pool is a lightweight operation (in terms of performance). I suggest going back and refactoring your code with the above in mind. That way, your connections will never time out (they are only open for a few milliseconds at a time).

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