Hibernate connection times out for long searches

What steps will reproduce the problem?
1. Query large amounts of text
2. Database connection gets stale

What is the expected output? What do you see instead?
Nothing. Excpetion

2011-11-29 14:07:58,259 WARN  JDBCExceptionReporter  - SQL Error: 0, SQLState: 
08S01
2011-11-29 14:07:58,259 ERROR JDBCExceptionReporter  - The last packet 
successfully received from the server was 62,825,445 milliseconds ago.  The 
last packet sent successfully to the server was 33,425,285 milliseconds ago. is 
longer than the server configured value of 'wait_timeout'. You should consider 
either expiring and/or testing connection validity before use in your 
application, increasing the server configured values for client timeouts, or 
using the Connector/J connection property 'autoReconnect=true' to avoid this 
problem.
2011-11-29 14:07:58,259 ERROR JDBCTransaction  - JDBC rollback failed
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: 
Communications link failure during rollback(). Transaction resolution unknown.
    at sun.reflect.GeneratedConstructorAccessor19.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:407)
    at com.mysql.jdbc.Util.getInstance(Util.java:382)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1013)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:987)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:982)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927)
    at com.mysql.jdbc.ConnectionImpl.rollback(ConnectionImpl.java:4751)
    at org.hibernate.transaction.JDBCTransaction.rollbackAndResetAutoCommit(JDBCTransaction.java:213)
    at org.hibernate.transaction.JDBCTransaction.rollback(JDBCTransaction.java:192)
    at de.uni_leipzig.simba.boa.backend.persistance.hibernate.HibernateFactory.rollback(HibernateFactory.java:151)
    at de.uni_leipzig.simba.boa.backend.dao.AbstractDao.findAllEntitiesByClass(AbstractDao.java:139)
    at de.uni_leipzig.simba.boa.backend.dao.pattern.PatternMappingDao.findAllPatternMappings(PatternMappingDao.java:87)
    at de.uni_leipzig.simba.boa.backend.configuration.command.impl.PatternScoreFeatureCommand.<init>(PatternScoreFeatureCommand.java:38)
    at de.uni_leipzig.simba.boa.backend.NLPedia.main(NLPedia.java:93)
Original issue reported on code.google.com by gerb...@googlemail.com on 29 Nov 2011 at 1:28
Thourayaaa / boa

Hibernate connection times out for long searches #3
