#58 DB connection lost on reposearch (project Reposearch on YellowGrass.org)

Caused the timer thread to go down.
[08:36:07 reposearch] ERROR exception message: could not update: [webdsl.generated.domain.GithubRepo#e1f89979-6102-47e7-ae76-bd294919ab5b]
org.hibernate.exception.JDBCConnectionException: could not update: [webdsl.generated.domain.GithubRepo#e1f89979-6102-47e7-ae76-bd294919ab5b]
        at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:99)
        at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
        at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2613)
        at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:2495)
        at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2822)
        at org.hibernate.action.EntityUpdateAction.execute(EntityUpdateAction.java:113)
        at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:273)
        at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:265)
        at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:185)
        at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
        at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:51)
        at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
        at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:383)
        at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:133)
        at utils.DispatchServlet$8.run(DispatchServlet.java:334)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 104,656,186 milliseconds ago.  The last packet sent successfully to the server was 104,
656,187 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.
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
        at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3938)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2551)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2815)
        at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2458)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2375)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2359)
        at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105)
        at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2595)
        ... 14 more
Caused by: java.net.SocketException: Broken pipe
        at java.net.SocketOutputStream.socketWrite0(Native Method)
        at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
        at java.net.SocketOutputStream.write(SocketOutputStream.java:153)
        at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
        at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
        at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3919)
        ... 23 more
[08:36:07 reposearch] ERROR JDBCTransaction:198 - JDBC rollback failed
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
        at com.mysql.jdbc.Util.getInstance(Util.java:386)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:975)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:920)
        at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1304)
        at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1296)
        at com.mysql.jdbc.ConnectionImpl.rollback(ConnectionImpl.java:5022)
        at com.mchange.v2.c3p0.impl.NewProxyConnection.rollback(NewProxyConnection.java:855)
        at org.hibernate.transaction.JDBCTransaction.rollbackAndResetAutoCommit(JDBCTransaction.java:213)
        at org.hibernate.transaction.JDBCTransaction.rollback(JDBCTransaction.java:192)
        at utils.DispatchServlet$8.run(DispatchServlet.java:342)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 104,656,186 milliseconds ago.  The last packet sent successfully to the server was 104,656,187 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.
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
        at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3938)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2551)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2815)
        at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2458)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2375)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2359)
        at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105)
        at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2595)
        at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:2495)
        at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2822)
        at org.hibernate.action.EntityUpdateAction.execute(EntityUpdateAction.java:113)
        at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:273)
        at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:265)
        at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:185)
        at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
        at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:51)
        at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
        at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:383)
        at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:133)
        at utils.DispatchServlet$8.run(DispatchServlet.java:334)
        ... 2 more
Caused by: java.net.SocketException: Broken pipe
        at java.net.SocketOutputStream.socketWrite0(Native Method)
        at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
        at java.net.SocketOutputStream.write(SocketOutputStream.java:153)
        at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
        at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
        at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3919)
        ... 23 more
Exception in thread "Timer for scheduled and recurring tasks" org.hibernate.TransactionException: JDBC rollback failed
        at org.hibernate.transaction.JDBCTransaction.rollback(JDBCTransaction.java:200)
        at utils.DispatchServlet$8.run(DispatchServlet.java:342)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
        at com.mysql.jdbc.Util.getInstance(Util.java:386)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:975)
        at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:920)
        at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1304)
        at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1296)
        at com.mysql.jdbc.ConnectionImpl.rollback(ConnectionImpl.java:5022)
        at com.mchange.v2.c3p0.impl.NewProxyConnection.rollback(NewProxyConnection.java:855)
        at org.hibernate.transaction.JDBCTransaction.rollbackAndResetAutoCommit(JDBCTransaction.java:213)
        at org.hibernate.transaction.JDBCTransaction.rollback(JDBCTransaction.java:192)
        ... 3 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 104,656,186 milliseconds ago.  The last packet sent successfully to the server was 104,656,187 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.
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
        at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3938)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2551)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2815)
        at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2458)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2375)
        at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2359)
        at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105)
        at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2595)
        at org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:2495)
        at org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2822)
        at org.hibernate.action.EntityUpdateAction.execute(EntityUpdateAction.java:113)
        at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:273)
        at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:265)
        at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:185)
        at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
        at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:51)
        at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
        at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:383)
        at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:133)
        at utils.DispatchServlet$8.run(DispatchServlet.java:334)
        ... 2 more
Caused by: java.net.SocketException: Broken pipe
        at java.net.SocketOutputStream.socketWrite0(Native Method)
        at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
        at java.net.SocketOutputStream.write(SocketOutputStream.java:153)
        at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
        at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
        at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3919)
        ... 23 more
Submitted by Elmer van Chastelet on 18 September 2013 at 14:49
On 18 September 2013 at 14:52 Elmer van Chastelet commented:
Seems to happen when updating the xwiki repository. This takes a long time, and probably the database connection is dropped in the meanwhile. Is this db connection bound to a single (?) session which is used during the execution of a function, as part of a recurring task?
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DB connection lost on reposearch

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