JMS TIMEOUT, cache out of synch

I have a message bean, weblogic 6.1 sp3, that's timing out. The transaction type is set to required. Cache is used with version stored in the cache. When the timeout occurs for whatever reason the version in the database table, Oracle 8.1.7 is updated but the version in the cache is not. On the next query an exception is thrown. Version in cache is out of synch with that in the database.
Exception thrown is below
####<Aug 3, 2003 4:05:18 PM CDT> <Error> <EDWhiteboard> <vumcportal1> <edisServer> <ExecuteThread: '10' for queue: 'default'> <guest> <> <000000>
<EXCEPTION: StatsCollectorDAO:updateCurrWbStats() 5:
EXCEPTION DESCRIPTION: Exception occurred within JTS.
INTERNAL EXCEPTION: weblogic.transaction.RollbackException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),
numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+,
Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+) - with nested exception:
[weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)]>
LOCAL EXCEPTION STACK:
EXCEPTION [TOPLINK-7061] (TopLink - 9.0.3 (Build 423)): oracle.toplink.exceptions.ValidationException
EXCEPTION DESCRIPTION: Exception occurred within JTS.
INTERNAL EXCEPTION: weblogic.transaction.RollbackException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+) - with nested exception:
[weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),
Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)]
     at oracle.toplink.exceptions.ValidationException.jtsExceptionRaised(Unknown Source)
     at oracle.toplink.jts.JTSExternalTransactionController.commitTransaction(Unknown Source)
at oracle.toplink.publicinterface.Session.commitExternalTransaction(Unknown Source)
     at oracle.toplink.publicinterface.UnitOfWork.commitInternallyStartedExternalTransaction(Unknown Source)
     at oracle.toplink.publicinterface.UnitOfWork.commit(Unknown Source)
     at vanderbilt.ed.stats.data.StatsCollectorDAO.updateCurrWbStats(StatsCollectorDAO.java:127)
     at vanderbilt.ed.stats.WbStatsDelegate.updateCurrWbStats(WbStatsDelegate.java:79)
     at vanderbilt.ed.stats.ejb.EdisStatsBean.onMessage(EdisStatsBean.java:147)
     at weblogic.ejb20.internal.MDListener.execute(MDListener.java:262)
     at weblogic.ejb20.internal.MDListener.onMessage(MDListener.java:214)
     at weblogic.jms.client.JMSSession.onMessage(JMSSession.java:1865)
     at weblogic.jms.client.JMSSession.execute(JMSSession.java:1819)
     at weblogic.kernel.ExecuteThread.execute(ExecuteThread.java:139)
     at weblogic.kernel.ExecuteThread.run(ExecuteThread.java:120)
INTERNAL EXCEPTION STACK:
weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)
     at weblogic.transaction.internal.ServerTransactionImpl.wakeUp(ServerTransactionImpl.java:1121)
     at weblogic.transaction.internal.ServerTransactionManagerImpl.processTimedOutTransactions(ServerTransactionManagerImpl.java:466)
     at weblogic.transaction.internal.TransactionManagerImpl.wakeUp(TransactionManagerImpl.java:1604)
     at weblogic.transaction.internal.ServerTransactionManagerImpl.wakeUp(ServerTransactionManagerImpl.java:429)
     at weblogic.transaction.internal.TransactionManagerImpl$1.run(TransactionManagerImpl.java:1570)
     at java.lang.Thread.run(Thread.java:479)
--------------- nested within: ------------------
weblogic.transaction.RollbackException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+) - with nested exception:
[weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)]
     at weblogic.transaction.internal.TransactionImpl.throwRollbackException(TransactionImpl.java:1481)
     at weblogic.transaction.internal.ServerTransactionImpl.internalCommit(ServerTransactionImpl.java:262)
     at weblogic.transaction.internal.ServerTransactionImpl.commit(ServerTransactionImpl.java:189)
     at weblogic.transaction.internal.TransactionManagerImpl.commit(TransactionManagerImpl.java:247)
     at weblogic.transaction.internal.TransactionManagerImpl.commit(TransactionManagerImpl.java:240)
     at oracle.toplink.jts.JTSExternalTransactionController.commitTransaction(Unknown Source)
     at oracle.toplink.publicinterface.Session.commitExternalTransaction(Unknown Source)
     at oracle.toplink.publicinterface.UnitOfWork.commitInternallyStartedExternalTransaction(Unknown Source)
     at oracle.toplink.publicinterface.UnitOfWork.commit(Unknown Source)
     at vanderbilt.ed.stats.data.StatsCollectorDAO.updateCurrWbStats(StatsCollectorDAO.java:127)
     at vanderbilt.ed.stats.WbStatsDelegate.updateCurrWbStats(WbStatsDelegate.java:79)
     at vanderbilt.ed.stats.ejb.EdisStatsBean.onMessage(EdisStatsBean.java:147)
     at weblogic.ejb20.internal.MDListener.execute(MDListener.java:262)
     at weblogic.ejb20.internal.MDListener.onMessage(MDListener.java:214)
     at weblogic.jms.client.JMSSession.onMessage(JMSSession.java:1865)
     at weblogic.jms.client.JMSSession.execute(JMSSession.java:1819)
     at weblogic.kernel.ExecuteThread.execute(ExecuteThread.java:139)
     at weblogic.kernel.ExecuteThread.run(ExecuteThread.java:120)
####<Aug 3, 2003 4:05:18 PM CDT> <Error> <EDWhiteboard> <vumcportal1> <edisServer> <ExecuteThread: '10' for queue: 'default'> <guest> <> <000000> <EdisStatsBean: updateCurrWbStats(): DataAccessException
EXCEPTION DESCRIPTION: Exception occurred within JTS.
INTERNAL EXCEPTION: weblogic.transaction.RollbackException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+) - with nested exception:
[weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)]>
vanderbilt.ed.dao.DataAccessException: DataAccessException
EXCEPTION DESCRIPTION: Exception occurred within JTS.
INTERNAL EXCEPTION: weblogic.transaction.RollbackException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+) - with nested exception:
[weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)]
     at vanderbilt.ed.stats.data.StatsCollectorDAO.updateCurrWbStats(StatsCollectorDAO.java:135)
     at vanderbilt.ed.stats.WbStatsDelegate.updateCurrWbStats(WbStatsDelegate.java:79)
     at vanderbilt.ed.stats.ejb.EdisStatsBean.onMessage(EdisStatsBean.java:147)
     at weblogic.ejb20.internal.MDListener.execute(MDListener.java:262)
     at weblogic.ejb20.internal.MDListener.onMessage(MDListener.java:214)
     at weblogic.jms.client.JMSSession.onMessage(JMSSession.java:1865)
     at weblogic.jms.client.JMSSession.execute(JMSSession.java:1819)
     at weblogic.kernel.ExecuteThread.execute(ExecuteThread.java:139)
     at weblogic.kernel.ExecuteThread.run(ExecuteThread.java:120)
####<Aug 3, 2003 4:05:18 PM CDT> <Error> <EDWhiteboard> <vumcportal1> <edisServer> <ExecuteThread: '10' for queue: 'default'> <guest> <> <000000> <EdisStatsBean:onMessage():vanderbilt.ed.dao.DataAccessException: DataAccessException DataAccessException
EXCEPTION DESCRIPTION: Exception occurred within JTS.
INTERNAL EXCEPTION: weblogic.transaction.RollbackException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+) - with nested exception:
[weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)] DataAccessException DataAccessException
EXCEPTION DESCRIPTION: Exception occurred within JTS.
INTERNAL EXCEPTION: weblogic.transaction.RollbackException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+) - with nested exception:
[weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)]>
vanderbilt.ed.dao.DataAccessException: DataAccessException DataAccessException
EXCEPTION DESCRIPTION: Exception occurred within JTS.
INTERNAL EXCEPTION: weblogic.transaction.RollbackException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+) - with nested exception:
[weblogic.transaction.internal.TimedOutException: Transaction timed out after 59 seconds
Xid=13474:af8a0fba65bcc42e(5631273),Status=Active (PrePreparing),numRepliesOwedMe=0,numRepliesOwedOthers=0,seconds since begin=59,seconds left=60,activeThread=Thread[ExecuteThread: '10' for queue: 'default',5,Thread Group for Queue: 'default'],SCInfo[edisdomain+edisServer]=(state=pre-preparing),OwnerTransactionManager=ServerTM[ServerCoordinatorDescriptor=(CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+, Resources={})],CoordinatorURL=edisServer+160.129.51.156:2206+edisdomain+)]
     at vanderbilt.ed.stats.WbStatsDelegate.updateCurrWbStats(WbStatsDelegate.java:86)
     at vanderbilt.ed.stats.ejb.EdisStatsBean.onMessage(EdisStatsBean.java:147)
     at weblogic.ejb20.internal.MDListener.execute(MDListener.java:262)
     at weblogic.ejb20.internal.MDListener.onMessage(MDListener.java:214)
     at weblogic.jms.client.JMSSession.onMessage(JMSSession.java:1865)
     at weblogic.jms.client.JMSSession.execute(JMSSession.java:1819)
     at weblogic.kernel.ExecuteThread.execute(ExecuteThread.java:139)
     at weblogic.kernel.ExecuteThread.run(ExecuteThread.java:120)
####<Aug 3, 2003 4:05:23 PM CDT> <Info> <JDBC> <vumcportal1> <edisServer> <ExecuteThread: '4' for queue: 'default'> <guest> <> <001068> <Connection for pool "oraclePool" created.>
####<Aug 3, 2003 4:05:23 PM CDT> <Info> <EDWhiteboard> <vumcportal1> <edisServer> <ExecuteThread: '9' for queue: 'CriticalAppQueue'> <> <> <000000> <CliniciansOnDuty:getNurseLookUpList IS NULL>
####<Aug 3, 2003 4:05:26 PM CDT> <Info> <JDBC> <vumcportal1> <edisServer> <ExecuteThread: '15' for queue: 'CriticalAppQueue'> <> <> <001068> <Connection for pool "oraclePool" created.>
####<Aug 3, 2003 4:05:26 PM CDT> <Info> <EDWhiteboard> <vumcportal1> <edisServer> <ExecuteThread: '7' for queue: 'default'> <system> <> <000000> <END: EDEncounterDAO:getEdAndWaitingRoomdata(): SUCCESSFUL>
####<Aug 3, 2003 4:05:28 PM CDT> <Info> <JDBC> <vumcportal1> <edisServer> <ExecuteThread: '16' for queue: 'CriticalAppQueue'> <> <> <001068> <Connection for pool "oraclePool" created.>
####<Aug 3, 2003 4:05:28 PM CDT> <Info> <EDWhiteboard> <vumcportal1> <edisServer> <ExecuteThread: '14' for queue: 'CriticalAppQueue'> <> <> <000000> <CliniciansOnDuty:getNurseLookUpList IS NULL>
####<Aug 3, 2003 4:05:34 PM CDT> <Error> <EDWhiteboard> <vumcportal1> <edisServer> <ExecuteThread: '4' for queue: 'default'> <guest> <> <000000> <WhiteboardServerDAO:updatePatient() 9 : Update ERROR: 8

Actually, what one or the developers in my group found out is two things:
1) The clone is a shallow copy.They copy the references but not objects themselves. This has been causing problems for us.
2) It seems that you don't work on a copy and you work on the original and they keep a copy. Now, this is fine IF you don't have multiple threads working on the same Entity bean and we moved our application from Weblogic where it throws an exception if that Entity bean is in use to OC4J which is suppose to copy the bean and doesn't so you have multiple threads possibly modifying the same object.

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