Hi,
I was trying to load the bct(bacteria) nucleotide genbank record from
NCBI to my own instance of biosql and I got an hibernate exception(see
it at the end of email):
The record which i tried to load is : LOCUS AL596172
248050 bp DNA linear BCT 16-APR-2005
I don't why I am getting this error because I am not doing any
manipulation to richSequence object I am simply reading it from file and
trying to load it to database.The part of program which is responsible
for loading the sequence is below:
while (seqs.hasNext()) {
try {
richSequence = seqs.nextRichSequence();
// hibernate work begins
// start a transaction session
tx = session.beginTransaction();
// if got exception go to proper exception catch
session.save("Sequence", richSequence);
tx.commit();
successFullRecord++; // one more record
successfully added to database
session.clear(); // clear out the resources
session.flush(); // force memory cache to go to
hardisk
RichObjectFactory.clearLRUCache(); // clear out LRU
cache
System.out.println("Changes committed. Records
added: " + successFullRecord);
richSequence = null; // clear out the memory
references to richsequence
} catch (HibernateException he) {
hibernateException++; // update the error count
he.printStackTrace();
richSequence = null; // reset the newRichSequence
tx.rollback(); // undo the changes before the
error occured
session.clear(); // clear out the session
session.flush(); // force the session cache to hard disk
RichObjectFactory.clearLRUCache(); // clear out the
LRU cache
} catch (BioException ex) {
bioJavaException++; // update the biojavaException
error count
RichObjectFactory.clearLRUCache();
session.clear();
session.flush();
RichObjectFactory.clearLRUCache();
richSequence = null;
} catch (Exception ex) {
otherException++; // update the otherError count
richSequence = null;
tx.rollback(); // rollBack the changes
//TODO make this to logger
System.out.println("Got general exception: " +
ex.getLocalizedMessage());
ex.printStackTrace();
session.clear();
session.flush();
RichObjectFactory.clearLRUCache();
richSequence = null;
}
}
Please help I am really stuck on this issue.
Thanks
Deepak Sheoran
[email protected]
_*Exception:*_
Jan 24, 2010 2:59:21 PM org.hibernate.jdbc.BatchingBatcher doExecuteBatch
SEVERE: Exception executing batch:
org.hibernate.StaleStateException: Batch update returned unexpected row
count from update [1]; actual row count: 0; expected: 1
at
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
at
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
at
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
at
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
at
org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660)
at
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
at
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
at
trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)
Jan 24, 2010 2:59:21 PM
org.hibernate.event.def.AbstractFlushingEventListener performExecutions
SEVERE: Could not synchronize database state with session
org.hibernate.StaleStateException: Batch update returned unexpected row
count from update [1]; actual row count: 0; expected: 1
at
org.hibernate.jdbc.Expectations$BasicExpectation.checkBatched(Expectations.java:61)
at
org.hibernate.jdbc.Expectations$BasicExpectation.verifyOutcome(Expectations.java:46)
at
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:68)
at
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:48)
at
org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2247)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2660)
at
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:56)
at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:250)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:234)
at
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:141)
at
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:298)
at
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000)
at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:338)
at
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)
at
trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:79)
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