Re: [Biojava-l] Hibernate Exception when persisting some richsequence object to biosql schema

Deepak Sheoran Mon, 25 Jan 2010 18:04:49 -0800

simon rayner wrote:

it sounds like there is something up with those sequences. are theylonger than some limit. if you grep the locus line of thesesequences, what are the lengths?

The average length for each record which are getting hibernate exceptionis around 14715 lines, which is kind of huge but I am able to get thethings working by the suggestion of Richard. i.e is create richSequenceafter you start a transaction. I don't if this was only the issue,because i am able to load the record which are causing the hibernateexception by creating them after I start a transaction. I don't knowwhat will be the statistics once I will change my program and run it onmy complete data set.



Thanks
Deepak Sheoran

On Mon, Jan 25, 2010 at 1:59 AM, Deepak Sheoran <[email protected]<mailto:[email protected]>> wrote:


    simon rayner wrote:

        do you get the error with this sequence only, or with any
        sequence you try to load?

    I get these error with around 2000 record out of 50000 record
    which i am able to load successfully. The record number which i
    sent you is one of the 2000 record with me waiting to enter my
    database, I can send the accession of all those record if you need
    them.

    Thanks for helping me out
    Deepak Sheoran


        On Sun, Jan 24, 2010 at 4:20 PM, Deepak Sheoran
        <[email protected] <mailto:[email protected]>
        <mailto:[email protected] <mailto:[email protected]>>>
        wrote:

           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] <mailto:[email protected]>
        <mailto:[email protected] <mailto:[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