[Biojava-l] loading multiple records for same organism and peristance in BioSQL
Mark Schreiber
markjschreiber at gmail.com
Tue Apr 22 01:27:51 UTC 2008
Hi Doug -
Has anyone provided a solution for this yet?
I haven't used the Hibernate bindings to BioSQL (I'm actually working
on a JPA binding with EntityBeans) but when I did they worked well.
However, I have seen this type of error before. Clearly the entry
'genbankBiosqlRich' is being duplicated somewhere where it should be
unique. This looks unusual because you call saveOrUpdate which should
be able to figure this out unless the way Hibernate determines
equality is not the same as the way BioJava does.
What happens if you try to save them one at a time (in sequential runs
of your program)? From the look of the stack trace you might see the
same error.
Also, it might pay to look at the biojavax documentation on
http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate.
Any Hibernate experts able to offer an opinion here??
- Mark
On Wed, Apr 16, 2008 at 7:57 PM, Doug Brown <debrown at unity.ncsu.edu> wrote:
> Greetings,
> I am happily climbing the learning curve for Biojava-live, Biojavax,
> and BioSQL. I believe that I am using the latest releases, Biojava 1.6
> and BioSQL 1.0, in that I have performed the installation within the
> past week.
>
> I am attempting to load, via Biojavax, multiple genbank records for the
> same organism (a whole genome's worth of annotations) and to save those
> into a BioSQL database via Biojavax's Hibernate persistence mechanism.
> Loading a second genbank file (same organism, different sequence) croaks
> with the error: SEVERE: Duplicate entry 'genbankBiosqlRich' for key 2
> ...... could not insert: [Namespace]. FYI two sample genbank records
> are CH476760.gb and CH476761.gb and were obtained directly from genbank.
>
> Never having used Hibernate before nor its type of database abstraction,
> I think that I am properly handling the transaction semantics. Either I
> am violating unspoken presumptions of the persistence paradigm or the
> behavior of RichSequence.IOTools.readGenbankDNA is not what I expected.
> I had presumed that the above routine would use the established
> RichObjectFactory to obtain new or extant objects and then populate
> those objects with values from the sequence file. This only seems to
> happen when I load multiple sequences from a single file. Multi file
> operations fail dismally.
>
> What is the proper way of using Biojava to load up a database with records?
>
> In advance, thank you all for the traffic on this list, it has been
> quite helpful in bringing me up to speed.
>
> Regards,
> Doug Brown
>
> Here is the relevant [hacked] subroutine:
> /**
> * This works for genbank files containing multiple sequences.
> * Originaly concept from:
> http://portal.open-bio.org/pipermail/biojava-l/2007-April/005824.html
> * It fails on inserting existant record(s) - does not replace...
> * This causes grief when loading multiple files...
> */
> public void loadNSave( Session session, File fileName)
> {
> boolean localSession = (session == null);
> Transaction tx = null;
>
> try
> {
> System.out.println( "*********** Loading "+fileName+"...");
> BufferedReader br = new BufferedReader( new FileReader( fileName) );
>
> if ( session == null) // create a local session
> {
> session = sessionFactory.openSession();
> RichObjectFactory.connectToBioSQL(session);
> }
>
> // load the objects. I expect this to use the established factory.
> RichSequenceIterator rsi = RichSequence.IOTools.readGenbankDNA(
> br, new
> SimpleNamespace( "genbankBiosqlRich") );
>
> while ( rsi.hasNext() )
> tx = session.beginTransaction(); // Hibernate requires transactions.
>
> System.out.println( "*********** Loading next sequence...");
> // ??should automatically fetch existing objects from the
> database...
> RichSequence sequence = rsi.nextRichSequence();
> System.out.println( "loaded sequence
> "+sequence.getAccession()+", identifier: "+ sequence.getIdentifier());
>
> try
> {
> System.out.println( "*********** saving...");
>
> // synchronize in-memory representation w/ the database
> // HUGE amounts of time spent doing selects on keys - really
> slows things down!!
> session.saveOrUpdate( "Sequence", sequence );
> tx.commit(); // save to database - does an automatic flush
> // batch operations overwhelm the cache - clear it out!
> session.flush(); // force in-memory to disk.
> session.clear(); // clean out cache.
> }
> catch (HibernateException ex)
> {
> tx.rollback(); // discard the sequence and all its annotations
> ex.printStackTrace();
> }
> }
> }
> catch (FileNotFoundException ex)
> {
> ex.printStackTrace();
> }
> catch ( BioException bex)
> {
> bex.printStackTrace();
> }
> finally
> {
> if ( localSession)
> {
> session.flush(); // force in-memory to disk.
> session.close(); // only for local sessions
> }
> }
> }
>
> and the following following is a sample stack dump:
>
> org.hibernate.exception.ConstraintViolationException: could not insert:
> [Namespace]
> at
> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:71)
>
> at
> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
>
> at
> org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:40)
>
> at
> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2163)
>
> at
> org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2643)
>
> at
> org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:51)
>
> at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279)
> at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:298)
>
> at
> org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
>
> at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:107)
>
> at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventLi
>
> stener.java:187)
> at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:1
>
> 72)
> at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java
>
> :94)
> at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>
> at
> org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
> at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
> at
> org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
> at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
> at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
> at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
> at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
> at
> org.hibernate.event.def.AbstractSaveEventListener.cascadeBeforeSave(AbstractSaveEventListener.java:431)
>
> at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:265)
>
> at
> org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
>
> at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:107)
>
> at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventLi
>
> stener.java:187)
> at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:1
>
> 72)
> at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java
>
> :94)
> at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>
> at
> org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
> at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
> at
> bioinformatics.biojava.BriefLoader.loadNSave(BriefLoader.java:108)
> at bioinformatics.biojava.BriefLoader.main(BriefLoader.java:72)
> Caused by: java.sql.SQLException: Duplicate entry 'genbankBiosqlRich'
> for key 2
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2975)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
> at
> com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1125)
>
> at
> com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:677)
>
> at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1357)
> at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1274)
> at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1259)
> at
> org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:73)
>
> at
> org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:33)
>
>
>
> --
> Doug Brown - Bioinformatics
> Fungal Genomics Laboratory
> Center for Integrated Fungal Research
> North Carolina State University
> Campus Box 7251, Raleigh, NC 27695-7251
> https://www.fungalgenomics.ncsu.edu/~debrown/
> Tel: (919) 513-0394, Fax (919) 513-0024
> e-mail: doug_brown at ncsu.edu
> _______________________________________________
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