[Biojava-l] [BioSQL-l] Load/Update Genbank sequence issue

Richard Holland dicknetherlands at gmail.com
Tue May 20 18:44:09 UTC 2008


Forgot to copy my reply back to the lists!


---------- Forwarded message ----------
From: Richard Holland <dicknetherlands at gmail.com>
Date: 2008/5/20
Subject: Re: [BioSQL-l] Load/Update Genbank sequence issue
To: gang wu <gwu at molbio.mgh.harvard.edu>


You need to substitute this line:

RichSequenceIterator rsi = RichSequence.IOTools.readGenbankDNA(br, new
SimpleNamespace(namespace));

with this line:

Namespace ns = (Namespace)RichObjectFactory.getObject(SimpleNamespace.class,new
Object[]{namespace});
RichSequenceIterator rsi = RichSequence.IOTools.readGenbankDNA(br, ns);

cheers,
Richard

PS. You're the second person who has quoted this section of code on
this list recently, and had the same problem with it. If you got it
from a website somewhere, could you send me the URL so I can get in
touch with the authors and get them to correct it? Thanks!

2008/5/20 gang wu <gwu at molbio.mgh.harvard.edu>:
> Hi all,
>
> I'm trying to load Genbank sequence into BioSQL database with
> BioJavax/Hibernate. It's Ok to load the first sequence. Then I got the
> exception when loading new sequences or reloading the same sequence. Seems
> the Hibernate is trying to insert "genbank" namespace again. Can anybody
> tell me what I did wrong? Thanks in advance.
>
> Gang
>
> ================================================================
> public class SequenceLoaderNew {
>   public void loadSeq(String fileName, String namespace) throws
> FileNotFoundException, BioException {
>       System.out.println("Start loading file " + fileName + " at " +
> System.currentTimeMillis());
>       BufferedReader br = new BufferedReader(new FileReader(fileName));
>       Session session = new
> Configuration().configure().buildSessionFactory().openSession();
>       RichObjectFactory.connectToBioSQL(session);
>       RichSequenceDB db = new BioSQLRichSequenceDB(session);
>       RichSequenceIterator rsi = RichSequence.IOTools.readGenbankDNA(br, new
> SimpleNamespace(namespace));
>       while (rsi.hasNext()) {
>           Transaction tx = session.beginTransaction();
>           RichSequence sequence = rsi.nextRichSequence();
>           System.out.println("Loaded sequence" + sequence.getAccession() +
> ", identifier: " + sequence.getIdentifier());
>           try {
>               System.out.println("Delete sequence" + sequence.getAccession()
> + " if exists.");
>               db.removeSequence(sequence.getAccession());
>           } catch (Exception ex) {
>           }
>           try {
>               System.out.println("Save sequence " +
> sequence.getAccession());
>               session.save("BioEntry", sequence);
>               tx.commit();
>               session.flush();
>               session.clear();
>           } catch (HibernateException ex) {
>               tx.rollback();
>               ex.printStackTrace();
>           }
>       }
>   }
>
>   public static void main(String[] args) throws BioException,
> FileNotFoundException {
>       SequenceLoaderNew sl = new SequenceLoaderNew();
>       //sl.loadSeq("/genomeseq/bacteria/NC_005813.gbk", "genbank");
>       sl.loadSeq("/genomeseq/bacteria/NC_004349.gbk", "genbank");
>   }
> }
> ================================================================
> 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(DefaultSaveOrUpdateEventListener.java:187)
>       at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
>       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(DefaultSaveOrUpdateEventListener.java:187)
>       at
> org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33)
>       at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
>       at
> org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:27)
>       at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
>       at org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)
>       at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)
>       at primerdb.SequenceLoaderNew.loadSeq(SequenceLoaderNew.java:38)
>       at primerdb.SequenceLoaderNew.main(SequenceLoaderNew.java:52)
> Caused by:
> com.mysql.jdbc.exceptions.MySQLIntegrityConstraintViolationException:
> Duplicate entry 'genbank' for key 'name'
>       at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1011)
>       at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
>       at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3491)
>       at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3423)
>       at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1936)
>       at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2060)
>       at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2542)
>       at
> com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1734)
>       at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2019)
>       at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1937)
>       at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1922)
>       at
> org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:73)
>       at
> org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:33)
>       ... 31 more
> ================================================================
>
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