[Biojava-l] Feature + BioJAVA-X + BioSQL ?

[mark.schreiber at novartis.com]

This could be a bug, this is bleeding edge development code.

Are you using the most up to date CVS code? Also which database are you 
using?

As a suggestion RichFeatures with the same Type, Source and Parent 
sequence can only be distinguished by rank (In BioSQL and BioJavaX). Can 
you persist them to the DB if you give one a different rank?

- Mark





Christian Köberle <koeberle at mpiib-berlin.mpg.de>
Sent by: biojava-l-bounces at lists.open-bio.org
03/14/2006 08:28 PM

 
        To:     bio java mailing list <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Feature + BioJAVA-X + BioSQL ?


Hi,
I try to write a Sequence-Object into BioSQL-DB using the Classes of 
BioJAVA-X.
This works well. But if I try to save a Sequence-Object with two (or 
more) Features and both Feature have equal Types and equal Sources, 
writing in DB fails.
Is the idea wrong to have more than one Feature with same type and 
source at one Sequence. Or is this a bug of BioJAVA / BioJAVA-X or BioSQL.

Thanks,
Christian

The Errormessage:
org.hibernate.StaleStateException: Batch update returned unexpected row 
count from update: 0 actual row count: 0 expected: 1
        at 
org.hibernate.jdbc.BatchingBatcher.checkRowCount(BatchingBatcher.java:93)
        at 
org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java:79)
        at 
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:58)
        at 
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:195)
        at 
org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:91)
        at 
org.hibernate.jdbc.AbstractBatcher.prepareStatement(AbstractBatcher.java:86)
        at 
org.hibernate.jdbc.AbstractBatcher.prepareBatchStatement(AbstractBatcher.java:171)
        at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2048)
        at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2427)
        at 
org.hibernate.action.EntityInsertAction.execute(EntityInsertAction.java:51)
        at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:243)
        at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:227)
        at 
org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:140)
        at 
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:296)
        at 
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
        at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1009)
        at 
org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:356)
        at 
org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:106)

-- 
Christian Köberle

Max Planck Institute for Infection Biology
Department: Immunology
Schumannstr. 21/22
10117 Berlin

Tel: +49 30 28 460 562
e-mail: koeberle at mpiib-berlin.mpg.de

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