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 <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
03/14/2006 08:28 PM
To: bio java mailing list <[email protected]>
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: [EMAIL PROTECTED]
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