[Biojava-l] BioSQL cvs versions

[mark.schreiber at novartis.com]

Dear Felix,

We have found a number of deficiencies in biojava's support of biosql. 
Therefore we have moved to a new model using hibernate to overcome several 
problems. This will be officially released in biojava1.5. In the meantime 
you can download the development version from CVS.

Having said that, the best supported database versions in biojava 1.4 are 
Oracle and MySQL. These have received the most testing and support. If you 
have a chance (and cannot use Hibernate) I would suggest using one of 
those. Although someone may offer a bug fix for this problem we do not 
plan to support the old biojava/biosql mappings after 1.5 is released. 
They have been deprecated in the CVS. The official way to interact with 
biosql will be via Hibernate.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





Felix Dreher <dreher at mpiib-berlin.mpg.de>
Sent by: biojava-l-bounces at portal.open-bio.org
01/20/2006 10:45 PM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] BioSQL cvs versions


Hello,
when I try to add a sequence to a BioSQL-DB, the following exception is 
thrown:

*Exception Details: * org.postgresql.util.PSQLException
  ERROR: column "seqfeature_key_id" of relation "seqfeature" does not 
exist

|org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512)
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297)
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188)
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:430)
org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:346)
org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:250)
org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:205)
org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:205)
org.biojava.bio.seq.db.biosql.FeaturesSQL.persistFeature(FeaturesSQL.java:804)
org.biojava.bio.seq.db.biosql.FeaturesSQL.persistFeatures(FeaturesSQL.java:760)
org.biojava.bio.seq.db.biosql.FeaturesSQL.persistFeatures(FeaturesSQL.java:729)
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB.java:481)
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB.java:374)
.
.
.

|
apparently the BioJava- and BioSQL-version don't really match.
I use the following cvs-version of the corresponding class: 
/BioSQLSequenceDB.java/1.70/Fri Jun 10 07:48:11 2005//
Further I use the latest cvs-version of the BioSQL-script 
'biosqldb-pg.sql' (it's from June 2005).
Are there any suggestions how this could be solved?

Thank you,
Felix






-- 
Felix Dreher
Max-Planck-Institute for Infection Biology
Campus Charité Mitte
Department of Immunology
Mailing address: Schumannstraße 21/22
Visitors: Virchowweg 12
10117 Berlin
Germany
Tel.: +49 (0)30 28460-254 / -494
Mobile: +49 (0)163 7542426

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