Hello Felix -
The best document is the BioJavaX docbook in the docs/ folder of the CVS
distribution of biojava.
- 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 <[EMAIL PROTECTED]>
02/01/2006 10:57 PM
To: Mark Schreiber/GP/[EMAIL PROTECTED]
cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] BioSQL cvs versions
Hello Mark,
thank you very much for your fast reply. In the meantime I was busy with
installing and configuring a new version of 'Sun Java Studio Creator',
which I use to develop at the time.
As you suggested, I would like to start using Hibernate. Is there any
documentation right now about the Hibernate-BioSQL interaction?
Thank you,
Felix
[EMAIL PROTECTED] wrote:
>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 <[EMAIL PROTECTED]>
>Sent by: [EMAIL PROTECTED]
>01/20/2006 10:45 PM
>
>
> To: biojava-l@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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