[Biojava-l] BioSQL cvs versions

[Janko Diminic]

Do you create database schema with <property
name="hbm2ddl.auto">create</property>?

Check if seqfeature_key_id exists.



2006/1/20, Felix Dreher <dreher at mpiib-berlin.mpg.de>:
> 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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>


--
Janko Diminic