[Biojava-l] (pre-Singapore) BioSQL ???

[Zagato]

Thanks for the answer, i will check the hibernate alternative :D

Alan

On 3/1/07, mark.schreiber at novartis.com <mark.schreiber at novartis.com> wrote:
>
> Hi -
>
> I think those scripts are particularly old. You could try getting the
> appropriate ones from
> http://code.open-bio.org/cgi/viewcvs.cgi/biosql-schema/sql/?cvsroot=biosql
>
> You should also know that we are no longer supporting the biojava 1.4
> bindings to biosql. As of biojava 1.5 we are using Hibernate to do a much
> better job of the ORM. You also get much better control over transactions.
> I strongly recommend you download biojava1.5-pre2 from
> http://biojava.org/wiki/BioJava:Download.
>
> For instructions on using Hibernate with Biojava take a look at
> http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate.
>
> Best regards,
>
> - Mark
>
> Mark Schreiber
> Research Investigator (Bioinformatics)
>
> Novartis Institute for Tropical Diseases (NITD)
> 10 Biopolis Road
> #05-01 Chromos
> Singapore 138670
> www.nitd.novartis.com
> www.dengueinfo.org
>
> phone +65 6722 2973
> fax  +65 6722 2910
>
>
>
>
>
> Zagato <zagato.gekko at gmail.com>
> Sent by: biojava-l-bounces at lists.open-bio.org
> 03/02/2007 10:27 AM
>
>
>         To:     Biojava-l at lists.open-bio.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] (pre-Singapore) BioSQL ???
>
>
> Hello everyone... i'm experimenting with connection to a BioSQL database
> on
> postgres, i'm follow this guide:
> http://www.biojava.org/wiki/BioJava:CookBook:BioSQL:Manage, and change the
> parameter to connect to postrges, but i get an error and i don't know why
> (i
> download the scripts for postgres from:
> http://www.biojava.org/download/biosql/), my error is:
>
> org.biojava.bio.BioException: This database appears to be an old
> (pre-Singapore) BioSQL. If you need to access it, try an older BioJava
> snapshot (1.3pre1 or earlier)
>         at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(
> BioSQLSequenceDB.java:227)
>         at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(
> BioSQLSequenceDB.java:195)
>         at Connect.main(Connect.java:40)
>
> I cannot using the CVS version of BioJava and can't use an older because a
> bug. Someone can give me some guide.... Thanks !!!
>
> Alan Acosta
>
> --
> Farewell.
> ruby << __EOF__
>   puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
> __EOF__
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>


-- 
Farewell.
ruby << __EOF__
  puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
__EOF__