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

[mark.schreiber at novartis.com]

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