[Biojava-l] Dazzle and Ensembl 34

[Ilari Scheinin]

Hello.

I am trying to install the DAS server Dazzle to serve data from a  
local copy of Ensembl, but it is not working. Does Dazzle not support  
the newest releases of Ensembl? I can get it to work with Ensembl 30  
from ensembldb.ensembl.org, but not with the 34 version we have  
mirrored.

I have setup three datasources in dazzlecfg.xml: "local" (local  
Ensembl 34), "new" (34 from ensembl.org), and "old" (30 from  
ensembl.org). The weird part is that datasources "local" and "new"  
give me different error messages even though the only difference in  
the config file is the host name. Getting the entry_points works for  
both of them, and so does getting the features for the first kb of  
chromosome 1:

$ curl http://localhost:8090/das/local/features?segment=1:1,1000
gives 3 features of the type "contig", and so does:
$ curl http://localhost:8090/das/new/features?segment=1:1,1000

But when I try to get features for the first 10 kb, I get two  
different error messages from the local and remote Ensembl 34 databases:

$ curl http://localhost:8090/das/local/features?segment=1:1,10000
...
javax.servlet.ServletException:  
org.biojava.bio.seq.db.ensembl.spi.AdaptorException:  
java.sql.SQLException: null,  message from server: "Unknown  
column 'exon.exon_id' in 'on clause'"
...

$ curl http://localhost:8090/das/new/features?segment=1:1,10000
...
javax.servlet.ServletException:  
org.biojava.bio.seq.db.ensembl.spi.AdaptorException:  
java.sql.SQLException: Base table or view not found,  message from  
server: "Table 'homo_sapiens_core_34_35g.gene_description'  
doesn't exist"
...

The first error message is really weird, because that column really  
does exist:
mysql> desc exon;
+-------------------+------------------+------+-----+--------- 
+----------------+
| Field             | Type             | Null | Key | Default |  
Extra          |
+-------------------+------------------+------+-----+--------- 
+----------------+
| exon_id           | int(10) unsigned | NO   | PRI | NULL    |  
auto_increment |
...

The second error message is caused, because the table  
gene_description is missing. Newest Ensembl releases don't seem to  
have it anymore and the newest one where I could find it was version  
30. That is why I also configured a datasource for that version from  
ensembldb.ensembl.org, which seems to work.

So, is Dazzle not compatible with the newest Ensembl releases? Any  
ideas why I get different error messages from a local mirror and  
ensembldb.ensembl.org?

I'm running J2SE 5.0, Tomcat 5.0.28 and the ensembl-das-webapp-1.4.30  
version of Dazzle.

Thanks,
Ilari


-- 
Ilari Scheinin, BSc.
Biomedicum Bioinformatics Unit
National Public Health Institute
Helsinki, Finland
ilari.scheinin at helsinki.fi
http://www.bioinfo.helsinki.fi/