[DAS] we just setup a DAS:"Error retrieving features"

[Thomas Down]

On Wed, Mar 27, 2002 at 07:33:39PM +0100, Haiyan Wang wrote:
> Hi, Everyone,
> 
> We set up a DAS Server and configured a data source to annotate Ensembl
> following the excellent instructions of Tony Cox.
> We ended up with a webpage at http://tomcat.molgen.mpg.de:8080/das and
> added it to the Ensembl DAS sources.
> However we get a "Error retrieving * .... features" in the contig-view
> of Ensembl, if we select our DAS-source.
> We also try to issue 'features' request at , for example
> http://tomcat.molgen.mpg.de:8080/das/EPD_promoters/features?segment=AC012462.5.1.143947:70000,72000

Hi...

In general, it's easier to debug servlet problems in general
(and Dazzle problems in particular) if you send your log files
along with the error report.  These generally contain the full
trace of the Java exception which caused the problem.

> (Here is our 'dazzlecfg.xml')
> 
> <dazzle xmlns="http://www.biojava.org/2000/dazzle">
> 
> <!-- Human 428 data bridge -->
> <resource id="ensembl428_bridge" jclass="ensembl.EnsemblHolder">
> <string name="dbURL" value="jdbc:mysql://kaka/homo_sapiens_core_4_28" />
> 
> <string name="dbUser" value="anonymous" />
> <string name="dbPass" value="" />
> <int name="schemaVersion" value="4" />
> </resource>


My best guess would be that the problem is being caused
by the servlet failing to connect to the database.  If you
want to continue using the ensembl database at sanger, try
using the fully-qualified name for the database server:

    kaka.sanger.ac.uk

Alternatively, if you have a copy of the ensembl databases locally,
you'll get better performance if you point the servlet
at that instead.


Hope this helps,

    Thomas.