[DAS] trouble attaching das source

[Thomas Down]

Hi Sean,

I'm afraid the version 20 databases include some major changed to the 
schema.  Updating the old biojava-ensembl and ensembl-das code wasn't 
going to be practical, since a lot of the internal assumptions about 
how assemblies work, etc., have been broken.

I've written some new code which should do the job -- unfortunately I 
haven't had a chance to put together a release yet.  But you can get 
the latest code using Subversion (http://subversion.tigris.org/) from:

     http://www.derkholm.net/svn/repos/biojava-ensembl/trunk/

Or send me an e-mail directly if you'd prefer me to send you a snapshot.

This includes both some new biojava-ensembl bridge code which can 
handle both schema-20+ and old-format database, and a new set of 
ensembl-das plugins which are compatible with dazzle 1.0x:

     http://www.biojava.org/dazzle/

A typical configuration for the new system looks something like:

<dazzle xmlns="http://www.biojava.org/2000/dazzle">
   <resource id="connection_hsa_core_20_34" 
jclass="org.ensembl.das.DatabaseHolder">
     <string name="dbURL" 
value="jdbc:mysql://noranti/homo_sapiens_core_20_34b" />
     <string name="dbUser" value="foo" />
     <string name="dbPass" value="bar" />
   </resource>

   <datasource id="hsa2034" 
jclass="org.ensembl.das.EnsemblCoreReference">
     <string name="name" value="Human assembly" />
     <string name="description" value="Human genome from Ensembl" />
     <string name="version" value="20.34" />

     <string name="coreHolder" value="connection_hsa_core_20_34" />
     <int name="schemaVersion" value="20" />

     <string name="ensemblWebURL" 
value="http://www.ensembl.org/Homo_sapiens/" />
   </datasource>
</dazzle>


Sorry I've been so slow getting this properly released -- give me a 
shout if you need any help with it,

      Thomas.



On 17 May 2004, at 16:53, Sean O'Keeffe wrote:

> Hi there,
> I'm a bioinformatics researcher at the GSF national research institute 
> in munich, germany.
> I have set-up a das server (dazzle 0.97a) according to instructions on 
> the ensembl site.
> It seems fine and shows up all the data-sources when I point to the 
> das server.
> My problem arises when i try to attach the server to the ensembl web 
> site - click on 'manage sources' on the das sources tab in contig 
> view. Nothing happens when i type in our server 
> 'andromeda.gsf.de:7070' and click on "show sources" - after about 5-10 
> seconds it just refreshes and is blank.
> I had it running fine on a previous ensembl version but this is now 
> version 20 and we've added extra data here also.
> My dazzle config xml file (part of it) is below:
> Any help would be great.
> Thanks, Sean.
>
> <?xml version="1.0" ?>
>
> <!-- Example configuration file for ensembl-das
>
>     Check all paths, database details, and mapMaster URLs before
>     deploying.
>
>     In case of problems, contact Thomas Down <td2 at sanger.ac.uk>
>
>  -->
> <dazzle xmlns="http://www.biojava.org/2000/dazzle">
>  <resource id="mouse20_32b_bridge" jclass="ensembl.EnsemblHolder">
>    <string name="dbURL" 
> value="jdbc:mysql://andromeda.gsf.de/mus_musculus_core_20_32b" />
>    <string name="dbUser" value="hmmmm" />
>    <string name="dbPass" value="whatever" />
>    <int name="schemaVersion" value="20" />
>  </resource>
>
>  <datasource id="mouse2032b" jclass="ensembl.EnsemblReferenceSource">
>    <string name="ensemblHolderID" value="mouse20_32b_bridge" />
>    <string name="name" value="Ensembl" />
>    <string name="description" value="The mouse genome from ensembl" />
>    <string name="version" value="20.32b" />
>    <string name="stylesheet" value="ensemblbase-style.xml" />
>    <set name="elideTypes">
>      <string value="repeat" />
>      <string value="similarity" />
>    </set>
> </datasource>
>
>   <datasource id="HNB_TF_mouse" 
> jclass="ensembl.EnsemblGenericSeqFeatureSource">
>    <string name="ensemblHolderID" value="mouse20_32b_bridge" />
>    <string name="name" value="Mouse TF binding sites" />
>    <string name="description" value="Mouse TF binding sites predicted 
> using MatInspector" />
>    <string name="version" value="1.0" />
>    <string name="mapMaster" 
> value="http://andromeda.gsf.de:7070/das/mouse2032b/" />
>    <string name="dbURL" 
> value="jdbc:mysql://andromeda.gsf.de/ensembl_generic/" />
>    <string name="dbUser" value="user" />
>    <string name="dbPass" value="***" />
>    <string name="tableName" value="TF_mouse" />
>    <string name="stylesheet" value="HNB-style.xml" />
>  </datasource>
>
>
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