[DAS] Dazzle with Ensembl 3.26.1

[Thomas Down]

On Thu, Feb 14, 2002 at 11:39:28AM -0500, jfreeman wrote:
> Hi Tony or to whom it may concern, on:
> 
> http://www.biojava.org/dazzle/ensembldas.html
> 
> You have an example dazzlecfg.xml file for a reference server shown here
> below:
> 
> <datasource id="ensembl110" jclass="ensembl.EnsemblReferenceSource">
>   <string name="ensemblHolderID" value="ensembl110_bridge" />
> 
>   <string name="name" value="Ensembl 1.10" />
>   <string name="description" value="The human genome from
> Ensembl" />
>   <string name="version" value="1.10" />
> 
>   <string name="stylesheet" value="ensemblbase-style.xml" />
> 
>   <set name="elideTypes">
>     <string value="repeat" />
>     <string value="similarity" />
>   </set
> </datasource>
> 
> Do you have the same example for ensembl-3.26.1?



That general recipe should work with the new version, too.
The only thing you'll want to do is change the version strings
to match the new release.

But you've left out the important bit

  <resource id="ensembl110_bridge" jclass="ensembl.EnsemblHolder">
    <string name="dbURL" value="jdbc:mysql://kaka.sanger.ac.uk/ensembl110" />
    <string name="dbUser" value="anonymous" />
    <string name="dbPass" value="" />
    <int name="schemaVersion" value="110" />
  </resource>

This is where you can point it to the new database.  You'll
also need to change the schemaVersion property.  For example:

  <resource id="ensembl326_bridge" jclass="ensembl.EnsemblHolder">
    <string name="dbURL" value="jdbc:mysql://kaka.sanger.ac.uk/homo_sapiens_core_130" />
    <string name="dbUser" value="anonymous" />
    <string name="dbPass" value="" />
    <int name="schemaVersion" value="130" />
  </resource>

Note that right now, you still need to use `old-style' schema versions.
Next time I do anything to the guts of the code, I'll update it to use
new-style `official' versions instead (so the current version is 3).
I'll warn people when this happens, and also add some kind of transitional
behaviour (e.g. `numbers greater than 100 are interpretted as old-style'' :-).


Hope this helps,

    Thomas.