[DAS] Config file?

[Warren, Jonathan]

Hi,

Can someone tell me what ( or if something ) is wrong with my config
file (this is driving me nuts!)

The following error comes up in the logs when I access the /das/ web
page. The MyDataSource comes up in this web page but no ensembl
stuff????


2003-04-10 16:33:56 Couldn't initialize datasource ensembl1030
java.lang.AbstractMethodError:
org/biojava/bio/program/ensembl/ImmutableSequenceDBBase.getName
        at ensembl.EnsemblReferenceSource.init(Unknown Source)
rethrown as org.biojava.servlets.dazzle.datasource.DataSourceException
        at
org.biojava.servlets.dazzle.datasource.BasicDazzleInstallation.initDataS
ource(Unknown Sou
rce)
        at
org.biojava.servlets.dazzle.datasource.BasicDazzleInstallation.getDataSo
urce(Unknown Sour
ce)
        at org.biojava.servlets.dazzle.DazzleServlet.welcomePage(Unknown
Source)
        at org.biojava.servlets.dazzle.DazzleServlet.doGet(Unknown
Source)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java,
Compiled Code)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java,
Compiled Code)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.j
ava, Compiled Code)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java, Com
piled Code)
        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java, Compiled
Code)
        at
org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.i
nvokeNext(Standar
dPipeline.java, Compiled Code)
        at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java,
Compiled Code)
        at
org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java,
Compiled Code)
        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java, Compiled
Code)
        at
org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.i
nvokeNext(Standar
dPipeline.java, Compiled Code)
        at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java,
Compiled Code)
        at
org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java,
Compiled Code)
        at
org.apache.catalina.core.StandardContext.invoke(StandardContext.java,
Compiled Code)
        at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
, Compiled Code)
        at
org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.i
nvokeNext(Standar
dPipeline.java, Compiled Code)
        at
org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherVa
lve.java, Compile
d Code)
        at
org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.i
nvokeNext(Standar
dPipeline.java, Compiled Code)
        at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
, Compiled Code)
        at
org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.i
nvokeNext(Standar
dPipeline.java, Compiled Code)
        at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java,
Compiled Code)
        at
org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java,
Compiled Code)
        at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java, Compiled Co
de)
        at
org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.i
nvokeNext(Standar
dPipeline.java, Compiled Code)
        at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java,
Compiled Code)
        at
org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java,
Compiled Code)
        at
org.apache.coyote.tomcat4.CoyoteAdapter.service(CoyoteAdapter.java,
Compiled Code)
        at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java,
Compiled Code)
        at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processC
onnection(Http11P
rotocol.java, Compiled Code)
        at
org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java,
Compiled Code)
        at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java, Compiled C
ode)
        at java.lang.Thread.run(Thread.java:484)

2003-04-10 16:33:56 DazzleServerMain: *** WARNING *** Lost a data source
ensembl1030





<?xml version="1.0" ?>

<!-- Example configuration file for ensembl-das

     Check all paths, database details, and mapMaster URLs before
     deploying.  More information can be found at:

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

     In case of problems, contact Thomas Down <td2 at sanger.ac.uk>

  -->

<dazzle xmlns="http://www.biojava.org/2000/dazzle">
  <!-- Define a connection to and Ensembl-format database -->

  <resource id="ensembl1030_bridge" jclass="ensembl.EnsemblHolder">
    <string name="dbURL"
value="jdbc:mysql://bifo6.agresearch.co.nz/homo_sapiens_core_10_30" />
    <string name="dbUser" value="user" />
    <string name="dbPass" value="password" />
    <int name="schemaVersion" value="10" />
  </resource>

  <!-- Reference server -->

  <datasource id="ensembl1030" jclass="ensembl.EnsemblReferenceSource">
    <string name="ensemblHolderID" value="ensembl1030_bridge" />

    <string name="name" value="Ensembl 10.30" />
    <string name="description" value="The human genome from ensembl" />
    <string name="version" value="10.30" />
    <string name="stylesheet" value="ensemblbase-style.xml" />
    <set name="elideTypes">
  <string value="repeat" />
  <string value="similarity" />
  </set>

  </datasource>

  <!-- Test Reference server -->

  <datasource id="MyDataSource"
jclass="ensembl.EnsemblGenericSeqFeatureSource">
    <string name="ensemblHolderID" value="ensembl1030_bridge" />
    <string name="name" value="Ensembl Test Source" />
    <string name="description" value="blah blah My DAS feature source"
/>
    <string name="version" value="1.00" />

    <string name="dbURL"
value="jdbc:mysql://bifo6.agresearch.co.nz/ensembl_generic" />
    <string name="dbUser" value="user" />
    <string name="dbPass" value="password" />
    <string name="tableName" value="my_feature" />
    <string name="stylesheet" value="ensemblbase-style.xml" />

    <string name="mapMaster"
value="http://bifo10.agresearch.co.nz:8080/das/ensembl1030/" />
  </datasource>

</dazzle>





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