[DAS] SEVERE: DazzleServerMain: DAS Error

[Warren, Jonathan]

Can anyone point me in the direction of why I would get the following
error?

We recently upgraded to the new version of dazzle and our old and new
data sources now don't work.

The reference servers for ensembl versions 25_34 and 18_34 work fine,
but our extra annotations in generic feature tables return the following
errors when a features?segment=1,1000 or something similar is used.
(They show up as sources just fine).


22/02/2005 16:23:44 org.apache.catalina.core.ApplicationContext log
SEVERE: DazzleServerMain: DAS Error
java.util.NoSuchElementException
        at java.util.StringTokenizer.nextToken(StringTokenizer.java:259)
        at
org.biojava.servlets.dazzle.DazzleServlet.getSegments(DazzleServlet.java
:617)
        at
org.biojava.servlets.dazzle.DazzleServlet.featuresCommand(DazzleServlet.
java:906)
        at
org.biojava.servlets.dazzle.DazzleServlet.doGet(DazzleServlet.java:257)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:237)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:157)
        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:214)
        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:178)
        at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:126)
        at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:105)
        at
org.apache.catalina.valves.FastCommonAccessLogValve.invoke(FastCommonAcc
essLogValve.java:481)
        at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java:107)
        at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
48)
        at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:82
5)
        at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processC
onnection(Http11Protocol.java:731)
        at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint
.java:526)
        at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollow
erWorkerThread.java:80)
        at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:684)
        at java.lang.Thread.run(Thread.java:534)

Config snippet below:

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

  <resource id="homo_sapiens_18_34_bridge"
jclass="org.ensembl.das.DatabaseHolder">
    <string name="dbURL"
value="jdbc:mysql://bifo6/homo_sapiens_core_18_34" />
    <string name="dbUser" value="ensembl" />
    <string name="dbPass" value="-------" />
  </resource>

  <!-- Reference server -->

  <datasource id="homo_sapiens_18_34"
jclass="org.ensembl.das.EnsemblCoreReference">
    <string name="coreHolder" value="homo_sapiens_18_34_bridge" />

    <string name="name" value="Ensembl" />
    <string name="description" value="The human genome from ensembl" />
    <string name="version" value="18.34" />

    <int name="schemaVersion" value="18" />

<!--    <set name="elideTypes">
      <string value="repeat" />
      <string value="similarity" />
    </set> -->
  </datasource>


  <resource id="homo_sapiens_25_34_bridge"
jclass="org.ensembl.das.DatabaseHolder">
    <string name="dbURL"
value="jdbc:mysql://bifo6/homo_sapiens_core_25_34e" />
    <string name="dbUser" value="ensembl" />
    <string name="dbPass" value="pass" />
  </resource>

  <!-- Reference server -->

  <datasource id="homo_sapiens_25_34"
jclass="org.ensembl.das.EnsemblCoreReference">
    <string name="coreHolder" value="homo_sapiens_25_34_bridge" />

    <string name="name" value="Ensembl" />
    <string name="description" value="The human schema 25 from ensembl"
/>
    <string name="version" value="25.34" />

    <int name="schemaVersion" value="25" />

<!--    <set name="elideTypes">
      <string value="repeat" />
      <string value="similarity" />
    </set> -->
  </datasource>

  <resource id="ensembl_generic"
jclass="org.ensembl.das.DatabaseHolder">
    <string name="dbURL" value="jdbc:mysql://bifo6/ensembl_generic" />
    <string name="dbUser" value="ensembl" />
    <string name="dbPass" value="-----" />
  </resource>

 <datasource id="BovineScaf1"
jclass="org.ensembl.das.GenericSeqFeatureSource">
    <string name="dbHolder" value="ensembl_generic" />
    <string name="name" value="Bovine draft type0" />
    <string name="description" value="Bovine draft genome assembly
contigs that only have hits to one chromosome " />
    <string name="version" value="1.00" />
    <string name="tableName" value="bovScaf1" />
    <string name="mapMaster"
value="http://imp23.agresearch.co.nz:8080/das/homo_sapiens_25_34/" />
  </datasource>

<datasource id="OvineDataSource"
jclass="org.ensembl.das.GenericSeqFeatureSource">
    <string name="dbHolder" value="ensembl_generic" />
    <string name="name" value="Ovine Contigs" />
    <string name="description" value="Our Ovine Contigs" />
    <string name="version" value="1.00" />
    <string name="tableName" value="cs18hg16" />
    <string name="mapMaster"
value="http://imp23.agresearch.co.nz:8080/das/homo_sapiens_18_34/" />
  </datasource>


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