[Taverna-hackers] class not found exception

Mon, 30 Mar 2009 08:00:59 -0700 

Hi All,

I am getting an exception when running a locally built t2 for the attached
workflow:

Exception in thread "Opening dataflow(s)
[C:\Users\Eddie\Desktop\biomoby-test.xml]" java.lang.NoClassDefFoundError:
org/biomoby/shared/MobySecondaryData
        at
org.biomoby.service.dashboard.data.ParametersTable$ParametersTableModel.<ini
t>(ParametersTable.java:298)
        at
org.biomoby.service.dashboard.data.ParametersTable.<init>(ParametersTable.ja
va:63)
        at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.generatePorts(BiomobyAc
tivity.java:1041)
        at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.configure(BiomobyActivi
ty.java:148)
        at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.configure(BiomobyActivi
ty.java:103)
        at
net.sf.taverna.t2.compatibility.activity.AbstractActivityTranslator.doTransl
ation(AbstractActivityTranslator.java:80)
        at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createActivity(Workf
lowModelTranslator.java:422)
        at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createProcessor(Work
flowModelTranslator.java:376)
        at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createProcessors(Wor
kflowModelTranslator.java:360)
        at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.doTranslation(Workfl
owModelTranslator.java:161)
        at
net.sf.taverna.t2.workbench.file.translator.T1OpenHandler.openDataflowStream
(T1OpenHandler.java:152)
        at
net.sf.taverna.t2.workbench.file.translator.T1OpenHandler.openDataflow(T1Ope
nHandler.java:122)
        at
net.sf.taverna.t2.workbench.file.impl.FileManagerImpl.openDataflow(FileManag
erImpl.java:327)
        at
net.sf.taverna.t2.workbench.file.impl.actions.OpenWorkflowAction.openWorkflo
ws(OpenWorkflowAction.java:154)
        at
net.sf.taverna.t2.workbench.file.impl.actions.OpenWorkflowAction$FileOpenerT
hread.run(OpenWorkflowAction.java:348)
Caused by: java.lang.ClassNotFoundException:
org.biomoby.shared.MobySecondaryData
        at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(Loca
lArtifactClassLoader.java:352)
        at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(Loca
lArtifactClassLoader.java:276)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)      
        at java.lang.ClassLoader.loadClassInternal(Unknown Source)
        ... 15 more

This exception happens when I download the latest snapshot from Hudson or
build it locally. Oddly enough, I don't get the exception when running t2
from within eclipse.

Eddie

<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"; version="0.2" log="0">
  <s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:742e5fca-b790-4c6e-8d90-180227d19ff8" author="" title="biomoby-test" />
  <s:processor name="Gene2PubMed">
    <s:description>Enter the EntrezGene ID (ie. 5211 for gene pfkl - phosphofructokinase, liver) to  lretrieve list of references and abstracts of publications related to the gene of your interest.</s:description>
    <s:defaults>
      <s:default name="input">&lt;moby:MOBY xmlns:moby="http://www.biomoby.org/moby"&gt;   &lt;moby:mobyContent&gt;     &lt;moby:mobyData moby:queryID="a0"&gt;       &lt;moby:Simple moby:articleName=""&gt;         &lt;Object articleName="" namespace="EntrezGene_EntrezGeneID" id="80332" /&gt;       &lt;/moby:Simple&gt;     &lt;/moby:mobyData&gt;   &lt;/moby:mobyContent&gt; &lt;/moby:MOBY&gt;</s:default>
    </s:defaults>
    <s:biomobywsdl>
      <s:mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:mobyEndpoint>
      <s:serviceName>Gene2PubMed</s:serviceName>
      <s:authorityName>icapture.ubc.ca</s:authorityName>
      <s:Parameter s:name="maxResults">20</s:Parameter>
    </s:biomobywsdl>
  </s:processor>
  <s:processor name="Parse_Moby_Data_Publication">
    <s:description>Processor to parse the datatype Publication</s:description>
    <s:biomobyparser>
      <s:endpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</s:endpoint>
      <s:datatype>Publication</s:datatype>
      <s:articleName>publications</s:articleName>
      <s:description>Processor to parse the datatype Publication</s:description>
    </s:biomobyparser>
  </s:processor>
  <s:link source="Gene2PubMed:Publication(Collection - 'publications' As Simples)" sink="Parse_Moby_Data_Publication:mobyData('Publication')" />
  <s:link source="Parse_Moby_Data_Publication:id" sink="id" />
  <s:link source="Parse_Moby_Data_Publication:publications_'Author'" sink="author" />
  <s:sink name="id" />
  <s:sink name="author" />
</s:scufl>


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