[MOBY-dev] Problems with biomoby plugins in taverna

[Jerzy Orlowski]

I am trying to execute an attached workflow with simple input (attached) 
using executeworkflow.sh

What I get is:
$ ./executeworkflow.sh -inputdoc 
/tmp/workflows/1653746517794550_input.xmml 
/tmp/workflows/1653746517794550_workflow_scufl.xml

Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects
  ... done
Fetching namespace ontology from 
http://biomoby.org/RESOURCES/MOBY-S/Namespaces
Exception in thread "Thread-15" java.lang.LinkageError: loader 
constraint violation: loader (instance of 
net/sf/taverna/raven/repository/impl/LocalArtifactClassLoader) 
previously initiated loading for a different type with name 
"org/apache/commons/logging/Log"
         at org.biomoby.shared.MobyException.<init>(MobyException.java:55)
         at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230)
         at org.biomoby.client.CentralImpl.call(CentralImpl.java:1525)
         at 
org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:521)
         at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576)
         at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517)
         at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436)
         at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642)
         at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353)
         at 
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280)
         at 
uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
 


And the system hangs (executeworkflow.sh produce no result, no progress 
report and does not terminate)

- Why do I get such errors?
- Why does the program hang? It should exit with non-zero value
- Why such workflow does not hang in taverna GUI version (it doesn't 
prosuce any result anyway), I attach the progress report from Taverna 
GUI version
- Why This workflow hangs executeworkflow.sh system? Most of the others 
work ok.


Jerzy Orlowski
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