myGrid

• Type: Bug
• Status: Open
• Priority: Critical
• Resolution: Unresolved
• Affects Version/s: 1.7.1
• Fix Version/s: None
• Component/s: None
• Labels:

  None

Reported by Jerzy Orlowski to moby-dev and taverna-hackers on 2008-10-02:

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)

Reproducable on my machine with 1.7.1 on OS X and Java 10.5:

: stain@mira ~/Downloads/mobydevproblemswithbiomobypluginsintaverna;/Applications/Taverna.app/Contents/MacOS/executeworkflow.sh -inputdoc 1653746517794550_input.xmml 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-16" java.lang.LinkageError: Class org/apache/commons/logging/Log violates loader constraints
	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)

1. 

   1653746517794550_input.xml

   2008-10-02 14:03

   0.6 kB

   Stian Soiland-Reyes

2. 

   1653746517794550_workflow_scufl.xml

   2008-10-02 14:04

   3 kB

   Stian Soiland-Reyes

3. 

   progress.xml

   2008-10-02 14:04

   0.1 kB

   Stian Soiland-Reyes

• Assignee:

  Alan Williams

  Reporter:

  Stian Soiland-Reyes

• Created:

  2008-10-02 14:03

  Updated:

  2008-10-02 14:05