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  1. Apache Taverna
  2. TAVERNA-94

Processors with looping fail

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    Details

    • Type: Bug
    • Status: To Do
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Taverna Engine
    • Labels:
      None

      Description

      Although it is not possible in alpha1 to create workflows with looping, loading them from t2flow should work.

      This impacts any workflow using asynchronous services, such as the EBI Interproscan example in the starter pack.

      However, the attached workflow (from http://www.myexperiment.org/workflows/1028/versions/3) fail to run in Taverna 3:

      WARN  2013-10-10 14:17:18,648 (net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:236) - Failed (INVOCATION) invoking net.sf.taverna.t2.activities.beanshell.BeanshellActivity@2d69627b for job DispatchJobEvent facade6:Dummy_example_of_looping:createJob[]: Uncaught exception while invoking net.sf.taverna.t2.activities.beanshell.BeanshellActivity@2d69627b
      java.lang.NullPointerException
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop.receiveJob(Loop.java:140)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce.receiveJob(ErrorBounce.java:117)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.AbstractDispatchLayer.receiveJob(AbstractDispatchLayer.java:69)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.IntermediateProvenance.receiveJob(IntermediateProvenance.java:409)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize$StateModel.fillFromQueue(Parallelize.java:387)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize.receiveJobQueue(Parallelize.java:137)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.impl.DispatchStackImpl.receiveEvent(DispatchStackImpl.java:144)
      	at net.sf.taverna.t2.workflowmodel.impl.ProcessorImpl$1.receiveEventFromStrategy(ProcessorImpl.java:121)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.impl.IterationStrategyImpl$TerminalNodeImpl.pushEvent(IterationStrategyImpl.java:106)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.impl.IterationStrategyImpl$TerminalNodeImpl.receiveJob(IterationStrategyImpl.java:92)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.AbstractIterationStrategyNode.pushJob(AbstractIterationStrategyNode.java:225)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.CrossProduct.innerReceiveJob(CrossProduct.java:57)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.CompletionHandlingAbstractIterationStrategyNode.receiveJob(CompletionHandlingAbstractIterationStrategyNode.java:96)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.AbstractIterationStrategyNode.pushJob(AbstractIterationStrategyNode.java:225)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.NamedInputPortNode.receiveJob(NamedInputPortNode.java:54)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.impl.IterationStrategyImpl.receiveData(IterationStrategyImpl.java:288)
      	at net.sf.taverna.t2.workflowmodel.processor.iteration.impl.IterationStrategyStackImpl.receiveData(IterationStrategyStackImpl.java:123)
      	at net.sf.taverna.t2.workflowmodel.impl.ProcessorInputPortImpl.pushData(ProcessorInputPortImpl.java:63)
      	at net.sf.taverna.t2.workflowmodel.impl.AbstractFilteringInputPort.receiveToken(AbstractFilteringInputPort.java:103)
      	at net.sf.taverna.t2.workflowmodel.impl.AbstractFilteringInputPort.receiveEvent(AbstractFilteringInputPort.java:57)
      	at net.sf.taverna.t2.workflowmodel.impl.BasicEventForwardingOutputPort.sendEvent(BasicEventForwardingOutputPort.java:70)
      	at net.sf.taverna.t2.workflowmodel.impl.ProcessorOutputPortImpl.receiveEvent(ProcessorOutputPortImpl.java:54)
      	at net.sf.taverna.t2.workflowmodel.impl.ProcessorCrystalizerImpl.jobCreated(ProcessorCrystalizerImpl.java:66)
      	at net.sf.taverna.t2.workflowmodel.impl.AbstractCrystalizer.receiveEvent(AbstractCrystalizer.java:90)
      	at net.sf.taverna.t2.workflowmodel.impl.ProcessorImpl$2.pushEvent(ProcessorImpl.java:144)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.impl.DispatchStackImpl$TopLayer.receiveResult(DispatchStackImpl.java:277)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize.receiveResult(Parallelize.java:174)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.AbstractDispatchLayer.receiveResult(AbstractDispatchLayer.java:85)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.IntermediateProvenance.receiveResult(IntermediateProvenance.java:472)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.AbstractDispatchLayer.receiveResult(AbstractDispatchLayer.java:85)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer.receiveResult(AbstractErrorHandlerLayer.java:136)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.AbstractErrorHandlerLayer.receiveResult(AbstractErrorHandlerLayer.java:136)
      	at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke$InvokeCallBack.receiveResult(Invoke.java:340)
      	at net.sf.taverna.t2.activities.beanshell.BeanshellActivity$1.run(BeanshellActivity.java:186)
      	at java.lang.Thread.run(Thread.java:724)
      

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        1. dummy_example_of_looping_582764.t2flow
          20 kB
          Stian Soiland-Reyes

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              • Assignee:
                Unassigned
                Reporter:
                stain Stian Soiland-Reyes
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                • Created:
                  Updated: