Taverna 2

• Type: Bug
• Status: Closed
• Priority: Critical
• Resolution: Fixed
• Affects Version/s: 2.1.0
• Fix Version/s: 2.1.2
• Component/s: Activity - Nested workflow, Engine - Workflow model
• Labels:

  None

WARN  2010-02-01 11:14:06,032 (net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke:196) - Failed (INVOCATION) invoking Local service org.embl.ebi.escience.scuflworkers.java.StringConcat for job DispatchJobEvent facade1071:Workflow1:Workflow19:invocation84429:facade2133:Workflow19:Concatenate_two_strings[]: Uncaught exception while invoking Local service org.embl.ebi.escience.scuflworkers.java.StringConcat
java.lang.NullPointerException
        at net.sf.taverna.t2.workflowmodel.impl.DataflowOutputPortImpl$1.receiveEvent(DataflowOutputPortImpl.java:65)
        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:88)
        at net.sf.taverna.t2.workflowmodel.impl.ProcessorImpl$2.pushEvent(ProcessorImpl.java:143)
        at net.sf.taverna.t2.workflowmodel.processor.dispatch.impl.DispatchStackImpl$TopLayer.receiveResult(DispatchStackImpl.java:277)
        at net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize.receiveResult(Parallelize.java:165)
        at net.sf.taverna.t2.workflowmodel.processor.dispatch.AbstractDispatchLayer.receiveResult(AbstractDispatchLayer.java:84)
        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:300)
        at net.sf.taverna.t2.activities.beanshell.BeanshellActivity$1.run(BeanshellActivity.java:181)
        at java.lang.Thread.run(Unknown Source)

due to: DataflowActivity doing:

facade.addResultListener(new ResultListener() {
					int outputPortCount = dataflow.getOutputPorts().size();

					Map<String, T2Reference> outputData = new HashMap<String, T2Reference>();

					public void resultTokenProduced(
							WorkflowDataToken dataToken, String port) {
						if (dataToken.getIndex().length == 0) {
							outputData.put(port, dataToken.getData());
							synchronized (this) {
								if (--outputPortCount == 0) {
									callback.receiveResult(outputData, dataToken.getIndex());
									facade.removeResultListener(this);
								}
							}
						}
					}
				})

notice that removeResultListener is called after receiveResults - meaning that it will be done after the output has been pushed up the stack and the next iteration of the nested workflow might already have started.

As net.sf.taverna.t2.workflowmodel.impl.DataflowOutputPortImpl don't synchronize access to it's resultListeners field it does not help that the WorkflowInstanceFacadeImpl does when calling addResultListener or removeResultListener, as they call down to add/remove on the dataflow port, which also internally does:

WorkflowDataToken newToken = token.popOwningProcess();
				sendEvent(newToken);
				for (ResultListener listener : resultListeners
						.toArray(new ResultListener[] {})) {
					listener.resultTokenProduced(newToken, this.getName());
				}

This can occur with iterations over nested workflows, for instance if running the workflow in T2-1124 including the T2-1124 fix.

1. 

   as.t2flow

   2010-02-01 11:28

   45 kB

   Stian Soiland-Reyes

• Assignee:

  Alex Nenadic

  Reporter:

  Stian Soiland-Reyes

• Created:

  2010-02-01 11:22

  Updated:

  2010-03-23 15:10

  Resolved:

  2010-03-22 09:58