[JAMESII-164] ML-Rules Reference Simulator crashes when simulating Yeast-Examples Created: 21/Jun/12  Updated: 27/Jun/12  Resolved: 26/Jun/12

Status: Resolved
Project: James II
Component/s: ML-Rules
Affects Version/s: James II 0.8.7
Fix Version/s: James II 0.8.7
Security Level: public (Visible to EVERYONE.)

Type: Bug Priority: Major
Reporter: re027 Assignee: Stefan Rybacki
Resolution: Fixed Votes: 0
Labels: None
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Attachments: File patch.diff    

 Description   

This problem occurs for all published Yeast Example models (#1-5), and always results in this exception:

 
java.util.ConcurrentModificationException
	at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372)
	at java.util.AbstractList$Itr.next(AbstractList.java:343)
	at simulator.mlrules.population.reference.MLRulesPopulationsSpecie.clone(MLRulesPopulationsSpecie.java:112)
	at simulator.mlrules.population.reference.MLRulesPopulationProcessor.removeSpeciesFromContexts(MLRulesPopulationProcessor.java:810)
	at simulator.mlrules.population.reference.MLRulesPopulationProcessor.executeRule(MLRulesPopulationProcessor.java:737)
	at simulator.mlrules.population.reference.MLRulesPopulationProcessor.nextStep(MLRulesPopulationProcessor.java:432)
	at james.core.processor.Processor.executeNextStep(Processor.java:148)
	at james.core.processor.execontrol.ExecutionControl.run(ExecutionControl.java:352)
	at james.core.processor.RunnableProcessor.run(RunnableProcessor.java:79)
	at james.core.simulationrun.SimulationRun.start(SimulationRun.java:719)
	at james.core.experiments.taskrunner.ComputationTaskHandler.runComputationTask(ComputationTaskHandler.java:135)
	at james.core.experiments.taskrunner.sequential.SequentialComputationTaskRunner.run(SequentialComputationTaskRunner.java:350)
	at james.core.experiments.taskrunner.sequential.SequentialComputationTaskRunner.executeConfiguration(SequentialComputationTaskRunner.java:197)
	at james.core.experiments.taskrunner.AbstractTaskRunner.run(AbstractTaskRunner.java:107)
	at java.lang.Thread.run(Thread.java:662)

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