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jsongraph / jgf-app

A cytoscape 3.x app to import and export BEL networks.
Apache License 2.0
3 stars 0 forks source link

ConcurrentModificationException exception occurs when importing network #1

Closed abargnesi closed 10 years ago

abargnesi commented 10 years ago

A ConcurrentModificationException error occurs when importing a JSON Graph format. The user will see a message popup indicating a "null" after importing.

The stacktrace reported is:

java.util.ConcurrentModificationException
        at java.util.IdentityHashMap$IdentityHashMapIterator.nextIndex(IdentityHashMap.java:732)
        at java.util.IdentityHashMap$EntryIterator.next(IdentityHashMap.java:838)
        at java.util.IdentityHashMap$EntryIterator.next(IdentityHashMap.java:832)
        at org.cytoscape.ding.impl.AbstractDViewModel.clearVisualProperties(AbstractDViewModel.java:198)
        at org.cytoscape.view.vizmap.internal.ApplyToNetworkHandler.apply(ApplyToNetworkHandler.java:77)
        at org.cytoscape.view.vizmap.internal.VisualStyleImpl.apply(VisualStyleImpl.java:157)
        at org.cytoscape.task.internal.loadnetwork.GenerateNetworkViewsTask.run(GenerateNetworkViewsTask.java:98)
        at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:337)
        at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
        at java.util.concurrent.FutureTask.run(FutureTask.java:262)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)

This is an issue in Cytoscape that was fixed in Cytoscape 3.1.1.

The Cytoscape-API-Compatibility manifest header will be set to 3.1, but keep in mind that this error can occur on Cytoscape 3.1.0 and previous.

abargnesi commented 10 years ago

Set compatibility header in 61c04e853bc747d3d6deaf5b3a0889280a195049.

This error can occur if using Cytoscape 3.1.0.