Repainting issue caused by java.util.ConcurrentModificationException

[Juan Garcia]

Hi all,

I have been facing a problem when trying to repaint the cytoscape network. In response to some interaction, I need to update some 

The problem starts when I try to repaint the graph in response of some events. If the repainting is so exhaustive, then I get the network as shown in the screenshot below:

The exception trace is shown below:

2017-05-02 11:14:47,191 [pool-3-thread-1] ERROR org.cytoscape.event.internal.CyListenerAdapter - Unexpected exception while handling listener: org.cytoscape.model.events.RowsSetListener

java.lang.reflect.InvocationTargetException

at sun.reflect.GeneratedMethodAccessor66.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.cytoscape.event.internal.CyListenerAdapter.fireEvent(CyListenerAdapter.java:120)

at org.cytoscape.event.internal.CyEventHelperImpl.flushPayloadEvents(CyEventHelperImpl.java:177)

at org.cytoscape.ding.impl.DGraphView.updateView(DGraphView.java:1098)

at org.cytoscape.internal.view.NetworkViewManager.updateView(NetworkViewManager.java:884)

at org.cytoscape.internal.view.NetworkViewManager.handleEvent(NetworkViewManager.java:614)

at sun.reflect.GeneratedMethodAccessor66.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.cytoscape.event.internal.CyListenerAdapter.fireEvent(CyListenerAdapter.java:120)

at org.cytoscape.event.internal.CyEventHelperImpl.flushPayloadEvents(CyEventHelperImpl.java:177)

at org.cytoscape.event.internal.CyEventHelperImpl$1.run(CyEventHelperImpl.java:70)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)

at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)

at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.util.ConcurrentModificationException

at java.util.IdentityHashMap$IdentityHashMapIterator.nextIndex(IdentityHashMap.java:734)

at java.util.IdentityHashMap$EntryIterator.next(IdentityHashMap.java:842)

at java.util.IdentityHashMap$EntryIterator.next(IdentityHashMap.java:836)

at org.cytoscape.ding.impl.AbstractDViewModel.clearVisualProperties(AbstractDViewModel.java:236)

at org.cytoscape.view.vizmap.internal.ApplyToNetworkHandler.apply(ApplyToNetworkHandler.java:80)

at org.cytoscape.view.vizmap.internal.VisualStyleImpl.apply(VisualStyleImpl.java:172)

at org.cytoscape.internal.view.NetworkViewManager.updateView(NetworkViewManager.java:883)

at org.cytoscape.internal.view.NetworkViewManager.handleEvent(NetworkViewManager.java:614)

... 21 more

2017-05-02 11:14:47,220 [pool-3-thread-1] ERROR org.cytoscape.event.internal.CyListenerAdapter - Unexpected exception while handling listener: org.cytoscape.model.events.RowsSetListener

java.lang.reflect.InvocationTargetException

at sun.reflect.GeneratedMethodAccessor66.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.cytoscape.event.internal.CyListenerAdapter.fireEvent(CyListenerAdapter.java:120)

at org.cytoscape.event.internal.CyEventHelperImpl.flushPayloadEvents(CyEventHelperImpl.java:177)

at org.cytoscape.event.internal.CyEventHelperImpl$1.run(CyEventHelperImpl.java:70)

at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)

at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)

at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)

at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.util.ConcurrentModificationException

at java.util.IdentityHashMap$IdentityHashMapIterator.nextIndex(IdentityHashMap.java:734)

at java.util.IdentityHashMap$EntryIterator.next(IdentityHashMap.java:842)

at java.util.IdentityHashMap$EntryIterator.next(IdentityHashMap.java:836)

at org.cytoscape.ding.impl.AbstractDViewModel.clearVisualProperties(AbstractDViewModel.java:236)

at org.cytoscape.view.vizmap.internal.ApplyToNetworkHandler.apply(ApplyToNetworkHandler.java:80)

at org.cytoscape.view.vizmap.internal.VisualStyleImpl.apply(VisualStyleImpl.java:172)

at org.cytoscape.internal.view.NetworkViewManager.updateView(NetworkViewManager.java:883)

at org.cytoscape.internal.view.NetworkViewManager.handleEvent(NetworkViewManager.java:614)

... 13 more

The interaction modifies some of the visual settings on the vertices:

       CyRow row = network.getRow(node);

        row.set(CyNetwork.NAME, nodeName);

        row.set(NODE_SIZE_, size);

        row.set(NODE_SHAPE_, shape);

        row.set(NODE_FILL_COLOR_, color);

        row.set(NODE_VISIBLE, visible);

        row.set(NODE_TRANSPARENCY, transparency);

        row.set(NODE_LABEL, nodeLabel);

        row.set(NODE_TYPE, type);

        row.set(NODE_BORDER_COLOR_, borderColor);

        row.set(NODE_BORDER_LINE_TYPE_, borderLineType);

        row.set(NODE_BORDER_WIDTH_, borderWidth);

...

nodeView.setVisualProperty(BasicVisualLexicon.NODE_SHAPE,shape);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR,nodeColor);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_TRANSPARENCY,transparency);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_BORDER_PAINT,borderColor);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_BORDER_LINE_TYPE,lineType);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_BORDER_WIDTH, borderWidth);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_SIZE,size);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_HEIGHT,size);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_WIDTH,size);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_LABEL_TRANSPARENCY, transparency);

        nodeView.setVisualProperty(BasicVisualLexicon.NODE_LABEL_FONT_SIZE,labelFontSize);

...

networkView.updateView();

To fix this problem, I have to force the repaint either with the option [Select] -> [Show all nodes and edges] on Cytoscape v3.2.1, or programatically for Cytoscape v3.4.0 with the following code:

...

nodeView.setVisualProperty(BasicVisualLexicon.NODE_VISIBLE,false);

...

nodeView.setVisualProperty(BasicVisualLexicon.NODE_VISIBLE,true);

The repainting process is ugly, due to it repaints so many times. My question is if is this ConcurrentModificationException a bug? or is there a way to do this repainting  process smoothly and correct?, Am I following the correct approach?

Thanks,

Juan

[Scooter Morris]

Hi Juan,
    Obviously, it's a little hard to debug just looking at the snippet of code, but since you are modifying a bunch of row values, and your getting an exception in RowsSetLIstener, I would suggest calling silenceEventSource on the table before you do all of your settings, then unsilenceEventSource when you've changed everything.

-- scooter

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[Juan Garcia]

Hi Dr. Scooter,

Fortunately, I have been able to remove this exception, but I'd like to know of there is a way to improve the interaction with Cytoscape I need.

The flow that I'm following is that I have a graph (most of times a huge one) in a DB but it is not shown all at a time, due to it cannot be fitted. Instead, I just show some nodes according to a set of criteria. Then, the most basic operation is "expansion", which means to query and retrieve the connected nodes and edges from the selected nodes displayed in Cytoscape. This is when programatically I add the new nodes/edges into Cytoscape. I have only one network and network view where I add the new elements as follows:

CyNetworkView networkView = this.adapter.getCyApplicationManager().getCurrentNetworkView();

  CyNetwork network = this.adapter.getCyApplicationManager().getCurrentNetwork();

PropertyGraph.cyEventHelper.silenceEventSource(network.getDefaultNodeTable());

CyNode node = network.addNode();

CyRow row = network.getRow(node);

        row.set(CyNetwork.NAME, nodeName);

        row.set(NODE_SIZE_, size);

        row.set(NODE_SHAPE_, shape);

        row.set(NODE_FILL_COLOR_, color);

        row.set(NODE_TRANSPARENCY, transparency);

        row.set(NODE_LABEL, nodeLabel);

        row.set(NODE_TYPE, type);

        row.set(NODE_BORDER_COLOR_, borderColor);

        row.set(NODE_BORDER_LINE_TYPE_, borderLineType);

        row.set(NODE_BORDER_WIDTH_, borderWidth);

        row.set(NODE_VISIBLE, visible);

...

// moving the nodes...

View<CyNode> nodeView = networkView.getNodeView(cyNode);

nodeView.setVisualProperty(BasicVisualLexicon.NODE_X_LOCATION,x);

                nodeView.setVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION,y);

PropertyGraph.cyEventHelper.unsilenceEventSource(network.getDefaultNodeTable());

This is the most important fragment of code and the flow I'm following. Right now, there is a flashing effect when the nodes are being added into Cytoscape, the effect is the same, the red circles appear while the network is being repainted, and the visual settings are applied to the vertices. I'd like to have all the new elements appearing smoothly in the network without this flashing behaviour. Is there a way to achieve this?, is there any way to get this smoothly transition in the network?

I'd appreciate your comments.

Thanks,

Juan

[Scooter Morris]

Hi Juan,
   OK, couple of suggestions.  First, make sure to add all of your nodes before getting any node views.   That might help a little.  Second, I'm not sure why you're writing all of your visual property information into the node row.  You can just set the visual properties directly using setLockedValue and that will minimize the time in the loop, I think.

-- scooter