Unexpected exception while handling listener: org.cytoscape.view.model.events.NetworkViewAddedListener

Juan Garcia

unread,

May 3, 2021, 1:23:14 PM5/3/21

to cytoscape-app-dev

Hi all,

I'm upgrading an old app developed some years ago to the new OSGi infastructure for Cytoscape 3.8.2.

I'm creating a new network and its corresponding networkView, but there is an exception:

2021-05-03 11:26:42,910 [SwingWorker-pool-23-thread-1] ERROR org.cytoscape.application.userlog - Unexpected exception while handling listener: org.cytoscape.view.model.events.NetworkViewAddedListener

java.lang.reflect.InvocationTargetException: null

at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]

at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]

at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]

at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]

at org.cytoscape.event.internal.CyListenerAdapter.fireEvent(CyListenerAdapter.java:120) [61:org.cytoscape.event-impl:3.8.2]

at org.cytoscape.event.internal.CyEventHelperImpl.fireEvent(CyEventHelperImpl.java:81) [61:org.cytoscape.event-impl:3.8.2]

at org.cytoscape.view.model.internal.CyNetworkViewManagerImpl.fireEvent(CyNetworkViewManagerImpl.java:205) [88:org.cytoscape.viewmodel-impl:3.8.2]

at org.cytoscape.view.model.internal.CyNetworkViewManagerImpl.addNetworkView(CyNetworkViewManagerImpl.java:194) [88:org.cytoscape.viewmodel-impl:3.8.2]

at org.cytoscape.view.model.internal.CyNetworkViewManagerImpl.addNetworkView(CyNetworkViewManagerImpl.java:165) [88:org.cytoscape.viewmodel-impl:3.8.2]

at oracle.graph.propertyGraph.client.visualization.cytoscape.CreatePropertyGraph.createPropertyGraph(CreatePropertyGraph.java:531) [121:oracle.spatial.propertyGraph.client.visualization.cytoscape:4.4.6]

at oracle.graph.propertyGraph.client.visualization.cytoscape.gui.LoadWindowRDBMSGraph.loadRandomNodes(LoadWindowRDBMSGraph.java:590) [121:oracle.spatial.propertyGraph.client.visualization.cytoscape:4.4.6]

at oracle.graph.propertyGraph.client.visualization.cytoscape.gui.LoadWindowRDBMSGraph.access$400(LoadWindowRDBMSGraph.java:80) [121:oracle.spatial.propertyGraph.client.visualization.cytoscape:4.4.6]

at oracle.graph.propertyGraph.client.visualization.cytoscape.gui.LoadWindowRDBMSGraph$DoLoad.doInBackground(LoadWindowRDBMSGraph.java:832) [121:oracle.spatial.propertyGraph.client.visualization.cytoscape:4.4.6]

at oracle.graph.propertyGraph.client.visualization.cytoscape.gui.LoadWindowRDBMSGraph$DoLoad.doInBackground(LoadWindowRDBMSGraph.java:796) [121:oracle.spatial.propertyGraph.client.visualization.cytoscape:4.4.6]

at javax.swing.SwingWorker$1.call(SwingWorker.java:304) [?:?]

at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]

at javax.swing.SwingWorker.run(SwingWorker.java:343) [?:?]

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]

at java.lang.Thread.run(Thread.java:834) [?:?]

Caused by: java.lang.NullPointerException

at org.cytoscape.internal.select.RowViewTracker.handleEvent(RowViewTracker.java:79) ~[?:?]

... 20 more

This is the main code that I have been using and perfectly worked in the previous version:

CyActivator.cyNetworkManager.reset();
this.network = CyActivator.cyNetworkFactory.createNetwork();

this.network.getRow(network).set(CyNetwork.NAME,networkID);//the network's identifier

createTable();// creates the node and edge tables
for each node...
this.network.addNode();

for each edge...
this.network.addEdge(nodeSource,nodeDestiny,true);

CyNetworkView view = CyActivator.networkViewFactory.createNetworkView(this.network);

CyActivator.cyNetworkManager.addNetwork(this.network);
CyActivator.networkViewManager.addNetworkView(view);

Even though the view seems to be there, it is not being shown. Not sure if I'm missing something...
any ideas?

Thanks,
Juan Garcia

Juan Garcia

unread,

May 4, 2021, 12:48:56 PM5/4/21

to cytoscape-app-dev

Hi all,

I tried exactly the sample-create-network-view code from the cytoscape-app-samples with the same error when trying to add the new network view.

public class CreateNetworkViewTask extends AbstractTask {

private final CyNetworkFactory cnf;

private final CyNetworkViewFactory cnvf;

private final CyNetworkViewManager networkViewManager;

private final CyNetworkManager networkManager;

private final CyNetworkNaming cyNetworkNaming;

public CreateNetworkViewTask(CyNetworkNaming cyNetworkNaming, CyNetworkFactory cnf, CyNetworkManager networkManager,

CyNetworkViewFactory cnvf, final CyNetworkViewManager networkViewManager) {

this.cnf = cnf;

this.cnvf = cnvf;

this.networkViewManager = networkViewManager;

this.networkManager = networkManager;

this.cyNetworkNaming = cyNetworkNaming;

}

@Override

public void run(TaskMonitor monitor) {

// Create an empty network

CyNetwork myNet = this.cnf.createNetwork();

if (myNet == null) {

return;

}

// add a node to the network

CyNode node1 = myNet.addNode();

// set name for the new node

myNet.getDefaultNodeTable().getRow(node1.getSUID()).set("name", "Node1");

myNet.getDefaultNetworkTable().getRow(myNet.getSUID()).set("name", cyNetworkNaming.getSuggestedNetworkTitle("My Network"));

this.networkManager.addNetwork(myNet);

final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(myNet);

CyNetworkView myView = null;

if (!views.isEmpty()) {

myView = views.iterator().next();

}

if (myView == null) {

// create a new view for my network

myView = cnvf.createNetworkView(myNet);

networkViewManager.addNetworkView(myView);

} else {

System.out.println("networkView already existed.");

}

// Set the variable destroyView to true, the following snippet of code

// will destroy a view

boolean destroyView = false;

if (destroyView) {

networkViewManager.destroyNetworkView(myView);

}

}

I also added a class that implements the NetworkViewAddedListener and the log successfully displays the corresponding output

public class PGNetworkViewAddedListener implements NetworkViewAddedListener{

@Override

public void handleEvent(NetworkViewAddedEvent e) {

CyNetworkView networkView = e.getNetworkView();

CyNetwork addedNetwork = networkView.getModel();

logger.log(Level.INFO, "Added the network view: {0} with model (network) {1} ", new Object[]{ networkView.getSUID(), addedNetwork.getSUID()});

}

The error is thrown in the line that registers the networkView to the networkViewManager object:

2021-05-04 11:31:36,850 [Task-Thread-3-Factory-0x174e86b4] ERROR org.cytoscape.application.userlog - Unexpected exception while handling listener: org.cytoscape.view.model.events.NetworkViewAddedListener