null pointer returned when accessing viewManager.getNodeView()

[M P]

Per title my view manager is returning null objects when requesting the View<> object equivalent of either CyNode or CyEdge. Here's my setup:

        network = networkFactory.createNetwork();
        network.getRow(network).set(CyNetwork.NAME, "Results");
       
        CyNetworkView view = viewFactory.createNetworkView(network);

        ...

        CyNode cy = network.addNode(); // Works
   
        network.getRow(cy).set(CyNetwork.NAME, name); // Works
        cynodes.put(name, cy); // Works
               
        View<CyNode> nodeDesign = view.getNodeView(cy); // nodeDesign is null!
        nodeDesign.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, Color.YELLOW); // null pointer exception thrown!

[Scooter Morris]

Hi M P,

   This sometimes happens as a result of Cytoscape's internal event mechanism.  See if explicitly calling flushPayloadEvents helps.  You'll need to get the CyEventHelper service first:

CyEventHelper helper = getService(CyEventHelper.class);

Then add:

helper.flushPayloadEvents();

right before your geNodeView(cy)...

-- scooter

[M P]

 This seemed to forever block a thread I was running from. I handle the calculations of a network in a worker thread and then invoke a callback function to display when the results are done. Here's my setup

// Callback from CyActivatorCalculationResponseThread.run()
    public void handleResults(Results results) {
        // Create a result model
        CyResultModel model = null; // Custom class that connects nodes to edges and modifies the visual of those nodes
       
        if(results != null) {
            CyNetworkViewFactory viewFactory = getService(bc, CyNetworkViewFactory.class);
            CyNetworkViewManager viewManager = getService(bc, CyNetworkViewManager.class);
            CyEventHelper helper             = getService(bc, CyEventHelper.class);
            helper.flushPayloadEvents(); // Adding this has blocked the thread as it never finishes
            model = new CyResultModel(networkFactory, viewFactory, viewManager, results);
           
            // add network to cytoscape
            CyNetworkManager networkManager = getService(bc, CyNetworkManager.class);

            // ========>> We never get here anymore!
            networkManager.addNetwork(model.getNetwork());
        }
       
        // Log status
        int numResults = 0;
        int numEvents = 0;
       
        if(results != null) {
            numResults = results.getResultCount();
           
            for(int i = 0; i < numResults; i++) {
                numEvents += results.getResult(i).getEventCount();
            }
        }
       
        this.AddLog("Returned " + numResults + " subnetworks, " + numEvents + " nodes\n");
   
        runButtonRef.setEnabled(true);;
        connectButtonRef.setEnabled(true);
        runButtonRef.setText(originalRunText);
    }

[M P]

bump

[M P]

hello still no help

[M P]

Scooter's offered solution blocks the thread it is called in. Is this a bug in cytoscape?

[David Otasek]

Have you tried running this on the Event Dispatch Thread using SwingUtilities.invokeLater()?

[M P]

No I have not. I've been using Future Tasks. I will try that and report back. Thank you so much for the lead. I felt like I was at a dead end.

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