Examples with Task org.cytoscape.work.Task used on opensource projects

Example 1 with Task

use of org.cytoscape.work.Task in project EnrichmentMapApp by BaderLab.

the class SerialTestTaskManager method execute.

@Override
public void execute(TaskIterator iterator, TaskObserver observer) {
    TaskMonitor monitor = mock(TaskMonitor.class);
    FinishStatus finishStatus = null;
    Task task = null;
    try {
        while (iterator.hasNext()) {
            task = iterator.next();
            if (tasksToIgnore.contains(task.getClass())) {
                //System.out.println("Task Ignored: " + task.getClass());
                continue;
            }
            task.run(monitor);
            if (task instanceof ObservableTask && observer != null) {
                observer.taskFinished((ObservableTask) task);
            }
        }
        finishStatus = FinishStatus.getSucceeded();
    } catch (Exception e) {
        finishStatus = FinishStatus.newFailed(task, e);
        throw new AssertionError("Task failed", e);
    } finally {
        if (observer != null) {
            observer.allFinished(finishStatus);
        }
    }
}

Example 2 with Task

use of org.cytoscape.work.Task in project EnrichmentMapApp by BaderLab.

the class SerialTestTaskManager method execute.

@Override
public void execute(TaskIterator iterator, TaskObserver observer) {
    TaskMonitor monitor = new NullTaskMonitor();
    FinishStatus finishStatus = null;
    Task task = null;
    try {
        while (iterator.hasNext()) {
            task = iterator.next();
            if (tasksToIgnore.contains(task.getClass())) {
                //System.out.println("Task Ignored: " + task.getClass());
                continue;
            }
            task.run(monitor);
            if (task instanceof ObservableTask && observer != null) {
                observer.taskFinished((ObservableTask) task);
            }
        }
        finishStatus = FinishStatus.getSucceeded();
    } catch (Exception e) {
        finishStatus = FinishStatus.newFailed(task, e);
        throw new AssertionError("Task failed", e);
    } finally {
        if (observer != null) {
            observer.allFinished(finishStatus);
        }
    }
}

Example 3 with Task

use of org.cytoscape.work.Task in project EnrichmentMapApp by BaderLab.

the class CreateDiseaseSignatureTaskParallel method run.

@Override
public void run(TaskMonitor tm) throws InterruptedException {
    int cpus = Runtime.getRuntime().availableProcessors();
    ExecutorService executor = Executors.newFixedThreadPool(cpus);
    // Compare enrichment gene sets to signature gene sets
    Set<String> enrichmentGeneSetNames = getEnrichmentGeneSetNames();
    Map<String, GeneSet> signatureGeneSets = getSignatureGeneSets();
    handleDuplicateNames(enrichmentGeneSetNames, signatureGeneSets);
    Map<SimilarityKey, GenesetSimilarity> geneSetSimilarities = startBuildDiseaseSignatureParallel(tm, executor, enrichmentGeneSetNames, signatureGeneSets);
    // Support cancellation
    Timer timer = new Timer();
    timer.scheduleAtFixedRate(new TimerTask() {

        public void run() {
            if (cancelled) {
                executor.shutdownNow();
            }
        }
    }, 0, 1000);
    executor.shutdown();
    executor.awaitTermination(3, TimeUnit.HOURS);
    timer.cancel();
    // create the network here
    if (!cancelled) {
        Task networkTask = networkTaskFactory.create(map, params, signatureGeneSets, geneSetSimilarities);
        insertTasksAfterCurrentTask(networkTask);
    }
}

Example 4 with Task

use of org.cytoscape.work.Task in project EnrichmentMapApp by BaderLab.

the class CreateEMViewTask method visualizeMap.

private void visualizeMap() {
    CyNetwork network = networkManager.getNetwork(map.getNetworkID());
    CyNetworkView view = networkViewFactory.createNetworkView(network);
    networkViewManager.addNetworkView(view);
    //apply force directed layout
    CyLayoutAlgorithm layout = layoutManager.getLayout("force-directed");
    if (layout == null)
        layout = layoutManager.getDefaultLayout();
    Task styleTask = applyStyleTaskFactory.create(new EMStyleOptions(view, map), null, false);
    TaskIterator layoutTasks = layout.createTaskIterator(view, layout.createLayoutContext(), CyLayoutAlgorithm.ALL_NODE_VIEWS, null);
    TaskIterator moreTasks = new TaskIterator();
    moreTasks.append(styleTask);
    moreTasks.append(layoutTasks);
    insertTasksAfterCurrentTask(moreTasks);
}

Example 5 with Task

use of org.cytoscape.work.Task in project EnrichmentMapApp by BaderLab.

the class EdgeWidthDialog method createButtonPanel.

private JPanel createButtonPanel() {
    JButton restoreDefaultsButton = new JButton("Restore Defaults");
    restoreDefaultsButton.addActionListener(e -> {
        setTextFieldValues(EdgeWidthParams.defaultValues());
    });
    JButton cancelButton = new JButton(new AbstractAction("Cancel") {

        @Override
        public void actionPerformed(ActionEvent e) {
            dispose();
        }
    });
    JButton okButton = new JButton(new AbstractAction("OK") {

        @Override
        public void actionPerformed(ActionEvent e) {
            double emLowerWidth = ((Number) emLowerWidthText.getValue()).doubleValue();
            double emUpperWidth = ((Number) emUpperWidthText.getValue()).doubleValue();
            double lessThan100 = ((Number) lessThan100Text.getValue()).doubleValue();
            double lessThan10 = ((Number) lessThan10Text.getValue()).doubleValue();
            double greaterThan = ((Number) greaterThanText.getValue()).doubleValue();
            EdgeWidthParams params = new EdgeWidthParams(emLowerWidth, emUpperWidth, lessThan100, lessThan10, greaterThan);
            params.save(network);
            Task task = new Task() {

                public void run(TaskMonitor taskMonitor) throws Exception {
                    taskMonitor.setTitle("EnrichmentMap");
                    taskMonitor.setStatusMessage("Calculating Post-Analysis Edge Widths");
                    WidthFunction widthFunction = widthFunctionProvider.get();
                    widthFunction.setEdgeWidths(network, prefix, taskMonitor);
                }

                public void cancel() {
                }
            };
            taskManager.execute(new TaskIterator(task));
            dispose();
        }
    });
    JPanel bottomPanel = LookAndFeelUtil.createOkCancelPanel(okButton, cancelButton, restoreDefaultsButton);
    LookAndFeelUtil.setDefaultOkCancelKeyStrokes(getRootPane(), okButton.getAction(), cancelButton.getAction());
    getRootPane().setDefaultButton(okButton);
    return bottomPanel;
}