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

Example 11 with ObservableTask

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

the class AddRanksDialog method loadRanksAndClose.

private void loadRanksAndClose() {
    String rankFileName = ranksFileText.getText();
    String ranksName = getRanksName();
    EMDataSet dataset = getDataSet();
    RanksFileReaderTask task = new RanksFileReaderTask(rankFileName, dataset, ranksName, true);
    dialogTaskManager.execute(new TaskIterator(task), new TaskObserver() {

        @Override
        public void taskFinished(ObservableTask task) {
        }

        @Override
        public void allFinished(FinishStatus finishStatus) {
            resultRanksName = ranksName;
            dispose();
        }
    });
}

Example 12 with ObservableTask

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

the class ClusterRankingOption method computeRanking.

@Override
public CompletableFuture<Optional<Map<Integer, RankValue>>> computeRanking(Collection<Integer> genes) {
    if (genes.size() < 2) {
        // The HierarchicalClusterTask requires at least 2 genes
        return CompletableFuture.completedFuture(Optional.of(Collections.emptyMap()));
    }
    HierarchicalClusterTask task = new HierarchicalClusterTask(map, genes, distance.getMetric());
    CompletableFuture<Optional<Map<Integer, RankValue>>> future = new CompletableFuture<>();
    taskManager.execute(new TaskIterator(task), new TaskObserver() {

        @Override
        public void taskFinished(ObservableTask task) {
            if (task instanceof HierarchicalClusterTask) {
                HierarchicalClusterTask clusterTask = (HierarchicalClusterTask) task;
                Optional<Map<Integer, RankValue>> ranking = clusterTask.getActualResults();
                future.complete(ranking);
            }
        }

        @Override
        public void allFinished(FinishStatus finishStatus) {
            // Don't see why this would ever happen
            if (!future.isDone()) {
                future.completeExceptionally(new RuntimeException("Failed"));
            }
        }
    });
    return future;
}

Example 13 with ObservableTask

use of org.cytoscape.work.ObservableTask in project cytoscape-impl by cytoscape.

the class CommandTaskRunner method runTasks.

private void runTasks(String command, MessageHandler messageHandler) {
    CommandExecutorTaskFactory commandFactory = serviceRegistrar.getService(CommandExecutorTaskFactory.class);
    TaskIterator taskIterator = commandFactory.createTaskIterator(Arrays.asList(command), new TaskObserver() {

        @Override
        public void taskFinished(ObservableTask task) {
            Object result = task.getResults(String.class);
            if (result != null) {
                messageHandler.appendResult(result.toString());
            }
        }

        @Override
        public void allFinished(FinishStatus status) {
            messageHandler.appendCommand(status.getType().toString());
        }
    });
    while (taskIterator.hasNext()) {
        Task task = taskIterator.next();
        try {
            task.run(new TaskMonitor() {

                @Override
                public void showMessage(Level level, String message) {
                    switch(level) {
                        default:
                        case ERROR:
                            messageHandler.appendError(message);
                            break;
                        case INFO:
                            messageHandler.appendMessage(message);
                            break;
                        case WARN:
                            messageHandler.appendWarning(message);
                            break;
                    }
                }

                @Override
                public void setTitle(String title) {
                }

                @Override
                public void setStatusMessage(String statusMessage) {
                }

                @Override
                public void setProgress(double progress) {
                }
            });
        } catch (Exception e) {
            messageHandler.appendError("Error handling command \"" + e.getMessage());
        }
    }
}

Example 14 with ObservableTask

use of org.cytoscape.work.ObservableTask in project cytoscape-impl by cytoscape.

the class DelegateTask method run.

public void run(TaskMonitor tm) throws Exception {
    // this ensures that we get a coherent task monitor
    DelegatingTaskMonitor dtm = new DelegatingTaskMonitor(tm, ti.getNumTasks());
    // this gives the tunable mutator what it needs to set
    // the tunables as the tasks get executed
    stm.setConfigurationContext(tunableValues);
    while (ti.hasNext()) {
        final Task task = ti.next();
        dtm.setTask(task);
        if (!setTunables(task))
            return;
        currentTask = task;
        task.run(dtm);
        if (currentTask instanceof ObservableTask && observer != null) {
            observer.taskFinished((ObservableTask) currentTask);
        }
        currentTask = null;
    }
// We don't call allfinished() since we're delegating...
}

Example 15 with ObservableTask

use of org.cytoscape.work.ObservableTask in project cytoscape-impl by cytoscape.

the class ImportDefaultVisualStylesCommand method execute.

@Override
public void execute(final INotification notification) {
    final TaskIterator iterator = new TaskIterator(new ImportDefaultVizmapTask(servicesUtil));
    final DialogTaskManager taskManager = servicesUtil.get(DialogTaskManager.class);
    final VizMapperProxy proxy = (VizMapperProxy) getFacade().retrieveProxy(VizMapperProxy.NAME);
    proxy.setIgnoreStyleEvents(true);
    taskManager.execute(iterator, new TaskObserver() {

        @Override
        public void taskFinished(ObservableTask task) {
        }

        @Override
        public void allFinished(FinishStatus finishStatus) {
            proxy.setIgnoreStyleEvents(false);
            proxy.loadVisualStyles();
            proxy.setCurrentVisualStyle(servicesUtil.get(VisualMappingManager.class).getDefaultVisualStyle());
        }
    });
}