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

Example 11 with TaskIterator

use of org.cytoscape.work.TaskIterator in project cytoscape-api by cytoscape.

the class AbstractWebServiceClientTest method testCreateTaskIterator.

@Test
public void testCreateTaskIterator() {
    final TaskIterator itr = client.createTaskIterator(queryObject);
    assertNotNull(itr);
    assertFalse(itr.getNumTasks() == 0);
}

Example 12 with TaskIterator

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

the class BaseIntegrationTest method importNetworkFromFile.

protected CyNetwork importNetworkFromFile(String path, String fileName) throws IOException {
    Set<CyNetwork> existingNetworks = networkManager.getNetworkSet();
    // import the network
    File file = TestUtils.createTempFile(path, fileName);
    TaskIterator taskIterator = loadNetworkFileTaskFactory.createTaskIterator(file);
    SerialTestTaskManager taskManager = new SerialTestTaskManager();
    taskManager.execute(taskIterator);
    // get a reference to the imported network
    Set<CyNetwork> networksAfterImport = networkManager.getNetworkSet();
    networksAfterImport.removeAll(existingNetworks);
    assertEquals(1, networksAfterImport.size());
    return networksAfterImport.iterator().next();
}

Example 13 with TaskIterator

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

the class MasterDetailDialogPage method finish.

@Override
public void finish() {
    if (!validateInput())
        return;
    String prefix = legacySupport.getNextAttributePrefix();
    SimilarityMetric similarityMetric = cutoffPanel.getSimilarityMetric();
    double pvalue = cutoffPanel.getPValue();
    double qvalue = cutoffPanel.getQValue();
    NESFilter nesFilter = cutoffPanel.getNESFilter();
    double cutoff = cutoffPanel.getCutoff();
    double combined = cutoffPanel.getCombinedConstant();
    Optional<Integer> minExperiments = cutoffPanel.getMinimumExperiments();
    EMCreationParameters params = new EMCreationParameters(prefix, pvalue, qvalue, nesFilter, minExperiments, similarityMetric, cutoff, combined);
    params.setCreateDistinctEdges(distinctEdgesCheckbox.isSelected());
    List<DataSetParameters> dataSets = dataSetListModel.toList().stream().map(DataSetListItem::getDetailPanel).map(DetailPanel::createDataSetParameters).filter(x -> x != null).collect(Collectors.toList());
    // Overwrite all the expression files if the common file has been provided
    String exprPath = commonPanel.getExpressionFile();
    if (!isNullOrEmpty(exprPath)) {
        for (DataSetParameters dsp : dataSets) {
            dsp.getFiles().setExpressionFileName(exprPath);
        }
    }
    // Overwrite all the gmt files if a common file has been provided
    String gmtPath = commonPanel.getGmtFile();
    if (!isNullOrEmpty(gmtPath)) {
        for (DataSetParameters dsp : dataSets) {
            dsp.getFiles().setGMTFileName(gmtPath);
        }
    }
    CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(params, dataSets);
    TaskIterator tasks = taskFactory.createTaskIterator();
    // Close this dialog after the progress dialog finishes normally
    tasks.append(new AbstractTask() {

        public void run(TaskMonitor taskMonitor) {
            callback.close();
        }
    });
    dialogTaskManager.execute(tasks);
}

Example 14 with TaskIterator

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

the class MasterDetailDialogPage method scan.

private void scan() {
    Optional<File> rootFolder = fileBrowser.browseForRootFolder(jframeProvider.get());
    if (rootFolder.isPresent()) {
        scanButton.setEnabled(false);
        ResolverTask task = new ResolverTask(rootFolder.get());
        dialogTaskManager.execute(new TaskIterator(task), new TaskObserver() {

            @Override
            public void taskFinished(ObservableTask task) {
                @SuppressWarnings("unchecked") List<DataSetParameters> datasets = task.getResults(List.class);
                if (!datasets.isEmpty()) {
                    datasets.forEach(MasterDetailDialogPage.this::addDataSetToList);
                    dataSetList.setSelectedValue(datasets.get(0), true);
                }
            }

            @Override
            public void allFinished(FinishStatus finishStatus) {
                scanButton.setEnabled(true);
                updateButtonEnablement();
            }
        });
    }
}

Example 15 with TaskIterator

use of org.cytoscape.work.TaskIterator 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();
        }
    });
}