Examples with SerialTestTaskManager org.baderlab.csplugins.enrichmentmap.SerialTestTaskManager used on opensource projects

Example 1 with SerialTestTaskManager

use of org.baderlab.csplugins.enrichmentmap.SerialTestTaskManager in project EnrichmentMapApp by BaderLab.

the class BaseNetworkTest method buildEnrichmentMap.

protected void buildEnrichmentMap(EMCreationParameters params, DataSetFiles datasetFiles, Method method, String datasetName) {
    List<DataSetParameters> dataSets = Arrays.asList(new DataSetParameters(datasetName, method, datasetFiles));
    CreateEnrichmentMapTaskFactory taskFactory = masterMapTaskFactoryFactory.create(params, dataSets);
    TaskIterator taskIterator = taskFactory.createTaskIterator();
    // make sure the task iterator completes
    TaskObserver observer = new TaskObserver() {

        public void taskFinished(ObservableTask task) {
        }

        public void allFinished(FinishStatus finishStatus) {
            if (finishStatus == null)
                fail();
            if (finishStatus.getType() != FinishStatus.Type.SUCCEEDED)
                throw new AssertionError("TaskIterator Failed", finishStatus.getException());
        }
    };
    SerialTestTaskManager testTaskManager = new SerialTestTaskManager();
    testTaskManager.ignoreTask(CreateEMViewTask.class);
    testTaskManager.execute(taskIterator, observer);
}

Example 2 with SerialTestTaskManager

use of org.baderlab.csplugins.enrichmentmap.SerialTestTaskManager in project EnrichmentMapApp by BaderLab.

the class BaseNetworkTest method runPostAnalysis.

protected void runPostAnalysis(CyNetwork emNetwork, PostAnalysisParameters.Builder builder, String dataSetName) throws Exception {
    // Set up mocks
    when(applicationManager.getCurrentNetwork()).thenReturn(emNetwork);
    CyNetworkView networkViewMock = mock(CyNetworkView.class);
    when(applicationManager.getCurrentNetworkView()).thenReturn(networkViewMock);
    when(networkViewManager.getNetworkViews(emNetwork)).thenReturn(Arrays.asList(networkViewMock));
    @SuppressWarnings("unchecked") View<CyNode> nodeViewMock = Mockito.mock(View.class);
    when(networkViewMock.getNodeView(Matchers.<CyNode>anyObject())).thenReturn(nodeViewMock);
    when(nodeViewMock.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION)).thenReturn(Double.valueOf(0.0));
    EnrichmentMap map = emManager.getEnrichmentMap(emNetwork.getSUID());
    assertNotNull(map);
    // Load the gene-sets from the file
    SerialTestTaskManager testTaskManager = new SerialTestTaskManager();
    File file = new File(builder.getSignatureGMTFileName());
    LoadSignatureSetsActionListener loader = loadSignatureSetsActionListenerFactory.create(file, new FilterMetric.None(), map);
    loader.setTaskManager(testTaskManager);
    loader.setGeneSetCallback(builder::setLoadedGMTGeneSets);
    loader.setFilteredSignatureSetsCallback(builder::addSelectedGeneSetNames);
    loader.actionPerformed(null);
    PostAnalysisParameters paParams = builder.build();
    // Run post-analysis
    EMDataSet dataSet = map.getDataSet(dataSetName);
    CreateDiseaseSignatureTaskParallel signatureTask = buildDiseaseSignatureTaskFactory.create(paParams, map, Arrays.asList(dataSet));
    testTaskManager = new SerialTestTaskManager();
    testTaskManager.execute(new TaskIterator(signatureTask));
}