Examples with EnrichmentMapManager org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager used on opensource projects

Example 1 with EnrichmentMapManager

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

the class LegacySessionLoadTest method testSavingSession.

@Ignore
@SessionFile("em_session_2.2.cys")
public void testSavingSession() throws Exception {
    EnrichmentMapManager emManager = injector.getInstance(EnrichmentMapManager.class);
    Map<Long, EnrichmentMap> maps = emManager.getAllEnrichmentMaps();
    assertEquals(1, maps.size());
    SessionModelIO listener = injector.getInstance(SessionModelIO.class);
    listener.saveModel();
}

Example 2 with EnrichmentMapManager

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

the class LegacySessionLoadTest method getEnrichmentMap.

private EnrichmentMap getEnrichmentMap() {
    EnrichmentMapManager emManager = injector.getInstance(EnrichmentMapManager.class);
    Map<Long, EnrichmentMap> maps = emManager.getAllEnrichmentMaps();
    assertEquals(1, maps.size());
    EnrichmentMap map = maps.values().iterator().next();
    return map;
}

Example 3 with EnrichmentMapManager

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

the class LegacySessionLoadTest method resetManager.

@After
public void resetManager() {
    // Don't save the model on shutdown, we want to do that in a test
    EnrichmentMapManager emManager = injector.getInstance(EnrichmentMapManager.class);
    emManager.reset();
}

Example 4 with EnrichmentMapManager

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

the class CyActivator method start.

@Override
public void start(BundleContext bc) {
    injector = Guice.createInjector(new OSGiModule(bc), new AfterInjectionModule(), new CytoscapeServiceModule(), new ApplicationModule(), new CommandModule());
    // register the injector as an OSGi service so the integration tests can access it
    registerService(bc, injector, Injector.class, new Properties());
    // manager
    EnrichmentMapManager manager = injector.getInstance(EnrichmentMapManager.class);
    registerAllServices(bc, manager, new Properties());
    // session save and restore
    SessionListener sessionListener = injector.getInstance(SessionListener.class);
    registerAllServices(bc, sessionListener, new Properties());
    // commands
    registerCommand(bc, "build", injector.getInstance(Key.get(TaskFactory.class, BuildCommand.class)));
    registerCommand(bc, "gsea", injector.getInstance(Key.get(TaskFactory.class, GSEACommand.class)));
    registerCommand(bc, "mastermap", injector.getInstance(Key.get(TaskFactory.class, ResolveCommand.class)));
    registerCommand(bc, "pa", injector.getInstance(Key.get(TaskFactory.class, PACommand.class)));
    registerService(bc, new MannWhitRanksTunableHandlerFactory(), StringTunableHandlerFactory.class, new Properties());
    // Don't load UI services if running headless
    boolean headless = injector.getInstance(Key.get(Boolean.class, Headless.class));
    if (!headless) {
        // register actions
        registerAllServices(bc, injector.getInstance(OpenEnrichmentMapAction.class), new Properties());
        // chart listener
        ChartFactoryManager chartFactoryManager = injector.getInstance(ChartFactoryManager.class);
        registerServiceListener(bc, chartFactoryManager, "addFactory", "removeFactory", CyCustomGraphics2Factory.class);
        // chart factories
        final Properties chartProps = new Properties();
        chartProps.setProperty(CyCustomGraphics2Factory.GROUP, "Charts");
        RadialHeatMapChartFactory radialHeatMapChartFactory = injector.getInstance(RadialHeatMapChartFactory.class);
        registerService(bc, radialHeatMapChartFactory, CyCustomGraphics2Factory.class, chartProps);
        // UI Mediators
        ControlPanelMediator controlPanelMediator = injector.getInstance(ControlPanelMediator.class);
        registerAllServices(bc, controlPanelMediator, new Properties());
        HeatMapMediator expressionViewerMediator = injector.getInstance(HeatMapMediator.class);
        registerAllServices(bc, expressionViewerMediator, new Properties());
    }
    // If the App is updated or restarted then we want to reload the model and view from the tables
    sessionListener.restore(null);
    Em21Handler.removeVersion21(bc, injector.getInstance(CyApplicationConfiguration.class));
}