Examples with CyServiceRegistrar org.cytoscape.service.util.CyServiceRegistrar used on opensource projects

Example 11 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.

the class MacCyActivator method start.

@Override
public void start(BundleContext context) throws Exception {
    final CyServiceRegistrar serviceRegistrar = getService(context, CyServiceRegistrar.class);
    final CyShutdown shutdown = getService(context, CyShutdown.class);
    final TaskFactory aboutTaskFactory = new HelpAboutTaskFactory(serviceRegistrar);
    final DialogTaskManager taskManager = getService(context, DialogTaskManager.class);
    final CyShutdownEvent[] lastShutdownEvent = new CyShutdownEvent[1];
    CyShutdownListener listener = (CyShutdownEvent e) -> {
        lastShutdownEvent[0] = e;
    };
    registerService(context, listener, CyShutdownListener.class, new Properties());
    Application application = Application.getApplication();
    application.setQuitHandler((QuitEvent event, QuitResponse response) -> {
        shutdown.exit(0);
        if (lastShutdownEvent[0] != null && !lastShutdownEvent[0].actuallyShutdown()) {
            response.cancelQuit();
        }
    });
    application.setAboutHandler((AboutEvent event) -> {
        taskManager.execute(aboutTaskFactory.createTaskIterator());
    });
}

Example 12 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.

the class CySubNetworkCyTableManagerTest method setUp.

@Before
public void setUp() {
    final CyEventHelper eh = new DummyCyEventHelper();
    final CyNetworkNaming namingUtil = mock(CyNetworkNaming.class);
    final CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    final EquationCompiler compiler = new EquationCompilerImpl(new EquationParserImpl(serviceRegistrar));
    final Interpreter interpreter = new InterpreterImpl();
    when(serviceRegistrar.getService(CyEventHelper.class)).thenReturn(eh);
    when(serviceRegistrar.getService(CyNetworkNaming.class)).thenReturn(namingUtil);
    when(serviceRegistrar.getService(EquationCompiler.class)).thenReturn(compiler);
    when(serviceRegistrar.getService(Interpreter.class)).thenReturn(interpreter);
    networkTableMgr = new CyNetworkTableManagerImpl();
    networkManager = new CyNetworkManagerImpl(serviceRegistrar);
    mgr = new CyTableManagerImpl(networkTableMgr, networkManager, serviceRegistrar);
    CyTableFactoryImpl tableFactory = new CyTableFactoryImpl(eh, serviceRegistrar);
    CyRootNetworkImpl baseNet = new CyRootNetworkImpl(eh, (CyTableManagerImpl) mgr, networkTableMgr, tableFactory, serviceRegistrar, true, SavePolicy.DO_NOT_SAVE);
    // This is a different subnetwork and not "baseNetwork" in ArrayGraph.
    goodNetwork = baseNet.addSubNetwork();
    globalTable = tableFactory.createTable("test table", CyIdentifiable.SUID, Long.class, true, true);
    networkManager.addNetwork(goodNetwork);
    assertNotNull(globalTable);
    assertNotNull(goodNetwork);
    assertEquals(1, networkManager.getNetworkSet().size());
}

Example 13 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.

the class CyActivator method start.

@Override
public void start(BundleContext bc) {
    final CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
    CommandTunableInterceptorImpl interceptor = new CommandTunableInterceptorImpl();
    StringTunableHandlerFactory<FileTunableHandler> fileTHF = new SimpleStringTunableHandlerFactory<>(FileTunableHandler.class, File.class);
    StringTunableHandlerFactory<IntTunableHandler> intTHF = new SimpleStringTunableHandlerFactory<>(IntTunableHandler.class, Integer.class, int.class);
    StringTunableHandlerFactory<DoubleTunableHandler> doubleTHF = new SimpleStringTunableHandlerFactory<>(DoubleTunableHandler.class, Double.class, double.class);
    StringTunableHandlerFactory<FloatTunableHandler> floatTHF = new SimpleStringTunableHandlerFactory<>(FloatTunableHandler.class, Float.class, float.class);
    StringTunableHandlerFactory<LongTunableHandler> longTHF = new SimpleStringTunableHandlerFactory<>(LongTunableHandler.class, Long.class, long.class);
    StringTunableHandlerFactory<BooleanTunableHandler> booleanTHF = new SimpleStringTunableHandlerFactory<>(BooleanTunableHandler.class, Boolean.class, boolean.class);
    StringTunableHandlerFactory<StringTunableHandlerImpl> stringTHF = new SimpleStringTunableHandlerFactory<>(StringTunableHandlerImpl.class, String.class);
    StringTunableHandlerFactory<BoundedIntTunableHandler> boundedIntTHF = new SimpleStringTunableHandlerFactory<>(BoundedIntTunableHandler.class, BoundedInteger.class);
    StringTunableHandlerFactory<BoundedDoubleTunableHandler> boundedDoubleTHF = new SimpleStringTunableHandlerFactory<>(BoundedDoubleTunableHandler.class, BoundedDouble.class);
    StringTunableHandlerFactory<BoundedFloatTunableHandler> boundedFloatTHF = new SimpleStringTunableHandlerFactory<>(BoundedFloatTunableHandler.class, BoundedFloat.class);
    StringTunableHandlerFactory<BoundedLongTunableHandler> boundedLongTHF = new SimpleStringTunableHandlerFactory<>(BoundedLongTunableHandler.class, BoundedLong.class);
    StringTunableHandlerFactory<URLTunableHandler> urlTHF = new SimpleStringTunableHandlerFactory<>(URLTunableHandler.class, URL.class);
    StringTunableHandlerFactory<ListSingleTunableHandler> listSingleTHF = new SimpleStringTunableHandlerFactory<>(ListSingleTunableHandler.class, ListSingleSelection.class);
    StringTunableHandlerFactory<ListMultipleTunableHandler> listMultipleTHF = new SimpleStringTunableHandlerFactory<>(ListMultipleTunableHandler.class, ListMultipleSelection.class);
    registerService(bc, fileTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, intTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, doubleTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, floatTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, longTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, booleanTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, stringTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, boundedIntTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, boundedDoubleTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, boundedFloatTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, boundedLongTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, urlTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, listSingleTHF, StringTunableHandlerFactory.class, new Properties());
    registerService(bc, listMultipleTHF, StringTunableHandlerFactory.class, new Properties());
    StringToModel stm = new StringToModelImpl(serviceRegistrar);
    registerService(bc, stm, StringToModel.class, new Properties());
    CyIdentifiableStringTunableHandlerFactory<CyNetworkTunableHandler> networkTHF = new CyIdentifiableStringTunableHandlerFactory<>(stm, CyNetworkTunableHandler.class, CyNetwork.class);
    registerService(bc, networkTHF, StringTunableHandlerFactory.class, new Properties());
    CyIdentifiableStringTunableHandlerFactory<CyNetworkViewTunableHandler> networkViewTHF = new CyIdentifiableStringTunableHandlerFactory<>(stm, CyNetworkViewTunableHandler.class, CyNetworkView.class);
    registerService(bc, networkViewTHF, StringTunableHandlerFactory.class, new Properties());
    CyIdentifiableStringTunableHandlerFactory<CyTableTunableHandler> tableTHF = new CyIdentifiableStringTunableHandlerFactory<>(stm, CyTableTunableHandler.class, CyTable.class);
    registerService(bc, tableTHF, StringTunableHandlerFactory.class, new Properties());
    CyIdentifiableStringTunableHandlerFactory<NodeListTunableHandler> nodeListTHF = new CyIdentifiableStringTunableHandlerFactory<>(stm, NodeListTunableHandler.class, NodeList.class);
    registerService(bc, nodeListTHF, StringTunableHandlerFactory.class, new Properties());
    CyIdentifiableStringTunableHandlerFactory<EdgeListTunableHandler> edgeListTHF = new CyIdentifiableStringTunableHandlerFactory<>(stm, EdgeListTunableHandler.class, EdgeList.class);
    registerService(bc, edgeListTHF, StringTunableHandlerFactory.class, new Properties());
    CyIdentifiableStringTunableHandlerFactory<RowListTunableHandler> rowListTHF = new CyIdentifiableStringTunableHandlerFactory<>(stm, RowListTunableHandler.class, RowList.class);
    registerService(bc, rowListTHF, StringTunableHandlerFactory.class, new Properties());
    BasicArgHandlerFactory argHandlerFactory = new BasicArgHandlerFactory();
    registerService(bc, argHandlerFactory, ArgHandlerFactory.class, new Properties());
    ArgRecorder argRec = new ArgRecorder();
    registerServiceListener(bc, argRec::addTunableHandlerFactory, argRec::removeTunableHandlerFactory, ArgHandlerFactory.class);
    AvailableCommandsImpl availableCommandsImpl = new AvailableCommandsImpl(argRec, serviceRegistrar);
    registerService(bc, availableCommandsImpl, AvailableCommands.class, new Properties());
    registerServiceListener(bc, availableCommandsImpl::addTaskFactory, availableCommandsImpl::removeTaskFactory, TaskFactory.class);
    registerServiceListener(bc, availableCommandsImpl::addNetworkTaskFactory, availableCommandsImpl::removeNetworkTaskFactory, NetworkTaskFactory.class);
    registerServiceListener(bc, availableCommandsImpl::addNetworkViewTaskFactory, availableCommandsImpl::removeNetworkViewTaskFactory, NetworkViewTaskFactory.class);
    registerServiceListener(bc, availableCommandsImpl::addNetworkViewCollectionTaskFactory, availableCommandsImpl::removeNetworkViewCollectionTaskFactory, NetworkViewCollectionTaskFactory.class);
    registerServiceListener(bc, availableCommandsImpl::addTableTaskFactory, availableCommandsImpl::removeTableTaskFactory, TableTaskFactory.class);
    CommandExecutorImpl commandExecutor = new CommandExecutorImpl(interceptor, availableCommandsImpl, serviceRegistrar);
    CommandExecutorTaskFactoryImpl commandExecutorTaskFactory = new CommandExecutorTaskFactoryImpl(commandExecutor, serviceRegistrar);
    Properties commandExecutorTaskFactoryProps = new Properties();
    commandExecutorTaskFactoryProps.setProperty(ID, "commandExecutorTaskFactory");
    registerService(bc, commandExecutorTaskFactory, TaskFactory.class, commandExecutorTaskFactoryProps);
    registerService(bc, commandExecutorTaskFactory, CommandExecutorTaskFactory.class, commandExecutorTaskFactoryProps);
    registerServiceListener(bc, commandExecutor::addTaskFactory, commandExecutor::removeTaskFactory, TaskFactory.class);
    registerServiceListener(bc, commandExecutor::addNetworkTaskFactory, commandExecutor::removeNetworkTaskFactory, NetworkTaskFactory.class);
    registerServiceListener(bc, commandExecutor::addNetworkViewTaskFactory, commandExecutor::removeNetworkViewTaskFactory, NetworkViewTaskFactory.class);
    registerServiceListener(bc, commandExecutor::addNetworkViewCollectionTaskFactory, commandExecutor::removeNetworkViewCollectionTaskFactory, NetworkViewCollectionTaskFactory.class);
    registerServiceListener(bc, commandExecutor::addTableTaskFactory, commandExecutor::removeTableTaskFactory, TableTaskFactory.class);
    registerServiceListener(bc, interceptor::addTunableHandlerFactory, interceptor::removeTunableHandlerFactory, StringTunableHandlerFactory.class);
    {
        Properties props = new Properties();
        props.setProperty(COMMAND, "sleep");
        props.setProperty(COMMAND_NAMESPACE, "command");
        props.setProperty(COMMAND_DESCRIPTION, "Stop command processing for a specified time");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "The **sleep** command will pause processing for a period of time as specified by *duration* seconds.");
        registerService(bc, new SleepCommandTaskFactory(), TaskFactory.class, props);
    }
    {
        Properties props = new Properties();
        props.setProperty(COMMAND, "echo");
        props.setProperty(COMMAND_NAMESPACE, "command");
        props.setProperty(COMMAND_DESCRIPTION, "Returns the value of the 'message' argument.");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Returns the value of the **message** argument.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "");
        registerService(bc, new EchoCommandTaskFactory(), TaskFactory.class, props);
    }
    {
        Properties props = new Properties();
        props.setProperty(COMMAND, "quit");
        props.setProperty(COMMAND_NAMESPACE, "command");
        props.setProperty(COMMAND_DESCRIPTION, "Exit Cytoscape");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "This command causes Cytoscape to exit. It is typically used at the end of a script file");
        registerService(bc, new QuitTaskFactory(serviceRegistrar), TaskFactory.class, props);
    }
    {
        Properties props = new Properties();
        props.setProperty(PREFERRED_MENU, "Tools");
        props.setProperty(TITLE, "Execute Command File...");
        props.setProperty(COMMAND, "run");
        props.setProperty(COMMAND_NAMESPACE, "command");
        props.setProperty(COMMAND_DESCRIPTION, "Run a series of commands from a file");
        props.setProperty(IN_MENU_BAR, "true");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "The **run** command will execute a command script from the " + "file pointed to by the ``file`` argument, which " + "should contain Cytoscape commands, one per line. " + "Arguments to the " + "script are provided by the *args* argument");
        registerService(bc, new RunCommandsTaskFactory(commandExecutorTaskFactory), TaskFactory.class, props);
    }
    // Get any command line arguments.  The "-S" and "-R" are ours
    AppsFinishedStartingListener scriptRunner = new AppsFinishedStartingListener() {

        public void handleEvent(AppsFinishedStartingEvent event) {
            @SuppressWarnings("unchecked") CyProperty<Properties> commandLineProps = getService(bc, CyProperty.class, "(cyPropertyName=commandline.props)");
            String scriptFile = commandLineProps.getProperties().getProperty("scriptFile");
            if (scriptFile != null) {
                TaskIterator tasks = commandExecutorTaskFactory.createTaskIterator(new File(scriptFile), null);
                SynchronousTaskManager<?> taskManager = serviceRegistrar.getService(SynchronousTaskManager.class);
                taskManager.execute(tasks);
            }
        }
    };
    registerService(bc, scriptRunner, AppsFinishedStartingListener.class, new Properties());
}

Example 14 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.

the class TestCyNetworkFactory method getPublicRootInstance.

public static CyRootNetwork getPublicRootInstance(DummyCyEventHelper deh, SavePolicy policy) {
    CyServiceRegistrar serviceRegistrar = mockCyServiceRegistrar(deh);
    final CyNetworkTableManagerImpl ntm = new CyNetworkTableManagerImpl();
    final CyTableManagerImpl tm = new CyTableManagerImpl(ntm, new CyNetworkManagerImpl(serviceRegistrar), serviceRegistrar);
    final CyTableFactoryImpl tableFactory = new CyTableFactoryImpl(deh, serviceRegistrar);
    return new CyRootNetworkImpl(deh, tm, ntm, tableFactory, serviceRegistrar, true, policy);
}

Example 15 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.

the class CyActivator method start.

public void start(BundleContext bc) {
    CyServiceRegistrar cyServiceRegistrarRef = getService(bc, CyServiceRegistrar.class);
    BookmarkReader bookmarksReader = new BookmarkReader("bookmarks", "bookmarks.xml");
    BookmarksUtilImpl bookmarksUtil = new BookmarksUtilImpl(cyServiceRegistrarRef);
    Properties bookmarksReaderProps = new Properties();
    bookmarksReaderProps.setProperty("cyPropertyName", "bookmarks");
    registerService(bc, bookmarksReader, CyProperty.class, bookmarksReaderProps);
    Properties bookmarksUtilProps = new Properties();
    registerService(bc, bookmarksUtil, BookmarksUtil.class, bookmarksUtilProps);
    PropsReader cyApplicationCoreProperty = new PropsReader(SimpleCyProperty.CORE_PROPRERTY_NAME, "cytoscape3.props");
    Properties cyApplicationCorePropertyProps = new Properties();
    cyApplicationCorePropertyProps.setProperty("cyPropertyName", "cytoscape3.props");
    registerAllServices(bc, cyApplicationCoreProperty, cyApplicationCorePropertyProps);
}