Examples with AppsFinishedStartingEvent org.cytoscape.app.event.AppsFinishedStartingEvent used on opensource projects

Example 1 with AppsFinishedStartingEvent

use of org.cytoscape.app.event.AppsFinishedStartingEvent 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 2 with AppsFinishedStartingEvent

use of org.cytoscape.app.event.AppsFinishedStartingEvent in project cytoscape-impl by cytoscape.

the class AppManager method initializeApps.

void initializeApps() {
    // Move apps from install-on-restart directory to install directory
    Set<App> installOnRestartApps = obtainAppsFromDirectory(new File(getInstallOnRestartAppsPath()), false);
    for (App app : installOnRestartApps) {
        try {
            app.moveAppFile(this, new File(getInstalledAppsPath()));
            userLogger.info("Moved app '" + app.getAppName() + "' that was marked for install on restart to the 'installed' directory.");
        } catch (IOException e) {
            userLogger.error("Cannot move app '" + app.getAppName() + "' that was marked for install on restart to the 'installed' directory:", e);
        }
    }
    // Remove the install-on-restart directory after apps were moved
    try {
        FileUtils.deleteDirectory(new File(getInstallOnRestartAppsPath()));
    } catch (IOException e) {
        userLogger.warn("Could not delete the directory of apps to install on restart:", e);
    }
    setupAlterationMonitor();
    // Obtain previously disabled, installed apps
    Set<App> disabledApps = obtainAppsFromDirectory(new File(getDisabledAppsPath()), false);
    for (App app : disabledApps) {
        try {
            boolean appRegistered = false;
            for (App regApp : apps) {
                if (regApp.heuristicEquals(app)) {
                    userLogger.warn("Disabled app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' is equal to an already registered app '" + regApp.getAppName() + "' in file '" + (regApp.getAppFile() == null ? "N/A" : regApp.getAppFile().getAbsolutePath()) + "'");
                    appRegistered = true;
                }
            }
            if (!appRegistered) {
                apps.add(app);
                app.setStatus(AppStatus.DISABLED);
            } else {
                // Delete the copy
                userLogger.info("Trying to delete the disabled copy of app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' because another copy exists.");
                FileUtils.deleteQuietly(app.getAppFile());
                app.setAppFile(null);
            }
        } catch (Throwable e) {
            userLogger.error("Error validating status of the disabled app '" + app.getAppName() + "'.", e);
        }
    }
    Set<App> uninstalledApps = obtainAppsFromDirectory(new File(getUninstalledAppsPath()), false);
    for (App app : uninstalledApps) {
        try {
            boolean appRegistered = false;
            for (App regApp : apps) {
                if (regApp.heuristicEquals(app)) {
                    userLogger.warn("Uninstalled app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' is equal to an already registered app '" + regApp.getAppName() + "' in file '" + (regApp.getAppFile() == null ? "N/A" : regApp.getAppFile().getAbsolutePath()) + "'");
                    appRegistered = true;
                }
            }
            if (!appRegistered) {
                apps.add(app);
                app.setStatus(AppStatus.UNINSTALLED);
            } else {
                // Delete the copy
                userLogger.info("Trying to delete the uninstalled copy of app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' because another copy exists.");
                FileUtils.deleteQuietly(app.getAppFile());
                app.setAppFile(null);
            }
        } catch (Throwable e) {
            userLogger.error("Error validating status of the uninstalled app '" + app.getAppName() + "'.", e);
        }
    }
    Set<App> installedApps = obtainAppsFromDirectory(getBundledAppsPath(), true);
    installedApps.addAll(obtainAppsFromDirectory(new File(getInstalledAppsPath()), false));
    Map<String, App> appsToStart = new HashMap<String, App>();
    for (App app : installedApps) {
        boolean appRegistered = false;
        for (App regApp : apps) {
            if (regApp.heuristicEquals(app)) {
                userLogger.warn("Installed app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' is equal to an already registered app '" + regApp.getAppName() + "' in file '" + (regApp.getAppFile() == null ? "N/A" : regApp.getAppFile().getAbsolutePath()) + "'");
                appRegistered = true;
            }
        }
        if (!appRegistered) {
            apps.add(app);
            String appName = app.getAppName().toLowerCase();
            App currentVersion = appsToStart.get(appName);
            if (app.isCompatible(version)) {
                if (currentVersion == null) {
                    appsToStart.put(appName, app);
                } else if (compareApps(currentVersion, app) > 0) {
                    userLogger.warn("Installed app '" + app.getAppName() + "' version  " + app.getVersion() + " will override an older version (" + currentVersion.getVersion() + ") that was registered previously.");
                    appsToStart.put(appName, app);
                } else {
                    userLogger.warn("Installed app '" + app.getAppName() + "' version " + app.getVersion() + " will not be started, because a newer version (" + currentVersion.getVersion() + ") was already registered.");
                }
            } else {
                userLogger.error("Installed app '" + app.getAppName() + "' is not compatible with the running version of Cytoscape (" + version.getVersion() + ").");
            }
        } else {
            // Delete the copy
            userLogger.info("Trying to delete the installed copy of app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' because another copy exists.");
            FileUtils.deleteQuietly(app.getAppFile());
            app.setAppFile(null);
        }
    }
    Set<App> coreAppsToStart = new HashSet<App>();
    App coreAppsMetaApp = appsToStart.get("core apps");
    if (coreAppsMetaApp != null && coreAppsMetaApp.getDependencies() != null) {
        for (App.Dependency dep : coreAppsMetaApp.getDependencies()) {
            String appName = dep.getName().toLowerCase();
            App app = appsToStart.get(appName);
            if (app != null) {
                coreAppsToStart.add(app);
            }
        }
        coreAppsToStart.add(coreAppsMetaApp);
    }
    if (!startApps(coreAppsToStart))
        userLogger.warn("One or more core apps failed to load or start");
    eventHelper.fireEvent(new CyStartEvent(this));
    Set<App> otherAppsToStart = new HashSet<App>(appsToStart.values());
    otherAppsToStart.removeAll(coreAppsToStart);
    if (!startApps(otherAppsToStart))
        userLogger.warn("One or more apps failed to load or start");
    eventHelper.fireEvent(new AppsFinishedStartingEvent(this));
}