Examples with FileUtil org.cytoscape.util.swing.FileUtil used on opensource projects

Example 1 with FileUtil

use of org.cytoscape.util.swing.FileUtil in project cytoscape-impl by cytoscape.

the class DataSourceSelectDialog method browseButtonActionPerformed.

private void browseButtonActionPerformed(ActionEvent evt) {
    File file = null;
    final FileUtil fileUtil = serviceRegistrar.getService(FileUtil.class);
    if (sourceType == ONTOLOGY_TYPE) {
        final FileChooserFilter filter = new FileChooserFilter("OBO File", "obo");
        List<FileChooserFilter> filterCollection = new ArrayList<FileChooserFilter>(1);
        filterCollection.add(filter);
        file = fileUtil.getFile(this.getParent(), "Select OBO Source File", FileUtil.LOAD, filterCollection);
    } else {
        // Currently, there is no pre-defined extension for this file type.
        final List<FileChooserFilter> filterCollection = new ArrayList<FileChooserFilter>();
        file = fileUtil.getFile(this.getParent(), "Select Gene Annotation Source File", FileUtil.LOAD, filterCollection);
    }
    if (file == null)
        return;
    sourceFileName = file.getName();
    if (sourceType == ONTOLOGY_TYPE) {
        ontologyNameTextField.setText("Local Ontology File: " + sourceFileName);
    } else {
        ontologyNameTextField.setText("Local Annotation File: " + sourceFileName);
    }
    try {
        dataSourceTextField.setText(file.toURI().toURL().toString());
    } catch (MalformedURLException e) {
        e.printStackTrace();
    }
    this.toFront();
}

Example 2 with FileUtil

use of org.cytoscape.util.swing.FileUtil in project cytoscape-impl by cytoscape.

the class SessionHandler method handleEvent.

@Override
public void handleEvent(final CyShutdownEvent e) {
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    // If there are no networks, just quit.
    if (netMgr.getNetworkSet().isEmpty() || e.forceShutdown())
        return;
    // Ask user whether to save current session or not.
    final String msg = "Do you want to save your session?";
    final String header = "Save Networks Before Quitting?";
    final Object[] options = { "Yes, save and quit", "No, just quit", "Cancel" };
    final int n = JOptionPane.showOptionDialog(desktop.getJFrame(), msg, header, JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE, null, options, options[0]);
    if (n == JOptionPane.NO_OPTION) {
        return;
    } else if (n == JOptionPane.YES_OPTION) {
        final CySessionManager sessionMgr = serviceRegistrar.getService(CySessionManager.class);
        final String sessionFileName = sessionMgr.getCurrentSessionFileName();
        final File file;
        if (sessionFileName == null || sessionFileName.isEmpty()) {
            FileChooserFilter filter = new FileChooserFilter("Session File", "cys");
            List<FileChooserFilter> filterCollection = new ArrayList<FileChooserFilter>(1);
            filterCollection.add(filter);
            final FileUtil fileUtil = serviceRegistrar.getService(FileUtil.class);
            file = fileUtil.getFile(desktop, "Save Session File", FileUtil.SAVE, filterCollection);
        } else {
            file = new File(sessionFileName);
        }
        if (file == null) {
            // just check the file again in case the file chooser dialoge task is canceled.
            e.abortShutdown("User canceled the shutdown request.");
            return;
        }
        final SynchronousTaskManager<?> syncTaskMgr = serviceRegistrar.getService(SynchronousTaskManager.class);
        final SaveSessionAsTaskFactory saveTaskFactory = serviceRegistrar.getService(SaveSessionAsTaskFactory.class);
        syncTaskMgr.execute(saveTaskFactory.createTaskIterator(file));
        return;
    } else {
        e.abortShutdown("User canceled the shutdown request.");
        return;
    }
}

Example 3 with FileUtil

use of org.cytoscape.util.swing.FileUtil in project cytoscape-impl by cytoscape.

the class CyActivator method start.

@Override
public void start(BundleContext bc) {
    CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
    CyApplicationConfiguration cyApplicationConfigurationRef = getService(bc, CyApplicationConfiguration.class);
    CyApplicationManager cyApplicationManagerRef = getService(bc, CyApplicationManager.class);
    CyEventHelper cyEventHelperRef = getService(bc, CyEventHelper.class);
    CyGroupAggregationManager cyGroupAggregationManagerRef = getService(bc, CyGroupAggregationManager.class);
    CyGroupFactory cyGroupFactoryRef = getService(bc, CyGroupFactory.class);
    CyGroupManager cyGroupManagerRef = getService(bc, CyGroupManager.class);
    CyLayoutAlgorithmManager cyLayoutAlgorithmManagerRef = getService(bc, CyLayoutAlgorithmManager.class);
    CyNetworkFactory cyNetworkFactoryRef = getService(bc, CyNetworkFactory.class);
    CyNetworkManager cyNetworkManagerRef = getService(bc, CyNetworkManager.class);
    CyNetworkViewFactory cyNetworkViewFactoryRef = getService(bc, CyNetworkViewFactory.class);
    CyNetworkViewManager cyNetworkViewManagerRef = getService(bc, CyNetworkViewManager.class);
    CyNetworkReaderManager cyNetworkViewReaderManagerRef = getService(bc, CyNetworkReaderManager.class);
    CyNetworkViewWriterManager cyNetworkViewWriterManagerRef = getService(bc, CyNetworkViewWriterManager.class);
    CyProperty<Properties> cyPropertyRef = getService(bc, CyProperty.class, "(cyPropertyName=cytoscape3.props)");
    CyPropertyReaderManager cyPropertyReaderManagerRef = getService(bc, CyPropertyReaderManager.class);
    CyPropertyWriterManager cyPropertyWriterManagerRef = getService(bc, CyPropertyWriterManager.class);
    CyRootNetworkManager cyRootNetworkFactoryRef = getService(bc, CyRootNetworkManager.class);
    CySessionManager cySessionManagerRef = getService(bc, CySessionManager.class);
    CySessionReaderManager cySessionReaderManagerRef = getService(bc, CySessionReaderManager.class);
    CySessionWriterManager cySessionWriterManagerRef = getService(bc, CySessionWriterManager.class);
    CySwingApplication cySwingApplicationRef = getService(bc, CySwingApplication.class);
    CyTableFactory cyTableFactoryRef = getService(bc, CyTableFactory.class);
    CyTableManager cyTableManagerRef = getService(bc, CyTableManager.class);
    CyTableReaderManager cyTableReaderManagerRef = getService(bc, CyTableReaderManager.class);
    CyTableWriterManager cyTableWriterManagerRef = getService(bc, CyTableWriterManager.class);
    PanelTaskManager panelTaskManagerRef = getService(bc, PanelTaskManager.class);
    DialogTaskManager dialogTaskManagerRef = getService(bc, DialogTaskManager.class);
    PresentationWriterManager presentationWriterManagerRef = getService(bc, PresentationWriterManager.class);
    RenderingEngineManager renderingEngineManagerRef = getService(bc, RenderingEngineManager.class);
    TaskManager taskManagerRef = getService(bc, TaskManager.class);
    UndoSupport undoSupportRef = getService(bc, UndoSupport.class);
    TunablePropertySerializerFactory tunablePropertySerializerFactoryRef = getService(bc, TunablePropertySerializerFactory.class);
    VisualMappingManager visualMappingManagerRef = getService(bc, VisualMappingManager.class);
    VisualStyleFactory visualStyleFactoryRef = getService(bc, VisualStyleFactory.class);
    CyVersion cytoscapeVersionService = getService(bc, CyVersion.class);
    CyApplicationConfiguration cyApplicationConfigurationServiceRef = getService(bc, CyApplicationConfiguration.class);
    VisualMappingFunctionFactory vmfFactoryC = getService(bc, VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
    VisualMappingFunctionFactory vmfFactoryD = getService(bc, VisualMappingFunctionFactory.class, "(mapping.type=discrete)");
    VisualMappingFunctionFactory vmfFactoryP = getService(bc, VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");
    DataSourceManager dataSourceManager = getService(bc, DataSourceManager.class);
    // Start of core-task services
    LoadVizmapFileTaskFactory loadVizmapFileTaskFactory = getService(bc, LoadVizmapFileTaskFactory.class);
    LoadNetworkFileTaskFactory loadNetworkFileTaskFactory = getService(bc, LoadNetworkFileTaskFactory.class);
    LoadNetworkURLTaskFactory loadNetworkURLTaskFactory = getService(bc, LoadNetworkURLTaskFactory.class);
    DeleteSelectedNodesAndEdgesTaskFactory deleteSelectedNodesAndEdgesTaskFactory = getService(bc, DeleteSelectedNodesAndEdgesTaskFactory.class);
    SelectAllTaskFactory selectAllTaskFactory = getService(bc, SelectAllTaskFactory.class);
    SelectAllEdgesTaskFactory selectAllEdgesTaskFactory = getService(bc, SelectAllEdgesTaskFactory.class);
    SelectAllNodesTaskFactory selectAllNodesTaskFactory = getService(bc, SelectAllNodesTaskFactory.class);
    SelectAdjacentEdgesTaskFactory selectAdjacentEdgesTaskFactory = getService(bc, SelectAdjacentEdgesTaskFactory.class);
    SelectConnectedNodesTaskFactory selectConnectedNodesTaskFactory = getService(bc, SelectConnectedNodesTaskFactory.class);
    SelectFirstNeighborsTaskFactory selectFirstNeighborsTaskFactory = getService(bc, SelectFirstNeighborsTaskFactory.class, "(title=Undirected)");
    SelectFirstNeighborsTaskFactory selectFirstNeighborsTaskFactoryInEdge = getService(bc, SelectFirstNeighborsTaskFactory.class, "(title=Directed: Incoming)");
    SelectFirstNeighborsTaskFactory selectFirstNeighborsTaskFactoryOutEdge = getService(bc, SelectFirstNeighborsTaskFactory.class, "(title=Directed: Outgoing)");
    DeselectAllTaskFactory deselectAllTaskFactory = getService(bc, DeselectAllTaskFactory.class);
    DeselectAllEdgesTaskFactory deselectAllEdgesTaskFactory = getService(bc, DeselectAllEdgesTaskFactory.class);
    DeselectAllNodesTaskFactory deselectAllNodesTaskFactory = getService(bc, DeselectAllNodesTaskFactory.class);
    InvertSelectedEdgesTaskFactory invertSelectedEdgesTaskFactory = getService(bc, InvertSelectedEdgesTaskFactory.class);
    InvertSelectedNodesTaskFactory invertSelectedNodesTaskFactory = getService(bc, InvertSelectedNodesTaskFactory.class);
    SelectFromFileListTaskFactory selectFromFileListTaskFactory = getService(bc, SelectFromFileListTaskFactory.class);
    SelectFirstNeighborsNodeViewTaskFactory selectFirstNeighborsNodeViewTaskFactory = getService(bc, SelectFirstNeighborsNodeViewTaskFactory.class);
    HideSelectedTaskFactory hideSelectedTaskFactory = getService(bc, HideSelectedTaskFactory.class);
    HideSelectedNodesTaskFactory hideSelectedNodesTaskFactory = getService(bc, HideSelectedNodesTaskFactory.class);
    HideSelectedEdgesTaskFactory hideSelectedEdgesTaskFactory = getService(bc, HideSelectedEdgesTaskFactory.class);
    UnHideAllTaskFactory unHideAllTaskFactory = getService(bc, UnHideAllTaskFactory.class);
    UnHideAllNodesTaskFactory unHideAllNodesTaskFactory = getService(bc, UnHideAllNodesTaskFactory.class);
    UnHideAllEdgesTaskFactory unHideAllEdgesTaskFactory = getService(bc, UnHideAllEdgesTaskFactory.class);
    NewEmptyNetworkViewFactory newEmptyNetworkTaskFactory = getService(bc, NewEmptyNetworkViewFactory.class);
    CloneNetworkTaskFactory cloneNetworkTaskFactory = getService(bc, CloneNetworkTaskFactory.class);
    NewNetworkSelectedNodesAndEdgesTaskFactory newNetworkSelectedNodesEdgesTaskFactory = getService(bc, NewNetworkSelectedNodesAndEdgesTaskFactory.class);
    NewNetworkSelectedNodesOnlyTaskFactory newNetworkSelectedNodesOnlyTaskFactory = getService(bc, NewNetworkSelectedNodesOnlyTaskFactory.class);
    DestroyNetworkTaskFactory destroyNetworkTaskFactory = getService(bc, DestroyNetworkTaskFactory.class);
    DestroyNetworkViewTaskFactory destroyNetworkViewTaskFactory = getService(bc, DestroyNetworkViewTaskFactory.class);
    NewSessionTaskFactory newSessionTaskFactory = getService(bc, NewSessionTaskFactory.class);
    OpenSessionTaskFactory openSessionTaskFactory = getService(bc, OpenSessionTaskFactory.class);
    SaveSessionAsTaskFactory saveSessionAsTaskFactory = getService(bc, SaveSessionAsTaskFactory.class);
    EditNetworkTitleTaskFactory editNetworkTitleTaskFactory = getService(bc, EditNetworkTitleTaskFactory.class);
    CreateNetworkViewTaskFactory createNetworkViewTaskFactory = getService(bc, CreateNetworkViewTaskFactory.class);
    ExportNetworkImageTaskFactory exportNetworkImageTaskFactory = getService(bc, ExportNetworkImageTaskFactory.class);
    ExportNetworkViewTaskFactory exportNetworkViewTaskFactory = getService(bc, ExportNetworkViewTaskFactory.class);
    ExportSelectedTableTaskFactory exportSelectedTableTaskFactory = getService(bc, ExportSelectedTableTaskFactory.class);
    ExportTableTaskFactory exportTableTaskFactory = getService(bc, ExportTableTaskFactory.class);
    ApplyPreferredLayoutTaskFactory applyPreferredLayoutTaskFactory = getService(bc, ApplyPreferredLayoutTaskFactory.class);
    DeleteColumnTaskFactory deleteColumnTaskFactory = getService(bc, DeleteColumnTaskFactory.class);
    RenameColumnTaskFactory renameColumnTaskFactory = getService(bc, RenameColumnTaskFactory.class);
    DeleteTableTaskFactory deleteTableTaskFactory = getService(bc, DeleteTableTaskFactory.class);
    ExportVizmapTaskFactory exportVizmapTaskFactory = getService(bc, ExportVizmapTaskFactory.class);
    ConnectSelectedNodesTaskFactory connectSelectedNodesTaskFactory = getService(bc, ConnectSelectedNodesTaskFactory.class);
    MapGlobalToLocalTableTaskFactory mapGlobal = getService(bc, MapGlobalToLocalTableTaskFactory.class);
    ApplyVisualStyleTaskFactory applyVisualStyleTaskFactory = getService(bc, ApplyVisualStyleTaskFactory.class);
    MapTableToNetworkTablesTaskFactory mapNetworkAttrTaskFactory = getService(bc, MapTableToNetworkTablesTaskFactory.class);
    GroupNodesTaskFactory groupNodesTaskFactory = getService(bc, GroupNodesTaskFactory.class);
    UnGroupTaskFactory unGroupTaskFactory = getService(bc, UnGroupTaskFactory.class);
    CollapseGroupTaskFactory collapseGroupTaskFactory = getService(bc, CollapseGroupTaskFactory.class);
    ExpandGroupTaskFactory expandGroupTaskFactory = getService(bc, ExpandGroupTaskFactory.class);
    UnGroupNodesTaskFactory unGroupNodesTaskFactory = getService(bc, UnGroupNodesTaskFactory.class);
    // End of core-task services
    // Command execution services
    CommandExecutorTaskFactory cyCommandExecutorTaskFactory = getService(bc, CommandExecutorTaskFactory.class);
    AvailableCommands availableCommands = getService(bc, AvailableCommands.class);
    StreamUtil streamUtilServiceRef = getService(bc, StreamUtil.class);
    FileUtil fileUtilServiceRef = getService(bc, FileUtil.class);
    CySwingAppAdapter cyAppAdapter = new CyAppAdapterImpl(cyApplicationConfigurationRef, cyApplicationManagerRef, cyEventHelperRef, cyGroupAggregationManagerRef, cyGroupFactoryRef, cyGroupManagerRef, cyLayoutAlgorithmManagerRef, cyNetworkFactoryRef, cyNetworkManagerRef, cyNetworkViewFactoryRef, cyNetworkViewManagerRef, cyNetworkViewReaderManagerRef, cyNetworkViewWriterManagerRef, cyPropertyRef, cyPropertyReaderManagerRef, cyPropertyWriterManagerRef, cyRootNetworkFactoryRef, serviceRegistrar, cySessionManagerRef, cySessionReaderManagerRef, cySessionWriterManagerRef, cySwingApplicationRef, cyTableFactoryRef, cyTableManagerRef, cyTableReaderManagerRef, cyTableWriterManagerRef, cytoscapeVersionService, dialogTaskManagerRef, panelTaskManagerRef, presentationWriterManagerRef, renderingEngineManagerRef, taskManagerRef, undoSupportRef, tunablePropertySerializerFactoryRef, vmfFactoryC, vmfFactoryD, vmfFactoryP, visualMappingManagerRef, visualStyleFactoryRef, dataSourceManager, // from core-task-api
    loadVizmapFileTaskFactory, loadNetworkFileTaskFactory, loadNetworkURLTaskFactory, deleteSelectedNodesAndEdgesTaskFactory, selectAllTaskFactory, selectAllEdgesTaskFactory, selectAllNodesTaskFactory, selectAdjacentEdgesTaskFactory, selectConnectedNodesTaskFactory, selectFirstNeighborsTaskFactory, selectFirstNeighborsTaskFactoryInEdge, selectFirstNeighborsTaskFactoryOutEdge, deselectAllTaskFactory, deselectAllEdgesTaskFactory, deselectAllNodesTaskFactory, invertSelectedEdgesTaskFactory, invertSelectedNodesTaskFactory, selectFromFileListTaskFactory, selectFirstNeighborsNodeViewTaskFactory, hideSelectedTaskFactory, hideSelectedNodesTaskFactory, hideSelectedEdgesTaskFactory, unHideAllTaskFactory, unHideAllNodesTaskFactory, unHideAllEdgesTaskFactory, newEmptyNetworkTaskFactory, cloneNetworkTaskFactory, newNetworkSelectedNodesEdgesTaskFactory, newNetworkSelectedNodesOnlyTaskFactory, destroyNetworkTaskFactory, destroyNetworkViewTaskFactory, newSessionTaskFactory, openSessionTaskFactory, saveSessionAsTaskFactory, editNetworkTitleTaskFactory, createNetworkViewTaskFactory, exportNetworkImageTaskFactory, exportNetworkViewTaskFactory, exportSelectedTableTaskFactory, exportTableTaskFactory, applyPreferredLayoutTaskFactory, deleteColumnTaskFactory, renameColumnTaskFactory, deleteTableTaskFactory, exportVizmapTaskFactory, connectSelectedNodesTaskFactory, mapGlobal, applyVisualStyleTaskFactory, mapNetworkAttrTaskFactory, groupNodesTaskFactory, unGroupTaskFactory, collapseGroupTaskFactory, expandGroupTaskFactory, unGroupNodesTaskFactory, cyCommandExecutorTaskFactory, availableCommands);
    registerService(bc, cyAppAdapter, CyAppAdapter.class);
    registerService(bc, cyAppAdapter, CySwingAppAdapter.class);
    WebQuerier webQuerier = new WebQuerier(streamUtilServiceRef, cytoscapeVersionService);
    registerService(bc, webQuerier, WebQuerier.class);
    StartLevel startLevel = getService(bc, StartLevel.class);
    // Instantiate new manager
    final AppManager appManager = new AppManager(cyAppAdapter, cyApplicationConfigurationServiceRef, cytoscapeVersionService, cyEventHelperRef, webQuerier, startLevel, bc);
    registerService(bc, appManager, AppManager.class);
    bc.addFrameworkListener(appManager);
    final DownloadSitesManager downloadSitesManager = new DownloadSitesManager(cyPropertyRef);
    final UpdateManager updateManager = new UpdateManager(appManager, downloadSitesManager);
    registerService(bc, updateManager, AppsFinishedStartingListener.class);
    final AppConflictHandlerFactory appConflictHandlerFactory = new AppConflictHandlerFactory();
    registerService(bc, appConflictHandlerFactory, GUITunableHandlerFactory.class);
    // AbstractCyAction implementation for updated app manager
    AppManagerAction appManagerAction = new AppManagerAction(appManager, downloadSitesManager, updateManager, cySwingApplicationRef, fileUtilServiceRef, dialogTaskManagerRef, serviceRegistrar);
    registerService(bc, appManagerAction, CyAction.class);
    // Show citations dialog
    final CitationsAction citationsAction = new CitationsAction(webQuerier, appManager, serviceRegistrar);
    registerService(bc, citationsAction, CyAction.class);
    // Start local server that reports app installation status to the app store when requested,
    // also able to install an app when told by the app store
    final AppGetResponder appGetResponder = new AppGetResponder(appManager, cytoscapeVersionService);
    final CyHttpd httpd = (new CyHttpdFactoryImpl()).createHttpd(new LocalhostServerSocketFactory(2607));
    httpd.addBeforeResponse(new ScreenOriginsBeforeResponse(WebQuerier.DEFAULT_APP_STORE_URL));
    httpd.addBeforeResponse(new OriginOptionsBeforeResponse("x-csrftoken"));
    httpd.addAfterResponse(new AddAllowOriginHeader());
    httpd.addResponder(appGetResponder.new StatusResponder());
    httpd.addResponder(appGetResponder.new InstallResponder());
    httpd.start();
    // Special case: handle yFiles app options
    final OpenBrowser openBrowser = getService(bc, OpenBrowser.class);
    YFilesChecker checker = new YFilesChecker(appManager, serviceRegistrar, openBrowser);
    bc.addBundleListener(checker);
    registerAllServices(bc, checker, new Properties());
    {
        AppStoreTaskFactory factory = new AppStoreTaskFactory(appManager, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "open appstore");
        props.setProperty(COMMAND_DESCRIPTION, "Open the app store page for an app");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Open the app store page for an app.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{}");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        DisableTaskFactory factory = new DisableTaskFactory(appManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "disable");
        props.setProperty(COMMAND_DESCRIPTION, "Disable an app");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Disable a currently installed app.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{\"appName\": \"appname\"}");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        EnableTaskFactory factory = new EnableTaskFactory(appManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "enable");
        props.setProperty(COMMAND_DESCRIPTION, "Enable a disabled app");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Enable a currently disabled app.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{\"appName\": \"appname\"}");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        InformationTaskFactory factory = new InformationTaskFactory(appManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "information");
        props.setProperty(COMMAND_DESCRIPTION, "Get app information");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Get information about an app.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{\"appName\": \"appname\"" + ", \"description\": \"App description\"" + ", \"version\": \"1.2.2\"}");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        InstallTaskFactory factory = new InstallTaskFactory(appManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "install");
        props.setProperty(COMMAND_DESCRIPTION, "Install an app");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Install an app given an app name or file.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{}");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        ListAvailableTaskFactory factory = new ListAvailableTaskFactory(appManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "list available");
        props.setProperty(COMMAND_DESCRIPTION, "List the available apps");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Return a list of the available apps in the app store");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "[{\"appName\":\"name\", " + "\"description\":\"descriptions\", " + "\"details\":\"app details\"}]");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        ListAppsTaskFactory factory = new ListAppsTaskFactory(appManager, AppStatus.DISABLED);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "list disabled");
        props.setProperty(COMMAND_DESCRIPTION, "List the disabled apps");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Return a list of the disabled apps in the current installation.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "[{ \"appName\": \"appname\"," + "\"version\": \"1.1.0\"," + "\"description\": \"descriptions\"," + "\"status\": \"Disabled\"}]");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        ListAppsTaskFactory factory = new ListAppsTaskFactory(appManager, AppStatus.INSTALLED);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "list installed");
        props.setProperty(COMMAND_DESCRIPTION, "List the installed apps");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Return a list of the installed apps in the current installation.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "[{\"appName\": \"appname\"," + "\"version\": \"1.1.0\"," + "\"description\": \"descriptions\"," + "\"status\": \"Installed\"}]");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        ListAppsTaskFactory factory = new ListAppsTaskFactory(appManager, AppStatus.UNINSTALLED);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "list uninstalled");
        props.setProperty(COMMAND_DESCRIPTION, "List the uninstalled apps");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Return a list of the uninstalled apps in the current installation.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "[{ \"appName\": \"appname\"," + "\"version\": \"1.1.0\"," + "\"description\": \"descriptions\"," + "\"status\": \"Uninstalled\"}]");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        ListUpdatesTaskFactory factory = new ListUpdatesTaskFactory(appManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "list updates");
        props.setProperty(COMMAND_DESCRIPTION, "List the apps available for updates");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Return a list of the apps that have updates in the app store.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "[{ \"appName\": \"appname\"," + "\"version\": \"1.1.10\"," + "\"information\": \"app information\"}]");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        StatusTaskFactory factory = new StatusTaskFactory(appManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "status");
        props.setProperty(COMMAND_DESCRIPTION, "Get the status of an app");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Get the status of an app.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{\"appName\": \"appname\", \"status\": \"Installed\"}");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        UninstallTaskFactory factory = new UninstallTaskFactory(appManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "uninstall");
        props.setProperty(COMMAND_DESCRIPTION, "Uninstall an app");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Uninstall a currently installed app.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{\"appName\": \"appname\"}");
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        UpdateTaskFactory factory = new UpdateTaskFactory(appManager, updateManager);
        Properties props = new Properties();
        props.setProperty(COMMAND_NAMESPACE, "apps");
        props.setProperty(COMMAND, "update");
        props.setProperty(COMMAND_DESCRIPTION, "Update an app or all apps");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Update an app or all apps.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{}");
        registerService(bc, factory, TaskFactory.class, props);
    }
}

Example 4 with FileUtil

use of org.cytoscape.util.swing.FileUtil in project PhenomeScape by soulj.

the class ExportMouseListener method actionPerformed.

@Override
public void actionPerformed(ActionEvent arg0) {
    this.summaryjTable = resultsPanel.getSummaryTable();
    this.parameterjTable = resultsPanel.getParameterTable();
    if (summaryjTable != null) {
        FileUtil fileUtil = resultsPanel.cyServiceRegistrar.getService(org.cytoscape.util.swing.FileUtil.class);
        File file = fileUtil.getFile(CytoPanelUtils.getJFrame(resultsPanel.cyServiceRegistrar), "Export Table", FileUtil.SAVE, filters);
        if (file != null) {
            try {
                ExportTable.toTSV(summaryjTable, parameterjTable, file);
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}