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

Example 1 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project EnrichmentMapApp by BaderLab.

the class TestUtils method mockServiceRegistrar.

public static CyServiceRegistrar mockServiceRegistrar() {
    CyNetworkManager netManager = mock(CyNetworkManager.class);
    CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyNetworkManager.class)).thenReturn(netManager);
    return serviceRegistrar;
}

Example 2 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) {
    CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
    CyEventHelper cyEventHelperRef = getService(bc, CyEventHelper.class);
    CyNetworkNaming cyNetworkNamingServiceRef = getService(bc, CyNetworkNaming.class);
    UndoSupport undoSupportServiceRef = getService(bc, UndoSupport.class);
    CyNetworkViewFactory cyNetworkViewFactoryServiceRef = getService(bc, CyNetworkViewFactory.class);
    CyNetworkFactory cyNetworkFactoryServiceRef = getService(bc, CyNetworkFactory.class);
    CyRootNetworkManager cyRootNetworkFactoryServiceRef = getService(bc, CyRootNetworkManager.class);
    VisualMappingManager visualMappingManagerServiceRef = getService(bc, VisualMappingManager.class);
    CyNetworkViewWriterManager networkViewWriterManagerServiceRef = getService(bc, CyNetworkViewWriterManager.class);
    CyNetworkManager cyNetworkManagerServiceRef = getService(bc, CyNetworkManager.class);
    CyNetworkViewManager cyNetworkViewManagerServiceRef = getService(bc, CyNetworkViewManager.class);
    CyApplicationManager cyApplicationManagerServiceRef = getService(bc, CyApplicationManager.class);
    CySessionManager cySessionManagerServiceRef = getService(bc, CySessionManager.class);
    CyTableFactory cyTableFactoryServiceRef = getService(bc, CyTableFactory.class);
    CyTableManager cyTableManagerServiceRef = getService(bc, CyTableManager.class);
    CyLayoutAlgorithmManager cyLayoutsServiceRef = getService(bc, CyLayoutAlgorithmManager.class);
    CyTableWriterManager cyTableWriterManagerRef = getService(bc, CyTableWriterManager.class);
    SynchronousTaskManager<?> synchronousTaskManagerServiceRef = getService(bc, SynchronousTaskManager.class);
    TunableSetter tunableSetterServiceRef = getService(bc, TunableSetter.class);
    CyRootNetworkManager rootNetworkManagerServiceRef = getService(bc, CyRootNetworkManager.class);
    CyNetworkTableManager cyNetworkTableManagerServiceRef = getService(bc, CyNetworkTableManager.class);
    RenderingEngineManager renderingEngineManagerServiceRef = getService(bc, RenderingEngineManager.class);
    CyNetworkViewFactory nullNetworkViewFactory = getService(bc, CyNetworkViewFactory.class, "(id=NullCyNetworkViewFactory)");
    CyGroupManager cyGroupManager = getService(bc, CyGroupManager.class);
    CyGroupFactory cyGroupFactory = getService(bc, CyGroupFactory.class);
    {
        DynamicTaskFactoryProvisionerImpl factory = new DynamicTaskFactoryProvisionerImpl(serviceRegistrar);
        registerAllServices(bc, factory);
    }
    createPreferencesTaskFactories(bc, serviceRegistrar);
    createFilterTaskFactories(bc, serviceRegistrar);
    createTableTaskFactories(bc, serviceRegistrar, undoSupportServiceRef, cyNetworkManagerServiceRef, cyApplicationManagerServiceRef, cyTableFactoryServiceRef, cyTableManagerServiceRef, cyTableWriterManagerRef, tunableSetterServiceRef, rootNetworkManagerServiceRef, cyNetworkTableManagerServiceRef);
    createNetworkTaskFactories(bc, serviceRegistrar, cyEventHelperRef, cyNetworkNamingServiceRef, undoSupportServiceRef, cyNetworkViewFactoryServiceRef, cyNetworkFactoryServiceRef, cyRootNetworkFactoryServiceRef, visualMappingManagerServiceRef, cyNetworkManagerServiceRef, cyNetworkViewManagerServiceRef, cyApplicationManagerServiceRef, synchronousTaskManagerServiceRef, rootNetworkManagerServiceRef, cyNetworkTableManagerServiceRef, renderingEngineManagerServiceRef, nullNetworkViewFactory, cyGroupManager, cyGroupFactory, networkViewWriterManagerServiceRef, tunableSetterServiceRef);
    createViewTaskFactories(bc, cyEventHelperRef, undoSupportServiceRef, visualMappingManagerServiceRef, networkViewWriterManagerServiceRef, cyNetworkViewManagerServiceRef, cyApplicationManagerServiceRef, cyLayoutsServiceRef, tunableSetterServiceRef, renderingEngineManagerServiceRef, cyNetworkManagerServiceRef, cySessionManagerServiceRef, serviceRegistrar);
    createVizmapTaskFactories(bc, serviceRegistrar);
    createSessionTaskFactories(bc, serviceRegistrar);
    createGroupTaskFactories(bc, undoSupportServiceRef, cyApplicationManagerServiceRef, cyGroupManager, cyGroupFactory, serviceRegistrar);
    createNodeEdgeTaskFactories(bc, serviceRegistrar, cyEventHelperRef, undoSupportServiceRef, cyNetworkViewManagerServiceRef, tunableSetterServiceRef, cyApplicationManagerServiceRef, cyTableManagerServiceRef, renderingEngineManagerServiceRef, visualMappingManagerServiceRef);
    createLayoutTaskFactories(bc, serviceRegistrar);
    createHelpTaskFactories(bc, serviceRegistrar);
}

Example 3 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);
    final StreamUtil streamUtil = getService(bc, StreamUtil.class);
    {
        // ".xls"
        WildCardCyFileFilter filter = new WildCardCyFileFilter(new String[] { "xls", "xlsx" }, new String[] { "application/excel" }, "Excel", TABLE, streamUtil);
        ImportAttributeTableReaderFactory factory = new ImportAttributeTableReaderFactory(filter, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty("readerDescription", "Attribute Table file reader");
        props.setProperty("readerId", "attributeTableReader");
        registerService(bc, factory, InputStreamTaskFactory.class, props);
    }
    {
        // ".txt"
        WildCardCyFileFilter filter = new WildCardCyFileFilter(new String[] { "csv", "tsv", "txt", "tab", "net", "" }, new String[] { "text/csv", "text/tab-separated-values", "text/plain", "" }, "Comma or Tab Separated Value", TABLE, streamUtil);
        filter.setBlacklist("xml", "xgmml", "rdf", "owl", "zip", "rar", "jar", "doc", "docx", "ppt", "pptx", "pdf", "jpg", "jpeg", "gif", "png", "svg", "tiff", "ttf", "mp3", "mp4", "mpg", "mpeg", "exe", "dmg", "iso", "cys");
        ImportAttributeTableReaderFactory factory = new ImportAttributeTableReaderFactory(filter, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty("readerDescription", "Attribute Table file reader");
        props.setProperty("readerId", "attributeTableReader_txt");
        registerService(bc, factory, InputStreamTaskFactory.class, props);
    }
    {
    // BasicCyFileFilter filter = new BasicCyFileFilter(
    // new String[] { "obo" },
    // new String[] { "text/obo" },
    // "OBO",
    // NETWORK,
    // streamUtil
    // );
    // OBONetworkReaderFactory factory = new OBONetworkReaderFactory(filter, serviceRegistrar);
    // Properties props = new Properties();
    // props.setProperty("readerDescription", "Open Biomedical Ontology (OBO) file reader");
    // props.setProperty("readerId", "oboReader");
    // registerService(bc, factory, InputStreamTaskFactory.class, props);
    // 
    // ImportOntologyAndAnnotationAction action = new ImportOntologyAndAnnotationAction(factory, serviceRegistrar);
    // registerService(bc, action, CyAction.class);
    }
    {
        // "txt"
        WildCardCyFileFilter filter = new WildCardCyFileFilter(new String[] { "csv", "tsv", "txt", "" }, new String[] { "text/csv", "text/tab-separated-values", "text/plain", "" }, "Comma or Tab Separated Value", NETWORK, streamUtil);
        filter.setBlacklist("xml", "xgmml", "rdf", "owl", "zip", "rar", "jar", "doc", "docx", "ppt", "pptx", "pdf", "jpg", "jpeg", "gif", "png", "svg", "tiff", "ttf", "mp3", "mp4", "mpg", "mpeg", "exe", "dmg", "iso", "cys");
        ImportNetworkTableReaderFactory factory = new ImportNetworkTableReaderFactory(filter, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty("readerDescription", "Network Table file reader");
        props.setProperty("readerId", "networkTableReader_txt");
        registerService(bc, factory, InputStreamTaskFactory.class, props);
    }
    {
        // ".xls"
        WildCardCyFileFilter filter = new WildCardCyFileFilter(new String[] { "xls", "xlsx" }, new String[] { "application/excel" }, "Excel", NETWORK, streamUtil);
        ImportNetworkTableReaderFactory factory = new ImportNetworkTableReaderFactory(filter, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty("readerDescription", "Network Table file reader");
        props.setProperty("readerId", "networkTableReader_xls");
        registerService(bc, factory, InputStreamTaskFactory.class, props);
    }
    {
        AttributeMappingParametersHandlerFactory factory = new AttributeMappingParametersHandlerFactory(ImportType.TABLE_IMPORT, serviceRegistrar);
        registerService(bc, factory, GUITunableHandlerFactory.class);
    }
    {
        NetworkTableMappingParametersHandlerFactory factory = new NetworkTableMappingParametersHandlerFactory(ImportType.NETWORK_IMPORT, serviceRegistrar);
        registerService(bc, factory, GUITunableHandlerFactory.class);
    }
    {
        TaskFactory factory = new ImportNoGuiTableReaderFactory(false, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty(COMMAND, "import file");
        props.setProperty(COMMAND_NAMESPACE, "table");
        props.setProperty(COMMAND_DESCRIPTION, "Import a table from a file");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "This uses a long list of input parameters to specify the attributes of the table, the mapping keys, and the destination table for the input.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{\"mappedTables\":[101,102]}");
        // Register the service as a TaskFactory for commands
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        TaskFactory importURLTableFactory = new ImportNoGuiTableReaderFactory(true, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty(COMMAND, "import url");
        props.setProperty(COMMAND_NAMESPACE, "table");
        props.setProperty(COMMAND_DESCRIPTION, "Import a table from a URL");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Similar to Import Table this uses a long list of input parameters to specify the attributes of the table, the mapping keys, and the destination table for the input.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, "{\"mappedTables\":[101,102]}");
        // Register the service as a TaskFactory for commands
        registerService(bc, importURLTableFactory, TaskFactory.class, props);
    }
    // {
    // TaskFactory mapColumnTaskFactory = new ImportNoGuiTableReaderFactory(true, serviceRegistrar);
    // Properties props = new Properties();
    // props.setProperty(COMMAND, "map column");
    // props.setProperty(COMMAND_NAMESPACE, "table");
    // props.setProperty(COMMAND_DESCRIPTION, "Map column content from one namespace to another");
    // props.setProperty(COMMAND_LONG_DESCRIPTION, "Uses the BridgeDB service to look up analogous identifiers from a wide selection of other databases");
    // props.setProperty(COMMAND_SUPPORTS_JSON, "true");
    // // Register the service as a TaskFactory for commands
    // registerService(bc, mapColumnTaskFactory, MapColumnTaskFactory.class, props);
    // }
    {
        TaskFactory factory = new ImportNoGuiNetworkReaderFactory(false, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty(COMMAND, "import file");
        props.setProperty(COMMAND_NAMESPACE, "network");
        props.setProperty(COMMAND_DESCRIPTION, "Import a network from a file");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Import a new network from a tabular formatted file type " + "(e.g. ``csv``, ``tsv``, ``Excel``, etc.).  Use ``network load file`` " + "to load network formatted files.  This command will create a " + "new network collection if no current network collection is selected, otherwise " + "it will add the network to the current collection. The SUIDs of the new networks " + "and views are returned.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, ImportNoGuiNetworkReaderFactory.JSON_EXAMPLE);
        // Register the service as a TaskFactory for commands
        registerService(bc, factory, TaskFactory.class, props);
    }
    {
        TaskFactory factory = new ImportNoGuiNetworkReaderFactory(true, serviceRegistrar);
        Properties props = new Properties();
        props.setProperty(COMMAND, "import url");
        props.setProperty(COMMAND_NAMESPACE, "network");
        props.setProperty(COMMAND_DESCRIPTION, "Import a network from a URL");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Import a new network from a URL that points to a tabular formatted file type " + "(e.g. ``csv``, ``tsv``, ``Excel``, etc.).  Use ``network load url`` " + "to load network formatted files.  This command will create a " + "new network collection if no current network collection is selected, otherwise " + "it will add the network to the current collection. The SUIDs of the new networks " + "and views are returned.");
        props.setProperty(COMMAND_SUPPORTS_JSON, "true");
        props.setProperty(COMMAND_EXAMPLE_JSON, ImportNoGuiNetworkReaderFactory.JSON_EXAMPLE);
        // Register the service as a TaskFactory for commands
        registerService(bc, factory, TaskFactory.class, props);
    }
}

Example 4 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);
    final OpenBrowserImpl openBrowser = new OpenBrowserImpl();
    registerService(bc, openBrowser, OpenBrowser.class, new Properties());
    final FileUtilImpl fileUtil = new FileUtilImpl(serviceRegistrar);
    registerService(bc, fileUtil, FileUtil.class, new Properties());
    final IconManagerImpl iconManager = new IconManagerImpl();
    registerService(bc, iconManager, IconManager.class, new Properties());
}

Example 5 with CyServiceRegistrar

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

the class CloneNetworkTaskFactoryTest method testObserver.

@Test
public void testObserver() throws Exception {
    NetworkViewTestSupport viewSupport = new NetworkViewTestSupport();
    NetworkTestSupport networkSupport = new NetworkTestSupport();
    CyNetworkManager networkMgr = Mockito.mock(CyNetworkManager.class);
    CyNetworkViewManager networkViewMgr = Mockito.mock(CyNetworkViewManager.class);
    VisualMappingManager vmm = Mockito.mock(VisualMappingManager.class);
    CyNetworkFactory netFactory = networkSupport.getNetworkFactory();
    CyNetworkViewFactory netViewFactory = viewSupport.getNetworkViewFactory();
    CyNetworkNaming naming = Mockito.mock(CyNetworkNaming.class);
    CyApplicationManager appMgr = Mockito.mock(CyApplicationManager.class);
    CyNetworkTableManager netTableMgr = Mockito.mock(CyNetworkTableManager.class);
    CyRootNetworkManager rootNetMgr = new CyRootNetworkManagerImpl();
    CyGroupManager groupMgr = Mockito.mock(CyGroupManager.class);
    CyGroupFactory groupFactory = Mockito.mock(CyGroupFactory.class);
    RenderingEngineManager renderingEngineMgr = Mockito.mock(RenderingEngineManager.class);
    CyNetworkViewFactory nullNetworkViewFactory = new NullCyNetworkViewFactory();
    CyServiceRegistrar serviceRegistrar = Mockito.mock(CyServiceRegistrar.class);
    CloneNetworkTaskFactoryImpl factory = new CloneNetworkTaskFactoryImpl(networkMgr, networkViewMgr, vmm, netFactory, netViewFactory, naming, appMgr, netTableMgr, rootNetMgr, groupMgr, groupFactory, renderingEngineMgr, nullNetworkViewFactory, serviceRegistrar);
    CyNetwork network = netFactory.createNetwork();
    TaskObserver observer = Mockito.mock(TaskObserver.class);
    TaskIterator iterator = factory.createTaskIterator(network);
    TaskMonitor taskMonitor = Mockito.mock(TaskMonitor.class);
    while (iterator.hasNext()) {
        Task t = iterator.next();
        t.run(taskMonitor);
        if (t instanceof ObservableTask)
            observer.taskFinished((ObservableTask) t);
    }
    Mockito.verify(observer, Mockito.times(1)).taskFinished(Mockito.any(ObservableTask.class));
}