Diff for "OSGI_Refactoring_Possibilities"

Cytoscape PUBLIC API

The core network and network view interfaces. We should consider rolling groups into network/view.

• org.cytoscape.network.CyNetwork

• org.cytoscape.network.CyNode

• org.cytoscape.network.CyEdge

• org.cytoscape.network.CyNetworkView

• org.cytoscape.network.CyNodeView

• org.cytoscape.network.CyEdgeView

• org.cytoscape.network.CyGroup

• org.cytoscape.network.CyGroupView

The core attribute interface.

• org.cytoscape.attributes.CyAttributes

Interfaces for writing various types to data. Session writing will not be provided as a service since on the internal core will ever write a session.

• org.cytoscape.io.export.CyNetworkWriter

• org.cytoscape.io.export.CyAttributesWriter

• org.cytoscape.io.export.GraphicsWriter

Interfaces for reading various types of data along with file filters that can be used to define how files get read.

• org.cytoscape.io.import.CyNetworkFileFilter

• org.cytoscape.io.import.CyNetworkReader

• org.cytoscape.io.import.CyAttributesReader

• org.cytoscape.io.import.CyAttributesFileFilter

The interfaces used for defining general actions in Cytoscape. Algorithms are strictly separated from any sort of UI.

• org.cytoscape.algorithm.Algorithm

• org.cytoscape.algorithm.AlgorithmFactory

The interfaces defining the user interface. Tunable objects are the primary mechanism for communicating data between Algorithms and the UI. If an Algorithm wants to be present in the UI, then it must provide its own SwingFactory. Eventually we'll have interfaces for things like CommandLineFactory (we could perhaps infer this automatically) or AJAXFactory.

• org.cytoscape.ui.TunableType

• org.cytoscape.ui.Tunable
• org.cytoscape.ui.Constraint
• org.cytoscape.ui.UIController

• org.cytoscape.ui.SwingFactory

The interface for defining a web service client.

• org.cytoscape.webservice.WebServiceClient

The (substantially simplified) interfaces for defining visual styles.

• org.cytoscape.vizmap.VisualStyle

• org.cytoscape.vizmap.Calculator
• org.cytoscape.vizmap.Mapping

• org.cytoscape.vizmap.VisualPropertyType

The service interfaces for Cytoscape. These interfaces represent much of the functionality that is currently included in Cytoscape.java as static methods. These services will be implemented by cytoscape.

• org.cytoscape.service.network.CyNetworkViewManager

• org.cytoscape.service.network.CyNetworkManager

• org.cytoscape.service.attributes.CyAttributesManager

• org.cytoscape.service.session.SessionManager

• org.cytoscape.service.ontology.OntologyManager

• org.cytoscape.service.bookmark.BookmarkManager

• org.cytoscape.service.proxy.ProxyManager

Plugin Implemented Services

The general mechanism for plugins to provide services to the rest of Cytoscape is to implement a public Cytoscape interface and register that object as a service with OSGi's service registry. The primary example of this is the Algorithm/AlgorithmFactory interface. Another example is the CyNetworkFileFilter.

Here is some example plugin code that would provide an SBML reader:

package sbmlreader;

import org.cytoscape.io.import.CyNetworkFileFilter;

import org.osgi.framework.BundleContext;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.ServiceReference;
import org.osgi.framework.ServiceRegistration;

import java.util.Hashtable;

public class SBMLReaderPlugin implements BundleActivator {

        private ServiceRegistration filterReg;

        public void start(BundleContext bc) {
                // defin the service metadata
                Hashtable metadata = new Hashtable();
                metadata.put("file.extensions",".sbml,.xml");
                metadata.put("description","SBML files");
                metadata.put("service.pid",SBMLFilter.class.getName());

                //                                               just an interface, implementation of interface, metadata
                filterReg = bc.registerService(CyNetworkFileFilter.class.getName(), new SBMLFilter(), metadata);
        }

        public void stop(BundleContext bc) {
                filterReg.unregister();
        }
}

Here is code that would exist in the Cytoscape core, consume services that have been registered as implementing CyNetworkFileFilter. Since SBMLReaderPlugin has done this, it will be found and used within the core normally.

package cytoscape;

import org.osgi.framework.BundleContext;
import org.osgi.framework.ServiceReference;
import org.cytoscape.io.import.CyNetworkFileFilter;

public class ServiceHandler {

    private BundleContext bc;

    // perhaps called at startup or some other time
    public ServiceHandler(BundleContext bc) {
        this.bc = bc;
        registerCyFileFilters();
    }

    public void registerCyFileFilters() {
        try {
           ServiceReference[] sr = bc.getServiceReferences(CyNetworkFileFilter.class.getName(), null);
           for (ServiceReference r : sr ) {
               CyNetworkFileFilter filter = (CyNetworkFileFilter)bc.getService(r));
               // do something with filter
           }
        } catch (Exception e) { e.printStackTrace(); }
    }

UI Services

Interactive - provide an option to bring up before or after action has run Action to create panel Action to be triggered by the panel

• Control Tab
• Results Tab
• Dialog

// the service interface
interface UIPanel {
  JPanel getJPanel();
}

// in the plugin
// meta data defining where/how to use the panel
Hashtable dict = new HashTable();
dict.put("panel.location","control");
dict.put("panel.name","hello world");
dict.put("service.pid","myuipanel.persistent.id");

bundleContext.registerService(UIPanel.class.getName(), new MyUIPanel(), dict);

Single Action

• Menu Item
• Button On Toolbar

// The factory is the service.  The factory will return individual action objects
// that can store internal state.  If we didn't have a factory, then the individual
// actions wouldn't be able to store their state because they'd persist as services.
interface CytoscapeActionFactory {
  CytoscapeAction createAction(context of some sort);
  List<Tunable> createParameters(possibly some context);
 boolean isEnabled(context of some sort);
}

interface CytoscapeAction {
   void run();
}

// meta data defining where/how to use the action
Hashtable dict = new HashTable();
dict.put("preferred.menu","whereever/submenu");
dict.put("action.panel","myuipanel.persistent.id"); // so that it can get the exact panel
dict.put("menu.label","asdfasdf");
dict.put("icon", new Icon("my.png"));

bundleContext.registerService(CytoscapeActionFactory.class.getName(), new MyCyActionFactory(), dict);

Menus

Menu Action flow of events

1. MenuItem is created.

2. Click on a menu

3. The menuSelected() method checks the CytoscapeActionFactory metadata to see if the menu item should be enabled/disabled. The Action could just declare what attributes need to exist in the world in the metadata of the CytoscapeActionFactory. For example, you could define metadata like requiresNetwork, requiresNetworkView, requiresNodeSelection, requiresEdgeSelection, etc.. There could also a overriding metadatum called isEnabled that could be forced to be true if necessary.

4. The menu would be displayed if the action is enabled.

5. The menu looks for a registered service for CytoscapeActionFactory. The individual factory returned is determined based on a parameter to the MenuItem. This happens dynamically based on how the CytoscapeActionFactories are defined.

6. First call createParameters() that creates some sort of UI (e.g. a GUI that allows input values or a command line that reads a config file or queries a database or reads a command line, etc.). This data is specified by the user and is then passed into the action that is created next.
7. The factory.createAction() method is called with all of the appropriate params (e.g. currentNetwork, currentNetworkView, etc.).

8. The CytoscapeAction object can now be run at your leisure.

CytoscapeAction can implement additional interfaces, e.g. ProgressTrackable, which would mean a progress monitor could be added.

A CytoscapeAction needs it's basic inputs (current network, current view, or possibly a DataManager), but it also may need separate parameters. These should be defined as some sort of Tunable or List<Tunable> or a JPanel that returns some sort of configuration object, e.g. a Dictionary of key -> value pairs.

The action context could be a DataManager interface that provides methods like getCurrentNetwork, getCurrentNetworkView, etc.. Alternatively, you could provide an Context object (e.g. CIShellContext) which could provide access to all Cytoscape services. This isn't an osgi context that worries about bundles, but is an application specific context that provides services appropriate for how the application is currently being run.

Scripting

This Action model needs to be separated from the GUI so that it can be used in a scripting context (i.e headless mode) as well.

MetaData could also be used to specify where the Action can be used. For example you could set a requiresGUI (or even requiresSwing) element that would disable the action if the current running context doesn't support a GUI.

the Solution

[http://cishell.org CIShell] does all of this now.

Action Services

• An action gets current context (network, view, etc.). Then the action does "something". The action should be independent of the UI. Make the actions chainable.

General Bundle Organization

• Each service described below will consist of a small number of interfaces. All service interfaces will be part of a single framework bundle.
• Each service implementation will (probably) have a separate bundle. This isn't necessary, but some organization is a good idea.
• There will be an initialization bundle that will handle starting and stopping all of the core services defined in the framework.
• The GUI will consist of separate bundles.
• Each service will (for the most part) have an associated GUI bundle.

Breakdown of Cytoscape Services

Currently supported by Cytoscape.java.

• handled by OSGi
  • void exit(int returnVal) {
• gui specific

  • CytoscapeDesktop getDesktop() {

  • VisualMappingManager getVisualMappingManager() {

• network service
  • Set getNetworkSet() {

  • CyNetwork getNetwork(String id) {

  • CyNetwork getNullNetwork() {

  • CyNetwork getCurrentNetwork() {

  • void setCurrentNetwork(String id) {

  • void destroyNetwork(CyNetwork network) {

  • CyNetwork createNetwork(String title, ...) {

  • encapsulate in CyNetwork:

    • List getCyNodesList() {
    • List getCyEdgesList() {

    • CyNode getCyNode(String alias)

    • CyEdge getCyEdge(Node node_1, Node node_2, ...)

• network view service
  • Map getNetworkViewMap() {

  • CyNetworkView getNetworkView(String network_id) {

  • CyNetworkView getNullNetworkView() {

  • boolean viewExists(String network_id) {

  • CyNetworkView getCurrentNetworkView() {

  • boolean setCurrentNetworkView(String id) {

  • CyNetworkView createNetworkView(CyNetwork network, ...) {

  • void destroyNetworkView(CyNetworkView view, ...) {

• session service
  • String getCurrentSessionFileName() {
  • void setCurrentSessionFileName(String newName) {
  • void setSessionState(int state) {
  • int getSessionstate() {
  • void createNewSession() {
• attribute service

  • CyAttributes getNodeAttributes() {

  • CyAttributes getEdgeAttributes() {

  • CyAttributes getNetworkAttributes() {

  • void loadAttributes(String[] nodeAttrLocations, String[] edgeAttrLocations) {
• import service

  • No need to exist. Imports are handled automatically by getting service references to all CyNetworkFileFilters.

• event handling service

  • SwingPropertyChangeSupport getSwingPropertyChangeSupport() {

  • PropertyChangeSupport getPropertyChangeSupport() {

  • void firePropertyChange(String property_type, Object old_value, Object new_value) {
• expression data service

  • ExpressionData getExpressionData() {

  • void setExpressionData(ExpressionData expData) {

  • boolean loadExpressionData(String filename, boolean copy_atts) {
• ontology service

  • OntologyServer buildOntologyServer() {

  • OntologyServer getOntologyServer() {

  • String getOntologyRootID() {
  • void setOntologyRootID(String id) {

  • CyAttributes getOntologyAttributes() {

• bookmark service
  • Bookmarks getBookmarks() throws JAXBException, IOException {
  • void setBookmarks(Bookmarks pBookmarks) {

NOT Currently provided by Cytoscape.java

• Export service
  • No need to exist. Imports are handled automatically by getting service references to all export filters.

"Services" currently existing elsewhere that would be transformed into OSGi services.

• Proxy handling service
• Layout service
• Web Service Service

• Groups - Perhaps this should be integrated with CyNetwork and CyNetworkView. CyGroup should be in/related to CyNetwork (CyNode?) and CyGroupView should in/related to CyNetworkView (CyNodeView?).

Visual Styles

A VisualStyle consists of a NodeAppearanceCalculator, EdgeAppearanceCalculator, and GlobalAppearanceCalculator.

NodeAppearanceCalculators and EdgeAppearanceCalculators consist of lists of Calculator objects. Each calculator has a specific VisualPropertyType. Only one Calculator of a given VisualPropertyType is allowed in either NodeAppearanceCalculators or EdgeAppearanceCalculators.

Possible Improvements for VisualStyles

• Get rid of the NodeAppearance and EdgeAppearance objects. Instead, operate directly on CyNodeView and CyEdgeView.

• Get rid of NodeAppearanceCalculator and EdgeAppearanceCalculator and just let VisualStyle keep a list of the individual Calculators.

• Make GlobalAppearanceCalculator based on VisualPropertyType. Perhaps with dummy calculators?

• Re-enable applyVisualStyle to CyNetworkView instead of applying the visual style in the VisualMappingManager. This would have the advantage of allowing different implementations of views to handle different visual properties as they deem appropriate.

• The Calculator objects must to be reworked to fetch attributes from CyAttributes rather than operating on their own attribute bundle model. The attribute in question should be an argument to the Calculator.

• Consider getting rid of CalculatorCatalog. Calculators are small objects and there won't be that many of them any way.

• Perhaps consolidate Mapping and Calculator since Calculator really just passes a mapping value through to an Appearance.

Current Cytoscape Actions

• SHOULD be gui independent

  • ListFromFileSelectionAction.java

  • ExportAction.java

  • ExportAsGMLAction.java

  • ExportAsGraphicsAction.java

  • ExportAsInteractionsAction.java

  • ExportAsXGMMLAction.java

  • ExportEdgeAttributesAction.java

  • ExportNodeAttributesAction.java

  • ExportVizmapAction.java

  • ExitAction.java

  • CloneGraphInNewWindowAction.java // misnamed

  • CreateNetworkViewAction.java

  • DestroyNetworkViewAction.java

  • DeSelectAllEdgesAction.java

  • DeSelectAllNodesAction.java

  • DeselectAllAction.java

  • DestroyNetworkAction.java

  • GraphObjectSelectionAction.java

  • AlphabeticalSelectionAction.java

  • InvertSelectedEdgesAction.java

  • InvertSelectedNodesAction.java

  • NewWindowSelectedNodesEdgesAction.java // new NETWORK from selected

  • NewWindowSelectedNodesOnlyAction.java // new NETWORK from selected

  • ImportBioDataServerAction.java

  • ImportEdgeAttributesAction.java

  • ImportExpressionMatrixAction.java

  • ImportGraphFileAction.java

  • ImportNodeAttributesAction.java

  • ImportVizmapAction.java

  • NewSessionAction.java

  • OpenSessionAction.java

  • ProxyServerAction.java

  • SaveSessionAction.java

  • SaveSessionAsAction.java

• pops up dialog

  • MapOntologyAction.java

  • PluginManagerAction.java

  • PluginUpdateAction.java

  • PreferenceAction.java

  • PrintAction.java

  • HelpAboutAction.java

  • HelpContactHelpDeskAction.java

  • HelpContentsAction.java

  • BookmarkAction.java

• gui specific view manipulation

  • FitContentAction.java

  • BendSelectedEdgesAction.java

  • HideSelectedAction.java

  • HideSelectedEdgesAction.java

  • HideSelectedNodesAction.java

  • AlignHorizontalAction.java

  • AlignVerticalAction.java

  • SelectAllAction.java

  • SelectAllEdgesAction.java

  • SelectAllNodesAction.java

  • SelectFirstNeighborsAction.java

  • SetVisualPropertiesAction.java

  • ShowAllAction.java

  • RotateSelectedNodesAction.java

  • StraightenSelectedEdgesAction.java

  • UnHideSelectedAction.java

  • UnHideSelectedEdgesAction.java

  • UnHideSelectedNodesAction.java

  • ZoomAction.java

  • ZoomSelectedAction.java

• gui specific state

  • SelectionModeAction.java

  • CytoPanelAction.java // pops up a cytopanel and takes a cyto panel type as arg

  • BirdsEyeViewAction.java

Algorithm Workflow

1. Click Top-level menu
2. Check algorithm meta data to see if menu item should be enabled.
3. Click menu item.

4. MenuManager checks Algorithm meta data to UI service id.

5. MenuManager associates a GUI instance with an Algorithm through Algorithm meta data.

6. MenuManager creates a GUIController object that knows about the Algorithm and the GUI.

7. MenuManager creates GUI based on the UI service id. MenuManager creates the GUI with a GUIController object.

8. GUI intializes itself from UI.getFallBackInterface().
9. User does stuff to the GUI setting the various Tunables.
10. User clicks submit().

11. GUI calls GUIController.execute(List<Tunables>).

12. GUIController.close() gets called some point to close the GUI.

13. GUIController gets all associated algorithms with GUI and calls AlgorithmFactory.createAlgorithm(List<Tunable>).execute().