fix currentnetwork selection

pom.xml

@@ -26,7 +26,7 @@
     <artifactId>enrichment</artifactId>
 
     <name>EnrichmentTable</name>
-    <version>2.0.6</version>
+    <version>2.0.7</version>
 
 
     <!--

src/main/java/org/nrnb/gsoc/enrichment/CyActivator.java

@@ -82,12 +82,11 @@ public void start(BundleContext context) throws Exception {
 
 		if (cytoPanel.getState() == CytoPanelState.HIDE)
 			cytoPanel.setState(CytoPanelState.DOCK);
-		cytoPanel.setSelectedIndex(
-				cytoPanel.indexOfComponent("org.cytoscape.NodeTables"));
-		TaskFactory myFactory = new EnrichmentTaskFactory(registrar,enrichmentPanel); // Implementation
-		registerService(context, myFactory,
-				TaskFactory.class, // Interface
-				properties); // Service properties
+			cytoPanel.setSelectedIndex(cytoPanel.indexOfComponent("org.cytoscape.NodeTables"));
+			TaskFactory myFactory = new EnrichmentTaskFactory(registrar,enrichmentPanel); // Implementation
+			registerService(context, myFactory,
+			TaskFactory.class, // Interface
+			properties); // Service properties
 
 	}
 }

src/main/java/org/nrnb/gsoc/enrichment/actions/ShowAppTableAction.java

@@ -21,6 +21,9 @@
 import org.cytoscape.session.events.SessionLoadedListener;
 import org.cytoscape.util.swing.TextIcon;
 import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskManager;
+import org.nrnb.gsoc.enrichment.tasks.EnrichmentTask;
 import org.nrnb.gsoc.enrichment.tasks.EnrichmentTaskFactory;
 import org.nrnb.gsoc.enrichment.ui.EnrichmentCytoPanel;
 import org.nrnb.gsoc.enrichment.utils.IconUtil;
@@ -42,34 +45,39 @@ public ShowAppTableAction(CyServiceRegistrar serviceRegistrar) {
 		var iconFont = IconUtil.getIconFont(30.0f);
 		var icon = new TextIcon(APP_ICON_LAYERS, iconFont, APP_ICON_COLORS, 32, 32, 1);
 
-		putValue(SHORT_DESCRIPTION, "Show Enrichment Table"); // Tooltip's short description
+		putValue(SHORT_DESCRIPTION, "Perform Gene Enrichment");
 		putValue(LARGE_ICON_KEY, icon);
 	}
 
 	@Override
 	public void actionPerformed(ActionEvent e) {
 		CySwingApplication swingApplication = serviceRegistrar.getService(CySwingApplication.class);
 		CytoPanel cytoPanel = swingApplication.getCytoPanel(CytoPanelName.SOUTH);
-		if (enrichmentPanel == null){
-		enrichmentPanel =  new EnrichmentCytoPanel(serviceRegistrar,false,null);
-		serviceRegistrar.registerService(enrichmentPanel, CytoPanelComponent.class,new Properties());
-		serviceRegistrar.registerService(enrichmentPanel, SelectedNodesAndEdgesListener.class, new Properties());
-		serviceRegistrar.registerService(enrichmentPanel, NetworkAboutToBeDestroyedListener.class, new Properties());
-		serviceRegistrar.registerService(enrichmentPanel, SessionLoadedListener.class, new Properties());
-		serviceRegistrar.registerService(enrichmentPanel, SetCurrentNetworkListener.class, new Properties());
-		//registrar.registerService(enrichmentPanel, SetCurrentNetworkListener.class, new Properties());
-		//registrar.registerService(enrichmentPanel, NetworkAddedListener.class, new Properties());
-		if (cytoPanel.getState() == CytoPanelState.HIDE)
-		cytoPanel.setState(CytoPanelState.DOCK);
-	cytoPanel.setSelectedIndex(
-			cytoPanel.indexOfComponent("org.nrnb.gsoc.enrichment"));
-
+		TaskManager<?, ?> tm = serviceRegistrar.getService(TaskManager.class);
+		if (enrichmentPanel == null) {
+			enrichmentPanel = new EnrichmentCytoPanel(serviceRegistrar, false, null);
+			serviceRegistrar.registerService(enrichmentPanel, CytoPanelComponent.class, new Properties());
+			serviceRegistrar.registerService(enrichmentPanel, SelectedNodesAndEdgesListener.class, new Properties());
+			serviceRegistrar.registerService(enrichmentPanel, NetworkAboutToBeDestroyedListener.class, new Properties());
+			serviceRegistrar.registerService(enrichmentPanel, SessionLoadedListener.class, new Properties());
+			serviceRegistrar.registerService(enrichmentPanel, SetCurrentNetworkListener.class, new Properties());
+			if (cytoPanel.getState() == CytoPanelState.HIDE)
+				cytoPanel.setState(CytoPanelState.DOCK);
+			cytoPanel.setSelectedIndex(cytoPanel.indexOfComponent("org.nrnb.gsoc.enrichment"));
 		} else {
 			if (cytoPanel.getState() == CytoPanelState.HIDE)
+				cytoPanel.setState(CytoPanelState.DOCK);
+			cytoPanel.setSelectedIndex(cytoPanel.indexOfComponent("org.nrnb.gsoc.enrichment"));
+		}
+
+		try {
+			tm.execute(new TaskIterator(new EnrichmentTask(serviceRegistrar, enrichmentPanel)));
+		} catch (Exception ex) {
+			System.err.println("Error executing EnrichmentTask: " + ex.getMessage());
+		}
+
+		if (cytoPanel.getState() == CytoPanelState.HIDE)
 			cytoPanel.setState(CytoPanelState.DOCK);
-		cytoPanel.setSelectedIndex(
-				cytoPanel.indexOfComponent("org.nrnb.gsoc.enrichment"));
-
-		}	
+		cytoPanel.setSelectedIndex(cytoPanel.indexOfComponent("org.nrnb.gsoc.enrichment"));
 	}
 }

src/main/java/org/nrnb/gsoc/enrichment/ui/EnrichmentCytoPanel.java

@@ -84,6 +84,7 @@ public class EnrichmentCytoPanel extends JPanel
     CyTable filteredEnrichmentTable = null;
     boolean clearSelection = false;
     JPopupMenu popupMenu;
+    private boolean registered = false;
 
     private String[] columnToolTips = {
             "the full name of the datasource for the term",
@@ -148,6 +149,7 @@ public EnrichmentCytoPanel(CyServiceRegistrar registrar, boolean noSignificant,
         enrichmentTables = new HashMap<String, JTable>();
         this.noSignificant = noSignificant;
         initPanel(this.noSignificant);
+        registered = true;
     }
 
     public void setEnrichmentTable(CyTable enrichmentTable){
@@ -874,13 +876,19 @@ private void clearNetworkSelection(CyNetwork network) {
         clearSelection = false;
     }
 
-    public void handleEvent(SetCurrentNetworkEvent event) {
-       CyNetwork network = event.getNetwork();
-       if (network != null) {
-           initPanel(network, false);
-           return;
-       }
-  	}
+	public void handleEvent(SetCurrentNetworkEvent event) {
+		CyNetwork network = event.getNetwork();
+		if (ModelUtils.ifHaveEnrichmentNS(network)) {
+			if (!registered) {
+				showCytoPanel();
+			} else {
+				initPanel(network, false);
+			}
+		} else {
+			hideCytoPanel();
+		}
+
+	}
 
     @Override
     public void handleEvent(SelectedNodesAndEdgesEvent event) {
@@ -942,6 +950,7 @@ public void handleEvent(NetworkAboutToBeDestroyedEvent e) {
                 cytoPanel.indexOfComponent("org.cytoscape.NodeTables"));
     }
 
+
     public void handleEvent(SessionLoadedEvent arg0) {
         CySwingApplication swingApplication = registrar.getService(CySwingApplication.class);
         CytoPanel cytoPanel = swingApplication.getCytoPanel(CytoPanelName.SOUTH);
@@ -983,6 +992,26 @@ public void drawCharts() {
     public boolean getIsChartEnabled() {
         return isChartEnabled;
     }
+	public void showCytoPanel() {
+		CySwingApplication swingApplication = registrar.getService(CySwingApplication.class);
+		CytoPanel cytoPanel = swingApplication.getCytoPanel(CytoPanelName.SOUTH);
+		if (!registered && cytoPanel.indexOfComponent("org.nrnb.gsoc.enrichment") < 0) {
+			// System.out.println("panel: register enrichment panel");
+			registrar.registerService(this, CytoPanelComponent.class, new Properties());
+			registered = true;
+		}
+		if (cytoPanel.getState() == CytoPanelState.HIDE)
+			cytoPanel.setState(CytoPanelState.DOCK);
+
+		initPanel(false);
+		cytoPanel
+				.setSelectedIndex(cytoPanel.indexOfComponent("edu.ucsf.rbvi.stringApp.Enrichment"));
+	}
+
+    public void hideCytoPanel() {
+		registrar.unregisterService(this, CytoPanelComponent.class);
+        registered = false;
+	}
 
     private boolean isEnrichmentMapInstalled() {
         return availableCommands.getNamespaces().contains("enrichmentmap");

src/main/java/org/nrnb/gsoc/enrichment/utils/ModelUtils.java

@@ -20,7 +20,6 @@
 import org.nrnb.gsoc.enrichment.model.EnrichmentTerm.TermSource;
 
 import java.util.*;
-import java.util.List;
 import java.util.stream.Collectors;
 
 import java.io.IOException;
@@ -831,4 +830,13 @@ public static class ConfigPropsReader extends AbstractConfigDirPropsReader {
         }
     }
 
+    	// This method will tell us if we have the new side panel functionality (i.e. namespaces)
+	public static boolean ifHaveEnrichmentNS(CyNetwork network) {
+		if (network == null) return false;
+		Collection<CyColumn> columns = network.getDefaultNetworkTable().getColumns(ENRICHMENT_NAMESPACE);
+		if (columns != null && columns.size() > 0)
+			return true;
+		return false;
+	}
+
 }