Don't save model when cytoscape is shutting down

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java

@@ -7,6 +7,7 @@
 import org.baderlab.csplugins.enrichmentmap.commands.BuildEnrichmentMapTuneableTaskFactory;
 import org.baderlab.csplugins.enrichmentmap.commands.EnrichmentMapGSEACommandHandlerTaskFactory;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
+import org.baderlab.csplugins.enrichmentmap.model.io.SessionListener;
 import org.baderlab.csplugins.enrichmentmap.style.ChartFactoryManager;
 import org.baderlab.csplugins.enrichmentmap.style.charts.radialheatmap.RadialHeatMapChartFactory;
 import org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator;
@@ -93,18 +94,21 @@ public void start(BundleContext bc) {
 		Em21Handler.removeVersion21(bc, injector.getInstance(CyApplicationConfiguration.class));
 	}
 
+	
 	@Override
 	public void shutDown() {
-		if (injector != null) {
-			// If the App gets updated or restarted we need to save all the data first
-			SessionListener sessionListener = injector.getInstance(SessionListener.class);
-			sessionListener.save();
-			
-			// Also close the legend panel
-			LegendPanelMediator legendPanelMediator = injector.getInstance(LegendPanelMediator.class);
-			legendPanelMediator.hideDialog();
+		try {
+			if (injector != null) {
+				// If the App gets updated or restarted we need to save all the data first
+				SessionListener sessionListener = injector.getInstance(SessionListener.class);
+				sessionListener.appShutdown();
+				
+				// Close the legend panel
+				LegendPanelMediator legendPanelMediator = injector.getInstance(LegendPanelMediator.class);
+				legendPanelMediator.hideDialog();
+			}
+		} finally {
+			super.shutDown();
 		}
-		
-		super.shutDown();
 	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/SessionListener.java renamed to EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/io/SessionListener.java

@@ -1,7 +1,8 @@
-package org.baderlab.csplugins.enrichmentmap;
+package org.baderlab.csplugins.enrichmentmap.model.io;
 
-import org.baderlab.csplugins.enrichmentmap.model.io.SessionModelIO;
 import org.baderlab.csplugins.enrichmentmap.view.control.io.SessionViewIO;
+import org.cytoscape.application.events.CyShutdownEvent;
+import org.cytoscape.application.events.CyShutdownListener;
 import org.cytoscape.session.CySession;
 import org.cytoscape.session.events.SessionAboutToBeSavedEvent;
 import org.cytoscape.session.events.SessionAboutToBeSavedListener;
@@ -12,15 +13,16 @@
 import com.google.inject.Singleton;
 
 @Singleton
-public class SessionListener implements SessionLoadedListener, SessionAboutToBeSavedListener {
+public class SessionListener implements SessionLoadedListener, SessionAboutToBeSavedListener, CyShutdownListener {
 
 	@Inject private SessionModelIO modelIO;
 	@Inject private SessionViewIO viewIO;
 
+	private boolean cytoscapeShuttingDown = false;
+	
 	@Override
 	public void handleEvent(SessionLoadedEvent event) {
-		CySession session = event.getLoadedSession();
-		restore(session);
+		restore(event.getLoadedSession());
 	}
 
 	@Override
@@ -37,4 +39,16 @@ public void restore(CySession session) {
 		modelIO.restoreModel(session);
 		viewIO.restoreView(session);
 	}
+	
+	@Override
+	public void handleEvent(CyShutdownEvent e) {
+		cytoscapeShuttingDown = e.actuallyShutdown();
+	}
+
+	public void appShutdown() {
+		if(!cytoscapeShuttingDown) {
+			// the App is being updated or restarted, we want to save all the data first
+			save();
+		}
+	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/io/SessionModelIO.java

@@ -1,8 +1,6 @@
 package org.baderlab.csplugins.enrichmentmap.model.io;
 
-import java.awt.event.ActionEvent;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -16,7 +14,6 @@
 import org.baderlab.csplugins.enrichmentmap.style.ColumnDescriptor;
 import org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapMediator;
-import org.cytoscape.application.swing.AbstractCyAction;
 import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyIdentifiable;
@@ -91,10 +88,6 @@ public void saveModel() {
 		});
 	}
 
-	public void restoreModel() {
-		restoreModel(null);
-	}
-	
 	public void restoreModel(CySession session) {
 		if(debug)
 			System.out.println("SessionModelListener.restoreModel()");
@@ -239,16 +232,4 @@ private void clearTable(CyTable table) {
 		table.deleteRows(rowKeys);
 	}
 
-	
-	@SuppressWarnings("serial")
-	public List<AbstractCyAction> getDebugActions() {
-		return Arrays.asList(
-			new AbstractCyAction(CyActivator.APP_NAME + ": Save Model") {
-				{setPreferredMenu("Apps");}
-				public void actionPerformed(ActionEvent e) {
-					saveModel();
-				}
-			}
-		);
-	}
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/control/io/SessionViewIO.java

@@ -64,10 +64,6 @@ public void saveView() {
 		});
 	}
 
-	public void restoreView() {
-		restoreView(null);
-	}
-	
 	public void restoreView(CySession session) {
 		if (!headless) {
 			CyTable table = getPrivateTable();