Handle problem with EM 2.1 using wrong Bundle-Name.

Author: mikekucera

EnrichmentMapPlugin/pom.xml

@@ -4,8 +4,9 @@
 
 	<groupId>org.baderlab.csplugins</groupId>
 	<artifactId>enrichmentmap</artifactId>
-	<version>2.2</version>
+	<version>2.2.0</version>
 	<packaging>bundle</packaging>
+	<name>EnrichmentMap</name>
 
 	<properties>
 	    <project.name>EnrichmentMap</project.name>

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

@@ -7,6 +7,10 @@
 import static org.cytoscape.work.ServiceProperties.PREFERRED_MENU;
 import static org.cytoscape.work.ServiceProperties.TITLE;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Properties;
@@ -26,6 +30,7 @@
 import org.baderlab.csplugins.enrichmentmap.view.HeatMapPanel;
 import org.baderlab.csplugins.enrichmentmap.view.ParametersPanel;
 import org.baderlab.csplugins.enrichmentmap.view.PostAnalysisPanel;
+import org.cytoscape.application.CyApplicationConfiguration;
 import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.application.events.SetCurrentNetworkListener;
 import org.cytoscape.application.events.SetCurrentNetworkViewListener;
@@ -64,7 +69,9 @@
 import org.cytoscape.work.SynchronousTaskManager;
 import org.cytoscape.work.TaskFactory;
 import org.cytoscape.work.swing.DialogTaskManager;
+import org.osgi.framework.Bundle;
 import org.osgi.framework.BundleContext;
+import org.osgi.framework.Version;
 
 
 
@@ -98,17 +105,7 @@ public void start(BundleContext bc) {
 		@SuppressWarnings("rawtypes")
 		SynchronousTaskManager syncTaskManager = getService(bc, SynchronousTaskManager.class);
 		DialogTaskManager dialogTaskManager = getService(bc, DialogTaskManager.class);
-		// Used with annotations to make Groups of nodes
-		CyGroupFactory groupFactory = getService(bc, CyGroupFactory.class);
-		CyGroupManager groupManager = getService(bc, CyGroupManager.class);
-		// Used to create/remove the annotations (ellipses and text labels)
-		AnnotationManager annotationManager = getService(bc, AnnotationManager.class);
-		@SuppressWarnings("unchecked")
-		AnnotationFactory<ShapeAnnotation> shapeFactory = (AnnotationFactory<ShapeAnnotation>) getService(bc, AnnotationFactory.class, "(type=ShapeAnnotation.class)");    	
-		@SuppressWarnings("unchecked")
-		AnnotationFactory<TextAnnotation> textFactory = (AnnotationFactory<TextAnnotation>) getService(bc, AnnotationFactory.class, "(type=TextAnnotation.class)");
-		CommandExecutorTaskFactory commandExecutor = getService(bc, CommandExecutorTaskFactory.class);
-		//get the service registrar so we can register new services in different classes
+		CyApplicationConfiguration applicationConfiguration = getService(bc, CyApplicationConfiguration.class);
 		CyServiceRegistrar registrar = getService(bc, CyServiceRegistrar.class);
 
 
@@ -142,8 +139,7 @@ public void start(BundleContext bc) {
 		serviceProperties.put(IN_MENU_BAR, "true");
 		serviceProperties.put(PREFERRED_MENU, APP_MENU);
 		serviceProperties.put(INSERT_SEPARATOR_BEFORE, "true");
-		HelpAction helpAction = new HelpAction(serviceProperties, cyApplicationManagerRef, cyNetworkViewManagerRef,
-				registrar);
+		HelpAction helpAction = new HelpAction(serviceProperties, cyApplicationManagerRef, cyNetworkViewManagerRef, registrar);
 		helpAction.setMenuGravity(2.1f);
 
 		//About Action
@@ -210,5 +206,7 @@ public void start(BundleContext bc) {
 		tableColumnTaskFactoryProps.setProperty("tableTypes", "edge");
 		registerService(bc, tableColumnTaskFactory, TableColumnTaskFactory.class, tableColumnTaskFactoryProps);
 
+		Em21Handler.removeVersion21(bc, applicationConfiguration);
 	}
+	
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/Em21Handler.java

@@ -0,0 +1,76 @@
+package org.baderlab.csplugins.enrichmentmap;
+
+import java.io.File;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.cytoscape.application.CyApplicationConfiguration;
+import org.osgi.framework.Bundle;
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.Version;
+
+
+
+/**
+ * Version 2.1.0 of EnrichmentMap on the app store has the wrong Bundle-Name in the manifest file.
+ * It was accidentally set to "enrichmentmap" when it should be "EnrichmentMap".
+ * That means the cytoscape app manager won't remove version 2.1 when installing version 2.2 or higher.
+ * The only fix is to manually remove the 2.1 app file programatically, sigh.
+ */
+public class Em21Handler {
+	
+	private static final String baseName = "EnrichmentMap-v2.1.0";
+	
+	public static void removeVersion21(BundleContext bc, CyApplicationConfiguration appConfig) {
+		try {
+			if(isEM21Installed(bc)) {
+				System.out.println("EnrichmentMap 2.1 is installed");
+				
+				Path installFolder = getAppInstallFolder(appConfig);
+				Path jarFile = installFolder.resolve(baseName + ".jar");
+				
+				boolean deleted = Files.deleteIfExists(jarFile);
+				if(deleted) {
+					System.out.println("Deleted EnrichmentMap 2.1 App Jar file: " + jarFile);
+				}
+				else {
+					// We know its installed but the above code didn't delete the file.
+					// Sometimes the App manager appends numbers to the end of the file name, lets try that.
+					for(int i = 1; i <= 5; i++) {
+						jarFile = installFolder.resolve(baseName + "-" + i + ".jar");
+						deleted = Files.deleteIfExists(jarFile);
+						if(deleted) {
+							System.out.println("Deleted App Jar file: " + jarFile);
+							break;
+						}
+					}
+					if(!deleted) {
+						// For some reason the file couldn't be deleted.
+						// Don't pop up a warning dialog, because we've had UI deadocks by throwing up dialogs
+						// during cytoscape initialization. Just log it.
+						System.out.println("Could not automatically uninstall EnrichmentMap 2.1, please uninstall it using the App Manager");
+					}
+				}
+			}
+		} catch(Exception e) {
+			e.printStackTrace();
+		}
+	}
+	
+	private static boolean isEM21Installed(BundleContext bc) {
+		for(Bundle bundle : bc.getBundles()) {
+			String name = bundle.getSymbolicName();
+			Version version = bundle.getVersion();
+			if(name.equals("org.baderlab.csplugins.enrichmentmap") && version.equals(new Version(2,1,0))) {
+				return true;
+			}
+		}
+		return false;
+	}
+	
+	private static Path getAppInstallFolder(CyApplicationConfiguration appConfig) {
+		File configFolder = appConfig.getConfigurationDirectoryLocation();
+		Path installFolder = configFolder.toPath().resolve("3/apps/installed");
+		return installFolder;
+	}
+}