Merge branch 'release/3.5.0'

app-impl/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>impl-parent</artifactId>
 		<groupId>org.cytoscape</groupId>
-		<version>3.4.0</version>
+		<version>3.5.0</version>
 	</parent>
 
 	<properties>
@@ -14,7 +14,7 @@
 
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>app-impl</artifactId>
-  <version>3.4.0</version>
+  <version>3.5.0</version>
 
 	<name>Cytoscape App Impl (${project.artifactId})</name>
 

app-impl/src/main/java/org/cytoscape/app/internal/CyAppAdapterImpl.java

@@ -38,6 +38,8 @@
 import org.cytoscape.command.util.NodeList;
 import org.cytoscape.command.util.RowList;
 import org.cytoscape.equations.AbstractFunction;
+import org.cytoscape.equations.event.EquationFunctionAddedEvent;
+import org.cytoscape.equations.event.EquationFunctionRemovedEvent;
 import org.cytoscape.event.CyEventHelper;
 import org.cytoscape.filter.TransformerManager;
 import org.cytoscape.filter.model.Transformer;
@@ -109,6 +111,7 @@
 import org.cytoscape.work.swing.DialogTaskManager;
 import org.cytoscape.work.swing.PanelTaskManager;
 import org.cytoscape.work.swing.undo.SwingUndoSupport;
+import org.cytoscape.work.swing.util.UserAction;
 import org.cytoscape.work.undo.UndoSupport;
 import org.cytoscape.work.util.BoundedDouble;
 
@@ -221,6 +224,8 @@ public class CyAppAdapterImpl implements CySwingAppAdapter {
 	private Transformers transformers;
 	private TransformerViewFactory transformerViewFactory;
 	private CyJobManager cyjobManager;
+	private EquationFunctionAddedEvent equationFunctionAddedEvent;
+	private EquationFunctionRemovedEvent equationFunctionRemovedEvent;
 
 /// from core-task api
 	private LoadVizmapFileTaskFactory loadVizmapFileTaskFactory;
@@ -295,6 +300,9 @@ public class CyAppAdapterImpl implements CySwingAppAdapter {
 	private CommandExecutorTaskFactory commandExecutorTaskFactory;
 	private AvailableCommands availableCommands;
 
+	// From work-swing-api
+	private UserAction userAction;
+
 	private LoadTableFileTaskFactory loadAttributesFileTaskFactory;
 	private LoadTableURLTaskFactory loadAttributesURLTaskFactory;
 

app-impl/src/main/java/org/cytoscape/app/internal/manager/AppManager.java

@@ -247,14 +247,17 @@ void initializeApps() {
 		for (App app: installOnRestartApps) {
 			try {
 				app.moveAppFile(this, new File(getInstalledAppsPath()));
+				userLogger.info("Moved app '" + app.getAppName() + "' that was marked for install on restart to the 'installed' directory.");				
 			} catch (IOException e) {
+				userLogger.error("Cannot move app '" + app.getAppName() + "' that was marked for install on restart to the 'installed' directory:", e);				
 			}
 		}
 
 		// Remove the install-on-restart directory after apps were moved
 		try {
 			FileUtils.deleteDirectory(new File(getInstallOnRestartAppsPath()));
 		} catch (IOException e) {
+			userLogger.warn("Could not delete the directory of apps to install on restart:", e);				
 		}
 
 		setupAlterationMonitor();
@@ -266,18 +269,22 @@ void initializeApps() {
 			try {
 				boolean appRegistered = false;
 				for (App regApp : apps) {
-					if (regApp.heuristicEquals(app))
+					if (regApp.heuristicEquals(app)) {
+						userLogger.warn("Disabled app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' is equal to an already registered app '" + regApp.getAppName() + "' in file '" + (regApp.getAppFile() == null ? "N/A" : regApp.getAppFile().getAbsolutePath()) + "'");
 						appRegistered = true;
+					}
 				}
 				if (!appRegistered) {
 					apps.add(app);
 					app.setStatus(AppStatus.DISABLED);
 				} else {
 					// Delete the copy
+					userLogger.info("Trying to delete the disabled copy of app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' because another copy exists.");				
 					FileUtils.deleteQuietly(app.getAppFile());
 					app.setAppFile(null);
 				}		
 			} catch (Throwable e) {
+				userLogger.error("Error validating status of the disabled app '" + app.getAppName() + "'.", e);				
 			}
 		}
 
@@ -286,18 +293,22 @@ void initializeApps() {
 			try {
 				boolean appRegistered = false;
 				for (App regApp : apps) {
-					if (regApp.heuristicEquals(app))
+					if (regApp.heuristicEquals(app)) {
+						userLogger.warn("Uninstalled app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' is equal to an already registered app '" + regApp.getAppName() + "' in file '" + (regApp.getAppFile() == null ? "N/A" : regApp.getAppFile().getAbsolutePath()) + "'");
 						appRegistered = true;
+					}
 				}
 				if (!appRegistered) {
 					apps.add(app);
 					app.setStatus(AppStatus.UNINSTALLED);
 				} else {
 					// Delete the copy
+					userLogger.info("Trying to delete the uninstalled copy of app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' because another copy exists.");				
 					FileUtils.deleteQuietly(app.getAppFile());
 					app.setAppFile(null);
 				}
 			} catch (Throwable e) {
+				userLogger.error("Error validating status of the uninstalled app '" + app.getAppName() + "'.", e);				
 			}
 		}
 
@@ -309,19 +320,35 @@ void initializeApps() {
 		for(App app: installedApps) {
 			boolean appRegistered = false;
 			for (App regApp : apps) {
-				if (regApp.heuristicEquals(app))
+				if (regApp.heuristicEquals(app)) {
+					userLogger.warn("Installed app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' is equal to an already registered app '" + regApp.getAppName() + "' in file '" + (regApp.getAppFile() == null ? "N/A" : regApp.getAppFile().getAbsolutePath()) + "'");
 					appRegistered = true;
+				}
 			}
 			if (!appRegistered) {
 				apps.add(app);
 				String appName = app.getAppName().toLowerCase();
 				App currentVersion = appsToStart.get(appName);
-				if(app.isCompatible(version) && (currentVersion == null ||  
-						compareApps(currentVersion, app) > 0))
-					appsToStart.put(appName, app);
+				if(app.isCompatible(version)) {
+					if (currentVersion == null) {
+						appsToStart.put(appName, app);
+					}
+					else if (compareApps(currentVersion, app) > 0) {
+						userLogger.warn("Installed app '" + app.getAppName() + "' version  " + app.getVersion() + " will override an older version (" + currentVersion.getVersion() + ") that was registered previously.");					
+						appsToStart.put(appName, app);						
+					}
+					else
+					{
+						userLogger.warn("Installed app '" + app.getAppName() + "' version " + app.getVersion() + " will not be started, because a newer version (" + currentVersion.getVersion() + ") was already registered.");					
+					}
+				}
+				else {
+					userLogger.error("Installed app '" + app.getAppName() + "' is not compatible with the running version of Cytoscape (" + version.getVersion() + ").");					
+				}
 			}
 			else {
 				// Delete the copy
+				userLogger.info("Trying to delete the installed copy of app '" + app.getAppName() + "' in file '" + app.getAppFile().getAbsolutePath() + "' because another copy exists.");				
 				FileUtils.deleteQuietly(app.getAppFile());
 				app.setAppFile(null);
 			}
@@ -365,6 +392,7 @@ private boolean startApps(Collection<App> apps) {
 			App app = i.next();
 			try {
 				app.load(this);
+				userLogger.info("Loaded app " + app.getAppName());
 			} catch (AppLoadingException e) {
 				i.remove();
 				success = false;
@@ -377,6 +405,7 @@ private boolean startApps(Collection<App> apps) {
 			try {
 				app.start(this);
 				app.setStatus(AppStatus.INSTALLED);
+				userLogger.info("Started app " + app.getAppName());
 			} catch (AppStartupException e) {
 				success = false;
 				app.setStatus(AppStatus.FAILED_TO_START);
@@ -409,36 +438,48 @@ public void onFileCreate(File file) {
 					parsedApp = appParser
 							.parseApp(file);
 				} catch (AppParsingException e) {
+					userLogger.error("Could not parse app from newly discovered file '" + file.getAbsolutePath() + "' :", e);
 					return;
 				}
 				boolean startApp = parsedApp.isCompatible(version);
+
+				if(!startApp) {
+					userLogger.error("Newly discovered app '" + parsedApp.getAppName() + "' is not compatible with the running version of Cytoscape (" + version + ").");					
+				}
+
 				App registeredApp = null;
 				for (App app : apps) {
 					if (parsedApp.heuristicEquals(app)) {
 						registeredApp = app;
 
+						userLogger.warn("Newly discovered app '" + parsedApp.getAppName() + "' in file '" + parsedApp.getAppFile().getAbsolutePath() + "' is equal to an already registered app '" + registeredApp.getAppName() + "' in file '" + (registeredApp.getAppFile() == null ? "N/A" : registeredApp.getAppFile().getAbsolutePath()) + "'");
+
 						// Delete old file if it was still there
 						File oldFile = registeredApp
 								.getAppFile();
 
 						if (oldFile != null && oldFile.exists() && !registeredApp
 								.getAppFile().equals(parsedApp
 										.getAppFile())) {
+							userLogger.info("Trying to delete the installed copy of app '" + registeredApp.getAppName() + "' in file '" + registeredApp.getAppFile().getAbsolutePath() + "' because another copy exists.");				
 							FileUtils.deleteQuietly(oldFile);
 						}
 
 						// Update file reference to reflect file having been moved
 						registeredApp.setAppFile(file);
 						registeredApp.setStatus(AppStatus.INACTIVE);
-					}
+					} 
 					else if(parsedApp.isCompatible(version) && parsedApp.getAppName().equals(app.getAppName())) {
 						try {
 							if(!app.isDetached() && app.isCompatible(version)) {
-								if(compareApps(parsedApp, app) > 0)
+								if(compareApps(parsedApp, app) > 0) {									
 									startApp = false;
+									userLogger.warn("Not starting newly discovered app '" + parsedApp.getAppName() + "' because a newer version is already loaded.");
+								}	
 								else {
 									app.unload(AppManager.this);
 									app.setStatus(AppStatus.INACTIVE);
+									userLogger.warn("Unloading app '" + app.getAppName() + "' because the newly discovered app '" + parsedApp.getAppName() + "' is a newer version.");
 								}
 							}
 						} catch (AppUnloadingException e) {
@@ -460,6 +501,7 @@ else if(parsedApp.isCompatible(version) && parsedApp.getAppName().equals(app.get
 						app.load(appManager);
 						app.start(appManager);
 						app.setStatus(AppStatus.INSTALLED);
+						userLogger.info("Started newly discovered app '" + app.getAppName() + "'.");
 					}
 				}
 				catch (AppLoadingException e) {
@@ -502,6 +544,7 @@ public void onFileDelete(File file) {
 				try {
 					registeredApp.unload(appManager);
 					registeredApp.setStatus(AppStatus.FILE_MOVED);
+					userLogger.info("Unloaded app '" + registeredApp.getAppName() + "', because its file is no longer available.");
 				}
 				catch (AppUnloadingException e) {
 					userLogger.warn("Failed to unload app " + registeredApp.getAppName(), e);
@@ -536,6 +579,7 @@ public void onFileDelete(File file) {
 						appToStart.load(appManager);
 						appToStart.start(appManager);
 						appToStart.setStatus(AppStatus.INSTALLED);
+						userLogger.info("Started app " + appToStart.getAppName() + " because a different version has been unloaded.");
 					}
 					catch (AppLoadingException e) {
 						appToStart.setStatus(AppStatus.FAILED_TO_LOAD);

app-impl/src/main/java/org/cytoscape/app/internal/ui/AppManagerDialog.java

@@ -24,9 +24,14 @@
 import org.cytoscape.app.internal.ui.downloadsites.DownloadSitesManager;
 import org.cytoscape.app.internal.ui.downloadsites.ManageDownloadSitesDialog;
 import org.cytoscape.util.swing.FileUtil;
+// import Help;
+// import org.cytoscape.util.swing.HelpImpl;
 import org.cytoscape.util.swing.LookAndFeelUtil;
 import org.cytoscape.work.TaskManager;
-
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import java.awt.Desktop;
+import java.net.URI;
 /*
  * #%L
  * Cytoscape App Impl (app-impl)
@@ -85,7 +90,7 @@ public AppManagerDialog(
         this.downloadSitesManager = downloadSitesManager;
         this.updateManager = updateManager;
         this.fileUtil = fileUtil;
-        this.taskManager = taskManager;
+        this.taskManager = taskManager;  
         initComponents();
 
         // Create new manage download sites dialog
@@ -128,7 +133,7 @@ public void actionPerformed(ActionEvent e) {
 			}
 		});
 
-        final JPanel buttonPanel = LookAndFeelUtil.createOkCancelPanel(null, closeButton);
+        final JPanel buttonPanel = LookAndFeelUtil.createOkCancelPanel(null, closeButton, "App_Manager");
 
         final GroupLayout layout = new GroupLayout(getContentPane());
         getContentPane().setLayout(layout);
@@ -185,4 +190,6 @@ public void run() {
             networkErrorLabel.setVisible(false);
         }
     }
-}
+
+
+ }

app-impl/src/main/java/org/cytoscape/app/internal/ui/CitationsDialog.java

@@ -207,7 +207,7 @@ public String toString(final String fmtString) {
  * Retrieves article summaries from PubMed and stores them in {@code Article} instances.
  */
 class PubMedParser {
-  static final String REQUEST_URL_BASE = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=";
+  static final String REQUEST_URL_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=";
 
   /**
    * Takes a sequence of PubMed IDs and returns a URL for requesting article summaries from PubMed.
@@ -405,4 +405,4 @@ private static void formatArticleAsHtmlDefinition(final String name, final Artic
 
   public void cancel() {
   }
-}
+}

app-impl/src/main/java/org/cytoscape/app/internal/util/DebugHelper.java

@@ -1,5 +1,8 @@
 package org.cytoscape.app.internal.util;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 /*
  * #%L
  * Cytoscape App Impl (app-impl)
@@ -28,13 +31,16 @@
  * A class used to manage print commands for aiding in debugging
  */
 public class DebugHelper {
+	private static final Logger sysLogger = LoggerFactory.getLogger(DebugHelper.class);
+
 	private static boolean debug = false;
 //	private static boolean debug = true;
 
 	public static void print(String message) {
 		if (debug) {
 			System.out.println("DebugHelper: " + message);
 		}
+		sysLogger.debug(message);
 	}
 
 	/**
@@ -46,5 +52,9 @@ public static void print(Object source, String message) {
 		if (debug) {
 			System.out.println("<" + source + ">: " + message);
 		}
+		if(sysLogger.isDebugEnabled())
+		{
+			sysLogger.debug("<" + source + ">: " + message);
+		}
 	}
 }

application-impl/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>impl-parent</artifactId>
 		<groupId>org.cytoscape</groupId>
-		<version>3.4.0</version>
+		<version>3.5.0</version>
 	</parent>
 
 	<properties>
@@ -14,7 +14,7 @@
 
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>application-impl</artifactId>
-  <version>3.4.0</version>
+  <version>3.5.0</version>
 
 	<name>Cytoscape Application Impl (${project.artifactId})</name>