Merge branch 'develop' of github.com:cytoscape/cytoscape-impl into de…

…velop
cytoscape · Nov 1, 2018 · a1aabf3 · a1aabf3
2 parents 8c5f877 + ecd205b
commit a1aabf3
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Showing 4 changed files with 66 additions and 56 deletions.
diff --git a/...ntation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/ui/AnnotationMediator.java b/...ntation-impl/src/main/java/org/cytoscape/ding/impl/cyannotator/ui/AnnotationMediator.java
@@ -196,6 +196,10 @@ public void handleEvent(SessionAboutToBeLoadedEvent evt) {
 	@Override
 	public void handleEvent(SessionLoadedEvent evt) {
 		loadingSession = false;
+
+		if (mainPanel == null)
+			return;
+
 		mainPanel.clearAnnotationButtonSelection();
 
 		final Set<CyNetworkView> allViews = serviceRegistrar.getService(CyNetworkViewManager.class).getNetworkViewSet();

diff --git a/gui-cmdline-parser-impl/pom.xml b/gui-cmdline-parser-impl/pom.xml
@@ -104,6 +104,10 @@
 			<groupId>org.cytoscape</groupId>
 			<artifactId>core-task-api</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.cytoscape</groupId>
+			<artifactId>app-api</artifactId>
+		</dependency>
 	</dependencies>
 
 

diff --git a/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/CyActivator.java b/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/CyActivator.java
@@ -1,12 +1,28 @@
 package org.cytoscape.cmdline.gui.internal;
 
+import java.util.Properties;
+
+import org.cytoscape.app.event.AppsFinishedStartingListener;
+import org.cytoscape.application.CyShutdown;
+import org.cytoscape.application.CyVersion;
+import org.cytoscape.cmdline.CommandLineArgs;
+import org.cytoscape.io.util.StreamUtil;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.service.util.AbstractCyActivator;
+import org.cytoscape.service.util.CyServiceRegistrar;
+import org.cytoscape.task.read.LoadNetworkFileTaskFactory;
+import org.cytoscape.task.read.LoadNetworkURLTaskFactory;
+import org.cytoscape.task.read.LoadVizmapFileTaskFactory;
+import org.cytoscape.task.read.OpenSessionTaskFactory;
+import org.osgi.framework.BundleContext;
+
 /*
  * #%L
  * Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl)
  * $Id:$
  * $HeadURL:$
  * %%
- * Copyright (C) 2006 - 2013 The Cytoscape Consortium
+ * Copyright (C) 2006 - 2018 The Cytoscape Consortium
  * %%
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as 
@@ -24,45 +40,28 @@
  * #L%
  */
 
-import java.util.Properties;
-
-import org.cytoscape.application.CyShutdown;
-import org.cytoscape.application.CyVersion;
-import org.cytoscape.cmdline.CommandLineArgs;
-import org.cytoscape.io.util.StreamUtil;
-import org.cytoscape.property.CyProperty;
-import org.cytoscape.service.util.AbstractCyActivator;
-import org.cytoscape.service.util.CyServiceRegistrar;
-import org.cytoscape.task.read.LoadNetworkFileTaskFactory;
-import org.cytoscape.task.read.LoadNetworkURLTaskFactory;
-import org.cytoscape.task.read.LoadVizmapFileTaskFactory;
-import org.cytoscape.task.read.OpenSessionTaskFactory;
-import org.cytoscape.work.TaskManager;
-import org.osgi.framework.BundleContext;
-
 public class CyActivator extends AbstractCyActivator {
-	public CyActivator() {
-		super();
-	}
 
+	@Override
+	@SuppressWarnings("unchecked")
 	public void start(BundleContext bc) {
-		CommandLineArgs args = getService(bc,CommandLineArgs.class);
-		CyVersion cyVersion = getService(bc,CyVersion.class);
-		CyShutdown cyShutdown = getService(bc,CyShutdown.class);
-		StreamUtil streamUtil = getService(bc,StreamUtil.class);
+		CommandLineArgs args = getService(bc, CommandLineArgs.class);
+		CyVersion cyVersion = getService(bc, CyVersion.class);
+		CyShutdown cyShutdown = getService(bc, CyShutdown.class);
+		StreamUtil streamUtil = getService(bc, StreamUtil.class);
 		OpenSessionTaskFactory loadSession = getService(bc, OpenSessionTaskFactory.class);
 		LoadNetworkFileTaskFactory networkFileLoader = getService(bc, LoadNetworkFileTaskFactory.class);
 		LoadNetworkURLTaskFactory networkURLLoader = getService(bc, LoadNetworkURLTaskFactory.class);
 		LoadVizmapFileTaskFactory visualStylesLoader = getService(bc, LoadVizmapFileTaskFactory.class);
-		TaskManager <?,?> taskManager = getService(bc, TaskManager.class);
 		CyServiceRegistrar registrar = getService(bc, CyServiceRegistrar.class);
-
-		CyProperty<Properties> props = (CyProperty<Properties>)getService(bc, CyProperty.class, "(cyPropertyName=cytoscape3.props)");
 
-		StartupConfig sc = new StartupConfig(props.getProperties(),streamUtil, loadSession, networkFileLoader, networkURLLoader, visualStylesLoader, taskManager, registrar);
+		CyProperty<Properties> props = (CyProperty<Properties>) getService(bc, CyProperty.class, "(cyPropertyName=cytoscape3.props)");
 
+		StartupConfig sc = new StartupConfig(props.getProperties(), streamUtil, loadSession, networkFileLoader,
+				networkURLLoader, visualStylesLoader, registrar);
+		registerService(bc, sc, AppsFinishedStartingListener.class);
 
-		Parser p = new Parser(args.getArgs(), cyShutdown, cyVersion, sc,props.getProperties());
+		Parser p = new Parser(args.getArgs(), cyShutdown, cyVersion, sc, props.getProperties());
 		sc.start();
 	}
 }
diff --git a/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/StartupConfig.java b/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/StartupConfig.java
@@ -9,6 +9,8 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.cytoscape.app.event.AppsFinishedStartingEvent;
+import org.cytoscape.app.event.AppsFinishedStartingListener;
 import org.cytoscape.application.CyUserLog;
 import org.cytoscape.io.util.StreamUtil;
 import org.cytoscape.property.CyProperty;
@@ -50,7 +52,7 @@
  * #L%
  */
 
-public class StartupConfig {
+public class StartupConfig implements AppsFinishedStartingListener {
 
 	private static final Logger logger = LoggerFactory.getLogger(CyUserLog.NAME);
 
@@ -62,14 +64,14 @@ public class StartupConfig {
 	private LoadNetworkFileTaskFactory networkFileLoader;
 	private LoadNetworkURLTaskFactory networkURLLoader;
 	private LoadVizmapFileTaskFactory visualStylesLoader;
-	private final TaskManager taskManager;
 
 	private final CyServiceRegistrar registrar;
 
 	private File sessionName;
 	private ArrayList<File> networkFiles;
 	private ArrayList<URL> networkURLs;
 	private ArrayList<File> vizmapFiles;
+	private ArrayList<TaskIterator> taskIteratorList;
 
 	public StartupConfig(
 			Properties globalProps,
@@ -78,7 +80,6 @@ public StartupConfig(
 			LoadNetworkFileTaskFactory networkFileLoader,
 			LoadNetworkURLTaskFactory networkURLLoader,
 			LoadVizmapFileTaskFactory visualStylesLoader,
-			TaskManager taskManager,
 			CyServiceRegistrar registrar
 	) {
 		this.globalProps = globalProps;
@@ -87,14 +88,32 @@ public StartupConfig(
 		this.networkFileLoader = networkFileLoader;
 		this.networkURLLoader = networkURLLoader;
 		this.visualStylesLoader = visualStylesLoader;
-		this.taskManager = taskManager;
-
 		this.registrar = registrar;
 		networkFiles= new ArrayList<>();
 		networkURLs = new ArrayList<>();
 		vizmapFiles = new ArrayList<>();
+		taskIteratorList = new ArrayList<>();
 	}
 
+	@Override
+	public void handleEvent(AppsFinishedStartingEvent evt) {
+		// We should only load sessions after Cytoscape and apps have been initialized!
+		if (!taskIteratorList.isEmpty()) {
+			Task initTask = new DummyTask();
+			TaskIterator taskIterator = new TaskIterator(taskIteratorList.size(), initTask);
+
+			for (int i = taskIteratorList.size() - 1; i >= 0; i--) {
+				TaskIterator ti = taskIteratorList.get(i);
+				taskIterator.insertTasksAfter(initTask, ti);
+			}
+
+			taskIteratorList.clear();
+
+			TaskManager <?,?> taskManager = registrar.getService(TaskManager.class);
+			taskManager.execute(taskIterator);
+		}
+	}
+
 	public void setProperties(String[] potentialProps) {
 		Properties argProps = new Properties();
 
@@ -205,32 +224,27 @@ public void setVizMapProps(String[] args){
 		taskStart = true;
 	}
 
-	public void start() {
+	protected void start() {
 		// set the properties
 		// no need to do this in a task since it's so fast
 		//globalProps.putAll(localProps);
 
 		CyProperty<Properties> commandline = new SimpleCyProperty<>("commandline", localProps,
 				Properties.class, CyProperty.SavePolicy.DO_NOT_SAVE);
 		Properties cmdlnProps = new Properties();
-		cmdlnProps.setProperty("cyPropertyName","commandline.props");
+		cmdlnProps.setProperty("cyPropertyName", "commandline.props");
 		registrar.registerService(commandline, CyProperty.class, cmdlnProps);
 
-		// Only proceed if we've specified tasks for execution
-		// on the command line.
-		if ( !taskStart )
+		// Only proceed if we've specified tasks for execution on the command line.
+		if (!taskStart)
 			return;
 
 		// Since we've set command line args we presumably
-		// don't want to see the welcome screen, so we
-		// disable it here.
-		globalProps.setProperty("tempHideWelcomeScreen","true");
-
-		ArrayList<TaskIterator> taskIteratorList = new ArrayList<>();
+		// don't want to see the welcome screen, so we disable it here.
+		globalProps.setProperty("tempHideWelcomeScreen", "true");
 
 		if (sessionName != null) {
 			taskIteratorList.add(loadSession.createTaskIterator(sessionName));
-
 		} else {
 			for (File network : networkFiles)
 				taskIteratorList.add(networkFileLoader.createTaskIterator(network));
@@ -239,16 +253,6 @@ public void start() {
 			for (File vizmap : vizmapFiles)
 				taskIteratorList.add(visualStylesLoader.createTaskIterator(vizmap));
 		}
-
-		Task initTask = new DummyTask();
-		TaskIterator taskIterator = new TaskIterator(taskIteratorList.size(), initTask);
-		for (int i= taskIteratorList.size()-1; i>= 0 ; i--){
-			TaskIterator ti = taskIteratorList.get(i);
-			taskIterator.insertTasksAfter(initTask, ti);
-		}
-
-		taskManager.execute(taskIterator);
-
 	}
 
 	private class DummyTask extends AbstractTask{
@@ -257,6 +261,5 @@ private class DummyTask extends AbstractTask{
 		public void run(TaskMonitor taskMonitor) throws Exception {
 			//DO nothing it is a dummy task just to initiate the iterator
 		}
-
 	}
 }