First working (messy) version of client/server split

FDA-1

ch.psi.fda/Readme.md

@@ -16,7 +16,7 @@ To use the FDA libary in an other project use:
 
 # Development
 When checking out the project from the repository there is the `target/generated-sources/xjc` folder missing.
-After checking out the project execute `mvn compile` to create the folder and the required classes.
+After checking out the project execute `mvn compile` to create the folder and the required classes. 
 
 To build project use `mvn clean install`.
 

ch.psi.fda/src/main/java/ch/psi/fda/AcquisitionRMain.java

@@ -0,0 +1,426 @@
+/**
+ * 
+ * Copyright 2010 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * This code is distributed in the hope that it will be useful,
+ * but without any warranty; without even the implied warranty of
+ * merchantability or fitness for a particular purpose. See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+package ch.psi.fda;
+
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.File;
+import java.io.PrintWriter;
+import java.util.HashMap;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.ScrollPaneLayout;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+
+import com.google.common.eventbus.AsyncEventBus;
+import com.google.common.eventbus.EventBus;
+
+import sun.misc.Signal;
+import sun.misc.SignalHandler;
+import ch.psi.fda.aq.VisualizationMapper;
+import ch.psi.fda.gui.ProgressPanel;
+import ch.psi.fda.gui.ScrollableFlowPanel;
+import ch.psi.fda.install.ApplicationConfigurator;
+import ch.psi.fda.model.ModelManager;
+import ch.psi.fda.model.v1.Configuration;
+import ch.psi.fda.model.v1.Data;
+import ch.psi.fda.rest.RestClient;
+import ch.psi.fda.visualizer.Visualizer;
+
+/**
+ * Entry class for command line based data acquisition
+ */
+@SuppressWarnings("restriction")
+public class AcquisitionRMain {
+
+	private static Logger logger = Logger.getLogger(AcquisitionRMain.class.getName());
+	
+	private static boolean abortedViaSignal = false;
+	
+	/**
+	 * Main Program
+	 * Process exit code: -1 if wrong number of arguments are passed
+	 * Process exit code: 3 if aborted via Ctrl+C
+	 * 
+	 * @param args	Arguments of the program
+	 */
+	public static void main(String[] args) {
+
+		String scriptname = "fda_scan";
+		
+		Integer iterations = null;
+		boolean autoclose = false;
+		boolean nogui = false;
+		String files[] = null;
+		
+		HashMap<String,String> varTable = new HashMap<String,String>();
+		
+		// Iterations option
+		OptionBuilder.hasArg();
+        OptionBuilder.withArgName("iterations");
+        OptionBuilder.withDescription("Number of iterations");
+        OptionBuilder.withType(new Integer(1));
+        Option o_iterations = OptionBuilder.create( "iterations");
+        
+        // Variables option
+        OptionBuilder.hasArg();
+        OptionBuilder.withArgName("variables");
+        OptionBuilder.withDescription("Scan variables - variables are specified in the form var=value,var2=value2");
+        OptionBuilder.withType(new Integer(1));
+        Option o_variables = OptionBuilder.create( "variables");
+        
+        Option o_autoclose = new Option( "autoclose", "Close down application after scan" );
+        Option o_init = new Option( "initialize", "Initialize application directories and configuration files" );
+        Option o_nogui = new Option( "nogui", "Do not show scan GUI" );
+        
+        Options options = new Options();
+        options.addOption(o_variables);
+        options.addOption(o_iterations);
+        options.addOption(o_autoclose);
+        options.addOption(o_init);
+        options.addOption(o_nogui);
+        
+        CommandLineParser parser = new GnuParser();
+        // Parse the command line arguments
+        try {
+			CommandLine line = parser.parse( options, args );
+			
+			// Initialize application
+			if( line.hasOption(o_init.getOpt()) ){
+				// Initialize application
+				ApplicationConfigurator ac = new ApplicationConfigurator();
+				ac.initializeApplication();
+				System.exit(0);
+			}
+			
+			if(line.getArgs().length<1){
+				throw new ParseException("One argument is required");
+			}
+			
+			files=line.getArgs();
+			
+			// Iterations option
+			if( line.hasOption(o_iterations.getOpt()) ){
+            	iterations = Integer.parseInt(line.getOptionValue(o_iterations.getOpt()));
+            }
+		
+			// Variables
+			if( line.hasOption(o_variables.getOpt()) ){
+				String variables = line.getOptionValue(o_variables.getOpt() );
+				String[] vars = variables.split(",");
+				for(String varp:vars){
+					String[] pair = varp.split("=");
+					if(pair.length!=2){
+						throw new ParseException("Variables are not specified the correct way. -variables var1=val1,var2=val2");
+					}
+					varTable.put(pair[0], pair[1]);
+				}
+			}
+			
+			// Autoclose option
+            if( line.hasOption( o_autoclose.getOpt() ) ) {
+                autoclose = true;
+            }
+            
+            // No GUI option
+            if( line.hasOption( o_nogui.getOpt() ) ) {
+                nogui = true;
+            }
+		
+        } catch (ParseException e) {
+			System.err.println(e.getMessage());
+			HelpFormatter formatter = new HelpFormatter();
+			formatter.printUsage(new PrintWriter(System.out, true), HelpFormatter.DEFAULT_WIDTH, scriptname, options);
+			System.exit(-1);
+		}
+		
+        // Run application
+        try{
+        	for(String file: files){
+        		run(new File(file), iterations, autoclose, nogui);
+        	}
+        	
+    		// Close application automatically if autoclose option is set (and visualizations are specified)
+    		if(nogui || autoclose ){	
+    			System.exit(0);
+    		}
+    		
+        }
+		catch(Exception ee){
+			System.out.println("Acquisition failed due to: "+ee.getMessage());
+			logger.log(Level.SEVERE, "Acquisition failed due to: ", ee); // Do not print stack trace
+			System.exit(-1);
+		}
+
+	}
+	
+	/**
+	 * Run scan
+	 * @param file			Scan file
+	 * @param iterations	Number of iterations
+	 * @param autoclose		Flag whether to close the application automatically after the scan
+	 * @param nogui			Flag whether to run the scan with a GUI
+	 */
+	public static void run(File file, Integer iterations, boolean autoclose, boolean nogui){
+		
+//		// Initialize application
+//		ApplicationConfigurator ac = new ApplicationConfigurator();
+//		ac.initializeApplication();
+		
+		if(!file.exists()){
+			throw new RuntimeException("File "+file.getAbsolutePath()+" does not exist");
+		}
+		
+		Configuration c;
+		try {
+			c = ModelManager.unmarshall(file);
+		} catch (Exception e) {
+			throw new RuntimeException("Unable to deserialize configuration: "+e.getMessage(), e);
+		}
+		
+		// Set data file name
+		// Determine name used for the data file
+		String name = file.getName();
+		name = name.replaceAll("\\.xml$", "");
+		
+		if(c.getData()!=null){
+			Data data = c.getData();
+			// Only update filename if no name is specified in xml file
+			if(data.getFileName()==null){
+				data.setFileName(name);
+			}
+		}
+		else{
+			Data data = new Data();
+			data.setFileName(name);
+			c.setData(data);
+		}
+		
+		
+		// Override number of executions
+		if(iterations != null){
+			c.setNumberOfExecution(iterations);
+		}
+		// Fix configuration if iterations is specified with 0 and no iterations option is specified
+		if(c.getNumberOfExecution()==0){
+			c.setNumberOfExecution(1);
+		}
+		
+		// Create/get acquisition engine
+//		final Acquisition acquisition = new Acquisition(new DefaultChannelService(), new AcquisitionConfiguration());
+		
+		boolean vis = false;
+		// Only register data visualization task/processor if there are visualizations
+		if(c.getVisualization().size()>0 && !nogui){
+			vis=true;
+		}
+		
+		EventBus b = new AsyncEventBus(Executors.newSingleThreadExecutor());
+		
+		final RestClient client = new RestClient();
+		
+		
+//		acquisition.initalize(b, c);
+		
+		Visualizer visualizer = null;
+		// Only register data visualization task/processor if there are visualizations
+		if(vis){
+			final StreamClient sclient = new StreamClient(b);
+			Executors.newSingleThreadExecutor().execute(new Runnable() {
+				@Override
+				public void run() {
+					sclient.listen();
+				}
+			});
+			
+			visualizer = new Visualizer(VisualizationMapper.mapVisualizations(c.getVisualization()));
+			b.register(visualizer);
+			
+			// TODO eventually set update on delimiter/dim boundary here
+			
+			// If there is a continous dimension only update plot at the end of a line
+			if(c.getScan() != null && c.getScan().getCdimension()!=null){
+                visualizer.setUpdateAtStreamElement(false);
+                visualizer.setUpdateAtStreamDelimiter(true);
+                visualizer.setUpdateAtEndOfStream(true);
+            }
+		}
+		
+		// GUI GUI GUI GUI GUI GUI GUI
+		ProgressPanel progressPanel = null;
+		if(visualizer != null){ // Only bring up GUI if there are some plots ...
+			// Visualizations
+			JPanel opanel = new ScrollableFlowPanel();
+	        opanel.setLayout(new FlowLayout());
+	        
+	        JScrollPane spane = new JScrollPane(opanel, ScrollPaneLayout.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneLayout.HORIZONTAL_SCROLLBAR_NEVER);
+	        JTabbedPane tpane = new JTabbedPane();
+	        tpane.addTab("Overview", spane);
+	        
+	        for(JPanel p: visualizer.getPlotPanels()){
+				opanel.add(p);
+			}
+	        
+				final JFrame frame = new JFrame("FDA: "+file);
+				frame.setSize(1200,800);
+				
+				// Create progress panel
+				progressPanel = new ProgressPanel();
+	            progressPanel.addActionListener(new ActionListener() {
+					
+					@Override
+					public void actionPerformed(ActionEvent e) {
+						try {
+							client.stop();
+						} catch (Exception e1) {
+							logger.log(Level.SEVERE, "Exception occured while aborting scan", e1);
+						}
+						
+					}
+				});
+				
+				
+				JSplitPane splitPane = new JSplitPane();
+				splitPane.setLeftComponent(progressPanel);
+				splitPane.setRightComponent(tpane);
+				
+				frame.add(splitPane);
+				frame.addWindowListener(new WindowAdapter(){
+					@Override
+					public void windowClosing(WindowEvent we){
+						if(client.isActive()){
+							// Abort acquisition
+							client.stop();
+						}
+						
+						// Wait until acquisition is aborted. Maximum wait 10*100milliseconds before forcefully
+						// terminate application
+						int count=0;
+						while(client.isActive()){
+							if(count == 10){
+								break;
+							}
+							
+							// Sleep 100 milliseconds
+							try {
+								Thread.sleep(100);
+							} catch (InterruptedException e) {
+								// TODO Auto-generated catch block
+								e.printStackTrace();
+							}
+							count++;
+						}
+						
+						// Terminate program
+						System.exit(0);
+					}
+				});
+				frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);//.DO_NOTHING_ON_CLOSE);
+//				frame.setVisible(true);
+				
+				java.awt.EventQueue.invokeLater(new Runnable() {
+		            public void run() {
+		                frame.setVisible(true);
+		            }
+		        });		
+		}
+		// GUI GUI GUI GUI GUI GUI GUI
+		
+		// CLI CLI CLI CLI
+		// Register the scan engine as Signal Handler
+		Signal.handle(new Signal("INT"), new SignalHandler() {
+			/**
+			 * Thread save signal counter
+			 */
+			private AtomicInteger signalCount= new AtomicInteger(0);
+			
+			/**
+			 * Testing signal handler (in Eclipse) use this after starting scan:
+			 *
+			 * SL5: A=`ps -ef | tail -10 | grep jav[a] | awk '{printf $2}'`;kill -2 $A
+			 * MacOS X: A=`ps -ef | grep AcquisitionMai[n] | awk '{printf $2}'`;kill -2 $A
+			 * 
+			 * on the command line use CTRL-C
+			 */
+			@Override
+			public void handle(Signal signal) {
+				
+				logger.finest("Received signal: "+signal);
+				
+				int count = signalCount.incrementAndGet();
+				
+				// If signal is received more than 1 time forcefully abort application
+				if(count>1){
+					logger.info("Terminate application");
+					System.exit(2);
+				}
+
+				abortedViaSignal = true;
+				// Abort acquisition engine
+				if(client.isActive()){
+					// Abort acquisition
+					client.stop();
+				}
+			}
+		});
+		// CLI CLI CLI CLI
+		
+		
+		if(visualizer != null){
+			visualizer.configure();
+		}
+		client.acquire(c);
+		
+		
+		// GUI GUI GUI GUI GUI GUI GUI
+		// Set progress panel to done
+//		if(progressPanel != null){
+//			// Can this be done via a Listener?
+//			progressPanel.done();
+//		}
+		// GUI GUI GUI GUI GUI GUI GUI
+		
+		if(abortedViaSignal){
+			System.exit(3);
+		}
+	}
+	
+	
+
+}

ch.psi.fda/src/main/java/ch/psi/fda/StreamClient.java

@@ -0,0 +1,73 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.ObjectInput;
+import java.io.ObjectInputStream;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.jeromq.ZMQ;
+
+import com.google.common.eventbus.EventBus;
+
+/**
+ * 
+ */
+public class StreamClient {
+	
+	private static final Logger logger = Logger.getLogger(StreamClient.class.getName());
+
+	private final EventBus bus;
+	
+	public StreamClient(EventBus bus){
+		this.bus = bus;
+	}
+	
+	public void listen() {
+		ZMQ.Context context = ZMQ.context();
+		zmq.ZError.clear(); // Clear error code
+		ZMQ.Socket socket = context.socket(ZMQ.SUB);
+		socket.connect("tcp://emac:10000");
+		socket.subscribe(""); // SUBSCRIBE !
+
+		while (true) {
+			byte[] content = null;
+			// String header = socket.recvStr(); // header
+			socket.recvStr(); // header
+			while (socket.hasReceiveMore()) {
+				content = socket.recv();
+			}
+			if (content == null) { // we lost something discard read messages
+				logger.warning("Lost some message - discard and continue");
+				continue;
+			}
+
+			try (ByteArrayInputStream bis = new ByteArrayInputStream(content); ObjectInput in = new ObjectInputStream(bis);) {
+				Object o = in.readObject();
+				bus.post(o);
+			} catch (IOException | ClassNotFoundException e) {
+				logger.log(Level.WARNING, "Unable to deserialize message", e);
+			}
+
+		}
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/ViewerMain.java

@@ -22,10 +22,6 @@ package ch.psi.fda;
 import java.awt.FlowLayout;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.ObjectInput;
-import java.io.ObjectInputStream;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Level;
@@ -37,8 +33,6 @@ import javax.swing.JScrollPane;
 import javax.swing.JTabbedPane;
 import javax.swing.ScrollPaneLayout;
 
-import org.jeromq.ZMQ;
-
 import com.google.common.eventbus.EventBus;
 
 import ch.psi.fda.gui.ScrollableFlowPanel;
@@ -107,35 +101,7 @@ public class ViewerMain {
 		bus.register(visualizer);
 		visualizer.configure();
 		
-		ZMQ.Context context = ZMQ.context();
-		zmq.ZError.clear(); // Clear error code
-		ZMQ.Socket socket = context.socket(ZMQ.SUB);
-		socket.connect("tcp://emac:10000");
-		socket.subscribe(""); // SUBSCRIBE !
-		
-		while(true){
-			byte[] content = null;
-//			String header = socket.recvStr(); // header
-			socket.recvStr(); // header
-			while(socket.hasReceiveMore()){
-				content = socket.recv();
-			}
-			if(content==null){ // we lost something discard read messages
-				logger.warning("Lost some message - discard and continue");
-				continue;
-			}
-			
-			try (
-					ByteArrayInputStream bis = new ByteArrayInputStream(content); 
-					ObjectInput in = new ObjectInputStream(bis);
-				) {
-				Object o = in.readObject();
-				bus.post(o);
-			} catch (IOException | ClassNotFoundException e) {
-				logger.log(Level.WARNING,"Unable to deserialize message",e);
-			}
-			
-		}
+		new StreamClient(bus).listen();
 	}	
 	
 	/**

ch.psi.fda/src/main/java/ch/psi/fda/rest/AcquisitionEngine.java

@@ -167,4 +167,14 @@ public class AcquisitionEngine {
 			}
 		}
 	}
+
+	/**
+	 * @return
+	 */
+	public boolean isActive() {
+		if(acquisition==null){
+			return false;
+		}
+		return acquisition.isActive();
+	}
 }

ch.psi.fda/src/main/java/ch/psi/fda/rest/RestClient.java

@@ -0,0 +1,58 @@
+/**
+ * 
+ * Copyright 2013 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.fda.rest;
+
+import javax.ws.rs.client.Client;
+import javax.ws.rs.client.ClientBuilder;
+import javax.ws.rs.client.Entity;
+import javax.ws.rs.client.WebTarget;
+import javax.ws.rs.core.MediaType;
+import javax.xml.bind.JAXBElement;
+import javax.xml.namespace.QName;
+
+import org.glassfish.jersey.jackson.JacksonFeature;
+
+import ch.psi.fda.model.v1.Configuration;
+
+/**
+ * 
+ */
+public class RestClient {
+
+	
+	
+	private Client client = ClientBuilder.newClient().register(JacksonFeature.class);
+	private WebTarget target = client.target("http://emac:8080").path("fda");
+	 
+
+	 
+	public String acquire(Configuration c){
+		// Wrap configuration in JAXBElement as there is no @XmlRootElement available within the generated Configuration class
+		JAXBElement<Configuration> jaxbElement = new JAXBElement<>(new QName("ROOT"), Configuration.class, c);
+		return target.request().post(Entity.entity(jaxbElement, MediaType.APPLICATION_XML), String.class);
+	}
+	
+	public void stop(){
+		target.request().delete();
+	}
+	
+	public boolean isActive(){
+		return target.request().get(Boolean.class);
+	}
+}

ch.psi.fda/src/main/java/ch/psi/fda/rest/RestServer.java

@@ -55,11 +55,17 @@ public class RestServer {
 
 		ResourceBinder binder = new ResourceBinder();
 		
-		ResourceConfig resourceConfig = new ResourceConfig(JacksonFeature.class);
+		ResourceConfig resourceConfig = new ResourceConfig();
 		resourceConfig.packages(RestServer.class.getPackage().getName()+".services"); // Services are located in services package
 		resourceConfig.register(binder);
+		
+		resourceConfig.register(JacksonFeature.class);
+		
+		
 		HttpServer server = GrizzlyHttpServerFactory.createHttpServer(baseUri, resourceConfig);
 
+		
+		
 		// Static content
 //		String home = System.getenv("FDA_BASE");
 //		if (home == null) {

ch.psi.fda/src/main/java/ch/psi/fda/rest/services/ScanService.java

@@ -22,6 +22,7 @@ package ch.psi.fda.rest.services;
 import javax.inject.Inject;
 import javax.ws.rs.Consumes;
 import javax.ws.rs.DELETE;
+import javax.ws.rs.GET;
 import javax.ws.rs.POST;
 import javax.ws.rs.Path;
 import javax.ws.rs.core.MediaType;
@@ -37,7 +38,6 @@ public class ScanService {
 	
 	@POST
 	@Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
-//	@Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
 	public String execute(Configuration configuration) throws InterruptedException{
 		return aengine.submit(configuration);
 	}
@@ -46,4 +46,10 @@ public class ScanService {
 	public void stop(){
 		aengine.terminate();
 	}
+	
+	@GET
+	public boolean isActive(){
+		return aengine.isActive();
+	}
+	
 }