Fix various deployment problems

build.gradle

@@ -104,7 +104,10 @@ project(":core") {
         compile group: 'com.thoughtworks.xstream', name: 'xstream', version: '1.4.8'
         compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.4'
         compile group: 'com.google.guava', name: 'guava', version: '18.0'
-        compile group: 'com.google.inject', name: 'guice', version: '4.0'
+        // We use the no_aop version of Guice because the aop isn't avaiable in arm java
+        // http://stackoverflow.com/a/15235190/3708426
+        // https://github.com/google/guice/wiki/OptionalAOP
+        compile group: 'com.google.inject', name: 'guice', version: '4.0', classifier: 'no_aop'
         compile group: 'com.google.inject.extensions', name: 'guice-assistedinject', version: '4.0'
     }
 

core/src/main/java/edu/wpi/grip/core/GRIPCoreModule.java

@@ -16,8 +16,8 @@
 import edu.wpi.grip.core.sources.MultiImageFileSource;
 import edu.wpi.grip.core.util.ExceptionWitness;
 
-import java.util.logging.Level;
-import java.util.logging.Logger;
+import java.io.IOException;
+import java.util.logging.*;
 
 /**
  * A Guice {@link com.google.inject.Module} for GRIP's core package.  This is where instances of {@link Pipeline},
@@ -29,6 +29,47 @@ public class GRIPCoreModule extends AbstractModule {
     private final EventBus eventBus = new EventBus(this::onSubscriberException);
 
     public GRIPCoreModule() {
+        //Set up the global level logger. This handles IO for all loggers.
+        final Logger globalLogger = LogManager.getLogManager().getLogger("");//This is our global logger
+
+        try {
+            // Remove the default handlers that stream to System.err
+            for(Handler handler : globalLogger.getHandlers()) {
+                globalLogger.removeHandler(handler);
+            }
+
+            final Handler fileHandler = new FileHandler("%h/GRIP.log");//Log to the file "GRIPlogger.log"
+
+            //Set level to handler and logger
+            fileHandler.setLevel(Level.FINE);
+            globalLogger.setLevel(Level.FINE);
+
+            // We need to stream to System.out instead of System.err
+            final StreamHandler sh = new StreamHandler(System.out,  new SimpleFormatter()) {
+
+                @Override
+                public synchronized void publish(final LogRecord record) {
+                    super.publish(record);
+                    // For some reason this doesn't happen automatically.
+                    // This will ensure we get all of the logs printed to the console immediately
+                    // when running on a remote device.
+                    flush();
+                }
+            };
+            sh.setLevel(Level.CONFIG);
+
+            globalLogger.addHandler(sh); // Add stream handler
+
+            globalLogger.addHandler(fileHandler);//Add the handler to the global logger
+
+            fileHandler.setFormatter(new SimpleFormatter());//log in text, not xml
+
+            globalLogger.config("Configuration done.");//Log that we are done setting up the logger
+
+        } catch (IOException exception) {//Something happened setting up file IO
+            throw new IllegalStateException("Failed to configure the Logger", exception);
+        }
+
         Thread.setDefaultUncaughtExceptionHandler(this::onThreadException);
     }
 
@@ -68,6 +109,7 @@ private void onSubscriberException(Throwable exception, SubscriberExceptionConte
             logger.log(Level.FINE, "EventBus Subscriber threw InterruptedException", exception);
             Thread.currentThread().interrupt();
         } else {
+            logger.log(Level.SEVERE, "An event subscriber threw an exception", exception);
             eventBus.post(new UnexpectedThrowableEvent(exception, "An event subscriber threw an exception"));
         }
     }
@@ -77,6 +119,8 @@ private void onThreadException(Thread thread, Throwable exception) {
             logger.log(Level.FINE, "InterruptedException from thread " + thread, exception);
             Thread.currentThread().interrupt();
         } else {
+            // This can potentially happen before the main class has even been loaded to handle these exceptions
+            logger.log(Level.SEVERE, "Uncaught Exception on thread " + thread, exception);
             eventBus.post(new UnexpectedThrowableEvent(exception, thread + " threw an exception"));
         }
     }

core/src/main/java/edu/wpi/grip/core/Main.java

@@ -28,7 +28,9 @@ public class Main {
     @Inject
     private Logger logger;
 
+    @SuppressWarnings("PMD.SystemPrintln")
     public static void main(String[] args) throws IOException, InterruptedException {
+        System.out.println("Loading Dependency Injection Framework");
         final Injector injector = Guice.createInjector(new GRIPCoreModule());
         injector.getInstance(Main.class).start(args);
     }
@@ -38,31 +40,10 @@ public void start(String[] args) throws IOException, InterruptedException {
         if (args.length != 1) {
             System.err.println("Usage: GRIP.jar project.grip");
             return;
+        } else {
+            logger.log(Level.INFO, "Loading file " + args[0]);
         }
 
-        //Set up the global level logger. This handles IO for all loggers.
-        Logger globalLogger = LogManager.getLogManager().getLogger("");//This is our global logger
-
-        Handler fileHandler = null;//This will be our handler for the global logger
-
-        try {
-            fileHandler = new FileHandler("%h/GRIP.log");//Log to the file "GRIPlogger.log"
-
-            globalLogger.addHandler(fileHandler);//Add the handler to the global logger
-
-            fileHandler.setFormatter(new SimpleFormatter());//log in text, not xml
-
-            //Set level to handler and logger
-            fileHandler.setLevel(Level.FINE);
-            globalLogger.setLevel(Level.FINE);
-
-            globalLogger.config("Configuration done.");//Log that we are done setting up the logger
-
-        } catch (IOException exception) {//Something happened setting up file IO
-            throw new IllegalStateException(exception);
-        }
-
-
         Operations.addOperations(eventBus);
         CVOperations.addOperations(eventBus);
 
@@ -73,7 +54,7 @@ public void start(String[] args) throws IOException, InterruptedException {
 
 
         // This is done in order to indicate to the user using the deployment UI that this is running
-        System.out.println("SUCCESS! The project is running in headless mode!");
+        logger.log(Level.INFO, "SUCCESS! The project is running in headless mode!");
         // There's nothing more to do in the main thread since we're in headless mode - sleep forever
         for (; ; ) {
             Thread.sleep(Integer.MAX_VALUE);

ui/src/main/java/edu/wpi/grip/ui/DeployerController.java

@@ -55,13 +55,13 @@ public StreamToTextArea(TextArea outputArea) {
         }
 
         public StreamToTextArea reset() {
-            outputArea.clear();
+            Platform.runLater(outputArea::clear);
             return this;
         }
 
         @Override
         public void write(int i) throws IOException {
-            outputArea.appendText(String.valueOf((char) i));
+            Platform.runLater(()-> outputArea.appendText(String.valueOf((char) i)));
         }
     }
 

ui/src/main/java/edu/wpi/grip/ui/Main.java

@@ -20,8 +20,6 @@
 import javafx.stage.Stage;
 
 import javax.inject.Inject;
-import java.io.IOException;
-import java.util.logging.*;
 
 public class Main extends Application {
 
@@ -53,29 +51,6 @@ public Main() {
     @Override
     @SuppressWarnings("PMD.SignatureDeclareThrowsException")
     public void start(Stage stage) throws Exception {
-
-        //Set up the global level logger. This handles IO for all loggers.
-        Logger globalLogger = LogManager.getLogManager().getLogger("");//This is our global logger
-
-        Handler fileHandler = null;//This will be our handler for the global logger
-
-        try {
-            fileHandler = new FileHandler("%h/GRIP.log");//Log to the file "GRIP.log"
-
-            globalLogger.addHandler(fileHandler);//Add the handler to the global logger
-
-            fileHandler.setFormatter(new SimpleFormatter());//log in text, not xml
-
-            //Set level to handler and logger
-            fileHandler.setLevel(Level.FINE);
-            globalLogger.setLevel(Level.FINE);
-
-            globalLogger.config("Configuration done.");//Log that we are done setting up the logger
-
-        } catch (IOException exception) {//Something happened setting up file IO
-            throw new IllegalStateException(exception);
-        }
-
         root = FXMLLoader.load(Main.class.getResource("MainWindow.fxml"), null, null, injector::getInstance);
         root.setStyle("-fx-font-size: " + DPIUtility.FONT_SIZE + "px");
 

ui/src/main/java/edu/wpi/grip/ui/util/deployment/DeployedInstanceManager.java

@@ -180,6 +180,7 @@ public synchronized void start() throws IOException {
                 synchronized (this) {
                     sshThread = Optional.empty();
                 }
+                eventBus.post(new StartedStoppedEvent(this));
             }
         }, "SSH Monitor Thread");
         launcher.setUncaughtExceptionHandler((thread, exception) -> {
@@ -216,7 +217,6 @@ public synchronized void stop() throws IOException {
             }
             runStop();
         } while (isStarted() && !Thread.interrupted());
-        eventBus.post(new StartedStoppedEvent(this));
     }
 
     /**