collectserver.java

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    // Setup menu
    JMenuBar menuBar = new JMenuBar();

    JMenu fileMenu = new JMenu("File");
    fileMenu.setMnemonic(KeyEvent.VK_F);
    menuBar.add(fileMenu);
    serialItem = new JMenuItem("Connect to serial");
    serialItem.addActionListener(new SerialItemHandler());
    fileMenu.add(serialItem);
    JMenuItem item = new JMenuItem("Program Sky nodes...");
    item.addActionListener(new ProgramItemHandler());
    fileMenu.add(item);

    fileMenu.addSeparator();
    final JMenuItem clearMapItem = new JMenuItem("Remove Map Background");
    clearMapItem.addActionListener(new ActionListener() {

      public void actionPerformed(ActionEvent e) {
        mapPanel.setMapBackground(null);
        clearMapItem.setEnabled(false);
        configTable.remove("collect.mapimage");
      }

    });
    clearMapItem.setEnabled(mapPanel.getMapBackground() != null);

    item = new JMenuItem("Select Map Background...");
    item.addActionListener(new ActionListener() {

      public void actionPerformed(ActionEvent e) {
        if (fileChooser == null) {
          fileChooser = new JFileChooser();
          int reply = fileChooser.showOpenDialog(window);
          if (reply == JFileChooser.APPROVE_OPTION) {
            File file = fileChooser.getSelectedFile();
            String name = file.getAbsolutePath();
            configTable.put("collect.mapimage", name);
            if (!mapPanel.setMapBackground(file.getAbsolutePath())) {
              JOptionPane.showMessageDialog(window, "Failed to set background image", "Error", JOptionPane.ERROR_MESSAGE);
            }
            clearMapItem.setEnabled(mapPanel.getMapBackground() != null);
            saveConfig(configTable, configFile);
          }
        }
      }

    });
    fileMenu.add(item);
    fileMenu.add(clearMapItem);

    fileMenu.addSeparator();
    item = new JMenuItem("Clear Sensor Data...");
    item.addActionListener(new ActionListener() {

      public void actionPerformed(ActionEvent e) {
        int reply = JOptionPane.showConfirmDialog(window, "Also clear the sensor data log file?");
        if (reply == JOptionPane.YES_OPTION) {
          // Clear data from both memory and sensor log file
          clearSensorDataLog();
          clearSensorData();
        } else if (reply == JOptionPane.NO_OPTION) {
          // Only clear data from memory
          clearSensorData();
        }
      }

    });
    fileMenu.add(item);

    fileMenu.addSeparator();
    item = new JMenuItem("Exit", KeyEvent.VK_X);
    item.addActionListener(new ActionListener() {

      public void actionPerformed(ActionEvent e) {
        exit();
      }

    });
    fileMenu.add(item);

    JMenu toolsMenu = new JMenu("Tools");
    toolsMenu.setMnemonic(KeyEvent.VK_T);
    menuBar.add(toolsMenu);

    runInitScriptItem = new JMenuItem("Run Init Script");
    runInitScriptItem.addActionListener(new ActionListener() {

      public void actionPerformed(ActionEvent e) {
        mainPanel.setSelectedComponent(serialConsole.getPanel());
        if (serialConnection != null && serialConnection.isOpen()) {
          runInitScript();
        } else {
          JOptionPane.showMessageDialog(mainPanel, "No serial port connection", "No connected node", JOptionPane.ERROR_MESSAGE);
        }
      }

    });
    runInitScriptItem.setEnabled(false);
    toolsMenu.add(runInitScriptItem);
    toolsMenu.addSeparator();

    final JCheckBoxMenuItem scrollItem = new JCheckBoxMenuItem("Scroll Layout");
    scrollItem.addActionListener(new ActionListener() {

      public void actionPerformed(ActionEvent e) {
        if (scrollItem.getState()) {
          mainPanel.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
        } else {
          mainPanel.setTabLayoutPolicy(JTabbedPane.WRAP_TAB_LAYOUT);
        }
      }

    });
    toolsMenu.add(scrollItem);

    window.setJMenuBar(menuBar);
    window.pack();

    String bounds = configTable.getProperty("collect.bounds");
    if (bounds != null) {
      String[] b = bounds.split(",");
      if (b.length == 4) {
        window.setBounds(Integer.parseInt(b[0]), Integer.parseInt(b[1]),
            Integer.parseInt(b[2]), Integer.parseInt(b[3]));
      }
    }

    for(Object key: configTable.keySet()) {
      String property = key.toString();
      if (!property.startsWith("collect")) {
        getNode(property, true);
      }
    }
    initSensorData();

    SwingUtilities.invokeLater(new Runnable() {
      public void run() {
        window.setVisible(true);
      }
    });

    serialConnection = new SerialConnection() {

      private boolean hasOpened;
      private boolean hasSentInit;

      @Override
      protected void serialOpened() {
        serialConsole.addSerialData("*** Serial console listening on port: " + getComPort() + " ***");
        hasOpened = true;
        // Remember the last selected serial port
        configTable.put("collect.serialport", getComPort());
        setSystemMessage("connected to " + getComPort());

        // Send any initial commands
        if (!hasSentInit) {
          hasSentInit = true;

          if (hasInitScript()) {
            // Wait a short time before running the init script
            sleep(3000);

            runInitScript();
          }
        }
      }

      @Override
      protected void serialClosed() {
        String comPort = getComPort();
        String prefix;
        if (hasOpened) {
          serialConsole.addSerialData("*** Serial connection terminated ***");
          prefix = "Serial connection terminated.\n";
          hasOpened = false;
          setSystemMessage("not connected");
        } else {
          prefix = "Failed to connect to " + getComPort() + '\n';
        }
        if (!isClosed) {
          String options[] = {"Retry", "Search for connected nodes", "Cancel"};
          int value = JOptionPane.showOptionDialog(window,
              prefix + "Do you want to retry or search for connected nodes?",
              "Reconnect to serial port?",
              JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
              null, options, options[0]);
          if (value == JOptionPane.CLOSED_OPTION || value == 2) {
//          exit();
          } else {
            if (value == 1) {
              // Select new serial port
              comPort = MoteFinder.selectComPort(window);
              if (comPort == null) {
//              exit();
              }
            }
            // Try to open com port again
            if (comPort != null) {
              open(comPort);
            }
          }
        }
      }

      @Override
      protected void serialData(String line) {
        parseIncomingLine(System.currentTimeMillis(), line);
      }

    };
    if (comPort != null) {
      serialConnection.setComPort(comPort);
    }
    connectToSerial();
  }

  protected void connectToSerial() {
    if (!serialConnection.isOpen()) {
      String comPort = serialConnection.getComPort();
      if (comPort == null) {
        comPort = MoteFinder.selectComPort(window);
      }
      if (comPort != null) {
        serialConnection.open(comPort);
      }
    }
  }

  private void exit() {
    /* TODO Clean up resources */
    if (configFile != null) {
      configTable.setProperty("collect.bounds", "" + window.getX() + ',' + window.getY() + ',' + window.getWidth() + ',' + window.getHeight());
      saveConfig(configTable, configFile);
    }
    if (serialConnection != null) {
      serialConnection.close();
    }
    PrintWriter output = this.sensorDataOutput;
    if (output != null) {
      output.close();
    }
    System.exit(0);
  }

  private void sleep(long delay) {
    try {
      Thread.sleep(delay);
    } catch (InterruptedException e1) {
      // Ignore
    }
  }

  protected boolean hasInitScript() {
    return initScript != null && new File(initScript).canRead();
  }

  protected void runInitScript() {
    if (initScript != null) {
      runScript(initScript);
    }
  }

  protected void runScript(final String scriptFileName) {
    new Thread("scripter") {
      public void run() {
        try {
          BufferedReader in = new BufferedReader(new FileReader(scriptFileName));
          String line;
          while ((line = in.readLine()) != null) {
            if (line.length() == 0 || line.charAt(0) == '#') {
              // Ignore empty lines and comments
            } else if (line.startsWith("echo ")) {
              line = line.substring(5).trim();
              if (line.indexOf('%') >= 0) {
                line = line.replace("%TIME%", "" + (System.currentTimeMillis() / 1000));
              }
              sendToNode(line);
            } else if (line.startsWith("sleep ")) {
              long delay = Integer.parseInt(line.substring(6).trim());
              Thread.sleep(delay * 1000);
            } else {
              System.err.println("Unknown script command: " + line);
              break;
            }
          }
          in.close();
        } catch (Exception e) {
          System.err.println("Failed to run script: " + scriptFileName);
          e.printStackTrace();
        }
      }
    }.start();
  }

  public String getConfig(String property) {
    return getConfig(property, null);
  }

  public String getConfig(String property, String defaultValue) {
    return configTable.getProperty(property, config.getProperty(property, defaultValue));
  }

  protected void setSystemMessage(final String message) {
    SwingUtilities.invokeLater(new Runnable() {

      public void run() {
        boolean isOpen = serialConnection.isOpen();
        if (message == null) {
          window.setTitle(WINDOW_TITLE);
        } else {
          window.setTitle(WINDOW_TITLE + " (" + message + ')');
        }
        serialItem.setText(isOpen ? "Disconnect from serial" : "Connect to serial");
        runInitScriptItem.setEnabled(isOpen && hasInitScript());
      }

    });
  }

  // -------------------------------------------------------------------
  // Node Handling
  // -------------------------------------------------------------------

  public synchronized Node[] getNodes() {
    if (nodeCache == null) {
      Node[] tmp = nodeTable.values().toArray(new Node[nodeTable.size()]);
      Arrays.sort(tmp);
      nodeCache = tmp;
    }
    return nodeCache;
  }

  public Node addNode(String nodeID) {
    return getNode(nodeID, true);
  }

  private Node getNode(final String nodeID, boolean notify) {
    Node node = nodeTable.get(nodeID);
    if (node == null) {
      node = new Node(nodeID);
      nodeTable.put(nodeID, node);
      updateNodeLocation(node);

      synchronized (this) {
        nodeCache = null;
      }

      if (notify) {
        final Node newNode = node;
        SwingUtilities.invokeLater(new Runnable() {
            public void run() {
              // Insert the node sorted by name
              String nodeName = newNode.getName();
              boolean added = false;
              for (int i = 0, n = nodeModel.size(); i < n; i++) {
                int cmp = nodeName.compareTo(((Node) nodeModel.get(i)).getName());
                if (cmp < 0) {