DBAnnotationViewerMain.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 * 
 *   http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

package org.barcelonamedia.uima.tools;

import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.prefs.Preferences;

import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JDialog;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextField;
import javax.swing.SpringLayout;
import javax.swing.UIManager;

import org.apache.uima.UIMAException;
import org.apache.uima.UIMAFramework;
import org.apache.uima.UIMARuntimeException;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.cas.CAS;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.metadata.FsIndexDescription;
import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.apache.uima.tools.images.Images;
import org.apache.uima.tools.util.gui.AboutDialog;
import org.apache.uima.tools.util.gui.Caption;
import org.apache.uima.tools.util.gui.FileSelector;
import org.apache.uima.tools.util.gui.SpringUtilities;
import org.apache.uima.tools.util.htmlview.AnnotationViewGenerator;
import org.apache.uima.util.CasCreationUtils;
import org.apache.uima.util.InvalidXMLException;
import org.apache.uima.util.XMLInputSource;

import org.barcelonamedia.uima.tools.DAO.DAOFactory;
import org.barcelonamedia.uima.tools.DAO.XMIDAO;
import org.barcelonamedia.uima.tools.docanalyzer.DBAnnotationViewerDialog;
import org.barcelonamedia.uima.tools.docanalyzer.DBPrefsMediator;


/**
 * Main Annotation Viewer GUI. Allows user to choose directory of XCAS or XMI files, then
 * launches the AnnotationViewerDialog.
 * 
 * 
 */
public class DBAnnotationViewerMain extends JFrame{

	private static final long serialVersionUID = -3201723535833938833L;

	private static final String HELP_MESSAGE = "Instructions for using DB Annotation Viewer:\n\n"
		+ "1) Specify MySQL database parameters, thats is, host, port, user, password and database.\n"         
		+ "Introduce the SQL query for selecting XMI ids as id field, and XMI files blobs as xmi fields.\n"
		+ "Check the uncompress checkbox in case stored XMI files are compressed.\n"
		+ "2) In the \"TypeSystem or AE Descriptor File\" field, either type or use the browse\n"
		+ "button to select the TypeSystem or AE descriptor for the AE that generated the\n"
		+ "XMI or XCAS files.  (This is needed for type system infornation only.\n"
		+ "Analysis will not be redone.)\n\n"
		+ "3) Click the \"View\" button at the buttom of the window.\n\n"
		+ "A list of the analyzed documents will be displayed.\n\n\n"
		+ "4) Select the view type -- either the Java annotation viewer, HTML,\n"
		+ "or XML.  The Java annotation viewer is recommended.\n\n"
		+ "5) Double-click on a document to view it.\n";


	private File uimaHomeDir;

	private JTextField inputHost;
	private JTextField inputPort;
	private JTextField inputUser;
	private JTextField inputPassword;
	private JTextField inputDatabase;
	private JTextField inputQuery;

	private JCheckBox checkBoxUncompress;

	private FileSelector taeDescriptorFileSelector;

	private JButton viewButton;

	private JDialog aboutDialog;

	/** Stores user preferences */
	private Preferences prefs = Preferences.userRoot().node("org/apache/uima/tools/AnnotationViewer");

	/** DAO Factory object. */
	private DAOFactory daoFactory;


	/**
	 * Constructor. Sets up the GUI.
	 */
	public DBAnnotationViewerMain(){

		super("DB Annotation Viewer");

		// set UIMA home dir
		uimaHomeDir = new File(System.getProperty("uima.home", "C:/Program Files/apache-uima"));

		this.daoFactory = DAOFactory.getDAOFactory(DAOFactory.MYSQL);

		try{

			UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
		}
		catch(Exception e){

			// I don't think this should ever happen, but if it does just print error and continue
			// with defalt look and feel
			System.err.println("Could not set look and feel: " + e.getMessage());
		}

		// Set frame icon image
		try{

			this.setIconImage(Images.getImage(Images.MICROSCOPE));
		}
		catch(IOException e){

			System.err.println("Image could not be loaded: " + e.getMessage());
		}

		this.getContentPane().setBackground(Color.WHITE);

		// create about dialog
		aboutDialog = new AboutDialog(this, "About DB Annotation Viewer");

		// Create Menu Bar
		JMenuBar menuBar = new JMenuBar();
		setJMenuBar(menuBar);

		JMenu fileMenu = new JMenu("File");
		JMenu helpMenu = new JMenu("Help");

		// Menu Items
		JMenuItem aboutMenuItem = new JMenuItem("About");
		JMenuItem helpMenuItem = new JMenuItem("Help");
		JMenuItem exitMenuItem = new JMenuItem("Exit");

		fileMenu.add(exitMenuItem);
		helpMenu.add(aboutMenuItem);
		helpMenu.add(helpMenuItem);
		menuBar.add(fileMenu);
		menuBar.add(helpMenu);

		// Labels to identify the text fields
		final Caption labelInputHost = new Caption("Host: ");
		final Caption labelInputPort = new Caption("Port: ");
		final Caption labelInputUser = new Caption("User: ");
		final Caption labelInputPassword = new Caption("Password: ");
		final Caption labelInputDatabase = new Caption("Database: ");
		final Caption labelInputQuery = new Caption("Query: ");
		final Caption labelCheckboxUncompress = new Caption("Uncompress: ");
		final Caption labelStyleMapFile = new Caption("TypeSystem or AE Descriptor File: ");

		JPanel controlPanel = new JPanel();
		controlPanel.setBorder(BorderFactory.createEmptyBorder(4, 4, 4, 4));
		controlPanel.setLayout(new SpringLayout());

		this.inputHost = new JTextField();
		this.inputPort = new JTextField();
		this.inputUser = new JTextField();
		this.inputPassword = new JTextField();
		this.inputDatabase = new JTextField();
		this.inputQuery = new JTextField();

		this.checkBoxUncompress = new JCheckBox();

		this.taeDescriptorFileSelector = new FileSelector("", "TAE Descriptor File", JFileChooser.FILES_ONLY, uimaHomeDir);

		File descriptorFile = new File(uimaHomeDir, "examples/descriptors/analysis_engine/PersonTitleAnnotator.xml");
		this.taeDescriptorFileSelector.setSelected(descriptorFile.getAbsolutePath());

		controlPanel.add(labelInputHost);
		controlPanel.add(this.inputHost);

		controlPanel.add(labelInputPort);
		controlPanel.add(this.inputPort);

		controlPanel.add(labelInputUser);
		controlPanel.add(this.inputUser);

		controlPanel.add(labelInputPassword);
		controlPanel.add(this.inputPassword);

		controlPanel.add(labelInputDatabase);
		controlPanel.add(this.inputDatabase);

		controlPanel.add(labelInputQuery);
		controlPanel.add(this.inputQuery);

		controlPanel.add(labelCheckboxUncompress);
		controlPanel.add(this.checkBoxUncompress);

		controlPanel.add(labelStyleMapFile);
		controlPanel.add(this.taeDescriptorFileSelector);

		// Once we add components to controlPanel, we'll
		// call SpringUtilities::makeCompactGrid on it.
		SpringUtilities.makeCompactGrid(controlPanel, 8, 2, // rows, cols
				4, 4, // initX, initY
				4, 4); // xPad, yPad

		// Event Handlling of "Exit" Menu Item
		exitMenuItem.addActionListener(new ActionListener() {
			public void actionPerformed(ActionEvent ae) {
				savePreferences();
				System.exit(0);
			}
		});

		// Event Handlling of "About" Menu Item
		aboutMenuItem.addActionListener(new ActionListener() {
			public void actionPerformed(ActionEvent ae) {
				aboutDialog.setVisible(true);
			}
		});

		// Event Handlling of "Help" Menu Item
		helpMenuItem.addActionListener(new ActionListener() {
			public void actionPerformed(ActionEvent ae) {
				JOptionPane.showMessageDialog(DBAnnotationViewerMain.this, HELP_MESSAGE, "DB Annotation Viewer Help", JOptionPane.PLAIN_MESSAGE);
			}
		});

		// Add the panels to the frame
		Container contentPanel = getContentPane();
		contentPanel.add(controlPanel, BorderLayout.CENTER);

		// add banner
		JLabel banner = new JLabel(Images.getImageIcon(Images.BANNER));
		contentPanel.add(banner, BorderLayout.NORTH);

		// Add the view Button to run TAE
		viewButton = new JButton("View");

		// Add the view button to another panel
		JPanel lowerButtonsPanel = new JPanel();
		lowerButtonsPanel.add(viewButton);

		contentPanel.add(lowerButtonsPanel, BorderLayout.SOUTH);
		setContentPane(contentPanel);
		
		JScrollPane jsp = new JScrollPane(controlPanel);
		this.add(jsp);

		// Event Handling of view Button
		viewButton.addActionListener(new ActionListener(){

			public void actionPerformed(ActionEvent ee){
				
				Hashtable<String, String> connectionParams = new Hashtable<String, String>();
				connectionParams.put("server", DBAnnotationViewerMain.this.inputHost.getText());
				connectionParams.put("port", DBAnnotationViewerMain.this.inputPort.getText());
				connectionParams.put("database", DBAnnotationViewerMain.this.inputDatabase.getText());
				connectionParams.put("user", DBAnnotationViewerMain.this.inputUser.getText());
				connectionParams.put("password", DBAnnotationViewerMain.this.inputPassword.getText());

				try{

					viewDocuments(connectionParams);
				}
				catch(Exception e){

					displayError(e);
				}
			}
		});

		// load user preferences
		if (System.getProperty("uima.noprefs") == null) {
			restorePreferences();
		}
	}

	public void viewDocuments(Hashtable<String, String> connectionParams) throws InvalidXMLException, IOException, ResourceInitializationException {

		File descriptorFile = new File(taeDescriptorFileSelector.getSelected());
		
		if (!descriptorFile.exists() || descriptorFile.isDirectory()) {
			displayError("Descriptor File \"" + descriptorFile.getPath() + "\" does not exist.");
			return;
		}

		XMIDAO xmiDAO = this.daoFactory.getDocumentDAO(connectionParams);
		xmiDAO.setSQLSentence(this.inputQuery.getText());

		// parse descriptor. Could be either AE or TypeSystem descriptor
		Object descriptor = UIMAFramework.getXMLParser().parse(new XMLInputSource(descriptorFile));
		// instantiate CAS to get type system. Also build style map file if there is none.
		CAS cas;
		File styleMapFile;
		
		if (descriptor instanceof AnalysisEngineDescription) {
			cas = CasCreationUtils.createCas((AnalysisEngineDescription) descriptor);
			styleMapFile = getStyleMapFile((AnalysisEngineDescription) descriptor, descriptorFile
					.getPath());
		} 
		else if (descriptor instanceof TypeSystemDescription) {
			TypeSystemDescription tsDesc = (TypeSystemDescription) descriptor;
			tsDesc.resolveImports();
			cas = CasCreationUtils.createCas(tsDesc, null, new FsIndexDescription[0]);
			styleMapFile = getStyleMapFile((TypeSystemDescription) descriptor, descriptorFile.getPath());
		} 
		else {
			displayError("Invalid Descriptor File \"" + descriptorFile.getPath() + "\""
					+ "Must be either an AnalysisEngine or TypeSystem descriptor.");
			return;
		}

		// create DB Annotation Viewer Main Panel
		DBPrefsMediator dbPrefsMed = new DBPrefsMediator();
		dbPrefsMed.setXmiDAO(xmiDAO);
		dbPrefsMed.setUmcompress(this.checkBoxUncompress.isSelected());
		
		DBAnnotationViewerDialog viewerDialog = new DBAnnotationViewerDialog(this, "Analyzed Documents", dbPrefsMed, styleMapFile, null, cas.getTypeSystem(), null, false, cas);
		viewerDialog.pack();
		viewerDialog.setModal(true);
		viewerDialog.setVisible(true);
	}

	/**
	 * @param tae // *
	 * @param taeDescFileName
	 * @return
	 * @throws IOException
	 */
	private File getStyleMapFile(AnalysisEngineDescription tad, String descFileName) throws IOException{

		File styleMapFile = getStyleMapFileName(descFileName);

		if (!styleMapFile.exists()) {
			// generate default style map
			String xml = AnnotationViewGenerator.autoGenerateStyleMap(tad.getAnalysisEngineMetaData());

			PrintWriter writer;
			writer = new PrintWriter(new BufferedWriter(new FileWriter(styleMapFile)));
			writer.println(xml);
			writer.close();
		}

		return styleMapFile;
	}

	/**
	 * @param tae // *
	 * @param taeDescFileName
	 * @return
	 * @throws IOException
	 */
	private File getStyleMapFile(TypeSystemDescription tsd, String descFileName) throws IOException {

		File styleMapFile = getStyleMapFileName(descFileName);

		if (!styleMapFile.exists()) {
			// generate default style map
			String xml = AnnotationViewGenerator.autoGenerateStyleMap(tsd);

			PrintWriter writer;
			writer = new PrintWriter(new BufferedWriter(new FileWriter(styleMapFile)));
			writer.println(xml);
			writer.close();
		}

		return styleMapFile;
	}

	/**
	 * Gets the name of the style map file for the given AE or TypeSystem descriptor filename.
	 */
	public File getStyleMapFileName(String aDescriptorFileName){

		String baseName;
		int index = aDescriptorFileName.lastIndexOf(".");

		if(index > 0){
			baseName = aDescriptorFileName.substring(0, index);
		} 
		else{
			baseName = aDescriptorFileName;
		}

		return new File(baseName + "StyleMap.xml");
	}

	public static void main(String[] args){

		final DBAnnotationViewerMain frame = new DBAnnotationViewerMain();

		frame.addWindowListener(new WindowAdapter(){

			public void windowClosing(WindowEvent e){

				frame.savePreferences();
				System.exit(0);
			}
		});

		frame.pack();
		frame.setVisible(true);
	}

	/**
	 * Save user's preferences using Java's Preference API.
	 */
	public void savePreferences(){

		prefs.put("host", this.inputHost.getText());
		prefs.put("port", this.inputPort.getText());
		prefs.put("user", this.inputUser.getText());
		prefs.put("password", this.inputPassword.getText());
		prefs.put("database", this.inputDatabase.getText());
		prefs.put("query", this.inputQuery.getText());
		prefs.put("uncompress", String.valueOf(this.checkBoxUncompress.isSelected()));		
		prefs.put("taeDescriptorFile", this.taeDescriptorFileSelector.getSelected());
	}

	/**
	 * Reset GUI to preferences last saved via {@link #savePreferences}.
	 */
	public void restorePreferences(){

		// figure defaults
		File defaultInputDir = new File(uimaHomeDir, "examples/data/processed");
		File defaultTaeDescriptorFile = new File(uimaHomeDir, "examples/descriptors/analysis_engine/PersonTitleAnnotator.xml");

		// restore preferences
		this.inputHost.setText(this.prefs.get("host", "localhost"));
		this.inputPort.setText(this.prefs.get("port", "3306"));
		this.inputUser.setText(this.prefs.get("user", ""));
		this.inputPassword.setText(this.prefs.get("password", ""));
		this.inputDatabase.setText(this.prefs.get("database", ""));
		this.inputQuery.setText(this.prefs.get("query", ""));
		
		if(this.prefs.get("uncompress", "false").equals("true")){
			
			this.checkBoxUncompress.setSelected(true);
		}
		
		this.taeDescriptorFileSelector.setSelected(prefs.get("taeDescriptorFile", defaultTaeDescriptorFile.toString()));
	}

	/**
	 * Displays an error message to the user.
	 * 
	 * @param aErrorString
	 *          error message to display
	 */
	public void displayError(String aErrorString){

		// word-wrap long mesages
		StringBuffer buf = new StringBuffer(aErrorString.length());
		final int CHARS_PER_LINE = 80;
		int charCount = 0;
		StringTokenizer tokenizer = new StringTokenizer(aErrorString, " \n", true);

		while (tokenizer.hasMoreTokens()) {
			String tok = tokenizer.nextToken();

			if (tok.equals("\n")) {
				buf.append("\n");
				charCount = 0;
			} else if ((charCount > 0) && ((charCount + tok.length()) > CHARS_PER_LINE)) {
				buf.append("\n").append(tok);
				charCount = tok.length();
			} else {
				buf.append(tok);
				charCount += tok.length();
			}
		}

		JOptionPane.showMessageDialog(DBAnnotationViewerMain.this, buf.toString(), "Error", JOptionPane.ERROR_MESSAGE);
	}

	/**
	 * Displays an error message to the user.
	 * 
	 * @param aThrowable
	 *          Throwable whose message is to be displayed.
	 */
	public void displayError(Throwable aThrowable){

		aThrowable.printStackTrace();

		String message = aThrowable.toString();

		// For UIMAExceptions or UIMARuntimeExceptions, add cause info.
		// We have to go through this nonsense to support Java 1.3.
		// In 1.4 all exceptions can have a cause, so this wouldn't involve
		// all of this typecasting.
		while ((aThrowable instanceof UIMAException) || (aThrowable instanceof UIMARuntimeException)) {

			if (aThrowable instanceof UIMAException) {
				aThrowable = ((UIMAException) aThrowable).getCause();
			} else if (aThrowable instanceof UIMARuntimeException) {
				aThrowable = ((UIMARuntimeException) aThrowable).getCause();
			}

			if (aThrowable != null) {
				message += ("\nCausedBy: " + aThrowable.toString());
			}
		}

		displayError(message);
	}

	/*
	 * (non-Javadoc)-
	 * 
	 * @see java.awt.Component#getPreferredSize()
	 */
	public Dimension getPreferredSize() {
		return new Dimension(640, 350);
	}  
}