ProjectProperty.java

/* ProjectProperty
 * This file is part of Artemis
 *
 * Copyright(C) 2012  Genome Research Limited
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or(at your option) any later version.
 *
 * This program 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
package uk.ac.sanger.artemis.components;

import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.net.URISyntaxException;

import java.util.HashMap;
import java.util.Properties;
import java.util.Vector;
import java.util.Map.Entry;
import java.util.Set;

import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.DefaultListModel;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JList;
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.ListSelectionModel;
import javax.swing.SwingUtilities;
import javax.swing.border.Border;
import javax.swing.border.TitledBorder;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;

import uk.ac.sanger.artemis.components.genebuilder.TextAreaDocumentListener;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.FileDocument;

/**
 * Project file management system using a properties file.
 * 
 * Example of the syntax for defining a project in the property file:
 * project.Pknowlsei.ref = Pknowlsei:Pk_strainH_chr01
 * project.Pknowlsei.chado =  genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro
 * project.Pknowlsei.title = Pknowlsei
 */
public class ProjectProperty extends JFrame
{
  private static final long serialVersionUID = 1L;
  private HashMap<String, HashMap<String, String>> projects;
  
  private final static int REFERENCE = 1;
  private final static int ANNOTATION = 2;
  private final static int NEXT_GEN_DATA = 3;
  private final static int CHADO = 4;
  private static org.apache.log4j.Logger logger4j = 
      org.apache.log4j.Logger.getLogger(ProjectProperty.class);
  
  private final static String[] TYPES = 
    { "title", "ref", "annotation", "bam", "vcf", "chado" };
  
  public ProjectProperty()
  {
    super("Project File Manager");
    InputStream ins = 
        this.getClass().getClassLoader().getResourceAsStream("etc/project.properties");
    
    try
    {
      logger4j.debug("Reading properties from: "+
          this.getClass().getClassLoader().getResource("etc/project.properties").toURI());
    }
    catch (URISyntaxException e1){}

    final Properties projectProps = new Properties();
    try
    {
      projectProps.load(ins);
      ins.close();
    }
    catch (IOException e)
    {
      e.printStackTrace();
    }
    
    final String [] propFiles = 
    {
      "project.properties",
      System.getProperty("user.home") + File.separator + ".project.properties"
    };
    
    for(int i=0; i<propFiles.length; i++)
    {
      final Document doc =
          new FileDocument(new File(propFiles[i]));
      if(doc.readable()) 
      {
        try
        {
          ins = doc.getInputStream();
          projectProps.load(ins);
        }
        catch (IOException e)
        {
          e.printStackTrace();
        }
        
        logger4j.debug("Reading properties from: "+propFiles[i]);
      }
    }

    projects = getProjectMap(projectProps);
    createProjectViewer((JPanel) getContentPane());
    pack();
    setVisible(true);
  }
  
  private void createProjectViewer(JPanel panel)
  {
    final DefaultListModel model = new DefaultListModel();
    
    final JList projectList = new JList(model);
    final JScrollPane jspList = new JScrollPane(projectList);
    Object[] items = projects.keySet().toArray();
    for (int i=0; i<items.length; i++)
      model.add(i, items[i]);

    final Box yBox = Box.createVerticalBox();
    final LaunchActionListener listener = new LaunchActionListener();
    projectList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
    projectList.setVisibleRowCount(-1);
    panel.add(jspList, BorderLayout.WEST);
    panel.add(yBox, BorderLayout.CENTER);
    
    // menus
    final JMenuBar menuBar = new JMenuBar();
    setJMenuBar(menuBar);
    final JMenu fileMenu = new JMenu("File");
    menuBar.add(fileMenu);
    final JMenuItem exitMenu = new JMenuItem("Exit");
    fileMenu.add(exitMenu);
    exitMenu.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent arg0)
      {
        int status = JOptionPane.showConfirmDialog(
            ProjectProperty.this, "Exit?", "Exit", JOptionPane.YES_NO_OPTION);
        if(status == JOptionPane.YES_OPTION)
          Splash.exitApp();
      }
    });

    final JMenu editMenu = new JMenu("Edit");
    menuBar.add(editMenu);
    final JMenuItem addProject = new JMenuItem("Add Project");
    addProject.addActionListener(new ActionListener(){
      public void actionPerformed(ActionEvent arg0)
      {
        String projName = 
            JOptionPane.showInputDialog(ProjectProperty.this,
                "Project Name", "New Project", JOptionPane.QUESTION_MESSAGE);
        if(projName == null)
          return;
        projects.put(projName, new HashMap<String, String>());
        model.add(model.getSize(), projName);
        projectList.repaint();
      }
    });
    editMenu.add(addProject);
    final JMenuItem removeProject = new JMenuItem("Remove Project");
    removeProject.addActionListener(new ActionListener(){
      public void actionPerformed(ActionEvent arg0)
      {
        projects.remove(projectList.getSelectedValue());
        model.remove(projectList.getSelectedIndex());
        projectList.repaint();
        yBox.removeAll();
        yBox.repaint();
      }
    });
    editMenu.add(removeProject);
    
    
    //
    panel.setPreferredSize(new Dimension(650,400));
    panel.setBackground(Color.WHITE);
    
    final JButton openArt = new JButton("OPEN");
    
    openArt.addActionListener(listener);
    panel.add(openArt, BorderLayout.SOUTH);
    
    final GridBagConstraints c = new GridBagConstraints();
    c.anchor = GridBagConstraints.NORTHWEST;
    c.fill = GridBagConstraints.VERTICAL;
    c.ipadx = 10;
    c.ipady = 10;
    
    
    projectList.addListSelectionListener(new ListSelectionListener()
    {
      public void valueChanged(ListSelectionEvent e)
      {
        if(e.getValueIsAdjusting() == false &&
           projectList.getSelectedIndex() > -1) 
          refreshProperties(projectList, yBox, listener);
      }
    });
  }
  
  /**
   * Refresh components in the properties panel.
   * @param projectList
   * @param yBox
   * @param listener
   */
  private void refreshProperties(final JList projectList, 
                                 final Box yBox, 
                                 final LaunchActionListener listener)
  {
    yBox.removeAll();
    
    final HashMap<String, String> projProps = projects.get(projectList.getSelectedValue());
    final HashMap<Integer, QualifierTextArea> settings = new HashMap<Integer, QualifierTextArea>();
    for(final String key: projProps.keySet())
    {
      Box xBox = Box.createHorizontalBox();
      final QualifierTextArea qta = new QualifierTextArea();
      Border loweredbevel = BorderFactory.createLoweredBevelBorder();
      TitledBorder title = BorderFactory.createTitledBorder(
          loweredbevel, key);
      title.setTitlePosition(TitledBorder.ABOVE_TOP);

      qta.setBorder(title);

      qta.setText(projProps.get(key));
      qta.getDocument().addDocumentListener(
          new TextAreaDocumentListener(qta));

      xBox.add(qta);
      
      // REMOVE PROPERTY
      final JButton removeProperty = new JButton("X");
      removeProperty.setOpaque(false);
      Font font = removeProperty.getFont().deriveFont(Font.BOLD);
      removeProperty.setFont(font);
      removeProperty.setToolTipText("REMOVE");
      removeProperty.setForeground(new Color(139, 35, 35));

      removeProperty.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          projProps.remove(key);
          refreshProperties(projectList, yBox, listener);
        }
      });
      xBox.add(removeProperty);
      //

      yBox.add(xBox);
      
      if(key.equals("ref"))
        settings.put(ProjectProperty.REFERENCE, qta);
      else if(key.equals("annotation"))
        settings.put(ProjectProperty.ANNOTATION, qta);
      else if(key.equals("bam") || key.equals("vcf") || key.equals("bcf"))
        settings.put(ProjectProperty.NEXT_GEN_DATA, qta);
      else if(key.equals("chado"))
        settings.put(ProjectProperty.CHADO, qta);
     
    }
    
    // ADD property
    Box xBox = Box.createHorizontalBox();
    final JButton addPropertyButton = new JButton("NEW PROPERTY");
    final JComboBox propertyList = new JComboBox(TYPES);
    xBox.add(addPropertyButton);
    xBox.add(propertyList);
    xBox.add(Box.createHorizontalGlue());
    yBox.add(xBox);
    addPropertyButton.addActionListener(new ActionListener(){
      public void actionPerformed(ActionEvent arg0)
      {
        String key = (String) propertyList.getSelectedItem();
        if(!projProps.containsKey(key))
        {
          projProps.put(key, "");
          refreshProperties(projectList, yBox, listener);
        }
      }
    });
    
    //
    yBox.add(Box.createVerticalGlue());
    yBox.revalidate();
    yBox.repaint();
    
    listener.setSettings(settings);
  }


  /**
   * Create a project hash of the properties.
   * @param projectProps
   * @return
   */
  private HashMap<String, HashMap<String, String>> getProjectMap(final Properties projectProps)
  {
    final HashMap<String, HashMap<String, String>> projects =
        new HashMap<String, HashMap<String, String>>();
    
    for (Entry<Object, Object> propItem : projectProps.entrySet())
    {
      String key = (String) propItem.getKey();
      String value = (String) propItem.getValue();

      if (key.startsWith("project."))
      {
        key = key.substring(8);
        int ind = key.indexOf(".");
        if (ind > -1)
        {
          String projName = key.substring(0, ind);
          key = key.substring(ind + 1);
          final HashMap<String, String> thisProj;
          if (projects.containsKey(projName))
            thisProj = projects.get(projName);
          else
            thisProj = new HashMap<String, String>();
          thisProj.put(key, value);
          
          projects.put(projName, thisProj);
        }
      }
    }
    return projects;
  }
  
  class LaunchActionListener implements ActionListener
  {
    private String args[] = new String[]{};
    private void setSettings(HashMap<Integer, QualifierTextArea> settings)
    {
      try
      {
        System.getProperties().remove("bam");
        System.getProperties().remove("chado");
      }
      catch(Exception e){ e.printStackTrace(); }
      
      final Set<Integer> keys = settings.keySet();
      final Vector<String> vargs = new Vector<String>();
      final Vector<String> vann = new Vector<String>();
      for(Integer key: keys)
      {
        switch(key)
        {
          case ProjectProperty.REFERENCE:
            vargs.add( settings.get(key).getText() );
            break;
          case ProjectProperty.ANNOTATION:
            vann.add( settings.get(key).getText() );
            break;
          case ProjectProperty.NEXT_GEN_DATA:
            System.setProperty("bam", settings.get(key).getText().replaceAll("\\s+", ","));
            break;
          case ProjectProperty.CHADO:
            System.setProperty("chado", settings.get(key).getText().trim());
            break;
        }
      }
      
      args = new String[vargs.size()+(vann.size()*2)];
      for(int i=0; i<vargs.size(); i++)
        args[i] = vargs.get(i);
      for(int i=0; i<vann.size(); i++)
      {
        args[vargs.size()+(i*2)] = "+";
        args[vargs.size()+(i*2)+1] = vann.get(i);
      }
    }
    
    public void actionPerformed(ActionEvent arg0)
    {
      SwingUtilities.invokeLater(new Runnable() 
      {
        public void run() 
        {
          final ArtemisMain main_window = new ArtemisMain(args);
          main_window.setVisible(true);
          main_window.readArgsAndOptions(args);
        }
      });
    }
  }
  
  public static void main(String args[])
  {
    new ProjectProperty();
  }
}