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    /* ExternalProgram.java
     *
     * created: Aug 2005
     *
     * This file is part of Artemis
     *
     * Copyright(C) 2005  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.j2ssh;
    
    
    import javax.swing.*;
    import java.awt.*;
    import java.io.*;
    import com.sshtools.j2ssh.SshClient;
    import com.sshtools.j2ssh.authentication.AuthenticationProtocolState;
    import com.sshtools.j2ssh.authentication.PasswordAuthenticationClient;
    import com.sshtools.j2ssh.io.UnsignedInteger32;
    import com.sshtools.j2ssh.session.SessionChannelClient;
    import com.sshtools.j2ssh.sftp.FileAttributes;
    import com.sshtools.j2ssh.sftp.SftpFile;
    import com.sshtools.j2ssh.sftp.SftpFileOutputStream;
    import com.sshtools.j2ssh.SftpClient;
    import com.sshtools.j2ssh.configuration.ConfigurationLoader;
    
    import java.util.Vector;
    import java.util.Properties;
    import java.util.logging.FileHandler;
    import java.util.logging.Handler;
    import java.util.logging.Level;
    import java.util.logging.Logger;
    import java.util.logging.SimpleFormatter;
    
    /**
     *
     */
    public class SshPSUClient extends Thread
    {
    
      private String hostname = null;
      private String user     = null;
      private String listfilepath = null;
      private String cmd      = null;
      private String bsub     = null;
      private String logfile  = null;
      private String db       = null;
      private String wdir     = "/nfs/pathscratch1/scratch";
      private int port        = -1;
    
      public SshPSUClient(String args[])
      {
        // process arguments
        if(args != null && args.length > 0)
        {
          for(int i=0; i<args.length; i++)
          {
            if(args[i].equals("-h") && i < args.length-1)
              hostname = args[i+1];
            else if(args[i].equals("-u") && i < args.length-1)
              user = args[i+1];
            else if(args[i].equals("-f") && i < args.length-1)
              listfilepath = args[i+1];
            else if(args[i].equals("-cmd") && i < args.length-1)
              cmd = args[i+1];
            else if(args[i].equals("-bsub") && i < args.length-1)
              bsub = args[i+1];
            else if(args[i].equals("-l") && i < args.length-1)
              logfile = args[i+1];
            else if(args[i].equals("-p") && i < args.length-1)
              port = Integer.parseInt(args[i+1]);
            else if(args[i].equals("-d") && i < args.length-1)
              db = args[i+1];
            else if(args[i].equals("-wdir") && i < args.length-1)
              wdir = args[i+1];
          }
        }
      }
    
      public void run()
      {
        String program = cmd;
        // get properties from j2ssh.properties
        Properties settings = getProperties();
        if(hostname == null && settings.getProperty("host") != null)
          hostname = settings.getProperty("host");
        if(port < 0 && settings.getProperty("port") != null)
          port = Integer.parseInt(settings.getProperty("port"));
        if(bsub == null && settings.getProperty("bsub") != null)
          bsub = settings.getProperty("bsub");
        if(user == null)
          user = System.getProperty("user.name");
        if(db == null)
        {
          if(settings.getProperty("default_db") != null)
            db = settings.getProperty("default_db");
          else
            db = "%uniprot";
        }
        if(cmd.equals("blastp") && settings.getProperty("blastp") != null)
          cmd = settings.getProperty("blastp");
        if(cmd.equals("fasta") && settings.getProperty("fasta") != null)
          cmd = settings.getProperty("fasta");
    
        try
        {
          // Setup a logfile
          if(logfile != null)
          {
            Handler fh = new FileHandler(logfile);
            fh.setFormatter(new SimpleFormatter());
            Logger.getLogger("com.sshtools").setUseParentHandlers(false);
            Logger.getLogger("com.sshtools").addHandler(fh);
            Logger.getLogger("com.sshtools").setLevel(Level.ALL);
          }
          else
            Logger.getLogger("com.sshtools").setLevel(Level.OFF);
    
          ConfigurationLoader.initialize(false);
    
    //    if(hostname == null)
    //      hostname = (String)JOptionPane.showInputDialog(
    //                           null, "Name of server machine:",
    //                           "Server hostname",
    //                           JOptionPane.PLAIN_MESSAGE, null,
    //                           null, null);
         
          BufferedReader reader =
              new BufferedReader(new InputStreamReader(System.in));
    
          // Create a password authentication instance
          PasswordAuthenticationClient pwd = new PasswordAuthenticationClient();
          // Get the users name
    
          JPanel promptPanel = new JPanel(new GridLayout(4,2));
    
          JTextField hostfield  = new JTextField(16);
          if(hostname != null)
            hostfield.setText(hostname);
          
          JTextField portfield  = new JTextField(16);
          if(port >-1)
            portfield.setText(Integer.toString(port));
    
          JTextField ufield  = new JTextField(16);
          if(user != null)
            ufield.setText(user);
          JPasswordField pfield = new JPasswordField(16);
    
          JLabel hostlab = new JLabel(" Hostname:", SwingConstants.LEFT);
          JLabel portlab = new JLabel("     Port:", SwingConstants.LEFT);
    
          JLabel ulab = new JLabel(" Username:", SwingConstants.LEFT);
          JLabel plab = new JLabel(" Password:", SwingConstants.LEFT);
          //add labels etc
          promptPanel.add(hostlab);
          promptPanel.add(hostfield);
    
          promptPanel.add(portlab);
          promptPanel.add(portfield);
    
          promptPanel.add(ulab);
          promptPanel.add(ufield);
    
          promptPanel.add(plab);
          promptPanel.add(pfield);
         
          Object[] options = { "CANCEL", "LOGIN"};
    
          int select = JOptionPane.showOptionDialog(null, promptPanel,
                                  "LOGIN",
                                   JOptionPane.YES_NO_CANCEL_OPTION,
                                   JOptionPane.QUESTION_MESSAGE,
                                   null,
                                   options,
                                   options[1]);
    
          if(select == 0)
            return;
    
          // Make a client connection
          SshClient ssh = new SshClient();
          hostname = hostfield.getText().trim();
          if(portfield.getText().trim().equals(""))
            port = -1;
          else
            port = Integer.parseInt(portfield.getText().trim());
    
          // Connect to the host
          if(port < 0)
            ssh.connect(hostname);
          else
            ssh.connect(hostname,port);
    
          user = ufield.getText().trim();
          pwd.setUsername(user);
          pwd.setPassword(new String(pfield.getPassword()));
    
          // Try the authentication
          int result = ssh.authenticate(pwd);
       
          // Evaluate the result
          if(result == AuthenticationProtocolState.COMPLETE)
          {
            if(listfilepath == null)
            {
              JFileChooser chooser = new JFileChooser();
              int returnVal = chooser.showOpenDialog(null);
              if(returnVal == JFileChooser.APPROVE_OPTION) 
                listfilepath = chooser.getSelectedFile().getAbsolutePath();
              else
                return;
            }
    
            SftpClient sftp = ssh.openSftpClient();
            Vector seqfile = readListFile(listfilepath);
            for(int i=0; i<seqfile.size();i++)
            {
              String filepath = (String)seqfile.get(i);
              int index = filepath.lastIndexOf(System.getProperty("file.separator"));
              String filename = filepath;
              if(index > -1)
                filename = filename.substring(index+1);
    
              wdir = wdir+"/"+user+"/";
              try
              {
                sftp.mkdir(wdir);
                sftp.put(filepath, wdir+filename);
              }
              catch(IOException ioe)
              {}
          
              SessionChannelClient session = ssh.openSessionChannel();
    
              String outputfile = wdir+filename+".out";
              final String actualCMD;
    
              if(cmd.indexOf("fasta33") > -1)
              {
                if(settings.getProperty(db) != null)
                  db = settings.getProperty(db);
                actualCMD = bsub+" -o "+ outputfile +" -e "+ outputfile + ".err " +
                               cmd+" "+wdir+filename+" "+db;
              }
              else
                actualCMD = bsub+" -o "+ outputfile +" -e "+ outputfile + ".err " +
                               cmd+" "+db+" "+wdir+filename;
    
              System.out.println(actualCMD);
              session.executeCommand(actualCMD);
    
              // Reading from the session InputStream
              StdoutStdErrHandler stdouth = new StdoutStdErrHandler(session, true);
              StdoutStdErrHandler stderrh = new StdoutStdErrHandler(session, false);
            
              stdouth.start();
              stderrh.start();
    
              boolean isFile = false;
              try
              {
                // make sure we hang around for stdout
                while(stdouth.isAlive() || stderrh.isAlive())
                  Thread.currentThread().sleep(10);
    
                int count = 0;
    
                while(!isFile && count < 100)
                {
                  Thread.currentThread().sleep(5000);
                  Object list[] = sftp.ls(wdir).toArray();
    
                  for(int j=0; j<list.length;j++)
                  {
                    if(((SftpFile)list[j]).getFilename().equals(filename+".out"))
                      isFile = true;
                  } 
                  count++;
                }
              }
              catch(InterruptedException ie)
              {
                ie.printStackTrace();
              }
              catch(java.io.IOException ioe)
              {
                ioe.printStackTrace();
              }
              
              // stdout
              System.out.println(stdouth.getOutput());
              System.out.println(stderrh.getOutput());
    
    //        ByteArrayOutputStream os = new ByteArrayOutputStream();
    //        sftp.get(outputfile, os);
    //        System.out.println(os.toString());
    
              sftp.get(outputfile, filepath+".out");
    
              session.close();
            }
    
            // Quit
            sftp.quit();
            ssh.disconnect();
          }
          else 
            JOptionPane.showMessageDialog(null, 
                "Problem logging in!\nCheck username and password.",
                "Authentication Problem",
                JOptionPane.ERROR_MESSAGE);
    
    
        } catch(IOException ioe){}
        finally
        {
          JOptionPane.showMessageDialog(null,
                "Finished \n" + program,
                "Process Finished",
                JOptionPane.INFORMATION_MESSAGE);
        }
      }
    
      private Vector readListFile(String file)
      {
        Vector seqfiles = new Vector();
        try
        {
          String line;
          BufferedReader in = new BufferedReader(new FileReader(file));
          while((line = in.readLine()) != null )
          {
            File seq = new File(line);
            if(seq.exists())
            {
              seqfiles.add(seq.getAbsolutePath());
            }
          }
        }
        catch (IOException e)
        {
          System.out.println("Problem reading list file");
        }
        return seqfiles;
      }
    
      private Properties getProperties()
      {
        Properties settings = new Properties();
        ClassLoader cl = this.getClass().getClassLoader();
        // try out of the classpath
        try
        {
          settings.load(cl.getResourceAsStream("j2ssh.properties"));
        }
        catch (Exception e)
        {
        }
        return settings;
      }
    
    
      class StdoutStdErrHandler extends Thread
      {
        private SessionChannelClient session;
        private boolean isStdout;
        private StringBuffer buff = new StringBuffer();
    
        protected StdoutStdErrHandler(SessionChannelClient session, 
                                      boolean isStdout)
        {
          this.session  = session;
          this.isStdout = isStdout;
        }
    
        public void run()
        {
          try
          {
            final InputStream in;
            if(isStdout)
              in = session.getInputStream();
            else
              in = session.getStderrInputStream();
    
            byte buffer[] = new byte[100];
            int read;
            while((read = in.read(buffer)) > 0)
              buff.append(new String(buffer, 0, read));
          }
          catch(IOException ioe){}
        }
    
        public String getOutput()
        {
          return buff.toString();
        }
    
      }
    
    
      /**
       * The main program for the PasswordConnect class
       *
       * @param args The command line arguments
       */
      public static void main(String args[]) 
      {
        new SshPSUClient(args);
      }
    }