/* 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;
private static JPasswordField pfield = new JPasswordField(16);
private static JTextField portfield = new JTextField(16);
private static JTextField hostfield = new JTextField(16);
private static JTextField ufield = new JTextField(16);
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");
else if(cmd.equals("blastn") && settings.getProperty("blastn") != null)
cmd = settings.getProperty("blastn");
else if(cmd.equals("blastx") && settings.getProperty("blastx") != null)
cmd = settings.getProperty("blastx");
else if(cmd.equals("tblastx") && settings.getProperty("tblastx") != null)
cmd = settings.getProperty("tblastx");
else if(cmd.equals("fasta") && settings.getProperty("fasta") != null)
cmd = settings.getProperty("fasta");
else if(cmd.equals("fastx") && settings.getProperty("fastx") != null)
cmd = settings.getProperty("fastx");
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);
BufferedReader reader =
new BufferedReader(new InputStreamReader(System.in));
// Create a password authentication instance
PasswordAuthenticationClient pwd = new PasswordAuthenticationClient();
JPanel promptPanel = new JPanel(new GridLayout(4,2));
if(hostname != null && hostfield.getText().equals(""))
hostfield.setText(hostname);
if(port >-1 && portfield.getText().equals(""))
portfield.setText(Integer.toString(port));
if(user != null && ufield.getText().equals(""))
ufield.setText(user);
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 AND RUN"};
int select = JOptionPane.showOptionDialog(null, promptPanel,
"LOGIN",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE,
null,
options,
options[1]);
if(select == 0)
return;
user = ufield.getText().trim();
pwd.setUsername(user);
pwd.setPassword(new String(pfield.getPassword()));
// 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());
if(port < 0)
ssh.connect(hostname);
else
ssh.connect(hostname,port);
// 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);
try
{
wdir = wdir+"/"+user;
sftp.mkdir(wdir);
wdir = wdir+"/"+program+"/";
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) ||
(cmd.indexOf("fastx33") > -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++;
}
Thread.currentThread().sleep(5000);
}
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);
}
}