file management

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3417 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/j2ssh/SshFileManager.java

+/* 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.JOptionPane;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.JPasswordField;
+import javax.swing.SwingConstants;
+
+import java.awt.GridLayout;
+import java.io.File;
+import java.io.FileReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.BufferedReader;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+
+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;
+
+import com.sshtools.j2ssh.SshClient;
+import com.sshtools.j2ssh.authentication.AuthenticationProtocolState;
+import com.sshtools.j2ssh.authentication.PasswordAuthenticationClient;
+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;
+
+
+/**
+*
+* Client to use ssh connection to server to run blast/fasta
+* remotely. 
+*
+*/
+public class SshFileManager
+{
+
+  private Vector dir_list;
+  private Vector file_list;
+
+  // defaults
+  private String logfile  = null;
+  private String wdir     = "/nfs/pathscratch1/scratch";
+
+  // login variables
+  private String hostname = null;
+  private String user     = null;
+  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);
+  private SshClient ssh;
+
+  public SshFileManager()
+  {
+    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);
+    }
+    catch(IOException ioe){}
+
+    Properties settings = getProperties();
+    try
+    {
+      ssh = login();
+    }
+    catch(IOException ioe){}
+  }
+
+  /**
+  *
+  * Log the user in.
+  *
+  */
+  private SshClient login()
+            throws IOException
+  {
+    SshClient ssh = null;
+    int result = AuthenticationProtocolState.FAILED;
+
+    while(result != AuthenticationProtocolState.COMPLETE)
+    {
+      if(!setLogin())
+        return null;
+
+      // Create a password authentication instance
+      PasswordAuthenticationClient pwd = new PasswordAuthenticationClient();
+      user = ufield.getText().trim();
+      pwd.setUsername(user);
+      pwd.setPassword(new String(pfield.getPassword()));
+
+      // Make a client connection
+      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
+      result = ssh.authenticate(pwd);
+    }
+    return ssh;
+  }
+
+  /**
+  *
+  * Set the login information.
+  *
+  */
+  private boolean setLogin()
+  {
+    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 false;
+
+    return true;
+  }
+
+
+  /**
+  *
+  * Get the properties from the j2ssh.properties file.
+  *
+  */
+  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)
+    {
+    }
+
+    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(user == null)
+      user = System.getProperty("user.name");
+
+    return settings;
+  }
+
+  public boolean remoteList(String remoteRootDir)
+                    throws IOException
+  {
+    SftpClient sftp = ssh.openSftpClient();
+
+    try
+    {
+      sftp.cd(remoteRootDir);
+    }
+    catch(java.io.FileNotFoundException fnf)
+    {
+    }
+
+    Object list[] = sftp.ls().toArray();
+    
+    dir_list  = new Vector();
+    file_list = new Vector();
+
+    for(int i=0; i < list.length; i++)
+    {
+      SftpFile sfile = (SftpFile)list[i];
+      if(sfile.isDirectory())
+        dir_list.add(sfile.getFilename());
+
+      file_list.add(sfile.getFilename());
+    }
+     
+    sftp.quit();
+    return true;
+  }
+
+  public boolean delete(String filename)
+  {
+    try
+    {
+      SftpClient sftp = ssh.openSftpClient();
+      sftp.rm(filename);
+      sftp.quit();
+    }
+    catch(IOException ioe)
+    {
+      ioe.printStackTrace();
+      return false;
+    }
+
+    return true;
+  }
+
+  public boolean mkdir(String dir)
+  {
+    try
+    {
+      SftpClient sftp = ssh.openSftpClient();
+      sftp.mkdir(dir);
+      sftp.quit();
+    }
+    catch(IOException ioe)
+    {
+      ioe.printStackTrace();
+      return false;
+    }
+
+    return true;
+  }
+
+  public String pwd()
+  {
+    String pwd = null;
+    try
+    {
+      SftpClient sftp = ssh.openSftpClient();
+      pwd = sftp.pwd();
+      sftp.quit();
+    }
+    catch(IOException ioe)
+    {
+      ioe.printStackTrace();
+    }
+
+    return pwd;
+  }
+
+  public boolean rename(String old_file, String new_file)
+  {
+    try
+    {
+      SftpClient sftp = ssh.openSftpClient();
+      sftp.rename(old_file,new_file);
+      sftp.quit();
+    }
+    catch(IOException ioe)
+    {
+      ioe.printStackTrace();
+      return false;
+    }
+
+    return true;
+  }
+
+
+  /**
+  *
+  * @param dir name of directory to write the file to
+  * @param local_file file to copy to the server
+  *
+  */
+  public boolean put(String dir, File local_file)
+  { 
+    SftpClient sftp = null;
+
+    try
+    {
+      sftp = ssh.openSftpClient();
+      FileAttributes attr = sftp.stat(dir+"/"+local_file.getName());
+
+      if(attr.isDirectory())
+      {
+        JOptionPane.showMessageDialog(null,
+               "Cannot overwrite the directory\n"+
+               dir+"/"+local_file.getName(),"Cannot Overwrite",
+               JOptionPane.ERROR_MESSAGE);
+        return false;
+      }
+      else
+      {
+        int n = JOptionPane.showConfirmDialog(null,
+               "Overwrite\n"+
+               dir+"/"+local_file.getName() + "\n?",
+               "Confirm the sequence entry",
+               JOptionPane.YES_NO_OPTION);
+        if(n == JOptionPane.NO_OPTION)
+          return false;
+      }      
+    }
+    catch(IOException ioe)
+    {
+      // remote file doesn't exist
+    }
+
+    if(sftp == null)
+      return false;
+
+    try
+    {
+      sftp.put(local_file.getCanonicalPath(), 
+               dir+"/"+local_file.getName());
+      sftp.quit();
+    }
+    catch(IOException ioe)
+    {
+      ioe.printStackTrace();
+      return false;
+    }
+
+    return true;
+  }
+
+
+
+  /**
+  *
+  * Return the file contents as a byte array
+  *
+  */
+  public byte[] getFileContents(String file)
+  {
+    try 
+    {
+      SftpClient sftp = ssh.openSftpClient();
+
+      ByteArrayOutputStream os = new ByteArrayOutputStream();
+      sftp.get(file, os);
+      sftp.quit();
+      return os.toByteArray();
+    }
+    catch(IOException ioe)
+    {
+      ioe.printStackTrace();
+      return null;
+    }
+  }
+
+
+  public Vector getFileList()
+  {
+    return file_list;
+  }
+
+  public Vector getDirList()
+  {
+    return dir_list;
+  }
+ 
+}