keep prompting for login of failure

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3390 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

@@ -142,139 +142,138 @@ public class SshPSUClient extends Thread
     {
       ConfigurationLoader.initialize(false);
 
-      if(!setLogin())
-        return;
-
-      // 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
-      SshClient ssh = new SshClient();
-      hostname = hostfield.getText().trim();
-      if(portfield.getText().trim().equals(""))
-        port = -1;
-      else
-        port = Integer.parseInt(portfield.getText().trim());
+      int result = AuthenticationProtocolState.FAILED;
+
+      SshClient ssh = null;
+
+      // login
+      while(result != AuthenticationProtocolState.COMPLETE)
+      {
+        if(!setLogin())
+          return;
+
+        // 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);
+        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)
+        // Try the authentication
+        result = ssh.authenticate(pwd);
+      }
+
+      // prompt for local listfile
+      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();
+
+      // loop over sequence files in the listfile
+      Vector seqfile = readListFile(listfilepath);
+      for(int i=0; i<seqfile.size();i++)
       {
-        if(listfilepath == null)
+        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
         {
-          JFileChooser chooser = new JFileChooser();
-          int returnVal = chooser.showOpenDialog(null);
-          if(returnVal == JFileChooser.APPROVE_OPTION) 
-            listfilepath = chooser.getSelectedFile().getAbsolutePath();
-          else
-            return;
+          wdir = wdir+"/"+user;
+          sftp.mkdir(wdir);
+          wdir = wdir+"/"+program+"/";
+          sftp.mkdir(wdir);
+
+          sftp.put(filepath, wdir+filename);
         }
+        catch(IOException ioe)
+        {}
+    
+        SessionChannelClient session = ssh.openSessionChannel();
 
-        SftpClient sftp = ssh.openSftpClient();
+        String outputfile = wdir+filename+".out";
+        final String actualCMD;
 
-        // loop over sequence files in the listfile
-        Vector seqfile = readListFile(listfilepath);
-        for(int i=0; i<seqfile.size();i++)
+        if( (cmd.indexOf("fasta33") > -1) ||
+            (cmd.indexOf("fastx33") > -1) )
         {
-          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)
-          {}
+          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;
+
+        // run the application
+        if(System.getProperty("debug") != null)
+          System.out.println(actualCMD);
+        session.executeCommand(actualCMD);
+
+        // Reading from the session InputStream
+        StdoutStdErrHandler stdouth = new StdoutStdErrHandler(session, true);
+        StdoutStdErrHandler stderrh = new StdoutStdErrHandler(session, false);
       
-          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;
-
-          // run the application
-          if(System.getProperty("debug") != null)
-            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);
-
-            isFile = waitUntilFileAppears(sftp, filename+".out");
-          }
-          catch(InterruptedException ie)
-          {
-            ie.printStackTrace();
-          }
+        stdouth.start();
+        stderrh.start();
+
+        boolean isFile = false;
+        try
+        {
+          // make sure we hang around for stdout
+          while(stdouth.isAlive() || stderrh.isAlive())
+            Thread.currentThread().sleep(10);
+
+          isFile = waitUntilFileAppears(sftp, filename+".out");
+        }
+        catch(InterruptedException ie)
+        {
+          ie.printStackTrace();
+        }
           
-          if(System.getProperty("debug") != null)
-          {
-            // stdout & stderr
-            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");
-          completed = true; 
-          session.close();
+        if(System.getProperty("debug") != null)
+        {
+          // stdout & stderr
+          System.out.println(stdouth.getOutput());
+          System.out.println(stderrh.getOutput());
         }
 
-        // Quit
-        sftp.quit();
-        ssh.disconnect();
-      }
-      else 
-        JOptionPane.showMessageDialog(null, 
-            "Problem logging in!\nCheck username and password.",
-            "Authentication Problem",
-            JOptionPane.ERROR_MESSAGE);
+//      ByteArrayOutputStream os = new ByteArrayOutputStream();
+//      sftp.get(outputfile, os);
+//      System.out.println(os.toString());
 
+        sftp.get(outputfile, filepath+".out");
+        completed = true; 
+        session.close();
+      }
 
-    } catch(IOException ioe){}
+      // Quit
+      sftp.quit();
+      ssh.disconnect();
+    }
+    catch(IOException ioe){}
     finally
     {
       if(completed)