Examples of com.trilead.ssh2.packets.PacketUserauthFailure

com.trilead.ssh2.StreamGobbler
PacketUserauthBanner. @author Christian Plattner, plattner@inf.ethz.ch @version $Id: PacketUserauthFailure.java,v 1.3 2005/08/24 17:54:09 cplattne Exp $

   * @see jSimMacs.gromacsrun.IGromacsRun#renameNdxGroup(java.util.List,
   *      java.util.List)
   */
  public void renameNdxGroup(List<String> commands, List<String> ndxCommands)
      throws IOException {
    Session sess = null;
    try {


      sess = startProcess(commands);


      OutputStuff ndxOutput = new OutputStuff();
      ndxOutput.output(sess.getStdin(), ndxCommands);


      outputStdout(sess.getStdout());
    } catch (IOException e) {
      throw e;
    } finally {
      if (sess != null)
        sess.close();
    }


    DataHandler handler = getHandler();
    handler.delete(commands.get(4));
  }

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  }


  private Session startProcess(List<String> commands) throws IOException {
    String command = ToolBox.createCommandString(commands);
    SSHDataHandler dataHandler = getHandler();
    Session sess = dataHandler.createSession();
    if (sess == null)
      throw new IOException("Session corrupt");
    sess.execCommand(command);
    return sess;
  }

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  public void startGromacsProgram(List<String> commands,
      OutputStream outStream, boolean interactive, OutputStream helperStream) throws IOException {
    SSHDataHandler dataHandler = getHandler();
    if (commands.get(0).equals(GromacsConstants.MDRUN)
        && remoteProject.isUseMPILib()) {
      Session mpiSess = dataHandler.createSession();
      mpiSess.execCommand(remoteProject.getMpiLib());
      outputSession(mpiSess);
      // outputStdout(mpiSess.getStdout());
      // outputStdout(mpiSess.getStderr());
      mpiSess.close();
      commands.add(0, Integer.toString(remoteProject.getNp()));
      commands.add(0, GromacsConstants.MPIRUNOPTION);
      commands.add(0, GromacsConstants.MPIRUN);
    }
    String command = ToolBox.createCommandString(commands);


    Session sess = dataHandler.createSession();
    SSHGromacsThread gromacsThread = new SSHGromacsThread(command, sess,
        outStream, interactive, helperStream);
    if (interactive)
      gromacsThread
          .setInputString(inputStringForInteractiveThread(commands

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      boolean interactive, OutputStream helperStream) throws IOException {
    SSHDataHandler dataHandler = getHandler();
    String gromacsCommand = command.substring(0, command.indexOf(" "));
    if (gromacsCommand.equals(GromacsConstants.MDRUN)
        && remoteProject.isUseMPILib()) {
      Session mpiSess = dataHandler.createSession();
      mpiSess.execCommand(remoteProject.getMpiLib());
      outputSession(mpiSess);
      // outputStdout(mpiSess.getStdout());
      // outputStdout(mpiSess.getStderr());
      mpiSess.close();
      String mpiCommand = GromacsConstants.MPIRUN + " "
          + GromacsConstants.MPIRUNOPTION + " " + remoteProject.getNp()
          + " " + command;
      command = mpiCommand;
    }


    Session sess = dataHandler.createSession();
    SSHGromacsThread gromacsThread = new SSHGromacsThread(command, sess,
        outStream, interactive, helperStream);
    if (interactive)
      gromacsThread
          .setInputString(inputStringForInteractiveThread(gromacsCommand));

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            if (isAuthenticated == false) {
              s_logger.info("Authentication failed for root with password");
              return false;
            }
            
            Session sess = conn.openSession();
            s_logger.info("Executing : " + commandElement.getTextContent());
            sess.execCommand(commandElement.getTextContent());
            Thread.sleep(60000);
            sess.close();
            conn.close();
            
            } catch (Exception ex) {
              s_logger.error(ex);
              return false;

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      objSSHSession = this.getSshConnection().openSession();
      logger.debug("Executing command " + checkShellCommand);
      objSSHSession.execCommand(checkShellCommand);


      logger.debug("output to stdout for remote command: " + checkShellCommand);
      ipsStdOut = new StreamGobbler(objSSHSession.getStdout());
      ipsStdErr = new StreamGobbler(objSSHSession.getStderr());
      BufferedReader stdoutReader = new BufferedReader(new InputStreamReader(ipsStdOut));
      String stdOut = "";
      while (true) {
        String line = stdoutReader.readLine();
        if (line == null)

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      }


      this.getSshSession().execCommand(strCmd);


      logger.debug("output to stdout for remote command: " + strCmd);
      ipsStdOut = new StreamGobbler(this.getSshSession().getStdout());
      ipsStdErr = new StreamGobbler(this.getSshSession().getStderr());
      BufferedReader stdoutReader = new BufferedReader(new InputStreamReader(ipsStdOut));
      strbStdoutOutput = new StringBuffer();
      while (true) {
        String line = stdoutReader.readLine();
        if (line == null)

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            spooler_log.debug5("executing remote command: " + command);
            this.setSshSession(this.getSshConnection().openSession());
            this.getSshSession().execCommand(command);


            spooler_log.debug5("output to stdout for remote command: " + command);
            InputStream stdout = new StreamGobbler(this.getSshSession().getStdout());
            BufferedReader stdoutReader = new BufferedReader(new InputStreamReader(stdout));
            while (true) {
                String line = stdoutReader.readLine();
                if (line == null) break;
                spooler_log.info(line);
            }


            spooler_log.debug5("output to stderr for remote command: " + command);
            InputStream stderr = new StreamGobbler(this.getSshSession().getStderr());
            BufferedReader stderrReader = new BufferedReader(new InputStreamReader(stderr));
            String stderrOutput = "";
            while (true) {
                String line = stderrReader.readLine();
                if (line == null) break;

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      spooler_log.debug5("fetching children");
      this.getSshSession().execCommand("/bin/ps -ef");


      spooler_log.debug9("output to stdout for ps command: ");
      stdout = new StreamGobbler(this.getSshSession().getStdout());
      stderr = new StreamGobbler(this.getSshSession().getStderr());
      BufferedReader stdoutReader = new BufferedReader(new InputStreamReader(stdout));
      String line = stdoutReader.readLine(); //Ueberschrift
      spooler_log.debug9(line);

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  private void executeCommand(String command, int logLevel) throws Exception{
    Session session = getSshConnection().openSession();
    try{
      session.execCommand(command);
      spooler_log.log(logLevel,"output to stdout for remote command: " + command);
      stdout = new StreamGobbler(this.getSshSession().getStdout());
      stderr = new StreamGobbler(this.getSshSession().getStderr());
      BufferedReader stdoutReader = new BufferedReader(new InputStreamReader(stdout));


      while (true) {
        String line = stdoutReader.readLine();
        if (line == null) break;

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