Package com.trilead.ssh2

Examples of com.trilead.ssh2.SFTPv3FileAttributes

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   * @see jSimMacs.gromacsrun.IGromacsRun#make_ndx(java.util.List,
   *      java.util.List, java.lang.String)
   */
  public List<String> make_ndx(List<String> commands,
      List<String> ndxCommands, String groupName) throws IOException {
    Session sess = null;
    BufferedReader commandResult = null;
    try {
      sess = startProcess(commands);

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

      InputStream stdout = new StreamGobbler(sess.getStdout());
      commandResult = new BufferedReader(new InputStreamReader(stdout));

      ndxCommands = GromacsCommandBuilder.getInstance()
          .createRenameGroupNdxCommand(commandResult, groupName);

    } catch (IOException e1) {
      throw e1;
    } finally {
      if (commandResult != null)
        commandResult.close();
      if (sess != null)
        sess.close();
    }
    return ndxCommands;
  }
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   * @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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            s_logger.info("Authentication failed for root with password");
            return false;
          }
         
          String restartCommand = "service cloud-management restart; service cloud-usage restart";
          Session sess = conn.openSession();
          s_logger.info("Executing : " + restartCommand);
          sess.execCommand(restartCommand);
          Thread.sleep(120000);
          sess.close();
          conn.close();
         
          } catch (Exception ex) {
            s_logger.error(ex);
            return false;
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        }
        SCPClient scp = new SCPClient(conn);
       
        scp.put("wget.exe", "");
       
        Session sess = conn.openSession();
        s_logger.info("Executing : wget http://172.16.0.220/dump.bin");
        sess.execCommand("wget http://172.16.0.220/dump.bin && dir dump.bin");
       
        InputStream stdout = sess.getStdout();
        InputStream stderr = sess.getStderr();
       
        byte[] buffer = new byte[8192];
        while (true) {
          if ((stdout.available() == 0) && (stderr.available() == 0)) {
            int conditions = sess.waitForCondition(ChannelCondition.STDOUT_DATA | ChannelCondition.STDERR_DATA
                | ChannelCondition.EOF, 120000);
           
            if ((conditions & ChannelCondition.TIMEOUT) != 0) {
              s_logger.info("Timeout while waiting for data from peer.");
              return null;
            }
           
            if ((conditions & ChannelCondition.EOF) != 0) {
              if ((conditions & (ChannelCondition.STDOUT_DATA | ChannelCondition.STDERR_DATA)) == 0) {
                break;
              }
            }
          }
         
          while (stdout.available() > 0) {
            success = true;
            int len = stdout.read(buffer);
            if (len > 0) // this check is somewhat paranoid
              s_logger.info(new String(buffer, 0, len));
          }
   
          while (stderr.available() > 0) {
            int len = stderr.read(buffer);
          }
        }
        sess.close();
        conn.close();
       
        if (success) {
          return null;
        } else {
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        if (isAuthenticated == false) {
          return "Authentication failed";
        }
        boolean success = false;
        Session sess = conn.openSession();
        s_logger.info("Executing : wget http://172.16.0.220/dump.bin");
        sess.execCommand("wget http://172.16.0.220/dump.bin && ls -al dump.bin");
       
        InputStream stdout = sess.getStdout();
        InputStream stderr = sess.getStderr();
       
        byte[] buffer = new byte[8192];
        while (true) {
          if ((stdout.available() == 0) && (stderr.available() == 0)) {
            int conditions = sess.waitForCondition(ChannelCondition.STDOUT_DATA | ChannelCondition.STDERR_DATA
                | ChannelCondition.EOF, 120000);
           
            if ((conditions & ChannelCondition.TIMEOUT) != 0) {
              s_logger.info("Timeout while waiting for data from peer.");
              return null;
            }
           
            if ((conditions & ChannelCondition.EOF) != 0) {
              if ((conditions & (ChannelCondition.STDOUT_DATA | ChannelCondition.STDERR_DATA)) == 0) {
                break;
              }
            }
          }
         
          while (stdout.available() > 0) {
            success = true;
            int len = stdout.read(buffer);
            if (len > 0) // this check is somewhat paranoid
              s_logger.info(new String(buffer, 0, len));
          }
   
          while (stderr.available() > 0) {
            int len = stderr.read(buffer);
          }
        }
       
        sess.close();
        conn.close();
       
        if (success) {
          return null;
        } else {
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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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