Esempio n. 1
0
  private void splitRead(LongWritable key, String line, Writer writer) throws IOException {
    String[] fields = line.split("\t");

    if (fields[1].length() != fields[3].length()) {
      logger.warn("Warning; mismatching seq and qual lengths in record " + key.toString() + "!");
      logger.warn("Seq:");
      logger.warn(fields[1]);
      logger.warn("Qual:");
      logger.warn(fields[3]);
      logger.warn("DONE WARNING");
    }
    writer.write(fields[0] + "\n");
    writer.write(fields[1] + "\n");
    writer.write(fields[2] + "\n");
    writer.write(fields[3] + "\n");
  }
Esempio n. 2
0
    @Override
    public Integer call() {
      int exitstatus = Integer.MAX_VALUE;
      Boolean useIdentityFile = null;
      String credentials = null;
      String userName = nodeCredentials.getUsername();

      if (nodeCredentials instanceof LoginCredentialsPassword) {
        useIdentityFile = false;
        credentials = ((LoginCredentialsPassword) nodeCredentials).getPassword();
      } else if (nodeCredentials instanceof LoginCredentialsPrivateKey) {
        useIdentityFile = true;
        credentials = ((LoginCredentialsPrivateKey) nodeCredentials).getKey().getKeyPath();
      }

      ChannelExec c = null;
      SshClient ssh = null;

      try {
        ssh = new SshClient();
        ssh.createSession(nodeAddress, userName, false);

        log.info("connecting with username: "******"connecting using identity file: " + credentials);
        } else {
          log.info("connecting using password: "******"executing command: " + command);
        c.connect();

        new Thread(
                new Runnable() {
                  public void run() {
                    String line;
                    BufferedReader bufferedInputReader =
                        new BufferedReader(new InputStreamReader(is));
                    try {
                      while ((line = bufferedInputReader.readLine()) != null) {
                        output.append(line);
                        synchronized (timeStamp) {
                          timeStamp = System.currentTimeMillis();
                        }
                      }
                    } catch (IOException e) {
                      e.printStackTrace();
                    }
                  }
                })
            .start();

        new Thread(
                new Runnable() {
                  public void run() {
                    String line;
                    BufferedReader bufferedErrorReader =
                        new BufferedReader(new InputStreamReader(err));
                    try {
                      while ((line = bufferedErrorReader.readLine()) != null) {
                        error.append(line);
                        synchronized (timeStamp) {
                          timeStamp = System.currentTimeMillis();
                        }
                      }
                    } catch (IOException e) {
                      e.printStackTrace();
                    }
                  }
                })
            .start();

        while (!c.isClosed()) {
          synchronized (this.timeStamp) {
            if (System.currentTimeMillis() - this.timeStamp > MAXIMUM_WAITING_TIME_INACTIVITY) {
              log.warn("command execution seems inactive, canceling!");
              break;
            }
          }
          log.info("waiting for command to finish.");
          try {
            Thread.sleep(SshClient.DEFAULT_WAITING_TIME_PER_CYCLE);
          } catch (InterruptedException e) {
            e.printStackTrace();
          }
        }
        exitstatus = c.getExitStatus();

      } catch (JSchException e) {
        e.printStackTrace();
      } catch (IOException e) {
        e.printStackTrace();
      } finally {
        if (c != null) {
          c.disconnect();
        }

        if (ssh != null) {
          try {
            ssh.disconnectSession();
          } catch (JSchException e) {
            e.printStackTrace();
          }
        }
      }
      return exitstatus;
    }