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"); }
@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; }