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;
}