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Process.getInputStream() doesnt return all lines

My code looks like this:
public List<String> linux(String... commands) throws Exception{
Process p = null;
ProcessBuilder builder = new ProcessBuilder(commands);
p = builder.start();
BufferedReader reader= new BufferedReader(new InputStreamReader(p.getInputStream(), StandardCharsets.UTF_8));
String line;
List<String> lines = new ArrayList<>();
while((line = reader.readLine()) != null) lines.add(line);
return lines;
}
But it didn't return all the outputs. I tried in the actual remote machine, there were about 100+ lines, but I only got 30 lines. Am I missing something ?

The code you have shown us will read all lines written by the process to its standard output. The readLine() call will only return a null when it has reached the end-of-stream for the pipe that it is reading from; i.e. after all reading all lines.
The readLine() call can only see the end-of-stream if the other end of the pipe (i.e. the external process) has closed it. You cannot get null by reading "too quickly". And conversely, if readLine() does return null for a given stream, any / all subsequent calls will return null. There is no point in retrying the readLine() if it returned null.
Also, you shouldn't use isAlive() to decide when to stop reading ... as suggested by someone else. The availability of unread output, and process termination are orthogonal issues.
Given that your code for reading the output is correct (I think so), there are just two possible explanations for the missing output:
Some of the process output was written to the processes standard error stream rather than its standard output.
Solution: You can get the contents of the standard error stream by reading from the stream returned by getErrorStream(). But a simpler alternative is to get ProcessBuilder to redirect the standard error output to standard output.
The external process terminated without flushing its output buffers. That could mean that some lines were never actually output by the process.
Solution: You need to fix the external application. This cannot be remedied from the Java application side.

It sounds like the Charset is not UTF-8 if it errors as soon as 'é' occurs. It's probably Extended ASCII, but if that doesn't work I'd try to figure out what Charset it really is.
It would fail on the entire line because of the BufferedReader.

Why does java.lang.process's readline() behave differently for reading inputstream on different boxes with the same os

I tested this code(below) on several different linux boxes(4+) and it worked fine. However, on one linux box I ran into an issue with readline() hanging for the error inputStream(errorStream). This stream should be empty so I suspected that box was not writing out a line terminator to the errorStream for the error. I changed my code to use read() instead of readline()...but read() also hung.
I tried retrieving the input inputStream first, and that worked and there was no hangs with readline()/read() for the error inputstream. I could not do this since I needed to obtain possible errors first. Appearing to be a deadlock, I was able to resolve this by having each inputstream read from it's own thread. Why did I only see this issue on one box? Is there a kernel setting or some other setting specific to this box that could have caused this?
ProcessBuilder processBuilder = new ProcessBuilder()
try
{
Process processA = null;
synchronized (processBuilder)
{
processBuilder.command("/bin/sh","-c"," . /Home/SomeScript.ksh");
processA = processBuilder.start();
}
inputStream = processA.getInputStream();
reader = new BufferedReader(new InputStreamReader(inputStream));
errorStream = processA.getErrorStream();
errorReader = new BufferedReader(new InputStreamReader(errorStream));
String driverError;
while ((driverError = errorReader.readLine()) != null)
{
//some code
}

Why did I only see this issue on one box?
Most likely because of something in the script that is being run ... and its interactions with its environment (e.g. files, environment variables, etc)
Is there a kernel setting or some other setting specific to this box that could have caused this?
It is possible but unlikely that it is a kernel setting. It might be "something else". Indeed, it has to be "something" outside of the Java application that is to blame, at least in part.
I suggest you do the following temporarily (at least):
ProcessBuilder processBuilder = new ProcessBuilder();
processBuilder.command("/bin/sh","-c"," . /Home/SomeScript.ksh");
processBuilder.redirectErrorStream(true);
processA = processBuilder.start();
inputStream = processA.getInputStream();
reader = new BufferedReader(new InputStreamReader(inputStream));
String line;
while ((line = reader.readLine()) != null) {
System.out.println(line);
}
System.out.println("Return code is " + processA.exitValue());
That way you can see what all of the output is.
There should not be a problem if the external process fails to put a newline at the end of the last line. The Java process will see an EOF on the input stream, and the BufferedReader will return what characters it has ... and return null on the next call.
Another possibility is that the external process is blocking because it is trying to read from its standard input.
UPDATE
The redirectErrorStream also resolved the issue, but I need the error stream separate.
OK so if it did (reliably) solve the problem then that (most likely) means that you have to read the external processes stdout and stderr streams in parallel. The simple way to do is to create 2 threads to read and buffer the two streams separately. For example: Capturing stdout when calling Runtime.exec
(Your problem is due to the fact that pipes have a finite buffering capacity. The external problem is most likely alternating between writing stuff to stdout and stderr. If it tries to write to one of the pipes when that pipe is "full", it will block. But if your application is reading all of the other pipe (to EOF) before it reads the blocked pipe, then everything will deadlock. The fact that the external process is stuck in PIPE_W state is more evidence for this explanation.
One possible reason that you are seeing different behaviour on different systems is that the amount of buffering in a pipe is system dependent. But it could also be due to differences in what the external process is doing; e.g. its inputs.)

You are running OS specific commands in a script, any one could be holding the error output. You can avoid this by discarding the errors, but that is unlikely to be a good idea.
I would check the version of the OS are the same and whether you have any significant differences in the command you run in the script. If this doesn't help, take out commands from the script until it starts working. I assume an empty script doesn't do this.

Java stuck in infinite loop executing a wmic command on Windows Server 2003

I'm trying to get a list of running processes and their file paths on a Windows Server 2003 machine. I'm using the following code to try and do that:
protected Map<String,String> getProcesses() {
Map<String,String> processes = new HashMap<String,String>();
try {
String line;
Process p = null;
// Windows
if (OS.indexOf("win") >= 0) {
p = Runtime.getRuntime().exec("wmic process get description,executablepath");
BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream()));
LOG.info("Entering while loop");
while ((line = input.readLine()) != null) {
LOG.info("blah");
String[] array = line.split("\\s+");
if (array.length > 1) {
processes.put(array[0], array[1]);
}
}
LOG.info("Exited while loop");
input.close();
}
} catch (Exception e) {
e.printStackTrace();
}
return processes;
}
The program gets stuck in an infinite loop at the while condition. "blah" and "Exited while loop" never output to the log. I've ran the command in command prompt on both my win7 local machine and the server which outputs the information just fine. I've also ran the above code on my local machine which also works fine. It looks like it's some issue between Java and Windows Server 2003 that I haven't been able to find in the past 3 hours of googling. Any help would be much appreciated.

You will need to get and close your OutputStream before getting and using your InputStream. That will confirm to the process that you've started that you have finished sending input (in this case, no input) to the process.
p.getOutputStream().close();
Remember that on the Process object, getInputStream() input comes from the output stream of the process, and getOutputStream() output goes to the input stream of the process.

Remember the BufferedReader.readLine() operation will block if there the end of input has not been reached, see here.
I think what you are experiencing is explained in the API for Process:
The methods that create processes may not work well for special processes on certain native platforms, such as native windowing processes, daemon processes, Win16/DOS processes on Microsoft Windows, or shell scripts. The created subprocess does not have its own terminal or console. All its standard io (i.e. stdin, stdout, stderr) operations will be redirected to the parent process through three streams (getOutputStream(), getInputStream(), getErrorStream()). The parent process uses these streams to feed input to and get output from the subprocess. Because some native platforms only provide limited buffer size for standard input and output streams, failure to promptly write the input stream or read the output stream of the subprocess may cause the subprocess to block, and even deadlock.

Reading error stream from a process

I am writing a java program to read the error stream from a process . Below is the structure of my code --
ProcessBuilder probuilder = new ProcessBuilder( command );
Process process = probuilder.start();
InputStream error = process.getErrorStream();
InputStreamReader isrerror = new InputStreamReader(error);
BufferedReader bre = new BufferedReader(isrerror);
while ((linee = bre.readLine()) != null) {
System.out.println(linee);
}
The above code works fine if anything is actually written to the error stream of the invoked process. However, if anything is not written to the error stream, then the call to readLine actually hangs indefinitely. However, I want to make my code generic so that it works for all scenarios. How can I modify my code to achieve the same.
Regards,
Dev

readline() is a blocking call. It will block until there's a line to be read (terminated by an end of line character) or the underlying stream is closed (returning EOF).
You need to have logic that is checking BufferedReader.ready() or just using BufferedReader.read() and bailing out if you decide you're waiting long enough (or want to do something else then check again).
Edit to add: That being said, it shouldn't hang "indefinitely" as-is; it should return once the invoked process terminates. By any chance is your invoked process also outputting something to stdout? If that's the case ... you need to be reading from that as well or the buffer will fill and will block the external process which will prevent it from exiting which ... leads to your problem.

This is a late reply, but the issue hasn't really solved and it's on the first page for some searches. I had the same issue, and BufferedReader.ready() would still set up a situation where it would lock.
The following workaround will not work if you need to get a persistent stream. However, if you're just running a program and waiting for it to close, this should be fine.
The workaround I'm using is to call ProcessBuilder.redirectError(File). Then I'd read the file and use that to present the error stream to the user. It worked fine, didn't lock. I did call Process.destroyForcibly() after Process.waitFor() but this is likely unnecessary.
Some pseudocode below:
File thisFile = new File("somefile.ext");
ProcessBuilder pb = new ProcessBuilder(yourStringList);
pb.redirectError(thisFile);
Process p = pb.start();
p.waitFor();
p.destroyForcibly();
ArrayList fileContents = getFileContents(thisFile);
I hope this helps with at least some of your use cases.

Something like this might also work and avoid the blocking behaviour (without requiring to create a File)
InputStream error = process.getErrorStream();
// Read from InputStream
for (int k = 0; k < error.available(); ++k)
System.out.println("Error stream = " + error.read());
From the Javadoc of InputStream.available
Returns an estimate of the number of bytes that can be read (orskipped over) from this input stream without blocking by the nextinvocation of a method for this input stream. The next invocationmight be the same thread or another thread. A single read or skip of thismany bytes will not block, but may read or skip fewer bytes.

The simplest answer would be to simply redirect the error stream to stdout:
process.getErrorStream().transferTo(System.out);

Read output from external process

I am trying to run a .csh script and read it's output into a StringBuffer.
the output sometime returns empty although running the script from console returns some output. the same running flow can sometimes returns output and sometimes not, although nothing is changed in the way the process starts (same script, path , args) and the script isn't changed as well.
I'm not getting any exceptions thrown.
what might cause output now to be read correctly/successfully ?
the code segment is
public static String getOutpoutScript(Process p) {
InputStream outpout = p.getInputStream();
logger.info("Retrived script output stream");
BufferedReader buf = new BufferedReader(new InputStreamReader(outpout));
String line = "";
StringBuffer write = new StringBuffer();
try {
while ((line = buf.readLine()) != null) {
write.append(line);
}
} catch (IOException e) {
// do something
}
return write.toString().trim();
}
beside the fact not closing the streams is not good, could this or something else in the code might prevent output from being read correctly under some circumstances ?
thanks,

If you launch it with ProcessBuilder, you can combine the error stream into the output stream. This way if the program prints to stderr you'll capture this too. Alternatively you could just read both. Additionally, you may not want to use readLine, you could be stuck for awhile if the program does not print end of line character at the end.

Maybe you must replace p.getInputStream() with p.getOutputStream()
Besides this sometimes processes can block waiting on input, so you must read and write asynchronously - one possible solution is to use different threads - e.g. one thread is reading, other is writing and one that is monitoring the process.

If you have an error, this will write to getErrorStream() by default. If you have a problem, I would ensure you are reading this somewhere.
If the buffer for this stream fills, your program will stop, waiting for you to read it.
A simple way around these issues is to use ProcessBuilder.redirectErrorStream(true)