Here is the way to go:

Runtime rt = Runtime.getRuntime();
String[] commands = {"system.exe", "-get t"};
Process proc = rt.exec(commands);

BufferedReader stdInput = new BufferedReader(new 
     InputStreamReader(proc.getInputStream()));

BufferedReader stdError = new BufferedReader(new 
     InputStreamReader(proc.getErrorStream()));

// Read the output from the command
System.out.println("Here is the standard output of the command:\n");
String s = null;
while ((s = stdInput.readLine()) != null) {
    System.out.println(s);
}

// Read any errors from the attempted command
System.out.println("Here is the standard error of the command (if any):\n");
while ((s = stdError.readLine()) != null) {
    System.out.println(s);
}

Read the Javadoc for more details here. ProcessBuilder would be a good choice to use.

I don't have a windows machine to test this on, but generally to get the output for those builtins you run cmd.exe as the program and pass it the command as an argument.

Now, this has some limitations, because when the command finishes the executable stops. So if you do a cd command, it will work, but it only affect the subprocess, not your process. For those sorts of things, if you want them to change the state of your process, you'll need to use other facilities.

This version works on a Mac:

import java.io.*;
public class cmd {
    public static void  
        main(String[] argv){
        String line;
        String[] cmd = {"bash","-c","ls"};
        System.out.println("Hello, world!\n");
        try {
            Process p = Runtime.getRuntime().exec(cmd);
            BufferedReader input =
                new BufferedReader(new InputStreamReader(p.getInputStream()));
            while ((line = input.readLine()) != null) {
                System.out.println(line);
            }
            input.close();
        } catch (Exception e) {
        }
        return ;
    }
}

You need to the OutputStream (InputStream) of your Process (and you should use a ProcessBuilder)... like so

public static void main(String[] args) {
  String filename = args[1].substring(0, args[1].length() - 5);
  String cmd1 = "javac " + args[1];
  String cmd2 = "java " + filename;

  try {
    // Use a ProcessBuilder
    ProcessBuilder pb = new ProcessBuilder(cmd1);

    Process p = pb.start();
    InputStream is = p.getInputStream();
    BufferedReader br = new BufferedReader(new InputStreamReader(is));
    String line = null;
    while ((line = br.readLine()) != null) {
      System.out.println(line);
    }
    int r = p.waitFor(); // Let the process finish.
    if (r == 0) { // No error
       // run cmd2.
    }
  } catch (Exception e) {
    e.printStackTrace();
  }
}

This is not Java question. Basically what you doing is running Java (Java Main Process A) and from it starting another process (Windows CMD B). This is fine and you can get input/output streams of this process (B) in Java(A). However this process (B) starts another process (again Windows CMD C) with its own standard input/output. This process has nothing common with processes A&B and uses Windows' standard Input/Output streams. So, there are no connections between A and C. I'm not sure but I think there are some ways to run Windows CMD with different or not standard IO. Maybe something like this will work:

cmd <tty >tty

but there is no tty in Windows. Pragmatically you can do this as described here - Creating a Child Process with Redirected Input and Output but that would not work for regular CMD.

Nevertheless it became even more problematic when you start your own process from the editorTemp.exe (process D). D has even more disconnection with process A. And all for what? What don't you simply start process D directly from A and have full control on the IO streams and process itself? Here is good example how to do so.

Solved the problem, the problem was that i did not have access to the output i wanted 'cause it was cause by a command calling another comman.

The way i solved it in code:

ProcessBuilder builder = new ProcessBuilder("cmd.exe");
Process  process = builder.start();
BufferedWriter out = new BufferedWriter(new 
OutputStreamWriter(process.getOutputStream()));
InputStream stdout = process.getInputStream();

BufferedReader reader = new BufferedReader(new InputStreamReader(stdout));

out.write("start /b new.bat\n");
out.flush();
out.close();

Scanner scanner = new Scanner(stdout);
while (scanner.hasNextLine()) {
    System.out.println(scanner.nextLine());
}
System.out.println("end");
scanner.close();

Awnser based on this .

Thanks for the help!

You need to read InputStream from the process, here is an example:

Edit I modified the code as suggested here to receive the errStream with the stdInput

ProcessBuilder builder = new ProcessBuilder("command goes here");
builder.redirectErrorStream(true);
Process process = builder.start();
InputStream is = process.getInputStream();
BufferedReader reader = new BufferedReader(new InputStreamReader(is));

String line = null;
while ((line = reader.readLine()) != null) {
   System.out.println(line);
}

For debugging purpose, you can read the input as bytes instead of using readLine just in case that the process does not terminate messages with newLine

You can use the following code for this

import java.io.*; 

    public class doscmd 
    { 
        public static void main(String args[]) 
        { 
            try 
            { 
                Process p=Runtime.getRuntime().exec("cmd /c dir"); 
                p.waitFor(); 
                BufferedReader reader=new BufferedReader(
                    new InputStreamReader(p.getInputStream())
                ); 
                String line; 
                while((line = reader.readLine()) != null) 
                { 
                    System.out.println(line);
                } 

            }
            catch(IOException e1) {e1.printStackTrace();} 
            catch(InterruptedException e2) {e2.printStackTrace();} 

            System.out.println("Done"); 
        } 
    }

 ProcessBuilder ps = new ProcessBuilder("java ", path);

You're executing java Second.java it should be java Second

replace path.replace(".java","") or create a variable without ".java"

nsaravanas@ubuntu:~$ pwd
/home/nsaravanas
nsaravanas@ubuntu:~$ javac com/test/Second.java
nsaravanas@ubuntu:~$ java com.test.Second
Hello world from Second.java
nsaravanas@ubuntu:~$

This full Java program example runs the command 'dir' (directory listing) on the command line and pulls the result into a String and prints it on the console.

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;

public class X {
    public static void main(String[] args) {
        try{
            String command = "dir";
            String s = get_commandline_results(command);
            System.out.println(s);
        }
        catch(Exception e){
            e.printStackTrace();
        }
        System.out.println("done");
    }

    public static String get_commandline_results(String cmd)
        throws IOException, InterruptedException, IllegalCommandException{

        //Do not remove the authorizedCommand method.  Be prepared 
        //to lose your hard drive if you have not white-listed the 
        //commands that can run.
        if (!authorizedCommand(cmd)) 
            throw new IllegalCommandException();

        String result = "";
        final Process p = Runtime.getRuntime().
            exec(String.format("cmd /c %s", cmd));
        final ProcessResultReader stderr = new ProcessResultReader(
                p.getErrorStream(), "STDERR");
        final ProcessResultReader stdout = new ProcessResultReader(
                p.getInputStream(), "STDOUT");
        stderr.start();
        stdout.start();
        final int exitValue = p.waitFor();
        if (exitValue == 0){
            result = stdout.toString();
        }
        else{
            result = stderr.toString();
        }
        return result;
    }
    public static boolean authorizedCommand(String cmd){
        //Do not allow any command to be run except for the ones 
        //that we have pre-approved here.  This lessens the 
        //likelihood that fat fingers will wreck your computer.
        if (cmd.equals("dir"))
            return true;
        //add the commands you want to authorize here.

        return false;
    }
}

class ProcessResultReader extends Thread{
    final InputStream is;
    final String type;
    final StringBuilder sb;

    ProcessResultReader(final InputStream is, String type){
        this.is = is;
        this.type = type;
        this.sb = new StringBuilder();
    }

    public void run()
    {
        try{
            final InputStreamReader isr = new InputStreamReader(is);
            final BufferedReader br = new BufferedReader(isr);
            String line = null;
            while ((line = br.readLine()) != null)
            {
                this.sb.append(line).append("\n");
            }
        }
        catch (final IOException ioe)
        {
            System.err.println(ioe.getMessage());
            throw new RuntimeException(ioe);
        }
    }
    @Override
    public String toString()
    {
        return this.sb.toString();
    }
}
class IllegalCommandException extends Exception{
    private static final long serialVersionUID = 1L;
    public IllegalCommandException(){   }
}

On Windows, this is the result I get

Directory of D:\projects\eric\eclipseworkspace\testing2
07/05/2012  01:06 PM    <DIR>          .
07/05/2012  01:06 PM    <DIR>          ..
06/05/2012  11:11 AM               301 .classpath
06/05/2012  11:11 AM               384 .project
06/05/2012  11:11 AM    <DIR>          .settings
07/05/2012  01:42 PM    <DIR>          bin
06/05/2012  11:11 AM    <DIR>          src
07/05/2012  01:06 PM             2,285 usernames.txt
               3 File(s)          2,970 bytes
               5 Dir(s)  45,884,035,072 bytes free

done

Use getErrorStream().

BufferedReader in = new BufferedReader(new InputStreamReader(pr.getErrorStream()));

EDIT:

You can use ProcessBuilder (and also read the documentation)

ProcessBuilder   ps=new ProcessBuilder("java.exe","-version");

//From the DOC:  Initially, this property is false, meaning that the 
//standard output and error output of a subprocess are sent to two 
//separate streams
ps.redirectErrorStream(true);

Process pr = ps.start();  

BufferedReader in = new BufferedReader(new InputStreamReader(pr.getInputStream()));
String line;
while ((line = in.readLine()) != null) {
    System.out.println(line);
}
pr.waitFor();
System.out.println("ok!");

in.close();
System.exit(0);

As one of the commenters mentioned this might result in quite complex setups you are running into. It is most likely in your case that an error happens in java and you just do not see the output since error messages are written to the STDERR stream instead of STDOUT.

So there are two options (1) you take the code you already have and also try to read from the process' ErrorStream.

Bufferedreader error = new BufferedReader(new InputStreamReader(p.getErrorStream());

Or if you do not care whether or not the process you were starting was writing to STDERR or to STDOUT you can also use a ProcessBuilder and just set it up to redirect the error stream.

ProcessBuilder pb = new ProcessBuilder("java", "helloworld");
pb.redirectErrorStream(true); // this redirects STDERR to STDOUT
Process p = pb.start();
BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream()));
while ((line = input.readLine()) != null) {
    output += (line + '\n');
}            
input.close();    

For the sake of simplicity I omitted all the boilerplate code and exception handling in the above. But I think you will get the idea.

When you use bash -c, the first argument after the -c is treated as a command, and any additional arguments are passed as positional parameters.

In your first fragment,

{"bash", "-c", "cd " + folder + "&& find . -type f | grep :*.txt "}

you are passing a single concatenated string argument "cd " + folder + "&& find . -type f | grep :*.txt " whereas in the second fragment,

{"bash", "-c", "~/Final-Year/src/query", "&& ./checkuser.sh", user}

you are passing 3 arguments:

• ~/Final-Year/src/query (which presumably should have been cd ~/Final-Year/src/query
• && ./checkuser.sh
• user

so it's equivalent to

bash -c '~/Final-Year/src/query' '&& ./checkuser.sh' user

which executes bash -c '~/Final-Year/src/query' or (corrected) bash -c 'cd ~/Final-Year/src/query' with literal string && ./checkuser.sh as positional parameter $0 and the substituted Java variable user as positional parameter $1

What you likely want is

bash -c 'cd ~/Final-Year/src/query && ./checkuser.sh user'

which would instead be

{"bash", "-c", "cd ~/Final-Year/src/query && ./checkuser.sh " + user}

Alternatively, you could make use of the positional parameter array like

{"bash", "-c", "cd ~/Final-Year/src/query && ./checkuser.sh \"$1\"", "bash", user}

where the shell's name bash is passed as $0 (you could use any arbitrary string here) and Java variable user as $1.

Instead of

while ((line = input.readLine()) != null) {
            output += (line + '\n');
        } 

To output the results to the command line immediately just print within the while loop

     while ((line = input.readLine()) != null) {
         System.out.println(line);               
         output += (line + '\n');
      }