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.

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

Use Process.getInputStream() to get an InputStream that represents the stdout of the newly created process.

Note that starting/running external processes from Java can be very tricky and has quite a few pitfalls.

They are described in this excellent article, which also describes ways around them.

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.

the code is right, just in the second line, I changed

"/bin/sh" to "/bin/bash"

And everything works!

sh == bash?

For a long time, /bin/sh used to point to /bin/bash on most GNU/Linux systems. As a result, it had almost become safe to ignore the difference between the two. But that started to change recently.

Some popular examples of systems where /bin/sh does not point to /bin/bash (and on some of which /bin/bash may not even exist) are:

1. Modern Debian and Ubuntu systems, which symlink sh to dash by default;

2. Busybox, which is usually run during the Linux system boot time as part of initramfs. It uses the ash shell implementation.

3. BSDs. OpenBSD uses pdksh, a descendant of the Korn shell. FreeBSD's sh is a descendant of the original UNIX Bourne shell.

For more information on this please refer to : Difference between sh and bash

Thanks to Abra I was able to find the solution. For anyone looking at this later, here is the code that worked:

// Create a new process and run the command
String[] command = new String[] {"mpw", "-u", "Name", "-t", "l", "Website"}; // Can also directly be put into the process builder as an argument without it being in an array
ProcessBuilder builder = new ProcessBuilder(command);
Process process = builder.start();

OutputStream stdin = process.getOutputStream();
InputStream stdout = process.getInputStream();
InputStream stderr = process.getErrorStream();

// Store the input and output streams in a buffer
BufferedReader reader = new BufferedReader(new InputStreamReader(stdout));
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(stdin));
BufferedReader error = new BufferedReader(new InputStreamReader(stderr));

// Send input
writer.write("password\n"); // Don't forget the '\n' here, otherwise it'll continue to wait for input
writer.flush();
//writer.close(); // Add if doesn't work without it

// Display the output
String line;
while ((line = reader.readLine()) != null) System.out.println(line);
// Display any errors
while ((line = error.readLine()) != null) System.out.println(line);

This should work for any command, I got the solution from Writing to InputStream of a Java Process