ProcessBuilder works starting jar but does not acknolwledge jar's arguments

Question

I am trying to run jmol's jar inside a running java program. This is how I run it in the command line and it runs fine.

$ java -jar Jmol.jar 1644_____.pdb -o -J "measure 3 4;measure 1 2"

I am using a ProcessBuilder and it calls the jar file and the first argument correctly but not the rest. What am I missing?

import java.io.IOException;

class test{
    public static void main(String [] ar) throws Exception{
        run();
    }

    public static void run() throws IOException, InterruptedException{
        String INPUTPDB = "1644_____.pdb";
        String args[] = {"java", "-jar", "Jmol.jar", INPUTPDB, "-o", "-J", "\"measure 3 4;measure1 2\""};
        ProcessBuilder pb = new ProcessBuilder(args);
        //Runtime.getRuntime().exec(args);
        Process p = pb.start();
        p.waitFor();
    }
}

[no idea from this question, maybe ordering of parameters, maybe exec(new String[] {"...."})](http://stackoverflow.com/a/6164084/714968) — mKorbel, Mar 02 '13 at 20:15
You don't appear to be handling the InputStream, OutputStream and error InputStream. The Error Stream in particular may show you important error messages. Also if you don't handle these Streams, you may fill up OS buffers rendering your process non-functioning. — Hovercraft Full Of Eels, Mar 02 '13 at 20:15
I could be wrong, but I'm pretty sure you don't need to "quote" argument groups like ` "\"measure 3 4;measure1 2\""`, ` "measure 3 4;measure1 2"` should be just fine — MadProgrammer, Mar 02 '13 at 20:38
@JulioDiaz I added an expanded answer, double check it and see if it sounds right — MadProgrammer, Mar 02 '13 at 20:53

MadProgrammer · Accepted Answer · 2013-03-04T01:01:26.503

As I understand it, each parameter you pass to ProcessBuilder will be passed to the process as a separate argument.

That means that when the process does an equivalent of args[x], your \"measure 3 4;measure1 2\" parameter will look like "measure 3 4;measure1 2" to the process (including the quotes).

Unless the command is expecting the quotes, there is no need to quote the parameters

Instead, try something like

String args[] = {"java", "-jar", "Jmol.jar", INPUTPDB, "-o", "-J", "measure 3 4;measure1 2"};

ProcessBuilder works starting jar but does not acknolwledge jar's arguments

1 Answers1