java process builder adding path to environment not working

Question

I am using intellij both on my imac and mac book. when i run the following code on my mac book, everything works.

import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;

public class Main {
    public ProcessBuilder pb;
     public Main(){
         try {
             pb = new ProcessBuilder();
             pb.directory(new File("~/IdeaProjects/test"));
             Map<String, String> env;
             env = pb.environment();
             env.put("PATH", "/usr/local/fsl/bin/");

         } catch (Exception e) {
             e.printStackTrace();
         }
     }

    public void getMeanImage(String base, String file){
        List<String> cmd = new LinkedList<>();
        cmd.add("fslmaths");
        cmd.add(base + file);
        cmd.add("-Tmean");
        cmd.add(base + file + "_mean");

        pb.command(cmd);

        try {
            String s = "";
            Process p = pb.start();
            BufferedReader stdInput = new BufferedReader(new
                    InputStreamReader(p.getInputStream()));

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

            // read the output from the command
            while ((s = stdInput.readLine()) != null) {
                System.out.println(s);
            }
            while ((s = stdError.readLine()) != null) {
                System.out.println(s);
            }

        } catch (IOException e) {
            e.printStackTrace();
        }

    }

    public static void main(String [ ] args) {
        Main m = new Main();
        m.getMeanImage("", "scan.nii.gz");
    }
}

On the imac I run into problems. I copied the PATH value used by printenv.

env.put("PATH", "/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin");

I get the exception:

java.io.IOException: Cannot run program "fslmaths" (in directory "~/IdeaProjects/test"): error=2, No such file or directory

Why can't the process builder find the program fslmaths in /usr/local/fsl/bin on the imac?

which fslmaths
/usr/local/fsl/bin/fslmaths

thanks in advance, Martin

Is pb.directory(new File("~/IdeaProjects/test")) actually creating a new subdirectory in your home directory, and not a directory literally named ~? — Andrew Henle
– Andrew Henle, Commented Jan 10, 2017 at 13:55

gimba · Accepted Answer · 2017-01-10 14:18:19Z

2

I found the solution. In the 'Run/Debug Configurations' of intellij under 'Environment Variables' the checkbox 'Include parent environment variables' was not enabled.

answered Jan 10, 2017 at 14:18

gimba

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