[kepler-dev] Running Shell Scripts inside Kepler

[Tobin Fricke]

On Wed, 6 Apr 2005, Dan Higgins wrote:

> Now here is where I ran into trouble!!! On Linux and the Mac, 'R' is a
> shell script, not a simple executable! And apparently, the Java
> runtime.exec() method WILL NOT START A SUBPROCESS SET UP THIS WAY WITH A
> SHELL SCRIPT!!!

The JavaDoc for the 'Process' class contains the following note:

  The Runtime.exec methods 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
  (Process.getOutputStream(), Process.getInputStream(),
  Process.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.

In my test, executing a shell script worked without problem:

[tobin at robin ~/proving]$ ls
foo.sh  RunShellScript.class  RunShellScript.java

[tobin at robin ~/proving]$ cat foo.sh
#!/bin/sh
echo Hello, World!

[tobin at robin ~/proving]$ cat RunShellScript.java

/* Tobin Fricke
   2005-04-06
*/

class RunShellScript {
  public static void main(String args[]) {
    try {
      Process p = Runtime.getRuntime().exec("./foo.sh");
      /* Note that 'input' and 'output' are from the perspective of the
         controlling Java class.  This 'input stream' refers to the process's
         stdout! */
      java.io.InputStream o = p.getInputStream();
      /* Wait for the process to exit. */
      p.waitFor();
      /* Collect its output. */
      int l = o.available();
      byte[] b = new byte[l];
      o.read(b, 0, l);
      System.out.print(new String(b));
    } catch (Exception e) {
      System.out.println("Woops! " + e);
    }
  }
}
[tobin at robin ~/proving]$ javac RunShellScript.java
[tobin at robin ~/proving]$ java RunShellScript
Hello, World!
[tobin at robin ~/proving]$

I'd make sure that the R shell script starts with the proper "#!" magic
cookie & interpreter signture.  Also, does anyone know how to simply dump
the 'InputStream' obtained from the process to the Java stdout without
doing the silly byte[] --> String business I did?

Tobin

http://web.pas.rochester.edu/~tobin/