import java.io.*;
/**
 * @author genepattern
 *
 * Runs a MATLAB function that exists in a directory passed in in the
 * first command line argument, with the remaining command-line args
 * being passed to the MATLAB function as String arguments.
 * 
 * Assumes that MATLAB is on the path.
 * 
 * operates by creating a startup.m file in the local working directory.
 * MATLAB reads this by default on startup. The startup.m it creates
 * adds the libdir to the path, calls the function (with args) and then quits matlab.
 * 
 * e.g. java RunMatlab c:\mystuff fooFunction one two
 * 
 * will write a startup.m that looks like this
 *
 * addpath c:\mystuff
 * fooFunction('one','two')
 * quit()
 *
 * and then exec
 * 	 matlab -nosplash -nodisplay
 */
public class RunMatlab {
 public static void main(String[] args) throws Exception {
 createStartupFile(args);
 
 String[] cmdArray = new String[3];
 cmdArray[0] = "matlab";
 cmdArray[1] = "-nosplash";
 cmdArray[2] = "-nodisplay";
 
 Process p = Runtime.getRuntime().exec(cmdArray);
 
 InputStream outs = p.getInputStream();
 
 	Thread stdoutReader = copyStream(p.getInputStream(), System.out);
		Thread stderrReader = copyStream(p.getErrorStream(), System.err);
		// drain the output and error streams
		stdoutReader.start();
		stderrReader.start();
		
		p.waitFor();
 }
 
 protected static void createStartupFile(String[] args){
 try {
 File startupM = new File("startup.m");
 BufferedWriter bw = new BufferedWriter(new FileWriter(startupM));
 bw.write("addpath "+args[0]);
 bw.write("\n");
 
 bw.write("try\n");
 
 bw.write(args[1]);
 bw.write("(");
 for (int i=2; i < args.length; i++){
 bw.write("'");
 bw.write(args[i]);
 bw.write("'"); 
 if ((i != (args.length - 1)) & (i != 0))
  bw.write(", ");
 }
 bw.write(")");
 bw.write("\n");

 bw.write("catch ME\n");
 bw.write("disp(ME.getReport);\n");
 bw.write("end\n");

 bw.write("quit();");
 bw.flush();
 bw.close();
 startupM.deleteOnExit();
 } catch (IOException e){
 e.printStackTrace();
	 System.err.println("Could not create startup.m file to execute. Exitting.");
	 System.exit(999);
 }
 }
 
	protected static Thread copyStream(final InputStream is, final PrintStream out) throws IOException {
	 // create thread to read from the a process' output or error stream
	 Thread copyThread = new Thread(new Runnable(){
	 	public void run() {
	 BufferedReader in = new BufferedReader(new InputStreamReader(is));
	 String line;
		 // copy inputstream to outputstream
		 try {
			boolean bNeedsBreak;
			while((line = in.readLine())!=null){
				out.println(line);
			}
		 } catch (IOException ioe) {
			System.err.println(ioe + " while reading from process stream");
	 }
	 	}
	 });
	 copyThread.setDaemon(true);
	 return copyThread;
 }
}

/* modified by Yuri Kotliarov (NOB/NCI/NIH)
 * Inserts try-catch block into startup.m to eliminate genepattern freeze 
 * if the user's MATLAB function generates an error.
 * startup.m then will look like this
 *
 * ============================
 * addpath c:\mystuff
 * try
 * fooFunction('one','two')
 * catch ME
 * disp(ME.getReport)
 * end
 * quit()
 * ============================
 *
 */