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SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by downstream projects in the SciJava ecosystem, such as ImageJ and SCIFIO.
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 * SciJava Common shared library for SciJava software.
 * %%
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 * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
 * Institute of Molecular Cell Biology and Genetics.
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 * 
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
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package org.scijava.util;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintStream;
import java.util.Arrays;

/**
 * Useful methods for working with processes.
 * 
 * @author Johannes Schindelin
 */
public final class ProcessUtils {

	private ProcessUtils() {
		// prevent instantiation of utility class
	}

	/**
	 * Executes a program. This is a convenience method mainly to be able to catch
	 * the output of programs as shell scripts can do by wrapping calls in $(...).
	 * 
	 * @param workingDirectory the directory in which to execute the program
	 * @param err the {@link PrintStream} to print the program's error stream to;
	 *          if null is passed, the error goes straight to Nirvana (not the
	 *          band, though).
	 * @param out the {@link PrintStream} to print the program's output to; if
	 *          null is passed, the output will be accumulated into a
	 *          {@link String} and returned upon exit.
	 * @param args the command-line to execute, split into components
	 * @return the output of the program if {@code out} is null, otherwise an
	 *         empty {@link String}
	 * @throws RuntimeException if interrupted or the program failed to execute
	 *           successfully.
	 */
	public static String exec(final File workingDirectory,
		final PrintStream err, final PrintStream out, final String... args)
	{
		return exec(workingDirectory, null, err, out, args);
	}

	/**
	 * Executes a program. This is a convenience method mainly to be able to catch
	 * the output of programs as shell scripts can do by wrapping calls in $(...).
	 * 
	 * @param workingDirectory the directory in which to execute the program
	 * @param in the {@link InputStream} which gets fed to the program as standard input;
	 * @param err the {@link PrintStream} to print the program's error stream to;
	 *          if null is passed, the error goes straight to Nirvana (not the
	 *          band, though).
	 * @param out the {@link PrintStream} to print the program's output to; if
	 *          null is passed, the output will be accumulated into a
	 *          {@link String} and returned upon exit.
	 * @param args the command-line to execute, split into components
	 * @return the output of the program if {@code out} is null, otherwise an
	 *         empty {@link String}
	 * @throws RuntimeException if interrupted or the program failed to execute
	 *           successfully.
	 */
	public static String exec(final File workingDirectory,
		final InputStream in, final PrintStream err, final PrintStream out,
		final String... args)
	{
		try {
			final Process process =
				Runtime.getRuntime().exec(args, null, workingDirectory);

			final ReadInto inThread;
			if (in == null) {
				inThread = null;
				process.getOutputStream().close();
			} else {
				final PrintStream print = new PrintStream(process.getOutputStream());
				inThread = new ReadInto(in, print, true);
			}

			final ReadInto errThread = new ReadInto(process.getErrorStream(), err);
			final ReadInto outThread = new ReadInto(process.getInputStream(), out);
			try {
				process.waitFor();
				if (inThread != null) {
					inThread.done();
					inThread.join();
				}
				errThread.join();
				outThread.join();
			}
			catch (final InterruptedException e) {
				process.destroy();
				if (inThread != null) inThread.interrupt();
				errThread.done();
				errThread.interrupt();
				outThread.done();
				outThread.interrupt();
				err.println("Interrupted!");
				throw new RuntimeException(e);
			}
			if (process.exitValue() != 0) {
				throw new RuntimeException("exit status " + process.exitValue() +
					": " + Arrays.toString(args) + "\n" + err);
			}
			return outThread.toString();
		}
		catch (final IOException e) {
			throw new RuntimeException(e);
		}
	}

}