//
// CombineAnnotations.java
//

/*
ImageJ software for multidimensional image processing and analysis.

Copyright (c) 2010, ImageJDev.org.
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
    * 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.
    * Neither the names of the ImageJDev.org developers nor the
      names of its contributors may be used to endorse or promote products
      derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/

package imagej.util;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.net.URL;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Set;
import java.util.regex.Pattern;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;

import net.java.sezpoz.impl.SerAnnotatedElement;

/**
 * Combines SezPoz annotations from all JAR files on the classpath.
 * 
 * @author Curtis Rueden
 */
public class CombineAnnotations {

	private static final String PREFIX = "META-INF/annotations";
	private static final String OUTPUT_DIR = "src/main/assembly/all";

	private final Set<String> annotationFiles;

	public CombineAnnotations() throws IOException {
		annotationFiles = getAnnotationFiles();
	}

	/** Reads in annotations from all available resources and combines them. */
	public void combine() throws IOException, ClassNotFoundException {
		final HashSet<SerAnnotatedElement> annotations =
			new HashSet<SerAnnotatedElement>();
		final ClassLoader loader = ClassLoader.getSystemClassLoader();

		log("");
		log("Writing annotations to " + new File(OUTPUT_DIR).getAbsolutePath());

		for (final String annotationFile : annotationFiles) {
			annotations.clear();

			// read in annotations from all classpath resources
			final Enumeration<URL> resources = loader.getResources(annotationFile);
			while (resources.hasMoreElements()) {
				final URL resource = resources.nextElement();
				final ObjectInputStream ois =
					new ObjectInputStream(resource.openStream());
				while (true) {
					final SerAnnotatedElement el = (SerAnnotatedElement) ois.readObject();
					if (el == null) break;
					annotations.add(el);
				}
				ois.close();
			}

			// write out annotations to combined file on disk
			final File outputFile = new File(OUTPUT_DIR, annotationFile);
			final ObjectOutputStream oos =
				new ObjectOutputStream(new FileOutputStream(outputFile));
			for (final SerAnnotatedElement el : annotations) {
				oos.writeObject(el);
			}
			oos.writeObject(null);
			oos.close();
			log(outputFile.getName() + ": " + annotations.size() + " items");
		}
	}

	/** Scans for annotations files in every resource on the classpath. */
	public Set<String> getAnnotationFiles() throws IOException {
		final HashSet<String> files = new HashSet<String>();

		final String classpath = System.getProperty("java.class.path");
		final String[] pathItems = classpath.split(File.pathSeparator);
		for (final String pathItem : pathItems) {
			log("Scanning " + pathItem);
			if (pathItem.toLowerCase().endsWith(".jar")) {
				// read index from JAR file
				final ZipInputStream zis =
					new ZipInputStream(new FileInputStream(pathItem));
				while (true) {
					final ZipEntry zipEntry = zis.getNextEntry();
					if (zipEntry == null) break;
					final String name = zipEntry.getName();
					if (!name.matches(Pattern.quote(PREFIX + "/") + ".")) continue;
					add(files, name);
				}
			}
			else {
				// read files from directory
				final File annDir = new File(pathItem + "/" + PREFIX);
				if (!annDir.exists() || !annDir.isDirectory()) continue;
				final File[] annItems = annDir.listFiles();
				for (final File annItem : annItems) {
					add(files, PREFIX + "/" + annItem.getName());
				}
			}
		}

		return files;
	}

	public static void main(final String[] args) throws Exception {
		new CombineAnnotations().combine();
	}

	// -- Helper methods --

	private void add(final HashSet<String> set, final String item) {
		log("\t" + item);
		set.add(item);
	}

	private void log(final String msg) {
		System.out.println(msg);
	}

}

@@ -4641,16 +4641,17 @@
 /%22) + %22.
++
 %22)) cont

Fix bug in JAR regex.