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// :tabSize=4:indentSize=4:noTabs=false:folding=explicit:collapseFolds=1:
// {{{ imports
import java.io.*;
import java.io.File;
import java.net.URL;
import java.net.URLClassLoader;
import java.util.HashMap;
import java.util.Vector;
import java.util.Enumeration;
import java.util.Iterator;
import java.util.StringTokenizer;
import java.util.zip.*;
 * Class loader used internally by rJava
 * The class manages the class paths and the native libraries (jri, ...)
public class RJavaClassLoader extends URLClassLoader {
	// {{{ fields 
	 * path of RJava
	String rJavaPath ;
	 * lib sub directory of rJava
	String rJavaLibPath;
	 * map of libraries
	HashMap/*<String,UnixFile>*/ libMap;
	 * The class path vector 
	Vector/*<UnixFile>*/ classPath;
	 * singleton
	public static RJavaClassLoader primaryLoader = null;
	 * Print debug messages if is set to <code>true</code>
	public static boolean verbose = false;
	 * Should the system class loader be used to resolve classes 
	 * as well as this class loader
	public boolean useSystem = true;
	// {{{ UnixFile class
	 * Light extension of File that handles file separators and updates
	class UnixFile extends File {
		 * cached "last time modified" stamp
		long lastModStamp;
		 * Constructor. Modifies the path so that 
		 * the proper path separator is used (most useful on windows)
		public UnixFile(String fn) {
			super( u2w(fn) ) ;
			lastModStamp=0;
		 * @return whether the file modified since last time the update method was called
		public boolean hasChanged() {
			long curMod = lastModified();
			return (curMod != lastModStamp);
		 * Cache the result of the lastModified stamp
		public void update() {
			lastModStamp = lastModified();
	// {{{ UnixJarFile
	 * Specialization of UnixFile that deals with jar files
	class UnixJarFile extends UnixFile {
		 * The cached jar file
		private ZipFile zfile ;
		 * common prefix for all URLs within this jar file
		private String urlPrefix ;
		public UnixJarFile( String filename ){
			super( filename );
		/* @Override */
		public void update(){
				if (zfile != null){
					zfile.close();
				zfile = new ZipFile( this ) ;
			} catch (Exception tryCloseX) {}
			/* time stamp */
			super.update( ) ; 
		 * Get an input stream for a resource contained in the jar file
		 * @param name file name of the resource within the jar file
		 * @return an input stream representing the resouce if it exists or null
		public InputStream getResourceAsStream( String name ){
			if (zfile==null || hasChanged()) {
				update(); 
				if (zfile == null) return null;
				ZipEntry e = zfile.getEntry(name);
				if (e != null)
					return zfile.getInputStream(e);
			} catch(Exception e) {
				if (verbose) System.err.println("RJavaClassLoader$UnixJarFile: exception: "+e.getMessage());
			return null;
		public URL getResource(String name ){
			if( zfile == null  || zfile.getEntry( name ) == null ){
				return null ;
			URL u = null ; 
			if( urlPrefix == null ){
					urlPrefix = "jar:" + toURL().toString() + "!" ;
				} catch( java.net.MalformedURLException ex){
				u = new URL( urlPrefix + name ) ;
			} catch( java.net.MalformedURLException ex ){
				/* not to worry */
			return u ;
	// {{{ UnixDirectory class
	 * Specialization of UnixFile representing a directory
	/* it is not really a specialization but makes possible to dispatch on instanceof*/
	class UnixDirectory extends UnixFile {
		public UnixDirectory( String dirname ){
			super( dirname ) ;
	// {{{ getPrimaryLoader
	 * Returns the singleton instance of RJavaClassLoader
	public static RJavaClassLoader getPrimaryLoader() {
		return primaryLoader;
	// {{{ constructor
	 * Constructor. The first time an RJavaClassLoader is created, it is
	 * cached as the primary loader.
	 * @param path path of the rJava package
	 * @param libpath lib sub directory of the rJava package
	public RJavaClassLoader(String path, String libpath) {
		this(path, libpath, null);
	 * Constructor. The first time an RJavaClassLoader is created, it is
	 * cached as the primary loader.
	 * @param path path of the rJava package
	 * @param libpath lib sub directory of the rJava package
	 * @param parent parent loader if we should fall back upstream or NULL
	public RJavaClassLoader(String path, String libpath, RJavaClassLoader parent) {
		super(new URL[] {}, (parent == null) ? ClassLoader.getSystemClassLoader() : parent);
		// respect rJava.debug level
		String rjd = System.getProperty("rJava.debug");
		if (rjd != null && rjd.length() > 0 && !rjd.equals("0")) verbose = true;
		if (verbose) System.out.println("RJavaClassLoader(\""+path+"\", \""+libpath+"\", "+ ((parent == null) ? "no parent" : parent) + ")");
		if (primaryLoader==null) {
			primaryLoader = this;
			if (verbose) System.out.println(" - primary loader");
			if (verbose) System.out.println(" - NOT primrary (this="+this+", primary="+primaryLoader+")");
		libMap = new HashMap/*<String,UnixFile>*/();
		classPath = new Vector/*<UnixFile>*/();
		classPath.add(new UnixDirectory(path+"/java"));
		rJavaPath = path;
		rJavaLibPath = libpath;
		/* load the rJava library */
		UnixFile so = new UnixFile(rJavaLibPath+"/rJava.so");
		if (!so.exists())
			so = new UnixFile(rJavaLibPath+"/rJava.dll");
		if (so.exists())
			libMap.put("rJava", so);
		/* load the jri library */
		UnixFile jri = new UnixFile(path+"/jri/libjri.so");
		String rarch = System.getProperty("r.arch");
		if (rarch != null && rarch.length()>0) {
			UnixFile af = new UnixFile(path+"/jri"+rarch+"/libjri.so");
			if (af.exists())
			    jri = af;
			    af = new UnixFile(path+"/jri"+rarch+"/jri.dll");
			    if (af.exists())
				jri = af;
		if (!jri.exists())
			jri = new UnixFile(path+"/jri/libjri.jnilib");
		if (!jri.exists())
			jri = new UnixFile(path+"/jri/jri.dll");
		if (jri.exists()) {
			libMap.put("jri", jri);
			if (verbose) System.out.println(" - registered JRI: "+jri);
		/* if we are the primary loader, make us the context loader so
		   projects that rely on the context loader pick us */
		if (primaryLoader == this)
			Thread.currentThread().setContextClassLoader(this);
		if (verbose) {
		    System.out.println("RJavaClassLoader initialized.\n\nRegistered libraries:");
		    for(Iterator entries = libMap.keySet().iterator(); entries.hasNext(); ) {
			Object key = entries.next(); System.out.println("  " + key + ": '" + libMap.get(key) + "'");
		    System.out.println("\nRegistered class paths:");
		    for (Enumeration e = classPath.elements() ; e.hasMoreElements() ;)
			System.out.println("  '"+e.nextElement()+"'");
		    System.out.println("\n-- end of class loader report --");
	// {{{ classNameToFile
	 * convert . to /
	String classNameToFile(String cls) {
		return cls.replace('.','/');
	// {{{ findClass
	protected Class findClass(String name) throws ClassNotFoundException {
		Class cl = null;
		if (verbose) System.out.println(""+this+".findClass("+name+")");
		if ("RJavaClassLoader".equals(name)) return getClass();
		// {{{ use the usual method of URLClassLoader
		if (useSystem) {
				cl = super.findClass(name);
				if (cl != null) {
					if (verbose) System.out.println("RJavaClassLoader: found class "+name+" using URL loader");
					return cl;
			} catch (Exception fnf) {
			    if (verbose) System.out.println(" - URL loader did not find it: " + fnf);
		if (verbose) System.out.println("RJavaClassLoader.findClass(\""+name+"\")");
		// {{{ iterate through the elements of the class path
		InputStream ins = null;
		Exception defineException = null;
		Enumeration/*<UnixFile>*/ e = classPath.elements() ;
		while( e.hasMoreElements() ){
			UnixFile cp = (UnixFile) e.nextElement();
			if (verbose) System.out.println(" - trying class path \""+cp+"\"");
				ins = null;
				/* a file - assume it is a jar file */
				if (cp instanceof UnixJarFile){
					ins = ((UnixJarFile)cp).getResourceAsStream( classNameToFile(name) + ".class" ) ;
					if (verbose) System.out.println("   JAR file, can get '" + classNameToFile(name) + "'? " + ((ins == null) ? "NO" : "YES"));
				} else if ( cp instanceof UnixDirectory ){
					UnixFile class_f = new UnixFile(cp.getPath()+"/"+classNameToFile(name)+".class");
					if (class_f.isFile() ) {
						ins = new FileInputStream(class_f);
					if (verbose) System.out.println("   Directory, can get '" + class_f + "'? " + ((ins == null) ? "NO" : "YES"));
				/* some comments on the following :
				   we could call ZipEntry.getSize in case of a jar file to 
				   find out the size of the byte[] directly
				   also ByteBuffer seems more efficient, but the ByteBuffer class
				   is java >= 1.4 and the defineClass method that uses the class
				   is java >= 1.5
				if (ins != null) {
					int al = 128*1024;
					byte fc[] = new byte[al];
					int n = ins.read(fc);
					int rp = n;
					if( verbose ) System.out.println("  loading class file, initial n = "+n);
					while (n > 0) {
						if (rp == al) {
							int nexa = al*2;
							if (nexa<512*1024) nexa=512*1024;
							byte la[] = new byte[nexa];
							System.arraycopy(fc, 0, la, 0, al);
							fc = la;
							al = nexa;
						n = ins.read(fc, rp, fc.length-rp);
						if( verbose ) System.out.println("  next n = "+n+" (rp="+rp+", al="+al+")");
						if (n>0) rp += n;
					ins.close();
					n = rp;
					if (verbose) System.out.println("RJavaClassLoader: loaded class "+name+", "+n+" bytes");
					    cl = defineClass(name, fc, 0, n);
					} catch (Exception dce) {
					    // we want to save this one so we can pass it on
					    defineException = dce;
					    break;
					if (verbose) System.out.println("  defineClass('" + name +"') returned " + cl);
					// System.out.println(" - class = "+cl);
					return cl;
			} catch (Exception ex) {
				// System.out.println(" * won't work: "+ex.getMessage());
		if (defineException != null) // we bailed out on class interpretation, re-throw it
		    throw (new ClassNotFoundException("Class not found - candidate class binary found but could not be loaded", defineException));
		// giving up
		if (cl == null) {
			if( verbose ) System.out.println("    >> ClassNotFoundException ");
			throw (new ClassNotFoundException());
		return cl;
	// {{{ findResource 
	public URL findResource(String name) {
		if (verbose) System.out.println("RJavaClassLoader: findResource('"+name+"')");
		// {{{ use the standard way
		if (useSystem) {
				URL u = super.findResource(name);
				if (u != null) {
					if (verbose) System.out.println("RJavaClassLoader: found resource in "+u+" using URL loader.");
					return u;
			} catch (Exception fre) {
		// {{{ iterate through the classpath
		if (verbose) System.out.println(" - resource not found with URL loader, trying alternative");
		Enumeration/*<UnixFile>*/ e = classPath.elements() ;
		while( e.hasMoreElements()) {
			UnixFile cp = (UnixFile) e.nextElement();
				/* is a file - assume it is a jar file */
				if (cp instanceof UnixJarFile ) {
					URL u = ( (UnixJarFile)cp ).getResource( name ) ;
					if (u != null) {
						if (verbose) System.out.println(" - found in a JAR file, URL "+u);
						return u;
				} else if(cp instanceof UnixDirectory ) {
					UnixFile res_f = new UnixFile(cp.getPath()+"/"+name);
					if (res_f.isFile()) {
						if (verbose) System.out.println(" - find as a file: "+res_f);
						return res_f.toURL();
			} catch (Exception iox) {
		return null;
	// {{{ addRLibrary
	/** add a library to path mapping for a native library */
	public void addRLibrary(String name, String path) {
		libMap.put(name, new UnixFile(path));
	// {{{ addClassPath
	 * adds an entry to the class path
	public void addClassPath(String cp) {
		UnixFile f = new UnixFile(cp);
		// use the URLClassLoader
		if (useSystem) {
				addURL(f.toURL());
				if (verbose) System.out.println("RJavaClassLoader: added '" + cp + "' to the URL class path loader");
				//return; // we need to add it anyway so it appears in .jclassPath()
			} catch (Exception ufe) {
		UnixFile g = null ;
		if( f.isFile() && (f.getName().endsWith(".jar") || f.getName().endsWith(".JAR"))) {
			g = new UnixJarFile(cp) ;
			if (verbose) System.out.println("RJavaClassLoader: adding Java archive file '"+cp+"' to the internal class path");
		} else if( f.isDirectory() ){
			g = new UnixDirectory(cp) ;
			if (verbose) System.out.println("RJavaClassLoader: adding class directory '"+cp+"' to the internal class path");
		} else if (verbose)
		    System.err.println(f.exists() ?
				       ("WARNING: the path '"+cp+"' is neither a directory nor a .jar file, it will NOT be added to the internal class path!") :
				       ("WARNING: the path '"+cp+"' does NOT exist, it will NOT be added to the internal class path!"));
		if (g != null && !classPath.contains(g)) {
			// this is the real meat - add it to our internal list
			classPath.add(g);
			// this is just cosmetics - it doesn't really have any meaning
			System.setProperty("java.class.path",
					System.getProperty("java.class.path")+File.pathSeparator+g.getPath());
	 * adds several entries to the class path
	public void addClassPath(String[] cp) {
		int i = 0;
		while (i < cp.length) addClassPath(cp[i++]);
	// {{{ getClassPath
	 * @return the array of class paths used by this class loader
	public String[] getClassPath() {
		int j = classPath.size();
		String[] s = new String[j];
		int i = 0;
		while (i < j) {
			s[i] = ((UnixFile) classPath.elementAt(i)).getPath();
		return s;
	// {{{ findLibrary
	protected String findLibrary(String name) {
		if (verbose) System.out.println("RJavaClassLoader.findLibrary(\""+name+"\")");
		//if (name.equals("rJava"))
		//    return rJavaLibPath+"/"+name+".so";
		UnixFile u = (UnixFile) libMap.get(name);
		String s = null;
		if (u!=null && u.exists()) s=u.getPath();
		if (verbose) System.out.println(" - mapping to "+((s==null)?"<none>":s));
		return s;
	// {{{ bootClass
	 * Boots the specified method of the specified class
	 * @param cName class to boot
	 * @param mName method to boot (typically main). The method must take a String[] as parameter
	 * @param args arguments to pass to the method
	public void bootClass(String cName, String mName, String[] args) throws java.lang.IllegalAccessException, java.lang.reflect.InvocationTargetException, java.lang.NoSuchMethodException, java.lang.ClassNotFoundException {
		Class c = findClass(cName);
		resolveClass(c);
		java.lang.reflect.Method m = c.getMethod(mName, new Class[] { String[].class });
		m.invoke(null, new Object[] { args });
	// {{{ setDebug
	 * Set the debug level. At the moment, there is only verbose (level &gt; 0)
	 * or quiet
	 * @param level debug level. verbose (&gt;0), quiet otherwise
	public static void setDebug(int level) {
		verbose=(level>0);
	// {{{ u2w
	 * Utility to convert paths for windows. Converts / to the path separator in use
	 * @param fn file name
	public static String u2w(String fn) {
		return (File.separatorChar != '/') ? fn.replace('/', File.separatorChar) : fn ;
	// {{{ main
	 * main method
	 * <p>This uses the system properties:</p>
	 * <li><code>rjava.path</code> : path of the rJava package</li>
	 * <li><code>rjava.lib</code>  : lib sub directory of the rJava package</li>
	 * <li><code>main.class</code> : main class to "boot", assumes Main if not specified</li>
	 * <li><code>rjava.class.path</code> : set of paths to populate the initiate the class path</li>
	 * <p>and boots the "main" method of the specified <code>main.class</code>, 
	 * passing the args down to the booted class</p>
	 * <p>This makes sure R and rJava are known by the class loader</p>
	public static void main(String[] args) {
		String rJavaPath = System.getProperty("rjava.path");
		if (rJavaPath  == null) {
			System.err.println("ERROR: rjava.path is not set");
			System.exit(2);
		String rJavaLib = System.getProperty("rjava.lib");
		if (rJavaLib == null) { // it is not really used so far, just for rJava.so, so we can guess
			rJavaLib = rJavaPath + File.separator + "libs";
		RJavaClassLoader cl = new RJavaClassLoader(u2w(rJavaPath), u2w(rJavaLib));
		String mainClass = System.getProperty("main.class");
		if (mainClass == null || mainClass.length()<1) {
			System.err.println("WARNING: main.class not specified, assuming 'Main'");
			mainClass = "Main";
		String classPath = System.getProperty("rjava.class.path");
		if (classPath != null) {
			StringTokenizer st = new StringTokenizer(classPath, File.pathSeparator);
			while (st.hasMoreTokens()) {
				String dirname = u2w(st.nextToken());
				cl.addClassPath(dirname);
			cl.bootClass(mainClass, "main", args);
		} catch (Exception ex) { 
			System.err.println("ERROR: while running main method: "+ex);
			ex.printStackTrace();
	//----- tools -----
	// {{{ RJavaObjectInputStream class
	class RJavaObjectInputStream extends ObjectInputStream {
		public RJavaObjectInputStream(InputStream in) throws IOException {
			super(in);
		protected Class resolveClass(ObjectStreamClass desc) throws ClassNotFoundException {
			return Class.forName(desc.getName(), false, RJavaClassLoader.getPrimaryLoader());
	// {{{ toByte
	 * Serialize an object to a byte array. (code by CB)
	 * @param object object to serialize
	 * @return byte array that represents the object
	 * @throws Exception 
	public static byte[] toByte(Object object) throws Exception {
		ByteArrayOutputStream os = new ByteArrayOutputStream();
		ObjectOutputStream   oos = new ObjectOutputStream((OutputStream) os);
		oos.writeObject(object);
		oos.close();
		return os.toByteArray();
	// {{{ toObject
	 * Deserialize an object from a byte array. (code by CB)
	 * @param byteArray
	 * @return the object that is represented by the byte array
	 * @throws Exception 
	public Object toObject(byte[] byteArray) throws Exception {
		InputStream        is = new ByteArrayInputStream(byteArray);
		RJavaObjectInputStream ois = new RJavaObjectInputStream(is);
		Object o = (Object) ois.readObject();
		ois.close();
		return o;
	// {{{ toObjectPL
	 * converts the byte array into an Object using the primary RJavaClassLoader
	public static Object toObjectPL(byte[] byteArray) throws Exception{
		return RJavaClassLoader.getPrimaryLoader().toObject(byteArray);
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