Jborat inclusion + additional changes - incomplete

.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="src-jborat"/>
+	<classpathentry kind="src" path="test/src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="lib/jborat-interface.jar"/>
-	<classpathentry kind="lib" path="lib/jborat-runtime.jar"/>
 	<classpathentry kind="lib" path="lib/asm-debug-all-4.0.jar"/>
+	<classpathentry kind="lib" path="/home/lukas/repos/disl/trunk/test/lib/stp.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

src-jborat/ch/usi/dag/dynamicbypass/Bootstrap.java

+package ch.usi.dag.dynamicbypass;
+
+public class Bootstrap {
+
+	public static void completed() {
+		// TODO jb ! redefinition of DynamicBypassCheck
+	}
+}

src-jborat/ch/usi/dag/dynamicbypass/CodeMerger.java

+package ch.usi.dag.dynamicbypass;
+
+import org.objectweb.asm.Opcodes;
+import org.objectweb.asm.Type;
+import org.objectweb.asm.tree.ClassNode;
+import org.objectweb.asm.tree.InsnList;
+import org.objectweb.asm.tree.JumpInsnNode;
+import org.objectweb.asm.tree.LabelNode;
+import org.objectweb.asm.tree.MethodInsnNode;
+import org.objectweb.asm.tree.MethodNode;
+
+public abstract class CodeMerger {
+
+	private static final String METHOD_FINALIZE = "finalize";
+
+	private static final String DBCHECK_CLASS = Type.getInternalName(
+			DynamicBypassCheck.class);
+	private static final String DBCHECK_METHOD = "executeUninstrumented";
+	private static final String DBCHECK_DESC = "()Z";
+
+	// NOTE: the instrumented class node will serve as an output
+	public static void mergeClasses(ClassNode originalCN,
+			ClassNode instrumentedCN) {
+
+		// do not merge interfaces
+		if ((originalCN.access & Opcodes.ACC_INTERFACE) != 0) {
+			return;
+		}
+
+		for (MethodNode instrMN : instrumentedCN.methods) {
+
+			// evaluation is done always but is more visible then in single if
+
+			boolean methodAbstract = (instrMN.access & Opcodes.ACC_ABSTRACT) != 0;
+			boolean methodNative = (instrMN.access & Opcodes.ACC_NATIVE) != 0;
+			// TODO jb ! test
+			boolean methodFinalizeInObject = instrumentedCN.name.equals(Type
+					.getInternalName(Object.class))
+					&& instrMN.name.equals(METHOD_FINALIZE);
+
+			// skip methods that should not be merged
+			if (methodAbstract | methodNative | methodFinalizeInObject) {
+				continue;
+			}
+
+			MethodNode origMN = getMethodNode(originalCN, instrMN.name,
+					instrMN.desc);
+
+			InsnList ilist = instrMN.instructions;
+
+			// TODO jb - check for similarity of the instructions
+
+			// add reference to the original code
+			LabelNode origCodeL = new LabelNode();
+			ilist.add(origCodeL);
+
+			// add original code
+			ilist.add(origMN.instructions);
+			// add exception handlers of the original code
+			instrMN.tryCatchBlocks.addAll(origMN.tryCatchBlocks);
+
+			// if the dynamic bypass is activated (non-zero value returned)
+			// then jump to original code
+			ilist.insert(new JumpInsnNode(Opcodes.IFNE, origCodeL));
+			ilist.insert(new MethodInsnNode(Opcodes.INVOKESTATIC,
+					DBCHECK_CLASS, DBCHECK_METHOD, DBCHECK_DESC));
+		}
+	}
+
+	private static MethodNode getMethodNode(ClassNode cnToSearch,
+			String methodName, String methodDesc) {
+
+		for (MethodNode mn : cnToSearch.methods) {
+			if (methodName.equals(mn.name) && methodDesc.equals(mn.desc)) {
+				return mn;
+			}
+		}
+
+		throw new RuntimeException(
+				"Code merger fatal error: method for merge not found");
+	}
+}

src-jborat/ch/usi/dag/dynamicbypass/DynamicBypass.java

+package ch.usi.dag.dynamicbypass;
+
+public class DynamicBypass {
+
+	private static final String PROP_DEBUG = "debug";
+	private static final boolean debug = Boolean.getBoolean(PROP_DEBUG);
+	
+	public static boolean isActivated() {
+		return Thread.currentThread().bypass;
+	}
+
+	public static void activate() {
+		
+		// bypass should be 0 in this state
+		if(debug && Thread.currentThread().bypass) {
+			throw new RuntimeException(
+					"Dynamic bypass fatal error: activated twice");
+		}
+		
+		Thread.currentThread().bypass = true;
+	}
+
+	public static void deactivate() {
+		
+		// bypass should be 1 in this state
+		if(debug && ! Thread.currentThread().bypass) {
+			throw new RuntimeException(
+					"Dynamic bypass fatal error: deactivated twice");
+		}
+		
+		Thread.currentThread().bypass = false;
+	}
+}

src-jborat/ch/usi/dag/dynamicbypass/DynamicBypassCheck.java

+package ch.usi.dag.dynamicbypass;
+
+public class DynamicBypassCheck {
+
+	// this version is executed before bootstrap phase
+	// and will be replaced by ...AfterBootstrap() after bootstrap
+	public static boolean executeUninstrumented() {
+		return true;
+	}
+	
+	public static boolean executeUninstrumentedAfterBootstrap() {
+		return DynamicBypass.isActivated();
+	}
+}

src-jborat/ch/usi/dag/jborat/agent/JavaAgent.java

+package ch.usi.dag.jborat.agent;
+
+import java.lang.instrument.Instrumentation;
+
+import ch.usi.dag.dynamicbypass.Bootstrap;
+
+public class JavaAgent {
+
+	public static void premain(String agentArguments,
+			Instrumentation instrumentation) {
+
+		if (!Boolean.getBoolean("jborat.noBootstrap")) {
+			Bootstrap.completed();
+		}
+	}
+}

src-jborat/ch/usi/dag/jborat/server/ClassAsBytes.java

+package ch.usi.dag.jborat.server;
+
+public class ClassAsBytes {
+    
+	private byte[] name;
+    private byte[] code;
+
+    public ClassAsBytes(byte[] name, byte[] code) {
+        this.name = name;
+        this.code = code;
+    }
+
+	public byte[] getName() {
+		return name;
+	}
+
+	public byte[] getCode() {
+		return code;
+	}
+}

src-jborat/ch/usi/dag/jborat/server/InstrumentationServer.java

+package ch.usi.dag.jborat.server;
+
+import java.net.ServerSocket;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import ch.usi.dag.disl.DiSL;
+import ch.usi.dag.disl.exception.DiSLException;
+
+public abstract class InstrumentationServer {
+
+	public static final String PROP_DEBUG = "debug";
+	private static final boolean debug = Boolean.getBoolean(PROP_DEBUG);
+
+	private static final String PROP_PORT = "jborat.port";
+	private static final int DEFAULT_PORT = 11217;
+	private static final int port = Integer.getInteger(PROP_PORT, DEFAULT_PORT);
+
+	private static final AtomicInteger aliveWorkers = new AtomicInteger();
+	private static DiSL disl;
+
+	public static void main(String args[]) {
+
+		try {
+
+			// use dynamic bypass
+			disl = new DiSL(true);
+
+			if (debug) {
+				System.out.println("Instrumentation server is starting on port "
+						+ port);
+			}
+
+			ServerSocket listenSocket = new ServerSocket(port);
+
+			while (true) {
+
+				NetClassReader sc = 
+						new NetClassReader(listenSocket.accept());
+				
+				aliveWorkers.incrementAndGet();
+				
+				new Worker(sc, disl).start();
+
+				if (debug) {
+					System.out.println("New connection accepted...");
+				}
+			}
+			
+		} catch (Exception e) {
+			reportError(e);
+		}
+	}
+
+	public static void reportError(Throwable e) {
+
+		if (e instanceof DiSLException) {
+
+			// Error reported in DiSL - just exit
+			return;
+		}
+
+		if (e instanceof JboratException) {
+
+			System.err.println("Jborat error: " + e.getMessage());
+
+			if (debug) {
+				e.printStackTrace();
+			}
+		}
+
+		// fatal exception (unexpected)
+		System.err.println("Fatal error: " + e.getMessage());
+
+		e.printStackTrace();
+	}
+	
+	public static void workerDone() {
+
+		if (aliveWorkers.decrementAndGet() == 0) {
+			
+			disl.terminate();
+			
+			if (debug) {
+				System.out.println("Instrumentation server is shutting down");
+			}
+			
+			// no workers - shutdown
+			System.exit(0);
+		}
+	}
+}

src-jborat/ch/usi/dag/jborat/server/JboratException.java

+package ch.usi.dag.jborat.server;
+
+public class JboratException extends Exception {
+
+	private static final long serialVersionUID = 5272000884539359236L;
+
+	public JboratException() {
+		super();
+	}
+
+	public JboratException(String message, Throwable cause,
+			boolean enableSuppression, boolean writableStackTrace) {
+		super(message, cause, enableSuppression, writableStackTrace);
+	}
+
+	public JboratException(String message, Throwable cause) {
+		super(message, cause);
+	}
+
+	public JboratException(String message) {
+		super(message);
+	}
+
+	public JboratException(Throwable cause) {
+		super(cause);
+	}
+}

src-jborat/ch/usi/dag/jborat/server/NetClassReader.java

+package ch.usi.dag.jborat.server;
+
+import java.io.BufferedOutputStream;
+import java.io.DataInputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.net.Socket;
+
+public class NetClassReader {
+
+	private final Socket socket;
+	private final DataInputStream is;
+	private final OutputStream os;
+
+	public NetClassReader(Socket socket) throws IOException {
+		
+		this.socket = socket;
+
+		is = new DataInputStream(socket.getInputStream());
+		os = new BufferedOutputStream(socket.getOutputStream());
+	}
+
+	public ClassAsBytes readClassAsBytes() throws IOException {
+
+		// protocol:
+		// java int - class name length (cnl)
+		// java int - code length (cl)
+		// bytes[cnl] - class name
+		// bytes[cl] - class code
+		
+		int nameLength = is.readInt();
+		int codeLength = is.readInt();
+
+		// end of communication
+		if(nameLength == 0 && codeLength == 0) {
+			return null;
+		}
+
+		// allocate buffer for class reading
+		byte[] name = new byte[nameLength];
+		byte[] code = new byte[codeLength];
+
+		// read class
+		is.readFully(name);
+		is.readFully(code);
+
+		return new ClassAsBytes(name, code);
+	}
+
+	public void close() throws IOException {
+
+		is.close();
+		socket.close();
+	}
+
+	public void sendClassAsBytes(ClassAsBytes cab) throws IOException {
+
+		// protocol:
+		// java int - class name length (cnl)
+		// java int - code length (cl)
+		// bytes[cnl] - class name
+		// bytes[cl] - class code
+		
+		os.write(cab.getName().length);
+		os.write(cab.getCode().length);
+		os.write(cab.getName());
+		os.write(cab.getCode());
+		os.flush();
+	}
+}

src-jborat/ch/usi/dag/jborat/server/Worker.java

+package ch.usi.dag.jborat.server;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.util.HashSet;
+import java.util.Scanner;
+import java.util.Set;
+
+import ch.usi.dag.disl.DiSL;
+import ch.usi.dag.disl.exception.DiSLException;
+import ch.usi.dag.disl.scope.WildCard;
+
+import com.sun.xml.internal.ws.org.objectweb.asm.Type;
+
+public class Worker extends Thread {
+
+	private static final boolean debug = Boolean
+			.getBoolean(InstrumentationServer.PROP_DEBUG);
+
+	private static final String PROP_EXCLIST = "jborat.exclusionList";
+	private static final String excListPath = 
+			System.getProperty(PROP_EXCLIST, null);
+
+	private static final String PROP_UNINSTR = "jborat.uninstrumented";
+	private static final String uninstrPath = 
+			System.getProperty(PROP_UNINSTR, null);
+
+	private static final String PROP_INSTR = "jborat.instrumented";
+	private static final String instrPath = 
+			System.getProperty(PROP_INSTR, null);
+
+	private static Set<String> exclusionList;
+
+	private final NetClassReader sc;
+	private final DiSL disl;
+
+	Worker(NetClassReader sc, DiSL disl) {
+		this.sc = sc;
+		this.disl = disl;
+	}
+
+	public void run() {
+
+		try {
+
+			instrumentationLoop();
+
+			sc.close();
+		}
+		catch (Throwable e) {
+			InstrumentationServer.reportError(e);
+		}
+		finally {
+			InstrumentationServer.workerDone();
+		}
+	}
+
+	private boolean filterClass(String className) throws JboratException {
+
+		// race condition can be here (invocation from multiple threads)
+		// but this is not serious problem
+		if(exclusionList == null) {
+			exclusionList = readExlusionList();
+		}
+		
+		// check the exclusion list for possible matches
+		for(String pattern : exclusionList) {
+			
+			if(WildCard.match(className, pattern)) {
+				return false;
+			}
+		}
+
+		if (debug) {
+			System.out.println("Excluding class: " + className);
+		}
+
+		if (className.equals(Type.getInternalName(Thread.class))) {
+			throw new JboratException(Thread.class.getName()
+					+ " cannot be excluded in exclusion list");
+		}
+
+		return true;
+	}
+
+	private Set<String> readExlusionList() throws JboratException {
+
+		final String COMMENT_START = "#";
+		
+		try {
+		
+			Set<String> exclSet = new HashSet<String>();
+
+			// read exclusion list line by line
+			Scanner scanner = new Scanner(new FileInputStream(excListPath));
+			while (scanner.hasNextLine()) {
+				
+				String line = scanner.nextLine();
+				
+				if(! line.startsWith(COMMENT_START)) {
+					exclSet.add(internClassName(line));
+				}
+			}
+
+			scanner.close();
+
+			// TODO jb ! add classes from agent and instrumentation jar
+			
+			return exclSet;
+		
+		} catch(FileNotFoundException e) {
+			throw new JboratException(e);
+		}
+	}
+	
+	private String internClassName(String normalClassName) {
+		
+		final char NORMAL_DELIM = '.';
+		final char INTERN_DELIM = '/';
+		
+		return normalClassName.replace(NORMAL_DELIM, INTERN_DELIM);
+	}
+	
+	private void instrumentationLoop() throws JboratException, DiSLException {
+
+		try {
+		
+		while (true) {
+
+			ClassAsBytes cab = sc.readClassAsBytes();
+
+			// communication closed by the client
+			if (cab == null) {
+				return;
+			}
+
+			byte[] instrClass;
+
+			try {
+				
+				// TODO jb - weave time stats
+				
+				instrClass = instrument(new String(cab.getName()),
+						cab.getCode());
+			}
+			catch (DiSLException e) {
+
+				// instrumentation error
+				// send the client a description of the server-side error
+
+				StringWriter sw = new StringWriter();
+				e.printStackTrace(new PrintWriter(sw));
+
+				// error protocol:
+				// class name contains the description of the server-side error
+				// class code is an array of size zero
+				String errMsg = "Error in class " + cab.getName() + ": "
+						+ sw.toString();
+
+				sc.sendClassAsBytes(new ClassAsBytes(errMsg.getBytes(),
+						new byte[0]));
+
+				throw e;
+			}
+
+			sc.sendClassAsBytes(new ClassAsBytes(cab.getName(), instrClass));
+		}
+		
+		}
+		catch (IOException e) {
+			throw new JboratException(e);
+		}
+	}
+	
+	private byte[] instrument(String className, byte[] origCode)
+			throws JboratException, DiSLException {
+		
+		// dump uninstrumented
+		if (uninstrPath != null) {
+			dump(className, origCode, uninstrPath);
+		}
+
+		// filter
+		if (filterClass(className)) {
+
+			if (debug) {
+				System.out.println("Excluding " + className);
+			}
+			
+			return origCode;
+		}
+
+		// instrument
+		byte[] instrCode = disl.instrument(origCode);
+
+		// dump instrumented
+		if (instrPath != null && instrCode != null) {
+			dump(className, instrCode, instrPath);
+		}
+
+		return instrCode;
+	}
+
+	private void dump(String className, byte[] codeAsBytes, String path)
+			throws JboratException {
+		
+		final String CLASS_DELIM = "/"; 
+		final String CLASS_EXT = ".class";
+		
+		try {
+		
+			// extract the class name and package name
+			int i = className.lastIndexOf(CLASS_DELIM);
+			String onlyClassName = className.substring(i + 1);
+			String packageName = className.substring(0, i + 1);
+			
+			// construct path to the class
+			String pathWithPkg = path + File.pathSeparator + packageName;
+
+			// create directories
+			new File(pathWithPkg).mkdirs();
+