Added simple README - needs more work

c-agent - some check_std_error replaced with check_error
first part of public API documentation

.project

 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>disl</name>
+	<name>DiSL</name>
 	<comment></comment>
 	<projects>
 	</projects>

README

+The DiSL language is hosted in Java using annotations, therefore, no special compiler is required.
+A convenient way to specify an instrumentation and to pass it to the DiSL framework is to pack the instrumentation classes with a manifest file into one jar.
+The DiSL framework will load the jar, parse the instrumentation specification, and instrument all classes used by an application at load-time.
+
+The examples of simple instrumentation are in src-test directory.
+The test can be invoked using runTest.sh script in the root directory.
+For user defined instrumentation, it is recommended to mimic the start and build script as they are provided for test.
+We are working on better setup scripts to ease the setup effort for developer.

runClient.sh

@@ -8,8 +8,6 @@ else
   C_AGENT="src-agent-c/libdislagent.so"
 fi
 
-# ipc.socket is the default communication
-# to enable shared memory, remove ",ipc.socket" from the options
 java -agentpath:${C_AGENT} \
      -javaagent:build/dislagent-unspec.jar \
      -Xbootclasspath/a:build/dislagent-unspec.jar:build/dislinstr.jar \

src-agent-c/dislagent.c

@@ -143,14 +143,14 @@ static void parse_agent_options(char *options) {
 
 		// convert number
 		int fitsP = strlen(port_start) < sizeof(port_number);
-		check_std_error(fitsP, FALSE, "Port number is too long");
+		check_error(! fitsP, "Port number is too long");
 
 		strcpy(port_number, port_start);
 	}
 
 	// check if host_name is big enough
 	int fitsH = strlen(options) < sizeof(host_name);
-	check_std_error(fitsH, FALSE, "Host name is too long");
+	check_error(! fitsH, "Host name is too long");
 
 	strcpy(host_name, options);
 }
@@ -237,7 +237,7 @@ static connection_item * open_connection() {
 	// get host address
 	struct addrinfo * addr;
 	int gai_res = getaddrinfo(host_name, port_number, NULL, &addr);
-	check_std_error(gai_res == 0, FALSE, gai_strerror(gai_res));
+	check_error(gai_res != 0, gai_strerror(gai_res));
 
 	// create stream socket
 	int sockfd = socket(addr->ai_family, SOCK_STREAM, 0);

src-agent-c/jvmtihelper.h

@@ -14,8 +14,22 @@
 #define FALSE 0
 
 // error nums
-#define ERR_JVMTI 10001
-#define ERR_COMM 10002
+#define ERR 10000
+#define ERR_STD 10002
+#define ERR_JVMTI 10003
+
+/*
+ * Reports error if condition is true
+ */
+void check_error(int cond, const char *str) {
+
+	if (cond) {
+
+		fprintf(stderr, "%s%s\n", ERR_PREFIX, str);
+
+		exit(ERR);
+	}
+}
 
 /*
  * Check error routine - reporting on one place
@@ -32,7 +46,7 @@ void check_std_error(int retval, int errorval, const char *str) {
 
 		perror(msgbuf);
 
-		exit(ERR_COMM);
+		exit(ERR_STD);
 	}
 }
 

src/ch/usi/dag/disl/DiSL.java

@@ -52,6 +52,10 @@ import ch.usi.dag.disl.utilinstr.tlvinserter.TLVInserter;
 import ch.usi.dag.disl.weaver.Weaver;
 
 // TODO javadoc comment all
+/**
+ * Main DiSL class providing interface for an instrumentation framework
+ * (normally DiSL Server)
+ */
 public class DiSL {
 
 	public final String PROP_DEBUG = "debug";
@@ -77,6 +81,10 @@ public class DiSL {
 	
 	private final List<Snippet> snippets;
 
+	/**
+	 * DiSL initialization 
+	 * @param useDynamicBypass enable or disable dynamic bypass instrumentation
+	 */
 	// this method should be called only once
 	public DiSL(boolean useDynamicBypass) throws DiSLException {
 
@@ -144,6 +152,10 @@ public class DiSL {
 		// specify this for InstructionMarker
 	}
 	
+	/**
+	 * Finds transformer class in configuration and allocates it.
+	 * @return newly allocated transformer.
+	 */
 	private Transformer resolveTransformer() throws ManifestInfoException,
 			ReflectionException {
 		
@@ -191,8 +203,6 @@ public class DiSL {
 	 *            class that will be instrumented
 	 * @param methodNode
 	 *            method in the classNode argument, that will be instrumented
-	 * @param staticContextInstances
-	 *
 	 */
 	private boolean instrumentMethod(ClassNode classNode, MethodNode methodNode)
 			throws ReflectionException, StaticContextGenException,
@@ -311,6 +321,13 @@ public class DiSL {
 		return true;
 	}
 
+	/**
+	 * Selects only shadows matching the passed guard.
+	 * 
+	 * @param guard guard, on witch conditions are the shadows selected
+	 * @param marking the list of shadows from where the gurads selects
+	 * @return selected shadows
+	 */
 	private List<Shadow> selectShadowsWithGuard(Method guard,
 			List<Shadow> marking) {
 		
@@ -332,6 +349,9 @@ public class DiSL {
 		return selectedMarking;
 	}
 
+	/**
+	 * Data holder for an instrumented class 
+	 */
 	private static class InstrumentedClass {
 		
 		private ClassNode classNode;
@@ -353,7 +373,15 @@ public class DiSL {
 		}
 	}
 	
-	// this method is thread safe after initialization
+	/**
+	 * Instruments class node.
+	 * 
+	 * Note: This method is thread safe. Parameter classNode is changed during
+	 * the invocation.
+	 * 
+	 * @param classNode class node to instrument
+	 * @return instrumented class
+	 */
 	private InstrumentedClass instrumentClass(ClassNode classNode)
 			throws DiSLException {
 
@@ -416,6 +444,12 @@ public class DiSL {
 		return null;
 	}
 
+	/**
+	 * Instruments array of bytes representing a class
+	 * 
+	 * @param classAsBytes class as array of bytes
+	 * @return instrumeted class as array of bytes
+	 */
 	public byte[] instrument(byte[] classAsBytes) throws DiSLException {
 	
 		// output bytes into the file
@@ -511,6 +545,9 @@ public class DiSL {
 		return cw.toByteArray();
 	}
 	
+	/**
+	 * Termination handler - should be invoked by the instrumentation framework
+	 */
 	public void terminate() {
 		
 	}

src/ch/usi/dag/disl/annotation/After.java

@@ -2,6 +2,22 @@ package ch.usi.dag.disl.annotation;
 
 import ch.usi.dag.disl.marker.Marker;
 
+/**
+ * The After annotation instructs DiSL to insert the snippet body after the
+ * marked region. The snippet will be invoked after a normal exit of the region
+ * or after an exit caused by an exception.
+ * 
+ * NOTE: This is only general contract. It depends on particular marker how the
+ * contract will be implemented.
+ *
+ * This annotation should be used with methods.
+ *
+ * The method should be static, not return any values and not throw any
+ * exceptions.
+ * 
+ * Method argument can be StaticContext, DynamicContext, ClassContext and
+ * ArgumentProcessorContext.
+ */
 public @interface After {
 	
 	// NOTE if you want to change names, you need to change 
@@ -9,13 +25,52 @@ public @interface After {
 	
 	// NOTE because of implementation of annotations in java the defaults
 	// are not retrieved from here but from class mentioned above
-	
+
+	/**
+	 * Marker class defines a region where the snippet is applied.
+	 */
 	Class<? extends Marker> marker();
+	
+	/**
+	 * Argument for the marker (as string).
+	 * 
+	 * Default value: ""
+	 */
 	String args() default ""; // cannot be null :(
+	
+	/**
+	 * Scope of the methods, where the snippet is applied.
+	 * 
+	 * @see ch.usi.dag.disl.scope package for more info about scoping language.
+	 * 
+	 * Default value: "*"
+	 */
 	String scope() default "*";
+	
+	/**
+	 * The guard class defining if the snippet will be inlined in particular
+	 * region or not.
+	 * 
+	 * Default value: Object.class - means none
+	 */
 	Class<? extends Object> guard() default Object.class; // cannot be null :(
+	
+	/**
+	 * Defines ordering of the snippets. Smaller number indicates that snippet
+	 * will be inlined closer to the instrumented code.
+	 * 
+	 * Default value: 100
+	 */
 	int order() default 100;
-	// NOTE that activation of dynamic bypass is decided by the instrumentation
-	// framework in first place
+
+	/**
+	 * Advanced option. You can in general disable dynamic bypass on snippets,
+	 * that are not using any other class.
+	 * 
+	 * NOTE Usage of dynamic bypass is determined by the underlying
+	 * instrumentation framework.
+	 * 
+	 * Default value: true
+	 */
 	boolean dynamicBypass() default true;
 }

src/ch/usi/dag/disl/annotation/AfterReturning.java

@@ -2,6 +2,22 @@ package ch.usi.dag.disl.annotation;
 
 import ch.usi.dag.disl.marker.Marker;
 
+/**
+ * The AfterReturning annotation instructs DiSL to insert the snippet body after
+ * the marked region. The snippet will be invoked after a normal exit of the
+ * region.
+ * 
+ * NOTE: This is only general contract. It depends on particular marker how the
+ * contract will be implemented.
+ * 
+ * This annotation should be used with methods.
+ * 
+ * The method should be static, not return any values and not throw any
+ * exceptions.
+ * 
+ * Method argument can be StaticContext, DynamicContext, ClassContext and
+ * ArgumentProcessorContext.
+ */
 public @interface AfterReturning {
 
 	// NOTE if you want to change names, you need to change 
@@ -10,12 +26,51 @@ public @interface AfterReturning {
 	// NOTE because of implementation of annotations in java the defaults
 	// are not retrieved from here but from class mentioned above
 	
+	/**
+	 * Marker class defines a region where the snippet is applied.
+	 */
 	Class<? extends Marker> marker();
+	
+	/**
+	 * Argument for the marker (as string).
+	 * 
+	 * Default value: ""
+	 */
 	String args() default ""; // cannot be null :(
+	
+	/**
+	 * Scope of the methods, where the snippet is applied.
+	 * 
+	 * @see ch.usi.dag.disl.scope package for more info about scoping language.
+	 * 
+	 * Default value: "*"
+	 */
 	String scope() default "*";
+	
+	/**
+	 * The guard class defining if the snippet will be inlined in particular
+	 * region or not.
+	 * 
+	 * Default value: Object.class - means none
+	 */
 	Class<? extends Object> guard() default Object.class; // cannot be null :(
+	
+	/**
+	 * Defines ordering of the snippets. Smaller number indicates that snippet
+	 * will be inlined closer to the instrumented code.
+	 * 
+	 * Default value: 100
+	 */
 	int order() default 100;
-	// NOTE that activation of dynamic bypass is decided by the instrumentation
-	// framework in first place
+
+	/**
+	 * Advanced option. You can in general disable dynamic bypass on snippets,
+	 * that are not using any other class.
+	 * 
+	 * NOTE Usage of dynamic bypass is determined by the underlying
+	 * instrumentation framework.
+	 * 
+	 * Default value: true
+	 */
 	boolean dynamicBypass() default true;
 }

src/ch/usi/dag/disl/annotation/AfterThrowing.java

@@ -2,6 +2,22 @@ package ch.usi.dag.disl.annotation;
 
 import ch.usi.dag.disl.marker.Marker;
 
+/**
+ * The AfterThrowing annotation instructs DiSL to insert the snippet body after
+ * the marked region. The snippet will be invoked after an exit caused by an
+ * exception.
+ * 
+ * NOTE: This is only general contract. It depends on particular marker how the
+ * contract will be implemented.
+ *
+ * This annotation should be used with methods.
+ *
+ * The method should be static, not return any values and not throw any
+ * exceptions.
+ * 
+ * Method argument can be StaticContext, DynamicContext, ClassContext and
+ * ArgumentProcessorContext.
+ */
 public @interface AfterThrowing {
 	
 	// NOTE if you want to change names, you need to change 
@@ -10,12 +26,51 @@ public @interface AfterThrowing {
 	// NOTE because of implementation of annotations in java the defaults
 	// are not retrieved from here but from class mentioned above
 	
+	/**
+	 * Marker class defines a region where the snippet is applied.
+	 */
 	Class<? extends Marker> marker();
+	
+	/**
+	 * Argument for the marker (as string).
+	 * 
+	 * Default value: ""
+	 */
 	String args() default ""; // cannot be null :(
+	
+	/**
+	 * Scope of the methods, where the snippet is applied.
+	 * 
+	 * @see ch.usi.dag.disl.scope package for more info about scoping language.
+	 * 
+	 * Default value: "*"
+	 */
 	String scope() default "*";
+	
+	/**
+	 * The guard class defining if the snippet will be inlined in particular
+	 * region or not.
+	 * 
+	 * Default value: Object.class - means none
+	 */
 	Class<? extends Object> guard() default Object.class; // cannot be null :(
+	
+	/**
+	 * Defines ordering of the snippets. Smaller number indicates that snippet
+	 * will be inlined closer to the instrumented code.
+	 * 
+	 * Default value: 100
+	 */
 	int order() default 100;
-	// NOTE that activation of dynamic bypass is decided by the instrumentation
-	// framework in first place
+
+	/**
+	 * Advanced option. You can in general disable dynamic bypass on snippets,
+	 * that are not using any other class.
+	 * 
+	 * NOTE Usage of dynamic bypass is determined by the underlying
+	 * instrumentation framework.
+	 * 
+	 * Default value: true
+	 */
 	boolean dynamicBypass() default true;
 }

src/ch/usi/dag/disl/annotation/ArgumentProcessor.java

 package ch.usi.dag.disl.annotation;
 
+/**
+ * Annotated class defines method for processing method arguments. The specified
+ * methods will be inlined into snippets to process one method argument value.
+ * 
+ * First argument of the method is a type, that will be processed by the method.
+ * The allowed types are all basic types, String and Object class. The processed
+ * type can be extend in some special cases by ProcessAlso annotation. 
+ * During run-time, the argument will contain a processed method argument value.
+ *
+ * ArgumentContext can be used to fetch additional data about the argument.
+ * 
+ * This annotation should be used with classes.
+ * 
+ * The method should be static, not return any values and not throw any
+ * exceptions.
+ * 
+ * Method argument can be StaticContext, DynamicContext, ClassContext and
+ * ArgumentContext.
+ */
 public @interface ArgumentProcessor {
 
 }

src/ch/usi/dag/disl/annotation/Before.java

@@ -2,6 +2,21 @@ package ch.usi.dag.disl.annotation;
 
 import ch.usi.dag.disl.marker.Marker;
 
+/**
+ * The Before annotation instructs DiSL to insert the snippet body before the
+ * marked region. The snippet will be invoked before the entry of the region.
+ * 
+ * NOTE: This is only general contract. It depends on particular marker how the
+ * contract will be implemented.
+ * 
+ * This annotation should be used with methods.
+ * 
+ * The method should be static, not return any values and not throw any
+ * exceptions.
+ * 
+ * Method argument can be StaticContext, DynamicContext, ClassContext and
+ * ArgumentProcessorContext.
+ */
 public @interface Before {
 	
 	// NOTE if you want to change names, you need to change 
@@ -10,12 +25,51 @@ public @interface Before {
 	// NOTE because of implementation of annotations in java the defaults
 	// are not retrieved from here but from class mentioned above
 	
+	/**
+	 * Marker class defines a region where the snippet is applied.
+	 */
 	Class<? extends Marker> marker();
+	
+	/**
+	 * Argument for the marker (as string).
+	 * 
+	 * Default value: ""
+	 */
 	String args() default ""; // cannot be null :(
+	
+	/**
+	 * Scope of the methods, where the snippet is applied.
+	 * 
+	 * @see ch.usi.dag.disl.scope package for more info about scoping language.
+	 * 
+	 * Default value: "*"
+	 */
 	String scope() default "*";
+	
+	/**
+	 * The guard class defining if the snippet will be inlined in particular
+	 * region or not.
+	 * 
+	 * Default value: Object.class - means none
+	 */
 	Class<? extends Object> guard() default Object.class; // cannot be null :(
+
+	/**
+	 * Defines ordering of the snippets. Smaller number indicates that snippet
+	 * will be inlined closer to the instrumented code.
+	 * 
+	 * Default value: 100
+	 */
 	int order() default 100;
-	// NOTE that activation of dynamic bypass is decided by the instrumentation
-	// framework in first place
+
+	/**
+	 * Advanced option. You can in general disable dynamic bypass on snippets,
+	 * that are not using any other class.
+	 * 
+	 * NOTE Usage of dynamic bypass is determined by the underlying
+	 * instrumentation framework.
+	 * 
+	 * Default value: true
+	 */
 	boolean dynamicBypass() default true;
 }

src/ch/usi/dag/disl/annotation/GuardMethod.java

@@ -6,10 +6,12 @@ import java.lang.annotation.RetentionPolicy;
 /**
  * Marks guard validation method.
  * 
+ * This annotation should be used with methods.
+ * 
  * Guard method should be static and state-less.
  * 
- * Method argument can be Shadow, StaticContext and for ArgumentProcessor guard
- * also ArgumentContext.
+ * Method argument can be Shadow, StaticContext, GuardContext and for
+ * ArgumentProcessor guard also ArgumentContext.
  */
 @Retention(RetentionPolicy.RUNTIME) // to resolve annotation using reflection 
 public @interface GuardMethod {

src/ch/usi/dag/disl/annotation/Guarded.java

 package ch.usi.dag.disl.annotation;
 
+/**
+ * Annotation used in ArgumentProcessor to guard specific methods.
+ * 
+ * This annotation should be used with methods.
+ */
 public @interface Guarded {
 
 	// NOTE if you want to change names, you need to change 
@@ -7,6 +12,8 @@ public @interface Guarded {
 	
 	// NOTE because of implementation of annotations in java the defaults
 	// are not retrieved from here but from class mentioned above
-
+	/**
+	 * The guard class defining if the processor method will be inlined or not.
+	 */
 	Class<? extends Object> guard();
 }

src/ch/usi/dag/disl/annotation/Instrumentation.java

@@ -2,6 +2,11 @@ package ch.usi.dag.disl.annotation;
 
 // TODO add tool that will look for Instrumentation annotation and create meta-data for jar
 // http://stackoverflow.com/questions/3644069/java-6-annotation-processing-configuration-with-ant
+/**
+ * This method denotes DiSL instrumentation class.
+ * 
+ * This annotation should be used with classes.
+ */
 public @interface Instrumentation {
 
 }

src/ch/usi/dag/disl/annotation/ProcessAlso.java

 package ch.usi.dag.disl.annotation;
 
-
+/**
+ * If attached to the processor method, it allows to process:
+ * short, byte and boolean in int processor,
+ * byte and boolean in short processor,
+ * boolean in byte processor.
+ */
 public @interface ProcessAlso {
 
 	// NOTE if you want to change names, you need to change 

src/ch/usi/dag/disl/annotation/SyntheticLocal.java

 package ch.usi.dag.disl.annotation;
 
-// NOTE: Initialization can be done only within field definition
-// - java static { } construct for initialization is not supported and
-//   will cause invalid instrumentation
+/**
+ * Indicates, that field is used for data passing between several snippets
+ * inlined into one method. The field is translated into local variable within
+ * a method. The local variable is by default always initialized to the assigned
+ * value or the default value of a corresponding type. It is possible to disable
+ * the  initialization using optional "initialize" annotation parameter.
+ * 
+ * NOTE: Initialization can be done only within field definition.
+ * Java static { } construct for initialization is not supported and
+ * could cause invalid instrumentation.
+ * 
+ * This annotation should be used with fields.
+ * 
+ * Field should be declared as static, and if not shared between multiple DiSL
+ * classes, also private.
+ */
 public @interface SyntheticLocal {
 
 	public enum Initialize {
@@ -15,5 +28,10 @@ public @interface SyntheticLocal {
 	// NOTE because of implementation of annotations in java the defaults
 	// are not retrieved from here but from class mentioned above
 	
+	/**
+	 * Initialization mode of the SyntheticLocal variable.
+	 * 
+	 * Default value: Initialize.ALWAYS
+	 */
 	Initialize initialize() default(Initialize.ALWAYS);
 }

src/ch/usi/dag/disl/annotation/ThreadLocal.java

 package ch.usi.dag.disl.annotation;
 
+/**
+ * Indicates, that field is used for data passing between several snippets
+ * inlined. The field is translated into thread local variable. The thread local
+ * variable is by default always initialized the default value of a