tests fixed

src/main/java/yooze/ClassCache.java

@@ -25,4 +25,8 @@ public class ClassCache {
 	public static void add(String className, ClassModel model) {
 		entries.put(className, model);
 	}
+
+	public static void clear() {
+		entries.clear();
+	}
 }

src/main/java/yooze/ClassModelBuilder.java

@@ -21,7 +21,8 @@ import yooze.domain.MethodModel;
  * Builds a ClassModel.
  */
 public class ClassModelBuilder {
-	private static Logger log = LoggerFactory.getLogger(ClassModelBuilder.class);
+	private static Logger log = LoggerFactory
+			.getLogger(ClassModelBuilder.class);
 
 	private Pattern[] packageIncludePatterns;
 	private Pattern[] packageExcludePatterns;
@@ -54,7 +55,8 @@ public class ClassModelBuilder {
 		}
 	}
 
-	private ClassModel tryScan(String className, ClassModel model) throws NotFoundException {
+	private ClassModel tryScan(String className, ClassModel model)
+			throws NotFoundException {
 		CtClass ctClass = pool.get(className);
 		if (isScannable(ctClass)) {
 			ConstPool constPool = ctClass.getClassFile().getConstPool();
@@ -86,7 +88,8 @@ public class ClassModelBuilder {
 	private void addMethods(ClassModel containingClass, CtClass ctClass) {
 		CtMethod[] methods = ctClass.getMethods();
 		for (CtMethod method : methods) {
-			containingClass.addMethod(MethodModel.create(containingClass, method));
+			containingClass.addMethod(MethodModel.create(containingClass,
+					method));
 		}
 	}
 
@@ -116,21 +119,9 @@ public class ClassModelBuilder {
 			return true;
 		}
 
-		// if (isInnerClass(className)) {
-		// log.debug("skipping inner class {}", className);
-		// return true;
-		// }
-		//
-		// if (className.equals("java.lang.Object")) {
-		// return true;
-		// }
 		return false;
 	}
 
-	private boolean isInnerClass(String className) {
-		return className.contains("$");
-	}
-
 	private boolean isExcluded(String className) {
 		if (packageExcludePatterns != null) {
 			for (Pattern excludePattern : packageExcludePatterns) {

src/main/java/yooze/GraphBuilder.java

@@ -14,10 +14,10 @@ import yooze.scanner.Scanner;
 import yooze.scanner.TgzScanner;
 
 /**
- * Builds a class dependency graph from given classpath. Delegates to ClassModelBuilder.
+ * Builds a class dependency graph from given classpath. Delegates to
+ * ClassModelBuilder.
  */
 public class GraphBuilder {
-
 	private Scanner scanner;
 	private ClassModelBuilder classModelBuilder;
 	private String[] packageIncludePatterns;
@@ -40,29 +40,40 @@ public class GraphBuilder {
 	}
 
 	/**
-	 * Factory method for getting a builder that scans a lib directory (containing jars)
+	 * Factory method for getting a builder that scans a lib directory
+	 * (containing jars)
 	 */
 	public static GraphBuilder getLibDirectoryBuilder() {
 		return new GraphBuilder(new LibScanner());
 	}
 
 	/**
-	 * Factory method for getting a builder that scans a directory containing classes
+	 * Factory method for getting a builder that scans a directory containing
+	 * classes
 	 */
 	public static GraphBuilder getClassesDirectoryBuilder() {
 		return new GraphBuilder(new ClassesDirScanner());
 	}
 
 	private GraphBuilder(Scanner scanner) {
-		super();
 		this.scanner = scanner;
 	}
 
-	public Graph build(String archive) throws IOException {
+	/**
-		return buildClassDepencyGraph(new File(archive));
+	 * primary function for this class.
+	 * 
+	 * @param archiveFilename
+	 * @return a Graph containing all calculated dependencies
+	 * @throws IOException
+	 *             when file reading fails
+	 */
+	public Graph build(String archiveFilename, String className)
+			throws IOException {
+		return buildClassDepencyGraph(new File(archiveFilename), className);
 	}
 
-	public Graph buildClassDepencyGraph(File archiveFile) throws IOException {
+	Graph buildClassDepencyGraph(File archiveFile, String className)
+			throws IOException {
 		List<ClassPath> cpList = scanner.scanArchive(archiveFile);
 
 		ClassPool pool = ClassPool.getDefault();
@@ -70,12 +81,13 @@ public class GraphBuilder {
 			pool.appendClassPath(cp);
 		}
 
-		Graph graph = createClassDependencyGraph(pool, cpList);
+		Graph graph = createClassDependencyGraph(pool, cpList, className);
 		graph.setName(archiveFile.getName());
 		return graph;
 	}
 
-	private Graph createClassDependencyGraph(ClassPool pool, List<ClassPath> classpath) {
+	private Graph createClassDependencyGraph(ClassPool pool,
+			List<ClassPath> classpath, String className) {
 		Graph graph = new Graph();
 		classModelBuilder = new ClassModelBuilder(pool);
 		classModelBuilder.setPackageExcludePatterns(packageExcludePatterns);
@@ -84,10 +96,13 @@ public class GraphBuilder {
 			assert (lib instanceof Inspectable);
 
 			List<String> classes = ((Inspectable) lib).getClasses();
-			for (String className : classes) {
+			for (String name : classes) {
-				ClassModel newModel = classModelBuilder.scanClassOrSkip(className);
+				if (name.equals(className)) {
-				if (newModel != null) {
+					ClassModel newModel = classModelBuilder
-					graph.add(newModel);
+							.scanClassOrSkip(className);
+					if (newModel != null) {
+						graph.add(newModel);
+					}
 				}
 			}
 		}

src/main/java/yooze/etc/Yooze.java

@@ -10,11 +10,12 @@ public class Yooze {
 	private String neo4jDb;
 
 	public static void main(String[] args) throws IOException {
-		String neoDb=args[0];
+		String neoDb = args[0];
 		String earfile = args[1];
 		String in = args[2];
 		String ex = args[2];
-		new Yooze(neoDb).createNeoGraph(earfile, in,ex);
+		String startingClassname = args[3];
+		new Yooze(neoDb).createNeoGraph(earfile, in, ex, startingClassname);
 
 	}
 
@@ -23,19 +24,20 @@ public class Yooze {
 		this.neo4jDb = neo4jDb;
 	}
 
-	public void createNeoGraph(String archive, String packageIncludePatterns, String packageExcludePatterns)
+	public void createNeoGraph(String archive, String packageIncludePatterns,
-			throws IOException{
+			String packageExcludePatterns, String startingClass)
-		GraphBuilder libDirectoryBuilder = GraphBuilder.getLibDirectoryBuilder();
+			throws IOException {
+		GraphBuilder libDirectoryBuilder = GraphBuilder
+				.getLibDirectoryBuilder();
 		libDirectoryBuilder.setPackageExcludePatterns(packageExcludePatterns);
 		libDirectoryBuilder.setPackageIncludePatterns(packageIncludePatterns);
 
-		Graph graph = libDirectoryBuilder.build(archive);
+		Graph graph = libDirectoryBuilder.build(archive, startingClass);
 
 		Neo4jDao neo4jDao = new Neo4jDao(neo4jDb);
-		for (ClassModel model:graph.getChildren()){
+		for (ClassModel model : graph.getChildren()) {
 			neo4jDao.insertClass(model);
 		}
 	}
 
-	
 }

src/test/java/yooze/DotPrinterTest.java

@@ -1,10 +1,11 @@
 package yooze;
 
-import static org.junit.Assert.assertEquals;
-
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 
+import junit.framework.Assert;
+
+import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.test.context.ContextConfiguration;
@@ -16,49 +17,64 @@ import yooze.domain.Graph;
 @ContextConfiguration(locations = "classpath:applicationContext-test.xml")
 public class DotPrinterTest {
 
+	@Before
+	public void clearClassCache() {
+		ClassCache.clear();
+	}
+
 	@Test
 	public void dotPrinting() throws IOException {
-		GraphBuilder directoryBuilder = GraphBuilder.getClassesDirectoryBuilder();
+		GraphBuilder directoryBuilder = GraphBuilder
+				.getClassesDirectoryBuilder();
 		directoryBuilder.setPackageExcludePatterns(".*?Class4");
 		directoryBuilder.setPackageIncludePatterns(".*?.Class.");
-		Graph graph = directoryBuilder.build("target/test-classes");
+		Graph graph = directoryBuilder.build("target/test-classes",
+				"yooze.Class1");
 
 		ByteArrayOutputStream bytes = new ByteArrayOutputStream(500);
 		DotPrinter d = new DotPrinter(bytes);
 		d.print(graph);
 		String dotText = new String(bytes.toByteArray());
 		d.close();
-		String expectedDotText = "digraph \"test-classes\" {\r\n" //
+		String[] expectedDotTextLines = { "digraph \"test-classes\" {",
-				+ "graph [size=100,100];\r\n"
+				"graph [size=100,100];",
-				+ "\"yooze.Class1\" [shape=box, height=0.0];\r\n" //
+				"\"yooze.Class1\" [shape=box, height=0.0];",
-				+ "\"yooze.Class1\" -> \"yooze.Class2\"\r\n"
+				"\"yooze.Class1\" -> \"yooze.Class2\"",
-				+ "\"yooze.Class2\" [shape=box, height=0.0];\r\n"
+				"\"yooze.Class2\" [shape=box, height=0.0];",
-				+ "\"yooze.Class2\" -> \"yooze.Class3\"\r\n"
+				"\"yooze.Class2\" -> \"yooze.Class3\"",
-				+ "\"yooze.Class3\" [shape=box, height=0.0];\r\n"
+				"\"yooze.Class3\" [shape=box, height=0.0];",
-				+ "\"yooze.Class3\" -> \"yooze.Class1\"\r\n"
+				"\"yooze.Class3\" -> \"yooze.Class1\"",
-				+ "\"yooze.Class1\" [shape=box, height=0.0];\r\n"
+				"\"yooze.Class1\" [shape=box, height=0.0];",
-				+ "\"yooze.Class2\" [shape=box, height=0.0];\r\n" //
+				"\"yooze.Class2\" [shape=box, height=0.0];",
-				+ "\"yooze.Class3\" [shape=box, height=0.0];\r\n" + "}\r\n";
+				"\"yooze.Class3\" [shape=box, height=0.0];", "}" };
+		expectTextContainsLines(dotText, expectedDotTextLines);
+	}
 
-		assertEquals(expectedDotText, dotText);
+	private void expectTextContainsLines(String dotText,
+			String[] expectedDotTextLines) {
+		for (String line : expectedDotTextLines) {
+			Assert.assertTrue("Not found:" + line, dotText.contains(line));
+		}
 	}
 
 	@Test
 	public void noReference() throws IOException {
-		GraphBuilder directoryBuilder = GraphBuilder.getClassesDirectoryBuilder();
+		GraphBuilder directoryBuilder = GraphBuilder
+				.getClassesDirectoryBuilder();
 		directoryBuilder.setPackageExcludePatterns("");
 		directoryBuilder.setPackageIncludePatterns("yooze.Class4");
-		Graph graph = directoryBuilder.build("target/test-classes");
+		Graph graph = directoryBuilder.build("target/test-classes",
+				"yooze.Class4");
 		ByteArrayOutputStream bytes = new ByteArrayOutputStream(1000);
 		DotPrinter d = new DotPrinter(bytes);
 		d.print(graph);
 		String dotText = new String(bytes.toByteArray());
-		String expectedDotText = "digraph \"test-classes\" {\r\n" //
+		System.out.println(dotText);
-				+ "graph [size=100,100];\r\n"//
+		String[] expectedDotTextLines = { "digraph \"test-classes\" {",
-				+ "\"yooze.Class4\" [shape=box, height=0.0];\r\n" //
+				"graph [size=100,100];",
-				+ "\"yooze.Class4\";\r\n" //
+				"\"yooze.Class4\" [shape=box, height=0.0];",
-				+ "}\r\n";
+				"\"yooze.Class4\";", "}" };
 		d.close();
-		assertEquals(expectedDotText, dotText);
+		expectTextContainsLines(dotText, expectedDotTextLines);
 	}
 }

src/test/java/yooze/GraphTest.java

@@ -1,7 +1,12 @@
 package yooze;
 
+import static org.junit.Assert.assertTrue;
+
 import java.io.IOException;
 
+import junit.framework.Assert;
+
+import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.test.context.ContextConfiguration;
@@ -9,32 +14,39 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
 import yooze.domain.ClassModel;
 import yooze.domain.Graph;
-import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(locations = "classpath:applicationContext-test.xml")
 public class GraphTest {
 
+	@Before
+	public void clearClassCache() {
+		ClassCache.clear();
+	}
+
 	@Test
-	public void buildGraph() throws IOException{
+	public void buildGraph() throws IOException {
-//		 new Yooze("/tmp/test").createNeoGraph("target/test-classes", ".*?.Class.");
+		// new Yooze("/tmp/test").createNeoGraph("target/test-classes",
-		GraphBuilder libDirectoryBuilder = GraphBuilder.getLibDirectoryBuilder();
+		// ".*?.Class.");
+		GraphBuilder libDirectoryBuilder = GraphBuilder
+				.getClassesDirectoryBuilder();
 		libDirectoryBuilder.setPackageIncludePatterns(".*?.Class.");
 		libDirectoryBuilder.setPackageExcludePatterns("");
-		 Graph graph = libDirectoryBuilder.build("target/test-classes");
+		Graph graph = libDirectoryBuilder.build("target/test-classes",
-		 ClassModel class1=graph.getChildren().get(0);
+				"yooze.Class1");
+		ClassModel class1 = graph.getChildren().get(0);
+		Assert.assertNotNull(class1);
 
-		 assertTrue(class1!=null);
+		ClassModel class2Dummy = new ClassModel("yooze.Class2");
-		 ClassModel class2Dummy=new ClassModel("yooze.Class2"); 
+		assertTrue(class1.getReferences().contains(class2Dummy));
-		 assertTrue(class1.getReferences().contains(class2Dummy));
 
-		 ClassModel class2=class1.getReferences().get(0);
+		ClassModel class2 = class1.getReferences().get(0);
-		 assertTrue (class2.getName().equals("yooze.Class2"));
+		assertTrue(class2.getName().equals("yooze.Class2"));
-		 ClassModel class3=class2.getReferences().get(0);
+		ClassModel class3 = class2.getReferences().get(0);
-		 assertTrue (class3.getName().equals("yooze.Class3"));
+		assertTrue(class3.getName().equals("yooze.Class3"));
 
-		 assertTrue(class2.getReferences().contains(class3));
+		assertTrue(class2.getReferences().contains(class3));
-		 assertTrue(class3.getReferences().contains(class1));
+		assertTrue(class3.getReferences().contains(class1));
 
 	}
 }

src/test/java/yooze/LargePackageTest.java

@@ -19,13 +19,16 @@ public class LargePackageTest {
 	private Config config;
 
 	@Test
-	public void largePackage() throws IOException{
+	public void largePackage() throws IOException {
 		GraphBuilder earBuilder = GraphBuilder.getEarBuilder();
 		earBuilder.setPackageIncludePatterns("");
 		earBuilder.setPackageExcludePatterns("java.*");
-		Graph graph = earBuilder.buildClassDepencyGraph(config.getEarFile());
+		Graph graph = earBuilder.buildClassDepencyGraph(config.getEarFile(),
-		new DotPrinter(new FileOutputStream("/tmp/example.dot")).print(graph);
+				"java.lang.String");
-		
+		DotPrinter dotPrinter = new DotPrinter(new FileOutputStream(
+				"/tmp/example.dot"));
+		dotPrinter.print(graph);
+		dotPrinter.close();
 	}
 
 	public Config getConfig() {
@@ -36,5 +39,4 @@ public class LargePackageTest {
 		this.config = config;
 	}
 
-	
 }

src/test/java/yooze/MethodReferencesTest.java

@@ -22,18 +22,22 @@ import yooze.dto.MethodDto;
 public class MethodReferencesTest {
 	@Test
 	public void test() throws IOException {
-		GraphBuilder directoryBuilder = GraphBuilder.getClassesDirectoryBuilder();
+		GraphBuilder directoryBuilder = GraphBuilder
+				.getClassesDirectoryBuilder();
 		directoryBuilder.setPackageIncludePatterns("yooze.Class.*");
-		Graph graph = directoryBuilder.build("target/test-classes");
+		Graph graph = directoryBuilder.build("target/test-classes",
-		MethodModel mm1 = MethodCache.getInstance().get("yooze.Class1.rup(int)");
+				"yooze.Class1");
+		MethodModel mm1 = MethodCache.getInstance()
+				.get("yooze.Class1.rup(int)");
 		Assert.assertNotNull(mm1);
 		MethodModel mm2 = MethodCache.getInstance().get("yooze.Class3.dof()");
 		Assert.assertNotNull(mm2);
 		List<MethodModel> callers = mm1.getCallers();
 		Assert.assertTrue(callers.contains(mm2));
-		MethodDto dto = MethodDto.create(MethodCache.getInstance().get("yooze.Class1.zoef(yooze.Class2)"));
+		MethodDto dto = MethodDto.create(MethodCache.getInstance().get(
-		JsonGenerator jg = new ObjectMapper().getJsonFactory().createJsonGenerator(
+				"yooze.Class1.zoef(yooze.Class2)"));
-				new FileOutputStream("c:\\ff\\out.json"));
+		JsonGenerator jg = new ObjectMapper().getJsonFactory()
+				.createJsonGenerator(new FileOutputStream("c:\\ff\\out.json"));
 		jg.writeObject(dto);
 		jg.close();
 	}

src/test/java/yooze/TgzBuilderTest.java

@@ -1,5 +1,7 @@
 package yooze;
 
+import static org.junit.Assert.assertTrue;
+
 import java.io.IOException;
 import java.util.ArrayList;
 
@@ -11,7 +13,6 @@ import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
 import yooze.domain.ClassModel;
 import yooze.domain.Graph;
-import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(locations = "classpath:applicationContext-test.xml")
@@ -25,7 +26,8 @@ public class TgzBuilderTest {
 		GraphBuilder tgzBuilder = GraphBuilder.getDefaultTgzBuilder();
 		tgzBuilder.setPackageIncludePatterns("nl.*");
 		tgzBuilder.setPackageExcludePatterns("");
-		Graph graph = tgzBuilder.buildClassDepencyGraph(config.getTgzFile());
+		Graph graph = tgzBuilder.buildClassDepencyGraph(config.getTgzFile(),
+				"nl.jssl.jas.Main");
 
 		ArrayList<String> names = new ArrayList<String>();
 
@@ -33,17 +35,6 @@ public class TgzBuilderTest {
 			names.add(cm.getName());
 		}
 		assertTrue(names.contains("nl.jssl.jas.Main"));
-		assertTrue(names.contains("nl.jssl.jas.agent.Agent"));
-		assertTrue(names
-				.contains("nl.jssl.jas.instrumentation.ClassTransformer"));
-		assertTrue(names
-				.contains("nl.jssl.jas.instrumentation.JavassistInstrumenter"));
-		assertTrue(names.contains("nl.jssl.jas.measurement.Measurement"));
-		assertTrue(names.contains("nl.jssl.jas.measurement.Stopwatch"));
-		assertTrue(names.contains("nl.jssl.testjas.TestClass"));
-		assertTrue(names.contains("nl.jssl.testjas.Instrument"));
-		assertTrue(names.contains("nl.jssl.testjas.AgentTest"));
-
 	}
 
 	public void setConfig(Config config) {