Reorganized classes

Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/BasicSourceSinkManager.java

@@ -21,6 +21,9 @@ public class BasicSourceSinkManager extends SourceSinkManager {
     private static final Map<String, Set<String>> taintThrough = new HashMap<>();
     // Maps class names to sets of class instances
     private static final Map<String, Set<Class<?>>> classMap = new HashMap<>();
+    public static InputStream sourcesFile;
+    public static InputStream sinksFile;
+    public static InputStream taintThroughFile;
     // Maps class names to a set of all methods listed as sources for the class or one of its supertypes or superinterfaces
     private static Map<String, Set<String>> inheritedSources = new HashMap<>();
     // Maps class names to a set of all methods listed as sinks for the class or one of its supertypes or superinterfaces
@@ -109,9 +112,9 @@ public String getBaseSink(String str) {
 
     /* Reads source, sink and taintThrough methods from their files into their respective maps. */
     public static synchronized void loadTaintMethods() {
-        readTaintMethods(Instrumenter.sourcesFile, AutoTaint.SOURCE);
-        readTaintMethods(Instrumenter.sinksFile, AutoTaint.SINK);
-        readTaintMethods(Instrumenter.taintThroughFile, AutoTaint.TAINT_THROUGH);
+        readTaintMethods(sourcesFile, AutoTaint.SOURCE);
+        readTaintMethods(sinksFile, AutoTaint.SINK);
+        readTaintMethods(taintThroughFile, AutoTaint.TAINT_THROUGH);
     }
 
     /* Provides access to the single instance of BasicSourceSinkManager */
@@ -263,7 +266,7 @@ private static synchronized Set<String> getAutoTaintMethods(String className, Ma
                 // Add any methods from this class that are directly listed as auto taint methods
                 set.addAll(baseMethods.get(className));
             }
-            ClassNode cn = Instrumenter.getClassNode(className);
+            ClassNode cn = ClassNodeCache.getClassNode(className);
             if (cn != null) {
                 if (cn.interfaces != null) {
                     // Add all auto taint methods from interfaces implemented by this class
@@ -295,7 +298,7 @@ private static synchronized String findSuperTypeAutoTaintProvider(String classNa
                 if (baseMethods.containsKey(curClassName) && baseMethods.get(curClassName).contains(methodName)) {
                     return curClassName;
                 }
-                ClassNode cn = Instrumenter.getClassNode(curClassName);
+                ClassNode cn = ClassNodeCache.getClassNode(curClassName);
                 if (cn != null) {
                     if (cn.interfaces != null) {
                         // Enqueue interfaces implemented by the current class

Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/ClassNodeCache.java

@@ -0,0 +1,79 @@
+package edu.columbia.cs.psl.phosphor;
+
+import edu.columbia.cs.psl.phosphor.struct.harmony.util.Collections;
+import edu.columbia.cs.psl.phosphor.struct.harmony.util.HashMap;
+import edu.columbia.cs.psl.phosphor.struct.harmony.util.Map;
+import org.objectweb.asm.ClassReader;
+import org.objectweb.asm.ClassVisitor;
+import org.objectweb.asm.MethodVisitor;
+import org.objectweb.asm.tree.ClassNode;
+import org.objectweb.asm.tree.MethodNode;
+
+import java.io.InputStream;
+
+public final class ClassNodeCache {
+    public static Map<String, ClassNode> classes = Collections.synchronizedMap(new HashMap<>());
+
+    static {
+        classes.putAll(ClassSupertypeReadingTransformer.classNodes);
+        ClassSupertypeReadingTransformer.classNodes = null;
+    }
+
+    private ClassNodeCache() {
+        throw new AssertionError("Tried to instantiate static utility class: " + getClass());
+    }
+
+    /* Returns the class node associated with the specified class name or null if none exists and a new one could not
+     * successfully be created for the class name. */
+    public static ClassNode getClassNode(String className) {
+        ClassNode cn = classes.get(className);
+        if (cn == null) {
+            // Class was loaded before ClassSupertypeReadingTransformer was added
+            return tryToAddClassNode(className);
+        } else {
+            return cn;
+        }
+    }
+
+    /* Attempts to create a ClassNode populated with supertype information for this class. */
+    private static ClassNode tryToAddClassNode(String className) {
+        try (InputStream is = ClassLoader.getSystemResourceAsStream(className + ".class")) {
+            if (is == null) {
+                return null;
+            }
+            ClassReader cr = new ClassReader(is);
+            cr.accept(
+                    new ClassVisitor(Configuration.ASM_VERSION) {
+                        private ClassNode cn;
+
+                        @Override
+                        public void visit(
+                                int version,
+                                int access,
+                                String name,
+                                String signature,
+                                String superName,
+                                String[] interfaces) {
+                            super.visit(version, access, name, signature, superName, interfaces);
+                            cn = new ClassNode();
+                            cn.name = name;
+                            cn.superName = superName;
+                            cn.interfaces = new java.util.ArrayList<>(java.util.Arrays.asList(interfaces));
+                            cn.methods = new java.util.LinkedList<>();
+                            classes.put(name, cn);
+                        }
+
+                        @Override
+                        public MethodVisitor visitMethod(
+                                int access, String name, String descriptor, String signature, String[] exceptions) {
+                            cn.methods.add(new MethodNode(access, name, descriptor, signature, exceptions));
+                            return super.visitMethod(access, name, descriptor, signature, exceptions);
+                        }
+                    },
+                    ClassReader.SKIP_CODE);
+            return classes.get(className);
+        } catch (Exception e) {
+            return null;
+        }
+    }
+}

Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/ClassSupertypeReadingTransformer.java

@@ -27,7 +27,7 @@ public void visit(int version, int access, String name, String signature, String
                 cn.superName = superName;
                 cn.interfaces = new ArrayList<>(Arrays.asList(interfaces));
                 if(classNodes == null) {
-                    Instrumenter.classes.put(name, cn);
+                    ClassNodeCache.classes.put(name, cn);
                 } else {
                     classNodes.put(name, cn);
                 }

Phosphor/src/main/java/edu/columbia/cs/psl/phosphor/PCLoggingTransformer.java

@@ -34,7 +34,7 @@ public byte[] transform(ClassLoader loader, final String className2, Class<?> cl
         ClassReader cr = (Configuration.READ_AND_SAVE_BCI ? new OffsetPreservingClassReader(classfileBuffer)
                 : new ClassReader(classfileBuffer));
         String className = cr.getClassName();
-        if (Instrumenter.isIgnoredClass(className)) {
+        if (Phosphor.isIgnoredClass(className)) {
             switch (className) {
                 case "java/lang/Boolean":
                 case "java/lang/Byte":