Merge branch 'develop' into develop

soot-oss · Aug 27, 2024 · 9a73239 · 9a73239
2 parents 1d5f9c5 + 027c7ba
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diff --git a/README.md b/README.md
@@ -2,7 +2,9 @@
 [![Gitpod Ready-to-Code](https://img.shields.io/badge/Gitpod-Ready--to--Code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/soot-oss/soot) 
 
 # IMPORTANT: Soot is now succeeded by SootUp!
-**In December 2022, we have officially released [SootUp](https://soot-oss.github.io/SootUp/announce/), a version of Soot with a completely overhauled, more modular, testable, maintainable and usable architecture. Please check this out in case you wish to start a new program-analysis project.**
+**In December 2022, we have officially released [SootUp](https://soot-oss.github.io/SootUp/), a version of Soot with a completely overhauled, more modular, testable, maintainable and usable architecture. Please check this out in case you wish to start a new program-analysis project.**
+
+Since there has been some confusion: SootUp is not yet feature-complete. Therefore, the "old" Soot needs to live on for the time being, especially for projects that require instrumentation capabilities or robust Android support. The "old" Soot is still being maintained until it can safely be dropped for a feature-complete successor.
 
 # Using Soot? Let us know about it!
 We are regularly applying for funding to help us maintain Soot. You can help us immensely by letting us know about [**projects that use Soot**](https://github.com/soot-oss/soot/wiki/Users-of-Soot), both commercially or in the form of research tools.
@@ -107,8 +109,6 @@ If you cannot work with the prebuild versions and need to build Soot on your own
 
 Soot follows the git-flow convention. Releases and hotfixes are maintained in the master branch.
 Development happens in the develop branch. To catch the bleeding edge of Soot, check out the latter.
-In case of any questions, please consult the Soot
-mailing list at: http://www.sable.mcgill.ca/mailman/listinfo/soot-list/
 
 # How do I contribute to Soot?
 

diff --git a/doc/soot_options.html b/doc/soot_options.html
@@ -684,6 +684,10 @@ <H2><A name="section_2">Input Options</A></H2>
             <td><tt>-drop-bodies-after-load </tt><br></td>
             <td colspan="2">Drop the method source after it has served its purpose of loading the method body</td>
          </tr>
+         <tr>
+            <td><tt>-nc </tt><br><tt>-native-code </tt><br></td>
+            <td colspan="2">Enables native methods to be concrete. Needed for analyzing the Java Native Interface.</td>
+         </tr>
       </table>
       <H2><A name="section_3">Output Options</A></H2>
       <table border="3">

diff --git a/eclipse/ca.mcgill.sable.soot/src/ca/mcgill/sable/soot/ui/PhaseOptionsDialog.java b/eclipse/ca.mcgill.sable.soot/src/ca/mcgill/sable/soot/ui/PhaseOptionsDialog.java
@@ -1206,6 +1206,12 @@ private boolean createNewConfig() {
 		if (boolRes != defBoolRes) {
 			getConfig().put(getInput_Optionsdrop_bodies_after_load_widget().getAlias(), new Boolean(boolRes));
 		}
+		boolRes = getInput_Optionsnative_code_widget().getButton().getSelection();
+		defBoolRes = false;
+
+		if (boolRes != defBoolRes) {
+			getConfig().put(getInput_Optionsnative_code_widget().getAlias(), new Boolean(boolRes));
+		}
 		stringRes = getInput_Optionssoot_classpath_widget().getText().getText();
 		defStringRes = "";
 
@@ -4899,6 +4905,16 @@ public BooleanOptionWidget getInput_Optionsdrop_bodies_after_load_widget() {
 		return Input_Optionsdrop_bodies_after_load_widget;
 	}	
 
+	private BooleanOptionWidget Input_Optionsnative_code_widget;
+
+	private void setInput_Optionsnative_code_widget(BooleanOptionWidget widget) {
+		Input_Optionsnative_code_widget = widget;
+	}
+
+	public BooleanOptionWidget getInput_Optionsnative_code_widget() {
+		return Input_Optionsnative_code_widget;
+	}	
+
 
 	private ListOptionWidget Input_Optionsprocess_dir_widget;
 
@@ -9020,6 +9036,17 @@ private Composite Input_OptionsCreate(Composite parent) {
 
 		setInput_Optionsdrop_bodies_after_load_widget(new BooleanOptionWidget(editGroupInput_Options, SWT.NONE, new OptionData("Drop method source after loading bodies", "", "","drop-bodies-after-load", "\nEach method is associated with a method source for loading its \nbody. When this option is disabled, a reference to this source \nis kept around even after the body has already been loaded. This \nis a waste of memory for most use cases. When this option is \nenabled, the reference is dropped, allowing for garbage \ncollection of the method source. On the other hand, if the body \nis ever released, it cannot easily be recovered (i.e., loaded \nagain) easily.", defaultBool)));
 
+		defKey = ""+" "+""+" "+"nc native-code";
+		defKey = defKey.trim();
+
+		if (isInDefList(defKey)) {
+			defaultBool = getBoolDef(defKey);	
+		} else {
+			defaultBool = false;
+		}
+
+		setInput_Optionsnative_code_widget(new BooleanOptionWidget(editGroupInput_Options, SWT.NONE, new OptionData("Enable native code", "", "","nc native-code", "\nThis option is needed, when analyzing native code. Particularly \nwhen using the Java Native Interface (JNI). If this option is \nenabled (set true), it allows native methods to be concrete. \nThis flag will be checked in the SootMethod.isConcrete() method, \nallowing native methods to have a body.", defaultBool)));
+
 		data = new OptionData [] {
 
 				new OptionData("Class File",

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
     <groupId>org.soot-oss</groupId>
     <artifactId>soot</artifactId>
     <name>Soot - a J*va Optimization Framework</name>
-    <version>4.5.0-SNAPSHOT</version>
+    <version>4.6.0-SNAPSHOT</version>
     <description>A Java Optimization Framework</description>
     <url>https://soot-oss.github.io/soot</url>
     <organization>
@@ -54,26 +54,26 @@
     <properties>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>1.8</maven.compiler.target>
-        <xml-maven-plugin.version>1.0.2</xml-maven-plugin.version>
-        <maven-resources-plugin.version>3.2.0</maven-resources-plugin.version>
-        <build-helper-maven-plugin.version>3.3.0</build-helper-maven-plugin.version>
-        <maven-compiler-plugin.version>3.10.1</maven-compiler-plugin.version>
-        <maven-surefire-plugin.version>3.0.0-M7</maven-surefire-plugin.version>
-        <maven-assembly-plugin.version>3.3.0</maven-assembly-plugin.version>
-        <maven-jar-plugin.version>3.2.2</maven-jar-plugin.version>
-        <maven-source-plugin.version>3.2.1</maven-source-plugin.version>
-        <maven-javadoc-plugin.version>3.4.0</maven-javadoc-plugin.version>
+        <xml-maven-plugin.version>1.1.0</xml-maven-plugin.version>
+        <maven-resources-plugin.version>3.3.1</maven-resources-plugin.version>
+        <build-helper-maven-plugin.version>3.5.0</build-helper-maven-plugin.version>
+        <maven-compiler-plugin.version>3.13.0</maven-compiler-plugin.version>
+        <maven-surefire-plugin.version>3.2.5</maven-surefire-plugin.version>
+        <maven-assembly-plugin.version>3.7.1</maven-assembly-plugin.version>
+        <maven-jar-plugin.version>3.3.0</maven-jar-plugin.version>
+        <maven-source-plugin.version>3.3.0</maven-source-plugin.version>
+        <maven-javadoc-plugin.version>3.6.3</maven-javadoc-plugin.version>
         <maven-nexus-staging-plugin.version>1.6.13</maven-nexus-staging-plugin.version>
-        <maven-gpg-plugin.version>3.0.1</maven-gpg-plugin.version>
+        <maven-gpg-plugin.version>3.2.2</maven-gpg-plugin.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <maven-checkstyle-plugin.version>3.1.2</maven-checkstyle-plugin.version>
+        <maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
         <checkstyle.version>8.18</checkstyle.version>
         <checkstyle.dir.path>${basedir}/codingstyle</checkstyle.dir.path>
         <checkstyle.file.path>${checkstyle.dir.path}/soot_checkstyle_checks.xml</checkstyle.file.path>
         <checkstyle.failOnViolation>true</checkstyle.failOnViolation>
         <licence-check.failOnMissingHeader>true</licence-check.failOnMissingHeader>
         <testcase.groups.excluded>categories.Java9Test,categories.Java11Test</testcase.groups.excluded>
-        <asm.version>9.6</asm.version>
+        <asm.version>9.7</asm.version>
     </properties>
     <build>
         <finalName>sootclasses-trunk</finalName>
@@ -576,12 +576,12 @@
         <dependency>
             <groupId>com.google.protobuf</groupId>
             <artifactId>protobuf-java</artifactId>
-            <version>3.21.7</version>
+            <version>3.25.3</version>
         </dependency>
         <dependency>
             <groupId>com.google.protobuf</groupId>
             <artifactId>protobuf-java-util</artifactId>
-            <version>3.21.2</version>
+            <version>3.25.3</version>
         </dependency>
     </dependencies>
 
@@ -657,6 +657,7 @@
                                 <configuration>
                                     <!-- This is necessary for gpg to not try to use the pinentry programs -->
                                     <gpgArguments>
+                                        <arg>--batch</arg>
                                         <arg>--pinentry-mode</arg>
                                         <arg>loopback</arg>
                                     </gpgArguments>

diff --git a/src/main/generated/options/soot/AntTask.java b/src/main/generated/options/soot/AntTask.java
@@ -342,6 +342,10 @@ public void setdrop_bodies_after_load(boolean arg) {
             if(arg) addArg("-drop-bodies-after-load");
         }
 
+        public void setnative_code(boolean arg) {
+            if(arg) addArg("-native-code");
+        }
+
         public void setoutput_dir(String arg) {
             addArg("-output-dir");
             addArg(arg);

diff --git a/src/main/generated/options/soot/options/Options.java b/src/main/generated/options/soot/options/Options.java
@@ -543,6 +543,11 @@ else if (false
                     || option.equals("no-drop-bodies-after-load")
             )
                 drop_bodies_after_load = false;
+            else if (false
+                    || option.equals("nc")
+                    || option.equals("native-code")
+            )
+                native_code = true;
             else if (false
                     || option.equals("d")
                     || option.equals("output-dir")
@@ -1656,6 +1661,10 @@ public int src_prec() {
     private boolean drop_bodies_after_load = true;
     public void set_drop_bodies_after_load(boolean setting) { drop_bodies_after_load = setting; }
 
+    public boolean native_code() { return native_code; }
+    private boolean native_code = false;
+    public void set_native_code(boolean setting) { native_code = setting; }
+
     public String output_dir() { return output_dir; }
     public void set_output_dir(String setting) { output_dir = setting; }
     private String output_dir = "";
@@ -1889,6 +1898,7 @@ public String getUsage() {
                 + padOpt("-polyglot", "Use Java 1.4 Polyglot frontend instead of JastAdd")
                 + padOpt("-permissive-resolving", "Use alternative sources when classes cannot be found using the normal resolving strategy")
                 + padOpt("-drop-bodies-after-load", "Drop the method source after it has served its purpose of loading the method body")
+                + padOpt("-nc, -native-code", "Enables native methods to be concrete. Needed for analyzing the Java Native Interface.")
                 + "\nOutput Options:\n"
                 + padOpt("-d ARG -output-dir ARG", "Store output files in ARG")
                 + padOpt("-f ARG -output-format ARG", "Set output format for Soot")

diff --git a/src/main/java/soot/AbstractASMBackend.java b/src/main/java/soot/AbstractASMBackend.java
@@ -344,10 +344,12 @@ protected void generateMethods() {
                 if (va == null) {
                   continue;
                 }
-                for (AnnotationTag at : va.getAnnotations()) {
-                  AnnotationVisitor av = mv.visitParameterAnnotation(j, at.getType(),
-                      (va.getVisibility() == AnnotationConstants.RUNTIME_VISIBLE));
-                  generateAnnotationElems(av, at.getElems(), true);
+                if (va.hasAnnotations()) {
+                  for (AnnotationTag at : va.getAnnotations()) {
+                    AnnotationVisitor av = mv.visitParameterAnnotation(j, at.getType(),
+                        (va.getVisibility() == AnnotationConstants.RUNTIME_VISIBLE));
+                    generateAnnotationElems(av, at.getElems(), true);
+                  }
                 }
               }
             }
@@ -503,17 +505,19 @@ protected void generateAnnotations(Object visitor, Host host) {
         // Find all VisibilityAnnotationTags
         VisibilityAnnotationTag vat = (VisibilityAnnotationTag) t;
         boolean runTimeVisible = (vat.getVisibility() == AnnotationConstants.RUNTIME_VISIBLE);
-        for (AnnotationTag at : vat.getAnnotations()) {
-          AnnotationVisitor av = null;
-          if (visitor instanceof ClassVisitor) {
-            av = ((ClassVisitor) visitor).visitAnnotation(at.getType(), runTimeVisible);
-          } else if (visitor instanceof FieldVisitor) {
-            av = ((FieldVisitor) visitor).visitAnnotation(at.getType(), runTimeVisible);
-          } else if (visitor instanceof MethodVisitor) {
-            av = ((MethodVisitor) visitor).visitAnnotation(at.getType(), runTimeVisible);
-          }
+        if (vat.hasAnnotations()) {
+          for (AnnotationTag at : vat.getAnnotations()) {
+            AnnotationVisitor av = null;
+            if (visitor instanceof ClassVisitor) {
+              av = ((ClassVisitor) visitor).visitAnnotation(at.getType(), runTimeVisible);
+            } else if (visitor instanceof FieldVisitor) {
+              av = ((FieldVisitor) visitor).visitAnnotation(at.getType(), runTimeVisible);
+            } else if (visitor instanceof MethodVisitor) {
+              av = ((MethodVisitor) visitor).visitAnnotation(at.getType(), runTimeVisible);
+            }
 
-          generateAnnotationElems(av, at.getElems(), true);
+            generateAnnotationElems(av, at.getElems(), true);
+          }
         }
       } else if (t instanceof AnnotationDefaultTag && host instanceof SootMethod) {
         // Visit AnnotationDefault on methods

diff --git a/src/main/java/soot/FastHierarchy.java b/src/main/java/soot/FastHierarchy.java
@@ -32,7 +32,6 @@
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.Queue;
@@ -58,6 +57,7 @@
 public class FastHierarchy {
 
   protected static final int USE_INTERVALS_BOUNDARY = 100;
+  private final boolean isDotNet = Options.v().src_prec() == Options.src_prec_dotnet;
 
   protected Table<SootClass, NumberedString, SootMethod> typeToVtbl = HashBasedTable.create();
 
@@ -306,8 +306,16 @@ public boolean canStoreType(final Type child, final Type parent) {
         // From Java Language Spec 2nd ed., Chapter 10, Arrays
         return base == rtObject || base == rtSerializable || base == rtCloneable;
       } else {
+        // We can story any_subtype_of(x) in a variable of type x
+        RefType childBase = ((AnySubType) child).getBase();
+        if (childBase == parent) {
+          return true;
+        }
+
+        // If the child is any_subtype_of(x) and the parent is not x, this only works if all known subclasses of x
+        // cast-compatible to the parent
         Deque<SootClass> worklist = new ArrayDeque<SootClass>();
-        SootClass base = ((AnySubType) child).getBase().getSootClass();
+        SootClass base = childBase.getSootClass();
         if (base.isInterface()) {
           worklist.addAll(getAllImplementersOfInterface(base));
         } else {
@@ -877,7 +885,7 @@ private SootMethod resolveMethod(final SootClass baseType, final SootClass decla
     // When there is no proper dispatch found, we simply return null to let the caller decide what to do
     SootMethod candidate = null;
     boolean calleeExist = declaringClass.getMethodUnsafe(subsignature) != null;
-    for (SootClass concreteType = baseType; concreteType != null && ignoreList.add(concreteType);) {
+    for (SootClass concreteType = baseType; concreteType != null;) {
       candidate = getSignaturePolymorphicMethod(concreteType, name, parameterTypes, returnType);
       if (candidate != null) {
         if (!calleeExist || isVisible(concreteType, declaringClass, candidate.getModifiers())) {
@@ -904,7 +912,7 @@ private SootMethod resolveMethod(final SootClass baseType, final SootClass decla
       // determining the most specific super interface
       HashSet<SootClass> interfaceIgnoreList = new HashSet<>();
       for (SootClass concreteType = baseType; concreteType != null;) {
-        Queue<SootClass> worklist = new LinkedList<>(concreteType.getInterfaces());
+        Queue<SootClass> worklist = new ArrayDeque<>(concreteType.getInterfaces());
         // we have to determine the "most specific super interface"
         while (!worklist.isEmpty()) {
           SootClass iFace = worklist.poll();
@@ -941,7 +949,7 @@ private SootMethod resolveMethod(final SootClass baseType, final SootClass decla
     return candidate;
   }
 
-  private boolean isHandleDefaultMethods() {
+  protected boolean isHandleDefaultMethods() {
     int version = Options.v().java_version();
     return version == 0 || version > 7;
   }
@@ -985,7 +993,7 @@ private SootMethod getSignaturePolymorphicMethod(SootClass concreteType, String
         returnType = method.getReturnType();
       }
       // if dotnet structs or generics
-      if (Options.v().src_prec() == Options.src_prec_dotnet) {
+      if (isDotNet) {
         if (method.getParameterCount() == parameterTypes.size() && canStoreType(returnType, method.getReturnType())) {
           boolean canStore = true;
           for (int i = 0; i < method.getParameterCount(); i++) {

diff --git a/src/main/java/soot/MethodToContexts.java b/src/main/java/soot/MethodToContexts.java
@@ -55,7 +55,9 @@ public MethodToContexts(Iterator<MethodOrMethodContext> it) {
   public void add(Iterator<MethodOrMethodContext> it) {
     while (it.hasNext()) {
       MethodOrMethodContext momc = it.next();
-      add(momc);
+      if (momc != null) {
+        add(momc);
+      }
     }
   }
 

diff --git a/src/main/java/soot/ModuleUtil.java b/src/main/java/soot/ModuleUtil.java
@@ -95,6 +95,15 @@ public final ModuleClassNameWrapper makeWrapper(String className) {
    * @return true, if module mode is used
    */
   public static boolean module_mode() {
+    return G.v().soot_ModuleUtil().isInModuleMode();
+  }
+
+  /**
+   * Check if Soot is run with module mode enabled.
+   *
+   * @return true, if module mode is used
+   */
+  public boolean isInModuleMode() {
     return !Options.v().soot_modulepath().isEmpty();
   }
 

diff --git a/src/main/java/soot/RefType.java b/src/main/java/soot/RefType.java
@@ -64,10 +64,11 @@ protected RefType(String className) {
   }
 
   public static RefType v() {
-    if (ModuleUtil.module_mode()) {
-      return G.v().soot_ModuleRefType();
+    G g = G.v();
+    if (g.soot_ModuleUtil().isInModuleMode()) {
+      return g.soot_ModuleRefType();
     } else {
-      return G.v().soot_RefType();
+      return g.soot_RefType();
     }
   }
 

diff --git a/src/main/java/soot/Scene.java b/src/main/java/soot/Scene.java
@@ -149,10 +149,11 @@ public Scene(Singletons.Global g) {
   }
 
   public static Scene v() {
-    if (ModuleUtil.module_mode()) {
-      return G.v().soot_ModuleScene();
+    G g = G.v();
+    if (g.soot_ModuleUtil().isInModuleMode()) {
+      return g.soot_ModuleScene();
     } else {
-      return G.v().soot_Scene();
+      return g.soot_Scene();
     }
   }
 
@@ -2072,7 +2073,7 @@ public void setDoneResolving() {
     doneResolving = true;
   }
 
-  void setResolving(boolean value) {
+  public void setResolving(boolean value) {
     doneResolving = value;
   }
 
@@ -2202,4 +2203,13 @@ public LocalCreation createLocalCreation(Chain<Local> locals) {
   public LocalCreation createLocalCreation(Chain<Local> locals, String prefix) {
     return new DefaultLocalCreation(locals, prefix);
   }
+
+  /**
+   * Resets the sootClassPath to null.
+   * This method allows for subsequent calls to {@link #loadNecessaryClasses()}
+   * to recompute and load the classes using updated configurations if provided.
+   */
+  public void resetSootClassPathCache() {
+    this.sootClassPath = null;
+  }
 }
diff --git a/src/main/java/soot/SootMethod.java b/src/main/java/soot/SootMethod.java
@@ -220,7 +220,7 @@ public boolean isPhantom() {
    * Returns true if this method is not phantom, abstract or native, i.e. this method can have a body.
    */
   public boolean isConcrete() {
-    return !isPhantom() && !isAbstract() && !isNative();
+    return !isPhantom() && !isAbstract() && (!isNative() || Options.v().native_code()); 
   }
 
   /**