Custom instrumentation pass not being run on methods that are part of the analyzed library

[prashast]

Describe the bug Soot is not performing the specified intra-procedural pass using jtp over classes that are part of the analyzed jar which is the rome library and simply ignoring them. I believe the reason this is happening is because the analyzed classes which are in the rome-1.0.jar are part of the standard Java API (com.sun.syndication.*). Is there a way to force Soot to run the instrumentation pass over these classes?

BaseAnalysis.java (The soot environment setup)

public class BaseAnalysis {

    public static void main(String[] args) {

        // Get the jarfile and source dir
        String jarFile = args[0];
        String sourceDirectory = Paths.get(jarFile).getParent().toString();

        System.out.println(String.format("Jar file:%s\nProcess dir:%s", jarFile, sourceDirectory));
        G.reset();
        Options.v().set_prepend_classpath(true); //-pp
        Options.v().set_whole_program(true); //-w
        Options.v().set_allow_phantom_refs(true);
        List<String> processdirs = new ArrayList<>();
        PackManager.v().getPack("jtp").add(new Transform("jtp.MethodPass", MethodPass.v()));
        processdirs.add(jarFile);
        Options.v().set_process_dir(processdirs);
        Options.v().set_soot_classpath(sourceDirectory);
        Options.v().set_output_jar(true); // Creates the output jar file with instrumented code
        Scene.v().loadNecessaryClasses();
        PackManager.v().runPacks();
        System.out.println("Writing processed jar file to sootOutput");
        PackManager.v().writeOutput();
    }
}

MethodPass.java (Simple custom pass that's just validating method bodies)

public class MethodPass extends BodyTransformer {

    private static MethodPass instance = new MethodPass();
    private MethodPass() {}

    public static MethodPass v() { return instance; }

	protected void internalTransform(Body body, String phase, Map options) {
            // body's method
            SootMethod method = body.getMethod();
            System.out.println("Validating body of:" + method.toString());
            body.validate();
	}

}

Input file debug_rome.tar.gz

To reproduce Steps to reproduce the behavior: The attached tarball contains a repro package to debug the issue in Rome where the classes and methods corresponding to the analyzed jar file are not being iterated over during the specified intra-procedural analysis. This in turn causes the output jar file to be empty.

• Untar the provided repro package.

• To run the test for the Rome library run the below set of commands

  • Perform the analysis pass which for the sake of simplicity is just iterating over the classes in the jar file and validating the bodies of the methods.

    cd src/static
    gradle run --args="$PWD/../../libs/rome/rome-1.0.jar"
    

  • If there were methods analyzed by the custom pass there would be messages of the form "Validating body of " to be printed but instead there is no such output

  • You can also see that the output jar is empty by checking the file generated ./sootOutput/out.jar

• To see the expected output, we provided a synthetic jar file as well containing some sample methods.

  • Perform the analysis pass which for the sake of simplicity is just iterating over the classes in the jar file and validating the bodies of the methods.

    gradle run --args="$PWD/../../libs/FizzBuzz/FizzBuzz.jar"
    

  • If there were methods analyzed by the custom pass there would be messages of the form "Validating body of " to be printed which indeed there are.

  • You can see that the output jar file is non-empty as well as seen in ./sootOutput/out.jar

Expected behavior For the rome library I would expect the classes belong to this library to be correctly processed by the specified intra-procedural analysis pass as provided using jtp.