Reflections including classes outside the given package (Dropwizard + Swagger)

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I am using reflections to obtain all the classes that have the Api annotation with the following code.

Reflections reflections = new Reflections(ClasspathHelper.forPackage("my.package"),new TypeAnnotationsScanner());
Set<Class<?>> annotated = reflections.getTypesAnnotatedWith(Api.class);

If I run the server from Eclipse everything works fine and getTypesAnnotatedWith is returning the correct classes. But If I run the server from command-line I am getting classes outside that package. Classes from the Swagger library.

I am trying to find out what is going on instead of making a wolk-around

Thanks in advance!

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Enrique Fernández-Polo On BEST ANSWER

I finally solve this just using the java ClassLoader. Some spaghetti code! Sorry..

package com.glass.core.doc;

import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Enumeration;
import java.util.List;

import com.wordnik.swagger.annotations.Api;

public class AnnotatedClassFinder {

    public Collection<Class> getAnnotatedClasess(Class annotation,
            String packageName) throws ClassNotFoundException, IOException {

        Collection<Class> allClasses = getClasses(packageName);
        List<Class> annotatedClass = new ArrayList<Class>();

        for (Class aClass : allClasses) {
            if (aClass.isAnnotationPresent(annotation)) {
                annotatedClass.add(aClass);
                System.out.println("!!!!!!!!!!!!!!!!!!!!!!!----------------!"
                        + aClass.getName());
            }
        }

        return annotatedClass;
    }

    /**
     * Scans all classes accessible from the context class loader which belong
     * to the given package and subpackages.
     * 
     * @param packageName
     *            The base package
     * @return The classes
     * @throws ClassNotFoundException
     * @throws IOException
     */
    private Collection<Class> getClasses(String packageName)
            throws ClassNotFoundException, IOException {

        ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
        String path = packageName.replace('.', '/');
        System.out.println("PATH:" + path);
        Enumeration<URL> resources = classLoader.getResources(path);
        List<File> dirs = new ArrayList<File>();
        while (resources.hasMoreElements()) {
            URL resource = resources.nextElement();
            dirs.add(new File(resource.getFile()));
        }
        List<Class> classes = new ArrayList<Class>();
        for (File directory : dirs) {
            classes.addAll(findClasses(directory, packageName));
        }

        return classes;
    }

    /**
     * Recursive method used to find all classes in a given directory and
     * subdirs.
     * 
     * @param directory
     *            The base directory
     * @param packageName
     *            The package name for classes found inside the base directory
     * @return The classes
     * @throws ClassNotFoundException
     */
    private List<Class> findClasses(File directory, String packageName)
            throws ClassNotFoundException {
        List<Class> classes = new ArrayList<Class>();
        if (!directory.exists()) {
            return classes;
        }
        File[] files = directory.listFiles();
        for (File file : files) {
            if (file.isDirectory()) {
                classes.addAll(findClasses(file,
                        packageName + "." + file.getName()));
            } else if (file.getName().endsWith(".class")) {
                classes.add(Class.forName(packageName
                        + '.'
                        + file.getName().substring(0,
                                file.getName().length() - 6)));
            }
        }
        return classes;
    }
}