New PackageUtils interferes with the packaging utility. Revert until Aaron and

I can get together to make this work.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1957 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/PackageUtils.java

@@ -3,30 +3,16 @@ package org.broadinstitute.sting.utils;
 import org.reflections.Reflections;
 import org.reflections.scanners.SubTypesScanner;
 import org.reflections.util.AbstractConfiguration;
-import org.apache.log4j.Logger;
+import org.reflections.util.ClasspathHelper;
 
 import java.util.Set;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Collection;
-import java.util.jar.Attributes;
-import java.util.jar.JarFile;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.io.File;
-import java.io.IOException;
-
-import com.google.common.collect.Lists;
 
 /**
  * PackageUtils contains some useful methods for package introspection.
  */
 public class PackageUtils {
-    /**
-     * our log, which we want to capture anything from this class
-     */
-    private static Logger logger = Logger.getLogger(PackageUtils.class);
-
     /**
      * A reference into our introspection utility.
      */
@@ -34,9 +20,9 @@ public class PackageUtils {
 
     static {
         // Initialize general-purpose source tree reflector.
-        reflections = new Reflections(new AbstractConfiguration() {
+        reflections = new Reflections( new AbstractConfiguration() {
             {
-                setUrls(PackageUtils.getUrlsForClasspath(System.getProperty("java.class.path")));
+                setUrls(ClasspathHelper.getUrlsForCurrentClasspath());
                 setScanners(new SubTypesScanner());
             }
         });
@@ -45,116 +31,25 @@ public class PackageUtils {
     /**
      * Private constructor.  No instantiating this class!
      */
-    private PackageUtils() {
+    private PackageUtils() {}
-    }
-
     {
     }
 
     /**
      * Return the classes that implement the specified interface.
      *
-     * @param iface the interface which returned classes should implement.
+     * @param iface  the interface which returned classes should implement.
-     * @return the list of classes that implement the interface.
+     * @return       the list of classes that implement the interface.
      */
     public static <T> List<Class<? extends T>> getClassesImplementingInterface(Class<T> iface) {
         // Load all classes implementing the given interface, then filter out any class that isn't concrete.
         Set<Class<? extends T>> allTypes = reflections.getSubTypesOf(iface);
         List<Class<? extends T>> concreteTypes = new ArrayList<Class<? extends T>>();
-        for (Class<? extends T> type : allTypes) {
+        for( Class<? extends T> type: allTypes ) {
-            if (JVMUtils.isConcrete(type))
+            if( JVMUtils.isConcrete(type) )
                 concreteTypes.add(type);
         }
 
         return concreteTypes;
     }
-
-    /**
-     * get a list of URL's, given the current classpath.  This function is a fix for the
-     * reflections package, which doesn't correctly expand the classpath from a jar (it doesn't
-     * get the manifest and parse out the embedded classpth).
-     * @param classpath the current classpath
-     * @return
-     */
-    public static Collection<URL> getUrlsForClasspath(String classpath) {
-        // if the classpath is null, we can't really do anything
-        if (classpath == null || classpath.equals(""))
-            throw new StingException("Classpath cannot be empty or null");
-        List<URL> urls = Lists.newArrayList();
-
-        // the current working directory
-        String baseDir = System.getProperty("user.dir");
-
-        // our collection of classpath's to expand
-        List<JarPath> javaClassPath = new ArrayList<JarPath>();
-
-        // the current classpath can be a list of path's seperated by a semicolon
-        String[] classPaths = classpath.split(File.pathSeparator);
-        for (String part : classPaths) {
-            extractJarClasspath(baseDir, javaClassPath, part);
-        }
-
-        // check to make sure each extracted path exists, if so add it to our list
-        if (javaClassPath.size() > 0)
-            for (JarPath path : javaClassPath) {
-                try {
-                    if (path.isValid())
-                        urls.add(path.toValidFile().toURL());
-                } catch (MalformedURLException e) {
-                    throw new StingException("could not create url from " + path, e);
-                }
-            }
-
-        return urls;
-    }
-
-    /**
-     * extract the classpath from a jar
-     *
-     * @param baseDir       the base
-     * @param javaClassPath the list of jar paths
-     * @param part          the current the subsection of the classpath we're processing
-     */
-    private static void extractJarClasspath(String baseDir, List<JarPath> javaClassPath, String part) {
-        try {
-            JarFile myJar = new JarFile(part);
-            Attributes.Name classPath = new Attributes.Name("Class-Path");
-            if (myJar.getManifest().getMainAttributes().containsKey(classPath)) {
-                for (String jar : myJar.getManifest().getMainAttributes().getValue(classPath).split(" "))
-                    javaClassPath.add(new JarPath(baseDir, new File(part).getParent(), jar));
-            }
-        } catch (IOException e) {
-            logger.warn("could not retreive manifest from " + part);
-        }
-    }
-
-    /**
-     * a simple helper class, to determine the absolute path to a jar file
-     */
-    static class JarPath {
-        private final String mPath;
-        private final String mFilename;
-        private final String mWorkingDir;
-
-        public JarPath(String workingDir, String path, String filename) {
-            this.mPath = path;
-            this.mFilename = filename;
-            mWorkingDir = workingDir;
-        }
-
-        public File toValidFile() {
-            if (new File(mFilename).exists())
-                return new File(mFilename);
-            if (new File(mPath + File.separator + mFilename).exists())
-                return new File(mPath + File.separator + mFilename);
-            if (new File(mWorkingDir + File.separator + mFilename).exists())
-                return new File(mWorkingDir + File.separator + mFilename);
-            return null;
-        }
-
-        public boolean isValid() {
-            return (toValidFile() != null) ? true : false;
-        }
-    }
-
 }