Lazy loading reflections so Queue can hack the classpath before the PluginManager looks for classes.

Removed extra quotes from 'cd' pre-exec command.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4067 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -35,7 +35,9 @@ import org.reflections.util.ClasspathHelper;
 import org.reflections.util.ConfigurationBuilder;
 import org.slf4j.LoggerFactory;
 
+import java.lang.reflect.Method;
 import java.net.URL;
+import java.net.URLClassLoader;
 import java.util.Set;
 import java.util.ArrayList;
 import java.util.List;
@@ -54,11 +56,6 @@ public class PackageUtils {
         // turn off logging in the reflections library - they talk too much (to the wrong logger factory as well, logback)
         Logger logger = (ch.qos.logback.classic.Logger)LoggerFactory.getLogger(Reflections.class);
         logger.setLevel(Level.OFF);
-
-        // Initialize general-purpose source tree reflector.
-        reflections = new Reflections( new ConfigurationBuilder()
-            .setUrls(getClassPathURLs())
-            .setScanners(new SubTypesScanner()));
     }
 
     /**
@@ -76,6 +73,7 @@ public class PackageUtils {
      */
     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.
+        initReflections();
         Set<Class<? extends T>> allTypes = reflections.getSubTypesOf(iface);
         List<Class<? extends T>> concreteTypes = new ArrayList<Class<? extends T>>();
         for( Class<? extends T> type: allTypes ) {
@@ -112,6 +110,7 @@ public class PackageUtils {
      */
     public static <T> List<Class<? extends T>> getInterfacesExtendingInterface(Class<T> iface) {
         // Load all classes extending the given interface, then filter out any class that is concrete.
+        initReflections();
         Set<Class<? extends T>> allTypes = reflections.getSubTypesOf(iface);
         List<Class<? extends T>> nonConcreteTypes = new ArrayList<Class<? extends T>>();
         for( Class<? extends T> type: allTypes ) {
@@ -125,4 +124,40 @@ public class PackageUtils {
     public static Set<URL> getClassPathURLs() {
         return ClasspathHelper.getUrlsForManifestsCurrentClasspath();
     }
+
+    /**
+     * Adds the URL to the system class loader classpath using reflection.
+     * HACK: Uses reflection to modify the class path, and assumes loader is a URLClassLoader.
+     * @param url URL to add to the system class loader classpath.
+     */
+    public static void addClasspath(URL url) {
+      try {
+          Method method = URLClassLoader.class.getDeclaredMethod("addURL", URL.class);
+          if (!method.isAccessible())
+            method.setAccessible(true);
+          method.invoke(ClassLoader.getSystemClassLoader(), url);
+          resetReflections();
+      } catch (Exception e) {
+          throw new StingException("Error adding url to the current classloader.", e);
+      }
+    }
+
+    /**
+     * Create new reflections object if it does not currently exists.
+     */
+    private static void initReflections() {
+        if (reflections == null) {
+            // Initialize general-purpose source tree reflector.
+            reflections = new Reflections( new ConfigurationBuilder()
+                .setUrls(getClassPathURLs())
+                .setScanners(new SubTypesScanner()));
+        }
+    }
+
+    /**
+     * Resets the reflections object after a class has been dynamically added to the classpath.
+     */
+    private static void resetReflections() {
+        reflections = null;
+    }
 }

scala/src/org/broadinstitute/sting/queue/QScriptManager.scala

@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.queue
 
-import org.broadinstitute.sting.utils.classloader.PluginManager
 import scala.tools.nsc.{Global, Settings}
 import scala.tools.nsc.io.PlainFile
-import org.broadinstitute.sting.queue.util.{Logging, ClasspathUtils, IOUtils}
+import org.broadinstitute.sting.queue.util.{Logging, IOUtils}
 import collection.JavaConversions
 import java.io.File
 import scala.tools.nsc.reporters.AbstractReporter
 import java.lang.String
 import org.apache.log4j.Level
 import scala.tools.nsc.util.{FakePos, NoPosition, Position}
+import org.broadinstitute.sting.utils.classloader.{PackageUtils, PluginManager}
 
 /**
  * Plugin manager for QScripts which loads QScripts into the current class loader.
@@ -52,7 +52,7 @@ object QScriptManager extends Logging {
       settings.outdir.value = outdir.getPath
 
       // Set the classpath to the current class path.
-      ClasspathUtils.manifestAwareClassPath.foreach(path => settings.classpath.append(path.getPath))
+      JavaConversions.asSet(PackageUtils.getClassPathURLs).foreach(url => settings.classpath.append(url.getPath))
 
       val reporter = new Log4JReporter(settings)
 
@@ -76,7 +76,7 @@ object QScriptManager extends Logging {
         logger.info("Compilation complete")
 
       // Add the new compilation output directory to the classpath.
-      ClasspathUtils.addClasspath(outdir)
+      PackageUtils.addClasspath(outdir.toURI.toURL)
     }
   }
 

scala/src/org/broadinstitute/sting/queue/engine/DispatchJobRunner.scala

@@ -64,7 +64,7 @@ trait DispatchJobRunner extends JobRunner {
     for (dir <- function.jobDirectories)
       dirs += IOUtils.dirLevel(dir, 2)
     if (dirs.size > 0)
-      Some("\'" + dirs.mkString("cd ", " && cd ", "") + "\'")
+      Some(dirs.mkString("cd ", " && cd ", ""))
     else
       None
   }

scala/src/org/broadinstitute/sting/queue/util/ClasspathUtils.scala

@@ -1,36 +0,0 @@
-package org.broadinstitute.sting.queue.util
-
-import collection.JavaConversions._
-import org.broadinstitute.sting.utils.classloader.PackageUtils
-import java.io.File
-import javax.print.URIException
-import java.net.{URL, URLClassLoader}
-
-/**
- * Builds the correct class path by examining the manifests
- */
-object ClasspathUtils {
-
-  /**
-   * Returns a list of files that build up the classpath, taking into account jar file manifests.
-   * @return List[File] that build up the current classpath.
-   */
-  def manifestAwareClassPath = {
-    var urls = PackageUtils.getClassPathURLs
-    urls.map(url => try {new File(url.toURI)} catch {case urie: URIException => new File(url.getPath)})
-  }
-
-  /**
-   * Adds the directory to the system class loader classpath using reflection.
-   * HACK: Uses reflection to modify the class path, and assumes loader is a URLClassLoader
-   * @param path Directory to add to the system class loader classpath.
-   */
-  def addClasspath(path: File): Unit = {
-    val url = path.toURI.toURL
-    val method = classOf[URLClassLoader].getDeclaredMethod("addURL", classOf[URL]);
-    if (!method.isAccessible)
-      method.setAccessible(true);
-    method.invoke(ClassLoader.getSystemClassLoader(), url);
-  }
-}
-