//
   //  ========================================================================
   //  Copyright (c) 1995-2015 Mort Bay Consulting Pty. Ltd.
   //  ------------------------------------------------------------------------
   //  All rights reserved. This program and the accompanying materials
   //  are made available under the terms of the Eclipse Public License v1.0
   //  and Apache License v2.0 which accompanies this distribution.
   //
   //      The Eclipse Public License is available at
  //      http://www.eclipse.org/legal/epl-v10.html
  //
  //      The Apache License v2.0 is available at
  //      http://www.opensource.org/licenses/apache2.0.php
  //
  //  You may elect to redistribute this code under either of these licenses.
  //  ========================================================================
  //
  
  package org.eclipse.jetty.annotations;
  
  import java.io.IOException;
  import java.net.MalformedURLException;
  import java.net.URI;
  import java.net.URL;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.Collections;
  import java.util.Comparator;
  import java.util.HashMap;
  import java.util.HashSet;
  import java.util.Iterator;
  import java.util.List;
  import java.util.Map;
  import java.util.ServiceLoader;
  import java.util.Set;
  import java.util.concurrent.Callable;
  import java.util.concurrent.ConcurrentHashMap;
  import java.util.concurrent.CountDownLatch;
  import java.util.concurrent.Semaphore;
  import java.util.concurrent.TimeUnit;
  import java.util.regex.Pattern;
  
  import javax.servlet.ServletContainerInitializer;
  import javax.servlet.annotation.HandlesTypes;
  
  import org.eclipse.jetty.annotations.AnnotationParser.Handler;
  import org.eclipse.jetty.plus.annotation.ContainerInitializer;
  import org.eclipse.jetty.util.ConcurrentHashSet;
  import org.eclipse.jetty.util.MultiException;
  import org.eclipse.jetty.util.StringUtil;
  import org.eclipse.jetty.util.log.Log;
  import org.eclipse.jetty.util.log.Logger;
  import org.eclipse.jetty.util.resource.Resource;
  import org.eclipse.jetty.util.statistic.CounterStatistic;
  import org.eclipse.jetty.webapp.AbstractConfiguration;
  import org.eclipse.jetty.webapp.FragmentDescriptor;
  import org.eclipse.jetty.webapp.MetaDataComplete;
  import org.eclipse.jetty.webapp.WebAppContext;
  import org.eclipse.jetty.webapp.WebDescriptor;
  
  /**
   * Configuration for Annotations
   */
  public class AnnotationConfiguration extends AbstractConfiguration
  {
      private static final Logger LOG = Log.getLogger(AnnotationConfiguration.class);
      
      public static final String SERVLET_CONTAINER_INITIALIZER_EXCLUSION_PATTERN = "org.eclipse.jetty.containerInitializerExclusionPattern";
      public static final String SERVLET_CONTAINER_INITIALIZER_ORDER = "org.eclipse.jetty.containerInitializerOrder";
      public static final String CLASS_INHERITANCE_MAP  = "org.eclipse.jetty.classInheritanceMap";
      public static final String CONTAINER_INITIALIZERS = "org.eclipse.jetty.containerInitializers";
      public static final String CONTAINER_INITIALIZER_STARTER = "org.eclipse.jetty.containerInitializerStarter";
      public static final String MULTI_THREADED = "org.eclipse.jetty.annotations.multiThreaded";
      public static final String MAX_SCAN_WAIT = "org.eclipse.jetty.annotations.maxWait";
      
      public static final int DEFAULT_MAX_SCAN_WAIT = 60; /* time in sec */  
      public static final boolean DEFAULT_MULTI_THREADED = true;
      
      protected List<AbstractDiscoverableAnnotationHandler> _discoverableAnnotationHandlers = new ArrayList<AbstractDiscoverableAnnotationHandler>();
      protected ClassInheritanceHandler _classInheritanceHandler;
      protected List<ContainerInitializerAnnotationHandler> _containerInitializerAnnotationHandlers = new ArrayList<ContainerInitializerAnnotationHandler>();
     
      protected List<ParserTask> _parserTasks;
      protected WebAppClassNameResolver _webAppClassNameResolver;
      protected ContainerClassNameResolver _containerClassNameResolver;
  
      protected CounterStatistic _containerPathStats;
      protected CounterStatistic _webInfLibStats;
      protected CounterStatistic _webInfClassesStats;
      protected Pattern _sciExcludePattern;
      protected ServiceLoader<ServletContainerInitializer> _loadedInitializers = null;
      /**
       * TimeStatistic
       *
       * Simple class to capture elapsed time of an operation.
       * 
       */
      public class TimeStatistic 
      {
         public long _start = 0;
         public long _end = 0;
         
         public void start ()
         {
             _start = System.nanoTime();
         }
         
         public void end ()
         {
             _end = System.nanoTime();
         }
         
         public long getStart()
         {
             return _start;
         }
         
         public long getEnd ()
         {
             return _end;
         }
         
         public long getElapsed ()
         {
             return (_end > _start?(_end-_start):0);
         }
     }
     
     
     /**
      * ParserTask
      *
      * Task to executing scanning of a resource for annotations.
      * 
      */
     public class ParserTask implements Callable<Void>
     {
         protected Exception _exception;
         protected final AnnotationParser _parser;
         protected final Set<? extends Handler> _handlers;
         protected final ClassNameResolver _resolver;
         protected final Resource _resource;
         protected TimeStatistic _stat;
         
         public ParserTask (AnnotationParser parser, Set<? extends Handler>handlers, Resource resource, ClassNameResolver resolver)
         {
             _parser = parser;
             _handlers = handlers;
             _resolver = resolver;
             _resource = resource;
         }
         
         public void setStatistic(TimeStatistic stat)
         {
            _stat = stat; 
         }
 
         public Void call() throws Exception
         {            
             if (_stat != null)
                 _stat.start();
             if (_parser != null)
                 _parser.parse(_handlers, _resource, _resolver); 
             if (_stat != null)
                 _stat.end();
             return null;
         }
         
         public TimeStatistic getStatistic()
         {
             return _stat;
         }
         
         public Resource getResource()
         {
             return _resource;
         }
         
     }
 
     /**
      * WebAppClassNameResolver
      *
      * Checks to see if a classname belongs to hidden or visible packages when scanning,
      * and whether a classname that is a duplicate should override a previously
      * scanned classname. 
      * 
      * This is analogous to the management of classes that the WebAppClassLoader is doing,
      * however we don't want to load the classes at this point so we are doing it on
      * the name only.
      * 
      */
     public class WebAppClassNameResolver implements ClassNameResolver
     {
         private WebAppContext _context;
 
         public WebAppClassNameResolver (WebAppContext context)
         {
             _context = context;
         }
 
         public boolean isExcluded (String name)
         {
             if (_context.isSystemClass(name)) return true;
             if (_context.isServerClass(name)) return false;
             return false;
         }
 
         public boolean shouldOverride (String name)
         {
             //looking at webapp classpath, found already-parsed class 
             //of same name - did it come from system or duplicate in webapp?
             if (_context.isParentLoaderPriority())
                 return false;
             return true;
         }
     }
 
     
     /**
      * ContainerClassNameResolver
      *
      * Checks to see if a classname belongs to a hidden or visible package
      * when scanning for annotations and thus whether it should be excluded from
      * consideration or not.
      * 
      * This is analogous to the management of classes that the WebAppClassLoader is doing,
      * however we don't want to load the classes at this point so we are doing it on
      * the name only.
      * 
      */
     public class ContainerClassNameResolver implements ClassNameResolver
     { 
         private WebAppContext _context;
         
         public ContainerClassNameResolver (WebAppContext context)
         {
             _context = context;
         }
         public boolean isExcluded (String name)
         {
             if (_context.isSystemClass(name)) return false;
             if (_context.isServerClass(name)) return true;
             return false;
         }
 
         public boolean shouldOverride (String name)
         {
             //visiting the container classpath, 
             if (_context.isParentLoaderPriority())
                 return true;
             return false;
         }
     }
     
     
     /**
      * ServletContainerInitializerOrdering
      *
      * A list of classnames of ServletContainerInitializers in the order in which
      * they are to be called back. One name only in the list can be "*", which is a
      * wildcard which matches any other ServletContainerInitializer name not already
      * matched.
      */
     public class ServletContainerInitializerOrdering 
     {
         private Map<String, Integer> _indexMap = new HashMap<String, Integer>();
         private Integer _star = null;
         private String _ordering = null;
         
         public ServletContainerInitializerOrdering (String ordering)
         {
             if (ordering != null)
             {
                 _ordering = ordering;
                 
                 String[] tmp = StringUtil.csvSplit(ordering);
                 
                 for (int i=0; i<tmp.length; i++)
                 {
                     String s = tmp[i].trim();
                     _indexMap.put(s, Integer.valueOf(i));
                     if ("*".equals(s))
                     {
                         if (_star != null)
                             throw new IllegalArgumentException("Duplicate wildcards in ServletContainerInitializer ordering "+ordering);
                         _star = Integer.valueOf(i);
                     }
                     
                 }
             }
         }
         
         /**
          * @return true if "*" is one of the values.
          */
         public boolean hasWildcard()
         {
             return _star != null;
         }
         
         /**
          * @return the index of the "*" element, if it is specified. -1 otherwise.
          */
         public int getWildcardIndex()
         {
             if (!hasWildcard())
                 return -1;
             return _star.intValue();
         }
         
         /**
          * @return true if the ordering contains a single value of "*"
          */
         public boolean isDefaultOrder ()
         {
             return (getSize() == 1 && hasWildcard());
         }
         
         /**
          * Get the order index of the given classname
          * @param name the classname to look up
          * @return the index of the class name (or -1 if not found)
          */
         public int getIndexOf (String name)
         {
             Integer i = _indexMap.get(name);
             if (i == null)
                 return -1;
             return i.intValue();
         }
         
         /**
          * Get the number of elements of the ordering
          * @return the size of the index
          */
         public int getSize()
         {
             return _indexMap.size();
         }
         
         public String toString()
         {
             if (_ordering == null)
                 return "";
             return _ordering;
         }
     }
     
     
     
     /**
      * ServletContainerInitializerComparator
      *
      * Comparator impl that orders a set of ServletContainerInitializers according to the
      * list of classnames (optionally containing a "*" wildcard character) established in a
      * ServletContainerInitializerOrdering.
      * @see ServletContainerInitializerOrdering
      */
     public class ServletContainerInitializerComparator implements Comparator<ServletContainerInitializer>
     {
         private ServletContainerInitializerOrdering _ordering;
         
         
         public ServletContainerInitializerComparator (ServletContainerInitializerOrdering ordering)
         {
             _ordering = ordering;
         }
 
         @Override
         public int compare(ServletContainerInitializer sci1, ServletContainerInitializer sci2)
         {
             String c1 = (sci1 != null? sci1.getClass().getName() : null);
             String c2 = (sci2 != null? sci2.getClass().getName() : null);
 
             if (c1 == null && c2 == null)
                 return 0;
             
             int i1 = _ordering.getIndexOf(c1);
             if (i1 < 0 && _ordering.hasWildcard())
                 i1 = _ordering.getWildcardIndex();
             int i2 = _ordering.getIndexOf(c2);
             if (i2 < 0 && _ordering.hasWildcard())
                 i2 = _ordering.getWildcardIndex();
            
             return Integer.compare(i1, i2);
         }
     }
     
     @Override
     public void preConfigure(final WebAppContext context) throws Exception
     {
         _webAppClassNameResolver = new WebAppClassNameResolver(context);
         _containerClassNameResolver = new ContainerClassNameResolver(context);
         String tmp = (String)context.getAttribute(SERVLET_CONTAINER_INITIALIZER_EXCLUSION_PATTERN);
         _sciExcludePattern = (tmp==null?null:Pattern.compile(tmp));
     }
 
    
     public void addDiscoverableAnnotationHandler(AbstractDiscoverableAnnotationHandler handler)
     {
         _discoverableAnnotationHandlers.add(handler);
     }
 
     @Override
     public void deconfigure(WebAppContext context) throws Exception
     {
         context.removeAttribute(CLASS_INHERITANCE_MAP);
         context.removeAttribute(CONTAINER_INITIALIZERS);
         ServletContainerInitializersStarter starter = (ServletContainerInitializersStarter)context.getAttribute(CONTAINER_INITIALIZER_STARTER);
         if (starter != null)
         {
             context.removeBean(starter);
             context.removeAttribute(CONTAINER_INITIALIZER_STARTER);
         }
         
         if (_loadedInitializers != null)
             _loadedInitializers.reload();
     }
     
     /** 
      * @see org.eclipse.jetty.webapp.AbstractConfiguration#configure(org.eclipse.jetty.webapp.WebAppContext)
      */
     @Override
     public void configure(WebAppContext context) throws Exception
     {
        context.getObjectFactory().addDecorator(new AnnotationDecorator(context));
 
        //Even if metadata is complete, we still need to scan for ServletContainerInitializers - if there are any
       
        if (!context.getMetaData().isMetaDataComplete())
        {
            //If metadata isn't complete, if this is a servlet 3 webapp or isConfigDiscovered is true, we need to search for annotations
            if (context.getServletContext().getEffectiveMajorVersion() >= 3 || context.isConfigurationDiscovered())
            {
                _discoverableAnnotationHandlers.add(new WebServletAnnotationHandler(context));
                _discoverableAnnotationHandlers.add(new WebFilterAnnotationHandler(context));
                _discoverableAnnotationHandlers.add(new WebListenerAnnotationHandler(context));
            }
        }
 
        //Regardless of metadata, if there are any ServletContainerInitializers with @HandlesTypes, then we need to scan all the
        //classes so we can call their onStartup() methods correctly
        createServletContainerInitializerAnnotationHandlers(context, getNonExcludedInitializers(context));
 
        if (!_discoverableAnnotationHandlers.isEmpty() || _classInheritanceHandler != null || !_containerInitializerAnnotationHandlers.isEmpty())
            scanForAnnotations(context);   
        
        // Resolve container initializers
        List<ContainerInitializer> initializers = 
                    (List<ContainerInitializer>)context.getAttribute(AnnotationConfiguration.CONTAINER_INITIALIZERS);
        if (initializers != null && initializers.size()>0)
        {
            Map<String, Set<String>> map = ( Map<String, Set<String>>) context.getAttribute(AnnotationConfiguration.CLASS_INHERITANCE_MAP);
            if (map == null)
                LOG.warn ("ServletContainerInitializers: detected. Class hierarchy: empty");
            for (ContainerInitializer i : initializers)
                    i.resolveClasses(context,map);
        }
     }
 
 
     /** 
      * @see org.eclipse.jetty.webapp.AbstractConfiguration#postConfigure(org.eclipse.jetty.webapp.WebAppContext)
      */
     @Override
     public void postConfigure(WebAppContext context) throws Exception
     {
         ConcurrentHashMap<String, ConcurrentHashSet<String>> classMap = (ClassInheritanceMap)context.getAttribute(CLASS_INHERITANCE_MAP);
         List<ContainerInitializer> initializers = (List<ContainerInitializer>)context.getAttribute(CONTAINER_INITIALIZERS);
         
         context.removeAttribute(CLASS_INHERITANCE_MAP);
         if (classMap != null)
             classMap.clear();
         
         context.removeAttribute(CONTAINER_INITIALIZERS);
         if (initializers != null)
             initializers.clear();
         
         if (_discoverableAnnotationHandlers != null)
             _discoverableAnnotationHandlers.clear();
 
         _classInheritanceHandler = null;
         if (_containerInitializerAnnotationHandlers != null)
             _containerInitializerAnnotationHandlers.clear();
 
         if (_parserTasks != null)
         {
             _parserTasks.clear();
             _parserTasks = null;
         }
         
         super.postConfigure(context);
     }
     
     
     
     /**
      * Perform scanning of classes for annotations
      * 
      * @param context the context for the scan
      * @throws Exception if unable to scan
      */
     protected void scanForAnnotations (WebAppContext context)
     throws Exception
     {
         AnnotationParser parser = createAnnotationParser();
         _parserTasks = new ArrayList<ParserTask>();
 
         long start = 0; 
 
 
         if (LOG.isDebugEnabled())
             LOG.debug("Annotation scanning commencing: webxml={}, metadatacomplete={}, configurationDiscovered={}, multiThreaded={}, maxScanWait={}", 
                       context.getServletContext().getEffectiveMajorVersion(), 
                       context.getMetaData().isMetaDataComplete(),
                       context.isConfigurationDiscovered(),
                       isUseMultiThreading(context),
                       getMaxScanWait(context));
 
              
         parseContainerPath(context, parser);
         //email from Rajiv Mordani jsrs 315 7 April 2010
         //    If there is a <others/> then the ordering should be
         //          WEB-INF/classes the order of the declared elements + others.
         //    In case there is no others then it is
         //          WEB-INF/classes + order of the elements.
         parseWebInfClasses(context, parser);
         parseWebInfLib (context, parser); 
         
         start = System.nanoTime();
         
         //execute scan, either effectively synchronously (1 thread only), or asynchronously (limited by number of processors available) 
         final Semaphore task_limit = (isUseMultiThreading(context)? new Semaphore(Runtime.getRuntime().availableProcessors()):new Semaphore(1));     
         final CountDownLatch latch = new CountDownLatch(_parserTasks.size());
         final MultiException me = new MultiException();
     
         for (final ParserTask p:_parserTasks)
         {
             task_limit.acquire();
             context.getServer().getThreadPool().execute(new Runnable()
             {
                 @Override
                 public void run()
                 {
                    try
                    {
                        p.call();
                    }
                    catch (Exception e)
                    {
                        me.add(e);
                    }
                    finally
                    {
                        task_limit.release();
                        latch.countDown();
                    }
                 }         
             });
         }
        
         boolean timeout = !latch.await(getMaxScanWait(context), TimeUnit.SECONDS);
           
         if (LOG.isDebugEnabled())
         {
             for (ParserTask p:_parserTasks)
                 LOG.debug("Scanned {} in {}ms", p.getResource(), TimeUnit.MILLISECONDS.convert(p.getStatistic().getElapsed(), TimeUnit.NANOSECONDS));
 
             LOG.debug("Scanned {} container path jars, {} WEB-INF/lib jars, {} WEB-INF/classes dirs in {}ms for context {}",
                     _containerPathStats.getTotal(), _webInfLibStats.getTotal(), _webInfClassesStats.getTotal(),
                     (TimeUnit.MILLISECONDS.convert(System.nanoTime()-start, TimeUnit.NANOSECONDS)),
                     context);
         }
 
         if (timeout)
             me.add(new Exception("Timeout scanning annotations"));
         me.ifExceptionThrow();   
     }
 
     
     
     /**
      * @return a new AnnotationParser. This method can be overridden to use a different implementation of
      * the AnnotationParser. Note that this is considered internal API.
      */
     protected AnnotationParser createAnnotationParser()
     {
         return new AnnotationParser();
     }
     
     /**
      * Check if we should use multiple threads to scan for annotations or not
      * @param context the context of the multi threaded setting
      * @return true if multi threading is enabled on the context, server, or via a System property.
      * @see #MULTI_THREADED
      */
     protected boolean isUseMultiThreading(WebAppContext context)
     {
         //try context attribute to see if we should use multithreading
         Object o = context.getAttribute(MULTI_THREADED);
         if (o instanceof Boolean)
         {
             return ((Boolean)o).booleanValue();
         }
         //try server attribute to see if we should use multithreading
         o = context.getServer().getAttribute(MULTI_THREADED);
         if (o instanceof Boolean)
         {
             return ((Boolean)o).booleanValue();
         }
         //try system property to see if we should use multithreading
         return Boolean.valueOf(System.getProperty(MULTI_THREADED, Boolean.toString(DEFAULT_MULTI_THREADED)));
     }
 
    
     
     /**
      * Work out how long we should wait for the async scanning to occur.
      * 
      * @param context the context of the max scan wait setting
      * @return the max scan wait setting on the context, or server, or via a System property.
      * @see #MAX_SCAN_WAIT
      */
     protected int getMaxScanWait (WebAppContext context)
     {
         //try context attribute to get max time in sec to wait for scan completion
         Object o = context.getAttribute(MAX_SCAN_WAIT);
         if (o != null && o instanceof Number)
         {
             return ((Number)o).intValue();
         }
         //try server attribute to get max time in sec to wait for scan completion
         o = context.getServer().getAttribute(MAX_SCAN_WAIT);
         if (o != null && o instanceof Number)
         {
             return ((Number)o).intValue();
         }
         //try system property to get max time in sec to wait for scan completion
         return Integer.getInteger(MAX_SCAN_WAIT, DEFAULT_MAX_SCAN_WAIT).intValue();
     }
     
     /** 
      * @see org.eclipse.jetty.webapp.AbstractConfiguration#cloneConfigure(org.eclipse.jetty.webapp.WebAppContext, org.eclipse.jetty.webapp.WebAppContext)
      */
     @Override
     public void cloneConfigure(WebAppContext template, WebAppContext context) throws Exception
     {
         context.getObjectFactory().addDecorator(new AnnotationDecorator(context));
     }
 
     public void createServletContainerInitializerAnnotationHandlers (WebAppContext context, List<ServletContainerInitializer> scis)
     throws Exception
     {
         if (scis == null || scis.isEmpty())
             return; // nothing to do
 
         List<ContainerInitializer> initializers = new ArrayList<ContainerInitializer>();
         context.setAttribute(CONTAINER_INITIALIZERS, initializers);
 
         for (ServletContainerInitializer service : scis)
         {
             HandlesTypes annotation = service.getClass().getAnnotation(HandlesTypes.class);
             ContainerInitializer initializer = null;
             if (annotation != null)
             {    
                 //There is a HandlesTypes annotation on the on the ServletContainerInitializer
                 Class<?>[] classes = annotation.value();
                 if (classes != null)
                 {
 
                     if (LOG.isDebugEnabled()){LOG.debug("HandlesTypes {} on initializer {}",Arrays.asList(classes),service.getClass());}
                     
                     initializer = new ContainerInitializer(service, classes);
 
                     //If we haven't already done so, we need to register a handler that will
                     //process the whole class hierarchy to satisfy the ServletContainerInitializer
                     if (context.getAttribute(CLASS_INHERITANCE_MAP) == null)
                     {
                         //MultiMap<String> map = new MultiMap<>();
                         ConcurrentHashMap<String, ConcurrentHashSet<String>> map = new ClassInheritanceMap();
                         context.setAttribute(CLASS_INHERITANCE_MAP, map);
                         _classInheritanceHandler = new ClassInheritanceHandler(map);
                     }
 
                     for (Class<?> c: classes)
                     {
                         //The value of one of the HandlesTypes classes is actually an Annotation itself so
                         //register a handler for it
                         if (c.isAnnotation())
                         {
                             if (LOG.isDebugEnabled()) LOG.debug("Registering annotation handler for "+c.getName());
                            _containerInitializerAnnotationHandlers.add(new ContainerInitializerAnnotationHandler(initializer, c));
                         }
                     }
                 }
                 else
                 {
                     initializer = new ContainerInitializer(service, null);
                     if (LOG.isDebugEnabled()) LOG.debug("No classes in HandlesTypes on initializer "+service.getClass());
                 }
             }
             else
             {
                 initializer = new ContainerInitializer(service, null);
                 if (LOG.isDebugEnabled()) LOG.debug("No HandlesTypes annotation on initializer "+service.getClass());
             }
             
             initializers.add(initializer);
         }
         
         
         //add a bean to the context which will call the servletcontainerinitializers when appropriate
         ServletContainerInitializersStarter starter = (ServletContainerInitializersStarter)context.getAttribute(CONTAINER_INITIALIZER_STARTER);
         if (starter != null)
             throw new IllegalStateException("ServletContainerInitializersStarter already exists");
         starter = new ServletContainerInitializersStarter(context);
         context.setAttribute(CONTAINER_INITIALIZER_STARTER, starter);
         context.addBean(starter, true);
     }
 
     public Resource getJarFor (ServletContainerInitializer service) 
     throws MalformedURLException, IOException
     {
         //try the thread context classloader to get the jar that loaded the class
         URL jarURL = Thread.currentThread().getContextClassLoader().getResource(service.getClass().getName().replace('.','/')+".class");
         
         //if for some reason that failed (eg we're in osgi and the TCCL does not know about the service) try the classloader that
         //loaded the class
         if (jarURL == null)
             jarURL = service.getClass().getClassLoader().getResource(service.getClass().getName().replace('.','/')+".class");
   
         String loadingJarName = jarURL.toString();
 
         int i = loadingJarName.indexOf(".jar");
         if (i < 0)
             return null; //not from a jar
         
         loadingJarName = loadingJarName.substring(0,i+4);
         loadingJarName = (loadingJarName.startsWith("jar:")?loadingJarName.substring(4):loadingJarName);
         return Resource.newResource(loadingJarName, false);
     }
     
     /**
      * Check to see if the ServletContainerIntializer loaded via the ServiceLoader came
      * from a jar that is excluded by the fragment ordering. See ServletSpec 3.0 p.85.
      * 
      * @param context the context for the jars
      * @param sci the servlet container initializer
      * @param sciResource  the resource for the servlet container initializer
      * @return true if excluded
      * @throws Exception if unable to determine exclusion
      */
     public boolean isFromExcludedJar (WebAppContext context, ServletContainerInitializer sci, Resource sciResource)
     throws Exception
     {
         if (sci == null)
             throw new IllegalArgumentException("ServletContainerInitializer null");
         if (context == null)
             throw new IllegalArgumentException("WebAppContext null");
         
         if (LOG.isDebugEnabled()) LOG.debug("Checking {} for jar exclusion", sci);
         
         //A ServletContainerInitializer that came from the container's classpath cannot be excluded by an ordering
         //of WEB-INF/lib jars
         if (isFromContainerClassPath(context, sci))
             return false;
         
         //If no ordering, nothing is excluded
         if (context.getMetaData().getOrdering() == null)
             return false;
         
         
         List<Resource> orderedJars = context.getMetaData().getOrderedWebInfJars();
 
         //there is an ordering, but there are no jars resulting from the ordering, everything excluded
         if (orderedJars.isEmpty())
             return true;
 
         if (sciResource == null)
             return false; //not from a jar therefore not from WEB-INF so not excludable
         
         URI loadingJarURI = sciResource.getURI();
         boolean found = false;
         Iterator<Resource> itor = orderedJars.iterator();
         while (!found && itor.hasNext())
         {
             Resource r = itor.next();
             found = r.getURI().equals(loadingJarURI);
         }
 
         return !found;
     }
 
 
     /**
      * Test if the ServletContainerIntializer is excluded by the 
      * o.e.j.containerInitializerExclusionPattern
      * 
      * @param sci the ServletContainerIntializer
      * @return true if the ServletContainerIntializer is excluded
      */
     public boolean matchesExclusionPattern(ServletContainerInitializer sci)
     {
         //no exclusion pattern, no SCI is excluded by it
         if (_sciExcludePattern == null)
             return false;
         
         //test if name of class matches the regex
         if (LOG.isDebugEnabled()) LOG.debug("Checking {} against containerInitializerExclusionPattern",sci.getClass().getName());
         return _sciExcludePattern.matcher(sci.getClass().getName()).matches();
     }
     
     
     /**
      * Test if the ServletContainerInitializer is from the container classpath
      * 
      * @param context the context for the webapp classpath
      * @param sci the ServletContainerIntializer
      * @return true if ServletContainerIntializer is from container classpath
      */
     public boolean isFromContainerClassPath (WebAppContext context, ServletContainerInitializer sci)
     {
         if (sci == null)
             return false;
         return sci.getClass().getClassLoader()==context.getClassLoader().getParent();
     }
 
     /**
      * Get SCIs that are not excluded from consideration
      * @param context the web app context 
      * @return the list of non-excluded servlet container initializers
      * @throws Exception if unable to get list 
      */
     public List<ServletContainerInitializer> getNonExcludedInitializers (WebAppContext context)
     throws Exception
     {
         ArrayList<ServletContainerInitializer> nonExcludedInitializers = new ArrayList<ServletContainerInitializer>();
       
         //We use the ServiceLoader mechanism to find the ServletContainerInitializer classes to inspect
         long start = 0;
 
         ClassLoader old = Thread.currentThread().getContextClassLoader();
        
         try
         {        
             if (LOG.isDebugEnabled())
                 start = System.nanoTime();
             Thread.currentThread().setContextClassLoader(context.getClassLoader());
             _loadedInitializers = ServiceLoader.load(ServletContainerInitializer.class);
         }
         finally
         {
             Thread.currentThread().setContextClassLoader(old);
         }
         
         if (LOG.isDebugEnabled())
             LOG.debug("Service loaders found in {}ms", (TimeUnit.MILLISECONDS.convert((System.nanoTime()-start), TimeUnit.NANOSECONDS)));
      
         
         Map<ServletContainerInitializer,Resource> sciResourceMap = new HashMap<ServletContainerInitializer,Resource>();
         ServletContainerInitializerOrdering initializerOrdering = getInitializerOrdering(context);
 
         //Get initial set of SCIs that aren't from excluded jars or excluded by the containerExclusionPattern, or excluded
         //because containerInitializerOrdering omits it
         for (ServletContainerInitializer sci:_loadedInitializers)
         { 
             
             if (matchesExclusionPattern(sci)) 
             {
                 if (LOG.isDebugEnabled()) LOG.debug("{} excluded by pattern", sci);
                 continue;
             }
 
             Resource sciResource = getJarFor(sci);
             if (isFromExcludedJar(context, sci, sciResource)) 
             { 
                 if (LOG.isDebugEnabled()) LOG.debug("{} is from excluded jar", sci);
                 continue;
             }
             
             //check containerInitializerOrdering doesn't exclude it
             String name = sci.getClass().getName();
             if (initializerOrdering != null
                 && (!initializerOrdering.hasWildcard() && initializerOrdering.getIndexOf(name) < 0))
             {
                 if (LOG.isDebugEnabled()) LOG.debug("{} is excluded by ordering", sci);
                 continue;
             }
             
             sciResourceMap.put(sci, sciResource);
         }
 
         //Order the SCIs that are included
         if (initializerOrdering != null && !initializerOrdering.isDefaultOrder())
         {
             if (LOG.isDebugEnabled())
                 LOG.debug("Ordering ServletContainerInitializers with "+initializerOrdering);
 
             //There is an ordering that is not just "*".
             //Arrange ServletContainerInitializers according to the ordering of classnames given, irrespective of coming from container or webapp classpaths
             nonExcludedInitializers.addAll(sciResourceMap.keySet());
             Collections.sort(nonExcludedInitializers, new ServletContainerInitializerComparator(initializerOrdering));
         }
         else
         {
             //No jetty-specific ordering specified, or just the wildcard value "*" specified.
             //Fallback to ordering the ServletContainerInitializers according to:
             //container classpath first, WEB-INF/classes then WEB-INF/lib (obeying any web.xml jar ordering)
              
             //no web.xml ordering defined, add SCIs in any order
             if (context.getMetaData().getOrdering() == null)
             {
                 if (LOG.isDebugEnabled())  LOG.debug("No web.xml ordering, ServletContainerInitializers in random order");
                 nonExcludedInitializers.addAll(sciResourceMap.keySet());
             }
             else
             {
                 if (LOG.isDebugEnabled())  LOG.debug("Ordering ServletContainerInitializers with ordering {}",context.getMetaData().getOrdering());
                 for (Map.Entry<ServletContainerInitializer, Resource> entry:sciResourceMap.entrySet())
                 {
                     //add in SCIs from the container classpath
                     if (entry.getKey().getClass().getClassLoader()==context.getClassLoader().getParent())
                         nonExcludedInitializers.add(entry.getKey());
                     else if (entry.getValue() == null) //add in SCIs not in a jar, as they must be from WEB-INF/classes and can't be ordered
                         nonExcludedInitializers.add(entry.getKey());
                 }
               
                 //add SCIs according to the ordering of its containing jar
                 for (Resource webInfJar:context.getMetaData().getOrderedWebInfJars())
                 {
                     for (Map.Entry<ServletContainerInitializer, Resource> entry:sciResourceMap.entrySet())
                     {
                       if (webInfJar.equals(entry.getValue()))
                             nonExcludedInitializers.add(entry.getKey());
                     }
                 }
             }
         }   
 
         if (LOG.isDebugEnabled()) 
         {
             int i=0;
             for (ServletContainerInitializer sci:nonExcludedInitializers)
                 LOG.debug("ServletContainerInitializer: {} {} from {}",(++i), sci.getClass().getName(), sciResourceMap.get(sci));
         }    
         
         return nonExcludedInitializers;
     }
 
 
     /**
      * Jetty-specific extension that allows an ordering to be applied across ALL ServletContainerInitializers.
      * 
      * @param context the context for the initializer ordering configuration 
      * @return the ordering of the ServletContainerIntializer's
      */
     public ServletContainerInitializerOrdering getInitializerOrdering (WebAppContext context)
     {
         if (context == null)
             return null;
         
         String tmp = (String)context.getAttribute(SERVLET_CONTAINER_INITIALIZER_ORDER);
         if (tmp == null || "".equals(tmp.trim()))
             return null;
         
         return new ServletContainerInitializerOrdering(tmp);
     }
 
 
     /**
      * Scan jars on container path.
      * 
      * @param context the context for the scan
      * @param parser the parser to scan with
      * @throws Exception if unable to scan
      */
     public void parseContainerPath (final WebAppContext context, final AnnotationParser parser) throws Exception
     {
         //always parse for discoverable annotations as well as class hierarchy and servletcontainerinitializer related annotations
         final Set<Handler> handlers = new HashSet<Handler>();
         handlers.addAll(_discoverableAnnotationHandlers);
         handlers.addAll(_containerInitializerAnnotationHandlers);
         if (_classInheritanceHandler != null)
             handlers.add(_classInheritanceHandler);
 
         _containerPathStats = new CounterStatistic();
 
         for (Resource r : context.getMetaData().getContainerResources())
         {
             //queue it up for scanning if using multithreaded mode
             if (_parserTasks != null)
             {
                 ParserTask task = new ParserTask(parser, handlers, r, _containerClassNameResolver);
                 _parserTasks.add(task);  
                 _containerPathStats.increment();
                 if (LOG.isDebugEnabled())
                     task.setStatistic(new TimeStatistic());
             }
         } 
     }
 
 
     /**
      * Scan jars in WEB-INF/lib
      * 
      * @param context the context for the scan
      * @param parser the annotation parser to use
      * @throws Exception if unable to scan and/or parse
      */
     public void parseWebInfLib (final WebAppContext context, final AnnotationParser parser) throws Exception
     {   
         List<FragmentDescriptor> frags = context.getMetaData().getFragments();
 
         //email from Rajiv Mordani jsrs 315 7 April 2010
         //jars that do not have a web-fragment.xml are still considered fragments
         //they have to participate in the ordering
         ArrayList<URI> webInfUris = new ArrayList<URI>();
 
         List<Resource> jars = null;
         
         if (context.getMetaData().getOrdering() != null)
             jars = context.getMetaData().getOrderedWebInfJars();
         else
             //No ordering just use the jars in any order
             jars = context.getMetaData().getWebInfJars();
 
         _webInfLibStats = new CounterStatistic();
 
         for (Resource r : jars)
         {
             //for each jar, we decide which set of annotations we need to parse for
             final Set<Handler> handlers = new HashSet<Handler>();
 
             FragmentDescriptor f = getFragmentFromJar(r, frags);
 
             //if its from a fragment jar that is metadata complete, we should skip scanning for @webservlet etc
             // but yet we still need to do the scanning for the classes on behalf of  the servletcontainerinitializers
             //if a jar has no web-fragment.xml we scan it (because it is not excluded by the ordering)
             //or if it has a fragment we scan it if it is not metadata complete
             if (f == null || !isMetaDataComplete(f) || _classInheritanceHandler != null ||  !_containerInitializerAnnotationHandlers.isEmpty())
             {
                 //register the classinheritance handler if there is one
                 if (_classInheritanceHandler != null)
                     handlers.add(_classInheritanceHandler);
 
                 //register the handlers for the @HandlesTypes values that are themselves annotations if there are any
                 handlers.addAll(_containerInitializerAnnotationHandlers);
 
                 //only register the discoverable annotation handlers if this fragment is not metadata complete, or has no fragment descriptor
                 if (f == null || !isMetaDataComplete(f))
                     handlers.addAll(_discoverableAnnotationHandlers);
 
                 if (_parserTasks != null)
                 {
                     ParserTask task = new ParserTask(parser, handlers,r, _webAppClassNameResolver);
                     _parserTasks.add (task);
                     _webInfLibStats.increment();
                     if (LOG.isDebugEnabled())
                         task.setStatistic(new TimeStatistic());
                 }
             }
         }
     }
 
 
     /**
      * Scan classes in WEB-INF/classes
      * 
      * @param context the context for the scan
      * @param parser the annotation parser to use
      * @throws Exception if unable to scan and/or parse
      */
     public void parseWebInfClasses (final WebAppContext context, final AnnotationParser parser)
     throws Exception
     {
         Set<Handler> handlers = new HashSet<Handler>();
         handlers.addAll(_discoverableAnnotationHandlers);
         if (_classInheritanceHandler != null)
             handlers.add(_classInheritanceHandler);
         handlers.addAll(_containerInitializerAnnotationHandlers);
 
         _webInfClassesStats = new CounterStatistic();
 
         for (Resource dir : context.getMetaData().getWebInfClassesDirs())
         {
             if (_parserTasks != null)
             {
                 ParserTask task = new ParserTask(parser, handlers, dir, _webAppClassNameResolver);
                 _parserTasks.add(task);
                 _webInfClassesStats.increment();
                 if (LOG.isDebugEnabled())
                     task.setStatistic(new TimeStatistic());
             }
         }
     }
 
 
 
     /**
      * Get the web-fragment.xml from a jar
      * 
      * @param jar the jar to look in for a fragment
      * @param frags the fragments previously found
      * @return true if the fragment if found, or null of not found
      * @throws Exception if unable to determine the the fragment contains
      */
     public FragmentDescriptor getFragmentFromJar (Resource jar,  List<FragmentDescriptor> frags)
     throws Exception
     {
         //check if the jar has a web-fragment.xml
         FragmentDescriptor d = null;
         for (FragmentDescriptor frag: frags)
         {
             Resource fragResource = frag.getResource(); //eg jar:file:///a/b/c/foo.jar!/META-INF/web-fragment.xml
             if (Resource.isContainedIn(fragResource,jar))
             {
                 d = frag;
                 break;
             }
         }
         return d;
     }
 
     public boolean isMetaDataComplete (WebDescriptor d)
     {
         return (d!=null && d.getMetaDataComplete() == MetaDataComplete.True);
     }
 
     public static class ClassInheritanceMap extends ConcurrentHashMap<String, ConcurrentHashSet<String>>
     {
         
         @Override
         public String toString()
         {
             return String.format("ClassInheritanceMap@%x{size=%d}",hashCode(),size());
         }
     }
 }