Payara 457 classloader work

appserver/ejb/ejb-container/src/main/java/com/sun/ejb/containers/EjbThreadPoolExecutor.java

@@ -37,6 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
+// Portions Copyright [2015] [C2B2 Consulting Limited]
 package com.sun.ejb.containers;
 
 import com.sun.enterprise.deployment.xml.RuntimeTagNames;
@@ -100,6 +101,9 @@ protected void afterExecute(Runnable r, Throwable t) {
             }
         } catch (Exception e) {
             e.printStackTrace();
+        } finally {
+            // clear our Context Classloader
+            Thread.currentThread().setContextClassLoader(null);
         }
     }
 

appserver/ejb/ejb-container/src/main/java/org/glassfish/ejb/startup/EjbApplication.java

@@ -37,6 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
+// Portions Copyright [2015] [C2B2 Consulting Limited]
 
 package org.glassfish.ejb.startup;
 
@@ -70,6 +71,8 @@
 import org.jvnet.hk2.annotations.Service;
 import org.glassfish.hk2.api.PerLookup;
 import org.glassfish.hk2.api.ServiceLocator;
+import org.glassfish.pfl.dynamic.codegen.impl.CurrentClassLoader;
+import org.glassfish.pfl.dynamic.codegen.spi.Wrapper;
 
 /**
  * This class represents a logical collection of EJB components contained in one ejb-jar
@@ -232,6 +235,11 @@ boolean loadContainers(ApplicationContext startupContext) {
         } catch(Throwable t) {
             abortInitializationAfterException();
             throw new RuntimeException("EJB Container initialization error", t);
+        } finally {
+            // clean up the thread local current classloader after codegen to ensure it isn't 
+            // referencing the deployed application
+            CurrentClassLoader.set(this.getClass().getClassLoader());
+            Wrapper._clear();
         }
 
         return true;

appserver/jms/jms-core/src/main/java/com/sun/enterprise/connectors/jms/system/ActiveJmsResourceAdapter.java

@@ -136,6 +136,7 @@
 import org.glassfish.hk2.api.ServiceLocator;
 
 import javax.inject.Singleton;
+import org.glassfish.api.invocation.InvocationManager;
 import org.jvnet.hk2.config.types.Property;
 
 //import com.sun.messaging.jmq.util.service.PortMapperClientHandler;
@@ -336,6 +337,9 @@ private static enum ClusterMode {
 
     @Inject
     private ApplicationRegistry appRegistry;
+
+    @Inject
+    InvocationManager invManager;
 
     /**
      * Constructor for an active Jms Adapter.
@@ -539,6 +543,8 @@ public Object run() throws
                                 //set the JMSRA system property to enable XA JOINS
                                 //disabling this due to issue - 8727
                                 //System.setProperty(XA_JOIN_ALLOWED, "true");
+
+                                // to prevent classloader leaks in new threads clear invocation manager before bootstrapping JMS
                                 resourceadapter_.start(bootStrapContextImpl);
                                 return null;
                             }

appserver/orb/orb-connector/src/main/java/org/glassfish/enterprise/iiop/api/GlassFishORBHelper.java

@@ -59,7 +59,6 @@
 
 import org.glassfish.hk2.api.PostConstruct;
 
-import org.glassfish.api.event.Events;
 import org.glassfish.api.event.EventTypes;
 import org.glassfish.api.event.Events;
 import org.glassfish.api.event.EventListener;

appserver/orb/orb-iiop/src/main/java/org/glassfish/enterprise/iiop/impl/GlassFishORBManager.java

@@ -37,7 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
-
+// Portions Copyright [2015] [C2B2 Consulting Limited]
 package org.glassfish.enterprise.iiop.impl;
 
 import com.sun.corba.ee.impl.javax.rmi.CORBA.StubDelegateImpl;
@@ -261,7 +261,8 @@ synchronized ORB getORB(Properties props) {
             finestLog( "GlassFishORBManager.getORB->: {0}", orb);
 
             if (orb == null) {
-                initORB(props);
+
+                initORB(props);                
             }
 
             return orb;
@@ -553,7 +554,7 @@ private void initORB(Properties props) {
             // OSGI mode and we're not in OSGI mode, orb initialization fails.  
             boolean useOSGI = false;
 
-            final ClassLoader prevCL = Utility.getClassLoader();
+            ClassLoader prevCL = Utility.getClassLoader();
             try {
                 Utility.setContextClassLoader(GlassFishORBManager.class.getClassLoader());
 
@@ -582,8 +583,14 @@ private void initORB(Properties props) {
 
             // Can't run with GlassFishORBManager.class.getClassLoader() as the context ClassLoader
             orb = ORBFactory.create() ;
-            ORBFactory.initialize( orb, args, orbInitProperties, useOSGI);
-
+            prevCL = Utility.getClassLoader();
+            try {
+                Utility.setContextClassLoader(prevCL.getParent());
+
+                ORBFactory.initialize( orb, args, orbInitProperties, useOSGI);
+            } finally {
+                Utility.setContextClassLoader(prevCL);
+            }
             // Done to indicate this is a server and
             // needs to create listen ports.
             try {
@@ -611,8 +618,12 @@ private void initORB(Properties props) {
 
                 rfm = (ReferenceFactoryManager) orb.resolve_initial_references(
                         ORBConstants.REFERENCE_FACTORY_MANAGER);
-
+
+                // ensure we don't inherit any Context Class Loaders when bootstrapping
+                ClassLoader cl = Thread.currentThread().getContextClassLoader();
+                Thread.currentThread().setContextClassLoader(this.getClass().getClassLoader());
                 new InitialGroupInfoService( orb ) ;
+                Thread.currentThread().setContextClassLoader(cl);
 
                 iiopUtils.setORB(orb);
             }

appserver/transaction/jts/src/main/java/com/sun/jts/CosTransactions/TimeoutManager.java

@@ -59,20 +59,18 @@
 //   This software contains confidential and proprietary information of
 //   IBM Corp.
 //----------------------------------------------------------------------------
-
+//Portions Copyright [2015] [C2B2 Consulting Limited]
 package com.sun.jts.CosTransactions;
 
 import java.util.*;
 
 import org.omg.CosTransactions.*;
 import com.sun.jts.jtsxa.XID;
 
-import com.sun.jts.trace.*;
 
 import java.util.logging.Logger;
 import java.util.logging.Level;
 import com.sun.logging.LogDomains;
-import com.sun.jts.utils.LogFormatter;
 
 /**
  * This class records state for timing out transactions, and runs a thread
@@ -150,7 +148,11 @@ static synchronized void initSetTimeout() {
 	if (isSetTimeout)
 	   return;
         isSetTimeout = true;
+
+        // to prevent classloader explicitly set context classloader
+
         timeoutThread = new TimeoutThread();
+        timeoutThread.setContextClassLoader(timeoutThread.getClass().getClassLoader());
         timeoutThread.start();
     }
 

appserver/web/war-util/src/main/java/com/sun/enterprise/glassfish/web/WarHandler.java

@@ -37,6 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
+// Portions Copyright [2015] [C2B2 Consulting Limited]
 
 package com.sun.enterprise.glassfish.web;
 
@@ -80,7 +81,6 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.security.PrivilegedActionException;
-import java.security.PrivilegedExceptionAction;
 
 import static javax.xml.stream.XMLStreamConstants.*;
 
@@ -350,6 +350,7 @@ public boolean accept(File pathname) {
                     } else {
                         cloader.addJar(file.getPath().substring(baseFileLen),
                                 new JarFile(file), file);
+                        cloader.closeJARs(true);
                     }
                 } catch (Exception e) {
                     // Catch and ignore any exception in case the JAR file

appserver/web/war-util/src/main/java/org/glassfish/web/loader/WebappClassLoader.java

@@ -55,7 +55,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
+// Portions Copyright [2015] [C2B2 Consulting Limited]
 package org.glassfish.web.loader;
 
 import com.sun.appserv.BytecodePreprocessor;
@@ -2041,6 +2041,32 @@ public void closeJARs(boolean force) {
                             }
                         }
                     }
+
+                    try {
+                        // aggressively close parent jars
+
+                        WeakHashMap<Closeable, Void> closeables;
+                        Field closeField = URLClassLoader.class.getDeclaredField("closeables");
+                        closeField.setAccessible(true);
+                        closeables = (WeakHashMap<Closeable, Void>) closeField.get(this);
+                        synchronized (closeables) {
+                            Set<Closeable> keys = closeables.keySet();
+                            for (Closeable c : keys) {
+                                try {
+                                    if (c instanceof JarFile) {
+                                        c.close();
+                                    }
+                                } catch (IOException ioex) {
+                                }
+                            }
+                            closeables.clear();
+                        }
+
+                    } catch (Exception ex) {
+                        Logger.getLogger(WebappClassLoader.class.getName()).log(Level.SEVERE, null, ex);
+                    }
+
+
                 }
             }
         }

appserver/web/weld-integration/src/main/java/org/glassfish/weld/BeanDeploymentArchiveImpl.java

@@ -44,7 +44,6 @@
 import org.glassfish.api.deployment.archive.ReadableArchive;
 import org.glassfish.cdi.CDILoggerInfo;
 import org.glassfish.weld.connector.WeldUtils;
-import org.glassfish.weld.connector.WeldUtils.*;
 import org.glassfish.weld.ejb.EjbDescriptorImpl;
 import org.jboss.weld.bootstrap.WeldBootstrap;
 import org.jboss.weld.bootstrap.api.ServiceRegistry;
@@ -58,6 +57,7 @@
 import javax.enterprise.inject.spi.InjectionTarget;
 import java.io.File;
 import java.io.IOException;
+import java.lang.reflect.Field;
 import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URL;
@@ -71,7 +71,9 @@
 import java.util.List;
 import java.util.ListIterator;
 import java.util.Map;
+import java.util.Set;
 import java.util.concurrent.CopyOnWriteArrayList;
+import java.util.jar.JarFile;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -752,7 +754,27 @@ private boolean isCDIAnnotatedClass(String className) {
     protected BeansXml parseBeansXML(ReadableArchive archive, String beansXMLPath) throws IOException {
         WeldBootstrap wb = context.getTransientAppMetaData(WeldDeployer.WELD_BOOTSTRAP,
                                                            WeldBootstrap.class);
-        return wb.parse(getBeansXMLFileURL(archive, beansXMLPath));
+        URL url = getBeansXMLFileURL(archive, beansXMLPath);
+        BeansXml result =  wb.parse(url);
+                try {
+            // Ensure JarFile is closed
+            Class clazz = Class.forName("sun.net.www.protocol.jar.JarFileFactory", true, URL.class.getClassLoader());
+            Field fields[] = clazz.getDeclaredFields();
+            for (Field field : fields) {
+                if ("fileCache".equals(field.getName())) {
+                    field.setAccessible(true);
+                    HashMap<String,JarFile> files = (HashMap<String,JarFile>) field.get(null);
+                    Set<JarFile> jars = new HashSet<>();
+                    jars.addAll(files.values());
+                    for (JarFile file : jars) {
+                        file.close();
+                    }
+                } 
+            }
+        } catch (ClassNotFoundException | IllegalAccessException | SecurityException | IllegalArgumentException | IOException ex) {
+            logger.log(Level.SEVERE, null, ex);
+        }   
+        return result;
     }
 
 

nucleus/common/glassfish-api/src/main/java/org/glassfish/api/invocation/InvocationManager.java

@@ -37,6 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
+// Portions Copyright [2015] [C2B2 Consulting Llimited]
 
 package org.glassfish.api.invocation;
 
@@ -92,7 +93,14 @@ public <T extends ComponentInvocation> T getPreviousInvocation()
     public boolean isInvocationStackEmpty();
 
     public java.util.List<? extends ComponentInvocation> getAllInvocations();
-
+
+    // useful to temp clear the invocation list for example when spawning a new Thread
+    // to prevent potential classloader leaks.
+     java.util.List<? extends ComponentInvocation> popAllInvocations();
+
+    // useful to temp clear the invocation list for example when spawning a new Thread
+    // to prevent potential classloader leaks.
+    public void putAllInvocations(java.util.List<? extends ComponentInvocation> invocations);
 
     public void registerComponentInvocationHandler(ComponentInvocationType type, 
             RegisteredComponentInvocationHandler handler);

nucleus/common/glassfish-api/src/main/java/org/glassfish/api/invocation/InvocationManagerImpl.java

@@ -37,6 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
+// Portions Copyright [2015] [C2B2 Consulting Llimited]
 
 package org.glassfish.api.invocation;
 
@@ -294,13 +295,33 @@ public <T extends ComponentInvocation> T getPreviousInvocation()
         return (T) v.get(i - 2);
     }
 
+    @Override
     public List getAllInvocations() {
         return frames.get();
     }
 
+    @Override
+    public List<? extends ComponentInvocation> popAllInvocations() {
+        List<? extends ComponentInvocation> result = frames.get();
+        frames.set(null);
+        return result;
+    }
+
+    @Override
+    public void putAllInvocations(List<? extends ComponentInvocation> invocations) {
+        frames.set(new InvocationArray<>((List<ComponentInvocation>) invocations));
+    }
+
     static class InvocationArray<T extends ComponentInvocation> extends java.util.ArrayList<T> {
         private ComponentInvocationType invocationAttribute;
 
+        private InvocationArray(List<T> invocations) {
+            super(invocations);
+        }
+
+        private InvocationArray() {
+        }
+
         public void setInvocationAttribute(ComponentInvocationType attribute) {
             this.invocationAttribute = attribute;
         }

nucleus/common/internal-api/src/main/java/org/glassfish/internal/data/ApplicationInfo.java

@@ -37,6 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
+// Portions Copyright [2015] [C2B2 Consulting Limited]
 
 package org.glassfish.internal.data;
 
@@ -448,11 +449,19 @@ public void clean(ExtendedDeploymentContext context) throws Exception {
         // clean up the app level classloader
         if (appClassLoader != null) {
             try {
-                appServiceLocator.preDestroy(appClassLoader);
+                if (appServiceLocator != null) {
+                    appServiceLocator.preDestroy(appClassLoader);
+                }
             }
             catch (Exception e) {
                 // Ignore, some failure in preDestroy
             }
+            try {
+                PreDestroy.class.cast(appClassLoader).preDestroy();
+            } catch (Exception e) {
+                        // ignore, the class loader does not need to be 
+                // explicitely stopped or already stopped
+            }
             appClassLoader = null;
         }
 

nucleus/core/kernel/src/main/java/com/sun/enterprise/v3/server/ApplicationLifecycle.java

@@ -1095,7 +1095,7 @@ public void undeploy(String appName, ExtendedDeploymentContext context) {
 
         // for DAS target, the undeploy should unload the application
         // as well
-        if (DeploymentUtils.isDASTarget(params.target)) {
+        if (DeploymentUtils.isDASTarget(params.target) || DeploymentUtils.isDomainTarget(params.target)) {
             unload(info, context);
         }