bugfix: fix EAR deployment failure when multiple WARs use multible CDI-enabled library JARs

    - correctly copy BDA sets for each war in EAR
    - Make WAR's CDI beans available in EAR-libs
    - read web-fragment.xml from EAR-libs
    - processing ear-lib manifest
    - de-duplicate BDAs in CDI processing by using LinkedHashSet intead of ArrayList
    - made some structures final (cleanup)
    - fixed ear and concurrent classloader leaks, including refactored reflection caching

Author: lprimak

appserver/concurrent/concurrent-impl/src/main/java/org/glassfish/concurrent/runtime/ContextSetupProviderImpl.java

@@ -37,7 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
-// Portions Copyright [2016-2023] [Payara Foundation and/or its affiliates]
+// Portions Copyright [2016-2024] [Payara Foundation and/or its affiliates]
 
 package org.glassfish.concurrent.runtime;
 
@@ -378,9 +378,7 @@ public void reset(ContextHandle contextHandle) {
             restorer.endContext();
         }
 
-        if (handle.getContextClassLoader() != null) {
-            Utility.setContextClassLoader(handle.getContextClassLoader());
-        }
+        Utility.setContextClassLoader(handle.getContextClassLoader());
         if (handle.getSecurityContext() != null) {
             SecurityContext.setCurrent(handle.getSecurityContext());
         }

appserver/deployment/javaee-full/src/main/java/org/glassfish/javaee/full/deployment/EarDeployer.java

@@ -37,6 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
+// Portions Copyright [2024] [Payara Foundation and/or its affiliates]
 
 package org.glassfish.javaee.full.deployment;
 
@@ -101,7 +102,7 @@
 @Service
 @PerLookup
 public class EarDeployer implements Deployer {
-
+    public static final String PER_BDA_METADATA_KEY = "[PerBDA]";
     //    private static final Class GLASSFISH_APPCLIENT_GROUP_FACADE_CLASS =
 //            org.glassfish.appclient.client.AppClientGroupFacade.class;
 // Currently using a string instead of a Class constant to avoid a circular
@@ -457,15 +458,21 @@ public <U extends OpsParams> U getCommandParameters(Class<U> commandParametersTy
         @Override
         public void addTransientAppMetaData(String metaDataKey,
                                             Object metaData) {
-            context.addTransientAppMetaData(metaDataKey,
-                metaData);
+            if (metaDataKey.startsWith(PER_BDA_METADATA_KEY)) {
+                super.addTransientAppMetaData(metaDataKey, metaData);
+            } else {
+                context.addTransientAppMetaData(metaDataKey, metaData);
+            }
         }
 
         @Override
         public <T> T getTransientAppMetaData(String metaDataKey,
                                              Class<T> metadataType) {
-            return context.getTransientAppMetaData(metaDataKey,
-                metadataType);
+            if (metaDataKey.startsWith(PER_BDA_METADATA_KEY)) {
+                return super.getTransientAppMetaData(metaDataKey, metadataType);
+            } else {
+                return context.getTransientAppMetaData(metaDataKey, metadataType);
+            }
         }
 
         @Override

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

@@ -42,60 +42,49 @@
 
 import java.lang.reflect.Field;
 import java.lang.reflect.Method;
-import java.util.Map;
-import java.util.concurrent.ConcurrentHashMap;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 
+/**
+ * @deprecated This class is not used and will be removed in a future release.
+ * Functionality has been moved to {@link com.sun.enterprise.loader.CachingReflectionUtil}.
+ */
+@Deprecated(forRemoval = true)
 public class CachingReflectionUtil {
-    private static final Logger logger = LogFacade.getLogger();
-    private static final Map<String, Class<?>> classCache = new ConcurrentHashMap<>();
-    private static final Map<String, Method> methodCache = new ConcurrentHashMap<>();
-    private static final Map<String, Field> fieldCache = new ConcurrentHashMap<>();
-
+    /**
+     * @deprecated This method is not used and will be removed in a future release.
+     * Functionality has been moved to {@link com.sun.enterprise.loader.CachingReflectionUtil}.
+     * @param className
+     * @param classLoader
+     * @return
+     */
+    @Deprecated(forRemoval = true)
     public static Class<?> getClassFromCache(String className, ClassLoader classLoader) {
-        var cls = classCache.computeIfAbsent(className, k -> {
-            try {
-                return classLoader.loadClass(className);
-            } catch (ClassNotFoundException e) {
-                logger.log(Level.FINE, "Class not found: " + className, e);
-                return null;
-            }
-        });
-        return cls;
+        return com.sun.enterprise.loader.CachingReflectionUtil.getClassFromCache(className, classLoader);
     }
 
+    /**
+     * @deprecated This method is not used and will be removed in a future release.
+     * Functionality has been moved to {@link com.sun.enterprise.loader.CachingReflectionUtil}.
+     * @param cls
+     * @param methodName
+     * @param isPrivate
+     * @param parameterTypes
+     * @return
+     */
+    @Deprecated(forRemoval = true)
     public static Method getMethodFromCache(Class<?> cls, String methodName, boolean isPrivate, Class<?>... parameterTypes) {
-        return methodCache.computeIfAbsent(methodName, k -> {
-            try {
-                if (isPrivate) {
-                    Method method = cls.getDeclaredMethod(methodName, parameterTypes);
-                    method.setAccessible(true);
-                    return method;
-                } else {
-                    return cls.getMethod(methodName, parameterTypes);
-                }
-            } catch (NoSuchMethodException e) {
-                logger.log(Level.FINE, "Method not found: " + methodName, e);
-                return null;
-            }
-        });
+        return com.sun.enterprise.loader.CachingReflectionUtil.getMethodFromCache(cls, methodName, isPrivate, parameterTypes);
     }
 
+    /**
+     * @deprecated This method is not used and will be removed in a future release.
+     * Functionality has been moved to {@link com.sun.enterprise.loader.CachingReflectionUtil}.
+     * @param cls
+     * @param fieldName
+     * @param isPrivate
+     * @return
+     */
+    @Deprecated(forRemoval = true)
     public static Field getFieldFromCache(Class<?> cls, String fieldName, boolean isPrivate) {
-        return fieldCache.computeIfAbsent(fieldName, k -> {
-            try {
-                if (isPrivate) {
-                    Field field = cls.getDeclaredField(fieldName);
-                    field.setAccessible(true);
-                    return field;
-                } else {
-                    return cls.getField(fieldName);
-                }
-            } catch (NoSuchFieldException e) {
-                logger.log(Level.FINE, "Field not found: " + fieldName, e);
-                return null;
-            }
-        });
+        return com.sun.enterprise.loader.CachingReflectionUtil.getFieldFromCache(cls, fieldName, isPrivate);
     }
 }

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

@@ -65,6 +65,7 @@
 import com.sun.enterprise.deployment.Application;
 import com.sun.enterprise.deployment.util.DOLUtils;
 import com.sun.enterprise.glassfish.bootstrap.MainHelper.HotSwapHelper;
+import com.sun.enterprise.loader.CacheCleaner;
 import com.sun.enterprise.security.integration.DDPermissionsLoader;
 import com.sun.enterprise.security.integration.PermsHolder;
 import com.sun.enterprise.util.io.FileUtils;
@@ -2051,7 +2052,7 @@ public void stop() throws Exception {
         // START SJSAS 6258619
         ClassLoaderUtil.releaseLoader(this);
         // END SJSAS 6258619
-        clearJaxRSCache();
+        CacheCleaner.clearCaches(this);
 
         synchronized(jarFilesLock) {
             started = false;
@@ -2658,23 +2659,6 @@ private void clearReferencesRmiTargets() {
         }
     }
 
-    private void clearJaxRSCache() {
-        try {
-            Class<?> cdiComponentProvider = CachingReflectionUtil
-                    .getClassFromCache("org.glassfish.jersey.ext.cdi1x.internal.CdiComponentProvider", this);
-            if (cdiComponentProvider != null) {
-                Field runtimeSpecificsField = CachingReflectionUtil.getFieldFromCache(cdiComponentProvider,
-                        "runtimeSpecifics", true);
-                Object runtimeSpecifics = runtimeSpecificsField.get(null);
-                CachingReflectionUtil.getMethodFromCache(runtimeSpecifics.getClass(),
-                                "clearJaxRsResource", true, ClassLoader.class)
-                        .invoke(runtimeSpecifics, this);
-            }
-        } catch (Exception e) {
-            logger.log(Level.WARNING, "Error clearing Jax-Rs cache", e);
-        }
-    }
-
     /**
      * Clear the {@link ResourceBundle} cache of any bundles loaded by this
      * class loader or any class loader where this loader is a parent class

appserver/web/web-glue/src/main/java/org/glassfish/web/deployment/archivist/WebArchivist.java

@@ -37,11 +37,12 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
-// Portions Copyright [2014-2021] [Payara Foundation and/or its affiliates]
+// Portions Copyright [2014-2024] [Payara Foundation and/or its affiliates]
 
 package org.glassfish.web.deployment.archivist;
 
 import com.sun.enterprise.deployment.Application;
+import com.sun.enterprise.deployment.EarType;
 import org.glassfish.deployment.common.RootDeploymentDescriptor;
 import com.sun.enterprise.deployment.EjbBundleDescriptor;
 import com.sun.enterprise.deployment.EjbDescriptor;
@@ -75,9 +76,10 @@
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.HashMap;
+import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Vector;
+import java.util.Set;
 import java.net.URL;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -296,24 +298,33 @@ protected String getArchiveExtension() {
     /**
      * @return a list of libraries included in the archivist
      */
-    public Vector<String> getLibraries(Archive archive) {
+    public Set<String> getLibraries(ReadableArchive archive) throws IOException {
+        Set<String> libraries = new LinkedHashSet<>();
+        // WAR libraries
+        extractLibraries(archive, true, libraries);
+        ReadableArchive parentArchive = archive.getParentArchive();
+        if (parentArchive != null && parentArchive.getExtraData(ArchiveType.class).toString().equals(EarType.ARCHIVE_TYPE)) {
+            // EAR shared libraries
+            extractLibraries(parentArchive.getSubArchive("lib"), false, libraries);
+        }
+        return libraries;
+    }
 
-        Enumeration<String> entries = archive.entries();
+    private static void extractLibraries(Archive archive, boolean hasWebInfPrefix, Set<String> libs) {
+        Enumeration<String> entries = archive != null ? archive.entries() : null;
         if (entries==null)
-            return null;
+            return;
 
-        Vector<String> libs = new Vector<String>();
         while (entries.hasMoreElements()) {
 
             String entryName = entries.nextElement();
-            if (!entryName.startsWith("WEB-INF/lib")) {
-                continue; // not in WEB-INF...
+            if (hasWebInfPrefix && !entryName.startsWith("WEB-INF/lib")) {
+                continue; // not in prefix (i.e. WEB-INF)...
             }
             if (entryName.endsWith(".jar")) {
                 libs.add(entryName);
             }
         }
-        return libs;
     }
 
     @Override
@@ -381,54 +392,50 @@ private List<WebFragmentDescriptor> readStandardFragments(WebBundleDescriptorImp
             ReadableArchive archive) throws IOException {
 
         List<WebFragmentDescriptor> wfList = new ArrayList<WebFragmentDescriptor>();
-        Vector libs = getLibraries(archive);
-        if (libs != null && libs.size() > 0) {
-
-            for (int i = 0; i < libs.size(); i++) {
-                String lib = (String)libs.get(i);
-                Archivist wfArchivist = new WebFragmentArchivist(this, habitat);
-                wfArchivist.setRuntimeXMLValidation(this.getRuntimeXMLValidation());
-                wfArchivist.setRuntimeXMLValidationLevel(
-                        this.getRuntimeXMLValidationLevel());
-                wfArchivist.setAnnotationProcessingRequested(false);
-
-                WebFragmentDescriptor wfDesc = null;
-                ReadableArchive embeddedArchive = archive.getSubArchive(lib);
-                try {
-                    if (embeddedArchive != null &&
-                            wfArchivist.hasStandardDeploymentDescriptor(embeddedArchive)) {
-                        try {
-                            wfDesc = (WebFragmentDescriptor)wfArchivist.open(embeddedArchive);
-                        } catch(SAXParseException ex) {
-                            IOException ioex = new IOException();
-                            ioex.initCause(ex);
-                            throw ioex;
-                        }
-                    } else {   
-                        wfDesc = new WebFragmentDescriptor();
-                        wfDesc.setExists(false);
-                    }
-                } finally {
-                    if (embeddedArchive != null) {
-                        embeddedArchive.close();
+        for (String lib : getLibraries(archive)) {
+            Archivist wfArchivist = new WebFragmentArchivist(this, habitat);
+            wfArchivist.setRuntimeXMLValidation(this.getRuntimeXMLValidation());
+            wfArchivist.setRuntimeXMLValidationLevel(
+                    this.getRuntimeXMLValidationLevel());
+            wfArchivist.setAnnotationProcessingRequested(false);
+
+            WebFragmentDescriptor wfDesc = null;
+            ReadableArchive embeddedArchive = lib.startsWith("WEB-INF")
+                    ? archive.getSubArchive(lib) : archive.getParentArchive().getSubArchive("lib").getSubArchive(lib);
+            try {
+                if (embeddedArchive != null &&
+                        wfArchivist.hasStandardDeploymentDescriptor(embeddedArchive)) {
+                    try {
+                        wfDesc = (WebFragmentDescriptor)wfArchivist.open(embeddedArchive);
+                    } catch(SAXParseException ex) {
+                        IOException ioex = new IOException();
+                        ioex.initCause(ex);
+                        throw ioex;
                     }
+                } else {
+                    wfDesc = new WebFragmentDescriptor();
+                    wfDesc.setExists(false);
+                }
+            } finally {
+                if (embeddedArchive != null) {
+                    embeddedArchive.close();
                 }
-                wfDesc.setJarName(lib.substring(lib.lastIndexOf('/') + 1));    
-                wfList.add(wfDesc);
+            }
+            wfDesc.setJarName(lib.substring(lib.lastIndexOf('/') + 1));
+            wfList.add(wfDesc);
 
-                descriptor.putJarNameWebFragmentNamePair(wfDesc.getJarName(), wfDesc.getName());
+            descriptor.putJarNameWebFragmentNamePair(wfDesc.getJarName(), wfDesc.getName());
 
-            }
+        }
 
-            if (((WebBundleDescriptorImpl)descriptor).getAbsoluteOrderingDescriptor() != null) {
-                wfList = ((WebBundleDescriptorImpl)descriptor).getAbsoluteOrderingDescriptor().order(wfList);
-            } else {
-                OrderingDescriptor.sort(wfList);
-            }
+        if (((WebBundleDescriptorImpl)descriptor).getAbsoluteOrderingDescriptor() != null) {
+            wfList = ((WebBundleDescriptorImpl)descriptor).getAbsoluteOrderingDescriptor().order(wfList);
+        } else {
+            OrderingDescriptor.sort(wfList);
+        }
 
-            for (WebFragmentDescriptor wf : wfList) {
-                descriptor.addOrderedLib(wf.getJarName());
-            }
+        for (WebFragmentDescriptor wf : wfList) {
+            descriptor.addOrderedLib(wf.getJarName());
         }
 
         return wfList;

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

@@ -37,7 +37,7 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  *
- * Portions Copyright [2017-2019] Payara Foundation and/or affiliates
+ * Portions Copyright [2017-2024] Payara Foundation and/or affiliates
  */
 
 package org.glassfish.weld;
@@ -108,11 +108,11 @@ public ClassLoader run()
       @Override
       public T get( String id )
       {
-        ClassLoader acl = getClassLoader();
-        T instance = store.get(acl);
+        T instance = storeById.get(id);
         if (instance == null)
         {
-            instance = storeById.get(id);
+            ClassLoader acl = getClassLoader();
+            instance = store.get(acl);
             if (instance == null) {
                 throw new IllegalStateException("Singleton not set for " + acl);
             }