FISH-10615 Fix deployment bugs discovered while implementing EAR enhancements

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

@@ -37,13 +37,14 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  */
-// Portions Copyright [2018-2021] [Payara Foundation and/or its affiliates]
+// Portions Copyright [2018-2025] [Payara Foundation and/or its affiliates]
 
 package org.glassfish.enterprise.iiop.impl;
 
 
 import jakarta.ejb.NoSuchObjectLocalException;
 
+import java.lang.ref.WeakReference;
 import java.rmi.Remote;
 
 import java.security.AccessController ;
@@ -135,7 +136,7 @@ public final class POARemoteReferenceFactory extends org.omg.CORBA.LocalObject
 
     private EjbContainerFacade container;
     private EjbDescriptor ejbDescriptor;
-    private ClassLoader appClassLoader;
+    private WeakReference<ClassLoader> appClassLoader;
 
     private ORB orb;
     private POAProtocolMgr protocolMgr;
@@ -180,7 +181,7 @@ public final class POARemoteReferenceFactory extends org.omg.CORBA.LocalObject
         this.ejbDescriptor = container.getEjbDescriptor();
         this.isRemoteHomeView = remoteHomeView;
 
-        appClassLoader = container.getClassLoader();
+        appClassLoader = new WeakReference<>(container.getClassLoader());
 
         // NOTE: ReferenceFactory creation happens in setRepositoryIds.
     }
@@ -217,12 +218,12 @@ public void setRepositoryIds(Class homeIntf, Class remoteIntf)
         // Home
         ejbHomeStubFactory = 
             sff.createStubFactory( homeIntf.getName(), false,
-                                   "", null, appClassLoader);
+                                   "", null, appClassLoader.get());
         String[] ejbHomeTypeIds = ejbHomeStubFactory.getTypeIds();
         ejbHomeRepositoryId = ejbHomeTypeIds[0];
 
         ejbObjectStubFactory = sff.createStubFactory
-            ( remoteIntf.getName(), false, "", null, appClassLoader);
+            ( remoteIntf.getName(), false, "", null, appClassLoader.get());
 
         String[] ejbObjectTypeIds = ejbObjectStubFactory.getTypeIds();
 

appserver/web/weld-integration/pom.xml

@@ -83,6 +83,7 @@
                     <include>**/faces-config.xml</include>
                     <include>**/com.sun.faces.spi.FacesConfigResourceProvider</include>
                     <include>**/jakarta.enterprise.inject.spi.Extension</include>
+                    <include>**/org.glassfish.jersey.internal.spi.*</include>
                 </includes>
             </resource>
         </resources>
@@ -200,6 +201,10 @@
             <groupId>fish.payara.server.internal.transaction</groupId>
             <artifactId>jta</artifactId>
             <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.json.bind</groupId>
+            <artifactId>jakarta.json.bind-api</artifactId>
         </dependency>
          <dependency>
              <groupId>jakarta.xml.ws</groupId>

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

@@ -37,21 +37,28 @@
  * only if the new code is made subject to such option by the copyright
  * holder.
  *
- * Portions Copyright [2017-2024] Payara Foundation and/or affiliates
+ * Portions Copyright [2017-2025] Payara Foundation and/or affiliates
  */
 
 package org.glassfish.weld;
 
+import org.glassfish.internal.deployment.Deployment;
 import org.glassfish.web.loader.WebappClassLoader;
 import org.jboss.weld.bootstrap.api.SingletonProvider;
 import org.jboss.weld.bootstrap.api.Singleton;
 import org.glassfish.internal.api.Globals;
 import org.glassfish.internal.api.ClassLoaderHierarchy;
+import org.jboss.weld.util.collections.Multimap;
+import org.jboss.weld.util.collections.SetMultimap;
 
+import java.util.Collection;
 import java.util.Map;
 import java.security.AccessController;
 import java.security.PrivilegedAction;
+import java.util.Objects;
 import java.util.concurrent.ConcurrentHashMap;
+import static org.glassfish.weld.ACLSingletonProvider.ACLSingleton.ValueAndClassLoaders.findByClassLoader;
+import static org.glassfish.weld.ACLSingletonProvider.ACLSingleton.ValueAndClassLoaders.findByIdOnly;
 
 /**
  * Singleton provider that uses Application ClassLoader to differentiate
@@ -83,11 +90,39 @@ public <T> ACLSingleton<T> create(Class<? extends T> expectedType) {
         return new ACLSingleton<T>();
     }
 
-    private static class ACLSingleton<T> implements Singleton<T> {
+    static class ACLSingleton<T> implements Singleton<T> {
 
       private final Map<ClassLoader, T> store = new ConcurrentHashMap<>();
-      private final Map<String, T> storeById = new ConcurrentHashMap<>();
+      private final Multimap<String, ValueAndClassLoaders<T>> storeById = SetMultimap.newConcurrentSetMultimap();
       private ClassLoader ccl = Globals.get(ClassLoaderHierarchy.class).getCommonClassLoader();
+      private final Deployment deployment = Globals.getDefaultHabitat().getService(Deployment.class);
+      static final class ValueAndClassLoaders<TT> {
+          final TT value;
+          final ClassLoader classLoader;
+          final ClassLoader backupClassLoader;
+
+          public ValueAndClassLoaders(TT value, ClassLoader classLoader, ClassLoader backupClassLoader) {
+              this.value = value;
+              this.classLoader = classLoader;
+              this.backupClassLoader = backupClassLoader;
+          }
+
+          public static <T> T findByClassLoader(Collection<ValueAndClassLoaders<T>> values, ClassLoader classLoader) {
+              return values.stream()
+                      .filter(v -> Objects.equals(v.classLoader, classLoader)
+                              || Objects.equals(v.backupClassLoader, classLoader))
+                      .findAny()
+                      .map(v -> v.value)
+                      .orElse(null);
+          }
+
+          public static <T> T findByIdOnly(Collection<ValueAndClassLoaders<T>> values) {
+              return values.stream()
+                      .findAny()
+                      .map(v -> v.value)
+                      .orElse(null);
+          }
+        }
 
       // Can't assume bootstrap loader as null. That's more of a convention.
       // I think either android or IBM JVM does not use null for bootstap loader
@@ -108,9 +143,11 @@ public ClassLoader run()
       @Override
       public T get( String id )
       {
-        T instance = storeById.get(id);
-        if (instance == null)
-        {
+        T instance = findByClassLoader(storeById.get(id), getDeploymentOrContextClassLoader());
+        if (instance == null) {
+            instance = findByIdOnly(storeById.get(id));
+        }
+        if (instance == null) {
             ClassLoader acl = getClassLoader();
             instance = store.get(acl);
             if (instance == null) {
@@ -120,6 +157,14 @@ public T get( String id )
         return instance;
       }
 
+      private ClassLoader getDeploymentOrContextClassLoader() {
+          if (deployment.getCurrentDeploymentContext() != null) {
+              return deployment.getCurrentDeploymentContext().getClassLoader();
+          } else {
+              return Thread.currentThread().getContextClassLoader();
+          }
+      }
+
       /**
        * This is the most significant method of this class. This is what
        * distingushes it from TCCLSIngleton. It tries to obtain a class loader
@@ -196,13 +241,16 @@ public boolean isSet(String id) {
       @Override
       public void set(String id, T object) {
         store.put(getClassLoader(), object);
-        storeById.put(id, object);
+        storeById.put(id, new ValueAndClassLoaders<>(object, getDeploymentOrContextClassLoader(),
+                Thread.currentThread().getContextClassLoader()));
       }
 
       @Override
       public void clear(String id) {
         store.remove(getClassLoader());
-        storeById.remove(id);
+        storeById.get(id).removeIf(v ->
+                Objects.equals(v.classLoader, getDeploymentOrContextClassLoader())
+                || Objects.equals(v.classLoader, Thread.currentThread().getContextClassLoader()));
       }
     }
 }

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

@@ -159,6 +159,7 @@ public DeploymentImpl(ReadableArchive archive,
         this.archiveFactory = archiveFactory;
         this.context = context;
         this.injectionManager = injectionManager;
+        this.contextId = moduleName != null? moduleName : archive.getName();
 
         // Collect /lib Jar BDAs (if any) from the parent module.
         // If we've produced BDA(s) from any /lib jars, <code>return</code> as
@@ -177,7 +178,6 @@ public DeploymentImpl(ReadableArchive archive,
             this.appName = "CDIApp";
         }
 
-        this.contextId = moduleName != null? moduleName : archive.getName();
         createModuleBda(archive, ejbs, context, contextId);
     }
 
@@ -274,7 +274,9 @@ private <TT extends BeanDeploymentArchive> Set<TT> filterBDAs(Set<TT> bdas, List
     }
 
     private void addBeanDeploymentArchives(RootBeanDeploymentArchive bda) {
-        rootBDAs(bda).add(bda);
+        if (bda.getModuleBDAType() != BDAType.UNKNOWN) {
+            rootBDAs(bda).add(bda);
+        }
     }
 
     private Set<RootBeanDeploymentArchive> rootBDAs(RootBeanDeploymentArchive bda) {
@@ -313,12 +315,16 @@ public void scanArchive(ReadableArchive archive, Collection<EjbDescriptor> ejbs,
      * <code>Deployment</code>.
      */
     public void buildDeploymentGraph() {
+        Set<BeanDeploymentArchive> ejbModuleAndRarBDAs = new HashSet<>();
+
         // Make jars accessible to each other - Example:
         //    /ejb1.jar <----> /ejb2.jar
         // If there are any application (/lib) jars, make them accessible
 
         for (RootBeanDeploymentArchive ejbRootBda : ejbRootBdas) {
             BeanDeploymentArchive ejbModuleBda = ejbRootBda.getModuleBda();
+            ejbModuleAndRarBDAs.add(ejbRootBda);
+            ejbModuleAndRarBDAs.add(ejbModuleBda);
 
             boolean modifiedArchive = false;
             for (RootBeanDeploymentArchive otherEjbRootBda : ejbRootBdas) {
@@ -345,6 +351,8 @@ public void buildDeploymentGraph() {
             // Make rars accessible to ejbs
             for (RootBeanDeploymentArchive rarRootBda : rarRootBdas) {
                 BeanDeploymentArchive rarModuleBda = rarRootBda.getModuleBda();
+                ejbModuleAndRarBDAs.add(rarRootBda);
+                ejbModuleAndRarBDAs.add(rarModuleBda);
                 ejbRootBda.getBeanDeploymentArchives().add(rarRootBda);
                 ejbRootBda.getBeanDeploymentArchives().add(rarModuleBda);
                 ejbModuleBda.getBeanDeploymentArchives().add(rarRootBda);
@@ -391,18 +399,6 @@ public void buildDeploymentGraph() {
                 warModuleBda.getBeanDeploymentArchives().add(libJarRootBda);
                 warModuleBda.getBeanDeploymentArchives().add(libJarModuleBda);
 
-                // make WAR's BDAs accessible to libJar BDAs
-                Set<BeanDeploymentArchive> seen = Collections.newSetFromMap(new IdentityHashMap<>());
-                beanDeploymentArchives.stream()
-                        .filter(RootBeanDeploymentArchive.class::isInstance)
-                        .map(RootBeanDeploymentArchive.class::cast)
-                        .forEach(bda -> recursivelyAdd(bda.getBeanDeploymentArchives(), warModuleBda, seen));
-                recursivelyAdd(beanDeploymentArchives, warModuleBda, seen);
-                libJarRootBda.getBeanDeploymentArchives().add(warRootBda);
-                libJarModuleBda.getBeanDeploymentArchives().add(warRootBda);
-                libJarRootBda.getBeanDeploymentArchives().add(warModuleBda);
-                libJarModuleBda.getBeanDeploymentArchives().add(warModuleBda);
-
                 for ( BeanDeploymentArchive oneBda : warModuleBda.getBeanDeploymentArchives() ) {
                     oneBda.getBeanDeploymentArchives().add( libJarRootBda );
                     oneBda.getBeanDeploymentArchives().add( libJarModuleBda );
@@ -458,15 +454,6 @@ private void addDependentBdas() {
         }
     }
 
-    private void recursivelyAdd(Collection<BeanDeploymentArchive> bdas, BeanDeploymentArchive bda, Set<BeanDeploymentArchive> seen) {
-        for (BeanDeploymentArchive subBda : new LinkedHashSet<>(bdas)) {
-            if (seen.add(subBda)) {
-                subBda.getBeanDeploymentArchives().add(bda);
-                recursivelyAdd(subBda.getBeanDeploymentArchives(), bda, seen);
-            }
-        }
-    }
-
     @Override
     public Set<BeanDeploymentArchive> getBeanDeploymentArchives() {
         if ( logger.isLoggable( FINE ) ) {

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

@@ -37,7 +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]
+// Portions Copyright [2024-2025] [Payara Foundation and/or its affiliates]
 
 package org.glassfish.weld;
 
@@ -49,26 +49,36 @@
 import org.jboss.weld.Container;
 import org.jboss.weld.SimpleCDI;
 import org.jboss.weld.bootstrap.spi.BeanDeploymentArchive;
+import org.jboss.weld.logging.BeanManagerLogger;
 import org.jboss.weld.manager.BeanManagerImpl;
 
 import jakarta.enterprise.inject.spi.CDI;
 import jakarta.enterprise.inject.spi.CDIProvider;
+import java.lang.StackWalker.StackFrame;
+import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
+import static java.lang.StackWalker.Option.RETAIN_CLASS_REFERENCE;
 
 /**
  * @author <a href="mailto:[email protected]">JJ Snyder</a>
  */
 public class GlassFishWeldProvider implements CDIProvider {
     private static final WeldDeployer weldDeployer = Globals.get(WeldDeployer.class);
     private static final InvocationManager invocationManager = Globals.get(InvocationManager.class);
+    private static final StackWalker stackWalker = StackWalker.getInstance(RETAIN_CLASS_REFERENCE);
 
     private static class GlassFishEnhancedWeld extends SimpleCDI {
+        private final Set<String> knownClassNames;
+
         GlassFishEnhancedWeld() {
+            knownClassNames = new HashSet<>(super.knownClassNames);
         }
 
         GlassFishEnhancedWeld(String contextId) {
             super(contextId == null ? Container.instance() : Container.instance(contextId));
+            knownClassNames = new HashSet<>(super.knownClassNames);
         }
 
         @Override
@@ -103,23 +113,40 @@ protected BeanManagerImpl unsatisfiedBeanManager(String callerClassName) {
 
             return super.unsatisfiedBeanManager(callerClassName);
         }
+
+        @Override
+        protected String getCallingClassName() {
+            boolean outerSubclassReached = false;
+            BundleDescriptor bundleDescriptor = getBundleDescriptor();
+            for (StackFrame element : stackWalker.walk(sf -> sf.collect(Collectors.toList()))) {
+                // the method call that leads to the first invocation of this class or its subclass is considered the caller
+                if (!knownClassNames.contains(element.getClassName())) {
+                    Class<?> declaringClass = element.getDeclaringClass();
+                    if (outerSubclassReached && declaringClass.getClassLoader() != null) {
+                        if (bundleDescriptor != null && declaringClass.getClassLoader() == bundleDescriptor.getClassLoader()) {
+                            // we are in the same class loader, so this is the caller
+                            return declaringClass.getName();
+                        } else {
+                            return getAnyClassFromBundleDescriptor(declaringClass.getName());
+                        }
+                    }
+                } else {
+                    outerSubclassReached = true;
+                }
+            }
+            throw BeanManagerLogger.LOG.unableToIdentifyBeanManager();
+        }
+
+        private static String getAnyClassFromBundleDescriptor(String backupClassName) {
+            BeanDeploymentArchive bda = weldDeployer.getBeanDeploymentArchiveForBundle(getBundleDescriptor());
+            return bda != null ? bda.getBeanClasses().stream().findAny().orElse(backupClassName) : backupClassName;
+        }
     }
 
     @Override
     public CDI<Object> getCDI() {
         try {
-            BundleDescriptor bundle = null;
-            Object componentEnv = invocationManager.getCurrentInvocation().getJNDIEnvironment();
-            if( componentEnv instanceof EjbDescriptor) {
-                bundle = (BundleDescriptor)
-                        ((EjbDescriptor) componentEnv).getEjbBundleDescriptor().
-                                getModuleDescriptor().getDescriptor();
-
-            } else if( componentEnv instanceof WebBundleDescriptor) {
-                bundle = (BundleDescriptor) componentEnv;
-            }
-
-            BeanDeploymentArchive bda = weldDeployer.getBeanDeploymentArchiveForBundle(bundle);
+            BeanDeploymentArchive bda = weldDeployer.getBeanDeploymentArchiveForBundle(getBundleDescriptor());
             if (bda == null) {
                 return new GlassFishEnhancedWeld();
             } else {
@@ -133,4 +160,18 @@ public CDI<Object> getCDI() {
             throw throwable;
         }
     }
+
+    private static BundleDescriptor getBundleDescriptor() {
+        BundleDescriptor bundle = null;
+        Object componentEnv = invocationManager.getCurrentInvocation().getJNDIEnvironment();
+        if( componentEnv instanceof EjbDescriptor) {
+            bundle = (BundleDescriptor)
+                    ((EjbDescriptor) componentEnv).getEjbBundleDescriptor().
+                            getModuleDescriptor().getDescriptor();
+
+        } else if( componentEnv instanceof WebBundleDescriptor) {
+            bundle = (BundleDescriptor) componentEnv;
+        }
+        return bundle;
+    }
 }