TOMEE-4650 - Guard undeploy against a closed EMF and add JPA 3.2 CDI qualifier beans

Two independent problems, both reproducing on Plume (EclipseLink) and the
webprofile distribution (OpenJPA), so neither is a provider defect.

1. When an application closes a container-managed EntityManagerFactory itself,
   TomEE's undeploy path closed it again, and Assembler.destroyApplication then
   failed with "Attempting to execute an operation on a closed
   EntityManagerFactory". ReloadableEntityManagerFactory.close() now checks
   isOpen() before delegating.

2. TomEE did not register the CDI beans required by the Jakarta Persistence 3.2 /
   Jakarta EE 11 CDI integration for persistence.xml-declared units, so injecting
   a qualified EntityManagerFactory / EntityManager / PersistenceUnitUtil failed
   with UnsatisfiedResolutionException. A new JpaCDIExtension registers, per
   persistence unit, an @ApplicationScoped EntityManagerFactory (bean name = PU
   name), an EntityManager in the <scope> element's scope (default
   TransactionScoped), and @dependent CriteriaBuilder, PersistenceUnitUtil, Cache,
   SchemaManager and Metamodel beans, all carrying the <qualifier> elements or
   @default when none is declared. Supporting this, <qualifier>/<scope> are added
   to the persistence.xml JAXB model (PersistenceUnit), to PersistenceUnitInfo,
   and copied through AppInfoBuilder, which also honours the
   jakarta.persistence.qualifiers / jakarta.persistence.scope override properties.

Bean-registration contract verified against the Jakarta EE 11 Platform spec
(CDI-JPA) and the Persistence 3.2 schema rather than from memory.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Author: jungm

container/openejb-core/src/main/java/org/apache/openejb/assembler/classic/PersistenceUnitInfo.java

@@ -27,6 +27,9 @@ public class PersistenceUnitInfo extends InfoObject {
     public String id;
     public String name;
     public String provider;
+    // Jakarta Persistence 3.2 CDI integration: <qualifier>/<scope> from persistence.xml
+    public final List<String> qualifiers = new ArrayList<>();
+    public String scope;
     public String transactionType;
     public String jtaDataSource;
     public String nonJtaDataSource;

container/openejb-core/src/main/java/org/apache/openejb/assembler/classic/ReloadableEntityManagerFactory.java

@@ -279,7 +279,8 @@ public boolean isOpen() {
 
     @Override
     public synchronized void close() {
-        if (delegate != null) {
+        // the application may have closed the EMF itself, closing it twice is an error
+        if (delegate != null && delegate.isOpen()) {
             delegate.close();
         }
     }

container/openejb-core/src/main/java/org/apache/openejb/cdi/OptimizedLoaderService.java

@@ -127,6 +127,7 @@ protected List<? extends Extension> loadExtensions(final ClassLoader classLoader
         }
 
         list.add(new org.apache.openejb.cdi.concurrency.ConcurrencyCDIExtension());
+        list.add(new org.apache.openejb.cdi.persistence.JpaCDIExtension());
 
         final Collection<Extension> extensionCopy = new ArrayList<>(list);
 

container/openejb-core/src/main/java/org/apache/openejb/cdi/persistence/JpaCDIExtension.java

@@ -0,0 +1,290 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.openejb.cdi.persistence;
+
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.enterprise.context.Dependent;
+import jakarta.enterprise.event.Observes;
+import jakarta.enterprise.inject.Any;
+import jakarta.enterprise.inject.Default;
+import jakarta.enterprise.inject.spi.AfterBeanDiscovery;
+import jakarta.enterprise.inject.spi.Extension;
+import jakarta.inject.Qualifier;
+import jakarta.persistence.Cache;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.EntityManagerFactory;
+import jakarta.persistence.PersistenceUnitUtil;
+import jakarta.persistence.SchemaManager;
+import jakarta.persistence.criteria.CriteriaBuilder;
+import jakarta.persistence.metamodel.Metamodel;
+import org.apache.openejb.assembler.classic.AppInfo;
+import org.apache.openejb.assembler.classic.PersistenceUnitInfo;
+import org.apache.openejb.cdi.OpenEJBLifecycle;
+import org.apache.openejb.loader.SystemInstance;
+import org.apache.openejb.spi.ContainerSystem;
+import org.apache.openejb.util.LogCategory;
+import org.apache.openejb.util.Logger;
+
+import javax.naming.NamingException;
+import java.lang.annotation.Annotation;
+import java.lang.reflect.InvocationHandler;
+import java.lang.reflect.Method;
+import java.lang.reflect.Proxy;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.function.Function;
+
+/**
+ * CDI extension registering the beans required by the Jakarta Persistence 3.2 /
+ * Jakarta EE 11 CDI integration (Platform specification, "Jakarta Persistence &
+ * Jakarta Context and Dependency Injection (CDI) Integration").
+ *
+ * <p>For each persistence unit the container must make available:
+ * <ul>
+ *   <li>an {@link EntityManagerFactory} bean, {@code @ApplicationScoped}, whose bean name
+ *       is the persistence unit name;</li>
+ *   <li>an {@link EntityManager} bean, in the scope given by the {@code <scope>} element
+ *       (defaulting to {@code jakarta.transaction.TransactionScoped});</li>
+ *   <li>{@link CriteriaBuilder}, {@link PersistenceUnitUtil}, {@link Cache},
+ *       {@link SchemaManager} and {@link Metamodel} beans, {@code @Dependent}, each simply
+ *       obtained from the matching getter of the {@code EntityManagerFactory}.</li>
+ * </ul>
+ *
+ * <p>All of them carry the qualifiers given by the {@code <qualifier>} elements of
+ * {@code persistence.xml}, or {@code @Default} when none is declared.
+ */
+public class JpaCDIExtension implements Extension {
+
+    private static final Logger logger = Logger.getInstance(LogCategory.OPENEJB.createChild("cdi"), JpaCDIExtension.class);
+
+    private static final String PERSISTENCE_UNIT_NAMING_CONTEXT = "openejb/PersistenceUnit/";
+
+    /**
+     * Default scope of the {@code EntityManager} bean. Resolved reflectively so that the
+     * extension keeps working on distributions without the Jakarta Transactions API.
+     */
+    private static final String TRANSACTION_SCOPED = "jakarta.transaction.TransactionScoped";
+
+    void registerBeans(@Observes final AfterBeanDiscovery afterBeanDiscovery) {
+        final AppInfo appInfo = OpenEJBLifecycle.CURRENT_APP_INFO.get();
+        if (appInfo == null) {
+            return;
+        }
+
+        for (final PersistenceUnitInfo unitInfo : appInfo.persistenceUnits) {
+            final Set<Annotation> qualifiers = validateAndCreateQualifiers(unitInfo, afterBeanDiscovery);
+            if (qualifiers == null) {
+                continue;
+            }
+
+            final Class<? extends Annotation> entityManagerScope = resolveEntityManagerScope(unitInfo, afterBeanDiscovery);
+            if (entityManagerScope == null) {
+                continue;
+            }
+
+            logger.debug("Registering CDI beans for persistence unit '" + unitInfo.name + "'");
+
+            afterBeanDiscovery.addBean()
+                    .id("tomee.jpa." + EntityManagerFactory.class.getName() + "#" + unitInfo.id)
+                    .beanClass(EntityManagerFactory.class)
+                    .types(Object.class, EntityManagerFactory.class)
+                    .qualifiers(qualifiers.toArray(new Annotation[0]))
+                    .scope(ApplicationScoped.class)
+                    .name(unitInfo.name)
+                    .createWith(cc -> lookupEntityManagerFactory(unitInfo.id));
+
+            // the EntityManager is created per contextual instance and closed when the context ends
+            afterBeanDiscovery.addBean()
+                    .id("tomee.jpa." + EntityManager.class.getName() + "#" + unitInfo.id)
+                    .beanClass(EntityManager.class)
+                    .types(Object.class, EntityManager.class)
+                    .qualifiers(qualifiers.toArray(new Annotation[0]))
+                    .scope(entityManagerScope)
+                    .produceWith(instance -> lookupEntityManagerFactory(unitInfo.id).createEntityManager())
+                    .disposeWith((em, cc) -> {
+                        if (em.isOpen()) {
+                            em.close();
+                        }
+                    });
+
+            addUtilityBean(afterBeanDiscovery, unitInfo, qualifiers, CriteriaBuilder.class, EntityManagerFactory::getCriteriaBuilder);
+            addUtilityBean(afterBeanDiscovery, unitInfo, qualifiers, PersistenceUnitUtil.class, EntityManagerFactory::getPersistenceUnitUtil);
+            addUtilityBean(afterBeanDiscovery, unitInfo, qualifiers, Cache.class, EntityManagerFactory::getCache);
+            addUtilityBean(afterBeanDiscovery, unitInfo, qualifiers, SchemaManager.class, EntityManagerFactory::getSchemaManager);
+            addUtilityBean(afterBeanDiscovery, unitInfo, qualifiers, Metamodel.class, EntityManagerFactory::getMetamodel);
+        }
+    }
+
+    /**
+     * The five utility beans are {@code @Dependent} and simply delegate to the matching
+     * getter of the {@code EntityManagerFactory}.
+     */
+    private <T> void addUtilityBean(final AfterBeanDiscovery afterBeanDiscovery,
+                                    final PersistenceUnitInfo unitInfo,
+                                    final Set<Annotation> qualifiers,
+                                    final Class<T> type,
+                                    final Function<EntityManagerFactory, T> accessor) {
+        afterBeanDiscovery.addBean()
+                .id("tomee.jpa." + type.getName() + "#" + unitInfo.id)
+                .beanClass(type)
+                .types(Object.class, type)
+                .qualifiers(qualifiers.toArray(new Annotation[0]))
+                .scope(Dependent.class)
+                .createWith(cc -> accessor.apply(lookupEntityManagerFactory(unitInfo.id)));
+    }
+
+    /**
+     * Builds the qualifier set of a persistence unit: the {@code <qualifier>} elements, or
+     * {@code @Default} when none is declared. {@code @Any} is always added, as for any bean.
+     *
+     * @return {@code null} if a qualifier is invalid, in which case a definition error has
+     * been reported
+     */
+    private Set<Annotation> validateAndCreateQualifiers(final PersistenceUnitInfo unitInfo,
+                                                        final AfterBeanDiscovery afterBeanDiscovery) {
+        final Set<Annotation> qualifiers = new LinkedHashSet<>();
+        qualifiers.add(Any.Literal.INSTANCE);
+
+        if (unitInfo.qualifiers.isEmpty()) {
+            qualifiers.add(Default.Literal.INSTANCE);
+            return qualifiers;
+        }
+
+        final ClassLoader loader = Thread.currentThread().getContextClassLoader();
+        for (final String qualifierName : unitInfo.qualifiers) {
+            final Class<?> qualifierClass;
+            try {
+                qualifierClass = loader.loadClass(qualifierName);
+            } catch (final ClassNotFoundException e) {
+                afterBeanDiscovery.addDefinitionError(new IllegalArgumentException("Qualifier class " + qualifierName
+                        + " of persistence unit " + unitInfo.name + " cannot be loaded", e));
+                return null;
+            }
+
+            if (!qualifierClass.isAnnotation()) {
+                afterBeanDiscovery.addDefinitionError(new IllegalArgumentException("Qualifier " + qualifierName
+                        + " of persistence unit " + unitInfo.name + " must be an annotation type"));
+                return null;
+            }
+
+            @SuppressWarnings("unchecked")
+            final Class<? extends Annotation> annotationClass = (Class<? extends Annotation>) qualifierClass;
+            if (!annotationClass.isAnnotationPresent(Qualifier.class)) {
+                afterBeanDiscovery.addDefinitionError(new IllegalArgumentException("Qualifier " + qualifierName
+                        + " of persistence unit " + unitInfo.name + " must be annotated with @Qualifier"));
+                return null;
+            }
+
+            qualifiers.add(createAnnotation(annotationClass));
+        }
+
+        return qualifiers;
+    }
+
+    /**
+     * Resolves the {@code <scope>} element of the persistence unit, defaulting to
+     * {@code jakarta.transaction.TransactionScoped}.
+     *
+     * @return {@code null} if the scope is invalid, in which case a definition error has
+     * been reported
+     */
+    @SuppressWarnings("unchecked")
+    private Class<? extends Annotation> resolveEntityManagerScope(final PersistenceUnitInfo unitInfo,
+                                                                  final AfterBeanDiscovery afterBeanDiscovery) {
+        final String scope = unitInfo.scope == null || unitInfo.scope.isBlank() ? TRANSACTION_SCOPED : unitInfo.scope.trim();
+        final ClassLoader loader = Thread.currentThread().getContextClassLoader();
+
+        final Class<?> scopeClass;
+        try {
+            scopeClass = loader.loadClass(scope);
+        } catch (final ClassNotFoundException e) {
+            if (unitInfo.scope == null || unitInfo.scope.isBlank()) {
+                // no Jakarta Transactions on the classpath, fall back to @Dependent
+                return Dependent.class;
+            }
+            afterBeanDiscovery.addDefinitionError(new IllegalArgumentException("Scope class " + scope
+                    + " of persistence unit " + unitInfo.name + " cannot be loaded", e));
+            return null;
+        }
+
+        if (!scopeClass.isAnnotation()) {
+            afterBeanDiscovery.addDefinitionError(new IllegalArgumentException("Scope " + scope
+                    + " of persistence unit " + unitInfo.name + " must be an annotation type"));
+            return null;
+        }
+
+        return (Class<? extends Annotation>) scopeClass;
+    }
+
+    private EntityManagerFactory lookupEntityManagerFactory(final String unitId) {
+        final ContainerSystem containerSystem = SystemInstance.get().getComponent(ContainerSystem.class);
+        if (containerSystem == null) {
+            throw new IllegalStateException("ContainerSystem is not available");
+        }
+
+        final Object instance;
+        try {
+            instance = containerSystem.getJNDIContext().lookup(PERSISTENCE_UNIT_NAMING_CONTEXT + unitId);
+        } catch (final NamingException e) {
+            throw new IllegalStateException("Unable to lookup persistence unit " + unitId, e);
+        }
+
+        if (!(instance instanceof EntityManagerFactory)) {
+            throw new IllegalStateException("Persistence unit " + unitId + " is not an EntityManagerFactory, found "
+                    + (instance == null ? "null" : instance.getClass().getName()));
+        }
+        return EntityManagerFactory.class.cast(instance);
+    }
+
+    /**
+     * Creates an instance of a member-less annotation type. Members are answered with their
+     * default value, which the CDI qualifier rules guarantee to exist.
+     */
+    private Annotation createAnnotation(final Class<? extends Annotation> annotationType) {
+        final Map<String, Object> values = new LinkedHashMap<>();
+        for (final Method method : annotationType.getDeclaredMethods()) {
+            values.put(method.getName(), method.getDefaultValue());
+        }
+
+        final InvocationHandler handler = (final Object proxy, final Method method, final Object[] args) -> {
+            final String name = method.getName();
+            if ("annotationType".equals(name) && method.getParameterCount() == 0) {
+                return annotationType;
+            }
+            if ("equals".equals(name) && method.getParameterCount() == 1) {
+                return annotationType.isInstance(args[0]);
+            }
+            if ("hashCode".equals(name) && method.getParameterCount() == 0) {
+                return annotationType.hashCode();
+            }
+            if ("toString".equals(name) && method.getParameterCount() == 0) {
+                return "@" + annotationType.getName() + "()";
+            }
+            if (values.containsKey(name)) {
+                return values.get(name);
+            }
+            throw new IllegalStateException("Unsupported annotation method: " + method);
+        };
+
+        return Annotation.class.cast(Proxy.newProxyInstance(
+                annotationType.getClassLoader(),
+                new Class<?>[]{annotationType},
+                handler));
+    }
+}

container/openejb-core/src/main/java/org/apache/openejb/config/AppInfoBuilder.java

@@ -691,6 +691,9 @@ private void buildPersistenceModules(final AppModule appModule, final AppInfo ap
                 info.jtaDataSource = persistenceUnit.getJtaDataSource();
                 info.nonJtaDataSource = persistenceUnit.getNonJtaDataSource();
 
+                info.qualifiers.addAll(persistenceUnit.getQualifier());
+                info.scope = persistenceUnit.getScope();
+
                 info.jarFiles.addAll(persistenceUnit.getJarFile());
                 info.classes.addAll(persistenceUnit.getClazz());
                 info.mappingFiles.addAll(persistenceUnit.getMappingFile());
@@ -704,6 +707,21 @@ private void buildPersistenceModules(final AppModule appModule, final AppInfo ap
 
                 PersistenceProviderProperties.apply(appModule, info);
 
+                // Jakarta Persistence 3.2: these properties override the corresponding XML elements
+                final String qualifiersProperty = info.properties.getProperty("jakarta.persistence.qualifiers");
+                if (qualifiersProperty != null) {
+                    info.qualifiers.clear();
+                    for (final String qualifier : qualifiersProperty.split(",")) {
+                        if (!qualifier.isBlank()) {
+                            info.qualifiers.add(qualifier.trim());
+                        }
+                    }
+                }
+                final String scopeProperty = info.properties.getProperty("jakarta.persistence.scope");
+                if (scopeProperty != null) {
+                    info.scope = scopeProperty;
+                }
+
 
                 // Persistence Unit Root Url
                 appInfo.persistenceUnits.add(info);