Merge pull request #250 from kbss-cvut/development

[2.0.1] Release

CHANGELOG.md

@@ -1,5 +1,13 @@
 # JOPA - Change Log
 
+## 2.0.1 - 2024-06-17
+- Proper implementation of `EntityManager.getReference` after 2.0.0 rewrite (Enhancement #233).
+- Log JOPA version and build date on persistence unit startup (Enhancement #243).
+- Prevent `AssertionError` on `EntityManager.flush` calls (Bug #240).
+- Fix incorrect SOQL to SPARQL translation when traversing reference and using identifier (Bug #234).
+- Fix issues with interaction of lazy loading with cascading (Bug #248).
+- Dependency updates: RDF4J 4.3.12.
+
 ## 2.0.0 - 2024-05-27
 - Move internal API from `jopa-api` to the `jopa-impl` module (Enhancement #146).
 - Modify name resolution in OWL2Java, support prefixes so that terms are better disambiguated without appending the useless `_A` suffix if possible (Enhancement #85).

datatype/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>jopa-all</artifactId>
         <groupId>cz.cvut.kbss.jopa</groupId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

jopa-api/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

jopa-api/src/main/java/cz/cvut/kbss/jopa/exceptions/EntityNotFoundException.java

@@ -20,9 +20,12 @@
 import cz.cvut.kbss.jopa.model.EntityManager;
 
 /**
- * Thrown when {@link EntityManager#refresh(Object)}  is called and the object no longer exists in the database.
+ * Thrown by the persistence provider when an entity reference obtained by
+ * {@link EntityManager#getReference(Class, Object)} is accessed but the entity does not exist. Thrown when
+ * {@link EntityManager#refresh} is called and the object no longer exists in the database.
  * <p>
- * The current transaction, if one is active and the persistence context has been joined to it, will be marked for rollback.
+ * The current transaction, if one is active and the persistence context has been joined to it, will be marked for
+ * rollback.
  */
 public class EntityNotFoundException extends OWLPersistenceException {
 

jopa-api/src/main/java/cz/cvut/kbss/jopa/model/metamodel/IdentifierVisitor.java

@@ -17,6 +17,7 @@
  */
 package cz.cvut.kbss.jopa.model.metamodel;
 
+@FunctionalInterface
 public interface IdentifierVisitor {
 
     void visit(IRIIdentifier i);

jopa-distribution/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

jopa-impl/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -49,6 +49,12 @@
 
 
     <build>
+        <resources>
+            <resource>
+                <directory>src/main/resources</directory>
+                <filtering>true</filtering>
+            </resource>
+        </resources>
         <plugins>
             <plugin>
                 <groupId>org.antlr</groupId>
@@ -63,6 +69,11 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+                <version>${maven.resources.plugin.version}</version>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>

jopa-impl/src/main/java/cz/cvut/kbss/jopa/loaders/DefaultClasspathScanner.java

@@ -88,9 +88,15 @@ protected void processElements(Enumeration<URL> urls, String scanPath) throws IO
                 continue;
             }
             visited.add(elemUri);
-            LOG.trace("Processing classpath element {}", url);
+            LOG.trace("Processing classpath element {}", elemUri);
             if (isJar(elemUri)) {
-                processJarFile(createJarFile(url));
+                final JarFile jarFile = createJarFile(url);
+                if (!elemUri.equals(jarFile.getName()) && visited.contains(jarFile.getName())) {
+                    LOG.trace("Classpath element {} maps to a JAR file {} and it has already been processed.", elemUri, jarFile.getName());
+                } else {
+                    visited.add(jarFile.getName());
+                    processJarFile(jarFile);
+                }
             } else {
                 processDirectory(new File(URI.create(elemUri).getPath()), scanPath);
             }

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/EntityManagerImpl.java

@@ -36,6 +36,7 @@
 import cz.cvut.kbss.jopa.utils.CollectionFactory;
 import cz.cvut.kbss.jopa.utils.Configuration;
 import cz.cvut.kbss.jopa.utils.EntityPropertiesUtils;
+import cz.cvut.kbss.jopa.utils.JOPALazyUtils;
 import cz.cvut.kbss.jopa.utils.Wrapper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -227,7 +228,7 @@ protected void exploreCascaded(Attribute<?, ?> at, Object merged, Object toMerge
 
     private void mergeX(Attribute<?, ?> at, Object merged, Object toMerge, Descriptor descriptor) {
         Object attVal = EntityPropertiesUtils.getAttributeValue(at, toMerge);
-        if (attVal == null) {
+        if (attVal == null || JOPALazyUtils.isLazyLoadingProxy(attVal)) {
             return;
         }
         if (at.isCollection()) {
@@ -261,7 +262,7 @@ public void remove(Object object) {
                     registerProcessedInstance(object);
                     // Intentional fall-through
                 case REMOVED:
-                    new SimpleOneLevelCascadeExplorer(this::remove).start(this, object, CascadeType.REMOVE);
+                    new OneLevelRemoveCascadeExplorer(this::remove).start(this, object, CascadeType.REMOVE);
                     break;
                 default:
                     throw new IllegalArgumentException("Entity " + object + " is not managed and cannot be removed.");

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/JOPAPersistenceProvider.java

@@ -17,19 +17,46 @@
  */
 package cz.cvut.kbss.jopa.model;
 
-import java.util.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Optional;
+import java.util.Properties;
+import java.util.Set;
 
 public class JOPAPersistenceProvider implements PersistenceProvider, ProviderUtil {
 
+    private static final Logger LOG = LoggerFactory.getLogger(JOPAPersistenceProvider.class);
+
     private static final Set<EntityManagerFactoryImpl> EMFS = Collections.synchronizedSet(new HashSet<>());
 
+    public JOPAPersistenceProvider() {
+        logVersionInfo();
+    }
+
     @Override
     public EntityManagerFactoryImpl createEntityManagerFactory(String emName, Map<String, String> properties) {
         final EntityManagerFactoryImpl emf = new EntityManagerFactoryImpl(properties, this::emfClosed);
         EMFS.add(emf);
         return emf;
     }
 
+    private static void logVersionInfo() {
+        try {
+            final Properties props = new Properties();
+            props.load(JOPAPersistenceProvider.class.getClassLoader().getResourceAsStream("jopa.properties"));
+            assert props.containsKey("cz.cvut.jopa.version");
+            assert props.containsKey("cz.cvut.jopa.build.timestamp");
+            LOG.info("This is JOPA {}, built on {}...", props.get("cz.cvut.jopa.version"), props.get("cz.cvut.jopa.build.timestamp"));
+        } catch (IOException e) {
+            LOG.warn("Unable to load properties file to log version info.", e);
+        }
+    }
+
     void emfClosed(EntityManagerFactoryImpl emf) {
         EMFS.remove(emf);
     }

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/MetamodelImpl.java

@@ -26,6 +26,7 @@
 import cz.cvut.kbss.jopa.model.metamodel.MetamodelBuilder;
 import cz.cvut.kbss.jopa.model.metamodel.StaticMetamodelInitializer;
 import cz.cvut.kbss.jopa.proxy.lazy.gen.LazyLoadingEntityProxyGenerator;
+import cz.cvut.kbss.jopa.proxy.reference.EntityReferenceProxyGenerator;
 import cz.cvut.kbss.jopa.query.NamedQueryManager;
 import cz.cvut.kbss.jopa.query.ResultSetMappingManager;
 import cz.cvut.kbss.jopa.sessions.MetamodelProvider;
@@ -55,6 +56,8 @@ public class MetamodelImpl implements Metamodel, MetamodelProvider {
     private TypeReferenceMap typeReferenceMap;
 
     private final Map<Class<?>, Class<?>> lazyLoadingProxyClasses = new ConcurrentHashMap<>();
+    // Proxy classes for results of EntityManager.getReference
+    private final Map<Class<?>, Class<?>> referenceProxyClasses = new ConcurrentHashMap<>();
 
     private NamedQueryManager namedQueryManager;
     private ResultSetMappingManager resultSetMappingManager;
@@ -151,10 +154,12 @@ public Set<Class<?>> getInferredClasses() {
         return Collections.unmodifiableSet(inferredClasses);
     }
 
+    @Override
     public NamedQueryManager getNamedQueryManager() {
         return namedQueryManager;
     }
 
+    @Override
     public ResultSetMappingManager getResultSetMappingManager() {
         return resultSetMappingManager;
     }
@@ -222,12 +227,24 @@ public Set<Class<?>> getReferringTypes(Class<?> cls) {
     /**
      * Gets a {@link cz.cvut.kbss.jopa.proxy.lazy.LazyLoadingProxy} type for the specified class.
      *
-     * @param cls Class to get lazy loading proxy for
+     * @param cls Class to get lazy loading proxy for, should be an entity class
      * @param <X> Type to proxy
      * @return Lazy loading proxy class
      */
     public <X> Class<? extends X> getLazyLoadingProxy(Class<X> cls) {
         assert isEntityType(cls);
         return (Class<? extends X>) lazyLoadingProxyClasses.computeIfAbsent(cls, c -> new LazyLoadingEntityProxyGenerator().generate(c));
     }
+
+    /**
+     * Gets a {@link cz.cvut.kbss.jopa.proxy.reference.EntityReferenceProxy} type for the specified class.
+     *
+     * @param cls Class to get reference proxy for, should be an entity class
+     * @param <X> Type to proxy
+     * @return Entity proxy class
+     */
+    public <X> Class<? extends X> getEntityReferenceProxy(Class<X> cls) {
+        assert isEntityType(cls);
+        return (Class<? extends X>) referenceProxyClasses.computeIfAbsent(cls, c -> new EntityReferenceProxyGenerator().generate(cls));
+    }
 }

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/OneLevelRemoveCascadeExplorer.java

@@ -0,0 +1,37 @@
+package cz.cvut.kbss.jopa.model;
+
+import cz.cvut.kbss.jopa.model.metamodel.Attribute;
+import cz.cvut.kbss.jopa.proxy.lazy.LazyLoadingProxy;
+import cz.cvut.kbss.jopa.utils.EntityPropertiesUtils;
+import cz.cvut.kbss.jopa.utils.JOPALazyUtils;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.function.Consumer;
+
+public class OneLevelRemoveCascadeExplorer extends OneLevelCascadeExplorer {
+
+    private final Consumer<Object> removeOperation;
+
+    public OneLevelRemoveCascadeExplorer(Consumer<Object> removeOperation) {
+        this.removeOperation = removeOperation;
+    }
+
+    @Override
+    protected void exploreCascaded(Attribute<?, ?> at, Object o) {
+        Object attVal = EntityPropertiesUtils.getAttributeValue(at, o);
+        if (attVal == null) {
+            return;
+        }
+        if (JOPALazyUtils.isLazyLoadingProxy(attVal)) {
+            attVal = ((LazyLoadingProxy<?>) attVal).triggerLazyLoading();
+        }
+        if (at.isCollection()) {
+            for (final Object ox2 : new HashSet<>((Collection<?>) attVal)) {
+                removeOperation.accept(ox2);
+            }
+        } else {
+            removeOperation.accept(attVal);
+        }
+    }
+}

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/metamodel/AbstractIdentifiableType.java

@@ -28,8 +28,8 @@
 import java.util.stream.Collectors;
 
 /**
- * Instances of the type AbstractIdentifiableType represent entity or mapped superclass
- * types which can be queried for attributes, subtypes and so on.
+ * Instances of the type AbstractIdentifiableType represent entity or mapped superclass types which can be queried for
+ * attributes, subtypes and so on.
  *
  * @param <X> Entity type being represented by this instance
  */
@@ -70,8 +70,8 @@ void addDeclaredQueryAttribute(final String name, final AbstractQueryAttribute<X
     }
 
     /**
-     * Set supertypes of this instance, and for all given supertypes add this as their subtype.
-     * This method should not be called multiple times on one instance.
+     * Set supertypes of this instance, and for all given supertypes add this as their subtype. This method should not
+     * be called multiple times on one instance.
      *
      * @param supertypes Supertypes to set
      */
@@ -138,9 +138,10 @@ public boolean hasSubtypes() {
 
     /**
      * Gets the Java type represented by the metamodel instance that can be instantiated.
-     *
+     * <p>
      * The purpose of this method is mainly to return the generated subclass of {@link #getJavaType()} that is used for
      * instantiation.
+     *
      * @return Instantiable Java type
      */
     public Class<? extends X> getInstantiableJavaType() {

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/metamodel/IdentifiableEntityType.java

@@ -21,10 +21,9 @@
 import cz.cvut.kbss.jopa.model.annotations.InheritanceType;
 
 /**
- *  Instances of the type IdentifiableEntityType represent entity
- *  types which can be saved to and read from storage.
+ * Instances of this type represent entity classes that can be saved to and read from storage.
  *
- * @param <X> Entity type being represented by this instance
+ * @param <X> Entity class being represented by this instance
  */
 public abstract class IdentifiableEntityType<X> extends AbstractIdentifiableType<X> implements EntityType<X> {
 
@@ -69,9 +68,10 @@ public IRI getIRI() {
     /**
      * Gets inheritance type of this entity type.
      * <p>
-     * If the entity type is a root if an inheritance hierarchy, the type can be defined using the {@link
-     * cz.cvut.kbss.jopa.model.annotations.Inheritance} annotation. If the entity is deeper in inheritance hierarchy, it
-     * is inherited from the supertype. Otherwise, it defaults to {@link cz.cvut.kbss.jopa.utils.Constants#DEFAULT_INHERITANCE_TYPE}.
+     * If the entity type is a root if an inheritance hierarchy, the type can be defined using the
+     * {@link cz.cvut.kbss.jopa.model.annotations.Inheritance} annotation. If the entity is deeper in inheritance
+     * hierarchy, it is inherited from the supertype. Otherwise, it defaults to
+     * {@link cz.cvut.kbss.jopa.utils.Constants#DEFAULT_INHERITANCE_TYPE}.
      *
      * @return Inheritance strategy for this entity type
      */

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/metamodel/RDFCollectionAttribute.java

@@ -84,6 +84,7 @@ public RDFCollectionAttributeBuilder<X, V> converter(ConverterWrapper converter)
             return this;
         }
 
+        @Override
         public RDFCollectionAttribute<X, V> build() {
             return new RDFCollectionAttribute<>(this);
         }

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/metamodel/gen/ManageableClassGenerator.java

@@ -87,7 +87,11 @@ private <T> void outputGeneratedClass(DynamicType.Unloaded<? extends T> typeDef)
 
     public static class SetterInterceptor {
 
-        public static void set(@This Manageable instance, @Origin Method setter) throws Exception {
+        private SetterInterceptor() {
+            throw new AssertionError();
+        }
+
+        public static void set(@This Manageable instance, @Origin Method setter) {
             final UnitOfWork pc = instance.getPersistenceContext();
             if (pc == null || !pc.isInTransaction()) {
                 return;

jopa-impl/src/main/java/cz/cvut/kbss/jopa/oom/DefaultInstanceLoader.java

@@ -35,12 +35,6 @@ <T> T loadEntity(LoadingParameters<T> loadingParameters) {
         return loadInstance(loadingParameters, et);
     }
 
-    @Override
-    <T> T loadReference(LoadingParameters<T> loadingParameters) {
-        final IdentifiableEntityType<T> et = metamodel.entity(loadingParameters.getEntityClass());
-        return loadReferenceInstance(loadingParameters, et);
-    }
-
     static DefaultInstanceLoaderBuilder builder() {
         return new DefaultInstanceLoaderBuilder();
     }

jopa-impl/src/main/java/cz/cvut/kbss/jopa/oom/EntityConstructor.java

@@ -203,6 +203,8 @@ private <T> void populateQueryAttributes(T instance, EntityType<T> et, LoadState
             if (queryAttribute.getFetchType() != FetchType.LAZY) {
                 populateQueryAttribute(instance, queryAttribute, queryFactory, et);
                 loadStateDescriptor.setLoaded(queryAttribute, LoadState.LOADED);
+            } else {
+                loadStateDescriptor.setLoaded(queryAttribute, LoadState.NOT_LOADED);
             }
         }
     }