Merge pull request #262 from kbss-cvut/development

[2.0.3] Release

CHANGELOG.md

@@ -1,5 +1,11 @@
 # JOPA - Change Log
 
+## 2.0.3 - 2024-07-22
+- Fix an issue with generating static metamodel under JDK 21 (Bug #257).
+- Support using URI/URL as data property values (as RDF simple literal) (Enhancement #256).
+- Support target ontology query hint (Enhancement #245).
+- Dependency updates: Jena 5.1.0, RDF4J 5.0.1.
+
 ## 2.0.2 - 2024-06-24
 - Fix a NPX when calling `EntityManager.isInferred` with lazy loading proxy (Bug #252).
 - Allow using multiple values for a query parameter that is written into SPARQL `VALUES` clause (Bug #246).
@@ -20,7 +26,7 @@
 - Modify name resolution in OWL2Java, support prefixes so that terms are better disambiguated without appending the useless `_A` suffix if possible (Enhancement #85).
 - Remove dependency on AspectJ by rewriting object change tracking and lazy loading (Enhancement #145, #231). See the [wiki](https://github.com/kbss-cvut/jopa/wiki/Change-Tracking-and-Lazy-Loading) for details.
 - Add support for RDF collections (Enhancement #51).
-- Update dependencies (Jena 5.0.0, RDF4J 4.3.11).
+- Dependency updates: Jena 5.0.0, RDF4J 4.3.11.
 - Require Java 17.
 
 ## 1.2.2 - 2024-01-30

datatype/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>jopa-all</artifactId>
         <groupId>cz.cvut.kbss.jopa</groupId>
-        <version>2.0.2</version>
+        <version>2.0.3</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>2.0.2</version>
+        <version>2.0.3</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

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

@@ -18,6 +18,7 @@
 package cz.cvut.kbss.jopa.model;
 
 import cz.cvut.kbss.jopa.NonJPA;
+import cz.cvut.kbss.jopa.exceptions.EntityNotFoundException;
 import cz.cvut.kbss.jopa.exceptions.OWLEntityExistsException;
 import cz.cvut.kbss.jopa.exceptions.OWLPersistenceException;
 import cz.cvut.kbss.jopa.exceptions.TransactionRequiredException;
@@ -136,16 +137,18 @@ public interface EntityManager extends AutoCloseable {
      * @return the found entity instance or {@code null} if the entity does not exist in the given ontology context
      * @throws IllegalArgumentException if the first argument does not denote an entity type or the second argument is
      *                                  not a valid type for that entity’s identifier
-     * @throws NullPointerException     If {@code entityClass}, {@code identifier} or {@code contextUri} is {@code
-     *                                  null}
+     * @throws NullPointerException     If {@code entityClass}, {@code identifier} or {@code contextUri} is
+     *                                  {@code null}
      * @see #getContexts()
      */
     <T> T find(final Class<T> entityClass, final Object identifier, final Descriptor descriptor);
 
     /**
      * Get an instance, whose state may be lazily fetched.
      * <p>
-     * If the requested instance does not exist in the database, {@code null} is returned.
+     * If the requested instance does not exist in the database, the {@link EntityNotFoundException} is thrown when the
+     * instance state is first accessed. (The persistence provider runtime is permitted to throw the
+     * {@code EntityNotFoundException} when getReference is called.)
      * <p>
      * The application should not expect that the instance state will be available upon detachment, unless it was
      * accessed by the application while the entity manager was open.
@@ -161,7 +164,9 @@ public interface EntityManager extends AutoCloseable {
     /**
      * Get an instance, whose state may be lazily fetched.
      * <p>
-     * If the requested instance does not exist in the database, {@code null} is returned.
+     * If the requested instance does not exist in the database, the {@link EntityNotFoundException} is thrown when the
+     * instance state is first accessed. (The persistence provider runtime is permitted to throw the
+     * {@code EntityNotFoundException} when getReference is called.)
      * <p>
      * The application should not expect that the instance state will be available upon detachment, unless it was
      * accessed by the application while the entity manager was open.

jopa-distribution/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>2.0.2</version>
+        <version>2.0.3</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>2.0.2</version>
+        <version>2.0.3</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

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

@@ -18,16 +18,35 @@
 package cz.cvut.kbss.jopa.model.metamodel;
 
 import cz.cvut.kbss.jopa.model.JOPAPersistenceProperties;
-import cz.cvut.kbss.jopa.oom.converter.*;
-import cz.cvut.kbss.jopa.oom.converter.datetime.*;
+import cz.cvut.kbss.jopa.oom.converter.ConverterWrapper;
+import cz.cvut.kbss.jopa.oom.converter.ObjectConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToDoubleConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToFloatConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToIntegerConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToLangStringConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToLongConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToShortConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToStringConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToURIConverter;
+import cz.cvut.kbss.jopa.oom.converter.ToURLConverter;
+import cz.cvut.kbss.jopa.oom.converter.datetime.DateConverter;
+import cz.cvut.kbss.jopa.oom.converter.datetime.InstantConverter;
+import cz.cvut.kbss.jopa.oom.converter.datetime.LocalDateTimeConverter;
+import cz.cvut.kbss.jopa.oom.converter.datetime.LocalTimeConverter;
+import cz.cvut.kbss.jopa.oom.converter.datetime.ZonedDateTimeConverter;
 import cz.cvut.kbss.jopa.utils.Configuration;
 import cz.cvut.kbss.ontodriver.model.LangString;
 
+import java.net.URI;
+import java.net.URL;
 import java.time.Instant;
 import java.time.LocalDateTime;
 import java.time.LocalTime;
 import java.time.ZonedDateTime;
-import java.util.*;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Optional;
 
 /**
  * Manages attribute converters.
@@ -70,7 +89,9 @@ void registerConverter(Class<?> attributeType, ConverterWrapper<?, ?> converter)
                 Map.entry(Float.class, new ToFloatConverter()),
                 Map.entry(Double.class, new ToDoubleConverter()),
                 Map.entry(String.class, new ToStringConverter()),
-                Map.entry(LangString.class, new ToLangStringConverter()));
+                Map.entry(LangString.class, new ToLangStringConverter()),
+                Map.entry(URI.class, new ToURIConverter()),
+                Map.entry(URL.class, new ToURLConverter()));
     }
 
     /**

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

@@ -71,9 +71,9 @@ private <T> void addAssertions(T entity, EntityType<T> et,
         fs.buildAxiomValuesFromInstance(entity, valueBuilder);
     }
 
-    <T> AxiomValueGatherer mapFieldToAxioms(URI primaryKey, T entity, FieldSpecification<? super T, ?> fieldSpec,
+    <T> AxiomValueGatherer mapFieldToAxioms(URI identifier, T entity, FieldSpecification<? super T, ?> fieldSpec,
                                             EntityType<T> et, Descriptor descriptor) {
-        final AxiomValueGatherer valueBuilder = createAxiomValueBuilder(primaryKey, descriptor);
+        final AxiomValueGatherer valueBuilder = createAxiomValueBuilder(identifier, descriptor);
         addAssertions(entity, et, fieldSpec, descriptor, valueBuilder);
         return valueBuilder;
     }

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

@@ -174,7 +174,7 @@ public <T> void loadFieldValue(T entity, FieldSpecification<? super T, ?> fieldS
         LOG.trace("Lazily loading value of field {} of entity {}.", fieldSpec, uow.stringify(entity));
 
         final EntityType<T> et = (EntityType<T>) getEntityType(entity.getClass());
-        final URI primaryKey = EntityPropertiesUtils.getIdentifier(entity, et);
+        final URI identifier = EntityPropertiesUtils.getIdentifier(entity, et);
 
         if (et.hasQueryAttribute(fieldSpec.getName())) {
             QueryAttribute<? super T, ?> queryAttribute = (QueryAttribute<? super T, ?>) fieldSpec;
@@ -183,7 +183,7 @@ public <T> void loadFieldValue(T entity, FieldSpecification<? super T, ?> fieldS
         }
 
         final AxiomDescriptor axiomDescriptor =
-                descriptorFactory.createForFieldLoading(primaryKey, fieldSpec, descriptor, et);
+                descriptorFactory.createForFieldLoading(identifier, fieldSpec, descriptor, et);
         try {
             final Collection<Axiom<?>> axioms = storageConnection.find(axiomDescriptor);
             entityBuilder.setFieldValue(entity, fieldSpec, axioms, et, descriptor);

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

@@ -0,0 +1,31 @@
+package cz.cvut.kbss.jopa.oom.converter;
+
+import cz.cvut.kbss.jopa.exception.UnsupportedTypeTransformationException;
+
+import java.net.URI;
+
+/**
+ * Converter to {@link java.net.URI}.
+ * <p>
+ * Only {@code String} values are supported.
+ */
+public class ToURIConverter implements ConverterWrapper<URI, Object> {
+    @Override
+    public boolean supportsAxiomValueType(Class<?> type) {
+        return String.class.equals(type);
+    }
+
+    @Override
+    public Object convertToAxiomValue(URI value) {
+        return value.toString();
+    }
+
+    @Override
+    public URI convertToAttribute(Object value) {
+        try {
+            return URI.create(value.toString());
+        } catch (IllegalArgumentException e) {
+            throw new UnsupportedTypeTransformationException("Unable to convert value " + value + " to URI.", e);
+        }
+    }
+}

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

@@ -0,0 +1,33 @@
+package cz.cvut.kbss.jopa.oom.converter;
+
+import cz.cvut.kbss.jopa.exception.UnsupportedTypeTransformationException;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+/**
+ * Converter to {@link java.net.URL}.
+ * <p>
+ * Only {@code String} values are supported.
+ */
+public class ToURLConverter implements ConverterWrapper<URL, Object> {
+
+    @Override
+    public boolean supportsAxiomValueType(Class<?> type) {
+        return String.class.equals(type);
+    }
+
+    @Override
+    public Object convertToAxiomValue(URL value) {
+        return value.toString();
+    }
+
+    @Override
+    public URL convertToAttribute(Object value) {
+        try {
+            return new URL(value.toString());
+        } catch (MalformedURLException e) {
+            throw new UnsupportedTypeTransformationException("Unable to convert value " + value + " to URL.", e);
+        }
+    }
+}

jopa-impl/src/test/java/cz/cvut/kbss/jopa/model/EntityManagerImplTest.java

@@ -189,7 +189,7 @@ void containsThrowsIllegalArgumentForNonEntity() {
     @Test
     void findThrowsIllegalArgumentForNonEntity() {
         final IllegalArgumentException ex = assertThrows(IllegalArgumentException.class,
-                () -> em.find(UnknownEntity.class, "primaryKey", new EntityDescriptor()));
+                () -> em.find(UnknownEntity.class, "identifier", new EntityDescriptor()));
         assertEquals(NON_ENTITY_CLASS_EXCEPTION_MESSAGE, ex.getMessage());
     }
 

jopa-impl/src/test/java/cz/cvut/kbss/jopa/sessions/cache/AbstractCacheManagerTest.java

@@ -288,7 +288,7 @@ public void evictInferredClassesRemovesInstancesOfInferredClasses() {
     }
 
     @Test
-    public void testEvictByContextClassAndPrimaryKey() throws Exception {
+    public void testEvictByContextClassAndIdentifier() throws Exception {
         final Descriptor descriptorOne = descriptor(CONTEXT_ONE);
         final Descriptor descriptorTwo = descriptor(CONTEXT_TWO);
         manager.add(testA.getUri(), testA, descriptors(descriptorTwo));

jopa-impl/src/test/java/cz/cvut/kbss/jopa/sessions/cache/LruCacheManagerTest.java

@@ -92,7 +92,7 @@ public void testEvictByContext() throws Exception {
     }
 
     @Test
-    public void testEvictByContextClassAndPrimaryKey() throws Exception {
+    public void testEvictByContextClassAndIdentifier() throws Exception {
         final LruCache lruCache = getLruCache();
         final Descriptor descriptorOne = descriptor(CONTEXT_ONE);
         final Descriptor descriptorTwo = descriptor(CONTEXT_TWO);

jopa-integration-tests-jena/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>2.0.2</version>
+        <version>2.0.3</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

jopa-integration-tests-jena/src/test/java/cz/cvut/kbss/jopa/test/query/jena/TypedQueryTest.java

@@ -47,6 +47,7 @@ void setUp() {
         final Map<String, String> properties = new HashMap<>();
         properties.put(JenaOntoDriverProperties.JENA_STORAGE_TYPE, JenaOntoDriverProperties.IN_MEMORY);
         properties.put(JenaOntoDriverProperties.JENA_TREAT_DEFAULT_GRAPH_AS_UNION, Boolean.toString(true));
+        properties.put(JenaOntoDriverProperties.JENA_ISOLATION_STRATEGY, JenaOntoDriverProperties.SNAPSHOT);
         em = persistenceFactory.getEntityManager("SPARQLTypedQueryTests", false, properties);
         QueryTestEnvironment.generateTestData(em);
         em.clear();

jopa-integration-tests-owlapi/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>2.0.2</version>
+        <version>2.0.3</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

jopa-integration-tests-rdf4j/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>2.0.2</version>
+        <version>2.0.3</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <artifactId>jopa-integration-tests-rdf4j</artifactId>

jopa-integration-tests-rdf4j/src/test/java/cz/cvut/kbss/jopa/test/query/rdf4j/TypedQueryTest.java

@@ -69,6 +69,6 @@ protected EntityManager getEntityManager() {
     @Test
     @Override
     public void askQueryAgainstTransactionalOntologyContainsUncommittedChangesAsWell() {
-        // This is not solved in RDF4J driver, yet
+        // RDF4J does not support queries against transactional snapshot because it does not use it
     }
 }

jopa-integration-tests/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>2.0.2</version>
+        <version>2.0.3</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

jopa-integration-tests/src/main/java/cz/cvut/kbss/jopa/test/OWLClassM.java

@@ -23,6 +23,7 @@
 import cz.cvut.kbss.jopa.test.environment.TestEnvironment;
 import cz.cvut.kbss.ontodriver.model.LangString;
 
+import java.net.URI;
 import java.time.LocalDate;
 import java.time.ZoneOffset;
 import java.util.*;
@@ -73,6 +74,9 @@ public class OWLClassM {
     @OWLDataProperty(iri = Vocabulary.p_m_simpleLiteral, simpleLiteral = true)
     private String simpleLiteral;
 
+    @OWLDataProperty(iri = Vocabulary.p_m_simpleLiteralUri, simpleLiteral = true)
+    private URI simpleLiteralUri;
+
     @OWLDataProperty(iri = Vocabulary.p_m_StringCollection)
     private Collection<String> stringCollection;
 
@@ -232,6 +236,14 @@ public void setEnumSimpleLiteral(Severity enumSimpleLiteral) {
         this.enumSimpleLiteral = enumSimpleLiteral;
     }
 
+    public URI getSimpleLiteralUri() {
+        return simpleLiteralUri;
+    }
+
+    public void setSimpleLiteralUri(URI simpleLiteralUri) {
+        this.simpleLiteralUri = simpleLiteralUri;
+    }
+
     public ZoneOffset getWithConverter() {
         return withConverter;
     }
@@ -279,6 +291,7 @@ public String toString() {
                 ", integerSet=" + integerSet +
                 ", lexicalForm=" + lexicalForm +
                 ", simpleLiteral=" + simpleLiteral +
+                ", simpleLiteralUri=" + simpleLiteralUri +
                 ", stringCollection=" + stringCollection +
                 ", explicitDatatype=" + explicitDatatype +
                 ", langString=" + langString +
@@ -305,6 +318,7 @@ public void initializeTestValues(boolean includingKey) {
         this.integerSet = IntStream.generate(Generators::randomInt).limit(10).boxed().collect(Collectors.toSet());
         this.stringCollection = new HashSet<>(Arrays.asList("test-one", "test-two", "test-three"));
         this.enumSimpleLiteral = Severity.HIGH;
+        this.simpleLiteralUri = Generators.generateUri();
         this.withConverter = ZoneOffset.UTC;
     }
 }

jopa-integration-tests/src/main/java/cz/cvut/kbss/jopa/test/Vocabulary.java

@@ -93,6 +93,7 @@ public class Vocabulary {
     public static final String p_m_IntegerSet = ATTRIBUTE_IRI_BASE + "m-pluralIntAttribute";
     public static final String p_m_lexicalForm = ATTRIBUTE_IRI_BASE + "m-lexicalForm";
     public static final String p_m_simpleLiteral = ATTRIBUTE_IRI_BASE + "m-simpleLiteral";
+    public static final String p_m_simpleLiteralUri = ATTRIBUTE_IRI_BASE + "m-simpleLiteralUri";
     public static final String p_m_StringCollection = ATTRIBUTE_IRI_BASE + "m-collectionStringAttribute";
     public static final String p_m_explicitDatatype = ATTRIBUTE_IRI_BASE + "m-explicitDatatype";
     public static final String p_m_langString = ATTRIBUTE_IRI_BASE + "m-langString";