Merge branch 'development'

CHANGELOG.md

@@ -1,5 +1,9 @@
 # JOPA - Release Notes
 
+## 0.19.1 - 2022-11-08
+- Fix issues in working with `BigInteger` and `BigDecimal` values.
+- Fix a warning about illegal reflective operations on newer JDKs.
+
 ## 0.19.0 - 2022-10-26
 - Add support for disabling inference via query hints (Enhancement #101).
 - Allow registering custom attribute converters (Enhancement #118).
@@ -10,7 +14,7 @@
 - Fix support for custom datatypes in Jena driver (Bug #113).
 - Fix mapping enums to simple literals (Bug #111).
 - Fix an issue with double-wrapped indirect collections when cloning singleton Maps (Bug #114).
-- Dependency updates: RDF4J 3.7.7
+- Dependency updates: RDF4J 3.7.7.
 
 ## 0.18.6 - 2022-05-09
 - Automatically resolve inferred statements contexts for GraphDB (Enhancement #106).

datatype/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>jopa-all</artifactId>
         <groupId>cz.cvut.kbss.jopa</groupId>
-        <version>0.19.0</version>
+        <version>0.19.1</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>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

jopa-distribution/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</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>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

jopa-impl/src/main/java/cz/cvut/kbss/jopa/sessions/CloneBuilderImpl.java

@@ -26,6 +26,8 @@
 import org.slf4j.LoggerFactory;
 
 import java.lang.reflect.Field;
+import java.math.BigDecimal;
+import java.math.BigInteger;
 import java.net.URI;
 import java.net.URL;
 import java.time.*;
@@ -284,6 +286,8 @@ private static Set<Class<?>> getImmutableTypes() {
                          Long.class,
                          Float.class,
                          Double.class,
+                         BigInteger.class,
+                         BigDecimal.class,
                          Void.class,
                          String.class,
                          URI.class,

jopa-impl/src/main/java/cz/cvut/kbss/jopa/sessions/CollectionInstanceBuilder.java

@@ -204,8 +204,13 @@ void mergeChanges(Field field, Object target, Object originalValue, Object clone
         if (clone instanceof IndirectCollection) {
             clone = ((IndirectCollection<Collection<Object>>) clone).unwrap();
         }
-        final Optional<Collection<?>> origOpt = createNewInstance(clone.getClass(), clone.size());
-        Collection<Object> orig = (Collection<Object>) origOpt.orElse(createDefaultCollection(clone.getClass()));
+        Collection<Object> orig;
+        if (clone == Collections.emptyList() || clone == Collections.emptySet()) {
+            orig = createDefaultCollection(clone.getClass());
+        } else {
+            final Optional<Collection<?>> origOpt = createNewInstance(clone.getClass(), clone.size());
+            orig = (Collection<Object>) origOpt.orElse(createDefaultCollection(clone.getClass()));
+        }
         EntityPropertiesUtils.setFieldValue(field, target, orig);
 
         if (clone.isEmpty()) {

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

@@ -1,16 +1,14 @@
 /**
  * Copyright (C) 2022 Czech Technical University in Prague
- *
- * This program is free software: you can redistribute it and/or modify it under
- * the terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
- * details. You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ * <p>
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ * <p>
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+ * details. You should have received a copy of the GNU General Public License along with this program. If not, see
+ * <http://www.gnu.org/licenses/>.
  */
 package cz.cvut.kbss.jopa.sessions;
 
@@ -19,10 +17,13 @@
 import cz.cvut.kbss.jopa.environment.OWLClassA;
 import cz.cvut.kbss.jopa.environment.OWLClassC;
 import cz.cvut.kbss.jopa.environment.OWLClassJ;
+import cz.cvut.kbss.jopa.environment.OWLClassM;
 import cz.cvut.kbss.jopa.environment.utils.Generators;
 import cz.cvut.kbss.jopa.exceptions.OWLPersistenceException;
 import cz.cvut.kbss.jopa.model.descriptors.Descriptor;
 import cz.cvut.kbss.jopa.model.descriptors.EntityDescriptor;
+import cz.cvut.kbss.jopa.model.metamodel.CollectionType;
+import cz.cvut.kbss.jopa.utils.CollectionFactory;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -33,7 +34,7 @@
 import java.util.*;
 import java.util.stream.IntStream;
 
-import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.CoreMatchers.*;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.ArgumentMatchers.any;
@@ -106,7 +107,7 @@ public void buildCloneThrowsUnsupportedCollectionTypeExceptionWhenCollectionIsNe
         final OWLPersistenceException ex = assertThrows(OWLPersistenceException.class, () -> builder
                 .buildClone(owner, CollectionOwner.queueField(), owner.queue, new CloneConfiguration(descriptor)));
         assertThat(ex.getMessage(),
-                containsString("Cannot clone unsupported collection instance of type " + owner.queue.getClass()));
+                   containsString("Cannot clone unsupported collection instance of type " + owner.queue.getClass()));
     }
 
     private static class CollectionOwner {
@@ -170,7 +171,7 @@ public void buildingSingletonSetCloneRegistersElementCloneInUoW() throws Excepti
         when(uowMock.registerExistingObject(aOrig, descriptor, Collections.emptyList())).thenReturn(aClone);
         when(uowMock.isEntityType(OWLClassA.class)).thenReturn(true);
         final Set<?> clone = (Set<?>) builder.buildClone(owner, OWLClassJ.getOwlClassAField(), owner.getOwlClassA(),
-                new CloneConfiguration(descriptor));
+                                                         new CloneConfiguration(descriptor));
         assertEquals(owner.getOwlClassA().size(), clone.size());
         assertSame(aClone, clone.iterator().next());
         verify(uowMock).registerExistingObject(aOrig, descriptor, Collections.emptyList());
@@ -187,7 +188,7 @@ public void buildCloneClonesSingletonListWithContent() throws Exception {
         when(uowMock.isEntityType(OWLClassA.class)).thenReturn(true);
 
         final List<?> clone = (List<?>) builder.buildClone(owner, OWLClassC.getSimpleListField(), owner.getSimpleList(),
-                new CloneConfiguration(descriptor));
+                                                           new CloneConfiguration(descriptor));
         assertEquals(1, clone.size());
         assertSame(aClone, clone.get(0));
         verify(uowMock).registerExistingObject(aOrig, descriptor, Collections.emptyList());
@@ -207,11 +208,20 @@ public void buildCloneClonesArrayAsListWithContent() throws Exception {
         when(uowMock.isEntityType(OWLClassA.class)).thenReturn(true);
 
         final List<?> clone = (List<?>) builder.buildClone(owner, OWLClassC.getSimpleListField(), owner.getSimpleList(),
-                new CloneConfiguration(descriptor));
+                                                           new CloneConfiguration(descriptor));
         assertEquals(2, clone.size());
         assertSame(aOneClone, clone.get(0));
         assertSame(aTwoClone, clone.get(1));
         verify(uowMock).registerExistingObject(aOneOrig, descriptor, Collections.emptyList());
         verify(uowMock).registerExistingObject(aTwoOrig, descriptor, Collections.emptyList());
     }
+
+    @Test
+    void mergeChangesReplacesEmptySetWithDefaultSet() throws Exception {
+        final OWLClassM target = new OWLClassM();
+        target.initializeTestValues(true);
+        builder.mergeChanges(OWLClassM.getIntegerSetField(), target, new HashSet<>(), Collections.emptySet());
+        assertThat(target.getIntegerSet(),
+                   instanceOf(CollectionFactory.createDefaultCollection(CollectionType.SET).getClass()));
+    }
 }

jopa-integration-tests-jena/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

jopa-integration-tests-owlapi/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</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>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <artifactId>jopa-integration-tests-rdf4j</artifactId>

jopa-integration-tests/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

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

@@ -16,6 +16,8 @@
 
 import cz.cvut.kbss.jopa.test.OWLClassA;
 
+import java.math.BigDecimal;
+import java.math.BigInteger;
 import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URL;
@@ -130,7 +132,7 @@ public static Map<URI, Set<Object>> createTypedProperties(int size) {
     }
 
     private static Object generateRandomPropertyValue(int valueIndex, int propertyIndex) {
-        final int random = randomInt(6);
+        final int random = randomInt(8);
         switch (random) {
             case 0: // boolean
                 return valueIndex % 2 == 0;
@@ -145,6 +147,10 @@ private static Object generateRandomPropertyValue(int valueIndex, int propertyIn
                 return OffsetDateTime.now().truncatedTo(ChronoUnit.MILLIS);
             case 5: // String
                 return "TypedProperty_" + propertyIndex + "Value_" + valueIndex;
+            case 6:
+                return BigInteger.valueOf(valueIndex);
+            case 7:
+                return BigDecimal.valueOf(Math.PI);
             default:
                 throw new IllegalArgumentException();
         }

jopa-maven-plugin/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>jopa-all</artifactId>
         <groupId>cz.cvut.kbss.jopa</groupId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

jopa-owl2java/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

jopa-owlapi-utils/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

ontodriver-api/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>jopa-all</artifactId>
         <groupId>cz.cvut.kbss.jopa</groupId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

ontodriver-jena/pom.xml

@@ -8,7 +8,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

ontodriver-owlapi/pom.xml

@@ -11,7 +11,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

ontodriver-rdf4j/pom.xml

@@ -10,7 +10,7 @@
     <parent>
         <artifactId>jopa-all</artifactId>
         <groupId>cz.cvut.kbss.jopa</groupId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
     </parent>
 
     <properties>

ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/StorageConnector.java

@@ -41,7 +41,7 @@
 import java.util.List;
 import java.util.Objects;
 
-class StorageConnector extends AbstractConnector {
+public class StorageConnector extends AbstractConnector {
 
     private static final Logger LOG = LoggerFactory.getLogger(StorageConnector.class);
 
@@ -310,8 +310,10 @@ private static boolean isInMemoryRepository(Repository repo) {
         if (!(repo instanceof SailRepository)) {
             return false;
         }
-        final Sail sail = ((SailRepository) repo).getSail();
-        return sail instanceof SailWrapper ? ((SailWrapper) sail).getBaseSail() instanceof MemoryStore :
-               sail instanceof MemoryStore;
+        Sail sail = ((SailRepository) repo).getSail();
+        while (sail instanceof SailWrapper) {
+            sail = ((SailWrapper) sail).getBaseSail();
+        }
+        return sail instanceof MemoryStore;
     }
 }

ontodriver-sesame/pom.xml

@@ -8,7 +8,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>0.19.0</version>
+        <version>0.19.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

pom.xml

@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>cz.cvut.kbss.jopa</groupId>
-    <version>0.19.0</version>
+    <version>0.19.1</version>
     <artifactId>jopa-all</artifactId>
     <packaging>pom</packaging>
     <name>JOPA</name>