Merge pull request #239 from kbss-cvut/development

[2.0.0] Release

.github/workflows/maven.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [ master ]
   pull_request:
-    branches: [ master, development ]
+    branches: [ master, development, release/** ]
 
 jobs:
   build:
@@ -13,10 +13,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up JDK 11
+      - name: Set up JDK
         uses: actions/setup-java@v3
         with:
           distribution: 'temurin'
-          java-version: 11
+          java-version: 17
       - name: Build with Maven
         run: mvn -B package --file pom.xml

CHANGELOG.md

@@ -1,5 +1,13 @@
 # JOPA - Change Log
 
+## 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).
+- 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).
+- Require Java 17.
+
 ## 1.2.2 - 2024-01-30
 - Modify `DefaultClasspathScanner` to handle Spring Boot nested JAR introduced in 3.2.0 (Bug #227).
 

README.md

@@ -15,6 +15,7 @@ The library architecture and API is similar to JPA (see [2]) so that Java develo
 * Explicit access to inferred knowledge
 * Access to unmapped properties and individual's types
 * Transactions
+* Multilingual strings
 * Separate storage access layer - Jena, OWLAPI, RDF4J drivers are available
 
 #### Object-ontological Mapping Based on Integrity Constraints
@@ -23,13 +24,13 @@ Similarly to object-relational mapping (ORM), OOM enables to map ontological con
 
 More specifically, OOM in JOPA maps (using the JLS [3] terminology):
 
-| Ontology            | OO Language                              |
-|---------------------|------------------------------------------|
-| OWL Class           | Reference type                           |
-| Object property     | Reference type member                    |
-| Data property       | Primitive type member (+ String, Date)   |
-| Annotation property | Reference or primitive type member       |
-| Class assertions    | Reference type instance or @Types record |
+| Ontology            | OO Language                                                |
+|---------------------|------------------------------------------------------------|
+| OWL Class           | Reference type                                             |
+| Object property     | Reference type member                                      |
+| Data property       | Primitive type member (+ String, Date, MultilingualString) |
+| Annotation property | Reference or primitive type member                         |
+| Class assertions    | Reference type instance or @Types record                   |
 
 All this means that individuals belonging to an OWL class can be retrieved as instances of a (Java) class.
 
@@ -101,15 +102,6 @@ Supported storages:
 * [OWLAPI](https://github.com/owlcs/owlapi)
 * [RDF4J](https://rdf4j.org/)
 
-### Not Supported, yet
-
-JOPA currently does not support referential integrity. This, for example, means that removing an instance that is referenced 
-by another instance is possible even though it should not. 
-Such feature is vital for object-oriented application, but not compatible with 
-the open-world nature of ontologies. Design possibilities and their implications are currently being studied.
-
-Other missing/planned stuff can be found in the GitHub issue tracker and in [TODO.md](TODO.md).
-
 ## Modules
 
 The whole framework consists of several modules:
@@ -141,14 +133,14 @@ JOPA examples can be found in a separate repository at [https://github.com/kbss-
 
 A real-world, up-to-date project using JOPA is [TermIt](https://github.com/kbss-cvut/termit) - a SKOS-compatible vocabulary manager.
 
-Note that JOPA requires **Java 11** or later.
+Note that JOPA requires **Java 17** or later.
 
 ## Getting JOPA
 
 There are two ways of getting JOPA for a project:
 
 * Clone repository/download zip and build it with Maven,
-* Use a Maven dependency from the [Maven central repository](http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22cz.cvut.kbss.jopa%22).
+* Use a Maven/Gradle dependency from the [Maven central repository](http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22cz.cvut.kbss.jopa%22).
 
 Basically, the _jopa-impl_ module and one of the OntoDriver implementations is all that is needed:
 
@@ -169,7 +161,7 @@ Basically, the _jopa-impl_ module and one of the OntoDriver implementations is a
 
 ## More Info
 
-More information about JOPA can be found for example in articles [4], [5], [6] and on the GitHub [Wiki](https://github.com/kbss-cvut/jopa/wiki).
+More information about JOPA can be found, for example, in articles [4], [5], [6] and on the GitHub [Wiki](https://github.com/kbss-cvut/jopa/wiki).
 
 JOPA build status and code metrics can be found at:
 
@@ -195,6 +187,7 @@ Some related libraries:
 
 Notable changes:
 
+* **2.0.0** - Major rewrite of change tracking and lazy loading, remove internal API from the `jopa-api` module etc.
 * **1.0.0** - Support for static metamodel generation and mapping multiple inheritance via Java interfaces.
 * **0.20.0** - Allow editing inferred attributes (See the [wiki](https://github.com/kbss-cvut/jopa/wiki) for more details). Support `IN`, `NOT LIKE`, `<>` operators in SOQL.
 * **0.19.0** - Add RDF4J driver (renaming of Sesame driver, which has been deprecated and will be removed in the future)

datatype/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>jopa-all</artifactId>
         <groupId>cz.cvut.kbss.jopa</groupId>
-        <version>1.2.2</version>
+        <version>2.0.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

datatype/src/main/java/cz/cvut/kbss/jopa/datatype/util/Pair.java

@@ -17,30 +17,11 @@
  */
 package cz.cvut.kbss.jopa.datatype.util;
 
-import java.util.AbstractMap;
-
 /**
  * Represents an ordered pair of values.
  *
  * @param <F> Type of the first value in the pair
  * @param <S> Type of the second value in the pair
  */
-public final class Pair<F, S> extends AbstractMap.SimpleEntry<F, S> {
-
-    public Pair(F first, S second) {
-        super(first, second);
-    }
-
-    public F getFirst() {
-        return getKey();
-    }
-
-    public S getSecond() {
-        return getValue();
-    }
-
-    @Override
-    public String toString() {
-        return "(" + getFirst() + ", " + getSecond() + ")";
-    }
+public record Pair<F, S>(F first, S second) {
 }

jopa-api/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>cz.cvut.kbss.jopa</groupId>
         <artifactId>jopa-all</artifactId>
-        <version>1.2.2</version>
+        <version>2.0.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

jopa-api/src/main/java/cz/cvut/kbss/jopa/NonJPA.java

@@ -18,7 +18,7 @@
 package cz.cvut.kbss.jopa;
 
 /**
- * Denotes class/member that is not present in JPA 2.0 
+ * Denotes class/member that is not present in JPA (Jakarta Persistence)
  */
 public @interface NonJPA {
 }

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

@@ -22,15 +22,8 @@
  */
 public class InvalidAssertionIdentifierException extends OWLPersistenceException {
 
-    public InvalidAssertionIdentifierException(String message) {
-        super(message);
-    }
-
     public InvalidAssertionIdentifierException(String message, Throwable cause) {
         super(message, cause);
     }
 
-    public InvalidAssertionIdentifierException(Throwable cause) {
-        super(cause);
-    }
 }

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

@@ -28,8 +28,6 @@
  */
 public class NoResultException extends OWLPersistenceException {
 
-    private static final long serialVersionUID = -1891852675684320722L;
-
     public NoResultException(String message) {
         super(message);
     }

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

@@ -28,8 +28,6 @@
  */
 public class NoUniqueResultException extends OWLPersistenceException {
 
-    private static final long serialVersionUID = -6340735954399074847L;
-
     public NoUniqueResultException(String message) {
         super(message);
     }

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

@@ -22,8 +22,6 @@
  */
 public class OWLEntityExistsException extends OWLPersistenceException {
 
-    private static final long serialVersionUID = 453666323423782580L;
-
     public OWLEntityExistsException(String message) {
         super(message);
     }

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

@@ -24,8 +24,6 @@
  */
 public class RollbackException extends OWLPersistenceException {
 
-    private static final long serialVersionUID = 8371285315001388603L;
-
     public RollbackException(String message) {
         super(message);
     }

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

@@ -22,8 +22,6 @@
  */
 public class StorageAccessException extends OWLPersistenceException {
 
-    private static final long serialVersionUID = 4661531292404254252L;
-
     public StorageAccessException(String message) {
         super(message);
     }

jopa-api/src/main/java/cz/cvut/kbss/jopa/sessions/Cache.java → jopa-api/src/main/java/cz/cvut/kbss/jopa/model/Cache.java

@@ -15,7 +15,7 @@
  * You should have received a copy of the GNU Lesser General Public
  * License along with this library.
  */
-package cz.cvut.kbss.jopa.sessions;
+package cz.cvut.kbss.jopa.model;
 
 import cz.cvut.kbss.jopa.model.descriptors.Descriptor;
 
@@ -26,8 +26,6 @@
  * <p>
  * If a cache is not in use, the methods of this interface have no effect, except for contains, which
  * returns false.
- * <p>
- * Taken from JPA 2.
  */
 public interface Cache {
 

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

@@ -27,14 +27,14 @@
 import cz.cvut.kbss.jopa.model.query.Query;
 import cz.cvut.kbss.jopa.model.query.TypedQuery;
 import cz.cvut.kbss.jopa.model.query.criteria.CriteriaQuery;
-import cz.cvut.kbss.jopa.sessions.CriteriaBuilder;
+import cz.cvut.kbss.jopa.model.query.criteria.CriteriaBuilder;
 import cz.cvut.kbss.jopa.transactions.EntityTransaction;
 
 import java.net.URI;
 import java.util.List;
 import java.util.Map;
 
-public interface EntityManager {
+public interface EntityManager extends AutoCloseable {
 
     /**
      * Make an instance managed and persistent.
@@ -140,14 +140,7 @@ public interface EntityManager {
      *                                  null}
      * @see #getContexts()
      */
-    <T> T find(final Class<T> entityClass, final Object identifier,
-               final Descriptor descriptor);
-
-    // TODO JPA 2.0 find with properties
-
-    // TODO JPA 2.0 find with lock mode
-
-    // TODO JPA 2.0 find with lock mode and properties
+    <T> T find(final Class<T> entityClass, final Object identifier, final Descriptor descriptor);
 
     /**
      * Get an instance, whose state may be lazily fetched.
@@ -192,33 +185,6 @@ <T> T find(final Class<T> entityClass, final Object identifier,
      */
     void flush();
 
-    // /**
-    // * Set the flush mode that applies to all objects contained in the
-    // * persistence context.
-    // *
-    // * @param flushMode
-    // */
-    // public void setFlushMode(FlushModeType flushMode);
-
-    // TODO JPA 2.0 getFlushMode
-
-    // /**
-    // * Set the lock mode for an entity object contained in the persistence
-    // * context.
-    // *
-    // * @param entity
-    // * @param lockMode
-    // * @throws PersistenceException
-    // * if an unsupported lock call is made
-    // * @throws IllegalArgumentException
-    // * if the instance is not an entity or is a detached entity
-    // * @throws TransactionRequiredException
-    // * if there is no transaction
-    // */
-    // public void lock(Object entity, LockModeType lockMode);
-
-    // TODO JPA 2.0 lock with lock mode and properties
-
     /**
      * Refresh the state of the instance from the data source, overwriting changes made to the entity, if any.
      *
@@ -229,10 +195,6 @@ <T> T find(final Class<T> entityClass, final Object identifier,
      */
     void refresh(final Object entity);
 
-    // TODO JPA 2.0 refresh with lock mode
-    // TODO JPA 2.0 refresh with properties
-    // TODO JPA 2.0 refresh with lock mode and properties
-
     /**
      * Clear the persistence context, causing all managed entities to become detached. Changes made to entities that
      * have not been flushed to the database will not be persisted.
@@ -285,8 +247,6 @@ <T> T find(final Class<T> entityClass, final Object identifier,
      */
     <T> boolean isInferred(T entity, FieldSpecification<? super T, ?> attribute, Object value);
 
-    // TODO JPA 2.0 public LockModeType getLockMode(Object entity)
-
     /**
      * Get the properties and hints and associated values that are in effect for the entity manager.
      * <p>