ont-api: 4.0.0-SNAPSHOT -- java-17 + jena-ontapi-5.1.0, related fixin…

…g and refactoring
owlcs · Aug 4, 2024 · be58554 · be58554
1 parent 8a95471
commit be58554
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# ONT-API (ver. 3.x.x)
+# ONT-API (ver. 4.x.x)
 
 <a href="https://maven-badges.herokuapp.com/maven-central/com.github.owlcs/ontapi"><img src="https://maven-badges.herokuapp.com/maven-central/com.github.owlcs/ontapi/badge.svg" height="25" alt="Maven Central"></a>
 <a href="https://javadoc.io/doc/com.github.owlcs/ontapi/latest/index.html"><img src="https://javadoc.io/badge2/com.github.owlcs/ontapi/javadoc.svg" height="25" alt="Javadoc"></a>
@@ -13,14 +13,13 @@ For more info about the library see the project [wiki](https://github.com/owlcs/
 
 ## Dependencies
 
-- **[Apache Jena](https://github.com/apache/jena)** (**4.x.x**)
+- **[Apache Jena](https://github.com/apache/jena)** (**5.x.x**)
 - **[OWL-API](https://github.com/owlcs/owlapi)** (**5.x.x**)
 - **[concurrent-rdf-graph](https://github.com/sszuev/concurrent-rdf-graph)** (jitpack)
-- **[jena-owl2](https://github.com/sszuev/jena-owl2)** (jitpack)
 
 ## Requirements
 
-- Java **11+**
+- Java **17+**
 
 ## License
 
@@ -33,13 +32,13 @@ For more info about the library see the project [wiki](https://github.com/owlcs/
 import com.github.owlcs.ontapi.OntManagers;
 import com.github.owlcs.ontapi.Ontology;
 import com.github.owlcs.ontapi.OntologyManager;
-import com.github.sszuev.jena.ontapi.OntSpecification;
-import com.github.sszuev.jena.ontapi.model.OntModel;
-import com.github.sszuev.jena.ontapi.vocabulary.OWL;
+import org.apache.jena.ontapi.OntSpecification;
+import org.apache.jena.ontapi.model.OntModel;
 import org.apache.jena.query.QueryExecution;
 import org.apache.jena.query.QueryExecutionFactory;
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.query.ResultSet;
+import org.apache.jena.vocabulary.OWL;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLDataFactory;
 

diff --git a/pom.xml b/pom.xml
@@ -20,46 +20,44 @@
 
     <groupId>com.github.owlcs</groupId>
     <artifactId>ontapi</artifactId>
-    <version>3.5.0</version>
+    <version>4.0.0-SNAPSHOT</version>
 
     <name>${project.groupId}:${project.artifactId}</name>
     <description>ONT-API is an RDF-centric library to work with OWL</description>
     <url>https://github.com/owlcs/ont-api</url>
 
     <properties>
-        <maven.compiler.target>11</maven.compiler.target>
-        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
+        <maven.compiler.source>17</maven.compiler.source>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
-        <!--https://mvnrepository.com/artifact/org.apache.jena/jena-arq-->
-        <version.jena>4.10.0</version.jena>
-        <!--https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-api-->
+        <!-- https://mvnrepository.com/artifact/org.apache.jena/jena-arq -->
+        <version.jena>5.1.0</version.jena>
+        <!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-api -->
         <version.owlapi>5.5.0</version.owlapi>
-        <!--https://mvnrepository.com/artifact/org.slf4j/slf4j-api-->
-        <version.slf4j>2.0.12</version.slf4j>
-        <!--https://mvnrepository.com/artifact/com.github.ben-manes.caffeine/caffeine-->
+        <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
+        <version.slf4j>2.0.13</version.slf4j>
+        <!-- https://mvnrepository.com/artifact/com.github.ben-manes.caffeine/caffeine -->
         <version.caffeine>3.1.8</version.caffeine>
-        <!--https://jitpack.io/#sszuev/concurrent-rdf-graph-->
+        <!-- https://jitpack.io/#sszuev/concurrent-rdf-graph -->
         <version.concurrent-rdf-graph>1.1.0-java</version.concurrent-rdf-graph>
-        <!--https://jitpack.io/#sszuev/jena-owl2-->
-        <version.jena-owl2>0.3.1-SNAPSHOT</version.jena-owl2>
-        <!--https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-->
-        <version.junit>5.10.2</version.junit>
-        <!--https://mvnrepository.com/artifact/org.mockito/mockito-core-->
-        <versio.mockito>5.11.0</versio.mockito>
+        <!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter -->
+        <version.junit>5.10.3</version.junit>
+        <!-- https://mvnrepository.com/artifact/org.mockito/mockito-core -->
+        <versio.mockito>5.12.0</versio.mockito>
 
-        <!--https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-gpg-plugin-->
-        <version.maven-gpg-plugin>3.2.2</version.maven-gpg-plugin>
-        <!--https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-source-plugin-->
-        <version.maven-source-plugin>3.3.0</version.maven-source-plugin>
-        <!--https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-javadoc-plugin-->
-        <version.maven-javadoc-plugin>3.6.3</version.maven-javadoc-plugin>
-        <!--https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-jar-plugin-->
-        <version.maven-jar-plugin>3.3.0</version.maven-jar-plugin>
-        <!--https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-compiler-plugin-->
-        <version.maven-compiler-plugin>3.12.1</version.maven-compiler-plugin>
-        <!--https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-surefire-plugin-->
-        <version.maven-surefire-plugin>3.2.5</version.maven-surefire-plugin>
+        <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-gpg-plugin -->
+        <version.maven-gpg-plugin>3.2.4</version.maven-gpg-plugin>
+        <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-source-plugin -->
+        <version.maven-source-plugin>3.3.1</version.maven-source-plugin>
+        <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-javadoc-plugin -->
+        <version.maven-javadoc-plugin>3.8.0</version.maven-javadoc-plugin>
+        <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-jar-plugin -->
+        <version.maven-jar-plugin>3.4.2</version.maven-jar-plugin>
+        <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-compiler-plugin -->
+        <version.maven-compiler-plugin>3.13.0</version.maven-compiler-plugin>
+        <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-surefire-plugin -->
+        <version.maven-surefire-plugin>3.3.1</version.maven-surefire-plugin>
     </properties>
 
     <licenses>
@@ -150,7 +148,7 @@
         <!-- Apache Jena: -->
         <dependency>
             <groupId>org.apache.jena</groupId>
-            <artifactId>jena-arq</artifactId>
+            <artifactId>jena-ontapi</artifactId>
             <version>${version.jena}</version>
         </dependency>
         <!-- OWL-API: -->
@@ -171,11 +169,6 @@
             <artifactId>concurrent-rdf-graph</artifactId>
             <version>${version.concurrent-rdf-graph}</version>
         </dependency>
-        <dependency>
-            <groupId>com.github.sszuev</groupId>
-            <artifactId>jena-owl2</artifactId>
-            <version>${version.jena-owl2}</version>
-        </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>

diff --git a/src/main/java/com/github/owlcs/ontapi/BlankNodeId.java b/src/main/java/com/github/owlcs/ontapi/BlankNodeId.java
@@ -0,0 +1,39 @@
+package com.github.owlcs.ontapi;
+
+import org.apache.jena.graph.Node;
+import org.apache.jena.graph.NodeFactory;
+
+import java.io.Serializable;
+
+public record BlankNodeId(String label) implements AsNode, Serializable {
+
+    public static BlankNodeId of(Node node) {
+        if (node.isBlank()) {
+            return new BlankNodeId(node.getBlankNodeLabel());
+        }
+        throw new IllegalArgumentException();
+    }
+
+    public static BlankNodeId of(String id) {
+        return new BlankNodeId(id);
+    }
+
+    public static BlankNodeId of() {
+        return new BlankNodeId(org.apache.jena.graph.BlankNodeId.createFreshId());
+    }
+
+    @Override
+    public Node asNode() {
+        return NodeFactory.createBlankNode(label);
+    }
+
+    @Override
+    public String toString() {
+        return label;
+    }
+
+    @Override
+    public int hashCode() {
+        return label.hashCode();
+    }
+}
diff --git a/src/main/java/com/github/owlcs/ontapi/DataFactory.java b/src/main/java/com/github/owlcs/ontapi/DataFactory.java
@@ -14,7 +14,6 @@
 
 package com.github.owlcs.ontapi;
 
-import org.apache.jena.graph.BlankNodeId;
 import org.apache.jena.graph.impl.LiteralLabel;
 import org.semanticweb.owlapi.model.OWLAnonymousIndividual;
 import org.semanticweb.owlapi.model.OWLDataFactory;

diff --git a/src/main/java/com/github/owlcs/ontapi/DataFactoryImpl.java b/src/main/java/com/github/owlcs/ontapi/DataFactoryImpl.java
@@ -100,14 +100,14 @@
 import com.github.owlcs.ontapi.owlapi.objects.swrl.ObjectPropertyAtomImpl;
 import com.github.owlcs.ontapi.owlapi.objects.swrl.SameIndividualAtomImpl;
 import com.github.owlcs.ontapi.owlapi.objects.swrl.VariableImpl;
-import org.apache.jena.graph.BlankNodeId;
 import org.apache.jena.graph.impl.LiteralLabel;
 import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.util.VersionInfo;
 import org.semanticweb.owlapi.vocab.OWL2Datatype;
 import org.semanticweb.owlapi.vocab.OWLFacet;
 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
 
+import java.io.Serial;
 import java.time.Instant;
 import java.util.Arrays;
 import java.util.Collection;
@@ -163,6 +163,7 @@
  */
 @SuppressWarnings("NullableProblems")
 public class DataFactoryImpl implements DataFactory {
+    @Serial
     private static final long serialVersionUID = -4032031232398404873L;
 
     private static final String LEXICAL_VALUE_CANNOT_BE_NULL = "lexicalValue cannot be null";
@@ -336,12 +337,12 @@ public OWLNamedIndividual getOWLNamedIndividual(IRI iri) {
 
     @Override
     public OWLAnonymousIndividual getOWLAnonymousIndividual(String id) {
-        return getOWLAnonymousIndividual(BlankNodeId.create(notNull(id, ID_CANNOT_BE_NULL)));
+        return getOWLAnonymousIndividual(BlankNodeId.of(notNull(id, ID_CANNOT_BE_NULL)));
     }
 
     @Override
     public OWLAnonymousIndividual getOWLAnonymousIndividual() {
-        return getOWLAnonymousIndividual(BlankNodeId.create());
+        return getOWLAnonymousIndividual(BlankNodeId.of());
     }
 
     /**
@@ -353,7 +354,7 @@ public OWLAnonymousIndividual getOWLAnonymousIndividual() {
      */
     @Override
     public OWLAnonymousIndividual getOWLAnonymousIndividual(BlankNodeId id) {
-        return new AnonymousIndividualImpl(notNull(id, ID_CANNOT_BE_NULL));
+        return new AnonymousIndividualImpl(notNull(id.label(), ID_CANNOT_BE_NULL));
     }
 
     @Override

diff --git a/src/main/java/com/github/owlcs/ontapi/ID.java b/src/main/java/com/github/owlcs/ontapi/ID.java
@@ -14,14 +14,13 @@
 
 package com.github.owlcs.ontapi;
 
-import com.github.sszuev.jena.ontapi.model.OntID;
-import com.github.sszuev.jena.ontapi.model.OntModel;
 import org.apache.jena.graph.Node;
 import org.apache.jena.graph.NodeFactory;
+import org.apache.jena.ontapi.model.OntID;
+import org.apache.jena.ontapi.model.OntModel;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLOntologyID;
 
-import java.lang.reflect.Field;
 import java.util.Objects;
 import java.util.Optional;
 
@@ -113,20 +112,10 @@ public ID(Node id, String version) throws OntApiException, IllegalStateException
         hashCode += 37 * internalID.hashCode();
         hashCode += 37 * ontologyIRI.hashCode();
         hashCode += 37 * versionIRI.hashCode();
-        setField("hashCode", hashCode);
-        setField("internalID", internalID);
-        setField("ontologyIRI", ontologyIRI);
-        setField("versionIRI", versionIRI);
-    }
-
-    private void setField(String name, Object value) {
-        try {
-            Field field = getClass().getSuperclass().getDeclaredField(name);
-            field.setAccessible(true);
-            field.set(this, value);
-        } catch (NoSuchFieldException | IllegalAccessException e) {
-            throw new IllegalStateException("Can't get access to " + name, e);
-        }
+        this.hashCode = hashCode;
+        this.internalID = internalID;
+        this.ontologyIRI = ontologyIRI;
+        this.versionIRI = versionIRI;
     }
 
     /**

diff --git a/src/main/java/com/github/owlcs/ontapi/ModelConfig.java b/src/main/java/com/github/owlcs/ontapi/ModelConfig.java
@@ -18,12 +18,13 @@
 import com.github.owlcs.ontapi.config.OntWriterConfiguration;
 import com.github.owlcs.ontapi.internal.InternalCache;
 import com.github.owlcs.ontapi.internal.InternalConfig;
-import com.github.sszuev.jena.ontapi.OntSpecification;
+import org.apache.jena.ontapi.OntSpecification;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
 import org.semanticweb.owlapi.model.OWLOntologyWriterConfiguration;
 import org.semanticweb.owlapi.model.OWLPrimitive;
 
+import java.io.Serial;
 import java.io.Serializable;
 import java.util.Map;
 import java.util.Objects;
@@ -39,6 +40,7 @@
  */
 @SuppressWarnings("WeakerAccess")
 public class ModelConfig implements InternalConfig, Serializable {
+    @Serial
     private static final long serialVersionUID = 3681978037818003272L;
 
     protected OntLoaderConfiguration readConf;

diff --git a/src/main/java/com/github/owlcs/ontapi/OWLFactoryWrapper.java b/src/main/java/com/github/owlcs/ontapi/OWLFactoryWrapper.java
@@ -16,9 +16,9 @@
 
 import com.github.owlcs.ontapi.config.CacheSettings;
 import com.github.owlcs.ontapi.config.OntLoaderConfiguration;
-import com.github.sszuev.jena.ontapi.UnionGraph;
 import javax.annotation.ParametersAreNonnullByDefault;
 import org.apache.jena.graph.Graph;
+import org.apache.jena.ontapi.UnionGraph;
 import org.semanticweb.owlapi.io.OWLOntologyCreationIOException;
 import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
 import org.semanticweb.owlapi.io.OWLOntologyInputSourceException;

diff --git a/src/main/java/com/github/owlcs/ontapi/OntApiException.java b/src/main/java/com/github/owlcs/ontapi/OntApiException.java
@@ -14,12 +14,12 @@
 
 package com.github.owlcs.ontapi;
 
-import com.github.sszuev.jena.ontapi.OntJenaException;
+import org.apache.jena.ontapi.OntJenaException;
 import org.semanticweb.owlapi.model.OWLRuntimeException;
 
 /**
  * A base {@code RuntimeException}, that must be used only in OWL-API part of implementation.
- * For a {@link com.github.sszuev.jena.ontapi Jena sybsustem}
+ * For a {@link org.apache.jena.ontapi Jena sybsustem}
  * there is its own exception: {@link OntJenaException}.
  * <p>
  * Created by @ssz on 27.09.2016.

diff --git a/src/main/java/com/github/owlcs/ontapi/OntBaseModel.java b/src/main/java/com/github/owlcs/ontapi/OntBaseModel.java
@@ -18,11 +18,11 @@
 import com.github.owlcs.ontapi.internal.InternalConfig;
 import com.github.owlcs.ontapi.internal.InternalGraphModel;
 import com.github.owlcs.ontapi.internal.InternalGraphModelImpl;
-import com.github.sszuev.jena.ontapi.OntSpecification;
-import com.github.sszuev.jena.ontapi.UnionGraph;
-import com.github.sszuev.jena.ontapi.impl.UnionGraphImpl;
-import com.github.sszuev.jena.ontapi.model.OntModel;
 import org.apache.jena.graph.Graph;
+import org.apache.jena.ontapi.OntSpecification;
+import org.apache.jena.ontapi.UnionGraph;
+import org.apache.jena.ontapi.impl.UnionGraphImpl;
+import org.apache.jena.ontapi.model.OntModel;
 import org.apache.jena.reasoner.ReasonerFactory;
 import org.semanticweb.owlapi.model.OWLPrimitive;
 

diff --git a/src/main/java/com/github/owlcs/ontapi/OntBaseModelImpl.java b/src/main/java/com/github/owlcs/ontapi/OntBaseModelImpl.java
@@ -16,12 +16,12 @@
 
 import com.github.owlcs.ontapi.internal.InternalGraphModel;
 import com.github.owlcs.ontapi.owlapi.OWLObjectImpl;
-import com.github.sszuev.jena.ontapi.model.OntModel;
-import com.github.sszuev.jena.ontapi.utils.Graphs;
 import javax.annotation.Nullable;
 import javax.annotation.ParametersAreNonnullByDefault;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.graph.GraphMemFactory;
+import org.apache.jena.ontapi.model.OntModel;
+import org.apache.jena.ontapi.utils.Graphs;
 import org.apache.jena.riot.RDFDataMgr;
 import org.semanticweb.owlapi.model.AxiomType;
 import org.semanticweb.owlapi.model.EntityType;
@@ -103,6 +103,7 @@
 import java.io.IOException;
 import java.io.ObjectInputStream;
 import java.io.ObjectOutputStream;
+import java.io.Serial;
 import java.util.Objects;
 import java.util.Set;
 import java.util.function.Function;
@@ -122,6 +123,7 @@
 public abstract class OntBaseModelImpl implements OWLOntology, OntBaseModel {
     // binary format to provide serialization:
     public static final OntFormat DEFAULT_SERIALIZATION_FORMAT = OntFormat.RDF_THRIFT;
+    @Serial
     private static final long serialVersionUID = 7605836729147058594L;
 
     protected transient InternalGraphModel base;
@@ -1182,6 +1184,7 @@ public Stream<OWLDifferentIndividualsAxiom> differentIndividualAxioms(OWLIndivid
      * @throws ClassNotFoundException if the class of a serialized object could not be found
      * @see OntologyManagerImpl#readObject(ObjectInputStream)
      */
+    @Serial
     @SuppressWarnings("JavadocReference")
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         in.defaultReadObject();
@@ -1202,6 +1205,7 @@ private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundE
      * @throws IOException     if I/O errors occur while writing to the underlying <code>OutputStream</code>
      * @throws OntApiException in case this instance encapsulates graph which is not plain in-memory graph
      */
+    @Serial
     private void writeObject(ObjectOutputStream out) throws IOException, OntApiException {
         Graph g = base.getBaseGraph();
         if (!Graphs.isGraphMem(g)) {