.github/workflows/maven-publish.yml

@@ -0,0 +1,35 @@
+# This workflow will build a package using Maven and then publish it to GitHub packages when a release is created
+# For more information see: https://github.com/actions/setup-java/blob/main/docs/advanced-usage.md#apache-maven-with-a-settings-path
+
+name: Maven Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK 14
+      uses: actions/setup-java@v2
+      with:
+        java-version: '14'
+        distribution: 'adopt'
+        cache: maven
+        server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
+        settings-path: ${{ github.workspace }} # location for the settings.xml file
+
+    - name: Build with Maven
+      run: mvn -B package --file pom.xml
+
+    - name: Publish to GitHub Packages Apache Maven
+      run: mvn deploy -s $GITHUB_WORKSPACE/settings.xml
+      env:
+        GITHUB_TOKEN: ${{ github.token }}

.github/workflows/maven.yml

@@ -16,10 +16,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up JDK 11
+    - name: Set up JDK 14
       uses: actions/setup-java@v2
       with:
-        java-version: '11'
+        java-version: '14'
         distribution: 'adopt'
         cache: maven
     - name: Build with Maven

README.md

@@ -1,10 +1,15 @@
-# OWLDiff
+# OWLDiff [![Java CI with Maven](https://github.com/psiotwo/owldiff/actions/workflows/maven.yml/badge.svg?branch=master)](https://github.com/psiotwo/owldiff/actions/workflows/maven.yml)
 
 A tool to perform a 2-way diff of OWL ontologies.
 
 ## Requirements
 - Java 14
 
+## Run
+In order to run OWLDiff run `mvn clean install` and
+- for CLI: `cd owldiff-cli && mvn assembly:assembly` to create an executable JAR file in `target/owldiff-cli-<VERSION>-jar-with-dependencies.jar`
+- for Desktop UI: `cd owldiff-standalone && mvn assembly:assembly` to create a ZIP file`target/owldiff-standalone-<VERSION>-dist-bin.zip`. Unzip it and run `bin/owldiff`.
+
 ## Features
 - syntactic diff/merge functionality
 - explanations for inferred axioms
@@ -40,5 +45,10 @@ A tool to perform a 2-way diff of OWL ontologies.
 - to perform the diff of file/URI <u1> and file/URI <u2> run
 			'java -jar owldiff.jar <u1> <u2>' (or the convenience script 'owldiff <u1> <u2>' on linux)
 
+## Resources
+- Kremen, P. & Šmíd, M. & Kouba, Z.. (2011). OWLDiff: A practical tool for comparison and merge of owl ontologies. Proceedings of the 10th International Workshop on Web Semantics. 229-233. 
+- Kremen, P. & Kouba, Z.. (2009). Incremental Approach to Error Explanations in Ontologies. Networked Knowledge - Networked Media - Integrating Knowledge Management 2009: 171-185
+
+
 * * *
 2020 Czech Technical University, Knowledge Based and Software Systems Group

owldiff-cli/pom.xml

@@ -11,13 +11,13 @@
   ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
   -->
 
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
     <parent>
         <groupId>cz.cvut.kbss</groupId>
         <artifactId>owldiff-parent</artifactId>
         <relativePath>../owldiff-parent/pom.xml</relativePath>
-        <version>0.2.1-SNAPSHOT</version>
+        <version>0.2.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>owldiff-cli</artifactId>
@@ -33,31 +33,30 @@
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
-            <version>1.7.26</version>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-core</artifactId>
         </dependency>
         <dependency>
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
-            <version>1.2.3</version>
         </dependency>
         <dependency>
             <groupId>org.projectlombok</groupId>
             <artifactId>lombok</artifactId>
-            <version>1.18.16</version>
         </dependency>
         <dependency>
-            <groupId>com.github.rvesse</groupId>
-            <artifactId>airline</artifactId>
-            <version>2.8.0</version>
+            <groupId>info.picocli</groupId>
+            <artifactId>picocli</artifactId>
         </dependency>
     </dependencies>
 
     <build>
         <plugins>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.1.0</version>
+                <version>3.3.0</version>
                 <configuration>
                     <archive>
                         <index>true</index>
@@ -71,9 +70,8 @@
                 </configuration>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-assembly-plugin</artifactId>
-                <version>2.4</version>
+                <version>3.6.0</version>
                 <configuration>
                     <archive>
                         <manifest>

owldiff-cli/src/main/java/cz/cvut/kbss/owldiff/cli/ChangeTypeUtils.java

@@ -0,0 +1,24 @@
+package cz.cvut.kbss.owldiff.cli;
+
+import cz.cvut.kbss.owldiff.change.OWLChangeType;
+
+public class ChangeTypeUtils {
+
+    public static String changeTypeName(OWLChangeType ct) {
+        switch (ct) {
+            case SYNTACTIC_ORIG_REST:
+                return "-";
+            case SYNTACTIC_UPD_REST:
+                return "+";
+            case ENTAILEXPL_INFERRED:
+            case ENTAILEXPL_POSSIBLY_REMOVE:
+            case CEX_ISIN_DIFFR_DIFFL:
+            case CEX_ISIN_DIFFR:
+            case CEX_ISIN_DIFFL:
+            case HEURISTIC_SAME_SUB_AND_SUPER_CLASSES:
+            case HEURISTIC_SINGLE_UNMATCHED_SIBLING:
+            default:
+                throw new UnsupportedOperationException();
+        }
+    }
+}

owldiff-cli/src/main/java/cz/cvut/kbss/owldiff/cli/Diff.java

@@ -1,153 +1,83 @@
 package cz.cvut.kbss.owldiff.cli;
 
-import com.github.rvesse.airline.annotations.Arguments;
-import com.github.rvesse.airline.annotations.Command;
-import cz.cvut.kbss.owldiff.change.OWLChangeType;
-import cz.cvut.kbss.owldiff.change.SyntacticAxiomChange;
 import cz.cvut.kbss.owldiff.diff.syntactic.SyntacticDiff;
 import cz.cvut.kbss.owldiff.diff.syntactic.SyntacticDiffOutput;
 import cz.cvut.kbss.owldiff.ontology.OntologyHandler;
 import cz.cvut.kbss.owldiff.syntax.ManchesterSyntax;
+import lombok.extern.slf4j.Slf4j;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.IRIDocumentSource;
+import org.semanticweb.owlapi.model.*;
+
 import java.io.File;
 import java.net.URI;
 import java.text.MessageFormat;
-import java.util.Comparator;
-import java.util.List;
 import java.util.regex.Pattern;
-import lombok.extern.slf4j.Slf4j;
-import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.io.IRIDocumentSource;
-import org.semanticweb.owlapi.io.OWLRendererException;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.MissingImportHandlingStrategy;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.model.OntologyConfigurator;
+
+import static cz.cvut.kbss.owldiff.cli.ChangeTypeUtils.changeTypeName;
 
 @Slf4j
-@Command(name = "diff")
 public class Diff {
 
-    @Arguments(title = "File paths", description = "Path of the oldFile and newFile")
-    private List<String> paths;
-
-    public void run() throws OWLOntologyCreationException, OWLRendererException {
-        if (paths.size() != 2) {
-            log.error("Exactly two files must be provided, but got {0} only", paths.size());
-            return;
-        }
-
-        String oldFF = paths.get(0);
-        String newFF = paths.get(1);
-
-        URI oldF;
-        URI newF;
-        if (new File(oldFF).exists()) {
-            oldF = new File(oldFF).getAbsoluteFile().toURI();
-        } else {
-            log.error("File does not exist {}");
-            throw new RuntimeException();
-        }
-
-        if (new File(newFF).exists()) {
-            newF = new File(newFF).getAbsoluteFile().toURI();
-        } else {
-            log.error("File does not exist {}");
-            throw new RuntimeException();
-        }
-
-        if (oldF.isAbsolute() && newF.isAbsolute()) {
-            final OWLOntologyManager originalM = OWLManager
-                .createOWLOntologyManager();
-            originalM.setOntologyConfigurator(
-                new OntologyConfigurator()
-                    .setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT)
-                    .setReportStackTraces(true)
-            .setStrict(false));
-            originalM.getIRIMappers().add( (ontologyIRI) -> {
-            if (Pattern.compile(oldFF).matcher(ontologyIRI.toString()).matches()) {
-                return ontologyIRI;
-            } else {
-                return IRI.create(String.format("file://%s", ontologyIRI.toString()));
-            }});
-            final OWLOntology originalO =
-                originalM.loadOntologyFromOntologyDocument(new IRIDocumentSource(
-                    IRI.create(oldF)));
-
-            final OWLOntologyManager updateM = OWLManager.createOWLOntologyManager();
-            updateM.setOntologyConfigurator(new OntologyConfigurator().setMissingImportHandlingStrategy(
-                MissingImportHandlingStrategy.SILENT)
-                .setReportStackTraces(true)
-                .setStrict(false)
-            );
-            updateM.getIRIMappers().add( (ontologyIRI) -> {
-                if (Pattern.compile(newFF).matcher(ontologyIRI.toString()).matches()) {
-                    return ontologyIRI;
-                } else {
-                    return IRI.create(String.format("file://%s", ontologyIRI.toString()));
-                }});
-
-            OWLOntology updateO =
-                updateM.loadOntologyFromOntologyDocument(new IRIDocumentSource(IRI.create(newF)));
+    public void run(final String original, final String updated) throws OWLOntologyCreationException {
+        final OWLOntology originalO = createFreshOntology(original);
+        final OWLOntology updateO = createFreshOntology(updated);
 
-            SyntacticDiff d = new SyntacticDiff(new OntologyHandler() {
-                @Override public OWLOntology getOriginalOntology() {
-                    return originalO;
-                }
-
-                @Override public OWLOntology getUpdateOntology() {
-                    return updateO;
-                }
-            });
+        final SyntacticDiff d = new SyntacticDiff(new OntologyHandler() {
+            @Override
+            public OWLOntology getOriginalOntology() {
+                return originalO;
+            }
 
-            final SyntacticDiffOutput o = d.diff();
+            @Override
+            public OWLOntology getUpdateOntology() {
+                return updateO;
+            }
+        });
 
-            ManchesterSyntax s = new ManchesterSyntax();
-            o.getOWLChanges()
+        final SyntacticDiffOutput o = d.diff();
+        final ManchesterSyntax s = new ManchesterSyntax();
+        o.getOWLChanges()
                 .stream().sorted(
-                new ChangeComparator()
-                    .thenComparing(SyntacticAxiomChange::getOWLChangeType))
+                        new SyntacticChangeComparator())
                 .forEach(c ->
-                    System.out.println(MessageFormat.format("{0} {1}", changeTypeName(c.getOWLChangeType()),
-                    s.writeAxiom(c.getAxiom(), false, null, false)))
+                        System.out.println(MessageFormat.format("{0} {1}",
+                                changeTypeName(c.getOWLChangeType()),
+                                s.writeAxiom(c.getAxiom(), false, null, false)))
                 );
-
-        } else {
-            log.error("Files are not absolute");
-        }
     }
 
-    private class ChangeComparator implements Comparator<SyntacticAxiomChange> {
-
-        private MainOwlEntityResolver resolver;
+    private URI ensureFileExists(final String file) {
+        final File f = new File(file);
 
-        public ChangeComparator() {
-            this.resolver = new MainOwlEntityResolver();
+        if (!f.exists()) {
+            throw new IllegalArgumentException(MessageFormat.format("File \"{0}\" does not exist.", file));
+        } else if (!f.isAbsolute()) {
+            throw new IllegalArgumentException(MessageFormat.format("File \"{0}\" is not absolute.", file));
+        } else {
+            return f.getAbsoluteFile().toURI();
         }
+    }
 
-        public int compare(SyntacticAxiomChange c1, SyntacticAxiomChange c2) {
-            c1.getAxiom().accept(resolver);
-            final IRI c1Iri = resolver.getEntity();
-
-            c2.getAxiom().accept(resolver);
-            final IRI c2Iri = resolver.getEntity();
-
-            if ( c1Iri != null && c1Iri.equals(c2Iri) ) {
-                return 0;
-            } else if (c1Iri != null && c2Iri != null) {
-                return c1Iri.compareTo(c2Iri);
-            } else {
-                return c1.getAxiom().compareTo(c2.getAxiom());
-            }
-        }
+    private OWLOntology createFreshOntology(final String original) throws OWLOntologyCreationException {
+        final OntologyConfigurator configurator = new OntologyConfigurator()
+                .setMissingImportHandlingStrategy(
+                        MissingImportHandlingStrategy.SILENT)
+                .setReportStackTraces(true)
+                .setStrict(false);
+        final OWLOntologyManager originalM = OWLManager
+                .createOWLOntologyManager();
+        originalM.setOntologyConfigurator(configurator);
+        originalM.getIRIMappers().add(createIRIMapper(original));
+        return
+                originalM.loadOntologyFromOntologyDocument(new IRIDocumentSource(
+                        IRI.create(ensureFileExists(original))));
     }
 
-    private String changeTypeName(OWLChangeType ct) {
-        switch (ct) {
-            case SYNTACTIC_ORIG_REST: return "-";
-            case SYNTACTIC_UPD_REST: return "+";
-            default: throw new UnsupportedOperationException();
-        }
+    private OWLOntologyIRIMapper createIRIMapper(final String file) {
+        final Pattern p = Pattern.compile(file);
+        return (ontologyIRI) -> p.matcher(ontologyIRI.toString()).matches() ?
+                ontologyIRI :
+                IRI.create(String.format("file://%s", ontologyIRI));
     }
 }

owldiff-cli/src/main/java/cz/cvut/kbss/owldiff/cli/DiffCommand.java

@@ -0,0 +1,33 @@
+package cz.cvut.kbss.owldiff.cli;
+
+import lombok.extern.slf4j.Slf4j;
+import picocli.CommandLine;
+
+import java.util.concurrent.Callable;
+
+@Slf4j
+@CommandLine.Command(name = "diff", mixinStandardHelpOptions = true,
+        description = "Compares OWL ontologies.")
+public class DiffCommand implements Callable<Integer> {
+
+    @CommandLine.Parameters(description = "Original ontology file.")
+    private String original;
+
+    @CommandLine.Parameters(description = "Updated ontology file.")
+    private String updated;
+
+    public static void main(String[] args) {
+        new CommandLine(new DiffCommand()).execute(args);
+    }
+
+    public Integer call() {
+        try {
+            new Diff().run(original, updated);
+        } catch (Exception e) {
+            log.error("Exception during command execution: {}", e.getMessage());
+            log.debug("Details:", e);
+            return -1;
+        }
+        return 0;
+    }
+}

owldiff-cli/src/main/java/cz/cvut/kbss/owldiff/cli/SyntacticChangeComparator.java

@@ -0,0 +1,26 @@
+package cz.cvut.kbss.owldiff.cli;
+
+import cz.cvut.kbss.owldiff.change.SyntacticAxiomChange;
+import org.semanticweb.owlapi.model.IRI;
+
+import java.util.Comparator;
+
+public class SyntacticChangeComparator implements Comparator<SyntacticAxiomChange> {
+
+    private IRI getIRI(SyntacticAxiomChange c) {
+        final MainOwlEntityResolver resolver = new MainOwlEntityResolver();
+        c.getAxiom().accept(resolver);
+        return resolver.getEntity();
+    }
+
+    public int compare(final SyntacticAxiomChange c1, final SyntacticAxiomChange c2) {
+        return Comparator.nullsFirst((cx1, cx2) -> {
+            final SyntacticAxiomChange cc1 = (SyntacticAxiomChange) cx1;
+            final SyntacticAxiomChange cc2 = (SyntacticAxiomChange) cx2;
+            // Compare entities first
+            int c = Comparator.nullsFirst(IRI::compareTo).compare(getIRI(cc1), getIRI(cc2));
+            // ... then axioms inside these entities.
+            return c != 0 ? c : cc1.getAxiom().compareTo(cc2.getAxiom());
+        }).compare(c1, c2);
+    }
+}

owldiff-cli/src/main/resources/logback.xml

@@ -8,7 +8,7 @@
         </layout>
     </appender>
 
-    <logger name="cz.cvut.kbss" level="info" additivity="false">
+    <logger name="cz.cvut.kbss" level="DEBUG" additivity="false">
         <appender-ref ref="CONSOLE"/>
     </logger>
 

owldiff-core/pom.xml

@@ -17,13 +17,29 @@
         <groupId>cz.cvut.kbss</groupId>
         <artifactId>owldiff-parent</artifactId>
         <relativePath>../owldiff-parent/pom.xml</relativePath>
-        <version>0.2.1-SNAPSHOT</version>
+        <version>0.2.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>owldiff-core</artifactId>
     <packaging>jar</packaging>
     <name>OWLDiff Core Library</name>
 
+    <dependencies>
+        <dependency>
+            <groupId>net.sourceforge.owlapi</groupId>
+            <artifactId>owlapi-distribution</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>cz.cvut.kbss</groupId>
+            <artifactId>explanations</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
     <build>
         <resources>
             <resource>
@@ -33,17 +49,15 @@
         </resources>
         <plugins>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-resources-plugin</artifactId>
-                <version>3.1.0</version>
+                <version>3.3.1</version>
                 <configuration>
                     <encoding>UTF-8</encoding>
                 </configuration>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-source-plugin</artifactId>
-                <version>3.2.1</version>
+                <version>3.3.0</version>
                 <executions>
                     <execution>
                         <phase>package</phase>
@@ -54,9 +68,8 @@
                 </executions>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-assembly-plugin</artifactId>
-                <version>2.4</version>
+                <version>3.6.0</version>
                 <configuration>
                     <descriptors>
                         <descriptor>
@@ -69,9 +82,8 @@
                 </configuration>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.5.0</version>
                 <configuration>
                     <encoding>UTF-8</encoding>
                 </configuration>
@@ -88,22 +100,4 @@
         <extensions>
         </extensions>
     </build>
-    <dependencies>
-        <dependency>
-            <groupId>net.sourceforge.owlapi</groupId>
-            <artifactId>owlapi-distribution</artifactId>
-            <version>5.1.16</version>
-        </dependency>
-        <dependency>
-            <groupId>cz.cvut.kbss</groupId>
-            <artifactId>explanations</artifactId>
-            <version>0.91</version>
-        </dependency>
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <version>4.13.1</version>
-            <scope>test</scope>
-        </dependency>
-    </dependencies>
 </project>

owldiff-core/src/test/java/cz/cvut/kbss/owldiff/diff/syntactic/SyntacticDiffTest.java

@@ -17,76 +17,59 @@
 import cz.cvut.kbss.owldiff.diff.OWLDiff;
 import cz.cvut.kbss.owldiff.diff.OWLDiffOutput;
 import cz.cvut.kbss.owldiff.ontology.OntologyHandler;
-import junit.framework.Assert;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.*;
 
 import java.util.Set;
 
-/**
- * Created with IntelliJ IDEA.
- * User: kremep1
- * Date: 10/3/12
- * Time: 8:01 AM
- * To change this template use File | Settings | File Templates.
- */
 public class SyntacticDiffTest {
 
-    OntologyHandler h;
+    private static final String iri = "http://kbss.felk.cvut.cz/ontologies/2012/owldiff-test-syntactic.owl";
+    private static final String ns = iri + "#";
 
-    @Before
-    public void setUp() throws Exception {
-        IRI iri = IRI.create("http://kbss.felk.cvut.cz/ontologies/2012/owldiff-test-syntactic.owl");
-        final OWLOntology o = OWLManager.createOWLOntologyManager().createOntology(iri);
-        final OWLDataFactory oF = o.getOWLOntologyManager().getOWLDataFactory();
-        final OWLClass oClassA1 = oF.getOWLClass(IRI.create(iri.toString() + "#A1"));
-        final OWLClass oClassA2 = oF.getOWLClass(IRI.create(iri.toString() + "#A2"));
-        final OWLObjectProperty oPropR = oF.getOWLObjectProperty(IRI.create(iri.toString() + "#R"));
+    @Test
+    public void testDiffBasic() throws Exception {
 
-        o.getOWLOntologyManager().addAxiom(o, oF.getOWLDeclarationAxiom(oClassA1));
-        o.getOWLOntologyManager().addAxiom(o, oF.getOWLDeclarationAxiom(oClassA2));
-        o.getOWLOntologyManager().addAxiom(o, oF.getOWLDeclarationAxiom(oPropR));
+        final OWLOntology o = OWLManager.createOWLOntologyManager().createOntology(IRI.create(iri));
+        final OWLDataFactory oF = o.getOWLOntologyManager().getOWLDataFactory();
+        final OWLClass oCA1 = oF.getOWLClass(ns, "A1");
+        final OWLClass oCA2 = oF.getOWLClass(ns, "A2");
+        final OWLObjectProperty oR = oF.getOWLObjectProperty(ns, "R");
 
-        o.getOWLOntologyManager().addAxiom(o, oF.getOWLSubClassOfAxiom(oClassA1, oF.getOWLObjectSomeValuesFrom(oPropR, oClassA2)));
+        final OWLOntologyManager om = o.getOWLOntologyManager();
+        om.addAxiom(o, oF.getOWLDeclarationAxiom(oCA1));
+        om.addAxiom(o, oF.getOWLDeclarationAxiom(oCA2));
+        om.addAxiom(o, oF.getOWLDeclarationAxiom(oR));
+        om.addAxiom(o, oF.getOWLSubClassOfAxiom(oCA1, oF.getOWLObjectSomeValuesFrom(oR, oCA2)));
 
-        final OWLOntology u = OWLManager.createOWLOntologyManager().createOntology(iri);
+        final OWLOntology u = OWLManager.createOWLOntologyManager().createOntology(IRI.create(iri));
 
         final OWLDataFactory uF = o.getOWLOntologyManager().getOWLDataFactory();
-        final OWLClass uClassA1 = uF.getOWLClass(IRI.create(iri.toString() + "#A1"));
-        final OWLObjectProperty uPropR = uF.getOWLObjectProperty(IRI.create(iri.toString() + "#R"));
-
-        u.getOWLOntologyManager().addAxiom(u, uF.getOWLDeclarationAxiom(uClassA1));
-        u.getOWLOntologyManager().addAxiom(u, uF.getOWLDeclarationAxiom(uPropR));
+        final OWLClass uCA1 = uF.getOWLClass(ns, "A1");
+        final OWLObjectProperty uR = uF.getOWLObjectProperty(ns, "R");
 
-        u.getOWLOntologyManager().addAxiom(u, uF.getOWLSubClassOfAxiom(uClassA1, uF.getOWLObjectSomeValuesFrom(uPropR, uClassA1)));
-        u.getOWLOntologyManager().addAxiom(u, uF.getOWLSubClassOfAxiom(uClassA1, uF.getOWLThing()));
+        final OWLOntologyManager um = u.getOWLOntologyManager();
+        um.addAxiom(u, uF.getOWLDeclarationAxiom(uCA1));
+        um.addAxiom(u, uF.getOWLDeclarationAxiom(uR));
+        um.addAxiom(u, uF.getOWLSubClassOfAxiom(uCA1, uF.getOWLObjectSomeValuesFrom(uR, uCA1)));
+        um.addAxiom(u, uF.getOWLSubClassOfAxiom(uCA1, uF.getOWLThing()));
 
-
-        h = new OntologyHandler() {
+        final OWLDiff diff = new SyntacticDiff(new OntologyHandler() {
             public OWLOntology getOriginalOntology() {
                 return o;
             }
 
             public OWLOntology getUpdateOntology() {
                 return u;
             }
-        };
-    }
-
-    @After
-    public void tearDown() throws Exception {
-    }
+        });
 
-    @Test
-    public void testDiffBasic() throws Exception {
-        OWLDiff diff = new SyntacticDiff(h);
-        OWLDiffOutput diffOutput = diff.diff();
-        Set<? extends OWLChange> changes = diffOutput.getOWLChanges();
+        final OWLDiffOutput diffOutput = diff.diff();
+        final Set<? extends OWLChange> changes = diffOutput.getOWLChanges();
 
-        Assert.assertNotNull(changes);
-        Assert.assertEquals(changes.size(), 4);
+        Assertions.assertNotNull(changes);
+        Assertions.assertEquals(4, changes.size());
     }
 }

owldiff-parent/pom.xml

@@ -19,12 +19,12 @@
     <artifactId>owldiff-parent</artifactId>
     <packaging>pom</packaging>
     <name>OWLDiff Parent POM</name>
-    <version>0.2.1-SNAPSHOT</version>
+    <version>0.2.1</version>
     <repositories>
         <repository>
             <id>kbss</id>
             <name>KBSS Maven 2 Repository</name>
-            <url>http://kbss.felk.cvut.cz/m2repo</url>
+            <url>https://kbss.felk.cvut.cz/m2repo</url>
         </repository>
     </repositories>
     <developers>
@@ -48,7 +48,7 @@
         </developer>
         <developer>
             <name>Peter Butka</name>
-            <email>peter. butka@gmail.com</email>
+            <email>peter.butka@gmail.com</email>
             <organization>CVUT</organization>
         </developer>
     </developers>
@@ -69,27 +69,89 @@
     <build>
         <plugins>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-source-plugin</artifactId>
-                <version>3.2.1</version>
+                <version>3.3.0</version>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.8.0</version>
+                <version>3.11.0</version>
                 <configuration>
                     <encoding>UTF-8</encoding>
                     <source>14</source>
                     <target>14</target>
                 </configuration>
             </plugin>
+            <plugin>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.2.3</version>
+            </plugin>
         </plugins>
         <extensions>
             <extension>
                 <groupId>org.apache.maven.wagon</groupId>
                 <artifactId>wagon-ssh</artifactId>
-                <version>3.4.1</version>
+                <version>3.5.2</version>
             </extension>
         </extensions>
     </build>
+
+    <distributionManagement>
+        <repository>
+            <id>github</id>
+            <name>GitHub Packages</name>
+            <url>https://maven.pkg.github.com/psiotwo/owldiff</url>
+        </repository>
+    </distributionManagement>
+
+    <dependencyManagement>
+        <dependencies>
+            <dependency>
+                <groupId>org.junit.jupiter</groupId>
+                <artifactId>junit-jupiter</artifactId>
+                <version>5.10.0</version>
+            </dependency>
+            <dependency>
+                <groupId>net.sourceforge.owlapi</groupId>
+                <artifactId>owlapi-distribution</artifactId>
+                <version>5.1.16</version>
+            </dependency>
+            <dependency>
+                <groupId>org.junit</groupId>
+                <artifactId>junit-bom</artifactId>
+                <version>5.9.1</version>
+                <type>pom</type>
+                <scope>import</scope>
+            </dependency>
+            <dependency>
+                <groupId>org.slf4j</groupId>
+                <artifactId>slf4j-api</artifactId>
+                <version>2.0.3</version>
+            </dependency>
+            <dependency>
+                <groupId>ch.qos.logback</groupId>
+                <artifactId>logback-core</artifactId>
+                <version>1.4.4</version>
+            </dependency>
+            <dependency>
+                <groupId>ch.qos.logback</groupId>
+                <artifactId>logback-classic</artifactId>
+                <version>1.4.4</version>
+            </dependency>
+            <dependency>
+                <groupId>org.projectlombok</groupId>
+                <artifactId>lombok</artifactId>
+                <version>1.18.24</version>
+            </dependency>
+            <dependency>
+                <groupId>info.picocli</groupId>
+                <artifactId>picocli</artifactId>
+                <version>4.7.0</version>
+            </dependency>
+            <dependency>
+                <groupId>cz.cvut.kbss</groupId>
+                <artifactId>explanations</artifactId>
+                <version>0.91</version>
+            </dependency>
+        </dependencies>
+    </dependencyManagement>
 </project>

owldiff-standalone/pom.xml

@@ -17,7 +17,7 @@
         <groupId>cz.cvut.kbss</groupId>
         <artifactId>owldiff-parent</artifactId>
         <relativePath>../owldiff-parent/pom.xml</relativePath>
-        <version>0.2.1-SNAPSHOT</version>
+        <version>0.2.1</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
@@ -34,12 +34,25 @@
         </license>
     </licenses>
 
+    <dependencies>
+        <dependency>
+            <groupId>cz.cvut.kbss</groupId>
+            <artifactId>owldiff-core</artifactId>
+            <version>${project.version}</version>
+            <type>jar</type>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
     <build>
         <plugins>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>2.22.2</version>
+                <version>3.2.3</version>
                 <configuration>
                     <includes>
                         <include>**/*Test.java</include>
@@ -48,9 +61,8 @@
                 </configuration>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.1.0</version>
+                <version>3.3.0</version>
                 <configuration>
                     <archive>
                         <index>true</index>
@@ -65,19 +77,19 @@
                 </configuration>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-assembly-plugin</artifactId>
-                <version>2.4</version>
+                <version>3.6.0</version>
                 <configuration>
-                    <descriptor>
-                        src/main/assembly/zip-bin-descriptor.xml
-                    </descriptor>
+                    <descriptors>
+                        <descriptor>
+                            src/main/assembly/zip-bin-descriptor.xml
+                        </descriptor>
+                    </descriptors>
                 </configuration>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-source-plugin</artifactId>
-                <version>2.0</version>
+                <version>3.3.0</version>
                 <executions>
                     <execution>
                         <phase>package</phase>
@@ -88,9 +100,8 @@
                 </executions>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.5.0</version>
                 <configuration>
                     <encoding>UTF-8</encoding>
                 </configuration>
@@ -104,27 +115,12 @@
                 </executions>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-resources-plugin</artifactId>
-                <version>3.1.0</version>
+                <version>3.3.1</version>
                 <configuration>
                     <encoding>UTF-8</encoding>
                 </configuration>
             </plugin>
         </plugins>
     </build>
-    <dependencies>
-        <dependency>
-            <groupId>cz.cvut.kbss</groupId>
-            <artifactId>owldiff-core</artifactId>
-            <version>${project.version}</version>
-            <type>jar</type>
-        </dependency>
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <version>4.13.1</version>
-            <scope>test</scope>
-        </dependency>
-    </dependencies>
 </project>

pom.xml

@@ -12,35 +12,36 @@
   -->
 
 <project xmlns="http://maven.apache.org/POM/4.0.0"
-         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-    <modelVersion>4.0.0</modelVersion>
-    <groupId>cz.cvut.kbss</groupId>
-    <artifactId>owldiff</artifactId>
-    <packaging>pom</packaging>
-    <name>OWLDiff</name>
-    <version>0.2.1-SNAPSHOT</version>
-    <description>OWLDiff - diff of OWL ontologies</description>
-    <distributionManagement>
-        <repository>
-            <id>kbss</id>
-            <url>http://kbss.felk.cvut.cz/var/www/m2repo</url>
-        </repository>
-    </distributionManagement>
-    <modules>
-        <module>owldiff-parent</module>
-        <module>owldiff-core</module>
-        <module>owldiff-cli</module>
-        <module>owldiff-standalone</module>
-        <module>owldiff-protege-plugin</module>
-    </modules>
-    <build>
-        <extensions>
-            <extension>
-                <groupId>org.apache.maven.wagon</groupId>
-                <artifactId>wagon-ssh</artifactId>
-                <version>3.4.1</version>
-            </extension>
-        </extensions>
-    </build>
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>cz.cvut.kbss</groupId>
+  <artifactId>owldiff</artifactId>
+  <packaging>pom</packaging>
+  <name>OWLDiff</name>
+  <version>0.2.1</version>
+  <description>OWLDiff - diff of OWL ontologies</description>
+  <distributionManagement>
+    <repository>
+      <id>github</id>
+      <name>GitHub Packages</name>
+      <url>https://maven.pkg.github.com/psiotwo/owldiff</url>
+    </repository>
+  </distributionManagement>
+  <modules>
+    <module>owldiff-parent</module>
+    <module>owldiff-core</module>
+    <module>owldiff-cli</module>
+    <module>owldiff-standalone</module>
+    <!--module>owldiff-protege-plugin</module-->
+  </modules>
+  <build>
+    <extensions>
+      <extension>
+        <groupId>org.apache.maven.wagon</groupId>
+        <artifactId>wagon-ssh</artifactId>
+        <version>3.5.2</version>
+      </extension>
+    </extensions>
+  </build>
 </project>