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ritarandazzo01owllink-owlapi's Issues
java.lang.NoClassDefFoundError: OWLlinkErrorResponseException
Hi,
My code works perfectly in Eclipse IDE but when I try to run from command line with this line:
mvn exec:java -Dexec.mainClass=ParenthoodExample_optimized -Dexec.args="C:\Users\Rita\Desktop\parenthood.owl HERMIT"
I get this exception:
java.lang.NoClassDefFoundError: org/semanticweb/owlapi/owllink/builtin/response/OWLlinkErrorResponseException
at java.lang.Class.getDeclaredMethods0 (Native Method)
at java.lang.Class.privateGetDeclaredMethods (Class.java:2701)
at java.lang.Class.privateGetMethodRecursive (Class.java:3048)
at java.lang.Class.getMethod0 (Class.java:3018)
at java.lang.Class.getMethod (Class.java:1784)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:270)
at java.lang.Thread.run (Thread.java:748)
Caused by: java.lang.ClassNotFoundException: org.semanticweb.owlapi.owllink.builtin.response.OWLlinkErrorResponseException
at java.net.URLClassLoader.findClass (URLClassLoader.java:382)
at java.lang.ClassLoader.loadClass (ClassLoader.java:418)
at java.lang.ClassLoader.loadClass (ClassLoader.java:351)
at java.lang.Class.getDeclaredMethods0 (Native Method)
at java.lang.Class.privateGetDeclaredMethods (Class.java:2701)
at java.lang.Class.privateGetMethodRecursive (Class.java:3048)
at java.lang.Class.getMethod0 (Class.java:3018)
at java.lang.Class.getMethod (Class.java:1784)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:270)
at java.lang.Thread.run (Thread.java:748)
I don't understand if it's an error that depends on my pom.xml or the class itself.
mypom:
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>OWLapi</groupId>
<artifactId>OWLapi</artifactId>
<version>0.0.1-SNAPSHOT</version>
<name>OWLapi</name>
<dependencies>
<dependency>
<groupId>com.github.galigator.openllet</groupId>
<artifactId>openllet-owlapi</artifactId>
<version>2.6.4</version>
</dependency>
<!-- https://mvnrepository.com/artifact/edu.stanford.protege/owl-diff -->
<dependency>
<groupId>edu.stanford.protege</groupId>
<artifactId>owl-diff</artifactId>
<version>6.0.2</version>
</dependency>
<!-- https://mvnrepository.com/artifact/uk.ac.manchester.cs/factplusplus -->
<dependency>
<groupId>uk.ac.manchester.cs</groupId>
<artifactId>factplusplus</artifactId>
<version>1.5.2</version>
</dependency>
<dependency>
<groupId>ignazioFork_OWLlink_for_OWLAPI5</groupId>
<artifactId>ignazioFork_OWLlink_for_OWLAPI5</artifactId>
<version>1.0</version>
<scope>system</scope>
<systemPath>${basedir}/ignazioFork_OWLlink_for_OWLAPI5.jar</systemPath>
</dependency>
<dependency>
<groupId>au.csiro</groupId>
<artifactId>snorocket-owlapi</artifactId>
<version>4.0.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/edu.stanford.protege/protege-editor-owl -->
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-apibinding</artifactId>
<version>5.1.13</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>org.semanticweb.hermit</artifactId>
<version>1.3.8.500</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>jfact</artifactId>
<version>5.0.3</version>
</dependency>
<dependency>
<groupId>org.semanticweb.elk</groupId>
<artifactId>elk-owlapi5</artifactId>
<version>0.5.0-SNAPSHOT</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>sonatype-nexus-snapshots</id>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
<repository>
<id>BBOP</id>
<name>BBOP</name>
<url>http://code.berkeleybop.org/maven/repository/</url>
</repository>
</repositories>
<build>
<sourceDirectory>src</sourceDirectory>
<plugins>
<!-- <plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.6.0</version>
<executions>
<execution>
<goals>
<goal>exec</goal>
</goals>
</execution>
</executions>
<configuration>
<executable>java</executable>
<arguments>
<argument>${basedir}/ignazioFork_OWLlink_for_OWLAPI5.jar</argument>
</arguments>
</configuration>
</plugin>
</plugins>
</build>
</project>
My java class:
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.empty;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import java.nio.file.Files;
import org.apache.commons.io.FilenameUtils;
import org.joda.time.DateTime;
import org.semanticweb.HermiT.Configuration;
import org.semanticweb.HermiT.ReasonerFactory;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDataPropertyAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLIndividualAxiom;
import org.semanticweb.owlapi.model.OWLObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory;
import org.semanticweb.owlapi.owllink.builtin.response.OWLlinkErrorResponseException;
import org.semanticweb.owlapi.reasoner.BufferingMode;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
import org.semanticweb.owlapi.reasoner.TimedConsoleProgressMonitor;
import org.semanticweb.owlapi.reasoner.UnsupportedEntailmentTypeException;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory;
import org.semanticweb.owlapi.util.InferredAxiomGenerator;
import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator;
import org.semanticweb.owlapi.util.InferredClassAxiomGenerator;
import org.semanticweb.owlapi.util.InferredDataPropertyAxiomGenerator;
import org.semanticweb.owlapi.util.InferredDataPropertyCharacteristicAxiomGenerator;
import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator;
import org.semanticweb.owlapi.util.InferredEntityAxiomGenerator;
import org.semanticweb.owlapi.util.InferredEquivalentClassAxiomGenerator;
import org.semanticweb.owlapi.util.InferredEquivalentDataPropertiesAxiomGenerator;
import org.semanticweb.owlapi.util.InferredEquivalentObjectPropertyAxiomGenerator;
import org.semanticweb.owlapi.util.InferredIndividualAxiomGenerator;
import org.semanticweb.owlapi.util.InferredInverseObjectPropertiesAxiomGenerator;
import org.semanticweb.owlapi.util.InferredObjectPropertyAxiomGenerator;
import org.semanticweb.owlapi.util.InferredObjectPropertyCharacteristicAxiomGenerator;
import org.semanticweb.owlapi.util.InferredOntologyGenerator;
import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator;
import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;
import au.csiro.snorocket.owlapi.SnorocketReasonerFactory;
import openllet.owlapi.OpenlletReasonerFactory;
import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasoner;
import uk.ac.manchester.cs.jfact.JFactFactory;
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
//import org.semanticweb.reasonerfactory.factpp.FaCTPlusPlusReasonerFactory;
public class ParenthoodExample_optimized {
public static void main(String[] args) throws Exception {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
File file = new File(args[0]);
OWLOntology ontology = logicalAxiomsOnly(file, manager);
System.out.println("axioms before reasoning" +ontology.getAxiomCount());
Set<OWLClass> classes = ontology.getClassesInSignature();
//File filename = FilenameUtils.removeExtension(args[0]);
OWLDataFactory df = manager.getOWLDataFactory();
String args1 = args[1];
Reasoner reasoner = Reasoner.valueOf(args1);
try {
System.out.println(RunReasoner(reasoner, df,ontology,manager,file));
}catch (final UnsupportedEntailmentTypeException e) {
System.out.println(e.getMessage());
}
catch (final OWLlinkErrorResponseException e) {
System.out.println(e.getMessage());
}
// Reasoner hermit = Reasoner.HERMIT;
// System.out.println(RunReasoner(hermit, df,ontology,manager,filename));
//
// Reasoner Structural = Reasoner.Structural;
// System.out.println(RunReasoner(Structural, df,ontology,manager,filename));
//
//
// Reasoner openllet = Reasoner.PELLET;
// System.out.println(RunReasoner(openllet, df,ontology,manager,filename));
//
// Reasoner konclude = Reasoner.KONCLUDE;
// System.out.println(RunReasoner(konclude, df,ontology,manager,filename));
//
// Reasoner elk = Reasoner.ELK;
// System.out.println(RunReasoner(elk, df,ontology,manager,filename));
// Reasoner jfact = Reasoner.JFACT;
// System.out.println(RunReasoner(jfact, df,ontology,manager,filename));
//
}
//CREATE AN ENUM REASONER
public enum Reasoner{
Structural,
HERMIT,
PELLET,
KONCLUDE,
JFACT,
FACT,
ELK,
SNOROCKET
}
public static String RunReasoner(Reasoner reasoner, OWLDataFactory df, OWLOntology ontology, OWLOntologyManager manager, File filename) throws OWLOntologyCreationException, FileNotFoundException, IOException, OWLOntologyStorageException {
String esito = "";
OWLReasoner reasoner_object = null;
//to measure execution time
long startTime = System.nanoTime();
if(reasoner == Reasoner.HERMIT) {
/****************HERMIT****************************************************************************************/
OWLReasonerFactory rf = new ReasonerFactory();
TimedConsoleProgressMonitor progressMonitor = new TimedConsoleProgressMonitor();
Configuration configuration = new Configuration();
configuration.reasonerProgressMonitor = progressMonitor;
configuration.ignoreUnsupportedDatatypes = true;
reasoner_object = rf.createReasoner(ontology, configuration);
}
else if(reasoner == Reasoner.Structural) {
StructuralReasonerFactory rf = new StructuralReasonerFactory();
TimedConsoleProgressMonitor progressMonitor = new TimedConsoleProgressMonitor();
Configuration configuration = new Configuration();
configuration.reasonerProgressMonitor = progressMonitor;
configuration.ignoreUnsupportedDatatypes = true;
reasoner_object = rf.createReasoner(ontology, configuration);
}
// //new entry
// else if(reasoner == Reasoner.SNOROCKET) {
//
// SnorocketReasonerFactory rf = new SnorocketReasonerFactory();
// TimedConsoleProgressMonitor progressMonitor = new TimedConsoleProgressMonitor();
// Configuration configuration = new Configuration();
// configuration.reasonerProgressMonitor = progressMonitor;
// configuration.ignoreUnsupportedDatatypes = true;
// reasoner_object = rf.createReasoner(ontology, configuration);
// }
//new entry
else if(reasoner == Reasoner.FACT) {
TimedConsoleProgressMonitor progressMonitor = new TimedConsoleProgressMonitor();
Configuration configuration = new Configuration();
configuration.reasonerProgressMonitor = progressMonitor;
configuration.ignoreUnsupportedDatatypes = true;
reasoner_object = new FaCTPlusPlusReasoner(ontology,configuration,BufferingMode.BUFFERING);
// reasoner_object = rf.
//.createReasoner(ontology, configuration);
}
else if(reasoner == Reasoner.KONCLUDE) {
// configure the server end-point
URL url = new URL("http://localhost:8080");
OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
TimedConsoleProgressMonitor progressMonitor = new TimedConsoleProgressMonitor();
//OWLlinkReasonerConfiguration conf = (OWLlinkReasonerConfiguration) new SimpleConfiguration(progressMonitor);
reasoner_object = factory.createNonBufferingReasoner(ontology);
}
else if(reasoner == Reasoner.JFACT) {
TimedConsoleProgressMonitor progressMonitor = new TimedConsoleProgressMonitor();
OWLReasonerConfiguration conf = new SimpleConfiguration(progressMonitor);
JFactFactory factory = new JFactFactory();
reasoner_object = factory.createNonBufferingReasoner(ontology,conf);
}
else if(reasoner == Reasoner.ELK) {
TimedConsoleProgressMonitor progressMonitor = new TimedConsoleProgressMonitor();
OWLReasonerConfiguration conf = new SimpleConfiguration(progressMonitor);
ElkReasonerFactory factory = new ElkReasonerFactory();
reasoner_object = factory.createNonBufferingReasoner(ontology,conf);
}
else if(reasoner == Reasoner.PELLET) {
TimedConsoleProgressMonitor progressMonitor = new TimedConsoleProgressMonitor();
OWLReasonerConfiguration conf = new SimpleConfiguration(progressMonitor);
reasoner_object = OpenlletReasonerFactory.getInstance().createReasoner(ontology,conf);
}
else{
esito = "Reasoner non valido";
}
System.out.println("UnsatisfiableClasses "+reasoner_object.getUnsatisfiableClasses().getSize());
System.out.println("TopClassNode "+reasoner_object.topClassNode());
boolean consistencyCheck = reasoner_object.isConsistent();
if (consistencyCheck) {
reasoner_object.precomputeInferences(InferenceType.CLASS_HIERARCHY,
InferenceType.CLASS_ASSERTIONS, InferenceType.OBJECT_PROPERTY_HIERARCHY,
InferenceType.DATA_PROPERTY_HIERARCHY, InferenceType.OBJECT_PROPERTY_ASSERTIONS);
reasoner_object.flush(); //Flushes any changes stored in the buffer, which causes the reasoner to take into consideration the changes the current root ontology specified by the changes. FROM RONALD's CODE
List<InferredAxiomGenerator<? extends OWLAxiom>> generators = new ArrayList<>();
generators.add(new InferredSubClassAxiomGenerator());
generators.add(new InferredClassAssertionAxiomGenerator());
generators.add(new InferredDataPropertyCharacteristicAxiomGenerator());
generators.add(new InferredEquivalentClassAxiomGenerator());
generators.add(new InferredEquivalentDataPropertiesAxiomGenerator());
generators.add(new InferredEquivalentObjectPropertyAxiomGenerator());
generators.add(new InferredInverseObjectPropertiesAxiomGenerator());
generators.add(new InferredObjectPropertyCharacteristicAxiomGenerator());
// NOTE: InferredPropertyAssertionGenerator significantly slows down
// inference computation
generators.add(new org.semanticweb.owlapi.util.InferredPropertyAssertionGenerator());
generators.add(new InferredSubDataPropertyAxiomGenerator());
generators.add(new InferredSubObjectPropertyAxiomGenerator());
List<InferredIndividualAxiomGenerator<? extends OWLIndividualAxiom>> individualAxioms =
new ArrayList<>();
generators.addAll(individualAxioms);
List<InferredDataPropertyAxiomGenerator<? extends OWLDataPropertyAxiom>> dataPropertyAxioms =
new ArrayList<>();
generators.addAll(dataPropertyAxioms);
List<InferredEntityAxiomGenerator<? extends OWLEntity,? extends OWLAxiom>> inferredEntityAxioms =
new ArrayList<>();
generators.addAll(inferredEntityAxioms);
List<InferredObjectPropertyAxiomGenerator<? extends OWLObjectPropertyAxiom>> objectPropertyAxioms =
new ArrayList<>();
generators.addAll(objectPropertyAxioms);
List<InferredClassAxiomGenerator<? extends OWLClassAxiom>> classAxioms =
new ArrayList<>();
generators.addAll(classAxioms);
generators.add(new InferredDisjointClassesAxiomGenerator());
//InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner_object, generators); //Generates an ontology based on inferred axioms which are essentially supplied by a reasoner
OWLOntology inferredAxiomsOntology = manager.createOntology();
//iog.fillOntology(df, inferredAxiomsOntology);
String path = filename.getParent();
String namefile = FilenameUtils.removeExtension(filename.getName());
//create main directory
File mainDir = new File(path+"/"+namefile);
if (!mainDir.exists()) mainDir.mkdirs();
//report file
File report = new File(mainDir,reasoner.toString()+".txt");
PrintWriter writer = new PrintWriter(report, "UTF-8");
writer.println("Reasoner: "+ reasoner.toString());
writer.println("Datetime: "+ DateTime.now());
for (InferredAxiomGenerator< ? extends OWLAxiom> inf : generators ) {
try{
Set< ? extends OWLAxiom> ax = inf.createAxioms(df, reasoner_object);
System.out.println(inf +" : " + ax.size());
writer.println(inf +" : " + ax.size());
//save single generator axioms in a little ontology
//create child directory
File childDir = new File(mainDir+"/"+inf.toString());
if (!childDir.exists()) childDir.mkdirs();
File newFile = new File(childDir,inf.toString()+"_"+reasoner.toString()+".owl");
// Now we create a stream since the ontology manager can then write to that stream.
try (OutputStream outputStream = new FileOutputStream(newFile)) {
// We use the same format as for the input ontol4ogy.
OWLOntology singleGeneratorOntology = manager.createOntology();
singleGeneratorOntology.addAxioms(ax);
manager.saveOntology(singleGeneratorOntology, outputStream);
inferredAxiomsOntology.addAxioms(ax);
}
} catch (Exception e) {
System.out.println("Error generating axioms using "+reasoner_object.getReasonerName()+", version " +reasoner_object.getReasonerVersion() +" Error:" +e);
}
}
//to measure runtime memory
Runtime runtime = Runtime.getRuntime(); //Returns the runtime object associated with the current Java application.
runtime.gc(); //Runs the garbage collector.
long memory = runtime.totalMemory() - runtime.freeMemory(); //total amount of memory in the Java virtual machine - the amount of free memory in the Java Virtual Machine
System.out.println("Used memory is bytes: " + memory);
writer.println("");
writer.println("Used memory is megabytes: " + memory/(1024L*1024L));
//to measure execution time
long endTime = System.nanoTime();
long timeElapsed = endTime - startTime;
System.out.println("Execution time in nanoseconds : " + timeElapsed);
writer.println("Execution time in seconds: " + TimeUnit.SECONDS.convert(timeElapsed, TimeUnit.NANOSECONDS)+ "''");
writer.println("Total Inferred Axioms: " + inferredAxiomsOntology.getAxiomCount());
writer.close();
System.out.println("numero inferred axioms " + inferredAxiomsOntology.getAxiomCount());
File inferredOntologyFile = new File(mainDir,namefile+"_inferredBy_"+reasoner.toString()+".owl");
System.out.println(inferredOntologyFile);
// Now we create a stream since the ontology manager can then write to that stream.
try (OutputStream outputStream = new FileOutputStream(inferredOntologyFile)) {
// We use the same format as for the input ontology.
manager.saveOntology(inferredAxiomsOntology, outputStream);
}
esito = "done "+ reasoner.toString();
reasoner_object.dispose();
} // End if consistencyCheck
else {
esito = reasoner.toString() +" -- Inconsistent input Ontology, Please check the OWL File";
}
return esito;
}
protected static OWLOntology logicalAxiomsOnly(File file, OWLOntologyManager manager)
throws OWLOntologyCreationException {
OWLOntology l = manager.loadOntology(IRI.create(file));
return manager.createOntology(
l.importsClosure().flatMap(OWLOntology::logicalAxioms).collect(Collectors.toSet()));
}
}
Thank you for all the suggestions
Rita
Error related to XML Parsing
I am getting an error when creating the reasoner. It seems to be related with XML parsing. The codes being used and the errors:
Codes
String path = "http://elite.polito.it/ontologies/dogont.owl";
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntology(
IRI.create(path));
OWLlinkReasonerConfigurationImpl reasonerConfiguration = new OWLlinkReasonerConfigurationImpl();
final OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
final OWLReasoner reasoner = factory.createReasoner(ontology, reasonerConfiguration);
Error
/opt/java/bin/java -javaagent:/home/noor/Documents/apps/idea/lib/idea_rt.jar=36367:/home/noor/Documents/apps/idea/bin -Dfile.encoding=UTF-8 -classpath /opt/java/jre/lib/charsets.jar:/opt/java/jre/lib/deploy.jar:/opt/java/jre/lib/ext/cldrdata.jar:/opt/java/jre/lib/ext/dnsns.jar:/opt/java/jre/lib/ext/jaccess.jar:/opt/java/jre/lib/ext/jfxrt.jar:/opt/java/jre/lib/ext/localedata.jar:/opt/java/jre/lib/ext/nashorn.jar:/opt/java/jre/lib/ext/sunec.jar:/opt/java/jre/lib/ext/sunjce_provider.jar:/opt/java/jre/lib/ext/sunpkcs11.jar:/opt/java/jre/lib/ext/zipfs.jar:/opt/java/jre/lib/javaws.jar:/opt/java/jre/lib/jce.jar:/opt/java/jre/lib/jfr.jar:/opt/java/jre/lib/jfxswt.jar:/opt/java/jre/lib/jsse.jar:/opt/java/jre/lib/management-agent.jar:/opt/java/jre/lib/plugin.jar:/opt/java/jre/lib/resources.jar:/opt/java/jre/lib/rt.jar:/home/noor/IdeaProjects/RDFInjectionAndAlignment/target/classes:/home/noor/.m2/repository/org/neo4j/neo4j-enterprise/3.4.13/neo4j-enterprise-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j/3.4.13/neo4j-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-kernel/3.4.13/neo4j-kernel-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-graphdb-api/3.4.13/neo4j-graphdb-api-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-resource/3.4.13/neo4j-resource-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-procedure-api/3.4.13/neo4j-procedure-api-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-kernel-api/3.4.13/neo4j-kernel-api-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-common/3.4.13/neo4j-common-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-collections/3.4.13/neo4j-collections-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-primitive-collections/3.4.13/neo4j-primitive-collections-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-unsafe/3.4.13/neo4j-unsafe-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-io/3.4.13/neo4j-io-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-csv/3.4.13/neo4j-csv-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-logging/3.4.13/neo4j-logging-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-lucene-upgrade/3.4.13/neo4j-lucene-upgrade-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-configuration/3.4.13/neo4j-configuration-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-index/3.4.13/neo4j-index-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-spatial-index/3.4.13/neo4j-spatial-index-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-lucene-index/3.4.13/neo4j-lucene-index-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-graph-algo/3.4.13/neo4j-graph-algo-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-udc/3.4.13/neo4j-udc-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher/3.4.13/neo4j-cypher-3.4.13.jar:/home/noor/.m2/repository/org/scala-lang/scala-library/2.11.12/scala-library-2.11.12.jar:/home/noor/.m2/repository/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar:/home/noor/.m2/repository/org/neo4j/neo4j-graph-matching/3.1.9/neo4j-graph-matching-3.1.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-codegen/3.4.13/neo4j-codegen-3.4.13.jar:/home/noor/.m2/repository/org/ow2/asm/asm-util/6.2/asm-util-6.2.jar:/home/noor/.m2/repository/org/ow2/asm/asm-analysis/6.2/asm-analysis-6.2.jar:/home/noor/.m2/repository/org/ow2/asm/asm-tree/6.2/asm-tree-6.2.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-compiler-2.3/2.3.12/neo4j-cypher-compiler-2.3-2.3.12.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-frontend-2.3/2.3.12/neo4j-cypher-frontend-2.3-2.3.12.jar:/home/noor/.m2/repository/com/googlecode/concurrentlinkedhashmap/concurrentlinkedhashmap-lru/1.4.2/concurrentlinkedhashmap-lru-1.4.2.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-compiler-3.1/3.1.9/neo4j-cypher-compiler-3.1-3.1.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-frontend-3.1/3.1.9/neo4j-cypher-frontend-3.1-3.1.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-compiler-3.3/3.3.9/neo4j-cypher-compiler-3.3-3.3.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-frontend-3.3/3.3.9/neo4j-cypher-frontend-3.3-3.3.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-ir-3.3/3.3.9/neo4j-cypher-ir-3.3-3.3.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-logical-plans-3.3/3.3.9/neo4j-cypher-logical-plans-3.3-3.3.9.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-util-3.4/3.4.13/neo4j-cypher-util-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-planner-3.4/3.4.13/neo4j-cypher-planner-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/openCypher-frontend-1/3.4.13/openCypher-frontend-1-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-expression-3.4/3.4.13/neo4j-cypher-expression-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-ir-3.4/3.4.13/neo4j-cypher-ir-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-logical-plans-3.4/3.4.13/neo4j-cypher-logical-plans-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-planner-spi-3.4/3.4.13/neo4j-cypher-planner-spi-3.4-3.4.13.jar:/home/noor/.m2/repository/org/neo4j/neo4j-cypher-runtime-util/3.4.13/neo4j-cypher-runtime-util-3.4.13.jar:/home/noor/.m2/repo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-hc/4.5.5/fluent-hc-4.5.5.jar:/home/noor/.m2/repository/org/apache/httpcomponents/httpcore-osgi/4.4.9/httpcore-osgi-4.4.9.jar:/home/noor/.m2/repository/org/apache/httpcomponents/httpcore-nio/4.4.9/httpcore-nio-4.4.9.jar:/home/noor/.m2/repository/com/github/vsonnier/hppcrt/0.7.5/hppcrt-0.7.5.jar:/home/noor/.m2/repository/com/google/guava/guava/22.0/guava-22.0.jar:/home/noor/.m2/repository/com/google/errorprone/error_prone_annotations/2.0.18/error_prone_annotations-2.0.18.jar:/home/noor/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar:/home/noor/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.14/animal-sniffer-annotations-1.14.jar:/home/noor/.m2/repository/com/google/code/findbugs/jsr305/3.0.2/jsr305-3.0.2.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-apibinding/5.1.10/owlapi-apibinding-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-api/5.1.10/owlapi-api-5.1.10.jar:/home/noor/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-impl/5.1.10/owlapi-impl-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-parsers/5.1.10/owlapi-parsers-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-oboformat/5.1.10/owlapi-oboformat-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-tools/5.1.10/owlapi-tools-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/owlapi-rio/5.1.10/owlapi-rio-5.1.10.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/org.semanticweb.hermit/1.4.3.517/org.semanticweb.hermit-1.4.3.517.jar:/home/noor/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar:/home/noor/.m2/repository/org/apache/ws/commons/axiom/axiom-api/1.2.14/axiom-api-1.2.14.jar:/home/noor/.m2/repository/org/apache/geronimo/specs/geronimo-activation_1.1_spec/1.1/geronimo-activation_1.1_spec-1.1.jar:/home/noor/.m2/repository/org/apache/geronimo/specs/geronimo-javamail_1.4_spec/1.7.1/geronimo-javamail_1.4_spec-1.7.1.jar:/home/noor/.m2/repository/jaxen/jaxen/1.1.4/jaxen-1.1.4.jar:/home/noor/.m2/repository/org/apache/geronimo/specs/geronimo-stax-api_1.0_spec/1.0.1/geronimo-stax-api_1.0_spec-1.0.1.jar:/home/noor/.m2/repository/org/apache/james/apache-mime4j-core/0.7.2/apache-mime4j-core-0.7.2.jar:/home/noor/.m2/repository/org/apache/ws/commons/axiom/axiom-c14n/1.2.14/axiom-c14n-1.2.14.jar:/home/noor/.m2/repository/org/apache/ws/commons/axiom/axiom-impl/1.2.14/axiom-impl-1.2.14.jar:/home/noor/.m2/repository/org/apache/ws/commons/axiom/axiom-dom/1.2.14/axiom-dom-1.2.14.jar:/home/noor/.m2/repository/dk/brics/automaton/automaton/1.11-8/automaton-1.11-8.jar:/home/noor/.m2/repository/gnu/getopt/java-getopt/1.0.13/java-getopt-1.0.13.jar:/home/noor/.m2/repository/net/sf/trove4j/trove4j/3.0.3/trove4j-3.0.3.jar:/home/noor/.m2/repository/net/sourceforge/owlapi/jfact/1.0.0/jfact-1.0.0.jar:/home/noor/.m2/repository/commons-cli/commons-cli/1.4/commons-cli-1.4.jar:/home/noor/.m2/repository/fr/emse/ci/sparql-generate/2.0-SNAPSHOT/sparql-generate-2.0-SNAPSHOT.jar:/home/noor/.m2/repository/us/monoid/web/resty/0.3.2/resty-0.3.2.jar:/home/noor/.m2/repository/net/java/dev/javacc/javacc/4.1/javacc-4.1.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkapi/target/owllinkapi-2.0.0.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkhttpxml/target/owllinkhttpxml-2.0.0.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkimpl/target/owllinkimpl-2.0.0.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkprotege/target/owllinkprotege-2.0.0.jar:/home/noor/Documents/repositories/github/owllink-owlapi/owllinkserver/target/owllinkserver-2.0.0.jar examples.TestKon
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/noor/.m2/repository/org/slf4j/slf4j-nop/1.7.25/slf4j-nop-1.7.25.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/noor/.m2/repository/org/apache/logging/log4j/log4j-slf4j-impl/2.11.0/log4j-slf4j-impl-2.11.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/noor/.m2/repository/fr/emse/ci/sparql-generate/2.0-SNAPSHOT/sparql-generate-2.0-SNAPSHOT.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.helpers.NOPLoggerFactory]
Exception in thread "main" org.semanticweb.owlapi.owllink.builtin.response.OWLlinkErrorResponseException: An error has occurred while processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command',
Error process protocol:
{notice}, [::Konclude::Command::Command]:Finish processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command' with all sub commands. Command closed.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Finish processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command'.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Stop processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command'.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Start processing 'Tell-'http://Konclude.com/Ontologies/UnnamedOntologies/1/1565623137724/'-Knowledge-Base-OWL2-XML-Axioms Command'.
{error}, An error has occurred while processing 'Parse-OWL2-XML-Ontology Command',
Sub-Error process protocol:
{notice}, [::Konclude::Command::Command]:Finish processing 'Parse-OWL2-XML-Ontology Command' with all sub commands. Command closed.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Finish processing 'Parse-OWL2-XML-Ontology Command'.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Stop processing 'Parse-OWL2-XML-Ontology Command'.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{error}, [::Konclude::Parser::OWL2QtXMLOntologyParser]:Node 'AnnotationProperty' is not supported and could not be processed.
{notice}, [::Konclude::Control::Interface::OWLlink::OWLlinkProcessor]:Start processing 'Parse-OWL2-XML-Ontology Command'.
at org.semanticweb.owlapi.owllink.parser.OWLlinkErrorResponseElementHandler.getOWLLinkObject(OWLlinkErrorResponseElementHandler.java:58)
at org.semanticweb.owlapi.owllink.parser.OWLlinkErrorResponseElementHandler.getOWLLinkObject(OWLlinkErrorResponseElementHandler.java:49)
at org.semanticweb.owlapi.owllink.parser.OWLlinkResponseMessageElementHandler.handleChild(OWLlinkResponseMessageElementHandler.java:96)
at org.semanticweb.owlapi.owllink.parser.AbstractOWLlinkErrorHandler.endElement(AbstractOWLlinkErrorHandler.java:75)
at org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:458)
at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
at org.apache.xerces.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
at org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
at org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:195)
at org.semanticweb.owlapi.owllink.HTTPSessionImpl.performRequests(HTTPSessionImpl.java:209)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.performRequests(OWLlinkHTTPXMLReasoner.java:526)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.performRequest(OWLlinkHTTPXMLReasoner.java:530)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.performRequestOWLAPI(OWLlinkHTTPXMLReasoner.java:544)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.<init>(OWLlinkHTTPXMLReasoner.java:92)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory.createReasoner(OWLlinkHTTPXMLReasonerFactory.java:80)
at examples.TestKon.main(TestKon.java:26)
Process finished with exit code 1
NullPointerException in OWLXMLWriter
Hi Ignazio,
thank you very much for updating the owllink-owlapi adapter. We also tried to update it to the OWL API version 4/5, but since Iām not really familiar with the OWL API, I probably wrote and copied a lot of odd and sub-optimal code (cf. branch owlapi5 of https://github.com/andreas-steigmiller/owllink-owlapi-adapter). I tested your update of the owllink-owlapi adapter with the following test
import java.net.URL;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.owllink.*;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
public class ClassSatisfiabilityTest01 {
public static void main(String[] args) {
try {
// create a test ontology
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.createOntology(IRI.create("http://test.de/"));
OWLDataFactory dfactory = manager.getOWLDataFactory();
OWLClass A = dfactory.getOWLClass(IRI.create("http://test.de/#A"));
OWLClass B = dfactory.getOWLClass(IRI.create("http://test.de/#B"));
OWLAxiom a = dfactory.getOWLSubClassOfAxiom(A, B);
manager.addAxiom(ontology, a);
// configure the server end-point
URL url = new URL("http://127.0.0.1:8081");
OWLlinkReasonerConfiguration reasonerConfiguration =
new OWLlinkReasonerConfiguration(url);
OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
OWLReasoner reasoner =
factory.createNonBufferingReasoner(ontology, reasonerConfiguration);
System.out.println("Satisfiability of class " + A.toString() +": " +
reasoner.isSatisfiable(A));
// adding additional axioms to our test ontology to make class A unsatisfiable
OWLAxiom b = dfactory.getOWLSubClassOfAxiom(A, manager.getOWLDataFactory()
.getOWLNothing());
manager.addAxiom(ontology, b);
System.out.println("After ontology changes, satisfiability of class " +
A.toString() +": " + reasoner.isSatisfiable(A));
} catch (Exception e) {
e.printStackTrace();
}
}
}
but it currently produces the following null pointer exception:
org.semanticweb.owlapi.owllink.OWLlinkReasonerRuntimeException
at org.semanticweb.owlapi.owllink.HTTPSessionImpl.performRequests(HTTPSessionImpl.java:222)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.performRequests(OWLlinkHTTPXMLReasoner.java:472)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.performRequest(OWLlinkHTTPXMLReasoner.java:476)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.createDefaultKB(OWLlinkHTTPXMLReasoner.java:460)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasoner.<init>(OWLlinkHTTPXMLReasoner.java:66)
at org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory.createNonBufferingReasoner(OWLlinkHTTPXMLReasonerFactory.java:55)
at ClassSatisfiabilityTest01.main(ClassSatisfiabilityTest01.java:35)
Caused by: java.lang.NullPointerException
at org.semanticweb.owlapi.owlxml.renderer.OWLXMLWriter.<init>(OWLXMLWriter.java:79)
at org.semanticweb.owlapi.owllink.renderer.OWLlinkXMLWriter.<init>(OWLlinkXMLWriter.java:76)
at org.semanticweb.owlapi.owllink.renderer.OWLlinkXMLRenderer.render(OWLlinkXMLRenderer.java:68)
at org.semanticweb.owlapi.owllink.HTTPSessionImpl.performRequests(HTTPSessionImpl.java:142)
... 6 more
In particular, the ontology given to the OWLXMLWriter must not be null. In our update, we passed a (new) ontology object through a lot of method calls/constructors to have it in the OWLXMLWriter, which was a little bit painful, too. (As OWLlink server, I used Konclude, e.g., with the command line ./Konclude owllinkserver -p 8081, but the exception is thrown before the owllink-owlapi adapter communicates with Konclude).
Unfortunately, I also cannot recommend our update since at least some queries for the owllink server are not working (and, as mentioned, some code is probably odd/sub-optimal). In the next days, I will try to have a closer look at the differences of our updates, but I think we should continue yours due to your experience with the OWL API.
Iām not really sure whether Protege 5.* already switched to version 5 of the OWL API. As long as this is not the case, it would be beneficial to have some easy to maintain compatibility with OWL API 4 (as well as for OWL API 4 reasoners). But on the other hand, our update to the OWL API version 4 seems to work as protege plugin, so I think a focus on OWL API 5 for the owllink-owlapi adapter should be fine.
Best, Andreas
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