owl api + pellet ignazio1977

Question

I am having problems running the Pellet together with the OWL-API. To debug the code, the following exception is thrown:

public class SemanticHelper{

private static final File file = new File("C:\\Users\\clayton\\Desktop\\testandoTopObjectProperty.owl");

public Set<OWLNamedIndividual> consultarInstanciasDeSuperClasse(String superClasse) {
    Set<OWLNamedIndividual> owlNamedIndividual = null;
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLOntology ontology;
    try {
        ontology = manager.loadOntologyFromOntologyDocument(IRI.create(file));
        OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance();
        OWLReasoner reasoner = reasonerFactory.createReasoner(ontology, new SimpleConfiguration());
        OWLClass owlClass =                 
                ontology
                .getOWLOntologyManager()
                .getOWLDataFactory()
                .getOWLClass(
                        IRI.create(Configuracoes.getIriBase() + "#" + superClasse));

        reasoner.precomputeInferences();

        Set<OWLClass> classes = reasoner.getSubClasses(owlClass, false).getFlattened();
        System.out.println(classes);

    } catch (OWLOntologyCreationException e) {
        e.printStackTrace();
    }

    return owlNamedIndividual;
}

public static void main(String args[]){
    SemanticHelper semanticHelper = new SemanticHelper();
    semanticHelper.consultarInstanciasDeSuperClasse("IntervaloDeDias");
}

}

the exception is thrown on the next line:

OWLReasoner reasoner = reasonerFactory.createReasoner(ontology, new SimpleConfiguration());

Exception in thread "main" java.lang.NoSuchMethodError: org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom.getProperty()Lorg/semanticweb/owlapi/model/OWLObjectPropertyExpression;
    at com.clarkparsia.pellet.owlapiv3.PelletVisitor.visit(PelletVisitor.java:478)
    at uk.ac.manchester.cs.owl.owlapi.OWLObjectSomeValuesFromImpl.accept(OWLObjectSomeValuesFromImpl.java:100)
    at com.clarkparsia.pellet.owlapiv3.PelletVisitor.visit(PelletVisitor.java:419)
    at uk.ac.manchester.cs.owl.owlapi.OWLObjectIntersectionOfImpl.accept(OWLObjectIntersectionOfImpl.java:90)
    at com.clarkparsia.pellet.owlapiv3.PelletVisitor.visit(PelletVisitor.java:1136)
    at uk.ac.manchester.cs.owl.owlapi.OWLObjectPropertyRangeAxiomImpl.accept(OWLObjectPropertyRangeAxiomImpl.java:107)
    at com.clarkparsia.pellet.owlapiv3.PelletVisitor.visit(PelletVisitor.java:839)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.accept(OWLOntologyImpl.java:1516)
    at com.clarkparsia.pellet.owlapiv3.PelletReasoner.refresh(PelletReasoner.java:967)
    at com.clarkparsia.pellet.owlapiv3.PelletReasoner.<init>(PelletReasoner.java:345)
    at com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory.createReasoner(PelletReasonerFactory.java:69)
    at com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory.createReasoner(PelletReasonerFactory.java:33)
    at br.com.ontologia.SemanticHelper.consultarInstanciasDeSuperClasse(SemanticHelper.java:58)
    at br.com.ontologia.SemanticHelper.main(SemanticHelper.java:94)

POM.XML:

<dependencies>
    <dependency>
        <groupId>junit</groupId>
        <artifactId>junit</artifactId>
        <version>3.8.1</version>
        <scope>test</scope>
    </dependency>

    <dependency>
        <groupId>net.sourceforge.owlapi</groupId>
        <artifactId>pellet-core-ignazio1977</artifactId>
        <version>2.4.0-ignazio1977</version>
    </dependency>

    <dependency>
        <groupId>net.sourceforge.owlapi</groupId>
        <artifactId>owlapi-distribution</artifactId>
        <version>4.1.3</version>
    </dependency>

    <dependency>
        <groupId>net.sourceforge.owlapi</groupId>
        <artifactId>pellet-owlapi-ignazio1977</artifactId>
        <version>2.4.0-ignazio1977</version>
    </dependency>

    <dependency>
        <groupId>asm</groupId>
        <artifactId>asm</artifactId>
        <version>3.3.1</version>
    </dependency>

    <dependency>
        <groupId>com.sun.jersey</groupId>
        <artifactId>jersey-bundle</artifactId>
        <version>1.19</version>
    </dependency>

    <dependency>
        <groupId>org.json</groupId>
        <artifactId>json</artifactId>
        <version>20140107</version>
    </dependency>

    <dependency>
        <groupId>com.sun.jersey</groupId>
        <artifactId>jersey-server</artifactId>
        <version>1.19</version>
    </dependency>

    <dependency>
        <groupId>com.sun.jersey</groupId>
        <artifactId>jersey-core</artifactId>
        <version>1.19</version>
    </dependency>

</dependencies>

Can anyone give me any hints on how to solve this problem?

main files of my classpath

owlapi-distribution-4.1.3
pellet-core-ignazio1977
pellet-owlapi-ignazio1977-2.4.0
pellet-query-ignazio1977-2.4.0
pellet-jena-ignazio1977-2.4.0
jena-arq-2.10.1
jena-core-2.10.1

Result of System.out.println(System.getProperty("java.class.path"));

C:\Users\clayton\workspace\SemanticMDX\target\classes;
C:\apache-tomcat-7.0.34\lib\annotations-api.jar;
C:\apache-tomcat-7.0.34\lib\catalina-ant.jar;
C:\apache-tomcat-7.0.34\lib\catalina-ha.jar;
C:\apache-tomcat-7.0.34\lib\catalina-tribes.jar;
C:\apache-tomcat-7.0.34\lib\catalina.jar;
C:\apache-tomcat-7.0.34\lib\ecj-4.2.1.jar;
C:\apache-tomcat-7.0.34\lib\el-api.jar;
C:\apache-tomcat-7.0.34\lib\jasper-el.jar;
C:\apache-tomcat-7.0.34\lib\jasper.jar;
C:\apache-tomcat-7.0.34\lib\jsp-api.jar;
C:\apache-tomcat-7.0.34\lib\owlapi-distribution-3.5.2.jar;
C:\apache-tomcat-7.0.34\lib\servlet-api.jar;
C:\apache-tomcat-7.0.34\lib\tomcat-api.jar;
C:\apache-tomcat-7.0.34\lib\tomcat-coyote.jar;
C:\apache-tomcat-7.0.34\lib\tomcat-dbcp.jar;
C:\apache-tomcat-7.0.34\lib\tomcat-i18n-es.jar;
C:\apache-tomcat-7.0.34\lib\tomcat-i18n-fr.jar;
C:\apache-tomcat-7.0.34\lib\tomcat-i18n-ja.jar;
C:\apache-tomcat-7.0.34\lib\tomcat-jdbc.jar;
C:\apache-tomcat-7.0.34\lib\tomcat-util.jar;
C:\Users\clayton\.m2\repository\net\sourceforge\owlapi\pellet-core-ignazio1977\2.4.0-ignazio1977\pellet-core-ignazio1977-2.4.0-ignazio1977.jar;
C:\Users\clayton\.m2\repository\com\github\ansell\aterms\aterm-java\1.8.2-p1\aterm-java-1.8.2-p1.jar;
C:\Users\clayton\.m2\repository\com\github\ansell\jjtraveler\jjtraveler\0.6\jjtraveler-0.6.jar;
C:\Users\clayton\.m2\repository\com\github\ansell\aterms\shared-objects\1.4.9-p1\shared-objects-1.4.9-p1.jar;
C:\Users\clayton\.m2\repository\org\jgrapht\jgrapht-jdk1.5\0.7.3\jgrapht-jdk1.5-0.7.3.jar;
C:\Users\clayton\.m2\repository\xerces\xercesImpl\2.11.0\xercesImpl-2.11.0.jar;
C:\Users\clayton\.m2\repository\xml-apis\xml-apis\1.4.01\xml-apis-1.4.01.jar;
C:\Users\clayton\.m2\repository\org\apache\jena\jena-arq\2.10.1\jena-arq-2.10.1.jar;
C:\Users\clayton\.m2\repository\org\apache\jena\jena-core\2.10.1\jena-core-2.10.1.jar;
C:\Users\clayton\.m2\repository\org\apache\jena\jena-iri\0.9.6\jena-iri-0.9.6.jar;
C:\Users\clayton\.m2\repository\org\apache\httpcomponents\httpclient\4.2.3\httpclient-4.2.3.jar;
C:\Users\clayton\.m2\repository\org\apache\httpcomponents\httpcore\4.2.2\httpcore-4.2.2.jar;
C:\Users\clayton\.m2\repository\commons-codec\commons-codec\1.6\commons-codec-1.6.jar;
C:\Users\clayton\.m2\repository\net\sourceforge\owlapi\owlapi-distribution\4.1.3\owlapi-distribution-4.1.3.jar;
C:\Users\clayton\.m2\repository\com\fasterxml\jackson\core\jackson-core\2.5.1\jackson-core-2.5.1.jar;
C:\Users\clayton\.m2\repository\com\fasterxml\jackson\core\jackson-databind\2.5.1\jackson-databind-2.5.1.jar;
C:\Users\clayton\.m2\repository\com\fasterxml\jackson\core\jackson-annotations\2.5.1\jackson-annotations-2.5.1.jar;
C:\Users\clayton\.m2\repository\org\tukaani\xz\1.5\xz-1.5.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-model\2.7.12\sesame-model-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-util\2.7.12\sesame-util-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-api\2.7.12\sesame-rio-api-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-languages\2.7.12\sesame-rio-languages-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-datatypes\2.7.12\sesame-rio-datatypes-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-binary\2.7.12\sesame-rio-binary-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-n3\2.7.12\sesame-rio-n3-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-nquads\2.7.12\sesame-rio-nquads-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-ntriples\2.7.12\sesame-rio-ntriples-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-rdfjson\2.7.12\sesame-rio-rdfjson-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-rdfxml\2.7.12\sesame-rio-rdfxml-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-trix\2.7.12\sesame-rio-trix-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-turtle\2.7.12\sesame-rio-turtle-2.7.12.jar;
C:\Users\clayton\.m2\repository\org\openrdf\sesame\sesame-rio-trig\2.7.12\sesame-rio-trig-2.7.12.jar;
C:\Users\clayton\.m2\repository\com\github\jsonld-java\jsonld-java-sesame\0.5.0\jsonld-java-sesame-0.5.0.jar;
C:\Users\clayton\.m2\repository\com\github\jsonld-java\jsonld-java\0.5.0\jsonld-java-0.5.0.jar;
C:\Users\clayton\.m2\repository\org\apache\httpcomponents\httpclient-cache\4.2.5\httpclient-cache-4.2.5.jar;
C:\Users\clayton\.m2\repository\org\slf4j\jcl-over-slf4j\1.7.7\jcl-over-slf4j-1.7.7.jar;
C:\Users\clayton\.m2\repository\org\semarglproject\semargl-sesame\0.6.1\semargl-sesame-0.6.1.jar;
C:\Users\clayton\.m2\repository\org\semarglproject\semargl-core\0.6.1\semargl-core-0.6.1.jar;
C:\Users\clayton\.m2\repository\org\semarglproject\semargl-rdfa\0.6.1\semargl-rdfa-0.6.1.jar;
C:\Users\clayton\.m2\repository\org\semarglproject\semargl-rdf\0.6.1\semargl-rdf-0.6.1.jar;
C:\Users\clayton\.m2\repository\net\sf\trove4j\trove4j\3.0.3\trove4j-3.0.3.jar;
C:\Users\clayton\.m2\repository\com\google\guava\guava\18.0\guava-18.0.jar;
C:\Users\clayton\.m2\repository\com\google\inject\guice\4.0\guice-4.0.jar;
C:\Users\clayton\.m2\repository\javax\inject\javax.inject\1\javax.inject-1.jar;
C:\Users\clayton\.m2\repository\aopalliance\aopalliance\1.0\aopalliance-1.0.jar;
C:\Users\clayton\.m2\repository\com\google\inject\extensions\guice-assistedinject\4.0\guice-assistedinject-4.0.jar;
C:\Users\clayton\.m2\repository\com\google\inject\extensions\guice-multibindings\4.0\guice-multibindings-4.0.jar;
C:\Users\clayton\.m2\repository\com\google\code\findbugs\jsr305\2.0.1\jsr305-2.0.1.jar;
C:\Users\clayton\.m2\repository\org\slf4j\slf4j-api\1.7.10\slf4j-api-1.7.10.jar;
C:\Users\clayton\.m2\repository\commons-io\commons-io\2.4\commons-io-2.4.jar;
C:\Users\clayton\.m2\repository\net\sourceforge\owlapi\pellet-owlapi-ignazio1977\2.4.0-ignazio1977\pellet-owlapi-ignazio1977-2.4.0-ignazio1977.jar;
C:\Users\clayton\.m2\repository\net\sourceforge\owlapi\pellet-query-ignazio1977\2.4.0-ignazio1977\pellet-query-ignazio1977-2.4.0-ignazio1977.jar;
C:\Users\clayton\.m2\repository\net\sourceforge\owlapi\pellet-jena-ignazio1977\2.4.0-ignazio1977\pellet-jena-ignazio1977-2.4.0-ignazio1977.jar;
C:\Users\clayton\.m2\repository\org\antlr\antlr-runtime\3.4\antlr-runtime-3.4.jar;
C:\Users\clayton\.m2\repository\org\antlr\stringtemplate\3.2.1\stringtemplate-3.2.1.jar;
C:\Users\clayton\.m2\repository\antlr\antlr\2.7.7\antlr-2.7.7.jar;
C:\Users\clayton\.m2\repository\asm\asm\3.3.1\asm-3.3.1.jar;
C:\Users\clayton\.m2\repository\com\sun\jersey\jersey-bundle\1.19\jersey-bundle-1.19.jar;
C:\Users\clayton\.m2\repository\javax\ws\rs\jsr311-api\1.1.1\jsr311-api-1.1.1.jar;
C:\Users\clayton\.m2\repository\org\json\json\20140107\json-20140107.jar;
C:\Users\clayton\.m2\repository\com\sun\jersey\jersey-server\1.19\jersey-server-1.19.jar;
C:\Users\clayton\.m2\repository\com\sun\jersey\jersey-core\1.19\jersey-core-1.19.jar

score 0 · Answer 1 · answered Apr 10 '16 at 07:19

0

The method not found has been part of OWLAPI since version 3.5.0, according to the javadoc. This seems to suggest you have multiple OWLAPI jars on the classpath, however your pom does not show them.

You should check to make sure only these libraries are in your actual runtime classpath - is this being run as part of a maven build, or is this run in another environment where the classpath might include other dependencies?

answered Apr 10 '16 at 07:19

Ignazio

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I compiled the code by command line, but I'm using eclipse. My eclipse also has the maven plugin. I will delete the Maven repository and redownload the eclipse. – Clayton Silva Apr 10 '16 at 18:37
Removal of the Maven directory did not work. The error still persists. – Clayton Silva Apr 10 '16 at 18:42
I edited the post and added the main files of my classpath. – Clayton Silva Apr 10 '16 at 19:09
Can you try adding this to your code and posting the result? System.out.println(System.getProperty("java.class.path")); – Ignazio Apr 10 '16 at 19:18
Thanks for the great help Ignazio. I posted the files of my classpath. – Clayton Silva Apr 11 '16 at 02:12
I realized that in the tomcat directory had a .jar owlapi 3.x. I removed that file and all returned to work perfectly! Thank ignazio, your valuable help was very important. If it were not for your help I would be still trying to solve the problem. – Clayton Silva Apr 11 '16 at 02:18

owl api + pellet ignazio1977

1 Answers1