ProcessOntology.groovy

@Grapes([
    @Grab(group="org.semanticweb.elk", module="elk-owlapi", version="0.4.3"),
    @Grab(group="net.sourceforge.owlapi", module="owlapi-api", version="4.2.5"),
    @Grab(group="net.sourceforge.owlapi", module="owlapi-apibinding", version="4.2.5"),
    @Grab(group="net.sourceforge.owlapi", module="owlapi-impl", version="4.2.5"),
    @Grab(group="net.sourceforge.owlapi", module="owlapi-parsers", version="4.2.5"),
    @Grab(group="org.codehaus.gpars", module="gpars", version="1.1.0"),
    @Grab(group="net.sourceforge.owlapi", module="org.semanticweb.hermit", version="1.3.8.413"),
    @GrabConfig(systemClassLoader=true)
])

import org.semanticweb.owlapi.model.parameters.*;
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.elk.owlapi.ElkReasonerConfiguration;
import org.semanticweb.elk.reasoner.config.*;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.reasoner.*;
import org.semanticweb.owlapi.reasoner.structural.StructuralReasoner
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.io.*;
import org.semanticweb.owlapi.owllink.*;
import org.semanticweb.owlapi.util.*;
import org.semanticweb.owlapi.search.*;
import org.semanticweb.owlapi.manchestersyntax.renderer.*;
import org.semanticweb.owlapi.reasoner.structural.*;
import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor;
import org.semanticweb.owlapi.manchestersyntax.renderer.*;
import java.io.*;
import java.io.PrintWriter;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.util.InferredAxiomGenerator;
import org.semanticweb.owlapi.util.InferredOntologyGenerator;
import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
import org.semanticweb.owlapi.util.InferredEquivalentClassAxiomGenerator;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.HermiT.Reasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
import groovyx.gpars.GParsPool;


OWLOntologyManager outputManager = OWLManager.createOWLOntologyManager();
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
String ontostring = args[0];
String prefreasoner =args[1];
OWLOntology ont = manager.loadOntologyFromOntologyDocument(new File(ontostring));
public class SimpleShortFormProvider1 implements ShortFormProvider, Serializable {

    private final SimpleIRIShortFormProvider uriShortFormProvider = new SimpleIRIShortFormProvider();

    @Override
    public String getShortForm(OWLEntity entity) {
	return '<'+entity.getIRI().toString()+'>';
    }
    public void dispose(){
	;
    }
}
if (prefreasoner.toLowerCase().equals("elk"))
    {

    OWLDataFactory dataFactory = manager.getOWLDataFactory()
    OWLDataFactory fac = manager.getOWLDataFactory()

    ConsoleProgressMonitor progressMonitor = new ConsoleProgressMonitor()
    OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor)


    ElkReasonerFactory f1 = new ElkReasonerFactory()
    OWLReasoner reasoner = f1.createReasoner(ont, config)
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY)

    List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
    gens.add(new InferredSubClassAxiomGenerator());
    gens.add(new InferredEquivalentClassAxiomGenerator());
    OWLOntology infOnt = outputManager.createOntology();


    InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner,gens);
    iog.fillOntology(outputManager.getOWLDataFactory(), infOnt);

    // Save the inferred ontology.
    //outputManager.saveOntology(infOnt,IRI.create((new File("inferredontologygo2.owl").toURI())));

    // Display Axioms
    OWLObjectRenderer renderer =new ManchesterOWLSyntaxOWLObjectRendererImpl ();
    renderer.setShortFormProvider(new SimpleShortFormProvider1());
    int numaxiom1= infOnt.getAxiomCount();
    Set<OWLClass> classes=infOnt.getClassesInSignature();

    //display original axioms
    //int numaxiom1= Ont.getAxiomCount();
    Set<OWLClass> classeso=ont.getClassesInSignature();

    FileWriter fwo= new FileWriter ("axiomsorig.lst");
    BufferedWriter bwo =new BufferedWriter (fwo);
    PrintWriter outo =new PrintWriter (bwo);

    for (OWLClass classo : classeso)
	{
	Set<OWLClassAxiom> ontoaxioms=ont.getAxioms (classo);
	for (OWLClassAxiom claxiom: ontoaxioms)
	    {
	    // classess=renderer.render(class1);
	    classaxiom=renderer.render (claxiom);
	    //out1.println (classess);
	    outo.println (classaxiom.replaceAll("\n"," ").replaceAll(","," "));
	}
    }
    outo.flush() //Tilman comment 
} else {
    OWLReasonerFactory reasonerFactory = new Reasoner.ReasonerFactory();
    OWLReasoner reasoner =reasonerFactory.createReasoner(ont);
    OWLDataFactory factory=manager.getOWLDataFactory();
    reasoner.precomputeInferences();
    InferredSubClassAxiomGenerator generator = new InferredSubClassAxiomGenerator();
    Set<OWLAxiom> axioms = generator.createAxioms(factory, reasoner);
    manager.addAxioms(ont,axioms);
    OWLObjectRenderer renderer =new ManchesterOWLSyntaxOWLObjectRendererImpl ();
    renderer.setShortFormProvider(new SimpleShortFormProvider1());
    Set<OWLClass> classes=ont.getClassesInSignature();

    FileWriter fw= new FileWriter ("axiomsinf.lst");
    BufferedWriter bw =new BufferedWriter (fw);
    PrintWriter out =new PrintWriter (bw);

    FileWriter fw1= new FileWriter ("classes.lst");
    BufferedWriter bw1 =new BufferedWriter (fw1);
    PrintWriter out1 =new PrintWriter (bw1);

    for (OWLClass class1 : classes)
	{
	Set<OWLClassAxiom> ontoaxioms=ont.getAxioms (class1);
	for (OWLClassAxiom claxiom: ontoaxioms)
	    {
	    classess=renderer.render(class1);
	    classaxiom=renderer.render (claxiom);
	    out1.println (classess);
	    out.println (classaxiom.replaceAll("\n"," ").replaceAll(","," "));
	}
    }

    FileWriter fwo= new FileWriter ("axiomsorig.lst"); BufferedWriter bwo =new BufferedWriter (fwo); PrintWriter outo =new PrintWriter (bwo);
    outo.println(" ");
    outo.flush()
    outo.close()
}