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[DL-Learner SVN] SF.net SVN: dl-learner:[2905] trunk
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From: <ku...@us...> - 2011-06-17 16:23:59
|
Revision: 2905
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2905&view=rev
Author: kurzum
Date: 2011-06-17 16:23:50 +0000 (Fri, 17 Jun 2011)
Log Message:
-----------
geizhals fixes
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/interfaces/src/main/java/org/dllearner/server/nke/Geizhals2OWL.java
trunk/interfaces/src/test/java/org/dllearner/test/junit/GeizhalsTest.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2011-06-17 15:57:04 UTC (rev 2904)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2011-06-17 16:23:50 UTC (rev 2905)
@@ -2,7 +2,7 @@
* Copyright (C) 2008, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -19,369 +19,307 @@
*/
package org.dllearner.reasoning;
-import java.io.File;
-import java.net.MalformedURLException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeMap;
-import java.util.TreeSet;
-
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.configurators.OWLAPIReasonerConfigurator;
-import org.dllearner.core.options.ConfigEntry;
-import org.dllearner.core.options.ConfigOption;
-import org.dllearner.core.options.InvalidConfigOptionValueException;
-import org.dllearner.core.options.StringConfigOption;
-import org.dllearner.core.options.URLConfigOption;
-import org.dllearner.core.owl.Axiom;
-import org.dllearner.core.owl.Constant;
-import org.dllearner.core.owl.Datatype;
-import org.dllearner.core.owl.DatatypeProperty;
-import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.Entity;
-import org.dllearner.core.owl.Individual;
-import org.dllearner.core.owl.KB;
-import org.dllearner.core.owl.NamedClass;
-import org.dllearner.core.owl.Nothing;
-import org.dllearner.core.owl.ObjectProperty;
-import org.dllearner.core.owl.Thing;
-import org.dllearner.core.owl.TypedConstant;
-import org.dllearner.core.owl.UntypedConstant;
+import org.dllearner.core.options.*;
+import org.dllearner.core.owl.*;
import org.dllearner.kb.OWLAPIOntology;
import org.dllearner.kb.OWLFile;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
-import org.dllearner.utilities.owl.ConceptComparator;
-import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
-import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
-import org.dllearner.utilities.owl.OWLAPIConverter;
-import org.dllearner.utilities.owl.OWLAPIDescriptionConvertVisitor;
-import org.dllearner.utilities.owl.RoleComparator;
+import org.dllearner.utilities.owl.*;
import org.semanticweb.HermiT.Reasoner.ReasonerFactory;
import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.AddAxiom;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLAnnotation;
-import org.semanticweb.owlapi.model.OWLAxiom;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLClassExpression;
-import org.semanticweb.owlapi.model.OWLDataFactory;
-import org.semanticweb.owlapi.model.OWLDataProperty;
-import org.semanticweb.owlapi.model.OWLDataRange;
-import org.semanticweb.owlapi.model.OWLDatatype;
-import org.semanticweb.owlapi.model.OWLEntity;
-import org.semanticweb.owlapi.model.OWLIndividual;
-import org.semanticweb.owlapi.model.OWLLiteral;
-import org.semanticweb.owlapi.model.OWLNamedIndividual;
-import org.semanticweb.owlapi.model.OWLNamedObject;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
-import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyChangeException;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyFormat;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.model.OWLOntologyStorageException;
-import org.semanticweb.owlapi.model.RemoveAxiom;
-import org.semanticweb.owlapi.model.UnknownOWLOntologyException;
+import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory;
import org.semanticweb.owlapi.owllink.OWLlinkReasonerConfiguration;
-import org.semanticweb.owlapi.reasoner.FreshEntityPolicy;
-import org.semanticweb.owlapi.reasoner.IndividualNodeSetPolicy;
-import org.semanticweb.owlapi.reasoner.InferenceType;
-import org.semanticweb.owlapi.reasoner.Node;
-import org.semanticweb.owlapi.reasoner.NodeSet;
-import org.semanticweb.owlapi.reasoner.NullReasonerProgressMonitor;
-import org.semanticweb.owlapi.reasoner.OWLReasoner;
-import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
-import org.semanticweb.owlapi.reasoner.ReasonerProgressMonitor;
-import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
+import org.semanticweb.owlapi.reasoner.*;
import org.semanticweb.owlapi.util.SimpleIRIMapper;
import org.semanticweb.owlapi.vocab.PrefixOWLOntologyFormat;
-
import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;
-import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.*;
+import java.util.Map.Entry;
/**
- * Mapping to OWL API reasoner interface. The OWL API currently
+ * Mapping to OWL API reasoner interface. The OWL API currently
* supports three reasoners: FaCT++, HermiT and Pellet. FaCT++ is connected
* using JNI and native libraries, while HermiT and Pellet are pure Java
* libraries.
- *
- * @author Jens Lehmann
*
+ * @author Jens Lehmann
*/
public class OWLAPIReasoner extends ReasonerComponent {
// private static Logger logger = Logger
// .getLogger(OWLAPIReasoner.class);
-
- //private String reasonerType = "pellet";
- private OWLAPIReasonerConfigurator configurator;
- @Override
- public OWLAPIReasonerConfigurator getConfigurator(){
- return configurator;
- }
-
- private OWLReasoner reasoner;
- private OWLOntologyManager manager;
- private OWLOntology ontology;
- // the data factory is used to generate OWL API objects
- private OWLDataFactory factory;
- // static factory
+ //private String reasonerType = "pellet";
+ private OWLAPIReasonerConfigurator configurator;
+
+ @Override
+ public OWLAPIReasonerConfigurator getConfigurator() {
+ return configurator;
+ }
+
+ private OWLReasoner reasoner;
+ private OWLOntologyManager manager;
+
+ private OWLOntology ontology;
+ // the data factory is used to generate OWL API objects
+ private OWLDataFactory factory;
+ // static factory
// private static OWLDataFactory staticFactory = OWLManager.createOWLOntologyManager().getOWLDataFactory();
-
- private ConceptComparator conceptComparator = new ConceptComparator();
- private RoleComparator roleComparator = new RoleComparator();
+
+ private ConceptComparator conceptComparator = new ConceptComparator();
+ private RoleComparator roleComparator = new RoleComparator();
// private ClassHierarchy subsumptionHierarchy;
// private ObjectPropertyHierarchy roleHierarchy;
// private DatatypePropertyHierarchy datatypePropertyHierarchy;
// private Set<Description> allowedConceptsInSubsumptionHierarchy;
-
- // primitives
- Set<NamedClass> atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
- Set<ObjectProperty> atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
- SortedSet<DatatypeProperty> datatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<DatatypeProperty> stringDatatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<Individual> individuals = new TreeSet<Individual>();
-
- // namespaces
- private Map<String, String> prefixes = new TreeMap<String,String>();
- private String baseURI;
-
- // references to OWL API ontologies
- private List<OWLOntology> owlAPIOntologies = new LinkedList<OWLOntology>();
-
- public OWLAPIReasoner(Set<KnowledgeSource> sources) {
- super(sources);
- this.configurator = new OWLAPIReasonerConfigurator(this);
- }
-
- public static String getName() {
- return "OWL API reasoner";
- }
-
-
- public static Collection<ConfigOption<?>> createConfigOptions() {
- Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
- StringConfigOption type = new StringConfigOption("reasonerType", "FaCT++, HermiT, OWLlink or Pellet, which means \"fact\", \"hermit\", \"owllink\" or \"pellet\"", "pellet", false, true);
- type.setAllowedValues(new String[] {"fact", "hermit", "owllink", "pellet" });
-
- // closure option? see:
- // http://owlapi.svn.sourceforge.net/viewvc/owlapi/owl1_1/trunk/tutorial/src/main/java/uk/ac/manchester/owl/tutorial/examples/ClosureAxiomsExample.java?view=markup
- options.add(type);
- try {
- URLConfigOption owlLinkURL = new URLConfigOption("owlLinkURL", "the URL to the remote OWLlink server", new URL("http://localhost:8080/"), false, true);
- options.add(owlLinkURL);
- } catch (MalformedURLException e) {
- e.printStackTrace();
- }
- return options;
- }
-
- /* (non-Javadoc)
- * @see org.dllearner.core.Component#applyConfigEntry(org.dllearner.core.config.ConfigEntry)
- */
- @Override
- public <T> void applyConfigEntry(ConfigEntry<T> entry) throws InvalidConfigOptionValueException {
-
- }
-
- @Override
- public void init() throws ComponentInitException {
- // reset variables (otherwise subsequent initialisation with
- // different knowledge sources will merge both)
- atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
- atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
- datatypeProperties = new TreeSet<DatatypeProperty>();
- booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
- doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
- intDatatypeProperties = new TreeSet<DatatypeProperty>();
- stringDatatypeProperties = new TreeSet<DatatypeProperty>();
- individuals = new TreeSet<Individual>();
-
- // create OWL API ontology manager
- manager = OWLManager.createOWLOntologyManager();
-
- // it is a bit cumbersome to obtain all classes, because there
- // are no reasoner queries to obtain them => hence we query them
- // for each ontology and add them to a set; a comparator avoids
- // duplicates by checking URIs
- Comparator<OWLNamedObject> namedObjectComparator = new Comparator<OWLNamedObject>() {
- public int compare(OWLNamedObject o1, OWLNamedObject o2) {
- return o1.getIRI().compareTo(o2.getIRI());
- }
- };
- Set<OWLClass> classes = new TreeSet<OWLClass>(namedObjectComparator);
- Set<OWLObjectProperty> owlObjectProperties = new TreeSet<OWLObjectProperty>(namedObjectComparator);
- Set<OWLDataProperty> owlDatatypeProperties = new TreeSet<OWLDataProperty>(namedObjectComparator);
- Set<OWLNamedIndividual> owlIndividuals = new TreeSet<OWLNamedIndividual>(namedObjectComparator);
-
- Set<OWLOntology> allImports = new HashSet<OWLOntology>();
- prefixes = new TreeMap<String,String>();
-
- for(KnowledgeSource source : sources) {
-
- if(source instanceof OWLFile || source instanceof SparqlKnowledgeSource || source instanceof OWLAPIOntology) {
- URL url=null;
- if(source instanceof OWLFile){
- url = ((OWLFile)source).getURL();
- }
- try {
-
- if(source instanceof OWLAPIOntology) {
- ontology = ((OWLAPIOntology)source).getOWLOntolgy();
+ // primitives
+ Set<NamedClass> atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
+ Set<ObjectProperty> atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
+ SortedSet<DatatypeProperty> datatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> stringDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<Individual> individuals = new TreeSet<Individual>();
+
+ // namespaces
+ private Map<String, String> prefixes = new TreeMap<String, String>();
+ private String baseURI;
+
+ // references to OWL API ontologies
+ private List<OWLOntology> owlAPIOntologies = new LinkedList<OWLOntology>();
+
+ public OWLAPIReasoner(Set<KnowledgeSource> sources) {
+ super(sources);
+ this.configurator = new OWLAPIReasonerConfigurator(this);
+ }
+
+ public static String getName() {
+ return "OWL API reasoner";
+ }
+
+
+ public static Collection<ConfigOption<?>> createConfigOptions() {
+ Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
+ StringConfigOption type = new StringConfigOption("reasonerType", "FaCT++, HermiT, OWLlink or Pellet, which means \"fact\", \"hermit\", \"owllink\" or \"pellet\"", "pellet", false, true);
+ type.setAllowedValues(new String[]{"fact", "hermit", "owllink", "pellet"});
+
+ // closure option? see:
+ // http://owlapi.svn.sourceforge.net/viewvc/owlapi/owl1_1/trunk/tutorial/src/main/java/uk/ac/manchester/owl/tutorial/examples/ClosureAxiomsExample.java?view=markup
+ options.add(type);
+ try {
+ URLConfigOption owlLinkURL = new URLConfigOption("owlLinkURL", "the URL to the remote OWLlink server", new URL("http://localhost:8080/"), false, true);
+ options.add(owlLinkURL);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+ return options;
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Component#applyConfigEntry(org.dllearner.core.config.ConfigEntry)
+ */
+ @Override
+ public <T> void applyConfigEntry(ConfigEntry<T> entry) throws InvalidConfigOptionValueException {
+
+ }
+
+ @Override
+ public void init() throws ComponentInitException {
+ // reset variables (otherwise subsequent initialisation with
+ // different knowledge sources will merge both)
+ atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
+ atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
+ datatypeProperties = new TreeSet<DatatypeProperty>();
+ booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
+ doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
+ intDatatypeProperties = new TreeSet<DatatypeProperty>();
+ stringDatatypeProperties = new TreeSet<DatatypeProperty>();
+ individuals = new TreeSet<Individual>();
+
+ // create OWL API ontology manager
+ manager = OWLManager.createOWLOntologyManager();
+
+ // it is a bit cumbersome to obtain all classes, because there
+ // are no reasoner queries to obtain them => hence we query them
+ // for each ontology and add them to a set; a comparator avoids
+ // duplicates by checking URIs
+ Comparator<OWLNamedObject> namedObjectComparator = new Comparator<OWLNamedObject>() {
+ public int compare(OWLNamedObject o1, OWLNamedObject o2) {
+ return o1.getIRI().compareTo(o2.getIRI());
+ }
+ };
+ Set<OWLClass> classes = new TreeSet<OWLClass>(namedObjectComparator);
+ Set<OWLObjectProperty> owlObjectProperties = new TreeSet<OWLObjectProperty>(namedObjectComparator);
+ Set<OWLDataProperty> owlDatatypeProperties = new TreeSet<OWLDataProperty>(namedObjectComparator);
+ Set<OWLNamedIndividual> owlIndividuals = new TreeSet<OWLNamedIndividual>(namedObjectComparator);
+
+ Set<OWLOntology> allImports = new HashSet<OWLOntology>();
+ prefixes = new TreeMap<String, String>();
+
+ for (KnowledgeSource source : sources) {
+
+ if (source instanceof OWLFile || source instanceof SparqlKnowledgeSource || source instanceof OWLAPIOntology) {
+ URL url = null;
+ if (source instanceof OWLFile) {
+ url = ((OWLFile) source).getURL();
+ }
+
+ try {
+
+ if (source instanceof OWLAPIOntology) {
+ ontology = ((OWLAPIOntology) source).getOWLOntolgy();
manager = ontology.getOWLOntologyManager();
- } else if (source instanceof SparqlKnowledgeSource) {
- ontology = ((SparqlKnowledgeSource)source).getOWLAPIOntology();
- manager = ontology.getOWLOntologyManager();
- } else {
- ontology = manager.loadOntologyFromOntologyDocument(IRI.create(url.toURI()));
- }
-
- owlAPIOntologies.add(ontology);
- // imports includes the ontology itself
- Set<OWLOntology> imports = manager.getImportsClosure(ontology);
- allImports.addAll(imports);
+ } else if (source instanceof SparqlKnowledgeSource) {
+ ontology = ((SparqlKnowledgeSource) source).getOWLAPIOntology();
+ manager = ontology.getOWLOntologyManager();
+ } else {
+ ontology = manager.loadOntologyFromOntologyDocument(IRI.create(url.toURI()));
+ }
+
+ owlAPIOntologies.add(ontology);
+ try {
+ // imports includes the ontology itself
+ //FIXME this line throws the strange error
+ Set<OWLOntology> imports = manager.getImportsClosure(ontology);
+ allImports.addAll(imports);
+
// System.out.println(imports);
- for(OWLOntology ont : imports) {
- classes.addAll(ont.getClassesInSignature());
- owlObjectProperties.addAll(ont.getObjectPropertiesInSignature());
- owlDatatypeProperties.addAll(ont.getDataPropertiesInSignature());
- owlIndividuals.addAll(ont.getIndividualsInSignature());
- }
-
- // if several knowledge sources are included, then we can only
- // guarantee that the base URI is from one of those sources (there
- // can't be more than one); but we will take care that all prefixes are
- // correctly imported
- OWLOntologyFormat format = manager.getOntologyFormat(ontology);
- if(format instanceof PrefixOWLOntologyFormat) {
- prefixes.putAll(((PrefixOWLOntologyFormat)format).getPrefixName2PrefixMap());
- baseURI = ((PrefixOWLOntologyFormat) format).getDefaultPrefix();
- prefixes.remove("");
- }
-
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- } catch (URISyntaxException e) {
- e.printStackTrace();
- }
- // all other sources are converted to KB and then to an
- // OWL API ontology
- } else {
- KB kb = source.toKB();
+ for (OWLOntology ont : imports) {
+ classes.addAll(ont.getClassesInSignature());
+ owlObjectProperties.addAll(ont.getObjectPropertiesInSignature());
+ owlDatatypeProperties.addAll(ont.getDataPropertiesInSignature());
+ owlIndividuals.addAll(ont.getIndividualsInSignature());
+ }
+
+ } catch (UnknownOWLOntologyException uooe) {
+ logger.error("UnknownOWLOntologyException occured, imports were not loaded! This is a bug, which has not been fixed yet.");
+ }
+
+ // if several knowledge sources are included, then we can only
+ // guarantee that the base URI is from one of those sources (there
+ // can't be more than one); but we will take care that all prefixes are
+ // correctly imported
+ OWLOntologyFormat format = manager.getOntologyFormat(ontology);
+ if (format instanceof PrefixOWLOntologyFormat) {
+ prefixes.putAll(((PrefixOWLOntologyFormat) format).getPrefixName2PrefixMap());
+ baseURI = ((PrefixOWLOntologyFormat) format).getDefaultPrefix();
+ prefixes.remove("");
+ }
+
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (URISyntaxException e) {
+ e.printStackTrace();
+ }
+ // all other sources are converted to KB and then to an
+ // OWL API ontology
+ } else {
+ KB kb = source.toKB();
// System.out.println(kb.toString(null,null));
-
- IRI ontologyURI = IRI.create("http://example.com");
- ontology = null;
- try {
- ontology = manager.createOntology(ontologyURI);
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- }
- OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, kb);
- owlAPIOntologies.add(ontology);
- allImports.add(ontology);
- atomicConcepts.addAll(kb.findAllAtomicConcepts());
- atomicRoles.addAll(kb.findAllAtomicRoles());
- individuals.addAll(kb.findAllIndividuals());
- // TODO: add method to find datatypes
- }
- }
- try {
- ontology = manager.createOntology(IRI.create("http://dl-learner/all"), new HashSet<OWLOntology>(owlAPIOntologies));
- } catch (OWLOntologyCreationException e1) {
- e1.printStackTrace();
- }
-
- //configure reasoner
- ReasonerProgressMonitor progressMonitor = new NullReasonerProgressMonitor();
- FreshEntityPolicy freshEntityPolicy = FreshEntityPolicy.ALLOW;
- long timeOut = Integer.MAX_VALUE;
- IndividualNodeSetPolicy individualNodeSetPolicy = IndividualNodeSetPolicy.BY_NAME;
- OWLReasonerConfiguration conf = new SimpleConfiguration(progressMonitor, freshEntityPolicy, timeOut, individualNodeSetPolicy);
-
- // create actual reasoner
- if(configurator.getReasonerType().equals("fact")) {
- try {
- reasoner = new FaCTPlusPlusReasonerFactory().createNonBufferingReasoner(ontology, conf);
- } catch (Exception e) {
- e.printStackTrace();
- }
- System.out.println("Using FaCT++.");
- } else if(configurator.getReasonerType().equals("hermit")){
- // instantiate HermiT reasoner
- reasoner = new ReasonerFactory().createNonBufferingReasoner(ontology, conf);
- } else if(configurator.getReasonerType().equals("pellet")){
- // instantiate Pellet reasoner
- reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(ontology, conf);
-
- // change log level to WARN for Pellet, because otherwise log
- // output will be very large
- Logger pelletLogger = Logger.getLogger("org.mindswap.pellet");
- pelletLogger.setLevel(Level.WARN);
- } else {
- try {
- OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
- URL url = getConfigurator().getOwlLinkURL();//Configure the server end-point
- OWLlinkReasonerConfiguration config = new OWLlinkReasonerConfiguration(url);
- reasoner = factory.createNonBufferingReasoner(ontology, config);
- System.out.println(reasoner.getReasonerName());
- } catch (Exception e) {
-// e.printStackTrace();
- throw new ComponentInitException(e);
- }
- }
- /*
- Set<OWLOntology> importsClosure = manager.getImportsClosure(ontology);
- System.out.println("imports closure : " + importsClosure);
+ IRI ontologyURI = IRI.create("http://example.com");
+ ontology = null;
+ try {
+ ontology = manager.createOntology(ontologyURI);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, kb);
+ owlAPIOntologies.add(ontology);
+ allImports.add(ontology);
+ atomicConcepts.addAll(kb.findAllAtomicConcepts());
+ atomicRoles.addAll(kb.findAllAtomicRoles());
+ individuals.addAll(kb.findAllIndividuals());
+ // TODO: add method to find datatypes
+ }
+ }
try {
- reasoner.loadOntologies(importsClosure);
- } catch (OWLReasonerException e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }*/
-
+ ontology = manager.createOntology(IRI.create("http://dl-learner/all"), new HashSet<OWLOntology>(owlAPIOntologies));
+ } catch (OWLOntologyCreationException e1) {
+ e1.printStackTrace();
+ }
+
+ //configure reasoner
+ ReasonerProgressMonitor progressMonitor = new NullReasonerProgressMonitor();
+ FreshEntityPolicy freshEntityPolicy = FreshEntityPolicy.ALLOW;
+ long timeOut = Integer.MAX_VALUE;
+ IndividualNodeSetPolicy individualNodeSetPolicy = IndividualNodeSetPolicy.BY_NAME;
+ OWLReasonerConfiguration conf = new SimpleConfiguration(progressMonitor, freshEntityPolicy, timeOut, individualNodeSetPolicy);
+
+ // create actual reasoner
+ if (configurator.getReasonerType().equals("fact")) {
+ try {
+ reasoner = new FaCTPlusPlusReasonerFactory().createNonBufferingReasoner(ontology, conf);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ System.out.println("Using FaCT++.");
+ } else if (configurator.getReasonerType().equals("hermit")) {
+ // instantiate HermiT reasoner
+ reasoner = new ReasonerFactory().createNonBufferingReasoner(ontology, conf);
+ } else if (configurator.getReasonerType().equals("pellet")) {
+ // instantiate Pellet reasoner
+ reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(ontology, conf);
+
+ // change log level to WARN for Pellet, because otherwise log
+ // output will be very large
+ Logger pelletLogger = Logger.getLogger("org.mindswap.pellet");
+ pelletLogger.setLevel(Level.WARN);
+ } else {
+ try {
+ OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
+ URL url = getConfigurator().getOwlLinkURL();//Configure the server end-point
+ OWLlinkReasonerConfiguration config = new OWLlinkReasonerConfiguration(url);
+ reasoner = factory.createNonBufferingReasoner(ontology, config);
+ System.out.println(reasoner.getReasonerName());
+ } catch (Exception e) {
+// e.printStackTrace();
+ throw new ComponentInitException(e);
+ }
+ }
+
+ /*
+ Set<OWLOntology> importsClosure = manager.getImportsClosure(ontology);
+ System.out.println("imports closure : " + importsClosure);
+ try {
+ reasoner.loadOntologies(importsClosure);
+ } catch (OWLReasonerException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }*/
+
// System.out.println(classes);
// System.out.println(properties);
// System.out.println(individuals);
-
- // compute class hierarchy and types of individuals
- // (done here to speed up later reasoner calls)
- boolean inconsistentOntology = !reasoner.isConsistent();
-
- if(!inconsistentOntology) {
- reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY, InferenceType.CLASS_ASSERTIONS);
- } else {
- throw new ComponentInitException("Inconsistent ontologies.");
- }
-
- factory = manager.getOWLDataFactory();
-
+
+ // compute class hierarchy and types of individuals
+ // (done here to speed up later reasoner calls)
+ boolean inconsistentOntology = !reasoner.isConsistent();
+
+ if (!inconsistentOntology) {
+ reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY, InferenceType.CLASS_ASSERTIONS);
+ } else {
+ throw new ComponentInitException("Inconsistent ontologies.");
+ }
+
+ factory = manager.getOWLDataFactory();
+
// try {
// if(reasoner.isDefined(factory.getOWLIndividual(URI.create("http://example.com/father#female"))))
// System.out.println("DEFINED.");
@@ -391,83 +329,79 @@
// // TODO Auto-generated catch block
// e.printStackTrace();
// }
-
- // read in primitives
- for(OWLClass owlClass : classes)
- atomicConcepts.add(new NamedClass(owlClass.toStringID()));
- for(OWLObjectProperty owlProperty : owlObjectProperties)
- atomicRoles.add(new ObjectProperty(owlProperty.toStringID()));
- for(OWLDataProperty owlProperty : owlDatatypeProperties) {
- DatatypeProperty dtp = new DatatypeProperty(owlProperty.toStringID());
- Set<OWLDataRange> ranges = owlProperty.getRanges(allImports);
- Iterator<OWLDataRange> it = ranges.iterator();
- if(it.hasNext()) {
- OWLDataRange range = it.next();
- if(range.isDatatype()) {
- URI uri = ((OWLDatatype)range).getIRI().toURI();
- if(uri.equals(Datatype.BOOLEAN.getURI()))
- booleanDatatypeProperties.add(dtp);
- else if(uri.equals(Datatype.DOUBLE.getURI()))
- doubleDatatypeProperties.add(dtp);
- else if(uri.equals(Datatype.INT.getURI()))
- intDatatypeProperties.add(dtp);
- else if(uri.equals(Datatype.STRING.getURI()))
- stringDatatypeProperties.add(dtp);
- }
- } else {
- stringDatatypeProperties.add(dtp);
- }
- datatypeProperties.add(dtp);
- }
- for(OWLNamedIndividual owlIndividual : owlIndividuals) {
- individuals.add(new Individual(owlIndividual.toStringID()));
- }
-
- // remove top and bottom properties (for backwards compatibility)
+
+ // read in primitives
+ for (OWLClass owlClass : classes)
+ atomicConcepts.add(new NamedClass(owlClass.toStringID()));
+ for (OWLObjectProperty owlProperty : owlObjectProperties)
+ atomicRoles.add(new ObjectProperty(owlProperty.toStringID()));
+ for (OWLDataProperty owlProperty : owlDatatypeProperties) {
+ DatatypeProperty dtp = new DatatypeProperty(owlProperty.toStringID());
+ Set<OWLDataRange> ranges = owlProperty.getRanges(allImports);
+ Iterator<OWLDataRange> it = ranges.iterator();
+ if (it.hasNext()) {
+ OWLDataRange range = it.next();
+ if (range.isDatatype()) {
+ URI uri = ((OWLDatatype) range).getIRI().toURI();
+ if (uri.equals(Datatype.BOOLEAN.getURI())) booleanDatatypeProperties.add(dtp);
+ else if (uri.equals(Datatype.DOUBLE.getURI())) doubleDatatypeProperties.add(dtp);
+ else if (uri.equals(Datatype.INT.getURI())) intDatatypeProperties.add(dtp);
+ else if (uri.equals(Datatype.STRING.getURI())) stringDatatypeProperties.add(dtp);
+ }
+ } else {
+ stringDatatypeProperties.add(dtp);
+ }
+ datatypeProperties.add(dtp);
+ }
+ for (OWLNamedIndividual owlIndividual : owlIndividuals) {
+ individuals.add(new Individual(owlIndividual.toStringID()));
+ }
+
+ // remove top and bottom properties (for backwards compatibility)
// atomicRoles.remove(new ObjectProperty("http://www.w3.org/2002/07/owl#bottomObjectProperty"));
// atomicRoles.remove(new ObjectProperty("http://www.w3.org/2002/07/owl#topObjectProperty"));
- }
+ }
- /* (non-Javadoc)
- * @see org.dllearner.core.Reasoner#getAtomicConcepts()
- */
- public Set<NamedClass> getNamedClasses() {
- return Collections.unmodifiableSet(atomicConcepts);
- }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#getAtomicConcepts()
+ */
+ public Set<NamedClass> getNamedClasses() {
+ return Collections.unmodifiableSet(atomicConcepts);
+ }
- /* (non-Javadoc)
- * @see org.dllearner.core.Reasoner#getAtomicRoles()
- */
- public Set<ObjectProperty> getObjectProperties() {
- return Collections.unmodifiableSet(atomicRoles);
- }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#getAtomicRoles()
+ */
+ public Set<ObjectProperty> getObjectProperties() {
+ return Collections.unmodifiableSet(atomicRoles);
+ }
- @Override
- public SortedSet<DatatypeProperty> getDatatypePropertiesImpl() {
- return datatypeProperties;
- }
-
- /* (non-Javadoc)
- * @see org.dllearner.core.Reasoner#getIndividuals()
- */
- public SortedSet<Individual> getIndividuals() {
- return individuals;
- }
+ @Override
+ public SortedSet<DatatypeProperty> getDatatypePropertiesImpl() {
+ return datatypeProperties;
+ }
- /* (non-Javadoc)
- * @see org.dllearner.core.Reasoner#getReasonerType()
- */
- @Override
- public ReasonerType getReasonerType() {
- if(configurator.getReasonerType().equals("fact")){
- return ReasonerType.OWLAPI_FACT;
- } else if(configurator.getReasonerType().equals("hermit")){
- return ReasonerType.OWLAPI_HERMIT;
- } else{
- return ReasonerType.OWLAPI_PELLET;
- }
- }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#getIndividuals()
+ */
+ public SortedSet<Individual> getIndividuals() {
+ return individuals;
+ }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#getReasonerType()
+ */
+ @Override
+ public ReasonerType getReasonerType() {
+ if (configurator.getReasonerType().equals("fact")) {
+ return ReasonerType.OWLAPI_FACT;
+ } else if (configurator.getReasonerType().equals("hermit")) {
+ return ReasonerType.OWLAPI_HERMIT;
+ } else {
+ return ReasonerType.OWLAPI_PELLET;
+ }
+ }
+
// @Override
// public ObjectPropertyHierarchy prepareRoleHierarchy() {
// // code copied from DIG reasoner
@@ -487,10 +421,10 @@
// roleHierarchyDown);
// return roleHierarchy;
// }
-
- /* (non-Javadoc)
- * @see org.dllearner.core.Reasoner#prepareRoleHierarchy(java.util.Set)
- */
+
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#prepareRoleHierarchy(java.util.Set)
+ */
// public void prepareRoleHierarchy(Set<ObjectProperty> allowedRoles) {
// // code copied from DIG reasoner
//
@@ -508,12 +442,12 @@
// roleHierarchy = new ObjectPropertyHierarchy(allowedRoles, roleHierarchyUp,
// roleHierarchyDown);
// }
-
+
// @Override
// public ObjectPropertyHierarchy getRoleHierarchy() {
// return roleHierarchy;
// }
-
+
// public void prepareDatatypePropertyHierarchyImpl(Set<DatatypeProperty> allowedRoles) {
// // code copied from DIG reasoner
//
@@ -531,583 +465,569 @@
// datatypePropertyHierarchy = new DatatypePropertyHierarchy(allowedRoles, datatypePropertyHierarchyUp,
// datatypePropertyHierarchyDown);
// }
-
+
// @Override
// public DatatypePropertyHierarchy getDatatypePropertyHierarchy() {
// return datatypePropertyHierarchy;
// }
-
- @Override
- public boolean isSuperClassOfImpl(Description superConcept, Description subConcept) {
- return reasoner.isEntailed(factory.getOWLSubClassOfAxiom(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(subConcept),
- OWLAPIDescriptionConvertVisitor.getOWLClassExpression(superConcept)));
- }
-
- @Override
- protected boolean isEquivalentClassImpl(Description class1, Description class2) {
- return reasoner.isEntailed(factory.getOWLEquivalentClassesAxiom(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(class1),
- OWLAPIDescriptionConvertVisitor.getOWLClassExpression(class2)));
- }
- @Override
- protected TreeSet<Description> getSuperClassesImpl(Description concept) {
- NodeSet<OWLClass> classes = null;
-
- classes = reasoner.getSuperClasses(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept), true);
-
- return getFirstClasses(classes);
- }
-
- @Override
- protected TreeSet<Description> getSubClassesImpl(Description concept) {
- NodeSet<OWLClass> classes = null;
-
- classes = reasoner.getSubClasses(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept), true);
-
- return getFirstClasses(classes);
- }
-
- @Override
- protected TreeSet<ObjectProperty> getSuperPropertiesImpl(ObjectProperty role) {
- NodeSet<OWLObjectPropertyExpression> properties = null;
-
- properties = reasoner.getSuperObjectProperties(OWLAPIConverter.getOWLAPIObjectProperty(role), true);
-
- return getFirstObjectProperties(properties);
- }
-
- @Override
- protected TreeSet<ObjectProperty> getSubPropertiesImpl(ObjectProperty role) {
- NodeSet<OWLObjectPropertyExpression> properties = null;
-
- properties = reasoner.getSubObjectProperties(OWLAPIConverter.getOWLAPIObjectProperty(role), true);
-
- return getFirstObjectProperties(properties);
- }
-
- @Override
- protected TreeSet<DatatypeProperty> getSuperPropertiesImpl(DatatypeProperty role) {
- NodeSet<OWLDataProperty> properties = null;
-
- properties = reasoner.getSuperDataProperties(OWLAPIConverter.getOWLAPIDataProperty(role), true);
-
- return getFirstDatatypeProperties(properties);
- }
-
- @Override
- protected TreeSet<DatatypeProperty> getSubPropertiesImpl(DatatypeProperty role) {
- NodeSet<OWLDataProperty> properties = null;
-
- properties = reasoner.getSubDataProperties(OWLAPIConverter.getOWLAPIDataProperty(role), true);
-
- return getFirstDatatypeProperties(properties);
- }
-
- @Override
- public boolean hasTypeImpl(Description concept, Individual individual) {
- OWLClassExpression d = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept);
- OWLIndividual i = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
- return reasoner.isEntailed(factory.getOWLClassAssertionAxiom(d, i));
- }
-
- @Override
- public SortedSet<Individual> getIndividualsImpl(Description concept) {
+ @Override
+ public boolean isSuperClassOfImpl(Description superConcept, Description subConcept) {
+ return reasoner.isEntailed(factory.getOWLSubClassOfAxiom(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(subConcept), OWLAPIDescriptionConvertVisitor.getOWLClassExpression(superConcept)));
+ }
+
+ @Override
+ protected boolean isEquivalentClassImpl(Description class1, Description class2) {
+ return reasoner.isEntailed(factory.getOWLEquivalentClassesAxiom(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(class1), OWLAPIDescriptionConvertVisitor.getOWLClassExpression(class2)));
+ }
+
+ @Override
+ protected TreeSet<Description> getSuperClassesImpl(Description concept) {
+ NodeSet<OWLClass> classes = null;
+
+ classes = reasoner.getSuperClasses(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept), true);
+
+ return getFirstClasses(classes);
+ }
+
+ @Override
+ protected TreeSet<Description> getSubClassesImpl(Description concept) {
+ NodeSet<OWLClass> classes = null;
+
+ classes = reasoner.getSubClasses(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept), true);
+
+ return getFirstClasses(classes);
+ }
+
+ @Override
+ protected TreeSet<ObjectProperty> getSuperPropertiesImpl(ObjectProperty role) {
+ NodeSet<OWLObjectPropertyExpression> properties = null;
+
+ properties = reasoner.getSuperObjectProperties(OWLAPIConverter.getOWLAPIObjectProperty(role), true);
+
+ return getFirstObjectProperties(properties);
+ }
+
+ @Override
+ protected TreeSet<ObjectProperty> getSubPropertiesImpl(ObjectProperty role) {
+ NodeSet<OWLObjectPropertyExpression> properties = null;
+
+ properties = reasoner.getSubObjectProperties(OWLAPIConverter.getOWLAPIObjectProperty(role), true);
+
+ return getFirstObjectProperties(properties);
+ }
+
+ @Override
+ protected TreeSet<DatatypeProperty> getSuperPropertiesImpl(DatatypeProperty role) {
+ NodeSet<OWLDataProperty> properties = null;
+
+ properties = reasoner.getSuperDataProperties(OWLAPIConverter.getOWLAPIDataProperty(role), true);
+
+ return getFirstDatatypeProperties(properties);
+ }
+
+ @Override
+ protected TreeSet<DatatypeProperty> getSubPropertiesImpl(DatatypeProperty role) {
+ NodeSet<OWLDataProperty> properties = null;
+
+ properties = reasoner.getSubDataProperties(OWLAPIConverter.getOWLAPIDataProperty(role), true);
+
+ return getFirstDatatypeProperties(properties);
+ }
+
+ @Override
+ public boolean hasTypeImpl(Description concept, Individual individual) {
+ OWLClassExpression d = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept);
+ OWLIndividual i = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
+ return reasoner.isEntailed(factory.getOWLClassAssertionAxiom(d, i));
+ }
+
+ @Override
+ public SortedSet<Individual> getIndividualsImpl(Description concept) {
// OWLDescription d = getOWLAPIDescription(concept);
- OWLClassExpression d = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept);
- Set<OWLNamedIndividual> individuals = reasoner.getInstances(d, false).getFlattened();
- SortedSet<Individual> inds = new TreeSet<Individual>();
- for(OWLNamedIndividual ind : individuals)
- //ugly code
- if(ind != null)
- inds.add(new Individual(ind.toStringID()));
- return inds;
- }
-
- @Override
- public Set<NamedClass> getTypesImpl(Individual individual) {
- Set<Node<OWLClass>> result = null;
-
- result = reasoner.getTypes(factory.getOWLNamedIndividual(IRI.create(individual.getName())),false).getNodes();
-
- return getFirstClassesNoTopBottom(result);
- }
-
- @Override
- public boolean isSatisfiableImpl() {
- return reasoner.isSatisfiable(factory.getOWLThing());
- }
-
- @Override
- public Description getDomainImpl(ObjectProperty objectProperty) {
- OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
-
- // Pellet returns a set of nodes of named classes, which are more
- // general than the actual domain/range
- NodeSet<OWLClass> set = reasoner.getObjectPropertyDomains(prop, false);
- return getDescriptionFromReturnedDomain(set);
-
- }
-
- @Override
- public Description getDomainImpl(DatatypeProperty datatypeProperty) {
- OWLDataProperty prop = OWLAPIConverter
- .getOWLAPIDataProperty(datatypeProperty);
+ OWLClassExpression d = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept);
+ Set<OWLNamedIndividual> individuals = reasoner.getInstances(d, false).getFlattened();
+ SortedSet<Individual> inds = new TreeSet<Individual>();
+ for (OWLNamedIndividual ind : individuals)
+ //ugly code
+ if (ind != null) inds.add(new Individual(ind.toStringID()));
+ return inds;
+ }
- NodeSet<OWLClass> set = reasoner.getDataPropertyDomains(prop, true);
- return getDescriptionFromReturnedDomain(set);
+ @Override
+ public Set<NamedClass> getTypesImpl(Individual individual) {
+ Set<Node<OWLClass>> result = null;
- }
-
- @Override
- public Description getRangeImpl(ObjectProperty objectProperty) {
- OWLObjectProperty prop = OWLAPIConverter
- .getOWLAPIObjectProperty(objectProperty);
+ result = reasoner.getTypes(factory.getOWLNamedIndividual(IRI.create(individual.getName())), false).getNodes();
- NodeSet<OWLClass> set = reasoner.getObjectPropertyRanges(prop, true);
- if (set.isEmpty())
- return new Thing();
- OWLClass oc = set.iterator().next().getRepresentativeElement();
- if(oc.isOWLThing()){
- return Thing.instance;
- }
- return new NamedClass(oc.toStringID());
+ return getFirstClassesNoTopBottom(result);
+ }
- }
-
- private Description getDescriptionFromReturnedDomain(NodeSet<OWLClass> set) {
- if(set.isEmpty())
- return new Thing();
-
- Set<OWLClassExpression> union = new HashSet<OWLClassExpression>();
- Set<OWLClassExpression> domains = new HashSet<OWLClassExpression>();
-
- for(Node<OWLClass> descs : set){
- for(OWLClassExpression desc : descs){
- union.add(desc);
- }
- }
- for(OWLClassExpression desc : union){
- boolean isSuperClass = false;
- for(Description d : getClassHierarchy().getSubClasses(OWLAPIConverter.convertClass(desc.asOWLClass()))){
- if(union.contains(OWLAPIConverter.getOWLAPIDescription(d))){
- isSuperClass = true;
- break;
- }
- }
- if(!isSuperClass){
- domains.add(desc);
- }
- }
-
- OWLClass oc = (OWLClass) domains.iterator().next();
- if(oc.isOWLThing()) {
- return new Thing();
- } else {
- return new NamedClass(oc.toStringID());
- }
- }
-
- @Override
- public Map<Individual, SortedSet<Individual>> getPropertyMembersImpl(ObjectProperty atomicRole) {
- OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(atomicRole);
- Map<Individual, SortedSet<Individual>> map = new TreeMap<Individual, SortedSet<Individual>>();
- for(Individual i : individuals) {
- OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(i.getName()));
-
- // get all related individuals via OWL API
- Set<OWLNamedIndividual> inds = reasoner.getObjectPropertyValues(ind, prop).getFlattened();
-
-
- // convert data back to DL-Learner structures
- SortedSet<Individual> is = new TreeSet<Individual>();
- for(OWLNamedIndividual oi : inds)
- is.add(new Individual(oi.toStringID()));
- map.put(i, is);
- }
- return map;
- }
-
- @Override
- protected Map<ObjectProperty,Set<Individual>> getObjectPropertyRelationshipsImpl(Individual individual) {
- OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
- Map<OWLObjectPropertyExpression, Set<OWLNamedIndividual>> mapAPI = new HashMap<OWLObjectPropertyExpression, Set<OWLNamedIndividual>>();
-
+ @Override
+ public boolean isSatisfiableImpl() {
+ return reasoner.isSatisfiable(factory.getOWLThing());
+ }
+
+ @Override
+ public Description getDomainImpl(ObjectProperty objectProperty) {
+ OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
+
+ // Pellet returns a set of nodes of named classes, which are more
+ // general than the actual domain/range
+ NodeSet<OWLClass> set = reasoner.getObjectPropertyDomains(prop, false);
+ return getDescriptionFromReturnedDomain(set);
+
+ }
+
+ @Override
+ public Description getDomainImpl(DatatypeProperty datatypeProperty) {
+ OWLDataProperty prop = OWLAPIConverter.getOWLAPIDataProperty(datatypeProperty);
+
+ NodeSet<OWLClass> set = reasoner.getDataPropertyDomains(prop, true);
+ return getDescriptionFromReturnedDomain(set);
+
+ }
+
+ @Override
+ public Description getRangeImpl(ObjectProperty objectProperty) {
+ OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
+
+ NodeSet<OWLClass> set = reasoner.getObjectPropertyRanges(prop, true);
+ if (set.isEmpty()) return new Thing();
+ OWLClass oc = set.iterator().next().getRepresentativeElement();
+ if (oc.isOWLThing()) {
+ return Thing.instance;
+ }
+ return new NamedClass(oc.toStringID());
+
+ }
+
+ private Description getDescriptionFromReturnedDomain(NodeSet<OWLClass> set) {
+ if (set.isEmpty()) return new Thing();
+
+ Set<OWLClassExpression> union = new HashSet<OWLClassExpression>();
+ Set<OWLClassExpression> domains = new HashSet<OWLClassExpression>();
+
+ for (Node<OWLClass> descs : set) {
+ for (OWLClassExpression desc : descs) {
+ union.add(desc);
+ }
+ }
+ for (OWLClassExpression desc : union) {
+ boolean isSuperClass = false;
+ for (Description d : getClassHierarchy().getSubClasses(OWLAPIConverter.convertClass(desc.asOWLClass()))) {
+ if (union.contains(OWLAPIConverter.getOWLAPIDescription(d))) {
+ isSuperClass = true;
+ break;
+ }
+ }
+ if (!isSuperClass) {
+ domains.add(desc);
+ }
+ }
+
+ OWLClass oc = (OWLClass) domains.iterator().next();
+ if (oc.isOWLThing()) {
+ return new Thing();
+ } else {
+ return new NamedClass(oc.toStringID());
+ }
+ }
+
+ @Override
+ public Map<Individual, SortedSet<Individual>> getPropertyMembersImpl(ObjectProperty atomicRole) {
+ OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(atomicRole);
+ Map<Individual, SortedSet<Individual>> map = new TreeMap<Individual, SortedSet<Individual>>();
+ for (Individual i : individuals) {
+ OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(i.getName()));
+
+ // get all related individuals via OWL API
+ Set<OWLNamedIndividual> inds = reasoner.getObjectPropertyValues(ind, prop).getFlattened();
+
+ // convert data back to DL-Learner structures
+ SortedSet<Individual> is = new TreeSet<Individual>();
+ for (OWLNamedIndividual oi : inds)
+ is.add(new Individual(oi.toStringID()));
+ map.put(i, is);
+ }
+ return map;
+ }
+
+ @Override
+ protected Map<ObjectProperty, Set<Individual>> getObjectPropertyRelationshipsImpl(Individual individual) {
+ OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
+ Map<OWLObjectPropertyExpression, Set<OWLNamedIndividual>> mapAPI = new HashMap<OWLObjectPropertyExpression, Set<OWLNamedIndividual>>();
+
// Map<OWLObjectPropertyExpression, Set<OWLIndividual>> mapAPI = ind.getObjectPropertyValues(ontology);
- //no method found in the new reasoner interface, so we have to ask the reasoner for each property in the ontology
- for(OWLObjectProperty prop : ontology.getObjectPropertiesInSignature(true)){
- mapAPI.put(prop, reasoner.getObjectPropertyValues(ind, prop).getFlattened());
- }
-
- Map<ObjectProperty,Set<Individual>> map = new TreeMap<ObjectProperty, Set<Individual>>();
- for(Entry<OWLObjectPropertyExpression,Set<OWLNamedIndividual>> entry : mapAPI.entrySet()) {
- ObjectProperty prop = OWLAPIConverter.convertObjectProperty(entry.getKey().asOWLObjectProperty());
- Set<Individual> inds = OWLAPIConverter.convertIndividuals(entry.getValue());
- map.put(prop, inds);
- }
- return map;
- }
-
- @Override
- public Set<Individual> getRelatedIndividualsImpl(Individual individual, ObjectProperty objectProperty) {
- OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
- OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
- Set<OWLNamedIndividual> inds = null;
-
- inds = reasoner.getObjectPropertyValues(ind, prop).getFlattened();
-
- // convert data back to DL-Learner structures
- SortedSet<Individual> is = new TreeSet<Individual>();
- for(OWLNamedIndividual oi : inds) {
- is.add(new Individual(oi.toStringID()));
- }
- return is;
- }
-
- @Override
- public Set<Constant> getRelatedValuesImpl(Individual individual, DatatypeProperty datatypeProperty) {
- OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
- OWLDataProperty prop = OWLAPIConverter.getOWLAPIDataProperty(datatypeProperty);
- Set<OWLLiteral> constants = null;
-
- constants = reasoner.getDataPropertyValues(ind, prop);
-
- return OWLAPIConverter.convertConstants(constants);
- }
-
- public Map<Individual, SortedSet<Double>> getDoubleValues(
- DatatypeProperty datatypeProperty) {
- OWLDataProperty prop = OWLAPIConverter
- .getOWLAPIDataProperty(datatypeProperty);
- Map<Individual, SortedSet<Double>> map = new TreeMap<Individual, SortedSet<Double>>();
- for (Individual i : individuals) {
- OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI
- .create(i.getName()));
+ //no method found in the new reasoner interface, so we have to ask the reasoner for each property in the ontology
+ for (OWLObjectProperty prop : ontology.getObjectPropertiesInSignature(true)) {
+ mapAPI.put(prop, reasoner.getObjectPropertyValues(ind, prop).getFlattened());
+ }
- // get all related individuals via OWL API
- Set<OWLLiteral> inds = null;
+ Map<ObjectProperty, Set<Individual>> map = new TreeMap<ObjectProperty, Set<Individual>>();
+ for (Entry<OWLObjectPropertyExpression, Set<OWLNamedIndividual>> entry : mapAPI.entrySet()) {
+ ObjectProperty prop = OWLAPIConverter.convertObjectProperty(entry.getKey().asOWLObjectProperty());
+ Set<Individual> inds = OWLAPIConverter.convertIndividuals(entry.getValue());
+ map.put(prop, inds);
+ }
+ return map;
+ }
- inds = reasoner.getDataPropertyValues(ind, prop);
+ @Override
+ public Set<Individual> getRelatedIndividualsImpl(Individual individual, ObjectProperty objectProperty) {
+ OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
+ OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
+ Set<OWLNamedIndividual> inds = null;
- // convert data back to DL-Learner structures
- SortedSet<Double> is = new TreeSet<Double>();
- for (OWLLiteral oi : inds) {
- Double d = Double.parseDouble(oi.getLiteral());
- is.add(d);
- }
- map.put(i, is);
- }
- return map;
- }
-
- @Override
- public Map<Individual, SortedSet<Constant>> getDatatypeMembersImpl(DatatypeProperty datatypeProperty) {
- OWLDataProperty prop = OWLAPIConverter.getOWLAPIDataProperty(datatypeProperty);
- Map<Individual, SortedSet<Constant>> map = new TreeMap<Individual, SortedSet<Constant>>();
- for(Individual i : individuals) {
- OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(i.getName()));
-
- // get all related values via OWL API
- Set<OWLLiteral> constants = null;
-
- constants = reasoner.getDataPropertyValues(ind, prop);
-
-
- // convert data back to DL-Learner structures
- SortedSet<Constant> is = new TreeSet<Constant>();
- for(OWLLiteral literal : constants) {
- // for typed constants we have to figure out the correct
- // data type and value
- if(!literal.isRDFPlainLiteral()) {
- Datatype dt = OWLAPIConverter.convertDatatype(literal.getDatatype());
- is.add(new TypedConstant(literal.getLiteral(), dt));
- // for untyped constants we have to figure out the value
- // and language tag (if any)
- } else {
- if(literal.hasLang())
- is.add(new UntypedConstant(literal.getLiteral(), literal.getLang()));
- else
- is.add(new UntypedConstant(literal.getLiteral()));
- }
- }
- // only add individuals using the datatype property
- if(is.size()>0)
- map.put(i, is);
- }
- return map;
- }
-
- // OWL API returns a set of nodes of classes, where each node
- // consists of equivalent classes; this method picks one class
- // from each node to flatten the set of nodes
- private TreeSet<Description> getFirstClasses(NodeSet<OWLClass> nodeSet) {
- TreeSet<Description> concepts = new TreeSet<Description>(conceptComparator);
- for(Node<OWLClass> node : nodeSet) {
- // take one element from the set and ignore the rest
- // (TODO: we need to make sure we always ignore the same concepts)
- OWLClass concept = node.getRepresentativeElement();
- if(concept.isOWLThing()) {
- concepts.add(new Thing());
- } else if(concept.isOWLNothing()) {
- concepts.add(new Nothing());
- } else {
- concepts.add(new NamedClass(concept.toStringID()));
- }
- }
- return concepts;
- }
-
- private Set<NamedClass> getFirstClassesNoTopBottom(Set<Node<OWLClass>> nodeSet) {
- Set<NamedClass> concepts = new HashSet<NamedClass>();
- for(Node<OWLClass> node : nodeSet) {
- // take one element from the set and ignore the rest
- // (TODO: we need to make sure we always ignore the same concepts)
- OWLClass concept = node.getRepresentativeElement();
- if(!concept.isOWLThing() && !concept.isOWLNothing())
- concepts.add(new NamedClass(concept.toStringID()));
- }
- return concepts;
- }
-
- private TreeSet<ObjectProperty> getFirstObjectProperties(NodeSet<OWLObjectPropertyExpression> nodeSet) {
- TreeSet<ObjectProperty> roles = new TreeSet<ObjectProperty>(roleComparator);
- for(Node<OWLObjectPropertyExpression> node : nodeSet) {
- if(node.isBottomNode() || node.isTopNode()){
- continue;
- }
- // take one element from the set and ignore the rest
- // (TODO: we need to make sure we always ignore the same concepts)
- OWLObjectPropertyExpression property = node.getRepresentativeElement();
- roles.add(new ObjectProperty(property.asOWLObjectProperty().toStringID()));
- }
- roles.remove(new ObjectProperty(factory.getOWLTopObjectProperty().toStringID()));
- roles.remove(new ObjectProperty(factory.getOWLBottomObjectProperty().toStringID()));
- return roles;
- }
-
- private TreeSet<DatatypeProperty> getFirstDatatypeProperties(NodeSet<OWLDataProperty> nodeSet) {
- TreeSet<DatatypeProperty> roles = new TreeSet<DatatypeProperty>(roleComparator);
- for(Node<OWLDataProperty> node : nodeSet) {
- if(node.isBottomNode() || node.isTopNode()){
- continue;
- }
- OWLDataProperty property = node.getRepresentativeElement();
- roles.add(new DatatypeProperty(property.toStringID()));
- }
- roles.remove(new DatatypeProperty(factory.getOWLTopDataProperty().toStringID()));
- roles.remove(new DatatypeProperty(factory.getOWLBottomDataProperty().toStringID()));
- return roles;
- }
-
- @SuppressWarnings({"unused"})
- private Set<Description> owlClassesToAtomicConcepts(Set<OWLClass> owlClasses) {
- Set<Description> concepts = new HashSet<Description>();
- for(OWLClass owlClass : owlClasses)
- concepts.add(OWLAPIConverter.convertClass(owlClass));
- return concepts;
- }
-
- public static void exportKBToOWL(File owlOutputFile, KB kb, IRI ontologyIRI) {
- OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
- //URI ontologyURI = URI.create("http://example.com");
- IRI physicalIRI = IRI.create(owlOutputFile.toURI());
- SimpleIRIMapper mapper = new SimpleIRIMapper(ontologyIRI, physicalIRI);
- manager.addIRIMapper(mapper);
- OWLOntology ontology;
- try {
- ontology = manager.createOntology(ontologyIRI);
- // OWLAPIReasoner.fillOWLAPIOntology(manager, ontology, kb);
- OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, kb);
- manager.saveOntology(ontology);
- } catch (OWLOntologyCreationException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (UnknownOWLOntologyException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (OWLOntologyStorageException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- /**
- * Test
- *
- * @param args
- */
- public static void main(String[] args) {
- String iri = "http://www.co-ode.org/ontologies/pizza/2007/02/12/pizza.owl";
-
- OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
- try {
- OWLOntology ontology = manager.loadOntologyFromOntologyDocument(IRI.create(iri));
- new PelletReasonerFactory().createReasoner(ontology);
- System.out.println("Reasoner loaded succesfully.");
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
+ inds = reasoner.getObjectPropertyValues(ind, prop).getFlattened();
- /...
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