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[DL-Learner SVN] SF.net SVN: dl-learner: [502] trunk
|
From: <jen...@us...> - 2008-02-06 16:36:39
|
Revision: 502
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=502&view=rev
Author: jenslehmann
Date: 2008-02-06 08:36:36 -0800 (Wed, 06 Feb 2008)
Log Message:
-----------
- removed KAON2 from project such that DL-Learner now builds solely upon open source libraries
- direct KAON2 reasoning no longer possible (KAON2 can still be used over DIG if desired)
- most of the other KAON2 functionality rewritten to OWL API, in particular KB to OWL export
Modified Paths:
--------------
trunk/lib/components.ini
trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
trunk/src/dl-learner/org/dllearner/kb/KBFile.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java
trunk/src/dl-learner/org/dllearner/utilities/OntologyClassRewriter.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/reasoning/KAON2Reasoner.java
Modified: trunk/lib/components.ini
===================================================================
--- trunk/lib/components.ini 2008-02-06 15:24:06 UTC (rev 501)
+++ trunk/lib/components.ini 2008-02-06 16:36:36 UTC (rev 502)
@@ -8,7 +8,6 @@
org.dllearner.reasoning.OWLAPIReasoner
org.dllearner.reasoning.DIGReasoner
org.dllearner.reasoning.FastRetrievalReasoner
-org.dllearner.reasoning.KAON2Reasoner
# learning problems
org.dllearner.learningproblems.PosNegDefinitionLP
org.dllearner.learningproblems.PosNegInclusionLP
Modified: trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-02-06 15:24:06 UTC (rev 501)
+++ trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-02-06 16:36:36 UTC (rev 502)
@@ -20,7 +20,6 @@
package org.dllearner.core;
-import java.io.File;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@@ -34,8 +33,6 @@
import org.dllearner.core.dl.Individual;
import org.dllearner.core.dl.RoleHierarchy;
import org.dllearner.core.dl.SubsumptionHierarchy;
-import org.dllearner.reasoning.DIGReasoner;
-import org.dllearner.reasoning.KAON2Reasoner;
import org.dllearner.reasoning.ReasonerType;
import org.dllearner.utilities.SortedSetTuple;
@@ -400,17 +397,6 @@
return result;
}
- // speichern einer Ontolgie wird speziell behandelt, da kein Reasoning
- public void saveOntology(File file, OntologyFormat format) {
- if (getReasonerType() == ReasonerType.KAON2) {
- ((KAON2Reasoner) reasoner).saveOntology(file, format);
- } else if (getReasonerType() == ReasonerType.DIG) {
- // DIG erzeugt momentan auch nur einen KAON2-Reasoner und
- // exportiert dann mit der obigen Funktion
- ((DIGReasoner) reasoner).saveOntology(file, format);
- }
- }
-
public Set<AtomicConcept> getAtomicConcepts() {
return reasoner.getAtomicConcepts();
}
Modified: trunk/src/dl-learner/org/dllearner/kb/KBFile.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-02-06 15:24:06 UTC (rev 501)
+++ trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-02-06 16:36:36 UTC (rev 502)
@@ -36,12 +36,20 @@
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
import org.dllearner.reasoning.DIGConverter;
-import org.dllearner.reasoning.KAON2Reasoner;
-import org.semanticweb.kaon2.api.KAON2Exception;
-import org.semanticweb.kaon2.api.formatting.OntologyFileFormat;
-import org.semanticweb.kaon2.api.reasoner.Reasoner;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyCreationException;
+import org.semanticweb.owl.model.OWLOntologyManager;
+import org.semanticweb.owl.model.OWLOntologyStorageException;
+import org.semanticweb.owl.model.UnknownOWLOntologyException;
+import org.semanticweb.owl.util.SimpleURIMapper;
/**
+ * KB files are an internal convenience format used in DL-Learner. Their
+ * syntax is close to Description Logics and easy to use. KB files can be
+ * exported to OWL for usage outside of DL-Learner.
+ *
* @author Jens Lehmann
*
*/
@@ -118,25 +126,47 @@
@Override
public void export(File file, org.dllearner.core.OntologyFormat format){
- Reasoner kaon2Reasoner = KAON2Reasoner.getKAON2Reasoner(kb);
-
- String kaon2Format = null;
- if(format.equals(org.dllearner.core.OntologyFormat.RDF_XML))
- kaon2Format = OntologyFileFormat.OWL_RDF;
- else {
- System.err.println("Warning: Cannot export format " + format + ". Exiting.");
- System.exit(0);
- }
-
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ URI ontologyURI = URI.create("http://example.com");
+ URI physicalURI = file.toURI();
+ SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
+ manager.addURIMapper(mapper);
+ OWLOntology ontology;
try {
- kaon2Reasoner.getOntology().saveOntology(kaon2Format,file,"ISO-8859-1");
- } catch (KAON2Exception e) {
+ ontology = manager.createOntology(ontologyURI);
+ OWLAPIReasoner.fillOWLAPIOntology(manager,ontology,kb);
+ manager.saveOntology(ontology);
+ } catch (OWLOntologyCreationException e) {
+ // TODO Auto-generated catch block
e.printStackTrace();
- } catch (IOException e) {
+ } catch (UnknownOWLOntologyException e) {
+ // TODO Auto-generated catch block
e.printStackTrace();
- } catch (InterruptedException e) {
+ } catch (OWLOntologyStorageException e) {
+ // TODO Auto-generated catch block
e.printStackTrace();
- }
+ }
+
+
+// Reasoner kaon2Reasoner = KAON2Reasoner.getKAON2Reasoner(kb);
+//
+// String kaon2Format = null;
+// if(format.equals(org.dllearner.core.OntologyFormat.RDF_XML))
+// kaon2Format = OntologyFileFormat.OWL_RDF;
+// else {
+// System.err.println("Warning: Cannot export format " + format + ". Exiting.");
+// System.exit(0);
+// }
+//
+// try {
+// kaon2Reasoner.getOntology().saveOntology(kaon2Format,file,"ISO-8859-1");
+// } catch (KAON2Exception e) {
+// e.printStackTrace();
+// } catch (IOException e) {
+// e.printStackTrace();
+// } catch (InterruptedException e) {
+// e.printStackTrace();
+// }
}
public URL getURL() {
Deleted: trunk/src/dl-learner/org/dllearner/reasoning/KAON2Reasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/KAON2Reasoner.java 2008-02-06 15:24:06 UTC (rev 501)
+++ trunk/src/dl-learner/org/dllearner/reasoning/KAON2Reasoner.java 2008-02-06 16:36:36 UTC (rev 502)
@@ -1,859 +0,0 @@
-package org.dllearner.reasoning;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URL;
-import java.util.Collection;
-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.Set;
-import java.util.SortedSet;
-import java.util.TreeMap;
-import java.util.TreeSet;
-
-import org.dllearner.core.ReasonerComponent;
-import org.dllearner.core.config.CommonConfigOptions;
-import org.dllearner.core.config.ConfigEntry;
-import org.dllearner.core.config.ConfigOption;
-import org.dllearner.core.config.InvalidConfigOptionValueException;
-import org.dllearner.core.dl.All;
-import org.dllearner.core.dl.AssertionalAxiom;
-import org.dllearner.core.dl.AtomicConcept;
-import org.dllearner.core.dl.AtomicRole;
-import org.dllearner.core.dl.Bottom;
-import org.dllearner.core.dl.Concept;
-import org.dllearner.core.dl.ConceptAssertion;
-import org.dllearner.core.dl.Conjunction;
-import org.dllearner.core.dl.Disjunction;
-import org.dllearner.core.dl.Equality;
-import org.dllearner.core.dl.Exists;
-import org.dllearner.core.dl.FunctionalRoleAxiom;
-import org.dllearner.core.dl.Inclusion;
-import org.dllearner.core.dl.Individual;
-import org.dllearner.core.dl.InverseRoleAxiom;
-import org.dllearner.core.dl.KB;
-import org.dllearner.core.dl.MultiConjunction;
-import org.dllearner.core.dl.MultiDisjunction;
-import org.dllearner.core.dl.Negation;
-import org.dllearner.core.dl.RBoxAxiom;
-import org.dllearner.core.dl.RoleAssertion;
-import org.dllearner.core.dl.SubRoleAxiom;
-import org.dllearner.core.dl.SymmetricRoleAxiom;
-import org.dllearner.core.dl.TerminologicalAxiom;
-import org.dllearner.core.dl.Top;
-import org.dllearner.core.dl.TransitiveRoleAxiom;
-import org.dllearner.utilities.ConceptComparator;
-import org.dllearner.utilities.Helper;
-import org.semanticweb.kaon2.api.DefaultOntologyResolver;
-import org.semanticweb.kaon2.api.KAON2Connection;
-import org.semanticweb.kaon2.api.KAON2Exception;
-import org.semanticweb.kaon2.api.KAON2Manager;
-import org.semanticweb.kaon2.api.Ontology;
-import org.semanticweb.kaon2.api.Request;
-import org.semanticweb.kaon2.api.formatting.OntologyFileFormat;
-import org.semanticweb.kaon2.api.logic.Formula;
-import org.semanticweb.kaon2.api.logic.Literal;
-import org.semanticweb.kaon2.api.logic.QueryDefinition;
-import org.semanticweb.kaon2.api.logic.Variable;
-import org.semanticweb.kaon2.api.owl.axioms.ObjectPropertyAttribute;
-import org.semanticweb.kaon2.api.owl.elements.Description;
-import org.semanticweb.kaon2.api.owl.elements.OWLClass;
-import org.semanticweb.kaon2.api.owl.elements.ObjectProperty;
-import org.semanticweb.kaon2.api.reasoner.Query;
-import org.semanticweb.kaon2.api.reasoner.SubsumptionHierarchy;
-import org.semanticweb.kaon2.api.reasoner.SubsumptionHierarchy.Node;
-
-/**
- *
- * Subsumption-Hierarchie wird automatisch beim ersten Aufruf von getMoreGeneral|SpecialConcept
- * berechnet.
- *
- * @author jl
- *
- */
-public class KAON2Reasoner extends ReasonerComponent {
-
- // configuration options
- private boolean una = false;
-
- ConceptComparator conceptComparator = new ConceptComparator();
-
- Set<AtomicConcept> atomicConcepts;
- Set<AtomicRole> atomicRoles;
- SortedSet<Individual> individuals;
- SubsumptionHierarchy kaon2SubsumptionHierarchy = null;
- org.dllearner.core.dl.SubsumptionHierarchy subsumptionHierarchy;
-
- private org.semanticweb.kaon2.api.reasoner.Reasoner kaon2Reasoner;
- private KAON2Connection kaon2Connection;
-
- public KAON2Reasoner(KB kb, Map<URL,org.dllearner.core.OntologyFormat> imports) {
-
- if(imports.size()>1)
- System.out.println("Warning: KAON2-Reasoner currently supports only one import file. Ignoring all other imports.");
-
- try {
- kaon2Connection = KAON2Manager.newConnection();
- } catch (KAON2Exception e2) {
- e2.printStackTrace();
- }
-
- DefaultOntologyResolver resolver = new DefaultOntologyResolver();
-
- // Set<String> ontologyURIs = new HashSet<String>();
- String ontologyURI = "";
- URL importFile = null;
- if (!imports.isEmpty()) {
- // alter Code - nicht empfehlenswert, da feste URI zugewiesen wird
- // resolver.registerReplacement("foo", imports.get(0).toURI().toString());
-
- // neuer Code - liest Dateien richtig ein
- // es ist aber noch nicht richtig klar, was bei mehreren eingelesenen
- // Ontologien passieren soll
- // for(File file : imports) {
- // String ontologyURI = resolver.registerOntology(file);
- // ontologyURIs.add(ontologyURI);
- //}
-
- // eine beliebige Datei auswählen
- importFile = imports.keySet().iterator().next();
-
- try {
- // System.out.println(imports.get(0));
- // resolver.r
-
- // TODO: testen, ob Umstellung von File auf URL funktioniert!
- // ontologyURI = resolver.registerOntology(importFile);
- ontologyURI = resolver.registerOntology(importFile.toString());
-
- } catch (KAON2Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- } else {
- // falls nur aus Config-Datei gelesen wird, dann wird resolver
- // eigentlich nicht gebraucht => trotzdem erwartet KAON2 ein physische
- // URI
- // resolver.registerReplacement("foo", "file:foo.xml");
- resolver.registerReplacement("http://localhost/foo", "file:nothing.xml");
- }
-
- kaon2Connection.setOntologyResolver(resolver);
- Ontology ontology = null;
-
- if (!imports.isEmpty()) {
- System.out.print("Importing Ontology " + importFile.toString() + " ... ");
- ontology = importKB(ontologyURI, imports.get(importFile), kaon2Connection);
- } else {
- try {
- // ontology = connection.createOntology("foo", new
- // HashMap<String, Object>());
- ontology = kaon2Connection.createOntology("http://localhost/foo",
- new HashMap<String, Object>());
- } catch (KAON2Exception e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
- }
-
- // System.out.println(importedFile.getPath().toURI().toString());
- // resolver.registerReplacement("foo", "file:" +
- // importedFile.getPath());
- // resolver.registerReplacement("foo",
- // importedFile.toURI().toString());
-
- kaon2Reasoner = getKAON2Reasoner(kb, ontology);
-
- // Individuals, Concepts und Roles aus Wissensbasis auslesen
- Request<ObjectProperty> requestRoles = ontology
- .createEntityRequest(ObjectProperty.class);
- Request<OWLClass> requestConcepts = ontology.createEntityRequest(OWLClass.class);
- Request<org.semanticweb.kaon2.api.owl.elements.Individual> requestIndividuals = ontology
- .createEntityRequest(org.semanticweb.kaon2.api.owl.elements.Individual.class);
-
- atomicConcepts = new HashSet<AtomicConcept>();
- atomicRoles = new HashSet<AtomicRole>();
- individuals = new TreeSet<Individual>();
-
- try {
- for (ObjectProperty role : requestRoles.get()) {
- atomicRoles.add(new AtomicRole(role.toString()));
- // getRole(role.toString());
- }
-
- for (OWLClass concept : requestConcepts.get()) {
- // Top und Bottom sind bei mir keine atomaren Konzepte, sondern
- // werden
- // extra behandelt
- if (!concept.equals(KAON2Manager.factory().thing())
- && !concept.equals(KAON2Manager.factory().nothing()))
- atomicConcepts.add(new AtomicConcept(concept.toString()));
- // System.out.println(concept.toString());
- }
- for (org.semanticweb.kaon2.api.owl.elements.Individual ind : requestIndividuals.get()) {
- // getIndividual(ind.toString());
- individuals.add(new Individual(ind.toString()));
- }
-
- // je nachdem, ob unique names assumption aktiviert ist, muss
- // man jetzt noch hinzuf�gen, dass die Individuen verschieden sind
- if (una) {
- Set<org.semanticweb.kaon2.api.owl.elements.Individual> individualsSet = new HashSet<org.semanticweb.kaon2.api.owl.elements.Individual>();
- for (Individual individual : individuals)
- individualsSet.add(KAON2Manager.factory().individual(individual.getName()));
- ontology.addAxiom(KAON2Manager.factory().differentIndividuals(
- individualsSet));
- }
-
- } catch (KAON2Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- // wandelt einen Bezeichner in eine URI für die interne KB
- // (http://localhost/foo) um;
- // die Umwandlungen machen KAON2 noch langsamer, aber sie sind notwendig
- // für eine korrekte Ontologie, die wiederum für den Export wichtig ist;
- // es wird einfach gesagt, dass alles was nicht mit "http://" beginnt ein
- // interner Bezeichner ist;
- // eine sauberere Lösung wäre für die internen Sachen auch immer eine URI
- // zu fordern bzw. eine ähnliche Heuristik wie hier schon beim parsen zu
- // verwenden; für DIG ist das allerdings nicht notwendig (basiert auf DLs,
- // also benötigt keine URIs) und erfordert relativ umfangreiche Änderungen
- // => es wird jetzt doch die saubere Lösung verwendet
- /*
- private String getInternalURI(String name) {
- if(name.startsWith("http://"))
- return name;
- else
- return internalNamespace + name;
- }
-
- // wandelt eine lokal vergebene URI in einen Bezeichner um
- private String getNameFromInternalURI(String uri) {
- if(uri.startsWith(internalNamespace))
- return uri.substring(internalNamespace.length());
- else
- return uri;
- }
- */
-
- public static String getName() {
- return "KAON2 reasoner";
- }
-
- // TODO: hier werden momentan keine allowed concepts berücksichtigt
- // (benötigt rekursive Aufrufe, da ein erlaubtes Konzept von einem nicht
- // erlaubten verdeckt werden könnte)
- public void prepareSubsumptionHierarchy(Set<AtomicConcept> allowedConcepts) {
- try {
- kaon2SubsumptionHierarchy = kaon2Reasoner.getSubsumptionHierarchy();
- } catch (KAON2Exception e) {
- e.printStackTrace();
- } catch (InterruptedException e) {
- e.printStackTrace();
- }
-
- // umwandeln in eine für die Lernalgorithmen verwertbare
- // Subsumptionhierarchie
- TreeMap<Concept,TreeSet<Concept>> subsumptionHierarchyUp = new TreeMap<Concept,TreeSet<Concept>>(conceptComparator);
- TreeMap<Concept,TreeSet<Concept>> subsumptionHierarchyDown = new TreeMap<Concept,TreeSet<Concept>>(conceptComparator);
-
- Top top = new Top();
- OWLClass kaon2Top = KAON2Manager.factory().thing();
- subsumptionHierarchyDown.put(top, (TreeSet<Concept>) getConceptsFromSubsumptionHierarchyNodes(kaon2SubsumptionHierarchy.getNodeFor(kaon2Top).getChildNodes()));
- // subsumptionHierarchyUp.put(top, new TreeSet<Concept>(conceptComparator));
-
- Bottom bottom = new Bottom();
- OWLClass kaon2Bottom = KAON2Manager.factory().nothing();
- subsumptionHierarchyUp.put(bottom, (TreeSet<Concept>) getConceptsFromSubsumptionHierarchyNodes(kaon2SubsumptionHierarchy.getNodeFor(kaon2Bottom).getParentNodes()));
- // subsumptionHierarchyDown.put(bottom, new TreeSet<Concept>(conceptComparator));
-
- for(AtomicConcept ac : atomicConcepts) {
- OWLClass kaon2Ac = (OWLClass) getKAON2Description(ac);
- subsumptionHierarchyDown.put(ac, (TreeSet<Concept>) getConceptsFromSubsumptionHierarchyNodes(kaon2SubsumptionHierarchy.getNodeFor(kaon2Ac).getChildNodes()));
- subsumptionHierarchyUp.put(ac, (TreeSet<Concept>) getConceptsFromSubsumptionHierarchyNodes(kaon2SubsumptionHierarchy.getNodeFor(kaon2Ac).getParentNodes()));
- }
-
- subsumptionHierarchy = new org.dllearner.core.dl.SubsumptionHierarchy(atomicConcepts, subsumptionHierarchyUp, subsumptionHierarchyDown);
- }
-
- @Override
- public SortedSet<Individual> retrieval(Concept c) {
- SortedSet<Individual> result = new TreeSet<Individual>();
- Description d = getKAON2Description(c);
-
- Query query = null;
- try {
- query = kaon2Reasoner.createQuery(d);
- query.open();
- while (!query.afterLast()) {
- // tupleBuffer = query.tupleBuffer();
- String individual = query.tupleBuffer()[0].toString();
- result.add(new Individual(individual));
- query.next();
- }
- query.close();
- query.dispose();
- } catch (KAON2Exception e) {
- e.printStackTrace();
- System.exit(0);
- } catch (InterruptedException e) {
- e.printStackTrace();
- System.exit(0);
- }
- return result;
- }
-
- public boolean instanceCheck(Concept c, String s) {
- boolean result;
-
- Description d = getKAON2Description(c);
- // ev. Aufruf Main.getIndividual g�nstiger??
- org.semanticweb.kaon2.api.owl.elements.Individual i = KAON2Manager.factory().individual(s);
-
- // Individual i = Main.getIndividual(s);
- // ClassMember cm = KAON2Manager.factory().classMember(d, i);
- // Formula f = KAON2Manager.factory().classMember(d,i);
- // Constant constant = KAON2Manager.factory().constant(i);
- // Predicate predicate = KAON2Manager.factory().p
- Literal l = KAON2Manager.factory().literal(true, d, i);
- // Formula f = KAON2Manager.factory().
-
- // TODO: mal mit Boris abkl�ren wie der Instance-Check
- // gemacht werden soll; eine Formel zu erstellen erscheint
- // mir ziemlich umst�ndlich und ist mir auch nicht ganz
- // klar wie das gemacht wird
-
- QueryDefinition qd = KAON2Manager.factory().queryDefinition(l, new Variable[] {});
-
- // kaon2Reasoner.createQuery(l, new Variable[] { });
- // Query q;
- result = true;
- try {
- Query query = kaon2Reasoner.createQuery(qd);
- query.open();
- if (query.afterLast())
- result = false;
- query.close();
- query.dispose();
- } catch (KAON2Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- return result;
- }
-
- @Override
- public boolean subsumes(Concept superConcept, Concept subConcept) {
- Description d1 = getKAON2Description(superConcept);
- Description d2 = getKAON2Description(subConcept);
- try {
- return kaon2Reasoner.subsumedBy(d2, d1);
- } catch (KAON2Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- throw new Error("Subsumption Error in KAON2.");
- }
-
- @Override
- public boolean isSatisfiable() {
- try {
- return kaon2Reasoner.isSatisfiable();
- } catch (KAON2Exception e1) {
- e1.printStackTrace();
- } catch (InterruptedException e2) {
- e2.printStackTrace();
- }
- throw new Error("Error in satisfiability check in KAON2.");
- }
-
- /*
- private SortedSet<Concept> getMoreGeneralConcepts(Concept concept) {
- // if (subsumptionHierarchy == null) {
- // computeSubsumptionHierarchy();
- // }
-
- Description d = getKAON2Description(concept);
- if(!(d instanceof OWLClass)) {
- System.out.println("description: " + d);
- System.out.println("concept:" + concept);
- }
- OWLClass owlClass = (OWLClass) d;
- return getConceptsFromSubsumptionHierarchyNodes(kaon2SubsumptionHierarchy.getNodeFor(
- owlClass).getParentNodes());
- }
-
- private SortedSet<Concept> getMoreSpecialConcepts(Concept concept) {
- // if (subsumptionHierarchy == null) {
- // computeSubsumptionHierarchy();
- // }
-
- OWLClass owlClass = (OWLClass) getKAON2Description(concept);
- return getConceptsFromSubsumptionHierarchyNodes(kaon2SubsumptionHierarchy.getNodeFor(
- owlClass).getChildNodes());
- }
- */
-
- @Override
- public org.dllearner.core.dl.SubsumptionHierarchy getSubsumptionHierarchy() {
- return subsumptionHierarchy;
- }
-
- private SortedSet<Concept> getConceptsFromSubsumptionHierarchyNodes(Set<Node> nodes) {
- SortedSet<Concept> ret = new TreeSet<Concept>(conceptComparator);
- for (Node node : nodes) {
- // es wird nur das erste Konzept unter mehreren �quivalenten
- // beachtet
- Iterator<OWLClass> it = node.getOWLClasses().iterator();
- ret.add(getConcept(it.next()));
- if (node.getOWLClasses().size() > 1)
- System.out
- .println("Warning: Ontology contains equivalent classes. Only one"
- + "representative of each equivalence class is used for learning. The others"
- + "are ignored.");
- }
- return ret;
- }
-
- public Concept getConcept(Description description) {
- if (description.equals(KAON2Manager.factory().thing())) {
- return new Top();
- } else if (description.equals(KAON2Manager.factory().nothing())) {
- return new Bottom();
- } else if (description instanceof OWLClass) {
- return new AtomicConcept(description.toString());
- } else {
- throw new Error("Transforming complex KAON2 descriptions not supported.");
- }
- }
-
- @Override
- public Map<org.dllearner.core.dl.Individual, SortedSet<org.dllearner.core.dl.Individual>> getRoleMembers(AtomicRole atomicRole) {
- Map<org.dllearner.core.dl.Individual, SortedSet<org.dllearner.core.dl.Individual>> returnMap = new TreeMap<org.dllearner.core.dl.Individual, SortedSet<org.dllearner.core.dl.Individual>>();
-
- Query query;
- Object[] tupleBuffer;
- ObjectProperty role = KAON2Manager.factory().objectProperty(atomicRole.getName());
- // positiver Query
- try {
- query = kaon2Reasoner.createQuery(role);
-
- query.open();
- while (!query.afterLast()) {
- tupleBuffer = query.tupleBuffer();
- org.dllearner.core.dl.Individual individual1 = new org.dllearner.core.dl.Individual(tupleBuffer[0].toString());
- org.dllearner.core.dl.Individual individual2 = new org.dllearner.core.dl.Individual(tupleBuffer[1].toString());
- // addIndividualToRole(aBox.rolesPos, name, individual1,
- // individual2);
- Helper.addMapEntry(returnMap, individual1, individual2);
- query.next();
- }
- query.close();
- query.dispose();
- } catch (KAON2Exception e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return returnMap;
- }
-
- public void saveOntology(File file, org.dllearner.core.OntologyFormat format) {
- // File exportFile = new File(baseDir, fileName);
- // String format = OntologyFileFormat.OWL_RDF;
- String kaon2Format = null;
- if(format.equals(org.dllearner.core.OntologyFormat.RDF_XML))
- kaon2Format = OntologyFileFormat.OWL_RDF;
- else {
- System.err.println("Warning: Cannot export format " + format + ". Exiting.");
- System.exit(0);
- }
-
- try {
- kaon2Reasoner.getOntology().saveOntology(kaon2Format,file,"ISO-8859-1");
- } catch (KAON2Exception e) {
- e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- } catch (InterruptedException e) {
- e.printStackTrace();
- }
- }
-
- public static Ontology importKB(File importFile) {
-
- Ontology ontology = null;
- try {
- System.out.print("Importing " + importFile + " ... ");
- long importStartTime = System.currentTimeMillis();
-
- // TODO: hier wird Ontologie richtig importiert; dass muss im
- // Konstruktor eventuell entsprechend angepasst werden
- DefaultOntologyResolver resolver = new DefaultOntologyResolver();
- String ontologyURI = resolver.registerOntology(importFile);
- KAON2Connection connection = KAON2Manager.newConnection();
- connection.setOntologyResolver(resolver);
- ontology = connection.openOntology(ontologyURI, new HashMap<String,Object>());
- long importDuration = System.currentTimeMillis() - importStartTime;
- System.out.println("OK (" + importDuration + " ms) [ontology URI " + ontologyURI + "]");
- } catch (KAON2Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return ontology;
- }
-
- private static Ontology importKB(String ontologyURI, org.dllearner.core.OntologyFormat format, KAON2Connection connection) {
- Ontology ontology = null;
- try {
- long importStartTime = System.currentTimeMillis();
- ontology = connection.openOntology(ontologyURI, new HashMap<String, Object>());
- long importDuration = System.currentTimeMillis() - importStartTime;
- System.out.println("OK (" + importDuration + " ms)");
- } catch (KAON2Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return ontology;
- }
-
- // Umwandlung eines Konzepts in eigener Darstellung zu einem
- // KAON2-Konzept (hat die st�ndige Umwandlung eine gro�e Auswirkung
- // auf die Effizienz? - es m�ssen zumindest h�ufig neue Konzepte
- // erzeugt werden)
- public static Description getKAON2Description(Concept concept) {
- if (concept instanceof AtomicConcept) {
- return KAON2Manager.factory().owlClass(((AtomicConcept) concept).getName());
- } else if (concept instanceof Bottom) {
- return KAON2Manager.factory().nothing();
- } else if (concept instanceof Top) {
- return KAON2Manager.factory().thing();
- } else if (concept instanceof Negation) {
- return KAON2Manager.factory().objectNot(
- getKAON2Description(concept.getChild(0)));
- } else if (concept instanceof Conjunction) {
- Description d1 = getKAON2Description(concept.getChild(0));
- Description d2 = getKAON2Description(concept.getChild(1));
- return KAON2Manager.factory().objectAnd(d1, d2);
- } else if (concept instanceof Disjunction) {
- Description d1 = getKAON2Description(concept.getChild(0));
- Description d2 = getKAON2Description(concept.getChild(1));
- return KAON2Manager.factory().objectOr(d1, d2);
- } else if (concept instanceof All) {
- ObjectProperty role = KAON2Manager.factory().objectProperty(
- ((All) concept).getRole().getName());
- Description d = getKAON2Description(concept.getChild(0));
- return KAON2Manager.factory().objectAll(role, d);
- } else if(concept instanceof Exists) {
- ObjectProperty role = KAON2Manager.factory().objectProperty(
- ((Exists) concept).getRole().getName());
- Description d = getKAON2Description(concept.getChild(0));
- return KAON2Manager.factory().objectSome(role, d);
- } else if(concept instanceof MultiConjunction) {
- List<Description> descriptions = new LinkedList<Description>();
- for(Concept child : concept.getChildren()) {
- descriptions.add(getKAON2Description(child));
- }
- return KAON2Manager.factory().objectAnd(descriptions);
- } else if(concept instanceof MultiDisjunction) {
- List<Description> descriptions = new LinkedList<Description>();
- for(Concept child : concept.getChildren()) {
- descriptions.add(getKAON2Description(child));
- }
- return KAON2Manager.factory().objectOr(descriptions);
- }
-
- throw new IllegalArgumentException("Unsupported concept type.");
- }
-
- public static org.semanticweb.kaon2.api.reasoner.Reasoner getKAON2Reasoner(KB kb) {
- try {
- KAON2Connection connection = KAON2Manager.newConnection();
-
- DefaultOntologyResolver resolver = new DefaultOntologyResolver();
- resolver.registerReplacement("http://localhost/foo", "file:nothing.xml");
- connection.setOntologyResolver(resolver);
- Ontology ontology = connection.createOntology("http://localhost/foo",
- new HashMap<String, Object>());
- return getKAON2Reasoner(kb, ontology);
-
- } catch (KAON2Exception e) {
- e.printStackTrace();
- return null;
- }
- }
-
- private static org.semanticweb.kaon2.api.reasoner.Reasoner getKAON2Reasoner(KB kb,
- Ontology ontology) {
-
- org.semanticweb.kaon2.api.reasoner.Reasoner reasoner = null;
-
- try {
-
- for (AssertionalAxiom axiom : kb.getAbox()) {
- if (axiom instanceof ConceptAssertion) {
- Description d = getKAON2Description(((ConceptAssertion) axiom)
- .getConcept());
- // TODO: checken ob unterschiedliche Objekte
- // unterschiedliche
- // Individuen sind, auch wenn sie den gleichen Namen haben
- org.semanticweb.kaon2.api.owl.elements.Individual i = KAON2Manager.factory().individual(
- ((ConceptAssertion) axiom).getIndividual().getName());
- ontology.addAxiom(KAON2Manager.factory().classMember(d, i));
- } else if (axiom instanceof RoleAssertion) {
- ObjectProperty role = KAON2Manager.factory().objectProperty(
- ((RoleAssertion) axiom).getRole().getName());
- org.semanticweb.kaon2.api.owl.elements.Individual i1 = KAON2Manager.factory().individual(
- ((RoleAssertion) axiom).getIndividual1().getName());
- org.semanticweb.kaon2.api.owl.elements.Individual i2 = KAON2Manager.factory().individual(
- ((RoleAssertion) axiom).getIndividual2().getName());
- // Code zur Unterst�tzung negierter Rollenzusicherungen,
- // falls sp�ter ben�tigt
- // Literal l = KAON2Manager.factory().literal(true, role,
- // i1, i2);
- // Rule r = KAON2Manager.factory().rule(new Formula[] {},
- // true, new Formula[] { l });
- // changes.add(new OntologyChangeEvent(r,
- // OntologyChangeEvent.ChangeType.ADD));
- ontology.addAxiom(KAON2Manager.factory().objectPropertyMember(role,
- i1, i2));
- }
- }
-
- for (RBoxAxiom axiom : kb.getRbox()) {
- if (axiom instanceof FunctionalRoleAxiom) {
- ObjectProperty role = KAON2Manager.factory().objectProperty(
- ((FunctionalRoleAxiom) axiom).getRole().getName());
- ontology.addAxiom(KAON2Manager.factory().objectPropertyAttribute(
- role, ObjectPropertyAttribute.OBJECT_PROPERTY_FUNCTIONAL));
- } else if (axiom instanceof SymmetricRoleAxiom) {
- ObjectProperty role = KAON2Manager.factory().objectProperty(
- ((SymmetricRoleAxiom) axiom).getRole().getName());
- ontology.addAxiom(KAON2Manager.factory().objectPropertyAttribute(
- role, ObjectPropertyAttribute.OBJECT_PROPERTY_SYMMETRIC));
-
- // alternative Implementierung ohne Hilfskonstrukt
- //ObjectProperty inverseRole = KAON2Manager.factory().objectProperty(
- // ((SymmetricRoleAxiom) axiom).getRole().getName());
- //ontology.addAxiom(KAON2Manager.factory().inverseObjectProperties(
- // role, inverseRole));
- //ontology.addAxiom(KAON2Manager.factory().equivalentObjectProperties(role,
- // inverseRole));
- } else if (axiom instanceof TransitiveRoleAxiom) {
- ObjectProperty role = KAON2Manager.factory().objectProperty(
- ((SymmetricRoleAxiom) axiom).getRole().getName());
- ontology.addAxiom(KAON2Manager.factory().objectPropertyAttribute(
- role, ObjectPropertyAttribute.OBJECT_PROPERTY_TRANSITIVE));
- } else if (axiom instanceof InverseRoleAxiom) {
- ObjectProperty role = KAON2Manager.factory().objectProperty(
- ((InverseRoleAxiom) axiom).getRole().getName());
- ObjectProperty inverseRole = KAON2Manager.factory().objectProperty(
- ((InverseRoleAxiom) axiom).getInverseRole().getName());
- ontology.addAxiom(KAON2Manager.factory().inverseObjectProperties(
- role, inverseRole));
- } else if (axiom instanceof SubRoleAxiom) {
- ObjectProperty role = KAON2Manager.factory().objectProperty(
- ((SubRoleAxiom) axiom).getRole().getName());
- ObjectProperty subRole = KAON2Manager.factory().objectProperty(
- ((SubRoleAxiom) axiom).getSubRole().getName());
- ontology.addAxiom(KAON2Manager.factory().subObjectPropertyOf(subRole,
- role));
- }
- }
-
- for (TerminologicalAxiom axiom : kb.getTbox()) {
- if (axiom instanceof Equality) {
- Description d1 = getKAON2Description(((Equality) axiom).getConcept1());
- Description d2 = getKAON2Description(((Equality) axiom).getConcept2());
- ontology.addAxiom(KAON2Manager.factory().equivalentClasses(d1, d2));
- } else if (axiom instanceof Inclusion) {
- Description subConcept = getKAON2Description(((Inclusion) axiom)
- .getSubConcept());
- Description superConcept = getKAON2Description(((Inclusion) axiom)
- .getSuperConcept());
- ontology.addAxiom(KAON2Manager.factory().subClassOf(subConcept,
- superConcept));
- }
- }
-
- // ontology.applyChanges(changes);
- reasoner = ontology.createReasoner();
- } catch (KAON2Exception e) {
- e.printStackTrace();
- System.out.println(e);
- }
-
- return reasoner;
- }
-
- public Map<String, SortedSet<String>> getNegatedRoleMembers(AtomicRole atomicRole) {
- Map<String, SortedSet<String>> returnMap = new TreeMap<String, SortedSet<String>>();
-
- Query query;
- Object[] tupleBuffer;
- ObjectProperty role = KAON2Manager.factory().objectProperty(atomicRole.getName());
- // negativer Query
- // wird �ber Rule-ML gemacht
- Variable X = KAON2Manager.factory().variable("X");
- Variable Y = KAON2Manager.factory().variable("Y");
- // ObjectProperty role = roles.get(name);
- Literal l = KAON2Manager.factory().literal(true, role, X, Y);
- Formula f = null;
-
- // falls closed world assumption, dann reicht default negation
-// if (Config.owa)
- // wegen BUG IN KAON2 momentan auskommentiert
- // f = KAON2Manager.factory().classicalNegation(l);
-// ;
-// else
- f = KAON2Manager.factory().defaultNegation(l);
-
- // if-Teil entf�llt, sobald Bug in KAON2 gefixt wurde
-// if (!Config.owa) {
- // ClassicalNegation cn =
- // KAON2Manager.factory().classicalNegation(l);
- try {
- query = kaon2Reasoner.createQuery(f, new Variable[] { X, Y }, null, null);
-
- // BUG IN KAON2, DESWEGEN AUSKOMMENTIERT
-
- // System.out.println();
- query.open();
- while (!query.afterLast()) {
- tupleBuffer = query.tupleBuffer();
- String individual1 = tupleBuffer[0].toString();
- String individual2 = tupleBuffer[1].toString();
- // addIndividualToRole(aBox.rolesNeg, name,
- // individual1,individual2);
- System.out.println(atomicRole.getName() + " " + individual1 + " "
- + individual2);
- query.next();
- }
- query.close();
- query.dispose();
- } catch (KAON2Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-// }
-
- return returnMap;
- }
-
- public void terminateReasoner() {
- kaon2Reasoner.dispose();
- try {
- kaon2Connection.close();
- } catch (KAON2Exception e) {
- e.printStackTrace();
- }
- }
-
- public ReasonerType getReasonerType() {
- return ReasonerType.KAON2;
- }
-
- public Set<AtomicConcept> getAtomicConcepts() {
- return atomicConcepts;
- }
-
- public Set<AtomicRole> getAtomicRoles() {
- return atomicRoles;
- }
-
- public SortedSet<Individual> getIndividuals() {
- return individuals;
- }
-
- public static Collection<ConfigOption<?>> createConfigOptions() {
- Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
- options.add(CommonConfigOptions.getUNA());
- return options;
- }
-
- /* (non-Javadoc)
- * @see org.dllearner.core.Component#applyConfigEntry(org.dllearner.core.ConfigEntry)
- */
- @Override
- public <T> void applyConfigEntry(ConfigEntry<T> entry) throws InvalidConfigOptionValueException {
- String name = entry.getOptionName();
- if(name.equals("una"))
- una = (Boolean) entry.getValue();
- }
-
- /* (non-Javadoc)
- * @see org.dllearner.core.Component#init()
- */
- @Override
- public void init() {
- // TODO Auto-generated method stub
-
- }
-
- // Problem: mit den eigenen Datenstrukturen wird OWL nicht vollständig
- // abgedeckt z.B. data types, d.h. ohne Erweiterung der internen Strukturen
- // kann nicht jede KAON2-Ontologie importiert werden
- // TODO: unvollständig
- /*
- public static void importKAON2Ontology(KB kb, Ontology ontology) throws KAON2Exception {
- Set<Axiom> axioms = ontology.createAxiomRequest().getAll();
-
- // KB kb = new KB();
- for(Axiom axiom : axioms) {
- if(axiom instanceof ClassMember) {
- String individual = ((ClassMember)axiom).getIndividual().toString();
- Concept concept = importKAON2Concept(((ClassMember)axiom).getDescription());
- ConceptAssertion ca = new ConceptAssertion(concept, individual);
- kb.addABoxAxiom(ca);
- // da es eine externe API ist, können wir nicht sicher sein alle
- // Axiome erwischt zu haben
- } else {
- throw new RuntimeException("Failed to import the following axiom: " + axiom);
- }
- }
- }
- */
-
- // TODO: unvollständig
- /*
- private static Concept importKAON2Concept(Description description) {
- if (description.equals(KAON2Manager.factory().thing())) {
- return new Top();
- } else if (description.equals(KAON2Manager.factory().nothing())) {
- return new Bottom();
- } else if (description instanceof OWLClass) {
- return new AtomicConcept(description.toString());
- } else {
- throw new RuntimeException("Failed to convert the following KAON2 description: " + description);
- }
- }
- */
-
-
-}
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-02-06 15:24:06 UTC (rev 501)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-02-06 16:36:36 UTC (rev 502)
@@ -38,26 +38,41 @@
import org.dllearner.core.config.InvalidConfigOptionValueException;
import org.dllearner.core.config.StringConfigOption;
import org.dllearner.core.dl.All;
+import org.dllearner.core.dl.AssertionalAxiom;
import org.dllearner.core.dl.AtomicConcept;
import org.dllearner.core.dl.AtomicRole;
import org.dllearner.core.dl.Bottom;
import org.dllearner.core.dl.Concept;
+import org.dllearner.core.dl.ConceptAssertion;
import org.dllearner.core.dl.Conjunction;
import org.dllearner.core.dl.Disjunction;
+import org.dllearner.core.dl.Equality;
import org.dllearner.core.dl.Exists;
+import org.dllearner.core.dl.FunctionalRoleAxiom;
+import org.dllearner.core.dl.Inclusion;
import org.dllearner.core.dl.Individual;
+import org.dllearner.core.dl.InverseRoleAxiom;
+import org.dllearner.core.dl.KB;
import org.dllearner.core.dl.MultiConjunction;
import org.dllearner.core.dl.MultiDisjunction;
import org.dllearner.core.dl.Negation;
+import org.dllearner.core.dl.RBoxAxiom;
+import org.dllearner.core.dl.RoleAssertion;
import org.dllearner.core.dl.RoleHierarchy;
+import org.dllearner.core.dl.SubRoleAxiom;
import org.dllearner.core.dl.SubsumptionHierarchy;
+import org.dllearner.core.dl.SymmetricRoleAxiom;
+import org.dllearner.core.dl.TerminologicalAxiom;
import org.dllearner.core.dl.Top;
+import org.dllearner.core.dl.TransitiveRoleAxiom;
import org.dllearner.kb.OWLFile;
import org.dllearner.utilities.ConceptComparator;
import org.dllearner.utilities.RoleComparator;
import org.semanticweb.owl.apibinding.OWLManager;
import org.semanticweb.owl.inference.OWLReasoner;
import org.semanticweb.owl.inference.OWLReasonerException;
+import org.semanticweb.owl.model.AddAxiom;
+import org.semanticweb.owl.model.OWLAxiom;
import org.semanticweb.owl.model.OWLClass;
import org.semanticweb.owl.model.OWLDataFactory;
import org.semanticweb.owl.model.OWLDescription;
@@ -65,6 +80,7 @@
import org.semanticweb.owl.model.OWLNamedObject;
import org.semanticweb.owl.model.OWLObjectProperty;
import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyChangeException;
import org.semanticweb.owl.model.OWLOntologyCreationException;
import org.semanticweb.owl.model.OWLOntologyManager;
@@ -85,6 +101,8 @@
private OWLReasoner reasoner;
// 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();
@@ -503,19 +521,19 @@
return new AtomicConcept(owlClass.getURI().toString());
}
- public OWLObjectProperty getOWLAPIDescription(AtomicRole role) {
- return factory.getOWLObjectProperty(URI.create(role.getName()));
+ public static OWLObjectProperty getOWLAPIDescription(AtomicRole role) {
+ return staticFactory.getOWLObjectProperty(URI.create(role.getName()));
}
- public OWLDescription getOWLAPIDescription(Concept concept) {
+ public static OWLDescription getOWLAPIDescription(Concept concept) {
if (concept instanceof AtomicConcept) {
- return factory.getOWLClass(URI.create(((AtomicConcept)concept).getName()));
+ return staticFactory.getOWLClass(URI.create(((AtomicConcept)concept).getName()));
} else if (concept instanceof Bottom) {
- return factory.getOWLNothing();
+ return staticFactory.getOWLNothing();
} else if (concept instanceof Top) {
- return factory.getOWLThing();
+ return staticFactory.getOWLThing();
} else if (concept instanceof Negation) {
- return factory.getOWLObjectComplementOf(
+ return staticFactory.getOWLObjectComplementOf(
getOWLAPIDescription(concept.getChild(0)));
} else if (concept instanceof Conjunction) {
OWLDescription d1 = getOWLAPIDescription(concept.getChild(0));
@@ -523,39 +541,133 @@
Set<OWLDescription> d = new HashSet<OWLDescription>();
d.add(d1);
d.add(d2);
- return factory.getOWLObjectIntersectionOf(d);
+ return staticFactory.getOWLObjectIntersectionOf(d);
} else if (concept instanceof Disjunction) {
OWLDescription d1 = getOWLAPIDescription(concept.getChild(0));
OWLDescription d2 = getOWLAPIDescription(concept.getChild(1));
Set<OWLDescription> d = new HashSet<OWLDescription>();
d.add(d1);
d.add(d2);
- return factory.getOWLObjectUnionOf(d);
+ return staticFactory.getOWLObjectUnionOf(d);
} else if (concept instanceof All) {
- OWLObjectProperty role = factory.getOWLObjectProperty(
+ OWLObjectProperty role = staticFactory.getOWLObjectProperty(
URI.create(((All) concept).getRole().getName()));
OWLDescription d = getOWLAPIDescription(concept.getChild(0));
- return factory.getOWLObjectAllRestriction(role, d);
+ return staticFactory.getOWLObjectAllRestriction(role, d);
} else if(concept instanceof Exists) {
- OWLObjectProperty role = factory.getOWLObjectProperty(
+ OWLObjectProperty role = staticFactory.getOWLObjectProperty(
URI.create(((Exists) concept).getRole().getName()));
OWLDescription d = getOWLAPIDescription(concept.getChild(0));
- return factory.getOWLObjectSomeRestriction(role, d);
+ return staticFactory.getOWLObjectSomeRestriction(role, d);
} else if(concept instanceof MultiConjunction) {
Set<OWLDescription> descriptions = new HashSet<OWLDescription>();
for(Concept child : concept.getChildren())
descriptions.add(getOWLAPIDescription(child));
- return factory.getOWLObjectIntersectionOf(descriptions);
+ return staticFactory.getOWLObjectIntersectionOf(descriptions);
} else if(concept instanceof MultiDisjunction) {
Set<OWLDescription> descriptions = new HashSet<OWLDescription>();
for(Concept child : concept.getChildren())
descriptions.add(getOWLAPIDescription(child));
- return factory.getOWLObjectUnionOf(descriptions);
+ return staticFactory.getOWLObjectUnionOf(descriptions);
}
throw new IllegalArgumentException("Unsupported concept type.");
}
+ public static void fillOWLAPIOntology(OWLOntologyManager manager, OWLOntology ontology, KB kb) {
+
+ // OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ OWLDataFactory factory = manager.getOWLDataFactory();
+ // OWLOntology ontology = manager.createOntology(ontologyURI);
+ try {
+ for (AssertionalAxiom axiom : kb.getAbox()) {
+ if (axiom instanceof ConceptAssertion) {
+ OWLDescription d = getOWLAPIDescription(((ConceptAssertion) axiom)
+ .getConcept());
+ OWLIndividual i = factory.getOWLIndividual(URI.create(
+ ((ConceptAssertion) axiom).getIndividual().getName()));
+ OWLAxiom axiomOWLAPI = factory.getOWLClassAssertionAxiom(i, d);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+
+ manager.applyChange(addAxiom);
+
+ } else if (axiom instanceof RoleAssertion) {
+ OWLObjectProperty role = factory.getOWLObjectProperty(
+ URI.create(((RoleAssertion) axiom).getRole().getName()));
+ OWLIndividual i1 = factory.getOWLIndividual(
+ URI.create(((RoleAssertion) axiom).getIndividual1().getName()));
+ OWLIndividual i2 = factory.getOWLIndividual(
+ URI.create(((RoleAssertion) axiom).getIndividual2().getName()));
+ OWLAxiom axiomOWLAPI = factory.getOWLObjectPropertyAssertionAxiom(i1, role, i2);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+ manager.applyChange(addAxiom);
+ }
+ }
+
+ for (RBoxAxiom axiom : kb.getRbox()) {
+ if (axiom instanceof FunctionalRoleAxiom) {
+ OWLObjectProperty role = factory.getOWLObjectProperty(
+ URI.create(((FunctionalRoleAxiom) axiom).getRole().getName()));
+ OWLAxiom axiomOWLAPI = factory.getOWLFunctionalObjectPropertyAxiom(role);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+ manager.applyChange(addAxiom);
+ } else if (axiom instanceof SymmetricRoleAxiom) {
+ OWLObjectProperty role = factory.getOWLObjectProperty(
+ URI.create(((SymmetricRoleAxiom) axiom).getRole().getName()));
+ OWLAxiom axiomOWLAPI = factory.getOWLSymmetricObjectPropertyAxiom(role);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+ manager.applyChange(addAxiom);
+ } else if (axiom instanceof TransitiveRoleAxiom) {
+ OWLObjectProperty role = factory.getOWLObjectProperty(
+ URI.create(((SymmetricRoleAxiom) axiom).getRole().getName()));
+ OWLAxiom axiomOWLAPI = factory.getOWLTransitiveObjectPropertyAxiom(role);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+ manager.applyChange(addAxiom);
+ } else if (axiom instanceof InverseRoleAxiom) {
+ OWLObjectProperty role = factory.getOWLObjectProperty(
+ URI.create(((InverseRoleAxiom) axiom).getRole().getName()));
+ OWLObjectProperty inverseRole = factory.getOWLObjectProperty(
+ URI.create(((InverseRoleAxiom) axiom).getInverseRole().getName()));
+ OWLAxiom axiomOWLAPI = factory.getOWLInverseObjectPropertiesAxiom(role, inverseRole);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+ manager.applyChange(addAxiom);
+ } else if (axiom instanceof SubRoleAxiom) {
+ OWLObjectProperty role = factory.getOWLObjectProperty(
+ URI.create(((SubRoleAxiom) axiom).getRole().getName()));
+ OWLObjectProperty subRole = factory.getOWLObjectProperty(
+ URI.create(((SubRoleAxiom) axiom).getSubRole().getName()));
+ OWLAxiom axiomOWLAPI = factory.getOWLSubObjectPropertyAxiom(subRole, role);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+ manager.applyChange(addAxiom);
+ }
+ }
+
+ for (TerminologicalAxiom axiom : kb.getTbox()) {
+ if (axiom instanceof Equality) {
+ OWLDescription d1 = getOWLAPIDescription(((Equality) axiom).getConcept1());
+ OWLDescription d2 = getOWLAPIDescription(((Equality) axiom).getConcept2());
+ Set<OWLDescription> ds = new HashSet<OWLDescription>();
+ ds.add(d1);
+ ds.add(d2);
+ OWLAxiom axiomOWLAPI = factory.getOWLEquivalentClassesAxiom(ds);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+ manager.applyChange(addAxiom);
+ } else if (axiom instanceof Inclusion) {
+ OWLDescription subConcept = getOWLAPIDescription(((Inclusion) axiom)
+ .getSubConcept());
+ OWLDescription superConcept = getOWLAPIDescription(((Inclusion) axiom)
+ .getSuperConcept());
+ OWLAxiom axiomOWLAPI = factory.getOWLSubClassAxiom(subConcept, superConcept);
+ AddAxiom addAxiom = new AddAxiom(ontology, axiomOWLAPI);
+ manager.applyChange(addAxiom);
+ }
+ }
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
/**
* Test
*
Modified: trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java 2008-02-06 15:24:06 UTC (rev 501)
+++ trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java 2008-02-06 16:36:36 UTC (rev 502)
@@ -25,7 +25,6 @@
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
-import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
Modified: trunk/src/dl-learner/org/dllearner/utilities/OntologyClassRewriter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/OntologyClassRewriter.java 2008-02-06 15:24:06 UTC (rev 501)
+++ trunk/src/dl-learner/org/dllearner/utilities/OntologyClassRewriter.java 2008-02-06 16:36:36 UTC (rev 502)
@@ -1,27 +1,51 @@
+/**
+ * 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
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
package org.dllearner.utilities;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
import java.net.MalformedURLException;
+import java.net.URI;
import java.net.URL;
-import java.util.HashMap;
-import java.util.Set;
import org.dllearner.core.dl.Concept;
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
-import org.dllearner.reasoning.KAON2Reasoner;
-import org.semanticweb.kaon2.api.DefaultOntologyResolver;
-import org.semanticweb.kaon2.api.KAON2Connection;
-import org.semanticweb.kaon2.api.KAON2Exception;
-import org.semanticweb.kaon2.api.KAON2Manager;
-import org.semanticweb.kaon2.api.Ontology;
-import org.semanticweb.kaon2.api.Request;
-import org.semanticweb.kaon2.api.formatting.OntologyFileFormat;
-import org.semanticweb.kaon2.api.owl.axioms.EquivalentClasses;
-import org.semanticweb.kaon2.api.owl.elements.Description;
-import org.semanticweb.kaon2.api.owl.elements.OWLClass;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.model.OWLClass;
+import org.semanticweb.owl.model.OWLDataFactory;
+import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyCreationException;
+import org.semanticweb.owl.model.OWLOntologyManager;
+/**
+ * Utility class to replace a definition in an OWL file by a learned
+ * definition.
+ *
+ * TODO: Class is currently not working. There is still some KAON2 specific
+ * code (commented out), which has to be converted to OWL API code.
+ *
+ * @author Jens Lehmann
+ *
+ */
public class OntologyClassRewriter {
public static void main(String[] args) {
@@ -37,6 +61,7 @@
System.out.println(rewrittenOntology);
}
+ @SuppressWarnings({"unused"})
public static String rewriteOntology(String urlString, String className, String newConceptString) {
try {
@@ -45,44 +70,54 @@
Concept newConceptInternal = KBParser.parseConcept(newConceptString);
// umwandeln in interne KAON2-Darstellung (bereits im DL-Learner implementiert)
- Description newConceptKAON2 = KAON2Reasoner.getKAON2Description(newConceptInternal);
+ // Description newConceptKAON2 = KAON2Reasoner.getKAON2Description(newConceptInternal);
+ OWLDescription newConceptOWLAPI = OWLAPIReasoner.getOWLAPIDescription(newConceptInternal);
// Umwandlung Klassenname in atomate KAON2-Klasse
- OWLClass classKAON2 = KAON2Manager.factory().owlClass(className);
+ // OWLClass classKAON2 = KAON2Manager.factory().owlClass(className);
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ OWLDataFactory factory = manager.getOWLDataFactory();
+ OWLClass classOWLAPI = factory.getOWLClass(URI.create(className));
// Test, ob es eine richtige URL ist (ansonsten wird Exception geworfen)
new URL(urlString);
// einlesen der Ontologie
- DefaultOntologyResolver resolver = new DefaultOntologyResolver();
- KAON2Connection connection = KAON2Manager.newConnection();
- connection.setOntologyResolver(resolver);
- Ontology ontology = connection.openOntology(urlString, new HashMap<String,Object>());
+ // DefaultOntologyResolver resolver = new DefaultOntologyResolver();
+ // KAON2Connection connection = KAON2Manager.newConnection();
+ // connection.setOntologyResolver(resolver);
+ // Ontology ontology = connection.openOntology(urlString, new HashMap<String,Object>());
- // suchen von Äquivalenzaxiomen
- Request<EquivalentClasses> equivalenceAxiomsRequest = ontology.createAxiomRequest(EquivalentClasses.class);
- Set<EquivalentClasses> equivalenceAxioms = equivalenceAxiomsRequest.get();
+ OWLOntology ontology = manager.loadOntologyFromPhysicalURI(URI.create(urlString));
- for(EquivalentClasses eq : equivalenceAxioms) {
- Set<Description> eqDescriptions = eq.getDescriptions();
- if(eqDescriptions.size() != 2)
- System.out.println("Warning: Rewriting more than two equivalent descriptions not supported yet." +
- " Possibly incorrect ontology returned.");
-
- // entfernen aller Äquivalenzaxiome, die die Klasse enthalten
- if(eqDescriptions.contains(classKAON2))
- ontology.removeAxiom(eq);
- }
+ // TODO
- // hinzufügen des neuen Äquivalenzaxioms
- EquivalentClasses eqNew = KAON2Manager.factory().equivalentClasses(classKAON2, newConceptKAON2);
- ontology.addAxiom(eqNew);
+ // suchen von Äquivalenzaxiomen
+// Request<EquivalentClasses> equivalenceAxiomsRequest = ontology.createAxiomRequest(EquivalentClasses.class);
+// Set<EquivalentClasses> equivalenceAxioms = equivalenceAxiomsRequest.get();
+//
+// for(EquivalentClasses eq : equivalenceAxioms) {
+// Set<Description> eqDescriptions = eq.getDescriptions();
+// if(eqDescriptions.size() != 2)
+// System.out.println("Warning: Rewriting more than two equivalent descriptions not supported yet." +
+// " Possibly incorrect ontology returned.");
+//
+// // entfernen aller Äquivalenzaxiome, die die Klasse enthalten
+// if(eqDescriptions.contains(classKAON2))
+// ontology.removeAxiom(eq);
+// }
+//
+// // hinzufügen des neuen Äquivalenzaxioms
+// EquivalentClasses eqNew = KAON2Manager.factory().equivalentClasses(classKAON2, newConceptKAON2);
+// ontology.addAxiom(eqNew);
+//
+// // umwandeln der Ontologie in einen String
+// ByteArrayOutputStream os = new ByteArrayOutputStream();
+// ontology.saveOntology(OntologyFileFormat.OWL_RDF,os,"ISO-8859-1");
+//
+// return os.toString();
+ return "";
- // umwandeln der Ontologie in einen String
- ByteArrayOutputStream os = new ByteArrayOutputStream();
- ontology.saveOntology(OntologyFileFormat.OWL_RDF,os,"ISO-8859-1");
- return os.toString();
-
// in einigen der folgenden Fälle sollten im Web-Service Exceptions geworfen
// werden (throws ...) z.B. bei ParseException
} catch (ParseException e) {
@@ -92,16 +127,10 @@
// TODO Auto-generated catch block
e.printStackTrace();
System.out.println("Syntactically incorrect URL.");
- } catch (KAON2Exception e) {
+ } catch (OWLOntologyCreationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
+ }
throw new Error("Ontology could not be rewritten. Exiting.");
}
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