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[DL-Learner SVN] SF.net SVN: dl-learner:[3562] trunk/components-core/src/main/java/org/ dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
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From: <lor...@us...> - 2012-02-01 14:31:35
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Revision: 3562
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3562&view=rev
Author: lorenz_b
Date: 2012-02-01 14:31:26 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
Started integration of debugging unsatisfiable object properties.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-01 11:36:50 UTC (rev 3561)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-01 14:31:26 UTC (rev 3562)
@@ -11,6 +11,8 @@
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.SortedSet;
+import java.util.TreeSet;
import java.util.Map.Entry;
import java.util.Set;
import java.util.logging.Level;
@@ -29,10 +31,12 @@
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLLogicalAxiom;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.RemoveAxiom;
import org.semanticweb.owlapi.reasoner.IllegalConfigurationException;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
@@ -47,6 +51,7 @@
import com.clarkparsia.owlapi.explanation.HSTExplanationGenerator;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
import com.clarkparsia.owlapiv3.OntologyUtils;
+import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
public class JustificationBasedCoherentOntologyExtractor implements CoherentOntologyExtractor{
@@ -62,10 +67,14 @@
private OWLDataFactory factory;
private Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
+ private Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
MessageDigest md5;
+ private Set<OWLTransitiveObjectPropertyAxiom> removedTransitiveAxioms;
+ private Set<OWLObjectProperty> unsatObjectProperties;
+
public JustificationBasedCoherentOntologyExtractor() {
try {
md5 = MessageDigest.getInstance("MD5");
@@ -83,25 +92,34 @@
@Override
public OWLOntology getCoherentOntology(OWLOntology ontology, boolean preferRoots){
- if(preferRoots){
- return computeCoherentOntologyRootBased(ontology);
- } else {
- return computeCoherentOntology(ontology);
- }
- }
-
- private OWLOntology computeCoherentOntologyRootBased(OWLOntology ontology) {
this.ontology = ontology;
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
//only for debugging
- ontology.getOWLOntologyManager().removeAxioms(ontology, ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
+ removedTransitiveAxioms = ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
+ incoherentOntology.getOWLOntologyManager().removeAxioms(ontology, removedTransitiveAxioms);
+ manager = incoherentOntology.getOWLOntologyManager();
+ factory = manager.getOWLDataFactory();
+
long startTime = System.currentTimeMillis();
reasoner = new IncrementalClassifier(incoherentOntology);
reasoner.classify();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ //compute the unsatisfiable object properties
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+
+ //start main process, either preferring root classes or not
+ if(preferRoots){
+ return computeCoherentOntologyRootBased(incoherentOntology);
+ } else {
+ return computeCoherentOntology(incoherentOntology);
+ }
+ }
+
+ private OWLOntology computeCoherentOntologyRootBased(OWLOntology ontology) {
+
// startTime = System.currentTimeMillis();
// hermitReasoner = new Reasoner(incoherentOntology);
// hermitReasoner.classifyClasses();
@@ -113,7 +131,7 @@
//compute the unsatisfiable classes
logger.info("Computing root/derived unsatisfiable classes...");
- startTime = System.currentTimeMillis();
+ long startTime = System.currentTimeMillis();
StructureBasedRootClassFinder rootFinder = new StructureBasedRootClassFinder(reasoner);
Set<OWLClass> unsatClasses = rootFinder.getRootUnsatisfiableClasses();
Set<OWLClass> derivedUnsatClasses = rootFinder.getDerivedUnsatisfiableClasses();
@@ -179,14 +197,7 @@
//save
if(cnt - (rootCnt+derivedCnt) >= 10){
cnt = rootCnt + derivedCnt;
- OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
- try {
- toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_" + cnt + ".owl")));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
+ save("log/dbpedia_" + cnt + ".owl");
cnt = rootCnt + derivedCnt;
}
@@ -211,23 +222,9 @@
}
private OWLOntology computeCoherentOntology(OWLOntology ontology) {
- this.ontology = ontology;
- this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
-
- //only for debugging
- ontology.getOWLOntologyManager().removeAxioms(ontology, ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
-
- long startTime = System.currentTimeMillis();
- reasoner = new IncrementalClassifier(incoherentOntology);
- reasoner.classify();
- logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
-
- OWLOntologyManager man = incoherentOntology.getOWLOntologyManager();
- factory = man.getOWLDataFactory();
-
//compute the unsatisfiable classes
logger.info("Computing unsatisfiable classes...");
- startTime = System.currentTimeMillis();
+ long startTime = System.currentTimeMillis();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
int cnt = unsatClasses.size();
@@ -247,6 +244,7 @@
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
+ Map<OWLObjectProperty, Set<Set<OWLAxiom>>> prop2Explanations = getInitialExplanationsForUnsatObjectProperties(unsatObjectProperties);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
@@ -261,8 +259,8 @@
//we remove the most frequent axiom from the ontology
OWLAxiom toRemove = sortedEntries.get(0).getKey();
logger.info("Removing axiom " + toRemove + ".");
- man.removeAxiom(incoherentOntology, toRemove);
- man.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
+ manager.removeAxiom(incoherentOntology, toRemove);
+ manager.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
removeFromExplanations(cls2Explanations, toRemove);
removeFromModules(toRemove);
@@ -277,14 +275,7 @@
//save
if(cnt - unsatClasses.size() >= 10){
cnt = unsatClasses.size();
- OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
- try {
- toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_" + cnt + ".owl")));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
+ save("log/dbpedia_" + cnt + ".owl");
}
//recompute explanations if necessary
@@ -307,6 +298,30 @@
return getOntologyWithAnnotations(incoherentOntology);
}
+ private void save(String fileName){
+ OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
+ try {
+ toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(fileName)));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private Set<OWLObjectProperty> getUnsatisfiableObjectProperties(IncrementalClassifier reasoner){
+ SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>();
+ OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
+ for(OWLObjectProperty p : reasoner.getRootOntology().getObjectPropertiesInSignature()){
+// boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectExactCardinality(1, p));
+ boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectSomeValuesFrom(p, factory.getOWLThing()));
+ if(!satisfiable){
+ properties.add(p);
+ }
+ }
+ return properties;
+ }
+
private void removeFromModules(OWLAxiom axiom){
OWLOntology module;
for(Entry<OWLClass, OWLOntology> entry : cls2ModuleMap.entrySet()){
@@ -366,6 +381,17 @@
return cls2Explanations;
}
+ private Map<OWLObjectProperty, Set<Set<OWLAxiom>>> getInitialExplanationsForUnsatObjectProperties(Set<OWLObjectProperty> unsatObjProperties){
+ Map<OWLObjectProperty, Set<Set<OWLAxiom>>> prop2Explanations = new HashMap<OWLObjectProperty, Set<Set<OWLAxiom>>>();
+
+ for(OWLObjectProperty unsatClass : unsatObjProperties){
+ Set<Set<OWLAxiom>> explanations = computeExplanations(unsatClass);
+ prop2Explanations.put(unsatClass, explanations);
+ }
+
+ return prop2Explanations;
+ }
+
private OWLOntology getOntologyWithoutAnnotations(OWLOntology ontology){
try {
OWLOntologyManager man = ontology.getOWLOntologyManager();
@@ -397,6 +423,11 @@
return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
}
+ private Set<Set<OWLAxiom>> computeExplanations(OWLObjectProperty unsatProp){
+ PelletExplanation expGen = new PelletExplanation(getModule(unsatProp));
+ return expGen.getUnsatisfiableExplanations(factory.getOWLObjectExactCardinality(1, unsatProp), numberOfJustifications);
+ }
+
private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass, int limit){
PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
@@ -415,7 +446,7 @@
// return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
// }
- private OWLOntology getModule(OWLClass cls){System.out.println(cls);
+ private OWLOntology getModule(OWLClass cls){
OWLOntology module = cls2ModuleMap.get(cls);
new File("log").mkdir();
if(module == null){
@@ -443,6 +474,35 @@
return module;
}
+ private OWLOntology getModule(OWLEntity entity){
+ OWLOntology module = entity2ModuleMap.get(entity);
+ new File("log").mkdir();
+ if(module == null){
+ md5.reset();
+ md5.update((ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toString() + entity.toStringID()).getBytes());
+ String hash = MD5.asHex(md5.digest());
+ String filename = "log/" + hash + ".owl";
+ File file = new File(filename);
+ if(file.exists()){
+ module = loadModule(file);
+ } else {
+ module = OntologyUtils.getOntologyFromAxioms(
+ ModularityUtils.extractModule(incoherentOntology, Collections.singleton(entity), ModuleType.TOP_OF_BOT));
+ try {
+ manager.saveOntology(module, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(filename)));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
+ entity2ModuleMap.put(entity, module);
+ }
+ return module;
+ }
+
+
private OWLOntology loadModule(File file){
OWLOntology module = null;
try {
@@ -453,13 +513,31 @@
return module;
}
- private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
- Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
- for(OWLClass cls : classes){
- OWLOntology module = getModule(cls);
- cls2ModuleMap.put(cls, module);
+// private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
+// Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
+// for(OWLClass cls : classes){
+// OWLOntology module = getModule(cls);
+// cls2ModuleMap.put(cls, module);
+// }
+// return cls2ModuleMap;
+// }
+//
+// private Map<OWLObjectProperty, OWLOntology> extractModules(Set<OWLObjectProperty> objectProperties){
+// Map<OWLObjectProperty, OWLOntology> prop2ModuleMap = new HashMap<OWLObjectProperty, OWLOntology>();
+// for(OWLObjectProperty prop : objectProperties){
+// OWLOntology module = getModule(prop);
+// prop2ModuleMap.put(prop, module);
+// }
+// return prop2ModuleMap;
+// }
+
+ private <T extends OWLEntity> Map<T, OWLOntology> extractModules(Set<T> entities){
+ Map<T, OWLOntology> entity2ModuleMap = new HashMap<T, OWLOntology>();
+ for(T entity : entities){
+ OWLOntology module = getModule(entity);
+ entity2ModuleMap.put(entity, module);
}
- return cls2ModuleMap;
+ return entity2ModuleMap;
}
public void setNumberOfJustifications(int numberOfJustifications) {
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