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[DL-Learner SVN] SF.net SVN: dl-learner:[3558] trunk/scripts/src/main/java/org/dllearner/ scripts/SPARQLSampleDebugging.java
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From: <lor...@us...> - 2012-01-27 11:51:34
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Revision: 3558
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3558&view=rev
Author: lorenz_b
Date: 2012-01-27 11:51:28 +0000 (Fri, 27 Jan 2012)
Log Message:
-----------
Small update.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-01-26 13:43:13 UTC (rev 3557)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-01-27 11:51:28 UTC (rev 3558)
@@ -1,8 +1,9 @@
package org.dllearner.scripts;
+import java.io.BufferedInputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
-import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
@@ -28,6 +29,8 @@
import java.util.TreeSet;
import java.util.prefs.Preferences;
+import org.apache.commons.compress.compressors.CompressorInputStream;
+import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
@@ -35,7 +38,8 @@
import org.apache.log4j.SimpleLayout;
import org.dllearner.algorithm.qtl.util.ModelGenerator;
import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy;
-import org.dllearner.core.owl.IrreflexiveObjectPropertyAxiom;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
@@ -52,14 +56,18 @@
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLIrreflexiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLObjectPropertyCharacteristicAxiom;
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.reasoner.InferenceType;
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
import com.clarkparsia.owlapi.explanation.PelletExplanation;
import com.clarkparsia.owlapi.explanation.io.manchester.ManchesterSyntaxExplanationRenderer;
import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
@@ -85,9 +93,9 @@
private ExtractionDBCache cache = new ExtractionDBCache("cache");
private int sampleSize = 10;
- private int depth = 2;
+ private int depth = 3;
private int nrOfChunks = 1;
- private int maxNrOfExplanations = 20;
+ private int maxNrOfExplanations = 10;
private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class);
@@ -98,6 +106,8 @@
private Connection conn;
private PreparedStatement ps;
+ private OWLDataFactory factory = new OWLDataFactoryImpl();
+
static {PelletExplanation.setup();}
public SPARQLSampleDebugging(SparqlEndpoint endpoint) {
@@ -184,7 +194,7 @@
for(int i = 0; i < nrOfChunks; i++){
int offset = (int)(Math.random() * max);
- offset = Math.min(offset, offset-(size/nrOfChunks));
+ offset = Math.min(offset, offset-(size/nrOfChunks));offset = 236242;
query = String.format("SELECT DISTINCT ?s WHERE {?s a ?type} LIMIT %d OFFSET %d", (size/nrOfChunks), offset);
logger.info(query);
@@ -236,10 +246,11 @@
private OWLOntology extractSampleModule(String resource){
logger.info("Extracting sample module...");
long startTime = System.currentTimeMillis();
- ModelGenerator modelGen = new ModelGenerator(endpoint, cache);
- Model model = modelGen.createModel(resource, Strategy.CHUNKS, depth);
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(endpoint, cache);
+ Model model = cbdGen.getConciseBoundedDescription(resource, 3);
+ OWLOntology data = convert(model);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- return convert(model);
+ return data;
}
@@ -257,7 +268,13 @@
logger.info("Computing explanations...");
long startTime = System.currentTimeMillis();
PelletExplanation expGen = new PelletExplanation(reasoner);
- Set<Set<OWLAxiom>> explanations = expGen.getInconsistencyExplanations(maxNrOfExplanations);
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>(maxNrOfExplanations);
+ try {
+ explanations = expGen.getInconsistencyExplanations(maxNrOfExplanations);
+ } catch (Exception e) {
+ e.printStackTrace();
+ logger.error(e);
+ }
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return explanations;
}
@@ -279,7 +296,7 @@
long startTime = System.currentTimeMillis();
logger.info("Loading reference ontology...");
OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(
- getClass().getClassLoader().getResourceAsStream("dbpedia_0.75_no_datapropaxioms.owl"));System.out.println(ontology.getLogicalAxiomCount());
+ getClass().getClassLoader().getResourceAsStream("dbpedia_0.75_no_datapropaxioms.owl"));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return ontology;
}
@@ -435,16 +452,26 @@
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
man.addOntologyChangeListener( reasoner );
Set<String> resources = extractSampleResourcesChunked(sampleSize);
+ Model model;
for(String resource : resources){
- logger.info("Resource " + resource);resource = "http://dbpedia.org/resource/The_Man_Who_Wouldn%27t_Die";
- module = extractSampleModule(Collections.singleton(resource));computeExplanations(convert(module).add(convert(extractSampleModule(resource))));
+ logger.info("###################################################################");
+ logger.info("Resource " + resource);//resource = "http://dbpedia.org/resource/The_Man_Who_Wouldn%27t_Die";
+ module = extractSampleModule(resource);
man.addAxioms(reference, module.getABoxAxioms(true));
+ man.removeAxioms(reference, reference.getAxioms(AxiomType.DATA_PROPERTY_ASSERTION));
boolean isConsistent = reasoner.isConsistent();
logger.info("Consistent: " + isConsistent);
Set<Set<OWLAxiom>> explanations = null;
if(!isConsistent){
explanations = computeExplanations(reasoner);
+ model = convert(reference);
+ explanations.addAll(computeInconsistencyExplanationsByAsymmetryPattern(reference, model));
+ explanations.addAll(computeInconsistencyExplanationsByIrreflexivityPattern(reference, model));
+ explanations.addAll(computeInconsistencyExplanationsByFunctionalityPattern(reference, model));
logger.info("Found " + explanations.size() + " explanations.");
+ for(Set<OWLAxiom> exp : explanations){
+ logger.info(exp + "\n");
+ }
Map<AxiomType, Integer> axiomType2CountMap = new HashMap<AxiomType, Integer>();
for(Set<OWLAxiom> explanation : explanations){
logger.info(explanation);
@@ -457,13 +484,14 @@
axiomType2CountMap.put(axiom.getAxiomType(), cnt);
}
}
+ logger.info("Axiom type count:");
for(Entry<AxiomType, Integer> entry : axiomType2CountMap.entrySet()){
logger.info(entry.getKey() + "\t: " + entry.getValue());
}
}
man.removeAxioms(reference, module.getABoxAxioms(true));
// writeToDB(resource, module.getLogicalAxiomCount(), isConsistent, explanations);
- break;
+// break;
}
}
@@ -501,10 +529,7 @@
} finally { qexec.close() ; }
}
- public void checkFunctionalityViolation(){
- try {
- OWLOntology ontology = loadReferenceOntology();
-
+ public void checkFunctionalityViolation(OWLOntology ontology){
Set<String> properties = new TreeSet<String>();
for(OWLAxiom ax : ontology.getAxioms(AxiomType.FUNCTIONAL_OBJECT_PROPERTY)){
OWLObjectProperty prop = ((OWLFunctionalObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
@@ -526,16 +551,9 @@
}
}
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- }
-
}
- public void checkIrreflexivityViolation(){
- try {
- OWLOntology ontology = loadReferenceOntology();
-
+ public void checkIrreflexivityViolation(OWLOntology ontology){
Set<String> properties = new TreeSet<String>();
for(OWLAxiom ax : ontology.getAxioms(AxiomType.IRREFLEXIVE_OBJECT_PROPERTY)){
OWLObjectProperty prop = ((OWLIrreflexiveObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
@@ -552,16 +570,9 @@
}
}
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- }
-
}
- public void checkAsymmetryViolation(){
- try {
- OWLOntology ontology = loadReferenceOntology();
-
+ public void checkAsymmetryViolation(OWLOntology ontology){
Set<String> properties = new TreeSet<String>();
for(OWLAxiom ax : ontology.getAxioms(AxiomType.ASYMMETRIC_OBJECT_PROPERTY)){
OWLObjectProperty prop = ((OWLAsymmetricObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
@@ -578,11 +589,102 @@
}
}
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
+ }
+
+ private Set<Set<OWLAxiom>> computeInconsistencyExplanationsByFunctionalityPattern(OWLOntology ontology, Model model){
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>();
+
+ for(OWLObjectProperty prop : extractObjectProperties(AxiomType.FUNCTIONAL_OBJECT_PROPERTY, ontology)){
+ OWLAxiom axiom = factory.getOWLFunctionalObjectPropertyAxiom(prop);
+ String queryString = "SELECT DISTINCT * WHERE {?s <%s> ?o1. ?s <%s> ?o2. FILTER(?o1 != ?o2)}".replace("%s", prop.toStringID());
+ Query query = QueryFactory.create(queryString) ;
+ QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
+ try {
+ ResultSet results = qexec.execSelect();
+ for (; results.hasNext();) {
+ Set<OWLAxiom> explanation = new HashSet<OWLAxiom>();
+ explanation.add(axiom);
+ QuerySolution qs = results.next();
+ OWLIndividual subject = factory.getOWLNamedIndividual(IRI.create(qs.getResource("s").getURI()));
+ OWLIndividual object1 = factory.getOWLNamedIndividual(IRI.create(qs.getResource("o1").getURI()));
+ OWLIndividual object2 = factory.getOWLNamedIndividual(IRI.create(qs.getResource("o2").getURI()));
+ OWLAxiom ax = factory.getOWLObjectPropertyAssertionAxiom(prop, subject, object1);
+ explanation.add(ax);
+ ax = factory.getOWLObjectPropertyAssertionAxiom(prop, subject, object2);
+ explanation.add(ax);
+ explanations.add(explanation);
+ }
+ } finally {
+ qexec.close();
+ }
}
+ return explanations;
}
+ private Set<Set<OWLAxiom>> computeInconsistencyExplanationsByAsymmetryPattern(OWLOntology ontology, Model model){
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>();
+
+ for(OWLObjectProperty prop : extractObjectProperties(AxiomType.ASYMMETRIC_OBJECT_PROPERTY, ontology)){
+ OWLAxiom axiom = factory.getOWLAsymmetricObjectPropertyAxiom(prop);
+ String queryString = "SELECT * WHERE {?s <%s> ?o. ?o <%s> ?s. FILTER(?o != ?s)}".replace("%s", prop.toStringID());
+ Query query = QueryFactory.create(queryString) ;
+ QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
+ try {
+ ResultSet results = qexec.execSelect();
+ for (; results.hasNext();) {
+ Set<OWLAxiom> explanation = new HashSet<OWLAxiom>();
+ explanation.add(axiom);
+ QuerySolution qs = results.nextSolution();
+ OWLIndividual subject = factory.getOWLNamedIndividual(IRI.create(qs.getResource("s").getURI()));
+ OWLIndividual object = factory.getOWLNamedIndividual(IRI.create(qs.getResource("o").getURI()));
+ OWLAxiom ax = factory.getOWLObjectPropertyAssertionAxiom(prop, subject, object);
+ explanation.add(ax);
+ ax = factory.getOWLObjectPropertyAssertionAxiom(prop, object, subject);
+ explanation.add(ax);
+ explanations.add(explanation);
+ }
+ } finally {
+ qexec.close();
+ }
+ }
+ return explanations;
+ }
+
+ private Set<Set<OWLAxiom>> computeInconsistencyExplanationsByIrreflexivityPattern(OWLOntology ontology, Model model){
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>();
+
+ for(OWLObjectProperty prop : extractObjectProperties(AxiomType.IRREFLEXIVE_OBJECT_PROPERTY, ontology)){
+ OWLAxiom axiom = factory.getOWLIrreflexiveObjectPropertyAxiom(prop);
+ String queryString = "SELECT * WHERE {?s <%s> ?s.}".replace("%s", prop.toStringID());
+ Query query = QueryFactory.create(queryString) ;
+ QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
+ try {
+ ResultSet results = qexec.execSelect();
+ for (; results.hasNext();) {
+ Set<OWLAxiom> explanation = new HashSet<OWLAxiom>();
+ explanation.add(axiom);
+ QuerySolution qs = results.nextSolution();
+ OWLIndividual subject = factory.getOWLNamedIndividual(IRI.create(qs.getResource("s").getURI()));
+ OWLAxiom ax = factory.getOWLObjectPropertyAssertionAxiom(prop, subject, subject);
+ explanation.add(ax);
+ explanations.add(explanation);
+ }
+ } finally {
+ qexec.close();
+ }
+ }
+ return explanations;
+ }
+
+ private SortedSet<OWLObjectProperty> extractObjectProperties(AxiomType<? extends OWLAxiom> axiomType, OWLOntology ontology){
+ SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>();
+ for(OWLAxiom ax : ontology.getAxioms(axiomType)){
+ properties.add(((OWLObjectPropertyCharacteristicAxiom)ax).getProperty().asOWLObjectProperty());
+ }
+// properties.retainAll(data.getObjectPropertiesInSignature());
+ return properties;
+ }
+
public void removeAxiomsWithNamespace(Set<String> namespaces){
}
@@ -611,24 +713,28 @@
System.exit(0);
}
- OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(IRI.create(new File(args[0]).toURI()));
+ InputStream is = new BufferedInputStream(new FileInputStream(args[0]));
+ CompressorInputStream in = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(in);
+
SPARQLSampleDebugging debug = new SPARQLSampleDebugging(endpoint);
- debug.checkFunctionalityViolation();
- debug.checkAsymmetryViolation();
- debug.checkIrreflexivityViolation();
+// debug.checkFunctionalityViolation(ontology);
+// debug.checkAsymmetryViolation(ontology);
+// debug.checkIrreflexivityViolation(ontology);
long s1 = System.currentTimeMillis();
debug.runOptimized(ontology);
long s2 = System.currentTimeMillis()-s1;
+ System.out.println(s2);
- long s3 = System.currentTimeMillis();
+ /*long s3 = System.currentTimeMillis();
debug.run(ontology);
long s4 = System.currentTimeMillis()-s3;
System.out.println(s2);
- System.out.println(s4);
+ System.out.println(s4);*/
}
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