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[DL-Learner SVN] SF.net SVN: dl-learner:[3468] trunk/scripts/src/main/java/org/dllearner/ scripts/SPARQLSampleDebugging.java
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From: <lor...@us...> - 2011-12-05 08:54:01
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Revision: 3468
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3468&view=rev
Author: lorenz_b
Date: 2011-12-05 08:53:54 +0000 (Mon, 05 Dec 2011)
Log Message:
-----------
Cleaned up script.
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 2011-12-04 15:50:59 UTC (rev 3467)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-12-05 08:53:54 UTC (rev 3468)
@@ -2,11 +2,12 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
+import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
-import java.io.ObjectOutputStream;
+import java.io.PrintWriter;
import java.io.StringReader;
import java.io.UnsupportedEncodingException;
import java.net.URL;
@@ -19,6 +20,7 @@
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
@@ -46,16 +48,17 @@
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
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.reasoner.InferenceType;
-import org.semanticweb.owlapi.reasoner.OWLReasoner;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
+import com.clarkparsia.owlapi.explanation.io.manchester.ManchesterSyntaxExplanationRenderer;
import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.hp.hpl.jena.query.Query;
@@ -64,8 +67,12 @@
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.rdf.model.InfModel;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.reasoner.Reasoner;
+import com.hp.hpl.jena.reasoner.ValidityReport;
+import com.hp.hpl.jena.reasoner.ValidityReport.Report;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDFS;
@@ -77,7 +84,7 @@
private int sampleSize = 10;
private int depth = 4;
private int nrOfChunks = 1;
- private int maxNrOfExplanations = 20;
+ private int maxNrOfExplanations = 60;
private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class);
@@ -105,7 +112,7 @@
conn = DriverManager.getConnection(url, dbUser, dbPass);
ps = conn.prepareStatement("INSERT INTO debugging_evaluation ("
- + "resource, fragement_size , consistent, nr_of_justifications, justifications, justificationsObject) " + "VALUES(?,?,?,?,?,?)");
+ + "resource, fragment_size , consistent, nr_of_justifications, justifications, justificationsObject) " + "VALUES(?,?,?,?,?,?)");
} catch (ClassNotFoundException e) {
e.printStackTrace();
@@ -219,6 +226,16 @@
}
+ 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);
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return convert(model);
+
+ }
+
private Set<Set<OWLAxiom>> computeExplanations(OWLOntology ontology){
logger.info("Computing explanations...");
long startTime = System.currentTimeMillis();
@@ -238,11 +255,24 @@
return explanations;
}
+ private void computeExplanations(Model model){
+ logger.info("Computing explanations...");
+ Reasoner reasoner = org.mindswap.pellet.jena.PelletReasonerFactory.theInstance().create();
+ InfModel infModel = ModelFactory.createInfModel(reasoner, model);
+ long startTime = System.currentTimeMillis();
+ ValidityReport report = infModel.validate();
+ Iterator<Report> i = report.getReports();
+ while(i.hasNext()){
+ System.out.println(i.next());
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ }
+
private OWLOntology loadReferenceOntology() throws OWLOntologyCreationException{
long startTime = System.currentTimeMillis();
logger.info("Loading reference ontology...");
OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(
- getClass().getClassLoader().getResourceAsStream("dbpedia_0.75.owl"));
+ getClass().getClassLoader().getResourceAsStream("dbpedia_0.75_no_datapropaxioms.owl"));System.out.println(ontology.getLogicalAxiomCount());
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return ontology;
}
@@ -284,69 +314,7 @@
return model;
}
- public void run() throws OWLOntologyCreationException{
- OWLOntology reference = loadReferenceOntology();
-
- Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
- ontologies.add(reference);
- OWLOntology sample;
- OWLOntology merged;
- OWLReasoner reasoner;
- for(int i = 0; i < 100; i++){
- Set<String> resources = extractSampleResourcesChunked(sampleSize);
- sample = extractSampleModule(resources);
-
- ontologies.add(sample);
-
- merged = OWLManager.createOWLOntologyManager().createOntology(IRI.create("http://merged.en"), ontologies);
-
- reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(merged);
- Logger pelletLogger = Logger.getLogger("org.mindswap.pellet");
- pelletLogger.setLevel(Level.OFF);
-
- boolean isConsistent = reasoner.isConsistent();
- logger.info("Consistent: " + isConsistent);
- reasoner.dispose();
- if(!isConsistent){
- Set<Set<OWLAxiom>> explanations = computeExplanations(merged);
- for(Set<OWLAxiom> explanation : explanations){
- System.out.println(explanation);
- }
- break;
-
- }
- ontologies.remove(sample);
-
- }
-
- }
- public void run2() throws OWLOntologyCreationException{
- OWLOntology reference = loadReferenceOntology();
- OWLReasoner reasoner = PelletReasonerFactory.getInstance().createReasoner(reference);
- OWLOntologyManager man = OWLManager.createOWLOntologyManager();
-
- Set<String> resources = extractSampleResourcesChunked(sampleSize);
- for(String resource : resources){
- logger.info("Resource " + resource);
- OWLOntology module = extractSampleModule(Collections.singleton(resource));
- man.addAxioms(reference, module.getLogicalAxioms());
- reasoner.flush();
- logger.info(reasoner.getRootOntology().getLogicalAxiomCount());
- boolean isConsistent = reasoner.isConsistent();
- logger.info("Consistent: " + isConsistent);
- if(!isConsistent){
- Set<Set<OWLAxiom>> explanations = computeExplanations(reference);
- for(Set<OWLAxiom> explanation : explanations){
- logger.info(explanation);
- }
- }
- man.removeAxioms(reference, module.getLogicalAxioms());
-
- }
-
- }
-
private Set<OWLObjectProperty> getUnsatisfiableObjectProperties(PelletReasoner reasoner){
SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>(new Comparator<OWLObjectProperty>() {
@Override
@@ -355,12 +323,29 @@
}
});
OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
+ ManchesterSyntaxExplanationRenderer renderer = new ManchesterSyntaxExplanationRenderer();
+ PrintWriter out = new PrintWriter( System.out );
for(OWLObjectProperty p : reasoner.getRootOntology().getObjectPropertiesInSignature()){
boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectExactCardinality(1, p));
if(!satisfiable){
properties.add(p);
+// PelletExplanation expGen = new PelletExplanation(reasoner);
+// try {
+// Set<Set<OWLAxiom>> explanations = expGen.getUnsatisfiableExplanations(f.getOWLObjectExactCardinality(1, p),1);
+// System.out.println(explanations);
+// renderer.startRendering( out );
+// renderer.render(explanations);
+// renderer.endRendering();
+// } catch (UnsupportedOperationException e) {
+// e.printStackTrace();
+// } catch (OWLException e) {
+// e.printStackTrace();
+// } catch (IOException e) {
+// e.printStackTrace();
+// }
}
}
+
return properties;
}
@@ -378,8 +363,7 @@
}
- public void run3() throws OWLOntologyCreationException{
- OWLOntology reference = loadReferenceOntology();
+ public void run(OWLOntology reference) throws OWLOntologyCreationException{
Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
ontologies.add(reference);
PelletReasoner reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(reference);
@@ -394,7 +378,7 @@
OWLOntology module;
Set<String> resources = extractSampleResourcesChunked(sampleSize);
- for(String resource : resources){
+ for(String resource : resources){resource = "http://dbpedia.org/resource/Leipzig";
logger.info("Resource " + resource);
module = extractSampleModule(Collections.singleton(resource));
ontologies.add(module);
@@ -424,17 +408,64 @@
}
ontologies.remove(module);
reasoner.dispose();
- writeToDB(resource, module.getLogicalAxiomCount(), isConsistent, explanations);
-
+// writeToDB(resource, module.getLogicalAxiomCount(), isConsistent, explanations);
+ break;
}
}
+ public void runOptimized(OWLOntology reference) throws OWLOntologyCreationException{
+ PelletReasoner reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(reference);
+ reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
+ Set<OWLClass> unsatisfiableClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ logger.info("Unsatisfiable classes(" + unsatisfiableClasses.size() + "): " + unsatisfiableClasses);
+ Set<OWLObjectProperty> unsatisfiableObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Unsatisfiable object properties(" + unsatisfiableObjectProperties.size() + "): " + unsatisfiableObjectProperties);
+ Set<OWLDataProperty> unsatisfiableDataProperties = getUnsatisfiableDataProperties(reasoner);
+ logger.info("Unsatisfiable data properties(" + unsatisfiableDataProperties.size() + "): " + unsatisfiableDataProperties);
+ OWLOntology module;
+ reasoner.isConsistent();
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ man.addOntologyChangeListener( reasoner );
+ Set<String> resources = extractSampleResourcesChunked(sampleSize);
+ for(String resource : resources){
+ logger.info("Resource " + resource);resource = "http://dbpedia.org/resource/Leipzig";
+ module = extractSampleModule(Collections.singleton(resource));
+ man.addAxioms(reference, module.getABoxAxioms(true));
+ boolean isConsistent = reasoner.isConsistent();
+ logger.info("Consistent: " + isConsistent);
+ Set<Set<OWLAxiom>> explanations = null;
+ if(!isConsistent){
+ explanations = computeExplanations(reasoner);
+ logger.info("Found " + explanations.size() + " explanations.");
+ Map<AxiomType, Integer> axiomType2CountMap = new HashMap<AxiomType, Integer>();
+ for(Set<OWLAxiom> explanation : explanations){
+ logger.info(explanation);
+ for(OWLAxiom axiom : explanation){
+ Integer cnt = axiomType2CountMap.get(axiom.getAxiomType());
+ if(cnt == null){
+ cnt = Integer.valueOf(0);
+ }
+ cnt = Integer.valueOf(cnt + 1);
+ axiomType2CountMap.put(axiom.getAxiomType(), cnt);
+ }
+ }
+ 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;
+ }
+
+ }
+
public void runPatternBasedDetection(){
Model model = ModelFactory.createDefaultModel();
//read schema
- InputStream in = getClass().getClassLoader().getResourceAsStream("dbpedia_0.75.owl");
+ InputStream in = getClass().getClassLoader().getResourceAsStream("dbpedia_0.75_no_datapropertyaxioms.owl");
model.read(in, null);
//read data
@@ -463,6 +494,41 @@
} finally { qexec.close() ; }
}
+ public void checkFunctionalityViolation(){
+ try {
+ OWLOntology ontology = loadReferenceOntology();
+
+ Set<String> properties = new TreeSet<String>();
+ for(OWLAxiom ax : ontology.getAxioms(AxiomType.FUNCTIONAL_OBJECT_PROPERTY)){
+ OWLObjectProperty prop = ((OWLFunctionalObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
+ properties.add(prop.toStringID());
+ }
+ for(OWLAxiom ax : ontology.getAxioms(AxiomType.FUNCTIONAL_DATA_PROPERTY)){
+ OWLDataProperty prop = ((OWLFunctionalDataPropertyAxiom)ax).getProperty().asOWLDataProperty();
+ properties.add(prop.toStringID());
+ }
+ for(String prop : properties){
+ String query = "SELECT * WHERE {?s <%s> ?o1. ?s <%s> ?o2. FILTER(?o1 != ?o2)} LIMIT 1".replaceAll("%s", prop);
+ ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+ while(rs.hasNext()){
+ QuerySolution qs = rs.next();
+ logger.info("********************************************************");
+ logger.info(prop);
+ logger.info(qs.get("s") + "-->" + qs.get("o1"));
+ logger.info(qs.get("s") + "-->" + qs.get("o2"));
+ }
+
+ }
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+
+ }
+
+ public void removeAxiomsWithNamespace(Set<String> namespaces){
+
+ }
+
/**
* @param args
* @throws Exception
@@ -478,8 +544,28 @@
SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://dbpedia.aksw.org:8902/sparql"),
Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList());
-// new SPARQLSampleDebugging(endpoint).runPatternBasedDetection();
- new SPARQLSampleDebugging(endpoint).run3();
+
+ if(args.length != 1){
+ System.out.println("Usage: SPARQLSampleDebugging <Schema-Ontology>");
+ System.exit(0);
+ }
+
+ OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(IRI.create(new File(args[0]).toURI()));
+
+ SPARQLSampleDebugging debug = new SPARQLSampleDebugging(endpoint);
+
+// debug.checkFunctionalityViolation();
+
+ long s1 = System.currentTimeMillis();
+ debug.runOptimized(ontology);
+ long s2 = System.currentTimeMillis()-s1;
+
+ long s3 = System.currentTimeMillis();
+ debug.run(ontology);
+ long s4 = System.currentTimeMillis()-s3;
+
+ System.out.println(s2);
+ System.out.println(s4);
}
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