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[DL-Learner SVN] SF.net SVN: dl-learner:[3429] trunk/scripts/src/main/java/org/dllearner/ scripts/SPARQLSampleDebugging.java
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From: <lor...@us...> - 2011-11-23 07:25:47
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Revision: 3429
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3429&view=rev
Author: lorenz_b
Date: 2011-11-23 07:25:39 +0000 (Wed, 23 Nov 2011)
Log Message:
-----------
Continued 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 2011-11-22 21:19:51 UTC (rev 3428)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-11-23 07:25:39 UTC (rev 3429)
@@ -4,11 +4,15 @@
import java.io.ByteArrayOutputStream;
import java.net.URL;
import java.util.Collections;
+import java.util.EnumSet;
import java.util.HashSet;
import java.util.Set;
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
import org.dllearner.algorithm.qtl.util.ModelGenerator;
import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy;
import org.dllearner.kb.sparql.ExtractionDBCache;
@@ -16,11 +20,14 @@
import org.dllearner.kb.sparql.SparqlQuery;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import com.clarkparsia.owlapi.explanation.PelletExplanation;
+import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Model;
@@ -31,32 +38,47 @@
private SparqlEndpoint endpoint;
private ExtractionDBCache cache = new ExtractionDBCache("cache");
- private int sampleSize = 1000;
- private int depth = 3;
+ private int sampleSize = 10;
+ private int depth = 5;
+ private int nrOfChunks = 10;
+ private int maxNrOfExplanations = 10;
private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class);
+ static {PelletExplanation.setup();}
+
public SPARQLSampleDebugging(SparqlEndpoint endpoint) {
this.endpoint = endpoint;
}
- private Set<String> extractSampleResources(int offset){
- logger.info("Extracting " + sampleSize + "sample resources...");
+ private Set<String> extractSampleResourcesChunked(int size){
+ logger.info("Extracting " + sampleSize + " sample resources...");
long startTime = System.currentTimeMillis();
Set<String> resources = new HashSet<String>();
- String query = String.format("SELECT DISTINCT ?s WHERE {?s a ?type} LIMIT %d OFFSET %d", sampleSize, offset);
+ String query = "SELECT COUNT(DISTINCT ?s) WHERE {?s a ?type}";
ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+ int max = rs.next().getLiteral(rs.getResultVars().get(0)).getInt();
- while(rs.hasNext()){
- resources.add(rs.next().getResource("s").getURI());
+ for(int i = 0; i < nrOfChunks; i++){
+ int offset = (int)(Math.random() * max);
+ offset = Math.min(offset, offset-(size/nrOfChunks));
+
+ query = String.format("SELECT DISTINCT ?s WHERE {?s a ?type} LIMIT %d OFFSET %d", (size/nrOfChunks), offset);
+ logger.info(query);
+ rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+
+ while(rs.hasNext()){
+ resources.add(rs.next().getResource("s").getURI());
+ }
}
+
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return resources;
}
- private Set<String> extractSampleResourcesRandom(int size){
- logger.info("Extracting " + sampleSize + "sample resources...");
+ private Set<String> extractSampleResourcesSingle(int size){
+ logger.info("Extracting " + sampleSize + " sample resources...");
long startTime = System.currentTimeMillis();
Set<String> resources = new HashSet<String>();
@@ -67,9 +89,8 @@
for(int i = 0; i < size; i++){
int random = (int)(Math.random() * max);
query = String.format("SELECT DISTINCT ?s WHERE {?s a ?type} LIMIT 1 OFFSET %d", random);
- System.out.println(random);
rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
- resources.add(rs.next().getResource("s").getURI());System.out.println(resources);
+ resources.add(rs.next().getResource("s").getURI());
}
@@ -90,9 +111,31 @@
}
+ private Set<Set<OWLAxiom>> computeExplanations(OWLOntology ontology){
+ logger.info("Computing explanations...");
+ long startTime = System.currentTimeMillis();
+ boolean useGlassBox = true;
+ PelletExplanation expGen = new PelletExplanation(ontology, useGlassBox);
+ Set<Set<OWLAxiom>> explanations = expGen.getInconsistencyExplanations(maxNrOfExplanations);
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return explanations;
+ }
+
+ private Set<Set<OWLAxiom>> computeExplanations(PelletReasoner reasoner){
+ logger.info("Computing explanations...");
+ long startTime = System.currentTimeMillis();
+ PelletExplanation expGen = new PelletExplanation(reasoner);
+ Set<Set<OWLAxiom>> explanations = expGen.getInconsistencyExplanations(maxNrOfExplanations);
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return explanations;
+ }
+
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"));
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return ontology;
}
@@ -113,38 +156,112 @@
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 < 1; i++){
- Set<String> resources = extractSampleResourcesRandom(sampleSize);
+ for(int i = 0; i < 100; i++){
+ Set<String> resources = extractSampleResourcesChunked(sampleSize);
sample = extractSampleModule(resources);
- Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
ontologies.add(sample);
- ontologies.add(reference);
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);
- System.out.println(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());
+
+ }
+
+ }
+
+ public void run3() throws OWLOntologyCreationException{
+ OWLOntology reference = loadReferenceOntology();
+ Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
+ ontologies.add(reference);
+ PelletReasoner reasoner;
+ OWLOntology merged;
+ OWLOntology module;
+
+ Set<String> resources = extractSampleResourcesChunked(sampleSize);
+ for(String resource : resources){
+ logger.info("Resource " + resource);
+ module = extractSampleModule(Collections.singleton(resource));
+ ontologies.add(module);
+ merged = OWLManager.createOWLOntologyManager().createOntology(IRI.create("http://merged.en"), ontologies);
+ reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(merged);
+ boolean isConsistent = reasoner.isConsistent();
+ logger.info("Consistent: " + isConsistent);
+ if(!isConsistent){
+ Set<Set<OWLAxiom>> explanations = computeExplanations(reasoner);
+ for(Set<OWLAxiom> explanation : explanations){
+ logger.info(explanation);
+ }
+ }
+ ontologies.remove(module);
+ reasoner.dispose();
+
+ }
+
+ }
+
/**
* @param args
* @throws Exception
*/
public static void main(String[] args) throws Exception {
Logger.getRootLogger().setLevel(Level.INFO);
+ Logger.getRootLogger().removeAllAppenders();
+ Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
+ Logger.getRootLogger().addAppender(new FileAppender(new SimpleLayout(), "log/debug.log"));
Logger.getLogger(SPARQLSampleDebugging.class).setLevel(Level.INFO);
+ java.util.logging.Logger pelletLogger = java.util.logging.Logger.getLogger("com.clarkparsia.pellet");
+ pelletLogger.setLevel(java.util.logging.Level.OFF);
+
SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://dbpedia.aksw.org:8902/sparql"),
Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList());
- new SPARQLSampleDebugging(endpoint).run();
+ new SPARQLSampleDebugging(endpoint).run3();
}
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