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From: <lor...@us...> - 2011-11-11 09:22:14
|
Revision: 3395
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3395&view=rev
Author: lorenz_b
Date: 2011-11-11 09:22:08 +0000 (Fri, 11 Nov 2011)
Log Message:
-----------
Added method to select resources randomly - very slow.
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 2011-11-10 14:58:27 UTC (rev 3394)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-11-11 09:22:08 UTC (rev 3395)
@@ -55,6 +55,28 @@
return resources;
}
+ private Set<String> extractSampleResourcesRandom(int size){
+ logger.info("Extracting " + sampleSize + "sample resources...");
+ long startTime = System.currentTimeMillis();
+ Set<String> resources = new HashSet<String>();
+
+ 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();
+
+ 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);
+ }
+
+
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return resources;
+ }
+
private OWLOntology extractSampleModule(Set<String> resources){
logger.info("Extracting sample module...");
long startTime = System.currentTimeMillis();
@@ -94,8 +116,8 @@
OWLOntology sample;
OWLOntology merged;
OWLReasoner reasoner;
- for(int i = 0; i < 10; i++){
- Set<String> resources = extractSampleResources(i * sampleSize);
+ for(int i = 0; i < 1; i++){
+ Set<String> resources = extractSampleResourcesRandom(sampleSize);
sample = extractSampleModule(resources);
Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
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|
|
From: <lor...@us...> - 2011-11-23 07:25:47
|
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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|
|
From: <lor...@us...> - 2011-11-27 22:14:28
|
Revision: 3438
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3438&view=rev
Author: lorenz_b
Date: 2011-11-27 22:14:21 +0000 (Sun, 27 Nov 2011)
Log Message:
-----------
Added simple method which checks consistency with anti-pattern.
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 2011-11-24 18:11:01 UTC (rev 3437)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-11-27 22:14:21 UTC (rev 3438)
@@ -2,10 +2,13 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
import java.net.URL;
import java.util.Collections;
-import java.util.EnumSet;
+import java.util.HashMap;
import java.util.HashSet;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import org.apache.log4j.ConsoleAppender;
@@ -19,6 +22,7 @@
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
@@ -29,19 +33,26 @@
import com.clarkparsia.owlapi.explanation.PelletExplanation;
import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+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.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.vocabulary.OWL;
public class SPARQLSampleDebugging {
private SparqlEndpoint endpoint;
private ExtractionDBCache cache = new ExtractionDBCache("cache");
- private int sampleSize = 10;
- private int depth = 5;
- private int nrOfChunks = 10;
- private int maxNrOfExplanations = 10;
+ private int sampleSize = 100;
+ private int depth = 4;
+ private int nrOfChunks = 100;
+ private int maxNrOfExplanations = 20;
private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class);
@@ -235,9 +246,22 @@
logger.info("Consistent: " + isConsistent);
if(!isConsistent){
Set<Set<OWLAxiom>> 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());
+ }
}
ontologies.remove(module);
reasoner.dispose();
@@ -246,6 +270,32 @@
}
+ public void runPatternBasedDetection(){
+ Model model = ModelFactory.createDefaultModel();
+
+ //read schema
+ InputStream in = getClass().getClassLoader().getResourceAsStream("dbpedia_0.75.owl");
+ model.read(in, null);
+
+ //read data
+ ModelGenerator modelGen = new ModelGenerator(endpoint, cache);
+ model.add(modelGen.createModel("http://dbpedia.org/resource/Leipzig", Strategy.CHUNKS, depth));
+
+ //query for conflicts
+ String queryString = "SELECT ?s WHERE {?type1 <" + OWL.disjointWith + "> ?type2. ?s a ?type1. ?s a ?type2.} LIMIT 1";
+ Query query = QueryFactory.create(queryString) ;
+ QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
+ try {
+ ResultSet results = qexec.execSelect() ;
+ for ( ; results.hasNext() ; )
+ {
+ QuerySolution soln = results.nextSolution() ;
+ Resource r = soln.getResource("s") ;
+ System.out.println(r.getURI());
+ }
+ } finally { qexec.close() ; }
+ }
+
/**
* @param args
* @throws Exception
@@ -261,7 +311,8 @@
SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://dbpedia.aksw.org:8902/sparql"),
Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList());
- new SPARQLSampleDebugging(endpoint).run3();
+ new SPARQLSampleDebugging(endpoint).runPatternBasedDetection();
+// new SPARQLSampleDebugging(endpoint).run3();
}
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|
|
From: <lor...@us...> - 2011-11-28 09:58:42
|
Revision: 3440
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3440&view=rev
Author: lorenz_b
Date: 2011-11-28 09:58:31 +0000 (Mon, 28 Nov 2011)
Log Message:
-----------
Extended script to write into database.
Added methods to compute unsatisfiable object and data properties.
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 2011-11-28 08:24:14 UTC (rev 3439)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-11-28 09:58:31 UTC (rev 3440)
@@ -2,14 +2,27 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
import java.io.InputStream;
+import java.io.ObjectOutputStream;
import java.net.URL;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.SQLException;
+import java.sql.Types;
import java.util.Collections;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+import java.util.prefs.Preferences;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
@@ -21,13 +34,20 @@
import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+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.reasoner.InferenceType;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
@@ -41,8 +61,8 @@
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDFS;
public class SPARQLSampleDebugging {
@@ -56,12 +76,69 @@
private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class);
+ private Connection conn;
+ private PreparedStatement ps;
+
static {PelletExplanation.setup();}
public SPARQLSampleDebugging(SparqlEndpoint endpoint) {
this.endpoint = endpoint;
+ initDBConnection();
}
+ private void initDBConnection() {
+ try {
+ String iniFile = "db_settings.ini";
+ Preferences prefs = new IniPreferences(new FileReader(iniFile));
+ String dbServer = prefs.node("database").get("server", null);
+ String dbName = prefs.node("database").get("name", null);
+ String dbUser = prefs.node("database").get("user", null);
+ String dbPass = prefs.node("database").get("pass", null);
+
+ Class.forName("com.mysql.jdbc.Driver");
+ String url = "jdbc:mysql://" + dbServer + "/" + dbName;
+ conn = DriverManager.getConnection(url, dbUser, dbPass);
+
+ ps = conn.prepareStatement("INSERT INTO debugging_evaluation ("
+ + "resource, fragement_size , consistent, nr_of_justifications, justifications, justificationsObject) " + "VALUES(?,?,?,?,?,?)");
+
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ } catch (InvalidFileFormatException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void writeToDB(String resource, int fragementSize, boolean consistent, Set<Set<OWLAxiom>> explanations) {
+ try {
+ ps.setString(1, resource);
+ ps.setInt(2, fragementSize);
+ ps.setBoolean(3, consistent);
+ if(explanations == null){
+ ps.setInt(4, 0);
+ ps.setNull(5, Types.NULL);
+ ps.setObject(6, Types.NULL);
+ } else {
+ ps.setInt(4, explanations.size());
+ ps.setString(5, explanations.toString());
+ ps.setObject(6, explanations);
+ }
+
+
+ ps.executeUpdate();
+ } catch (SQLException e) {
+ logger.error("Error while writing to DB.", e);
+ e.printStackTrace();
+ }
+
+ }
+
private Set<String> extractSampleResourcesChunked(int size){
logger.info("Extracting " + sampleSize + " sample resources...");
long startTime = System.currentTimeMillis();
@@ -227,11 +304,49 @@
}
+ private Set<OWLObjectProperty> getUnsatisfiableObjectProperties(PelletReasoner reasoner){
+ SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>(new Comparator<OWLObjectProperty>() {
+ @Override
+ public int compare(OWLObjectProperty o1, OWLObjectProperty o2) {
+ return o1.toString().compareTo(o2.toString());
+ }
+ });
+ OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
+ for(OWLObjectProperty p : reasoner.getRootOntology().getObjectPropertiesInSignature()){
+ boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectExactCardinality(1, p));
+ if(!satisfiable){
+ properties.add(p);
+ }
+ }
+ return properties;
+
+ }
+
+ private Set<OWLDataProperty> getUnsatisfiableDataProperties(PelletReasoner reasoner){
+ SortedSet<OWLDataProperty> properties = new TreeSet<OWLDataProperty>();
+ OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
+ for(OWLDataProperty p : reasoner.getRootOntology().getDataPropertiesInSignature()){
+ boolean satisfiable = reasoner.isSatisfiable(f.getOWLDataExactCardinality(1, p));
+ if(!satisfiable){
+ properties.add(p);
+ }
+ }
+ return properties;
+
+ }
+
public void run3() throws OWLOntologyCreationException{
OWLOntology reference = loadReferenceOntology();
Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
ontologies.add(reference);
- PelletReasoner reasoner;
+ 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 merged;
OWLOntology module;
@@ -244,8 +359,9 @@
reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(merged);
boolean isConsistent = reasoner.isConsistent();
logger.info("Consistent: " + isConsistent);
+ Set<Set<OWLAxiom>> explanations = null;
if(!isConsistent){
- Set<Set<OWLAxiom>> explanations = computeExplanations(reasoner);
+ explanations = computeExplanations(reasoner);
logger.info("Found " + explanations.size() + " explanations.");
Map<AxiomType, Integer> axiomType2CountMap = new HashMap<AxiomType, Integer>();
for(Set<OWLAxiom> explanation : explanations){
@@ -265,6 +381,7 @@
}
ontologies.remove(module);
reasoner.dispose();
+ writeToDB(resource, module.getLogicalAxiomCount(), isConsistent, explanations);
}
@@ -283,6 +400,11 @@
//query for conflicts
String queryString = "SELECT ?s WHERE {?type1 <" + OWL.disjointWith + "> ?type2. ?s a ?type1. ?s a ?type2.} LIMIT 1";
+ queryString = "SELECT ?s ?p ?type1 ?type2 WHERE {" +
+ "?type1 <" + OWL.disjointWith + "> ?type2." +
+ "?p <" + RDFS.domain + "> ?type1. ?p <" + RDFS.domain + "> ?type2." +
+ " ?s ?p ?o1." +
+ " ?s ?p ?o2.} LIMIT 10";
Query query = QueryFactory.create(queryString) ;
QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
try {
@@ -290,8 +412,10 @@
for ( ; results.hasNext() ; )
{
QuerySolution soln = results.nextSolution() ;
- Resource r = soln.getResource("s") ;
- System.out.println(r.getURI());
+ for(String var : results.getResultVars()){
+ System.out.print(soln.get(var) + "|");
+ }
+ System.out.println();
}
} finally { qexec.close() ; }
}
@@ -312,7 +436,7 @@
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();
+ new SPARQLSampleDebugging(endpoint).run3();
}
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|
|
From: <lor...@us...> - 2011-11-28 10:43:16
|
Revision: 3442
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3442&view=rev
Author: lorenz_b
Date: 2011-11-28 10:43:10 +0000 (Mon, 28 Nov 2011)
Log Message:
-----------
Changed database writing because OWLAxioms are not serializable.
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 2011-11-28 10:01:07 UTC (rev 3441)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-11-28 10:43:10 UTC (rev 3442)
@@ -7,6 +7,8 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.ObjectOutputStream;
+import java.io.StringReader;
+import java.io.UnsupportedEncodingException;
import java.net.URL;
import java.sql.Connection;
import java.sql.DriverManager;
@@ -47,6 +49,7 @@
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 org.semanticweb.owlapi.reasoner.OWLReasoner;
@@ -127,7 +130,22 @@
} else {
ps.setInt(4, explanations.size());
ps.setString(5, explanations.toString());
- ps.setObject(6, explanations);
+ try {
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology ont = OWLManager.createOWLOntologyManager().createOntology();
+ for(Set<OWLAxiom> axioms : explanations){
+ man.addAxioms(ont, axioms);
+ }
+ Model model = convert(ont);
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ model.write(baos, "N-TRIPLE");
+ String modelStr = baos.toString("UTF-8");
+ ps.setClob(6, new StringReader(modelStr));
+ } catch (UnsupportedEncodingException e) {
+ logger.error("ERROR", e);
+ } catch (OWLOntologyCreationException e) {
+ logger.error("ERROR", e);
+ }
}
@@ -241,6 +259,29 @@
return retOnt;
}
+ private Model convert(OWLOntology ontology) {
+ Model model = ModelFactory.createDefaultModel();
+ ByteArrayInputStream bais = null;
+ try {
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ man.saveOntology(ontology, baos);
+ bais = new ByteArrayInputStream(baos.toByteArray());
+ model.read(bais, null);
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } finally {
+ try {
+ if(bais != null){
+ bais.close();
+ }
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ return model;
+ }
+
public void run() throws OWLOntologyCreationException{
OWLOntology reference = loadReferenceOntology();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-11-28 11:22:09
|
Revision: 3443
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3443&view=rev
Author: lorenz_b
Date: 2011-11-28 11:22:01 +0000 (Mon, 28 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 2011-11-28 10:43:10 UTC (rev 3442)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-11-28 11:22:01 UTC (rev 3443)
@@ -39,6 +39,7 @@
import org.ini4j.IniPreferences;
import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
@@ -48,6 +49,7 @@
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;
@@ -72,9 +74,9 @@
private SparqlEndpoint endpoint;
private ExtractionDBCache cache = new ExtractionDBCache("cache");
- private int sampleSize = 100;
+ private int sampleSize = 10;
private int depth = 4;
- private int nrOfChunks = 100;
+ private int nrOfChunks = 1;
private int maxNrOfExplanations = 20;
private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class);
@@ -265,7 +267,7 @@
try {
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
ByteArrayOutputStream baos = new ByteArrayOutputStream();
- man.saveOntology(ontology, baos);
+ man.saveOntology(ontology, new RDFXMLOntologyFormat(), baos);
bais = new ByteArrayInputStream(baos.toByteArray());
model.read(bais, null);
} catch (OWLOntologyStorageException e) {
@@ -476,7 +478,7 @@
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).runPatternBasedDetection();
new SPARQLSampleDebugging(endpoint).run3();
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-12-05 08:54:01
|
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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|
|
From: <lor...@us...> - 2011-12-05 15:20:22
|
Revision: 3473
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3473&view=rev
Author: lorenz_b
Date: 2011-12-05 15:20:13 +0000 (Mon, 05 Dec 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 2011-12-05 13:08:51 UTC (rev 3472)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2011-12-05 15:20:13 UTC (rev 3473)
@@ -35,6 +35,7 @@
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.ExtractionDBCache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
@@ -44,12 +45,14 @@
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLAxiom;
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.OWLIrreflexiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -82,12 +85,16 @@
private ExtractionDBCache cache = new ExtractionDBCache("cache");
private int sampleSize = 10;
- private int depth = 4;
+ private int depth = 2;
private int nrOfChunks = 1;
- private int maxNrOfExplanations = 60;
+ private int maxNrOfExplanations = 20;
private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class);
+ private Logger functionalLogger = Logger.getLogger("functionality");
+ private Logger asymmetricLogger = Logger.getLogger("asymmetry");
+ private Logger irreflexiveLogger = Logger.getLogger("irreflexivity");
+
private Connection conn;
private PreparedStatement ps;
@@ -429,8 +436,8 @@
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));
+ 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))));
man.addAxioms(reference, module.getABoxAxioms(true));
boolean isConsistent = reasoner.isConsistent();
logger.info("Consistent: " + isConsistent);
@@ -512,10 +519,10 @@
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"));
+ functionalLogger.info("********************************************************");
+ functionalLogger.info(prop);
+ functionalLogger.info(qs.get("s") + "-->" + qs.get("o1"));
+ functionalLogger.info(qs.get("s") + "-->" + qs.get("o2"));
}
}
@@ -525,6 +532,57 @@
}
+ public void checkIrreflexivityViolation(){
+ try {
+ OWLOntology ontology = loadReferenceOntology();
+
+ Set<String> properties = new TreeSet<String>();
+ for(OWLAxiom ax : ontology.getAxioms(AxiomType.IRREFLEXIVE_OBJECT_PROPERTY)){
+ OWLObjectProperty prop = ((OWLIrreflexiveObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
+ properties.add(prop.toStringID());
+ }
+ for(String prop : properties){
+ String query = "SELECT * WHERE {?s <%s> ?s.} LIMIT 1".replaceAll("%s", prop);
+ ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+ while(rs.hasNext()){
+ QuerySolution qs = rs.next();
+ irreflexiveLogger.info("********************************************************");
+ irreflexiveLogger.info(prop);
+ irreflexiveLogger.info(qs.get("s"));
+ }
+
+ }
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+
+ }
+
+ public void checkAsymmetryViolation(){
+ try {
+ OWLOntology ontology = loadReferenceOntology();
+
+ Set<String> properties = new TreeSet<String>();
+ for(OWLAxiom ax : ontology.getAxioms(AxiomType.ASYMMETRIC_OBJECT_PROPERTY)){
+ OWLObjectProperty prop = ((OWLAsymmetricObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
+ properties.add(prop.toStringID());
+ }
+ for(String prop : properties){
+ String query = "SELECT * WHERE {?s <%s> ?o.?o <%s> ?s.FILTER(?s != ?o)} LIMIT 1".replaceAll("%s", prop);
+ ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+ while(rs.hasNext()){
+ QuerySolution qs = rs.next();
+ asymmetricLogger.info("********************************************************");
+ asymmetricLogger.info(prop);
+ asymmetricLogger.info(qs.get("s") + "<-->" + qs.get("o"));
+ }
+
+ }
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ }
+
public void removeAxiomsWithNamespace(Set<String> namespaces){
}
@@ -538,6 +596,9 @@
Logger.getRootLogger().removeAllAppenders();
Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
Logger.getRootLogger().addAppender(new FileAppender(new SimpleLayout(), "log/debug.log"));
+ Logger.getLogger("functionality").addAppender(new FileAppender(new SimpleLayout(), "log/functionality_violations.log"));
+ Logger.getLogger("irreflexivity").addAppender(new FileAppender(new SimpleLayout(), "log/irreflexivity_violations.log"));
+ Logger.getLogger("asymmetry").addAppender(new FileAppender(new SimpleLayout(), "log/asymmetry_violations.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);
@@ -554,7 +615,9 @@
SPARQLSampleDebugging debug = new SPARQLSampleDebugging(endpoint);
-// debug.checkFunctionalityViolation();
+ debug.checkFunctionalityViolation();
+ debug.checkAsymmetryViolation();
+ debug.checkIrreflexivityViolation();
long s1 = System.currentTimeMillis();
debug.runOptimized(ontology);
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|
|
From: <lor...@us...> - 2012-01-27 11:51:34
|
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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From: <lor...@us...> - 2012-01-27 11:55:52
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Revision: 3559
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3559&view=rev
Author: lorenz_b
Date: 2012-01-27 11:55:41 +0000 (Fri, 27 Jan 2012)
Log Message:
-----------
Option to load bzip2 compressed.
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 2012-01-27 11:51:28 UTC (rev 3558)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-01-27 11:55:41 UTC (rev 3559)
@@ -714,10 +714,11 @@
}
InputStream is = new BufferedInputStream(new FileInputStream(args[0]));
- CompressorInputStream in = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ if(args[0].endsWith("bz2")){
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ }
+ OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(is);
- OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(in);
-
SPARQLSampleDebugging debug = new SPARQLSampleDebugging(endpoint);
// debug.checkFunctionalityViolation(ontology);
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From: <lor...@us...> - 2012-02-07 21:43:27
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Revision: 3575
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3575&view=rev
Author: lorenz_b
Date: 2012-02-07 21:43:20 +0000 (Tue, 07 Feb 2012)
Log Message:
-----------
Added method to check if axiom is already entailed by DBpedia ontology.
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 2012-02-07 09:53:33 UTC (rev 3574)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-02-07 21:43:20 UTC (rev 3575)
@@ -12,6 +12,7 @@
import java.io.PrintWriter;
import java.io.StringReader;
import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
import java.net.URL;
import java.sql.Connection;
import java.sql.DriverManager;
@@ -30,6 +31,7 @@
import java.util.TreeSet;
import java.util.prefs.Preferences;
+import org.apache.commons.compress.compressors.CompressorException;
import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
@@ -65,7 +67,13 @@
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.reasoner.ClassExpressionNotInProfileException;
+import org.semanticweb.owlapi.reasoner.FreshEntitiesException;
+import org.semanticweb.owlapi.reasoner.InconsistentOntologyException;
import org.semanticweb.owlapi.reasoner.InferenceType;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.ReasonerInterruptedException;
+import org.semanticweb.owlapi.reasoner.TimeOutException;
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
@@ -109,11 +117,18 @@
private OWLDataFactory factory = new OWLDataFactoryImpl();
+ private OWLOntology dbpediaOntology;
+ private OWLReasoner dbpediaReasoner;
+ private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+
static {PelletExplanation.setup();}
public SPARQLSampleDebugging(SparqlEndpoint endpoint) {
this.endpoint = endpoint;
initDBConnection();
+ dbpediaOntology = loadDBpediaOntology();
+ dbpediaReasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(dbpediaOntology);
+ dbpediaReasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
}
private void initDBConnection() {
@@ -302,6 +317,30 @@
return ontology;
}
+ private OWLOntology loadDBpediaOntology() {
+ long startTime = System.currentTimeMillis();
+ logger.info("Loading DBpedia reference ontology...");
+ OWLOntology ontology = null;
+ try {
+ URL dbpediaURL = new URL("http://downloads.dbpedia.org/3.7/dbpedia_3.7.owl.bz2");
+ InputStream is = dbpediaURL.openStream();
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(is);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (CompressorException e) {
+ e.printStackTrace();
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return ontology;
+ }
+
+
+
private OWLOntology convert(Model model) {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
model.write(baos, "N-TRIPLE");
@@ -470,16 +509,13 @@
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>();
ManchesterSyntaxExplanationRenderer renderer = new ManchesterSyntaxExplanationRenderer();
try {
FileWriter out = new FileWriter( "log/justifications.txt" );
renderer.startRendering(out );
for(Set<OWLAxiom> explanation : explanations){
- logger.info(explanation);
+ logger.info(explanation + "\n");
out.flush();
try {
renderer.render( Collections.singleton(explanation) );
@@ -702,6 +738,42 @@
return properties;
}
+ private boolean isLearnedAxiom(OWLAxiom axiom){
+ return !dbpediaReasoner.isEntailed(axiom);
+ }
+
+ private boolean containsUnsatisfiableObjectProperty(Set<OWLAxiom> justification){
+ boolean value = false;
+
+ OWLReasoner reasoner = null;
+ try {
+ OWLOntology ontology = manager.createOntology(justification);
+ manager.removeAxioms(ontology, ontology.getABoxAxioms(true));
+ reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(ontology);
+ for(OWLObjectProperty p : ontology.getObjectPropertiesInSignature()){
+ boolean satisfiable = reasoner.isSatisfiable(factory.getOWLObjectExactCardinality(1, p));
+ if(!satisfiable){
+ value = true;
+ break;
+ }
+ }
+ } catch (TimeOutException e) {
+ e.printStackTrace();
+ } catch (ClassExpressionNotInProfileException e) {
+ e.printStackTrace();
+ } catch (FreshEntitiesException e) {
+ e.printStackTrace();
+ } catch (InconsistentOntologyException e) {
+ e.printStackTrace();
+ } catch (ReasonerInterruptedException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ reasoner.dispose();
+ return value;
+ }
+
public void removeAxiomsWithNamespace(Set<String> namespaces){
}
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From: <lor...@us...> - 2012-04-28 14:41:55
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Revision: 3661
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3661&view=rev
Author: lorenz_b
Date: 2012-04-28 14:41:49 +0000 (Sat, 28 Apr 2012)
Log Message:
-----------
Removed unused method.
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 2012-04-28 14:02:44 UTC (rev 3660)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-04-28 14:41:49 UTC (rev 3661)
@@ -24,7 +24,6 @@
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.Random;
@@ -88,12 +87,8 @@
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;
@@ -304,19 +299,6 @@
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...");
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From: <lor...@us...> - 2012-07-05 07:24:36
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Revision: 3772
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3772&view=rev
Author: lorenz_b
Date: 2012-07-05 07:24:27 +0000 (Thu, 05 Jul 2012)
Log Message:
-----------
Removed old class.
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 2012-07-04 15:42:53 UTC (rev 3771)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-07-05 07:24:27 UTC (rev 3772)
@@ -39,8 +39,8 @@
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.common.index.ModelGenerator;
+import org.dllearner.common.index.ModelGenerator.Strategy;
import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
import org.dllearner.kb.sparql.ExtractionDBCache;
@@ -258,10 +258,10 @@
private OWLOntology extractSampleModule(Set<String> resources){
logger.info("Extracting sample module...");
long startTime = System.currentTimeMillis();
- ModelGenerator modelGen = new ModelGenerator(endpoint, cache);
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(endpoint, cache);
Model model = ModelFactory.createDefaultModel();
for(String resource : resources){
- model.add(modelGen.createModel(resource, Strategy.CHUNKS, depth));
+ model.add(cbdGen.getConciseBoundedDescription(resource, depth));
}
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return convert(model);
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