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[DL-Learner SVN] SF.net SVN: dl-learner:[3915] trunk/components-core/src/main/java/org/ dllearner
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From: <lor...@us...> - 2013-04-10 10:06:41
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Revision: 3915
http://sourceforge.net/p/dl-learner/code/3915
Author: lorenz_b
Date: 2013-04-10 10:06:38 +0000 (Wed, 10 Apr 2013)
Log Message:
-----------
Fixed bug.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java
trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/LabelShortFormProvider.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -58,7 +58,7 @@
public class OWLAxiomRenamer implements OWLAxiomVisitor {
private OWLDataFactory df;
- private OWLClassExpressionRenamer renamer;
+ private OWLClassExpressionRenamer expressionRenamer;
private OWLAxiom renamedAxiom;
public OWLAxiomRenamer(OWLDataFactory df) {
@@ -67,7 +67,7 @@
public OWLAxiom rename(OWLAxiom axiom){
Map<OWLEntity, OWLEntity> renaming = new HashMap<OWLEntity, OWLEntity>();
- renamer = new OWLClassExpressionRenamer(df, renaming);
+ expressionRenamer = new OWLClassExpressionRenamer(df, renaming);
axiom.accept(this);
return renamedAxiom;
}
@@ -75,9 +75,9 @@
@Override
public void visit(OWLSubClassOfAxiom axiom) {
OWLClassExpression subClass = axiom.getSubClass();
- subClass = renamer.rename(subClass);
+ subClass = expressionRenamer.rename(subClass);
OWLClassExpression superClass = axiom.getSuperClass();
- superClass = renamer.rename(superClass);
+ superClass = expressionRenamer.rename(superClass);
renamedAxiom = df.getOWLSubClassOfAxiom(subClass, superClass);
}
@@ -120,18 +120,18 @@
@Override
public void visit(OWLDataPropertyDomainAxiom axiom) {
OWLDataPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
OWLClassExpression domain = axiom.getDomain();
- domain = renamer.rename(domain);
+ domain = expressionRenamer.rename(domain);
renamedAxiom = df.getOWLDataPropertyDomainAxiom(property, domain);
}
@Override
public void visit(OWLObjectPropertyDomainAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
OWLClassExpression domain = axiom.getDomain();
- domain = renamer.rename(domain);
+ domain = expressionRenamer.rename(domain);
renamedAxiom = df.getOWLObjectPropertyDomainAxiom(property, domain);
}
@@ -158,9 +158,9 @@
@Override
public void visit(OWLObjectPropertyRangeAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
OWLClassExpression range = axiom.getRange();
- range = renamer.rename(range);
+ range = expressionRenamer.rename(range);
renamedAxiom = df.getOWLObjectPropertyDomainAxiom(property, range);
}
@@ -171,7 +171,7 @@
@Override
public void visit(OWLFunctionalObjectPropertyAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLFunctionalObjectPropertyAxiom(property);
}
@@ -186,23 +186,23 @@
@Override
public void visit(OWLSymmetricObjectPropertyAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLSymmetricObjectPropertyAxiom(property);
}
@Override
public void visit(OWLDataPropertyRangeAxiom axiom) {
OWLDataPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
OWLDataRange range = axiom.getRange();
- range = renamer.rename(range);
+ range = expressionRenamer.rename(range);
renamedAxiom = df.getOWLDataPropertyRangeAxiom(property, range);
}
@Override
public void visit(OWLFunctionalDataPropertyAxiom axiom) {
OWLDataPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLFunctionalDataPropertyAxiom(property);
}
@@ -213,9 +213,9 @@
@Override
public void visit(OWLClassAssertionAxiom axiom) {
OWLClassExpression classExpression = axiom.getClassExpression();
- classExpression = renamer.rename(classExpression);
+ classExpression = expressionRenamer.rename(classExpression);
OWLIndividual individual = axiom.getIndividual();
- individual = renamer.rename(individual);
+ individual = expressionRenamer.rename(individual);
renamedAxiom = df.getOWLClassAssertionAxiom(classExpression, individual);
}
@@ -224,7 +224,7 @@
List<OWLClassExpression> classExpressions = axiom.getClassExpressionsAsList();
List<OWLClassExpression> renamedClassExpressions = new ArrayList<OWLClassExpression>();
for (OWLClassExpression expr : classExpressions) {
- renamedClassExpressions.add(renamer.rename(expr));
+ renamedClassExpressions.add(expressionRenamer.rename(expr));
}
renamedAxiom = df.getOWLEquivalentClassesAxiom(new TreeSet<OWLClassExpression>(renamedClassExpressions));
}
@@ -236,14 +236,14 @@
@Override
public void visit(OWLTransitiveObjectPropertyAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLTransitiveObjectPropertyAxiom(property);
}
@Override
public void visit(OWLIrreflexiveObjectPropertyAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLIrreflexiveObjectPropertyAxiom(property);
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -20,6 +20,7 @@
package org.dllearner.algorithms.properties;
import java.util.ArrayList;
+import java.util.List;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
import org.dllearner.core.ComponentAnn;
@@ -29,6 +30,8 @@
import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.FunctionalDatatypePropertyAxiom;
import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.learningproblems.AxiomScore;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -109,7 +112,7 @@
all = qs.getLiteral("all").getInt();
}
// get number of instances of s with <s p o> <s p o1> where o != o1
- query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o1)} }";
+ query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o2)} }";
query = query.replace("%s", propertyToDescribe.getURI().toString());
rs = executeSelectQuery(query, workingModel);
int functional = 1;
@@ -140,7 +143,7 @@
if (numberOfSubjects > 0) {
int functional = 0;
- String query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o1)} }";
+ String query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o2)} }";
query = query.replace("%s", propertyToDescribe.getURI().toString());
ResultSet rs = executeSelectQuery(query);
if (rs.hasNext()) {
@@ -153,4 +156,23 @@
declaredAsFunctional));
}
}
+
+ public static void main(String[] args) throws Exception {
+ FunctionalDataPropertyAxiomLearner l = new FunctionalDataPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia()));
+ l.setPropertyToDescribe(new DatatypeProperty("http://dbpedia.org/ontology/birthDate"));
+ l.setMaxExecutionTimeInSeconds(10);
+ l.setForceSPARQL_1_0_Mode(true);
+ l.init();
+ l.start();
+ List<EvaluatedAxiom> axioms = l.getCurrentlyBestEvaluatedAxioms(5);
+ System.out.println(axioms);
+
+ for(EvaluatedAxiom axiom : axioms){
+ printSubset(l.getPositiveExamples(axiom), 10);
+ printSubset(l.getNegativeExamples(axiom), 10);
+ l.explainScore(axiom);
+ System.out.println(((AxiomScore)axiom.getScore()).getTotalNrOfExamples());
+ System.out.println(((AxiomScore)axiom.getScore()).getNrOfPositiveExamples());
+ }
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -198,22 +198,24 @@
org.apache.log4j.Logger.getRootLogger().setLevel(Level.INFO);
org.apache.log4j.Logger.getLogger(DataPropertyDomainAxiomLearner.class).setLevel(Level.INFO);
- SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
+ SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia());
+
SPARQLReasoner reasoner = new SPARQLReasoner(ks);
reasoner.prepareSubsumptionHierarchy();
ObjectPropertyDomainAxiomLearner l = new ObjectPropertyDomainAxiomLearner(ks);
l.setReasoner(reasoner);
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/anthem"));
- l.setMaxExecutionTimeInSeconds(40);
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/birthPlace"));
+ l.setMaxExecutionTimeInSeconds(10);
// l.addFilterNamespace("http://dbpedia.org/ontology/");
// l.setReturnOnlyNewAxioms(true);
+ l.setForceSPARQL_1_0_Mode(true);
l.init();
l.start();
- System.out.println(l.getCurrentlyBestEvaluatedAxioms());
+ System.out.println(l.getCurrentlyBestEvaluatedAxioms(0.7));
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -307,7 +307,7 @@
}
protected ResultSet executeSelectQuery(String query) {
- logger.debug("Sending query\n{} ...", query);
+ logger.info("Sending query\n{} ...", query);
if(ks.isRemote()){
SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -27,10 +27,11 @@
import java.util.Map;
import java.util.concurrent.TimeUnit;
-import org.openjena.atlas.io.IO;
-import org.openjena.riot.Lang;
-import org.openjena.riot.RiotReader;
-import org.openjena.riot.WebContent;
+import org.apache.jena.atlas.io.IO;
+import org.apache.jena.riot.Lang;
+import org.apache.jena.riot.RDFLanguages;
+import org.apache.jena.riot.RiotReader;
+import org.apache.jena.riot.WebContent;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -267,7 +268,7 @@
private Model execModel(Model model)
{
HttpQuery httpQuery = makeHttpQuery() ;
- httpQuery.setAccept(WebContent.contentTypeNTriples) ;
+ httpQuery.setAccept(WebContent.contentTypeNTriplesAlt) ;
InputStream in = httpQuery.exec() ;
//Don't assume the endpoint actually gives back the content type we asked for
@@ -282,7 +283,7 @@
//Try to select language appropriately here based on the model content type
Lang lang = WebContent.contentTypeToLang(actualContentType);
- if (!lang.isTriples()) throw new QueryException("Endpoint returned Content Type: " + actualContentType + " which is not a valid RDF Graph syntax");
+ if (! RDFLanguages.isTriples(lang)) throw new QueryException("Endpoint returned Content Type: " + actualContentType + " which is not a valid RDF Graph syntax");
model.read(in, null, "N-TRIPLES") ;
return model ;
@@ -306,7 +307,7 @@
//Try to select language appropriately here based on the model content type
Lang lang = WebContent.contentTypeToLang(actualContentType);
- if (!lang.isTriples()) throw new QueryException("Endpoint returned Content Type: " + actualContentType + " which is not a valid RDF Graph syntax");
+ if (! RDFLanguages.isTriples(lang)) throw new QueryException("Endpoint returned Content Type: " + actualContentType + " which is not a valid RDF Graph syntax");
return RiotReader.createIteratorTriples(in, lang, null);
}
@@ -527,9 +528,20 @@
//Check that this is a valid setting
Lang lang = WebContent.contentTypeToLang(contentType);
if (lang == null) throw new IllegalArgumentException("Given Content Type '" + contentType + "' is not supported by RIOT");
- if (!lang.isTriples()) throw new IllegalArgumentException("Given Content Type '" + contentType + " is not a RDF Graph format");
+ if (! RDFLanguages.isTriples(lang)) throw new IllegalArgumentException("Given Content Type '" + contentType + " is not a RDF Graph format");
modelContentType = contentType;
}
+
+ @Override
+ public long getTimeout1() { return asMillis(readTimeout, readTimeoutUnit) ; }
+
+ @Override
+ public long getTimeout2() { return asMillis(connectTimeout, connectTimeoutUnit) ; }
+
+ private static long asMillis(long duration, TimeUnit timeUnit)
+ {
+ return (duration < 0 ) ? duration : timeUnit.toMillis(duration) ;
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -61,7 +61,7 @@
return totalNrOfExamples;
}
- public int getNrOfpositiveExamples() {
+ public int getNrOfPositiveExamples() {
return nrOfpositiveExamples;
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -451,7 +451,7 @@
//
Comparator<OWLNamedObject> namedObjectComparator = new Comparator<OWLNamedObject>() {
public int compare(OWLNamedObject o1, OWLNamedObject o2) {
- return o1.getIRI().compareTo(o2.getIRI());
+ return o1.compareTo(o2);
}
};
Set<OWLClass> classes = new TreeSet<OWLClass>(namedObjectComparator);
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -460,6 +460,39 @@
}
return types;
}
+
+ public Set<NamedClass> getOWLClasses() {
+ Set<NamedClass> types = new HashSet<NamedClass>();
+ String query = String.format("SELECT DISTINCT ?class WHERE {?class a <%s>.}",OWL.Class.getURI());
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ types.add(new NamedClass(qs.getResource("class").getURI()));
+ }
+ return types;
+ }
+
+ /**
+ * Returns a set of classes which are siblings, i.e. on the same level
+ * in the class hierarchy.
+ * @param cls
+ * @param limit
+ * @return
+ */
+ public Set<NamedClass> getSiblingClasses(NamedClass cls) {
+ Set<NamedClass> siblings = new HashSet<NamedClass>();
+ String query = "SELECT ?sub WHERE { <" + cls.getName() + "> <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
+ query += "?sub <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
+ query += "FILTER( !SAMETERM(?sub, <" + cls.getName() + ">)) . }";
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ siblings.add(new NamedClass(qs.getResource("sub").getURI()));
+ }
+ return siblings;
+ }
@Override
public boolean hasType(Description description, Individual individual) {
@@ -490,12 +523,14 @@
if(limit != 0) {
query += " LIMIT " + limit;
}
-
+ System.out.println(query);
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
qs = rs.next();
- individuals.add(new Individual(qs.getResource("ind").getURI()));
+ if(qs.get("ind").isURIResource()){
+ individuals.add(new Individual(qs.getResource("ind").getURI()));
+ }
}
return individuals;
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/LabelShortFormProvider.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/LabelShortFormProvider.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/LabelShortFormProvider.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -9,7 +9,9 @@
import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.hp.hpl.jena.vocabulary.RDFS;
@@ -23,7 +25,12 @@
private ExtractionDBCache cache;
private SparqlEndpoint endpoint;
+ private Model model;
+ public LabelShortFormProvider(Model model) {
+ this.model = model;
+ }
+
public LabelShortFormProvider(SparqlEndpoint endpoint) {
this.endpoint = endpoint;
}
@@ -59,15 +66,20 @@
protected ResultSet executeSelect(Query query){
ResultSet rs = null;
- if(cache != null){
- rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query.toString()));
+ if(endpoint != null){
+ if(cache != null){
+ rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query.toString()));
+ } else {
+ QueryEngineHTTP qe = new QueryEngineHTTP(endpoint.getURL().toString(), query);
+ for(String uri : endpoint.getDefaultGraphURIs()){
+ qe.addDefaultGraph(uri);
+ }
+ rs = qe.execSelect();
+ }
} else {
- QueryEngineHTTP qe = new QueryEngineHTTP(endpoint.getURL().toString(), query);
- for(String uri : endpoint.getDefaultGraphURIs()){
- qe.addDefaultGraph(uri);
- }
- rs = qe.execSelect();
+ rs = QueryExecutionFactory.create(query, model).execSelect();
}
+
return rs;
}
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