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[DL-Learner SVN] SF.net SVN: dl-learner:[3483] trunk
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From: <lor...@us...> - 2011-12-07 15:24:24
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Revision: 3483
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3483&view=rev
Author: lorenz_b
Date: 2011-12-07 15:24:10 +0000 (Wed, 07 Dec 2011)
Log Message:
-----------
Some changes for release.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/IrreflexiveObjectPropertyAxiomLearner.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/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
trunk/interfaces/pom.xml
trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
trunk/interfaces/src/main/java/org/dllearner/cli/QuickStart.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -226,7 +226,7 @@
l.setReasoner(reasoner);
ConfigHelper.configure(l, "maxExecutionTimeInSeconds", 10);
- l.setClassToDescribe(new NamedClass("http://dbpedia.org/ontology/AdministrativeRegion"));
+ l.setClassToDescribe(new NamedClass("http://dbpedia.org/ontology/Olympics"));
l.init();
l.start();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -19,7 +19,9 @@
package org.dllearner.algorithms.properties;
+import java.net.URL;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -36,6 +38,7 @@
import org.dllearner.core.owl.EquivalentObjectPropertiesAxiom;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.learningproblems.AxiomScore;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -132,5 +135,15 @@
return axioms;
}
+ public static void main(String[] args) throws Exception{
+ EquivalentObjectPropertyAxiomLearner l = new EquivalentObjectPropertyAxiomLearner(new SparqlEndpointKS(new SparqlEndpoint(
+ new URL("http://dbpedia.aksw.org:8902/sparql"), Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList())));//.getEndpointDBpediaLiveAKSW()));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/country"));
+ l.setMaxExecutionTimeInSeconds(10);
+ l.init();
+ l.start();
+ System.out.println(l.getCurrentlyBestEvaluatedAxioms(5, 0.75));
+ }
+
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/IrreflexiveObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/IrreflexiveObjectPropertyAxiomLearner.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/IrreflexiveObjectPropertyAxiomLearner.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -19,6 +19,8 @@
package org.dllearner.algorithms.properties;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.util.ArrayList;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
@@ -101,10 +103,14 @@
logger.info("...finished in {}ms.", (System.currentTimeMillis()-startTime));
}
- public static void main(String[] args) {
- IrreflexiveObjectPropertyAxiomLearner l = new IrreflexiveObjectPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW()));
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/thumbnail"));
+ public static void main(String[] args) throws Exception {
+ SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(new URL("http://dbpedia.aksw.org:8902/sparql")));
+
+ IrreflexiveObjectPropertyAxiomLearner l = new IrreflexiveObjectPropertyAxiomLearner(ks);
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/author"));
l.start();
+
+ System.out.println(l.getCurrentlyBestEvaluatedAxioms(10, 0.75));
}
}
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 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -176,21 +176,21 @@
}
public static void main(String[] args) throws Exception{
- SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(new URL("http://factforge.net/sparql")));//.getEndpointDBpediaLiveAKSW()));
+ SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(new URL("http://dbpedia.aksw.org:8902/sparql")));//.getEndpointDBpediaLiveAKSW()));
SPARQLReasoner reasoner = new SPARQLReasoner(ks);
-// reasoner.prepareSubsumptionHierarchy();
+ reasoner.prepareSubsumptionHierarchy();
ObjectPropertyDomainAxiomLearner l = new ObjectPropertyDomainAxiomLearner(ks);
l.setReasoner(reasoner);
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/industry"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/officialLanguage"));
l.setMaxExecutionTimeInSeconds(10);
- l.setReturnOnlyNewAxioms(true);
+// l.setReturnOnlyNewAxioms(true);
l.init();
l.start();
- System.out.println(l.getCurrentlyBestEvaluatedAxioms(5));
+ System.out.println(l.getCurrentlyBestEvaluatedAxioms(10, 0.75));
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -28,6 +28,7 @@
import java.util.SortedSet;
import java.util.TreeSet;
+import org.aksw.commons.jena.CollectionResultSet;
import org.dllearner.core.config.BooleanEditor;
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.config.IntegerEditor;
@@ -190,6 +191,13 @@
queryExecution.setDefaultGraphURIs(ks.getEndpoint().getDefaultGraphURIs());
queryExecution.setNamedGraphURIs(ks.getEndpoint().getNamedGraphURIs());
+// ResultSet resultSet = null;
+// try {
+// resultSet = queryExecution.execSelect();
+// } catch (Exception e) {
+// logger.error("Got a timeout during query execution.", e);
+// resultSet = new CollectionResultSet(Collections.<String>emptyList(), Collections.<QuerySolution>emptyList());
+// }
ResultSet resultSet = queryExecution.execSelect();
return resultSet;
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -80,15 +80,19 @@
StringBuilder sb = new StringBuilder();
sb.append("CONSTRUCT {\n");
sb.append("<").append(resource).append("> ").append("?p0 ").append("?o0").append(".\n");
+ sb.append("?p0 a ?type0.\n");
for(int i = 1; i < depth; i++){
sb.append("?o").append(i-1).append(" ").append("?p").append(i).append(" ").append("?o").append(i).append(".\n");
+ sb.append("?p").append(i).append(" ").append("a").append(" ").append("?type").append(i).append(".\n");
}
sb.append("}\n");
sb.append("WHERE {\n");
sb.append("<").append(resource).append("> ").append("?p0 ").append("?o0").append(".\n");
+ sb.append("?p0 a ?type0.\n");
for(int i = 1; i < depth; i++){
sb.append("OPTIONAL{\n");
sb.append("?o").append(i-1).append(" ").append("?p").append(i).append(" ").append("?o").append(i).append(".\n");
+ sb.append("?p").append(i).append(" ").append("a").append(" ").append("?type").append(i).append(".\n");
}
for(int i = 1; i < depth; i++){
sb.append("}");
@@ -96,7 +100,6 @@
sb.append("}\n");
sb.append("LIMIT ").append(limit).append("\n");
sb.append("OFFSET ").append(offset);
-
return sb.toString();
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -514,7 +514,11 @@
// policy: returned sets are clones, i.e. can be modified
// (of course we only have to clone the leafs of a class description tree)
if (description instanceof NamedClass) {
- return (TreeSet<Individual>) classInstancesPos.get((NamedClass) description).clone();
+ if(classInstancesPos.containsKey((NamedClass) description)){
+ return (TreeSet<Individual>) classInstancesPos.get((NamedClass) description).clone();
+ } else {
+ return new TreeSet<Individual>();
+ }
} else if (description instanceof Negation) {
if(description.getChild(0) instanceof NamedClass) {
return (TreeSet<Individual>) classInstancesNeg.get((NamedClass) description.getChild(0)).clone();
Modified: trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -351,7 +351,7 @@
// we do not need the temporary set anymore and let the
// garbage collector take care of it
valueFrequency = null;
- dataValueFrequency = null;
+ dataValueFrequency.clear();// = null;
// System.out.println("freqDataValues: " + frequentDataValues);
Modified: trunk/interfaces/pom.xml
===================================================================
--- trunk/interfaces/pom.xml 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/interfaces/pom.xml 2011-12-07 15:24:10 UTC (rev 3483)
@@ -15,7 +15,7 @@
</parent>
<properties>
- <release.name>1.0-alpha-2</release.name>
+ <release.name>1.0-beta-1</release.name>
</properties>
<profiles>
@@ -202,12 +202,10 @@
<groupId>org.dllearner</groupId>
<artifactId>components-core</artifactId>
</dependency>
- <!--
- <dependency>
+ <!--dependency>
<groupId>org.dllearner</groupId>
<artifactId>components-ext</artifactId>
- </dependency>
- -->
+ </dependency-->
<!-- Added the dependency of the core tests so that they will be accessible
from the tests in this component -->
<dependency>
@@ -279,6 +277,12 @@
<groupId>org.json</groupId>
<artifactId>json</artifactId>
</dependency>
+
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.3</version>
+</dependency>
<!--BEGIN Logging Dependencies-->
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -123,7 +123,7 @@
AbstractCELA la = context.getBean(AbstractCELA.class);
new CrossValidation(la,lp,rs,nrOfFolds,false);
} else {
- knowledgeSource = context.getBean(KnowledgeSource.class);
+ knowledgeSource = context.getBeansOfType(KnowledgeSource.class).entrySet().iterator().next().getValue();
algorithm = context.getBean(LearningAlgorithm.class);
algorithm.start();
}
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -128,6 +128,7 @@
import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLIndividual;
@@ -223,6 +224,7 @@
AbstractReasonerComponent rcCached;
private Set<OWLAxiom> learnedOWLAxioms;
+ private Set<EvaluatedAxiom> learnedEvaluatedAxioms;
public Enrichment(SparqlEndpoint se, Entity resource, double threshold, int nrOfAxiomsToLearn, boolean useInference, boolean verbose) {
this.se = se;
@@ -263,6 +265,7 @@
algorithmRuns = new LinkedList<AlgorithmRun>();
learnedOWLAxioms = new HashSet<OWLAxiom>();
+ learnedEvaluatedAxioms = new HashSet<EvaluatedAxiom>();
}
public void start() throws ComponentInitException, IllegalArgumentException, SecurityException, InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException, LearningProblemUnsupportedException, MalformedURLException {
@@ -444,7 +447,7 @@
learnedAxioms.add(new EvaluatedAxiom(axiom, score));
}
System.out.println(prettyPrint(learnedAxioms));
-
+ learnedEvaluatedAxioms.addAll(learnedAxioms);
algorithmRuns.add(new AlgorithmRun(CELOE.class, learnedAxioms, ConfigHelper.getConfigOptionValues(la)));
return learnedAxioms;
}
@@ -485,7 +488,7 @@
List<EvaluatedAxiom> learnedAxioms = learner
.getCurrentlyBestEvaluatedAxioms(nrOfAxiomsToLearn, threshold);
System.out.println(prettyPrint(learnedAxioms));
-
+ learnedEvaluatedAxioms.addAll(learnedAxioms);
for(EvaluatedAxiom evAx : learnedAxioms){
learnedOWLAxioms.add(OWLAPIAxiomConvertVisitor.convertAxiom(evAx.getAxiom()));
}
@@ -665,7 +668,7 @@
return model;
}
- private OWLOntology getGeneratedOntology(){
+ public OWLOntology getGeneratedOntology(){
OWLOntology ontology = null;
try {
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
@@ -677,6 +680,31 @@
return ontology;
}
+ public OWLOntology getGeneratedOntology(boolean withConfidenceAsAnnotations){
+ OWLOntology ontology = null;
+ try {
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLDataFactory factory = man.getOWLDataFactory();
+ if(withConfidenceAsAnnotations){
+ OWLAnnotationProperty confAnnoProp = factory.getOWLAnnotationProperty(IRI.create(EnrichmentVocabulary.NS + "confidence"));
+ Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
+ for(EvaluatedAxiom evAx : learnedEvaluatedAxioms){
+ OWLAxiom ax = OWLAPIAxiomConvertVisitor.convertAxiom(evAx.getAxiom());
+ ax = ax.getAnnotatedAxiom(Collections.singleton(
+ factory.getOWLAnnotation(confAnnoProp, factory.getOWLLiteral(evAx.getScore().getAccuracy()))));
+ axioms.add(ax);
+ }
+ ontology = man.createOntology(axioms);
+ } else {
+ ontology = man.createOntology(learnedOWLAxioms);
+ }
+ } catch (OWLOntologyCreationException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return ontology;
+ }
+
/*
* Write axioms in Turtle syntax.
*/
@@ -748,6 +776,8 @@
"Specifies whether to use inference. If yes, the schema will be loaded into a reasoner and used for computing the scores.").withOptionalArg().ofType(Boolean.class).defaultsTo(true);
parser.acceptsAll(asList("s", "serialize"), "Specify a file where the ontology with all axioms can be written.")
.withRequiredArg().ofType(File.class);
+ parser.acceptsAll(asList("a", "annotations"),
+ "Specifies whether to save scores as annotations.").withOptionalArg().ofType(Boolean.class).defaultsTo(true);
// parse options and display a message for the user in case of problems
OptionSet options = null;
try {
@@ -885,7 +915,7 @@
if(options.has("s")){
File file = (File)options.valueOf("s");
try {
- OWLOntology ontology = e.getGeneratedOntology();
+ OWLOntology ontology = e.getGeneratedOntology(options.has("a"));
OutputStream os = new BufferedOutputStream(new FileOutputStream(file));
OWLManager.createOWLOntologyManager().saveOntology(ontology, new RDFXMLOntologyFormat(), os);
} catch (OWLOntologyStorageException e1) {
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/QuickStart.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/QuickStart.java 2011-12-07 15:18:27 UTC (rev 3482)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/QuickStart.java 2011-12-07 15:24:10 UTC (rev 3483)
@@ -177,7 +177,7 @@
public static void getAllConfs(File f, String path, Map<String, ArrayList<String>> confs) {
path = path + File.separator;
// System.out.println(path);
- String[] act = f.list();
+ String[] act = f.list();System.out.println(f);
for (int i = 0; i < act.length; i++) {
// System.out.println(act[i]);
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