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From: <lor...@us...> - 2011-01-18 12:25:36
|
Revision: 2619
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2619&view=rev
Author: lorenz_b
Date: 2011-01-18 12:25:29 +0000 (Tue, 18 Jan 2011)
Log Message:
-----------
Added 2 methods to cache which have a max execution time for SPARQL queries.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-01-18 10:22:55 UTC (rev 2618)
+++ trunk/components-core/pom.xml 2011-01-18 12:25:29 UTC (rev 2619)
@@ -164,6 +164,11 @@
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
</dependency>
+
+ <dependency>
+ <groupId>org.aksw.commons</groupId>
+ <artifactId>commons</artifactId>
+ </dependency>
</dependencies>
</project>
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2011-01-18 10:22:55 UTC (rev 2618)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2011-01-18 12:25:29 UTC (rev 2619)
@@ -32,13 +32,13 @@
import java.sql.SQLException;
import java.sql.Statement;
+import org.aksw.commons.jena.ExtendedQueryEngineHTTP;
import org.dllearner.utilities.Helper;
import com.hp.hpl.jena.query.ResultSetFactory;
import com.hp.hpl.jena.query.ResultSetRewindable;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
@@ -99,6 +99,10 @@
}
public Model executeConstructQuery(SparqlEndpoint endpoint, String query) throws SQLException, UnsupportedEncodingException {
+ return executeConstructQuery(endpoint, query, 0);
+ }
+
+ public Model executeConstructQuery(SparqlEndpoint endpoint, String query, int maxExecutionTimeInSeconds) throws SQLException, UnsupportedEncodingException {
mon.start();
byte[] md5 = md5(query);
// Timestamp currTS = new Timestamp(new java.util.Date().getTime());
@@ -128,7 +132,8 @@
// System.out.println("Posing new query");
// String endpoint = "http://139.18.2.37:8890/sparql";
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(), query);
+ ExtendedQueryEngineHTTP queryExecution = new ExtendedQueryEngineHTTP(endpoint.getURL().toString(), query);
+ queryExecution.setTimeOut(maxExecutionTimeInSeconds * 1000);
for (String dgu : endpoint.getDefaultGraphURIs()) {
queryExecution.addDefaultGraph(dgu);
}
@@ -164,6 +169,10 @@
}
public String executeSelectQuery(SparqlEndpoint endpoint, String query) {
+ return executeSelectQuery(endpoint, query, 0);
+ }
+
+ public String executeSelectQuery(SparqlEndpoint endpoint, String query, int maxExecutionTimeInSeconds) {
try {
@@ -182,7 +191,8 @@
return clob.getSubString(1, (int) clob.length());
} else {
// System.out.println("no-cache");
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(), query);
+ ExtendedQueryEngineHTTP queryExecution = new ExtendedQueryEngineHTTP(endpoint.getURL().toString(), query);
+ queryExecution.setTimeOut(maxExecutionTimeInSeconds * 1000);
for (String dgu : endpoint.getDefaultGraphURIs()) {
queryExecution.addDefaultGraph(dgu);
}
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|
|
From: <ji...@us...> - 2011-05-02 14:56:57
|
Revision: 2778
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2778&view=rev
Author: jialva
Date: 2011-05-02 14:56:50 +0000 (Mon, 02 May 2011)
Log Message:
-----------
New update of fuzzyDL-Learner
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest.java
Added Paths:
-----------
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-04-28 17:44:44 UTC (rev 2777)
+++ trunk/components-core/pom.xml 2011-05-02 14:56:50 UTC (rev 2778)
@@ -201,7 +201,7 @@
<version>1.0</version>
</dependency>
- <dependency>
+ <dependency>
<groupId>fuzzydll</groupId>
<artifactId>fuzzyowl2fuzzydlparser</artifactId>
<version>1.0</version>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java 2011-04-28 17:44:44 UTC (rev 2777)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java 2011-05-02 14:56:50 UTC (rev 2778)
@@ -54,6 +54,7 @@
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.learningproblems.PosNegLPStandard;
import org.dllearner.learningproblems.PosOnlyLP;
+import org.dllearner.learningproblems.fuzzydll.FuzzyPosNegLP;
import org.dllearner.learningproblems.fuzzydll.FuzzyPosNegLPStandard;
import org.dllearner.refinementoperators.OperatorInverter;
import org.dllearner.refinementoperators.RefinementOperator;
@@ -308,9 +309,13 @@
}
} else if(learningProblem instanceof PosOnlyLP) {
examples = ((PosOnlyLP)learningProblem).getPositiveExamples();
- } else if(learningProblem instanceof PosNegLP) {
+ // changed by Josue
+ } else if (learningProblem instanceof PosNegLP) {
examples = Helper.union(((PosNegLP)learningProblem).getPositiveExamples(),((PosNegLP)learningProblem).getNegativeExamples());
+ } else if (learningProblem instanceof FuzzyPosNegLP) {
+ examples = Helper.union(((FuzzyPosNegLP)learningProblem).getPositiveExamples(),((FuzzyPosNegLP)learningProblem).getNegativeExamples());
}
+
}
@Override
Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java 2011-04-28 17:44:44 UTC (rev 2777)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java 2011-05-02 14:56:50 UTC (rev 2778)
@@ -73,6 +73,8 @@
private boolean useOldDIGOptions = false;
private HeuristicType heuristic = HeuristicType.PRED_ACC;
+
+ private int errorIndex = 0;
@Override
public FuzzyPosNegLPStandardConfigurator getConfigurator() {
@@ -506,10 +508,10 @@
* @see org.dllearner.core.LearningProblem#getAccuracyOrTooWeak(org.dllearner.core.owl.Description, double)
*/
public double getPredAccuracyOrTooWeakExact(Description description, double noise) {
-
+
double crispAccuracy = crispAccuracy(description, noise);
// if I erase next line, fuzzy reasoning fails
- // if (crispAccuracy == -1) return -1;
+ if (crispAccuracy == -1) return -1;
// BEGIN
// added by Josue
@@ -527,27 +529,17 @@
double fuzzyAccuracy = descriptionMembership / (double)fuzzyExamples.size();
- // double fuzzyAccuracy = (posMembership + (negativeExamples.size() - negMembership)) / (double) allExamples.size();
- // END
-
-// if(useFMeasure) {
-// double recall = (positiveExamples.size() - notCoveredPos) / (double) positiveExamples.size();
-// double precision = (positiveExamples.size() - notCoveredPos) / (double) (allExamples.size() - notCoveredPos - notCoveredNeg);
-// return getFMeasure(recall, precision);
-// } else {
- // double crispAccuracy = crispAccuracy(description, noise);
-// }
-
- crispAccuracy = fuzzyAccuracy;
-
if (crispAccuracy != fuzzyAccuracy) {
System.err.println("***********************************************");
- System.err.println("* (crispAccuracy[" + crispAccuracy + "] != fuzzyAccuracy)[" + fuzzyAccuracy + "] *");
+ System.err.println("* " + (errorIndex++));
+ System.err.println("* (crispAccuracy[" + crispAccuracy + "] != fuzzyAccuracy[" + fuzzyAccuracy + "])");
+ System.err.println("* DESC: " + description);
System.err.println("***********************************************");
- Scanner sc = new Scanner(System.in);
- sc.nextLine(); }
+// Scanner sc = new Scanner(System.in);
+// sc.nextLine();
+ }
- return crispAccuracy;
+ return fuzzyAccuracy;
}
// added by Josue
@@ -581,6 +573,7 @@
double totalMembershipDegree = 0;
double invertedCoveredMembershipDegree = 0;
+ // TODO to optimize
for (FuzzyIndividual ind: fuzzyExamples) {
coveredMembershipDegree += reasoner.hasTypeFuzzyMembership(description, ind) * ind.getBeliefDegree();
totalMembershipDegree += ind.getBeliefDegree();
@@ -620,7 +613,7 @@
// return getFMeasure(recall, precision);
double crispFmeasure = Heuristics.getFScore(recall, precision);
- crispFmeasure = fuzzyFmeasure;
+ // crispFmeasure = fuzzyFmeasure;
if (crispFmeasure != fuzzyFmeasure) {
System.err.println("************************");
@@ -631,7 +624,7 @@
sc.nextLine();
}
- return crispFmeasure;
+ return fuzzyFmeasure;
}
// instead of using the standard operation, we use optimisation
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java 2011-04-28 17:44:44 UTC (rev 2777)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java 2011-05-02 14:56:50 UTC (rev 2778)
@@ -1,9 +1,8 @@
package org.dllearner.reasoning.fuzzydll;
import java.io.FileInputStream;
-import java.util.ArrayList;
+import java.util.Iterator;
import java.util.Scanner;
-
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLIndividual;
@@ -12,40 +11,37 @@
import fuzzydl.exception.FuzzyOntologyException;
import fuzzydl.milp.Solution;
import fuzzydl.parser.*;
-import fuzzydll.fuzzyowl2fuzzydlparser.FuzzyOwl2toFuzzyDL;
+import fuzzydll.fuzzyowl2fuzzydlparser.*;
public class FuzzyDLReasonerManager {
private static final String CHANGING_JUST_HIERARCHI_PROBLEM = "/Users/josue/Documents/PhD/AKSW/fuzzySemanticTools/FuzzyDLMacOSX/FuzzyDL/examples/output/fuzzyOWL2fuzzyDLparserOutput_manual.fuzzyDL.txt";
private static final String FUZZYOWL2FUZZYDLPARSEROUTPUT = "/Users/josue/Documents/PhD/AKSW/fuzzySemanticTools/FuzzyDLMacOSX/FuzzyDL/examples/output/fuzzyOWL2fuzzyDLparserOutput.fuzzyDL.txt";
private static String CONFIG_FILENAME = "/Users/josue/Documents/PhD/AKSW/fuzzySemanticTools/FuzzyDLMacOSX/FuzzyDL/CONFIG";
-
+
private Solution queryResult;
private KnowledgeBase fuzzyKB;
private Parser parser;
private SimpleShortFormProvider shortFormParser;
-
- // private OWLAPI2fuzzyDLConvertVisitor converter;
-
- private FuzzyOwl2toFuzzyDL fuzzyParser;
-
+
+ private FuzzyOwl2toFuzzyDL fuzzyFileParser;
+ private int auxCounter = 0;
+
public FuzzyDLReasonerManager(String ontologyFile) throws Exception {
queryResult = null;
parser = null;
-
+
shortFormParser = new SimpleShortFormProvider();
- // converter = new OWLAPI2fuzzyDLConvertVisitor();
-
+
ConfigReader.loadParameters(CONFIG_FILENAME, new String[0]);
-
- fuzzyKB = parseOWLontologyToFuzzyDLsyntax(ontologyFile);
+ fuzzyKB = parseOWLontologyToFuzzyDLsyntax(ontologyFile);
+// fuzzyFileParser.setBaseKB(fuzzyKB);
+ OWLAPI_fuzzyDLObjectParser.setParsingFuzzyKB(fuzzyFileParser, fuzzyKB);
+
solveKB();
-
- // testAux();
-
}
-
+
private void solveKB() {
try {
fuzzyKB.solveKB();
@@ -54,71 +50,67 @@
}
}
- private void testAux() {
- // query stored in the KB
- ArrayList <Query> queries = parser.getQueries();
- Query q1 = queries.get(0);
- System.out.println(q1);
-
- try {
- queryResult = q1.solve(fuzzyKB);
- } catch (FuzzyOntologyException e) {
- e.printStackTrace();
- }
-
- if (queryResult.isConsistentKB())
- System.out.println(q1.toString() + queryResult.getSolution());
- else
- System.out.println("KB is inconsistent");
- }
-
private KnowledgeBase parseOWLontologyToFuzzyDLsyntax(String ontologyFile) throws Exception {
// TODO added by Josue: we may use an in-memory file in the future and not a HD one
// As the parser doesn't work at 100% a manually-edited fuzzyDL-file is used
-
- // String fuzzyOnt = "/Users/josue/Documents/PhD/AKSW/ontologies/foodItems_v1.1.owl";
-
- fuzzyParser = new FuzzyOwl2toFuzzyDL(ontologyFile, FUZZYOWL2FUZZYDLPARSEROUTPUT);
- fuzzyParser.translateOwl2Ontology();
- // return Parser.getKB(FUZZYOWL2FUZZYDLPARSEROUTPUT);
-
- // ontologyFile = CHANGING_JUST_HIERARCHI_PROBLEM;
-
- parser = new Parser(new FileInputStream(FUZZYOWL2FUZZYDLPARSEROUTPUT));
+ fuzzyFileParser = new FuzzyOwl2toFuzzyDL(ontologyFile, FUZZYOWL2FUZZYDLPARSEROUTPUT);
+ fuzzyFileParser.translateOwl2Ontology();
+
+ System.err.println("WARNING: you're using a particular fuzzy ontology");
+ parser = new Parser(new FileInputStream(CHANGING_JUST_HIERARCHI_PROBLEM));
+ // parser = new Parser(new FileInputStream(FUZZYOWL2FUZZYDLPARSEROUTPUT));
+
parser.Start();
return parser.getKB();
}
// added by Josue
- // TODO use beliefDegree
- public double getFuzzyMembership(OWLClassExpression oce, OWLIndividual i, double beliefDegree) {
-
- Individual fIndividual = fuzzyKB.getIndividual(shortFormParser.getShortForm((OWLEntity) i));
- Concept fConcept = fuzzyParser.getFuzzyDLExpresion(oce);
-
- // Concept auxfConcept = Concept.l_or(new Concept("Item"), new Concept("MediumSizeItem"));
-
- Query q = new MinInstanceQuery(fConcept, fIndividual);
-
- try {
- KnowledgeBase clonedFuzzyKB = fuzzyKB.clone();
- queryResult = q.solve(clonedFuzzyKB);
- if (!queryResult.isConsistentKB()){
- System.err.println("Fuzzy KB is inconsistent.");
- System.err.println("This may be a fuzzyDL reasoner bug. Press enter to continue.");
- System.err.println("concept: " + fConcept + " individual: " + fIndividual);
- Scanner sc = new Scanner(System.in);
- sc.nextLine();
- // System.exit(0);
+ public double getFuzzyMembership(OWLClassExpression oce, OWLIndividual i, double truthDegree) {
+
+ Individual fIndividual = fuzzyKB.getIndividual(shortFormParser.getShortForm((OWLEntity) i));
+ Concept fConcept = OWLAPI_fuzzyDLObjectParser.getFuzzyDLExpresion(oce);
+
+ // added by Josue
+ // this if is to jump a fuzyDL's bug
+ if (!fConcept.toString().equalsIgnoreCase("SOME_hasCar_SOME_hasLoad_*top*") &&
+ !fConcept.toString().equalsIgnoreCase("SOME_hasCar_ALL_hasLoad_*top*") &&
+ !fConcept.toString().equalsIgnoreCase("SOME_hasCar_(LongCar)_OR_(ShortCar)") &&
+ !fConcept.toString().equalsIgnoreCase("(Car)_OR_(SOME_hasCar_*top*)") &&
+ !fConcept.toString().equalsIgnoreCase("(Load)_OR_(SOME_hasCar_*top*)") &&
+ !fConcept.toString().equalsIgnoreCase("(Train)_OR_(SOME_hasCar_*top*)") &&
+ !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_SOME_hasLoad_*top*)") &&
+ !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_ALL_hasLoad_*top*)") &&
+ !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_LongCar)") &&
+ !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_(LongCar)_OR_(ShortCar))") &&
+ !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_*top*)") &&
+ !fConcept.toString().equalsIgnoreCase("SOME_hasCar_LongCar")) {
+
+ System.err.println(fConcept);
+
+ Query q = new MinInstanceQuery(fConcept, fIndividual);
+
+ try {
+ KnowledgeBase clonedFuzzyKB = fuzzyKB.clone();
+ queryResult = q.solve(clonedFuzzyKB);
+ if (!queryResult.isConsistentKB()){
+ System.err.println("Fuzzy KB is inconsistent.");
+ System.err.println("This may be a fuzzyDL reasoner bug. Press enter to continue.");
+ System.err.println("concept: " + fConcept + " individual: " + fIndividual);
+ Scanner sc = new Scanner(System.in);
+ sc.nextLine();
+ // System.exit(0);
+ }
+ } catch (FuzzyOntologyException e) {
+ e.printStackTrace();
}
- } catch (FuzzyOntologyException e) {
- e.printStackTrace();
+
+ return (1 - Math.abs(truthDegree - queryResult.getSolution()));
}
-
- return (1 - Math.abs(beliefDegree - queryResult.getSolution()));
+ System.err.println("* " + fConcept);
+ return 0;
}
-
+
public KnowledgeBase getFuzzyKB() {
return fuzzyKB;
}
Modified: trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest.java 2011-04-28 17:44:44 UTC (rev 2777)
+++ trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest.java 2011-05-02 14:56:50 UTC (rev 2778)
@@ -20,36 +20,20 @@
*
*/
-import java.io.File;
import java.io.IOException;
import java.net.URL;
-import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
-
-import org.dllearner.algorithms.celoe.CELOE;
import org.dllearner.algorithms.fuzzydll.FuzzyCELOE;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.ComponentManager;
import org.dllearner.core.LearningProblemUnsupportedException;
-import org.dllearner.core.OntologyFormat;
import org.dllearner.core.ReasonerComponent;
-import org.dllearner.core.configurators.CELOEConfigurator;
import org.dllearner.core.options.fuzzydll.FuzzyExample;
import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.EquivalentClassesAxiom;
-import org.dllearner.core.owl.Individual;
-import org.dllearner.core.owl.KB;
-import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.OWLFile;
-import org.dllearner.kb.sparql.SparqlKnowledgeSource;
-import org.dllearner.learningproblems.PosNegLPStandard;
import org.dllearner.learningproblems.fuzzydll.FuzzyPosNegLPStandard;
-import org.dllearner.reasoning.FastInstanceChecker;
-import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.reasoning.fuzzydll.FuzzyOWLAPIReasoner;
-import org.dllearner.utilities.datastructures.Datastructures;
-import org.dllearner.utilities.datastructures.SortedSetTuple;
/**
* A script, which learns definitions / super classes of classes in the DBpedia ontology.
@@ -98,7 +82,7 @@
ComponentManager cm = ComponentManager.getInstance();
OWLFile ks = cm.knowledgeSource(OWLFile.class);
- ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyFoodItems_v1.owl"));
+ ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/foodItems_v1.owl"));
ks.init();
//ReasonerComponent rc = cm.reasoner(OWLAPIReasoner.class, ks);
@@ -120,9 +104,10 @@
// Set<String> aaaaaaaaaa = new TreeSet<String>();
// aaaaaaaaaa.add("Nothing");
// fc.getConfigurator().setIgnoredConcepts(aaaaaaaaaa);
- fc.getConfigurator().setMaxClassDescriptionTests(50);
+ fc.getConfigurator().setMaxClassDescriptionTests(1000);
fc.getConfigurator().setMaxExecutionTimeInSeconds(0);
fc.getConfigurator().setUseDoubleDatatypes(false);
+ fc.getConfigurator().setUseCardinalityRestrictions(false);
fc.init();
fc.start();
Added: trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java 2011-05-02 14:56:50 UTC (rev 2778)
@@ -0,0 +1,118 @@
+package org.dllearner.test;
+
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+import java.io.IOException;
+import java.net.URL;
+import java.util.SortedSet;
+import java.util.TreeSet;
+import org.dllearner.algorithms.fuzzydll.FuzzyCELOE;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.options.fuzzydll.FuzzyExample;
+import org.dllearner.core.owl.Description;
+import org.dllearner.kb.OWLFile;
+import org.dllearner.learningproblems.fuzzydll.FuzzyPosNegLPStandard;
+import org.dllearner.reasoning.fuzzydll.FuzzyOWLAPIReasoner;
+
+/**
+ * A script, which learns definitions / super classes of classes in the DBpedia ontology.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class FuzzyDLLTest_Trains {
+
+ String[] posEx = {
+ "http://www.example.com/fuzzyTrains.owl#east1"
+ };
+ String[] negEx = {
+ "http://www.example.com/fuzzyTrains.owl#west6"
+ };
+
+ public Description learn() throws LearningProblemUnsupportedException, IOException, ComponentInitException {
+
+ //
+ // positive and negative examples
+ //
+ SortedSet<String> positiveExamples = new TreeSet<String>();
+ SortedSet<String> negativeExamples = new TreeSet<String>();
+ for (int i=0; i<posEx.length; i++) {
+ positiveExamples.add(posEx[i]);
+ }
+ for (int i=0; i<negEx.length; i++) {
+ negativeExamples.add(negEx[i]);
+ }
+
+ //
+ // fuzzy examples
+ //
+ SortedSet<Object> fuzzyExamples = new TreeSet<Object>();
+ for (int i=0; i<posEx.length; i++) {
+ fuzzyExamples.add(new FuzzyExample(posEx[i],1.0));
+ }
+ for (int i=0; i<negEx.length; i++) {
+ fuzzyExamples.add(new FuzzyExample(negEx[i],0.0));
+ }
+
+ ComponentManager cm = ComponentManager.getInstance();
+
+ OWLFile ks = cm.knowledgeSource(OWLFile.class);
+ ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyTrains/noFuzzyTrains_v1.2.owl"));
+ ks.init();
+
+ //ReasonerComponent rc = cm.reasoner(OWLAPIReasoner.class, ks);
+ ReasonerComponent rc = cm.reasoner(FuzzyOWLAPIReasoner.class, ks);
+ rc.init();
+
+ FuzzyPosNegLPStandard lp = cm.learningProblem(FuzzyPosNegLPStandard.class, rc);
+ //PosNegLPStandard lp = cm.learningProblem(PosNegLPStandard.class, rc);
+ lp.getConfigurator().setPositiveExamples(positiveExamples);
+ lp.getConfigurator().setNegativeExamples(negativeExamples);
+ lp.getConfigurator().setFuzzyExamples(fuzzyExamples);
+ lp.init();
+
+ FuzzyCELOE fc = cm.learningAlgorithm(FuzzyCELOE.class, lp, rc);
+ //CELOE fc = cm.learningAlgorithm(CELOE.class, lp, rc);
+// Set<String> kkkkkkkkkk = new TreeSet<String>();
+// kkkkkkkkkk.add("kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk");
+// fc.getConfigurator().setAllowedConcepts(kkkkkkkkkk);
+// Set<String> aaaaaaaaaa = new TreeSet<String>();
+// aaaaaaaaaa.add("Nothing");
+// fc.getConfigurator().setIgnoredConcepts(aaaaaaaaaa);
+ fc.getConfigurator().setMaxClassDescriptionTests(1000);
+ fc.getConfigurator().setMaxExecutionTimeInSeconds(0);
+ fc.getConfigurator().setUseDoubleDatatypes(false);
+ fc.getConfigurator().setUseCardinalityRestrictions(false);
+ fc.init();
+ fc.start();
+
+ return fc.getCurrentlyBestDescription();
+ }
+
+ public static void main(String args[]) throws LearningProblemUnsupportedException, IOException, ComponentInitException {
+ FuzzyDLLTest_Trains test = new FuzzyDLLTest_Trains();
+ test.learn();
+ }
+
+}
\ No newline at end of file
Added: trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java 2011-05-02 14:56:50 UTC (rev 2778)
@@ -0,0 +1,123 @@
+package org.dllearner.test;
+
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+import java.io.IOException;
+import java.net.URL;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.algorithms.fuzzydll.FuzzyCELOE;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.options.fuzzydll.FuzzyExample;
+import org.dllearner.core.owl.Description;
+import org.dllearner.kb.OWLFile;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.learningproblems.fuzzydll.FuzzyPosNegLPStandard;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.dllearner.reasoning.fuzzydll.FuzzyOWLAPIReasoner;
+
+/**
+ * A script, which learns definitions / super classes of classes in the DBpedia ontology.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class FuzzyDLLTest_noFuzzyTrains {
+
+ String[] posEx = {
+ "http://www.example.com/fuzzyTrains.owl#east1"
+ };
+ String[] negEx = {
+ "http://www.example.com/fuzzyTrains.owl#west6"
+ };
+
+ public Description learn() throws LearningProblemUnsupportedException, IOException, ComponentInitException {
+
+ //
+ // positive and negative examples
+ //
+ SortedSet<String> positiveExamples = new TreeSet<String>();
+ SortedSet<String> negativeExamples = new TreeSet<String>();
+ for (int i=0; i<posEx.length; i++) {
+ positiveExamples.add(posEx[i]);
+ }
+ for (int i=0; i<negEx.length; i++) {
+ negativeExamples.add(negEx[i]);
+ }
+
+ //
+ // fuzzy examples
+ //
+ SortedSet<Object> fuzzyExamples = new TreeSet<Object>();
+ for (int i=0; i<posEx.length; i++) {
+ fuzzyExamples.add(new FuzzyExample(posEx[i],1.0));
+ }
+ for (int i=0; i<negEx.length; i++) {
+ fuzzyExamples.add(new FuzzyExample(negEx[i],0.0));
+ }
+
+ ComponentManager cm = ComponentManager.getInstance();
+
+ OWLFile ks = cm.knowledgeSource(OWLFile.class);
+ // ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyTrains/fuzzyTrains_v1.0.owl"));
+ ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyTrains/noFuzzyTrains_v1.2.owl"));
+ ks.init();
+
+ ReasonerComponent rc = cm.reasoner(OWLAPIReasoner.class, ks);
+ //ReasonerComponent rc = cm.reasoner(FuzzyOWLAPIReasoner.class, ks);
+ rc.init();
+
+ //FuzzyPosNegLPStandard lp = cm.learningProblem(FuzzyPosNegLPStandard.class, rc);
+ PosNegLPStandard lp = cm.learningProblem(PosNegLPStandard.class, rc);
+ lp.getConfigurator().setPositiveExamples(positiveExamples);
+ lp.getConfigurator().setNegativeExamples(negativeExamples);
+ //lp.getConfigurator().setFuzzyExamples(fuzzyExamples);
+ lp.init();
+
+ //FuzzyCELOE fc = cm.learningAlgorithm(FuzzyCELOE.class, lp, rc);
+ CELOE fc = cm.learningAlgorithm(CELOE.class, lp, rc);
+// Set<String> kkkkkkkkkk = new TreeSet<String>();
+// kkkkkkkkkk.add("kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk");
+// fc.getConfigurator().setAllowedConcepts(kkkkkkkkkk);
+// Set<String> aaaaaaaaaa = new TreeSet<String>();
+// aaaaaaaaaa.add("Nothing");
+// fc.getConfigurator().setIgnoredConcepts(aaaaaaaaaa);
+ fc.getConfigurator().setMaxClassDescriptionTests(1000);
+ fc.getConfigurator().setMaxExecutionTimeInSeconds(0);
+ fc.getConfigurator().setUseDoubleDatatypes(false);
+ fc.getConfigurator().setUseCardinalityRestrictions(false);
+ fc.init();
+ fc.start();
+
+ return fc.getCurrentlyBestDescription();
+ }
+
+ public static void main(String args[]) throws LearningProblemUnsupportedException, IOException, ComponentInitException {
+ FuzzyDLLTest_noFuzzyTrains test = new FuzzyDLLTest_noFuzzyTrains();
+ test.learn();
+ }
+
+}
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ji...@us...> - 2011-05-03 14:57:32
|
Revision: 2780
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2780&view=rev
Author: jialva
Date: 2011-05-03 14:57:22 +0000 (Tue, 03 May 2011)
Log Message:
-----------
New update of fuzzyDL-Learner
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-05-03 14:22:29 UTC (rev 2779)
+++ trunk/components-core/pom.xml 2011-05-03 14:57:22 UTC (rev 2780)
@@ -200,12 +200,12 @@
<artifactId>fuzzydl</artifactId>
<version>1.0</version>
</dependency>
-
+
<dependency>
<groupId>fuzzydll</groupId>
<artifactId>fuzzyowl2fuzzydlparser</artifactId>
<version>1.0</version>
</dependency>
-
+
</dependencies>
</project>
Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java 2011-05-03 14:22:29 UTC (rev 2779)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java 2011-05-03 14:57:22 UTC (rev 2780)
@@ -511,7 +511,10 @@
double crispAccuracy = crispAccuracy(description, noise);
// if I erase next line, fuzzy reasoning fails
- if (crispAccuracy == -1) return -1;
+ if (crispAccuracy == -1) {
+ System.out.println("crisp return -1");
+ // return -1;
+ }
// BEGIN
// added by Josue
@@ -520,15 +523,20 @@
// double negMembership = 0;
double descriptionMembership = 0;
- //System.out.println("d: " + description);
- //System.out.println();
+ System.out.println("noise = " + noise);
+ int individualCounter = fuzzyExamples.size();
for (FuzzyIndividual fuzzyExample : fuzzyExamples) {
descriptionMembership += reasoner.hasTypeFuzzyMembership(description, fuzzyExample);
+ individualCounter--;
+ if ((descriptionMembership + individualCounter) / fuzzyExamples.size() < noise)
+ return -1;
}
double fuzzyAccuracy = descriptionMembership / (double)fuzzyExamples.size();
+
+
if (crispAccuracy != fuzzyAccuracy) {
System.err.println("***********************************************");
System.err.println("* " + (errorIndex++));
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java 2011-05-03 14:22:29 UTC (rev 2779)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java 2011-05-03 14:57:22 UTC (rev 2780)
@@ -1,6 +1,9 @@
package org.dllearner.reasoning.fuzzydll;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
import java.util.Iterator;
import java.util.Scanner;
import org.semanticweb.owlapi.model.OWLClassExpression;
@@ -26,6 +29,7 @@
private FuzzyOwl2toFuzzyDL fuzzyFileParser;
private int auxCounter = 0;
+ private FileOutputStream errorFile;
public FuzzyDLReasonerManager(String ontologyFile) throws Exception {
queryResult = null;
@@ -40,6 +44,8 @@
OWLAPI_fuzzyDLObjectParser.setParsingFuzzyKB(fuzzyFileParser, fuzzyKB);
solveKB();
+
+ errorFile = new FileOutputStream("errorFile.txt");
}
private void solveKB() {
@@ -71,21 +77,25 @@
Individual fIndividual = fuzzyKB.getIndividual(shortFormParser.getShortForm((OWLEntity) i));
Concept fConcept = OWLAPI_fuzzyDLObjectParser.getFuzzyDLExpresion(oce);
- // added by Josue
- // this if is to jump a fuzyDL's bug
- if (!fConcept.toString().equalsIgnoreCase("SOME_hasCar_SOME_hasLoad_*top*") &&
- !fConcept.toString().equalsIgnoreCase("SOME_hasCar_ALL_hasLoad_*top*") &&
- !fConcept.toString().equalsIgnoreCase("SOME_hasCar_(LongCar)_OR_(ShortCar)") &&
- !fConcept.toString().equalsIgnoreCase("(Car)_OR_(SOME_hasCar_*top*)") &&
- !fConcept.toString().equalsIgnoreCase("(Load)_OR_(SOME_hasCar_*top*)") &&
- !fConcept.toString().equalsIgnoreCase("(Train)_OR_(SOME_hasCar_*top*)") &&
- !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_SOME_hasLoad_*top*)") &&
- !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_ALL_hasLoad_*top*)") &&
- !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_LongCar)") &&
- !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_(LongCar)_OR_(ShortCar))") &&
- !fConcept.toString().equalsIgnoreCase("(Train)_AND_(SOME_hasCar_*top*)") &&
- !fConcept.toString().equalsIgnoreCase("SOME_hasCar_LongCar")) {
-
+ try {
+ errorFile.write(fConcept.toString().getBytes());
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+// try {
+// fuzzyKB.saveToFile("file.txt");
+// Parser parser = new Parser(new FileInputStream("file.txt"));
+// parser.Start();
+// fuzzyKB = parser.getKB();
+// } catch (Exception e1) {
+// e1.printStackTrace();
+// }
+
+ if (fConcept.toString().equalsIgnoreCase("SOME_hasFirstCar_SOME_inFrontOf_LongCar"))
+ System.err.println(fConcept);
+
System.err.println(fConcept);
Query q = new MinInstanceQuery(fConcept, fIndividual);
@@ -101,14 +111,24 @@
sc.nextLine();
// System.exit(0);
}
- } catch (FuzzyOntologyException e) {
+ } catch (Exception e) {
e.printStackTrace();
+ try {
+ errorFile.write(" 1".getBytes());
+ } catch (IOException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
}
-
+
+ try {
+ errorFile.write("\n".getBytes());
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
return (1 - Math.abs(truthDegree - queryResult.getSolution()));
- }
- System.err.println("* " + fConcept);
- return 0;
}
public KnowledgeBase getFuzzyKB() {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ji...@us...> - 2011-05-10 12:31:46
|
Revision: 2788
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2788&view=rev
Author: jialva
Date: 2011-05-10 12:31:35 +0000 (Tue, 10 May 2011)
Log Message:
-----------
New update of fuzzyDL-Learner
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-05-09 13:37:35 UTC (rev 2787)
+++ trunk/components-core/pom.xml 2011-05-10 12:31:35 UTC (rev 2788)
@@ -195,11 +195,13 @@
<artifactId>h2</artifactId>
</dependency>
+ <!--
<dependency>
<groupId>fuzzydll</groupId>
<artifactId>fuzzydl</artifactId>
<version>1.0</version>
</dependency>
+ -->
<dependency>
<groupId>fuzzydll</groupId>
Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java 2011-05-09 13:37:35 UTC (rev 2787)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java 2011-05-10 12:31:35 UTC (rev 2788)
@@ -508,12 +508,14 @@
* @see org.dllearner.core.LearningProblem#getAccuracyOrTooWeak(org.dllearner.core.owl.Description, double)
*/
public double getPredAccuracyOrTooWeakExact(Description description, double noise) {
-
+
+ System.out.println(errorIndex++);
+
double crispAccuracy = crispAccuracy(description, noise);
// if I erase next line, fuzzy reasoning fails
if (crispAccuracy == -1) {
- System.out.println("crisp return -1");
- // return -1;
+// System.out.println("crisp return -1");
+ return -1;
}
// BEGIN
@@ -523,7 +525,7 @@
// double negMembership = 0;
double descriptionMembership = 0;
- System.out.println("noise = " + noise);
+// System.out.println("noise = " + noise);
int individualCounter = fuzzyExamples.size();
for (FuzzyIndividual fuzzyExample : fuzzyExamples) {
@@ -535,11 +537,12 @@
double fuzzyAccuracy = descriptionMembership / (double)fuzzyExamples.size();
+ System.err.println("crispAccuracy = fuzzyAccuracy");
+ crispAccuracy = fuzzyAccuracy;
-
if (crispAccuracy != fuzzyAccuracy) {
System.err.println("***********************************************");
- System.err.println("* " + (errorIndex++));
+ //System.err.println("* " + (errorIndex++));
System.err.println("* (crispAccuracy[" + crispAccuracy + "] != fuzzyAccuracy[" + fuzzyAccuracy + "])");
System.err.println("* DESC: " + description);
System.err.println("***********************************************");
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java 2011-05-09 13:37:35 UTC (rev 2787)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java 2011-05-10 12:31:35 UTC (rev 2788)
@@ -4,6 +4,9 @@
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.PrintStream;
+import java.io.PrintWriter;
+import java.io.StringWriter;
import java.util.Iterator;
import java.util.Scanner;
import org.semanticweb.owlapi.model.OWLClassExpression;
@@ -18,7 +21,7 @@
public class FuzzyDLReasonerManager {
- // private static final String CHANGING_JUST_HIERARCHI_PROBLEM = "/Users/josue/Documents/PhD/AKSW/fuzzySemanticTools/FuzzyDLMacOSX/FuzzyDL/examples/output/fuzzyOWL2fuzzyDLparserOutput_manual.fuzzyDL.txt";
+ private static final String CHANGING_JUST_HIERARCHI_PROBLEM = "/Users/josue/Documents/PhD/AKSW/fuzzySemanticTools/FuzzyDLMacOSX/FuzzyDL/examples/output/fuzzyOWL2fuzzyDLparserOutput_manual.fuzzyDL.txt";
private static final String FUZZYOWL2FUZZYDLPARSEROUTPUT = "fuzzyOWL2fuzzyDLparserOutput.fuzzyDL.txt";
private static String CONFIG_FILENAME = "/Users/josue/Documents/PhD/AKSW/fuzzySemanticTools/FuzzyDLMacOSX/FuzzyDL/CONFIG";
@@ -45,7 +48,7 @@
solveKB();
- errorFile = new FileOutputStream("errorFile.txt");
+ errorFile = new FileOutputStream("errorFile.txt");
}
private void solveKB() {
@@ -77,27 +80,6 @@
Individual fIndividual = fuzzyKB.getIndividual(shortFormParser.getShortForm((OWLEntity) i));
Concept fConcept = OWLAPI_fuzzyDLObjectParser.getFuzzyDLExpresion(oce);
- try {
- errorFile.write(fConcept.toString().getBytes());
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
-// try {
-// fuzzyKB.saveToFile("file.txt");
-// Parser parser = new Parser(new FileInputStream("file.txt"));
-// parser.Start();
-// fuzzyKB = parser.getKB();
-// } catch (Exception e1) {
-// e1.printStackTrace();
-// }
-
- if (fConcept.toString().equalsIgnoreCase("SOME_hasFirstCar_SOME_inFrontOf_LongCar"))
- System.err.println(fConcept);
-
- System.err.println(fConcept);
-
Query q = new MinInstanceQuery(fConcept, fIndividual);
try {
@@ -112,26 +94,35 @@
// System.exit(0);
}
} catch (Exception e) {
- e.printStackTrace();
+ // e.printStackTrace();
try {
- errorFile.write(" 1".getBytes());
+ errorFile.write(fIndividual.toString().getBytes());
+ errorFile.write("\n".getBytes());
+ errorFile.write(fConcept.toString().getBytes());
+ errorFile.write("\n".getBytes());
+ errorFile.write(getStackTrace(e).getBytes());
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
+// Scanner sc = new Scanner(System.in);
+// sc.nextLine();
}
- try {
- errorFile.write("\n".getBytes());
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
return (1 - Math.abs(truthDegree - queryResult.getSolution()));
}
public KnowledgeBase getFuzzyKB() {
return fuzzyKB;
}
+
+ public static String getStackTrace(Throwable t)
+ {
+ StringWriter sw = new StringWriter();
+ PrintWriter pw = new PrintWriter(sw, true);
+ t.printStackTrace(pw);
+ pw.flush();
+ sw.flush();
+ return sw.toString();
+ }
}
Modified: trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java 2011-05-09 13:37:35 UTC (rev 2787)
+++ trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java 2011-05-10 12:31:35 UTC (rev 2788)
@@ -44,10 +44,12 @@
public class FuzzyDLLTest_Trains {
String[] posEx = {
- "http://www.example.com/fuzzyTrains.owl#east1"
+ "http://www.example.com/fuzzyTrains.owl#east1",
+ "http://www.example.com/fuzzyTrains.owl#east2"
};
String[] negEx = {
- "http://www.example.com/fuzzyTrains.owl#west6"
+ "http://www.example.com/fuzzyTrains.owl#west6",
+ "http://www.example.com/fuzzyTrains.owl#west7"
};
public Description learn() throws LearningProblemUnsupportedException, IOException, ComponentInitException {
@@ -78,7 +80,7 @@
ComponentManager cm = ComponentManager.getInstance();
OWLFile ks = cm.knowledgeSource(OWLFile.class);
- ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyTrains/fuzzyTrains_v1.2.owl"));
+ ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyTrains/fuzzyTrains_v1.3.owl"));
ks.init();
//ReasonerComponent rc = cm.reasoner(OWLAPIReasoner.class, ks);
Modified: trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java 2011-05-09 13:37:35 UTC (rev 2787)
+++ trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java 2011-05-10 12:31:35 UTC (rev 2788)
@@ -48,10 +48,12 @@
public class FuzzyDLLTest_noFuzzyTrains {
String[] posEx = {
- "http://www.example.com/fuzzyTrains.owl#east1"
+ "http://www.example.com/fuzzyTrains.owl#east1",
+ "http://www.example.com/fuzzyTrains.owl#east2"
};
String[] negEx = {
- "http://www.example.com/fuzzyTrains.owl#west6"
+ "http://www.example.com/fuzzyTrains.owl#west6",
+ "http://www.example.com/fuzzyTrains.owl#west7"
};
public Description learn() throws LearningProblemUnsupportedException, IOException, ComponentInitException {
@@ -83,7 +85,7 @@
OWLFile ks = cm.knowledgeSource(OWLFile.class);
// ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyTrains/fuzzyTrains_v1.0.owl"));
- ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyTrains/noFuzzyTrains_v1.2.owl"));
+ ks.getConfigurator().setUrl(new URL("file:///Users/josue/Documents/PhD/AKSW/ontologies/fuzzyTrains/noFuzzyTrains_v1.3.owl"));
ks.init();
ReasonerComponent rc = cm.reasoner(OWLAPIReasoner.class, ks);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ji...@us...> - 2011-06-03 17:02:48
|
Revision: 2849
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2849&view=rev
Author: jialva
Date: 2011-06-03 17:02:41 +0000 (Fri, 03 Jun 2011)
Log Message:
-----------
New update of fuzzyDL-Learner
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java
Added Paths:
-----------
trunk/components-core/log/
Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java 2011-06-03 14:57:18 UTC (rev 2848)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java 2011-06-03 17:02:41 UTC (rev 2849)
@@ -513,10 +513,11 @@
double crispAccuracy = crispAccuracy(description, noise);
// if I erase next line, fuzzy reasoning fails
- if (crispAccuracy == -1) {
-// System.out.println("crisp return -1");
- // return -1;
- }
+// if (crispAccuracy == -1) {
+// System.out.print(description);
+// System.out.println();
+// // return -1;
+// }
// BEGIN
// added by Josue
@@ -524,6 +525,10 @@
// double posMembership = 0;
// double negMembership = 0;
double descriptionMembership = 0;
+ double singleMembership = 0;
+ // double accumulatedSingleMembership = 0;
+ double nonAccumulativeDescriptionMembership = 0;
+ double accumulativeDescriptionMembership = 0;
// System.out.println("noise = " + noise);
@@ -531,15 +536,15 @@
// int individualCounter = fuzzyExamples.size();
double individualCounter = totalTruth;
for (FuzzyIndividual fuzzyExample : fuzzyExamples) {
- descriptionMembership += reasoner.hasTypeFuzzyMembership(description, fuzzyExample);
- // individualCounter--;
- if (individualCounter >= 1) individualCounter -= fuzzyExample.getTruthDegree(); // before it was individual--;
- // before
-// if ((descriptionMembership + individualCounter) / fuzzyExamples.size() < noise)
-// return -1;
- // after (to match the noise management of the crisp part)
- if ((descriptionMembership + individualCounter) < ((1 - noise) * totalTruth))
+ singleMembership = reasoner.hasTypeFuzzyMembership(description, fuzzyExample);
+ // accumulatedSingleMembership += singleMembership;
+ nonAccumulativeDescriptionMembership = 1 - Math.abs(fuzzyExample.getTruthDegree() - singleMembership);
+ descriptionMembership += nonAccumulativeDescriptionMembership;
+ individualCounter -= fuzzyExample.getTruthDegree();
+ if ((accumulativeDescriptionMembership + (nonAccumulativeDescriptionMembership * fuzzyExample.getTruthDegree()) + individualCounter) < ((1 - noise) * totalTruth))
return -1;
+ accumulativeDescriptionMembership += nonAccumulativeDescriptionMembership * fuzzyExample.getTruthDegree();
+
}
double fuzzyAccuracy = descriptionMembership / (double)fuzzyExamples.size();
@@ -590,12 +595,14 @@
double coveredMembershipDegree = 0;
double totalMembershipDegree = 0;
double invertedCoveredMembershipDegree = 0;
+ double lastMembershipDegree = 0;
// TODO to optimize
for (FuzzyIndividual ind: fuzzyExamples) {
- coveredMembershipDegree += reasoner.hasTypeFuzzyMembership(description, ind) * ind.getTruthDegree();
+ lastMembershipDegree = (1 - Math.abs(ind.getTruthDegree() - reasoner.hasTypeFuzzyMembership(description, ind)));
+ coveredMembershipDegree += lastMembershipDegree * ind.getTruthDegree();
totalMembershipDegree += ind.getTruthDegree();
- invertedCoveredMembershipDegree += (1 - ind.getTruthDegree()) * (1 - reasoner.hasTypeFuzzyMembership(description, ind));
+ invertedCoveredMembershipDegree += (1 - ind.getTruthDegree()) * (1 - lastMembershipDegree);
}
double fuzzyRecall = totalMembershipDegree == 0 ? 0 :coveredMembershipDegree/totalMembershipDegree;
// TODO this is like this??? not sure
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java 2011-06-03 14:57:18 UTC (rev 2848)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java 2011-06-03 17:02:41 UTC (rev 2849)
@@ -143,7 +143,7 @@
}
// added by Josue
- public double getFuzzyMembership(OWLClassExpression oce, OWLIndividual i, double truthDegree) {
+ public double getFuzzyMembership(OWLClassExpression oce, OWLIndividual i) {
Individual fIndividual = fuzzyKB.getIndividual(shortFormParser.getShortForm((OWLEntity) i));
Concept fConcept = OWLAPI_fuzzyDLObjectParser.getFuzzyDLExpresion(oce);
@@ -177,7 +177,8 @@
// sc.nextLine();
}
- return (1 - Math.abs(truthDegree - queryResult.getSolution()));
+ // return (1 - Math.abs(truthDegree - queryResult.getSolution()));
+ return queryResult.getSolution();
}
public KnowledgeBase getFuzzyKB() {
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java 2011-06-03 14:57:18 UTC (rev 2848)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java 2011-06-03 17:02:41 UTC (rev 2849)
@@ -624,7 +624,7 @@
// return crispReasonerOutput;
// added by Josue to make be fuzzyDL and not Pellet to answer this method
- double fuzzyReasonerOutput = ((FuzzyDLReasonerManager) reasoner).getFuzzyMembership(d, i, 1);
+ double fuzzyReasonerOutput = ((FuzzyDLReasonerManager) reasoner).getFuzzyMembership(d, i);
return fuzzyReasonerOutput == 0 ? false : true;
}
@@ -1138,7 +1138,7 @@
OWLClassExpression desc = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(description);
OWLIndividual ind = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
- double fuzzyReasonerOutput = ((FuzzyDLReasonerManager) reasoner).getFuzzyMembership(desc, ind, individual.getTruthDegree());
+ double fuzzyReasonerOutput = ((FuzzyDLReasonerManager) reasoner).getFuzzyMembership(desc, ind);
// System.out.println("- d: " + d);
// System.out.println("- i: " + i);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sha...@us...> - 2011-07-27 04:46:49
|
Revision: 2968
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2968&view=rev
Author: shadowtm
Date: 2011-07-27 04:46:43 +0000 (Wed, 27 Jul 2011)
Log Message:
-----------
Added example showing how to use annotations for fields which were not of a basic type.
Modified Paths:
--------------
trunk/components-core/pom.xml
Added Paths:
-----------
trunk/components-core/src/test/java/org/dllearner/examples/
trunk/components-core/src/test/java/org/dllearner/examples/AnnotationExample.java
trunk/components-core/src/test/java/org/dllearner/examples/ConfigOption.java
trunk/components-core/src/test/java/org/dllearner/examples/ConfiguredObject.java
trunk/components-core/src/test/java/org/dllearner/examples/ObjectPropertyEditor.java
trunk/components-core/src/test/java/org/dllearner/examples/OurStringTrimmerEditor.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-07-26 11:37:49 UTC (rev 2967)
+++ trunk/components-core/pom.xml 2011-07-27 04:46:43 UTC (rev 2968)
@@ -247,5 +247,11 @@
<version>1.0</version>
</dependency>
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-beans</artifactId>
+ <version>3.0.5.RELEASE</version>
+ <scope>test</scope>
+ </dependency>
</dependencies>
</project>
Added: trunk/components-core/src/test/java/org/dllearner/examples/AnnotationExample.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/examples/AnnotationExample.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/examples/AnnotationExample.java 2011-07-27 04:46:43 UTC (rev 2968)
@@ -0,0 +1,58 @@
+package org.dllearner.examples;
+
+
+import javax.xml.transform.Source;
+import java.beans.PropertyEditor;
+import java.lang.reflect.Field;
+import java.lang.reflect.Method;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: Chris
+ * Date: 7/26/11
+ * Time: 9:03 PM
+ * <p/>
+ * An example showing the use of Annotations with non basic types/classes.
+ */
+public class AnnotationExample {
+
+
+ public static void main(String[] args) throws Exception {
+
+ /** The Configuration map comes in from somewhere - The keys here correspond to the configuration options in ConfiguredObject*/
+ Map<String, String> propertiesMap = new HashMap<String, String>();
+ propertiesMap.put("initString", "My Initialization String");
+ propertiesMap.put("objectProperty", "My Object Property");
+
+ /** Here's my new configured object */
+ ConfiguredObject obj = new ConfiguredObject();
+
+ Method[] methods = obj.getClass().getMethods();
+ for (Method method : methods) {
+ ConfigOption option = method.getAnnotation(ConfigOption.class);
+ /** If Annotated with Config Option*/
+ if (option != null) {
+
+ /** Retrieve the actual String value from the properties map */
+ String configValue = propertiesMap.get(option.name());
+
+ /** Might be a good idea to catch a class cast exception here if we're wrong */
+ PropertyEditor editor = (PropertyEditor) option.propertyEditorClass().newInstance();
+
+ /** This line causes the property editors to convert the string to the object*/
+ editor.setAsText(configValue);
+
+ /** This line grabs the object we want and invokes the method we're currently working on - with this scheme, only annotations should go on set methods */
+ method.invoke(obj, editor.getValue());
+ }
+ }
+
+ /** Now show that we actually stored the objects on the ConfiguredObject itself */
+ System.out.println("Information on Configured Object:");
+ System.out.println("Initialization String: " + obj.getInitializationString());
+ System.out.println("ObjectProperty: " + obj.getObjectProperty().getName());
+
+ }
+}
Added: trunk/components-core/src/test/java/org/dllearner/examples/ConfigOption.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/examples/ConfigOption.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/examples/ConfigOption.java 2011-07-27 04:46:43 UTC (rev 2968)
@@ -0,0 +1,36 @@
+package org.dllearner.examples;
+
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: Chris
+ * Date: 7/26/11
+ * Time: 8:55 PM
+ *
+ * This is an example annotation class allowing one to configure a field with a name, description, and corresponding property editor.
+ *
+ * Note: Only put this on Setters that take the actual object you want to end up with as the example expects it to be on the setter
+ */
+@Retention(RetentionPolicy.RUNTIME)
+public @interface ConfigOption {
+
+ /**
+ * The name of this config option.
+ * @return The name of this config option.
+ */
+ String name();
+
+ /**
+ * The description of this config option
+ * @return
+ */
+ String description();
+
+ /**
+ * An implementation of the Property Editor to use
+ * @return
+ */
+ Class propertyEditorClass();
+}
Added: trunk/components-core/src/test/java/org/dllearner/examples/ConfiguredObject.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/examples/ConfiguredObject.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/examples/ConfiguredObject.java 2011-07-27 04:46:43 UTC (rev 2968)
@@ -0,0 +1,59 @@
+package org.dllearner.examples;
+
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.examples.ConfigOption;
+import org.springframework.beans.propertyeditors.StringTrimmerEditor;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: Chris
+ * Date: 7/26/11
+ * Time: 8:57 PM
+ *
+ * In this example, this is the object that is actually getting configured. It has the fields that we want to define
+ * configuration on and hence that's why we use the annotations.
+ */
+public class ConfiguredObject {
+
+
+
+
+ /** Two options that can be configured for this object */
+ private String initializationString;
+ private ObjectProperty objectProperty;
+
+
+ /**
+ * Default constructor
+ */
+ public ConfiguredObject() {
+
+ }
+
+
+ /**
+ * Get the Initialization String.
+ * @return The Initialization String
+ */
+ public String getInitializationString() {
+ return initializationString;
+ }
+
+ /**
+ * Set the Initialization String
+ * @param initializationString
+ */
+ @ConfigOption(name="initString", description = "An Initialization String", propertyEditorClass = OurStringTrimmerEditor.class)
+ public void setInitializationString(String initializationString) {
+ this.initializationString = initializationString;
+ }
+
+ /** Corresponds with the name above */
+ public ObjectProperty getObjectProperty() {
+ return objectProperty;
+ }
+ @ConfigOption(name="objectProperty", description = "Some Object Property", propertyEditorClass = ObjectPropertyEditor.class)
+ public void setObjectProperty(ObjectProperty objectProperty) {
+ this.objectProperty = objectProperty;
+ }
+}
Added: trunk/components-core/src/test/java/org/dllearner/examples/ObjectPropertyEditor.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/examples/ObjectPropertyEditor.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/examples/ObjectPropertyEditor.java 2011-07-27 04:46:43 UTC (rev 2968)
@@ -0,0 +1,88 @@
+package org.dllearner.examples;
+
+import org.dllearner.core.owl.ObjectProperty;
+
+import java.awt.*;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyEditor;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: Chris
+ * Date: 7/26/11
+ * Time: 9:42 PM
+ * <p/>
+ * Basic Property Editor for the Object Property DL-Learner class. Doesn't have GUI support yet but we could add that later if we wanted.
+ */
+public class ObjectPropertyEditor implements PropertyEditor {
+
+
+ private ObjectProperty value;
+
+ @Override
+ public void setValue(Object value) {
+ this.value = (ObjectProperty) value;
+ }
+
+ @Override
+ public Object getValue() {
+ return value;
+ }
+
+ @Override
+ public boolean isPaintable() {
+ /** Not right now, we're doing non gui work */
+ return false;
+ }
+
+ @Override
+ public void paintValue(Graphics gfx, Rectangle box) {
+
+ }
+
+ @Override
+ public String getJavaInitializationString() {
+ /** This returns the value needed to reconstitute the object from a string */
+ return value.getName();
+ }
+
+ @Override
+ public String getAsText() {
+ /** Get the text value of this object - for displaying in GUIS, etc */
+ return value.getName();
+ }
+
+ @Override
+ public void setAsText(String text) throws IllegalArgumentException {
+ value = new ObjectProperty(text);
+ }
+
+ @Override
+ public String[] getTags() {
+ /** If there was a known set of values it had to have, we could add that list here */
+ return new String[0];
+ }
+
+ @Override
+ public Component getCustomEditor() {
+ /** GUI stuff, if you wanted to edit it a custom way */
+ return null;
+ }
+
+ @Override
+ public boolean supportsCustomEditor() {
+ /** We don't support this right now, but maybe later */
+ return false;
+
+ }
+
+ @Override
+ public void addPropertyChangeListener(PropertyChangeListener listener) {
+ /** More gui stuff, we don't need this for our basic example */
+ }
+
+ @Override
+ public void removePropertyChangeListener(PropertyChangeListener listener) {
+ /** More gui stuff, we don't need this for our basic example */
+ }
+}
Added: trunk/components-core/src/test/java/org/dllearner/examples/OurStringTrimmerEditor.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/examples/OurStringTrimmerEditor.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/examples/OurStringTrimmerEditor.java 2011-07-27 04:46:43 UTC (rev 2968)
@@ -0,0 +1,22 @@
+package org.dllearner.examples;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: Chris
+ * Date: 7/26/11
+ * Time: 10:17 PM
+ * <p/>
+ * Making a basic extension so I can get a default constructor so that using reflection is simpler.
+ *
+ * I'm extending a Spring provided class for this.
+ */
+public class OurStringTrimmerEditor extends org.springframework.beans.propertyeditors.StringTrimmerEditor {
+
+
+ /**
+ * Default Constructor
+ */
+ public OurStringTrimmerEditor() {
+ super(true);
+ }
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-08-02 10:53:03
|
Revision: 2973
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2973&view=rev
Author: lorenz_b
Date: 2011-08-02 10:52:56 +0000 (Tue, 02 Aug 2011)
Log Message:
-----------
Changed dependency scope.
Extended reasoner.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/PropertyDomainAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/SubPropertyOfAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-07-28 13:02:01 UTC (rev 2972)
+++ trunk/components-core/pom.xml 2011-08-02 10:52:56 UTC (rev 2973)
@@ -251,7 +251,6 @@
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>3.0.5.RELEASE</version>
- <scope>test</scope>
</dependency>
</dependencies>
</project>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/PropertyDomainAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/PropertyDomainAxiomLearner.java 2011-07-28 13:02:01 UTC (rev 2972)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/PropertyDomainAxiomLearner.java 2011-08-02 10:52:56 UTC (rev 2973)
@@ -1,33 +1,80 @@
package org.dllearner.algorithms.properties;
+import java.beans.PropertyEditor;
+import java.lang.reflect.Field;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedSet;
import org.dllearner.core.AxiomLearningAlgorithm;
import org.dllearner.core.Component;
import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.config.ConfigOption;
+import org.dllearner.core.config.IntegerEditor;
+import org.dllearner.core.config.ObjectPropertyEditor;
import org.dllearner.core.configurators.Configurator;
import org.dllearner.core.owl.Axiom;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
+
public class PropertyDomainAxiomLearner extends Component implements AxiomLearningAlgorithm {
- private String propertyToDescribe;
+ private static final Logger logger = LoggerFactory.getLogger(PropertyDomainAxiomLearner.class);
- public String getPropertyToDescribe() {
+ @ConfigOption(name="propertyToDescribe", description="", propertyEditorClass=ObjectPropertyEditor.class)
+ private ObjectProperty propertyToDescribe;
+ @ConfigOption(name="maxExecutionTimeInSeconds", description="", propertyEditorClass=IntegerEditor.class)
+ private int maxExecutionTimeInSeconds;
+
+ private SPARQLReasoner reasoner;
+ private SparqlEndpointKS ks;
+
+ public PropertyDomainAxiomLearner(SparqlEndpointKS ks){
+ this.ks = ks;
+ }
+
+ public int getMaxExecutionTimeInSeconds() {
+ return maxExecutionTimeInSeconds;
+ }
+
+ public void setMaxExecutionTimeInSeconds(int maxExecutionTimeInSeconds) {
+ this.maxExecutionTimeInSeconds = maxExecutionTimeInSeconds;
+ }
+
+ public ObjectProperty getPropertyToDescribe() {
return propertyToDescribe;
}
- public void setPropertyToDescribe(String propertyToDescribe) {
+ public void setPropertyToDescribe(ObjectProperty propertyToDescribe) {
this.propertyToDescribe = propertyToDescribe;
}
-
- public PropertyDomainAxiomLearner(SparqlEndpointKS ks){
-
- }
@Override
public void start() {
- // TODO Auto-generated method stub
+ //get existing domains
+ Description existingDomain = reasoner.getDomain(propertyToDescribe);
+ logger.debug("Existing domain: " + existingDomain);
+
+ //get subjects with types
+ Map<Individual, Set<NamedClass>> individual2Types = getSubjectsWithTypes();
+
+ //get subjects of property
+ Map<Individual, SortedSet<Individual>> members = reasoner.getPropertyMembers(propertyToDescribe);
+
}
@@ -45,8 +92,76 @@
@Override
public void init() throws ComponentInitException {
- // TODO Auto-generated method stub
+ reasoner = new SPARQLReasoner(ks);
}
+
+ private Map<Individual, Set<NamedClass>> getSubjectsWithTypes(){
+ Map<Individual, Set<NamedClass>> individual2Types = new HashMap<Individual, Set<NamedClass>>();
+ int limit = 1000;
+ int offset = 135000;
+ boolean executeAgain = true;
+
+ while(executeAgain){
+ String query = String.format("SELECT ?ind ?type WHERE {?ind %s ?o. ?ind a ?type.} LIMIT %d OFFSET %d", inAngleBrackets(propertyToDescribe.getURI().toString()), limit, offset);
+ ResultSet rs = executeQuery(query);
+ QuerySolution qs;
+ Individual ind;
+ Set<NamedClass> types;
+ executeAgain = rs.hasNext();
+ while(executeAgain && rs.hasNext()){
+ qs = rs.next();
+ ind = new Individual(qs.getResource("ind").getURI());
+ types = individual2Types.get(ind);
+ if(types == null){
+ types = new HashSet<NamedClass>();
+ }
+ types.add(new NamedClass(qs.getResource("type").getURI()));
+ }
+ offset += 1000;
+ }
+
+ return individual2Types;
+ }
+
+ private String inAngleBrackets(String s){
+ return "<" + s + ">";
+ }
+
+ private ResultSet executeQuery(String query){
+ logger.info("Sending query \n {}", query);
+
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(ks.getEndpoint().getURL().toString(), query);
+ for (String dgu : ks.getEndpoint().getDefaultGraphURIs()) {
+ queryExecution.addDefaultGraph(dgu);
+ }
+ for (String ngu : ks.getEndpoint().getNamedGraphURIs()) {
+ queryExecution.addNamedGraph(ngu);
+ }
+ ResultSet resultSet = queryExecution.execSelect();
+ return resultSet;
+ }
+
+ public static void main(String[] args) throws Exception{
+ Map<String, String> propertiesMap = new HashMap<String, String>();
+ propertiesMap.put("propertyToDescribe", "http://dbpedia.org/ontology/league");
+ propertiesMap.put("maxExecutionTimeInSeconds", "20");
+
+ PropertyDomainAxiomLearner l = new PropertyDomainAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia()));
+
+ Field[] fields = l.getClass().getDeclaredFields();
+ for(Field f : fields){
+ ConfigOption option = f.getAnnotation(ConfigOption.class);
+ if(option != null){
+ String configValue = propertiesMap.get(option.name());
+ PropertyEditor editor = (PropertyEditor) option.propertyEditorClass().newInstance();
+ editor.setAsText(configValue);
+ f.set(l, editor.getValue());
+ }
+ }
+
+ l.init();
+ l.start();
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/SubPropertyOfAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/SubPropertyOfAxiomLearner.java 2011-07-28 13:02:01 UTC (rev 2972)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/SubPropertyOfAxiomLearner.java 2011-08-02 10:52:56 UTC (rev 2973)
@@ -3,8 +3,10 @@
import java.beans.PropertyEditor;
import java.lang.reflect.Field;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import org.dllearner.core.AxiomLearningAlgorithm;
import org.dllearner.core.Component;
@@ -17,8 +19,12 @@
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.springframework.beans.propertyeditors.CustomNumberEditor;
+import org.dllearner.reasoning.SPARQLReasoner;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
+
public class SubPropertyOfAxiomLearner extends Component implements AxiomLearningAlgorithm {
@ConfigOption(name="propertyToDescribe", description="", propertyEditorClass=ObjectPropertyEditor.class)
@@ -26,7 +32,7 @@
@ConfigOption(name="maxExecutionTimeInSeconds", description="", propertyEditorClass=IntegerEditor.class)
private int maxExecutionTimeInSeconds;
-
+ private SPARQLReasoner reasoner;
private SparqlEndpointKS ks;
public SubPropertyOfAxiomLearner(SparqlEndpointKS ks){
@@ -35,8 +41,17 @@
@Override
public void start() {
- // TODO Auto-generated method stub
-
+ //get
+ Set<ObjectProperty> properties = new HashSet<ObjectProperty>();
+ String query = String.format("SELECT ?p ?p1 WHERE {?s %s ?o. ?s ?p ?o1. ?s1 ?p1 ?o.}", inAngleBrackets(propertyToDescribe.getURI().toString()));
+ ResultSet rs = executeQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ properties.add(new ObjectProperty(qs.getResource("p").getURI()));
+ properties.add(new ObjectProperty(qs.getResource("p1").getURI()));
+ }
+ System.out.println(properties);
}
@Override
@@ -53,8 +68,7 @@
@Override
public void init() throws ComponentInitException {
- // TODO Auto-generated method stub
-
+ reasoner = new SPARQLReasoner(ks);
}
public int getMaxExecutionTimeInSeconds() {
@@ -73,9 +87,26 @@
this.propertyToDescribe = propertyToDescribe;
}
+ private String inAngleBrackets(String s){
+ return "<" + s + ">";
+ }
+
+ private ResultSet executeQuery(String query){
+ System.out.println(query);
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(ks.getEndpoint().getURL().toString(), query);
+ for (String dgu : ks.getEndpoint().getDefaultGraphURIs()) {
+ queryExecution.addDefaultGraph(dgu);
+ }
+ for (String ngu : ks.getEndpoint().getNamedGraphURIs()) {
+ queryExecution.addNamedGraph(ngu);
+ }
+ ResultSet resultset = queryExecution.execSelect();
+ return resultset;
+ }
+
public static void main(String[] args) throws Exception{
Map<String, String> propertiesMap = new HashMap<String, String>();
- propertiesMap.put("propertyToDescribe", "http://dbpedia.org/ontology/locatedIn");
+ propertiesMap.put("propertyToDescribe", "http://dbpedia.org/ontology/league");
propertiesMap.put("maxExecutionTimeInSeconds", "20");
SubPropertyOfAxiomLearner l = new SubPropertyOfAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW()));
@@ -91,8 +122,9 @@
}
}
- System.out.println(l.getPropertyToDescribe());
- System.out.println(l.getMaxExecutionTimeInSeconds());
+ l.init();
+ l.start();
+
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java 2011-07-28 13:02:01 UTC (rev 2972)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java 2011-08-02 10:52:56 UTC (rev 2973)
@@ -748,7 +748,9 @@
Set<OWLNamedIndividual> individuals = reasoner.getInstances(d, false).getFlattened();
SortedSet<Individual> inds = new TreeSet<Individual>();
for(OWLNamedIndividual ind : individuals)
- inds.add(new Individual(ind.toStringID()));
+ if(ind != null){
+ inds.add(new Individual(ind.toStringID()));
+ }
return inds;
}
@@ -1280,8 +1282,16 @@
}
// take one element from the set and ignore the rest
// (TODO: we need to make sure we always ignore the same concepts)
- OWLObjectPropertyExpression property = node.getRepresentativeElement();
- roles.add(new ObjectProperty(property.asOWLObjectProperty().toStringID()));
+
+ for(OWLObjectPropertyExpression property : node.getEntities()){
+ if(!property.isAnonymous()){
+ roles.add(new ObjectProperty(property.asOWLObjectProperty().toStringID()));
+ break;
+ }
+ }
+ //TODO: We get a problem when the returned representative element is anonymous, so we now use the code above
+// OWLObjectPropertyExpression property = node.getRepresentativeElement();
+// roles.add(new ObjectProperty(property.asOWLObjectProperty().toStringID()));
}
roles.remove(new ObjectProperty(factory.getOWLTopObjectProperty().toStringID()));
roles.remove(new ObjectProperty(factory.getOWLBottomObjectProperty().toStringID()));
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2011-07-28 13:02:01 UTC (rev 2972)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2011-08-02 10:52:56 UTC (rev 2973)
@@ -9,6 +9,7 @@
import java.util.SortedSet;
import java.util.TreeSet;
+import org.dllearner.algorithms.properties.PropertyDomainAxiomLearner;
import org.dllearner.core.IndividualReasoner;
import org.dllearner.core.SchemaReasoner;
import org.dllearner.core.owl.ClassHierarchy;
@@ -25,6 +26,8 @@
import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.utilities.datastructures.SortedSetTuple;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import com.clarkparsia.owlapiv3.XSD;
import com.hp.hpl.jena.query.QuerySolution;
@@ -36,6 +39,8 @@
public class SPARQLReasoner implements SchemaReasoner, IndividualReasoner{
+ private static final Logger logger = LoggerFactory.getLogger(PropertyDomainAxiomLearner.class);
+
private SparqlEndpointKS ks;
public SPARQLReasoner(SparqlEndpointKS ks) {
@@ -117,7 +122,7 @@
@Override
public Map<ObjectProperty, Set<Individual>> getObjectPropertyRelationships(Individual individual) {
Map<ObjectProperty, Set<Individual>> prop2individuals = new HashMap<ObjectProperty, Set<Individual>>();
- String query = String.format("select ?prop ?ind WHERE {" +
+ String query = String.format("SELECT ?prop ?ind WHERE {" +
"%s ?prop ?ind." +
" FILTER(isIRI(?ind) && ?prop != %s && ?prop != %s)}",
inAngleBrackets(individual.getName()), inAngleBrackets(RDF.type.getURI()), inAngleBrackets(OWL.sameAs.getURI()));
@@ -145,7 +150,7 @@
@Override
public Map<Individual, SortedSet<Individual>> getPropertyMembers(ObjectProperty objectProperty) {
Map<Individual, SortedSet<Individual>> subject2objects = new HashMap<Individual, SortedSet<Individual>>();
- String query = String.format("select ?s ?o WHERE {" +
+ String query = String.format("SELECT ?s ?o WHERE {" +
"?s %s ?o." +
" FILTER(isIRI(?o))}",
inAngleBrackets(objectProperty.getName()));
@@ -179,7 +184,7 @@
@Override
public Map<Individual, SortedSet<Double>> getDoubleDatatypeMembers(DatatypeProperty datatypeProperty) {
Map<Individual, SortedSet<Double>> subject2objects = new HashMap<Individual, SortedSet<Double>>();
- String query = String.format("select ?s ?o WHERE {" +
+ String query = String.format("SELECT ?s ?o WHERE {" +
"?s %s ?o." +
" FILTER(DATATYPE(?o) = %s)}",
inAngleBrackets(datatypeProperty.getName()), inAngleBrackets(XSD.DOUBLE.toStringID()));
@@ -207,7 +212,7 @@
@Override
public Map<Individual, SortedSet<Integer>> getIntDatatypeMembers(DatatypeProperty datatypeProperty) {
Map<Individual, SortedSet<Integer>> subject2objects = new HashMap<Individual, SortedSet<Integer>>();
- String query = String.format("select ?s ?o WHERE {" +
+ String query = String.format("SELECT ?s ?o WHERE {" +
"?s %s ?o." +
" FILTER(DATATYPE(?o) = %s)}",
inAngleBrackets(datatypeProperty.getName()), inAngleBrackets(XSD.INT.toStringID()));
@@ -235,7 +240,7 @@
@Override
public Map<Individual, SortedSet<Boolean>> getBooleanDatatypeMembers(DatatypeProperty datatypeProperty) {
Map<Individual, SortedSet<Boolean>> subject2objects = new HashMap<Individual, SortedSet<Boolean>>();
- String query = String.format("select ?s ?o WHERE {" +
+ String query = String.format("SELECT ?s ?o WHERE {" +
"?s %s ?o." +
" FILTER(DATATYPE(?o) = %s)}",
inAngleBrackets(datatypeProperty.getName()), inAngleBrackets(XSD.BOOLEAN.toStringID()));
@@ -263,7 +268,7 @@
@Override
public SortedSet<Individual> getTrueDatatypeMembers(DatatypeProperty datatypeProperty) {
SortedSet<Individual> members = new TreeSet<Individual>();
- String query = String.format("select ?ind WHERE {" +
+ String query = String.format("SELECT ?ind WHERE {" +
"?ind %s ?o." +
" FILTER(isLiteral(?o) && DATATYPE(?o) = %s && ?o=%s)}",
inAngleBrackets(datatypeProperty.getName()), inAngleBrackets(XSD.BOOLEAN.toStringID()),
@@ -282,7 +287,7 @@
@Override
public SortedSet<Individual> getFalseDatatypeMembers(DatatypeProperty datatypeProperty) {
SortedSet<Individual> members = new TreeSet<Individual>();
- String query = String.format("select ?ind WHERE {" +
+ String query = String.format("SELECT ?ind WHERE {" +
"?ind %s ?o." +
" FILTER(isLiteral(?o) && DATATYPE(?o) = %s && ?o=%s)}",
inAngleBrackets(datatypeProperty.getName()), inAngleBrackets(XSD.BOOLEAN.toStringID()),
@@ -311,7 +316,7 @@
@Override
public Description getDomain(ObjectProperty objectProperty) {
- String query = String.format("select ?domain WHERE {" +
+ String query = String.format("SELECT ?domain WHERE {" +
"%s %s ?domain. FILTER(isIRI(?domain))" +
"}",
inAngleBrackets(objectProperty.getName()), inAngleBrackets(RDFS.domain.getURI()));
@@ -334,7 +339,7 @@
@Override
public Description getDomain(DatatypeProperty datatypeProperty) {
- String query = String.format("select ?domain WHERE {" +
+ String query = String.format("SELECT ?domain WHERE {" +
"%s %s ?domain. FILTER(isIRI(?domain))" +
"}",
inAngleBrackets(datatypeProperty.getName()), inAngleBrackets(RDFS.domain.getURI()));
@@ -357,7 +362,7 @@
@Override
public Description getRange(ObjectProperty objectProperty) {
- String query = String.format("select ?range WHERE {" +
+ String query = String.format("SELECT ?range WHERE {" +
"%s %s ?range. FILTER(isIRI(?range))" +
"}",
inAngleBrackets(objectProperty.getName()), inAngleBrackets(RDFS.range.getURI()));
@@ -413,7 +418,7 @@
@Override
public Set<Description> getAssertedDefinitions(NamedClass namedClass) {
Set<Description> definitions = new HashSet<Description>();
- String query = String.format("SELECT ?class {%s %s ?class. FILTER(isIRI(?class))} UNION {?class. %s %s. FILTER(isIRI(?class))}",
+ String query = String.format("SELECT ?class { {%s %s ?class. FILTER(isIRI(?class))} UNION {?class. %s %s. FILTER(isIRI(?class))} }",
inAngleBrackets(namedClass.getURI().toString()),
inAngleBrackets(OWL.equivalentClass.getURI()),
inAngleBrackets(OWL.equivalentClass.getURI()),
@@ -535,14 +540,35 @@
@Override
public SortedSet<DatatypeProperty> getSuperProperties(DatatypeProperty dataProperty) {
- // TODO Auto-generated method stub
- return null;
+ SortedSet<DatatypeProperty> superProperties = new TreeSet<DatatypeProperty>();
+ String query = String.format("SELECT ?sup {%s %s ?sup. FILTER(isIRI(?sup))}",
+ inAngleBrackets(dataProperty.getURI().toString()),
+ inAngleBrackets(RDFS.subPropertyOf.getURI())
+ );
+ ResultSet rs = executeQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ superProperties.add(new DatatypeProperty(qs.getResource("sup").getURI()));
+ }
+ return superProperties;
}
@Override
public SortedSet<DatatypeProperty> getSubProperties(DatatypeProperty dataProperty) {
- // TODO Auto-generated method stub
- return null;
+ SortedSet<DatatypeProperty> subProperties = new TreeSet<DatatypeProperty>();
+ String query = String.format("SELECT ?sub {?sub %s %s. FILTER(isIRI(?sub))}",
+ inAngleBrackets(RDFS.subPropertyOf.getURI()),
+ inAngleBrackets(dataProperty.getURI().toString())
+
+ );
+ ResultSet rs = executeQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ subProperties.add(new DatatypeProperty(qs.getResource("sub").getURI()));
+ }
+ return subProperties;
}
@Override
@@ -556,7 +582,7 @@
}
private ResultSet executeQuery(String query){
- System.out.println(query);
+ logger.info("Sending query \n {}", query);
QueryEngineHTTP queryExecution = new QueryEngineHTTP(ks.getEndpoint().getURL().toString(), query);
for (String dgu : ks.getEndpoint().getDefaultGraphURIs()) {
queryExecution.addDefaultGraph(dgu);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2011-08-04 08:40:11
|
Revision: 2986
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2986&view=rev
Author: jenslehmann
Date: 2011-08-04 08:40:05 +0000 (Thu, 04 Aug 2011)
Log Message:
-----------
removed log folder from SVN (please re-create the components-core/log/ folder locally)
Removed Paths:
-------------
trunk/components-core/log/
Property Changed:
----------------
trunk/components-core/
Property changes on: trunk/components-core
___________________________________________________________________
Modified: svn:ignore
- components-core.iml
target
.classpath
.project
.settings
+ components-core.iml
target
log
.classpath
.project
.settings
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-08-11 14:20:56
|
Revision: 3032
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3032&view=rev
Author: lorenz_b
Date: 2011-08-11 14:20:49 +0000 (Thu, 11 Aug 2011)
Log Message:
-----------
Added preliminary utility class for vocabulary of enrichments.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/utilities/EnrichmentVocabulary.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-08-11 12:56:45 UTC (rev 3031)
+++ trunk/components-core/pom.xml 2011-08-11 14:20:49 UTC (rev 3032)
@@ -225,6 +225,11 @@
<groupId>com.jamonapi</groupId>
<artifactId>jamon</artifactId>
</dependency>
+
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-digester3</artifactId>
+ </dependency>
<!--JENA ARQ is in central - we use the latest-->
<dependency>
@@ -276,5 +281,10 @@
<artifactId>slf4j-api</artifactId>
<version>1.5.8</version>
</dependency>
+ <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>20041127.091804</version>
+ </dependency>
</dependencies>
</project>
Modified: trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java 2011-08-11 12:56:45 UTC (rev 3031)
+++ trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java 2011-08-11 14:20:49 UTC (rev 3032)
@@ -1,7 +1,15 @@
package org.dllearner.core;
+import org.apache.commons.codec.digest.DigestUtils;
import org.dllearner.core.owl.Axiom;
+import org.dllearner.utilities.EnrichmentVocabulary;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
public class EvaluatedAxiom {
private Axiom axiom;
@@ -25,6 +33,18 @@
return axiom + "(" + score.getAccuracy()+ ")";
}
+ public void toRDF(){
+ OWLDataFactory f = new OWLDataFactoryImpl();
+
+ String id = DigestUtils.md5Hex(axiom.toString()) + score.getAccuracy();
+ OWLNamedIndividual ind = f.getOWLNamedIndividual(IRI.create(EnrichmentVocabulary.NS + id));
+
+ OWLAxiom ax1 = f.getOWLClassAssertionAxiom(EnrichmentVocabulary.Suggestion, ind);
+ OWLAxiom ax2 = f.getOWLObjectPropertyAssertionAxiom(EnrichmentVocabulary.hasAxiom, ind, null);
+ OWLAxiom ax3 = f.getOWLDataPropertyAssertionAxiom(EnrichmentVocabulary.confidence, ind, score.getAccuracy());
+
+ System.out.println(ax1);
+ }
}
Added: trunk/components-core/src/main/java/org/dllearner/utilities/EnrichmentVocabulary.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/EnrichmentVocabulary.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/EnrichmentVocabulary.java 2011-08-11 14:20:49 UTC (rev 3032)
@@ -0,0 +1,52 @@
+package org.dllearner.utilities;
+
+import org.semanticweb.owlapi.model.IRI;
+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 uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
+public class EnrichmentVocabulary {
+
+ private static final OWLDataFactory factory = new OWLDataFactoryImpl();
+
+ public static final String NS = "http://www.dl-learner.org/enrichment.owl#";
+
+ //the classes
+ public static final OWLClass ChangeSet = factory.getOWLClass(IRI.create(NS + "ChangeSet"));
+
+ public static final OWLClass Suggestion = factory.getOWLClass(IRI.create(NS + "Suggestion"));
+
+ public static final OWLClass Parameter = factory.getOWLClass(IRI.create(NS + "Parameter"));
+
+
+ //the object properties
+ public static final OWLObjectProperty creation = factory.getOWLObjectProperty(IRI.create(NS + "creation"));
+
+ public static final OWLObjectProperty hasAxiom = factory.getOWLObjectProperty(IRI.create(NS + "hasAxiom"));
+
+ public static final OWLObjectProperty hasChange = factory.getOWLObjectProperty(IRI.create(NS + "hasChange"));
+
+ public static final OWLObjectProperty hasInput = factory.getOWLObjectProperty(IRI.create(NS + "hasInput"));
+
+ public static final OWLObjectProperty hasParameter = factory.getOWLObjectProperty(IRI.create(NS + "hasParameter"));
+
+ public static final OWLObjectProperty usedAlgorithm = factory.getOWLObjectProperty(IRI.create(NS + "usedAlgorithm"));
+
+
+ //the data properties
+ public static final OWLDataProperty confidence = factory.getOWLDataProperty(IRI.create(NS + "confidence"));
+
+ public static final OWLDataProperty explanation = factory.getOWLDataProperty(IRI.create(NS + "explanation"));
+
+ public static final OWLDataProperty parameterName = factory.getOWLDataProperty(IRI.create(NS + "parameterName"));
+
+ public static final OWLDataProperty parameterValue = factory.getOWLDataProperty(IRI.create(NS + "parameterValue"));
+
+ public static final OWLDataProperty timestamp = factory.getOWLDataProperty(IRI.create(NS + "timestamp"));
+
+ public static final OWLDataProperty version = factory.getOWLDataProperty(IRI.create(NS + "version"));
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-08-21 20:31:46
|
Revision: 3078
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3078&view=rev
Author: lorenz_b
Date: 2011-08-21 20:31:32 +0000 (Sun, 21 Aug 2011)
Log Message:
-----------
Added maven-license-plugin to automatically create/update license headers (USAGE: mvn license:format -Dyear=${currentYear} ).
Added header file.
Updated license headers for release.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/Info.java
trunk/components-core/src/main/java/org/dllearner/algorithms/BruteForceLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/RandomGuesser.java
trunk/components-core/src/main/java/org/dllearner/algorithms/SearchTreeNode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/DisjunctiveHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELDescriptionEdge.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELDescriptionEdgeComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELDescriptionNode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELDescriptionNodeComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELDescriptionTree.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELDescriptionTreeComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithm.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/SearchTreeNode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/Simulation.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/StableHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/TreeAndRoleSet.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/TreeAndRoleSetComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/TreeTuple.java
trunk/components-core/src/main/java/org/dllearner/algorithms/el/package.html
trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyCELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyOEHeuristicRuntime.java
trunk/components-core/src/main/java/org/dllearner/algorithms/fuzzydll/FuzzyOENode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/gp/ADC.java
trunk/components-core/src/main/java/org/dllearner/algorithms/gp/GP.java
trunk/components-core/src/main/java/org/dllearner/algorithms/gp/GPUtilities.java
trunk/components-core/src/main/java/org/dllearner/algorithms/gp/Program.java
trunk/components-core/src/main/java/org/dllearner/algorithms/gp/package.html
trunk/components-core/src/main/java/org/dllearner/algorithms/hybridgp/GeneticRefinementOperator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/hybridgp/Psi.java
trunk/components-core/src/main/java/org/dllearner/algorithms/hybridgp/package.html
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/EntityTextRetriever.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/ISLE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneDocument.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneIndexer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneSearcher.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/NLPHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/Relevances.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/ExampleBasedHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/ExampleBasedNode.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/FlexibleHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/LexicographicHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/MultiHeuristic.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/NodeComparatorStable.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/OCEL.java
trunk/components-core/src/main/java/org/dllearner/algorithms/ocel/ROLearner2.java
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trunk/components-core/src/main/java/org/dllearner/kb/manipulator/DBpediaNavigatorOtherRule.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/Manipulator.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/ObjectReplacementRule.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/PredicateReplacementRule.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/Rule.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/SimpleObjectFilterRule.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/SimplePredicateFilterRule.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/StringToResource.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/TypeFilterRule.java
trunk/components-core/src/main/java/org/dllearner/kb/manipulator/package.html
trunk/components-core/src/main/java/org/dllearner/kb/package.html
trunk/components-core/src/main/java/org/dllearner/kb/sparql/Cache.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtendedQueryEngineHTTP.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/HttpQuery.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/NaturalLanguageDescriptionConvertVisitor.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQuery.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertRDFS.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQueryException.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQueryMaker.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/package.html
trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/ClassLearningProblem.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/ClassScore.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/EvaluatedDescriptionClass.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/EvaluatedDescriptionPosNeg.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/EvaluatedDescriptionPosOnly.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/EvaluationCache.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/Heuristics.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/PosNegLP.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/PosNegLPStandard.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/PosNegLPStrict.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/PosOnlyLP.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/ScorePosNeg.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/ScorePosOnly.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/ScoreThreeValued.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/ScoreTwoValued.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLP.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/fuzzydll/FuzzyPosNegLPStandard.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/package.html
trunk/components-core/src/main/java/org/dllearner/package.html
trunk/components-core/src/main/java/org/dllearner/parser/KBParser.java
trunk/components-core/src/main/java/org/dllearner/parser/KBParserConstants.java
trunk/components-core/src/main/java/org/dllearner/parser/KBParserTokenManager.java
trunk/components-core/src/main/java/org/dllearner/parser/ParseException.java
trunk/components-core/src/main/java/org/dllearner/parser/PrologParser.java
trunk/components-core/src/main/java/org/dllearner/parser/PrologParserConstants.java
trunk/components-core/src/main/java/org/dllearner/parser/PrologParserTokenManager.java
trunk/components-core/src/main/java/org/dllearner/parser/SimpleCharStream.java
trunk/components-core/src/main/java/org/dllearner/parser/Token.java
trunk/components-core/src/main/java/org/dllearner/parser/TokenMgrError.java
trunk/components-core/src/main/java/org/dllearner/parser/package.html
trunk/components-core/src/main/java/org/dllearner/prolog/ArrayListSet.java
trunk/components-core/src/main/java/org/dllearner/prolog/Atom.java
trunk/components-core/src/main/java/org/dllearner/prolog/Body.java
trunk/components-core/src/main/java/org/dllearner/prolog/Clause.java
trunk/components-core/src/main/java/org/dllearner/prolog/Constant.java
trunk/components-core/src/main/java/org/dllearner/prolog/Function.java
trunk/components-core/src/main/java/org/dllearner/prolog/FunctionDefinition.java
trunk/components-core/src/main/java/org/dllearner/prolog/List.java
trunk/components-core/src/main/java/org/dllearner/prolog/Literal.java
trunk/components-core/src/main/java/org/dllearner/prolog/Number.java
trunk/components-core/src/main/java/org/dllearner/prolog/PredicateDefinition.java
trunk/components-core/src/main/java/org/dllearner/prolog/Program.java
trunk/components-core/src/main/java/org/dllearner/prolog/PrologConstant.java
trunk/components-core/src/main/java/org/dllearner/prolog/StringConstant.java
trunk/components-core/src/main/java/org/dllearner/prolog/Term.java
trunk/components-core/src/main/java/org/dllearner/prolog/Variable.java
trunk/components-core/src/main/java/org/dllearner/prolog/package.html
trunk/components-core/src/main/java/org/dllearner/reasoning/DIGConverter.java
trunk/components-core/src/main/java/org/dllearner/reasoning/DIGHTTPConnector.java
trunk/components-core/src/main/java/org/dllearner/reasoning/DIGReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
trunk/components-core/src/main/java/org/dllearner/reasoning/FastRetrieval.java
trunk/components-core/src/main/java/org/dllearner/reasoning/FastRetrievalReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIDIGConverter.java
trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/ReasonerType.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyDLReasonerManager.java
trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/package.html
trunk/components-core/src/main/java/org/dllearner/refinementoperators/ELDown.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/ELDown2.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/MathOperations.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/OperatorInverter.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/PsiDown.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/PsiUp.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RefinementOperator.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RefinementOperatorAdapter.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDown.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/Utility.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/fuzzydll/FuzzyRhoDRDown.java
trunk/components-core/src/main/java/org/dllearner/refinementoperators/package.html
trunk/components-core/src/main/java/org/dllearner/utilities/CSVFileToArray.java
trunk/components-core/src/main/java/org/dllearner/utilities/CommonPrefixMap.java
trunk/components-core/src/main/java/org/dllearner/utilities/EnrichmentVocabulary.java
trunk/components-core/src/main/java/org/dllearner/utilities/Files.java
trunk/components-core/src/main/java/org/dllearner/utilities/Helper.java
trunk/components-core/src/main/java/org/dllearner/utilities/JamonMonitorLogger.java
trunk/components-core/src/main/java/org/dllearner/utilities/Logging.java
trunk/components-core/src/main/java/org/dllearner/utilities/StringFormatter.java
trunk/components-core/src/main/java/org/dllearner/utilities/URLencodeUTF8.java
trunk/components-core/src/main/java/org/dllearner/utilities/analyse/CountInstances.java
trunk/components-core/src/main/java/org/dllearner/utilities/analyse/Hierarchy.java
trunk/components-core/src/main/java/org/dllearner/utilities/analyse/ScriptDoAll.java
trunk/components-core/src/main/java/org/dllearner/utilities/components/ComponentCombo.java
trunk/components-core/src/main/java/org/dllearner/utilities/components/ReasonerComponentFactory.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/Datastructures.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/DescriptionSubsumptionTree.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/Maps.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/RDFNodeTuple.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/ResultConceptSorter.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SortedSetTuple.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/StringTuple.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/TrainTestList.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/package.html
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderOWL.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderOWL.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/ExMakerHelper.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/ExampleContainer.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/ExampleDataCollector.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/package.html
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/ExMakerCrossFolds.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/ExMakerFixedSize.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/ExMakerRandomizer.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/Examples.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/ExperimentConfiguration.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/FinalizedMonitor.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/Jamon.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/MyMonKey.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/Table.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/TableRowColumn.java
trunk/components-core/src/main/java/org/dllearner/utilities/experiments/Units.java
trunk/components-core/src/main/java/org/dllearner/utilities/learn/ConfWriter.java
trunk/components-core/src/main/java/org/dllearner/utilities/learn/LearnConfiguration.java
trunk/components-core/src/main/java/org/dllearner/utilities/learn/LearnOWLFileConfiguration.java
trunk/components-core/src/main/java/org/dllearner/utilities/learn/LearnSPARQLConfiguration.java
trunk/components-core/src/main/java/org/dllearner/utilities/learn/UsedEntitiesDetection.java
trunk/components-core/src/main/java/org/dllearner/utilities/learn/package.html
trunk/components-core/src/main/java/org/dllearner/utilities/owl/ConceptComparator.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/ConceptTransformation.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/DLLearnerDescriptionConvertVisitor.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionMinimizer.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/DescriptionSet.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/EvaluatedDescriptionComparator.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/EvaluatedDescriptionPosNegComparator.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/EvaluatedDescriptionSet.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/ManchesterOWLSyntaxParser.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWL2SPARULConverter.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIAxiomConvertVisitor.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIConverter.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIDescriptionConvertVisitor.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIRenderers.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLVocabulary.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OntologyClassRewriter.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OntologyCloser.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OntologyCloserOWLAPI.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/PropertyContext.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/RoleComparator.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/package.html
trunk/components-core/src/main/java/org/dllearner/utilities/package-info.java
trunk/components-core/src/main/java/org/dllearner/utilities/statistics/FleissKappa.java
trunk/components-core/src/main/java/org/dllearner/utilities/statistics/RawAgreement.java
trunk/components-core/src/main/java/org/dllearner/utilities/statistics/SimpleClock.java
trunk/components-core/src/main/java/org/dllearner/utilities/statistics/Stat.java
trunk/components-core/src/main/java/org/dllearner/utilities/statistics/Statistics.java
trunk/components-core/src/main/java/org/dllearner/utilities/statistics/Table.java
trunk/components-core/src/main/java/org/dllearner/utilities/statistics/TableColumn.java
trunk/components-core/src/main/java/org/dllearner/utilities/statistics/package.html
trunk/components-core/src/test/java/org/dllearner/examples/AnnotationExample.java
trunk/components-core/src/test/java/org/dllearner/examples/ConfigOption.java
trunk/components-core/src/test/java/org/dllearner/examples/ConfiguredObject.java
trunk/components-core/src/test/java/org/dllearner/examples/ObjectPropertyEditor.java
trunk/components-core/src/test/java/org/dllearner/examples/OurStringTrimmerEditor.java
trunk/components-core/src/test/java/org/dllearner/test/ClassCastExceptionTest.java
trunk/components-core/src/test/java/org/dllearner/test/ComponentTest.java
trunk/components-core/src/test/java/org/dllearner/test/FaCTBugDemo.java
trunk/components-core/src/test/java/org/dllearner/test/FilterTest.java
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest.java
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains.java
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_Trains_noFuzzyIndividuals.java
trunk/components-core/src/test/java/org/dllearner/test/FuzzyDLLTest_noFuzzyTrains.java
trunk/components-core/src/test/java/org/dllearner/test/HermitTest.java
trunk/components-core/src/test/java/org/dllearner/test/JenaConstruct.java
trunk/components-core/src/test/java/org/dllearner/test/JenaHTTPTest.java
trunk/components-core/src/test/java/org/dllearner/test/JenaLongQueryTest.java
trunk/components-core/src/test/java/org/dllearner/test/JenaQueryToResultSpeedTest.java
trunk/components-core/src/test/java/org/dllearner/test/OWLAPIBugDemo.java
trunk/components-core/src/test/java/org/dllearner/test/OWLAPIConsistency.java
trunk/components-core/src/test/java/org/dllearner/test/OWLLinkReasonerTest.java
trunk/components-core/src/test/java/org/dllearner/test/PelletBug.java
trunk/components-core/src/test/java/org/dllearner/test/PelletBug2.java
trunk/components-core/src/test/java/org/dllearner/test/PelletBug3.java
trunk/components-core/src/test/java/org/dllearner/test/PelletPerformanceProblem.java
trunk/components-core/src/test/java/org/dllearner/test/SparqlEndpointTest.java
trunk/components-core/src/test/java/org/dllearner/test/SparqlExtractionTest.java
trunk/components-core/src/test/java/org/dllearner/test/SparqlQueryConverter.java
trunk/components-core/src/test/java/org/dllearner/test/SworeTest.java
trunk/components-core/src/test/java/org/dllearner/test/TestGetExampleBug.java
trunk/components-core/src/test/java/org/dllearner/test/TestOneQueryForMusicRecommender.java
trunk/components-core/src/test/java/org/dllearner/test/TripleTypeTest.java
trunk/components-core/src/test/java/org/dllearner/test/ValueKBParserTest.java
trunk/components-core/src/test/java/org/dllearner/test/junit/AllTestsRunner.java
trunk/components-core/src/test/java/org/dllearner/test/junit/ClassExpressionTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/ComponentTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/ELDescriptionTreeTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/ELDownTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/HeuristicTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/PropertyLearningTest.java
trunk/components-core/src/test/java/org/dllearner/test/junit/RefinementOperatorTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/SimulationTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/TestOntologies.java
trunk/components-core/src/test/java/org/dllearner/test/junit/UtilitiesTests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/package.html
trunk/components-core/src/test/java/org/dllearner/test/package.html
Added Paths:
-----------
trunk/components-core/src/etc/
trunk/components-core/src/etc/header.txt
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/pom.xml 2011-08-21 20:31:32 UTC (rev 3078)
@@ -4,7 +4,6 @@
<groupId>org.dllearner</groupId>
<artifactId>components-core</artifactId>
- <packaging>jar</packaging>
<name>DL Learner Core Components</name>
<url>http://aksw.org/Projects/DLLearner</url>
@@ -109,6 +108,15 @@
</distroConfigurations>
</configuration>
</plugin>
+ <plugin>
+ <groupId>com.mycila.maven-license-plugin</groupId>
+ <artifactId>maven-license-plugin</artifactId>
+ <configuration>
+ <header>src/etc/header.txt</header>
+ </configuration>
+ </plugin>
+
+
</plugins>
</build>
Added: trunk/components-core/src/etc/header.txt
===================================================================
--- trunk/components-core/src/etc/header.txt (rev 0)
+++ trunk/components-core/src/etc/header.txt 2011-08-21 20:31:32 UTC (rev 3078)
@@ -0,0 +1,16 @@
+Copyright (C) 2007-${year}, Jens Lehmann
+
+This file is part of DL-Learner.
+
+DL-Learner is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 3 of the License, or
+(at your option) any later version.
+
+DL-Learner is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
\ No newline at end of file
Property changes on: trunk/components-core/src/etc/header.txt
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Modified: trunk/components-core/src/main/java/org/dllearner/Info.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/Info.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/Info.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -1,4 +1,23 @@
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
// File is updated automatically when a new version is created
package org.dllearner;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/BruteForceLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/BruteForceLearner.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/BruteForceLearner.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -1,8 +1,8 @@
/**
- * Copyright (C) 2007, Jens Lehmann
+ * Copyright (C) 2007-2011, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -15,7 +15,6 @@
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
*/
package org.dllearner.algorithms;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -2,7 +2,7 @@
* Copyright (C) 2007-2011, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -15,8 +15,8 @@
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
*/
+
package org.dllearner.algorithms;
import java.util.ArrayList;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/RandomGuesser.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/RandomGuesser.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/RandomGuesser.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -1,8 +1,8 @@
/**
- * Copyright (C) 2007, Jens Lehmann
+ * Copyright (C) 2007-2011, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -15,8 +15,8 @@
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
*/
+
package org.dllearner.algorithms;
import java.util.Collection;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/SearchTreeNode.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/SearchTreeNode.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/SearchTreeNode.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -1,8 +1,8 @@
/**
- * Copyright (C) 2007-2010, Jens Lehmann
+ * Copyright (C) 2007-2011, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -15,8 +15,8 @@
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
*/
+
package org.dllearner.algorithms;
import java.util.Collection;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -2,7 +2,7 @@
* Copyright (C) 2007-2011, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -15,8 +15,8 @@
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
*/
+
package org.dllearner.algorithms;
import java.util.ArrayList;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -1,8 +1,8 @@
/**
- * Copyright (C) 2007-2009, Jens Lehmann
+ * Copyright (C) 2007-2011, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -15,8 +15,8 @@
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
*/
+
package org.dllearner.algorithms.celoe;
import java.io.File;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -1,8 +1,8 @@
/**
- * Copyright (C) 2007-2009, Jens Lehmann
+ * Copyright (C) 2007-2011, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -15,8 +15,8 @@
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
*/
+
package org.dllearner.algorithms.celoe;
import java.util.Comparator;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -1,8 +1,8 @@
/**
- * Copyright (C) 2007-2009, Jens Lehmann
+ * Copyright (C) 2007-2011, Jens Lehmann
*
* This file is part of DL-Learner.
- *
+ *
* DL-Learner is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
@@ -15,8 +15,8 @@
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
- *
*/
+
package org.dllearner.algorithms.celoe;
import java.text.DecimalFormat;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/el/DisjunctiveHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/el/DisjunctiveHeuristic.java 2011-08-20 17:04:42 UTC (rev 3077)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/el/DisjunctiveHeuristic.java 2011-08-21 20:31:32 UTC (rev 3078)
@@ -1,3 +1,22 @@
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it...
[truncated message content] |
|
From: <lor...@us...> - 2011-08-22 09:18:04
|
Revision: 3083
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3083&view=rev
Author: lorenz_b
Date: 2011-08-22 09:17:56 +0000 (Mon, 22 Aug 2011)
Log Message:
-----------
Cleaned up pom.xml.
Removed unused classes.
Modified Paths:
--------------
trunk/components-core/pom.xml
Removed Paths:
-------------
trunk/components-core/src/main/java/org/dllearner/core/config/OurStringTrimmerEditor.java
trunk/components-core/src/test/java/org/dllearner/examples/
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-08-22 07:28:14 UTC (rev 3082)
+++ trunk/components-core/pom.xml 2011-08-22 09:17:56 UTC (rev 3083)
@@ -152,12 +152,6 @@
</dependency>
<dependency>
- <groupId>org.projectlombok</groupId>
- <artifactId>lombok</artifactId>
- <scope>provided</scope>
- </dependency>
-
- <dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</dependency>
@@ -177,38 +171,22 @@
</exclusions>
</dependency>
- <!--SwingX is in central-->
- <dependency>
- <groupId>org.swinglabs</groupId>
- <artifactId>swingx</artifactId>
- </dependency>
-
-
<!--JSON is in Central-->
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
</dependency>
-
<dependency>
<groupId>net.sf.jopt-simple</groupId>
<artifactId>jopt-simple</artifactId>
</dependency>
-
- <!--Lucene is in Central-->
<dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-core</artifactId>
- </dependency>
-
- <dependency>
<groupId>org.ini4j</groupId>
<artifactId>ini4j</artifactId>
</dependency>
-
<dependency>
<groupId>xmlbeans</groupId>
<artifactId>xbean</artifactId>
@@ -275,12 +253,8 @@
<version>1.0</version>
</dependency>
+
<dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-beans</artifactId>
- <version>3.0.5.RELEASE</version>
- </dependency>
- <dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.5.8</version>
Deleted: trunk/components-core/src/main/java/org/dllearner/core/config/OurStringTrimmerEditor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/config/OurStringTrimmerEditor.java 2011-08-22 07:28:14 UTC (rev 3082)
+++ trunk/components-core/src/main/java/org/dllearner/core/config/OurStringTrimmerEditor.java 2011-08-22 09:17:56 UTC (rev 3083)
@@ -1,41 +0,0 @@
-/**
- * Copyright (C) 2007-2011, Jens Lehmann
- *
- * This file is part of DL-Learner.
- *
- * DL-Learner is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * DL-Learner is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-
-package org.dllearner.core.config;
-
-/**
- * Created by IntelliJ IDEA.
- * User: Chris
- * Date: 7/26/11
- * Time: 10:17 PM
- * <p/>
- * Making a basic extension so I can get a default constructor so that using reflection is simpler.
- *
- * I'm extending a Spring provided class for this.
- */
-public class OurStringTrimmerEditor extends org.springframework.beans.propertyeditors.StringTrimmerEditor {
-
-
- /**
- * Default Constructor
- */
- public OurStringTrimmerEditor() {
- super(true);
- }
-}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-08-22 11:08:09
|
Revision: 3085
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3085&view=rev
Author: lorenz_b
Date: 2011-08-22 11:08:02 +0000 (Mon, 22 Aug 2011)
Log Message:
-----------
Added javadoc-plugin and 2 style files.
Modified Paths:
--------------
trunk/components-core/pom.xml
Added Paths:
-----------
trunk/components-core/src/etc/javadoc.css
trunk/components-core/src/etc/overview.html
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2011-08-22 09:19:36 UTC (rev 3084)
+++ trunk/components-core/pom.xml 2011-08-22 11:08:02 UTC (rev 3085)
@@ -16,31 +16,26 @@
<build>
<plugins>
- <!--Surefire - for JUnits-->
+ <!--Surefire - for JUnits -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
- <!--
- Uncomment this when the junits are independent of a runtime
- directory
- -->
- <!--<includes>-->
- <!--<include>org/dllearner/test/junit/*</include>-->
- <!--</includes>-->
+ <!-- Uncomment this when the junits are independent of a runtime directory -->
+ <!--<includes> -->
+ <!--<include>org/dllearner/test/junit/*</include> -->
+ <!--</includes> -->
<excludes>
<exclude>org/dllearner/test/*</exclude>
<exclude>org/dllearner/test/junit/TestOntologies.java</exclude>
<exclude>org/dllearner/test/junit/PropertyLearningTest.java</exclude>
- <!--This line excludes inner classes-->
+ <!--This line excludes inner classes -->
<exclude>**/*$*</exclude>
</excludes>
</configuration>
</plugin>
- <!--
- Jar the tests up into a separate jar so other components tests' can
- leverage them
- -->
+ <!-- Jar the tests up into a separate jar so other components tests' can
+ leverage them -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
@@ -108,15 +103,43 @@
</distroConfigurations>
</configuration>
</plugin>
- <plugin>
- <groupId>com.mycila.maven-license-plugin</groupId>
- <artifactId>maven-license-plugin</artifactId>
- <configuration>
- <header>src/etc/header.txt</header>
- </configuration>
- </plugin>
-
-
+ <plugin>
+ <groupId>com.mycila.maven-license-plugin</groupId>
+ <artifactId>maven-license-plugin</artifactId>
+ <configuration>
+ <header>src/etc/header.txt</header>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.8</version>
+ <configuration>
+ <show>public</show>
+ <nohelp>true</nohelp>
+ <destDir>doc/javadoc</destDir>
+ <doctitle>DL-Learner Javadoc</doctitle>
+ <author>true</author>
+ <nodeprecated>false</nodeprecated>
+ <nodeprecatedlist>false</nodeprecatedlist>
+ <noindex>false</noindex>
+ <nonavbar>false</nonavbar>
+ <notree>false</notree>
+ <overview>src/etc/overview.html</overview>
+ <source>1.6</source>
+ <sourcepath>src/main/java</sourcepath>
+ <splitindex>true</splitindex>
+ <stylesheetfile>src/etc/javadoc.css</stylesheetfile>
+ <use>true</use>
+ <version>true</version>#
+ <linksource>true</linksource>
+ <bottom><img style='float:right' src='http://sflogo.sourceforge.net/sflogo.php?group_id=203619&type=1' width='88' height='31' border='0' alt='SourceForge.net Logo' /> DL-Learner is licenced under the terms of the GNU General Public License.<br />Copyright &#169; 2007-2011 Jens Lehmann</bottom>
+ <encoding>ISO-8859-1</encoding>
+ <windowtitle>DL-Learner Javadoc</windowtitle>
+ </configuration>
+ </plugin>
+
+
</plugins>
</build>
@@ -133,13 +156,13 @@
</exclusions>
</dependency>
- <!-- THIS IS FROM THE UNIBAS REPO-->
+ <!-- THIS IS FROM THE UNIBAS REPO -->
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi</artifactId>
</dependency>
- <!-- THIS IS FROM THE UNIBAS REPO-->
+ <!-- THIS IS FROM THE UNIBAS REPO -->
<dependency>
<groupId>com.owldl</groupId>
<artifactId>pellet</artifactId>
@@ -156,10 +179,8 @@
<artifactId>log4j</artifactId>
</dependency>
- <!--
- Available via central, we use the latest with minor mods to DL
- Learner source (IE Dig related code)
- -->
+ <!-- Available via central, we use the latest with minor mods to DL Learner
+ source (IE Dig related code) -->
<dependency>
<groupId>com.hp.hpl.jena</groupId>
<artifactId>jena</artifactId>
@@ -171,7 +192,7 @@
</exclusions>
</dependency>
- <!--JSON is in Central-->
+ <!--JSON is in Central -->
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
@@ -211,9 +232,9 @@
<groupId>com.jamonapi</groupId>
<artifactId>jamon</artifactId>
</dependency>
-
- <!--JENA ARQ is in central - we use the latest-->
+
+ <!--JENA ARQ is in central - we use the latest -->
<dependency>
<groupId>com.hp.hpl.jena</groupId>
<artifactId>arq</artifactId>
@@ -253,16 +274,16 @@
<version>1.0</version>
</dependency>
-
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-api</artifactId>
- <version>1.5.8</version>
- </dependency>
- <dependency>
- <groupId>commons-codec</groupId>
- <artifactId>commons-codec</artifactId>
- <version>20041127.091804</version>
- </dependency>
+
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ <version>1.5.8</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>20041127.091804</version>
+ </dependency>
</dependencies>
</project>
Added: trunk/components-core/src/etc/javadoc.css
===================================================================
--- trunk/components-core/src/etc/javadoc.css (rev 0)
+++ trunk/components-core/src/etc/javadoc.css 2011-08-22 11:08:02 UTC (rev 3085)
@@ -0,0 +1,351 @@
+
+
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!-- ViewVC :: http://www.viewvc.org/ -->
+<head>
+<title>SourceForge.net Repository - [dl-learner] Log of /tags/premaven/javadoc.css</title>
+<meta name="generator" content="ViewVC 1.1.6" />
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<meta name="description" content="The world's largest development and download repository of Open Source code and applications" />
+<meta name="keywords" content="Open Source, Development, Developers, Projects, Downloads, OSTG, VA Software, SF.net, SourceForge" />
+<title>SourceForge.net Repository - dl-learner Index of /</title>
+<link rel="shortcut icon" href="http://a.fsdn.com/con/img/favicon.ico" />
+<link rel="stylesheet" href="http://a.fsdn.com/con/css/sf.min.css?1256826599" type="text/css" />
+<link rel="stylesheet" href="/viewvc-static/styles.css" type="text/css" />
+<style type="text/css">
+#doc3 { max-width: 1000px; margin: 0 auto; }
+#hd .logo {
+background: url("http://a.fsdn.com/sf/images/phoneix/sf_phoneix.png") no-repeat;
+color: transparent;
+display: inline-block;
+height: 36px;
+}
+#hd .search { display: none; }
+#breadcrumbs { margin-bottom: 1em; }
+#fad83 { float: right; }
+#yui-main { min-height: 100px; }
+#ft .yui-u { display: inline-block; margin-right: 2em; }
+</style>
+
+<!-- BEGIN: AdSolution-Tag 4.2: Global-Code [PLACE IN HTML-HEAD-AREA!] -->
+<!-- DoubleClick Random Number -->
+<script language="JavaScript" type="text/javascript">
+dfp_ord=Math.random()*10000000000000000;
+dfp_tile = 1;
+</script>
+<!-- End DoubleClick Random Number -->
+<script type="text/javascript">
+var google_page_url = 'http://sourceforge.net/projects/dl-learner/';
+var sourceforge_project_name = 'dl-learner';
+var sourceforge_project_description = '';
+</script>
+<!-- END: AdSolution-Tag 4.2: Global-Code -->
+<!-- after META tags -->
+<script type="text/javascript">
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+</script>
+</head>
+<body class="short-head">
+<!--[if IE 7]><div id="ie7only"><![endif]-->
+<!--[if IE 6]><div id="ie6only"><![endif]-->
+<!--[if IE]><div id="ieonly"><![endif]-->
+<div id="doc3">
+<div id="hd">
+<div class="yui-b">
+<div class="yui-gc">
+<div class="yui-u first">
+<a href="http://sourceforge.net/" class="logo">Find and develop open source software</a>
+</div>
+<div class="yui-u">
+<div class="search">
+<form action="http://sourceforge.net/search/" method="get" name="searchform" id="searchform">
+<input type="hidden" name="type_of_search" value="soft" />
+<input type="text" class="text clear hint" name="words" id="words" value="enter keyword" />
+<span class="yui-button yui-push-button default"><span class="first-child"><button type="submit" value="Search">Search</button></span></span>
+</form>
+</div>
+</div>
+</div>
+</div>
+</div>
+<div id="bd" class="inner-bd">
+<div id="doc4" class="yui-t6">
+<div id="breadcrumbs">
+
+<a href="http://sourceforge.net/">SourceForge.net</a>
+> <a href="http://sourceforge.net/softwaremap/">Find Software</a>
+> <a href="http://sourceforge.net/projects/dl-learner/">dl-learner</a>
+> SCM Repositories
+
+
+<a href="/viewvc/dl-learner/">
+
+
+> dl-learner
+
+
+</a>
+
+
+
+<a href="/viewvc/dl-learner/tags/">
+
+
+> tags
+
+
+</a>
+
+
+
+<a href="/viewvc/dl-learner/tags/premaven/">
+
+
+> premaven
+
+
+</a>
+
+
+
+
+> javadoc.css
+
+
+
+
+</div>
+
+
+
+
+
+
+
+
+
+
+<div id="project_nav_container">
+<small><div>
+
+<a href="/viewvc/dl-learner/tags/premaven/"><img src="/viewvc-static/images/back_small.png" width="16" height="16" alt="Parent Directory" /> Parent Directory</a>
+
+| <a href="/viewvc/dl-learner/tags/premaven/javadoc.css?view=log"><img src="/viewvc-static/images/log.png" width="16" height="16" alt="Revision Log" /> Revision Log</a>
+
+
+
+
+</div>
+</small>
+<h1>SCM Repositories - <a href="http://sourceforge.net/projects/dl-learner">dl-learner</a></h1>
+</div>
+<hr class="clear">
+<div class="yui-b">
+<div id="fad83">
+<!-- DoubleClick Ad Tag -->
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+dfp_tile++;
+//]]>
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+<!-- End DoubleClick Ad Tag -->
+</div>
+</div>
+<div id="yui-main">
+<div class="yui-b sfBox">
+<table class="auto">
+
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+<tr>
+<td>Links to HEAD:</td>
+<td>
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+mime-type: text/css
+</td>
+</tr>
+
+
+
+<tr>
+<td>Sticky Revision:</td>
+<td><form method="get" action="/viewvc/dl-learner" style="display: inline">
+<div style="display: inline">
+<input type="hidden" name="orig_pathtype" value="FILE"/><input type="hidden" name="orig_view" value="log"/><input type="hidden" name="orig_path" value="tags/premaven/javadoc.css"/><input type="hidden" name="view" value="redirect_pathrev"/>
+
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+
+<input type="submit" value="Set" />
+</div>
+</form>
+
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+</table>
+
+
+
+</div>
+</div>
+<hr class="clear">
+<div>
+
+
+
+
+
+
+<div>
+<hr />
+
+<a name="rev2309"></a>
+
+
+Revision <a href="/viewvc/dl-learner?view=revision&revision=2309"><strong>2309</strong></a> -
+
+
+(<a href="/viewvc/dl-learner/tags/premaven/javadoc.css?revision=2309&view=markup">view</a>)
+
+
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+(<a href="/viewvc/dl-learner/tags/premaven/javadoc.css?annotate=2309">annotate</a>)
+
+
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+- <a href="/viewvc/dl-learner/tags/premaven/javadoc.css?r1=2309&view=log">[select for diffs]</a>
+
+
+
+
+<br />
+
+Added
+
+<em>Fri Sep 17 09:17:53 2010 UTC</em>
+(11 months ago)
+by <em>kurzum</em>
+
+
+
+
+
+
+
+<br />File length: 1969 byte(s)
+
+
+
+
+
+
+
+
+
+
+
+<pre class="vc_log">DL-Learner before the transition to maven</pre>
+</div>
+
+
+
+
+
+ <div class="sfBox">
+<hr class="clear"/>
+<a name="diff"></a>
+This form allows you to request diffs between any two revisions of this file.
+For each of the two "sides" of the diff,
+
+enter a numeric revision.
+
+<form method="get" action="/viewvc/dl-learner/tags/premaven/javadoc.css" id="diff_select">
+<table cellpadding="2" cellspacing="0" class="auto">
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+<td> </td>
+<td>
+
+<input type="hidden" name="view" value="diff"/>
+
+Diffs between
+
+<input type="text" size="12" name="r1"
+value="2309" />
+
+and
+
+<input type="text" size="12" name="r2" value="2309" />
+
+</td>
+</tr>
+<tr>
+<td> </td>
+<td>
+Type of Diff should be a
+<select name="diff_format" onchange="submit()">
+<option value="h" selected="selected">Colored Diff</option>
+<option value="l" >Long Colored Diff</option>
+<option value="f" >Full Colored Diff</option>
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+<option value="c" >Context Diff</option>
+<option value="s" >Side by Side</option>
+</select>
+<input type="submit" value=" Get Diffs " />
+</td>
+</tr>
+</table>
+</form>
+</div>
+
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+<form method="get" action="/viewvc/dl-learner/tags/premaven/javadoc.css">
+<div>
+<hr />
+<a name="logsort"></a>
+<input type="hidden" name="view" value="log"/>
+Sort log by:
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+<div class="yui-u" style="text-align: center;"> <strong><a href="/viewvc-static/help_log.html">ViewVC Help</a></strong> </div>
+<div class="yui-u" style="text-align: center;"> <a href="http://viewvc.tigris.org/">Powered by ViewVC 1.1.6</a> </div>
+</div>
+<p class="copyright">Copyright © 2010 <a title="Network which provides and promotes Open Source software downloads, development, discussion and news." href="http://geek.net">Geeknet, Inc.</a> All rights reserved. <a href="http://p.sf.net/sourceforge/terms">Terms of Use</a></p>
+</div>
+</div>
+</div>
+<!--[if IE]></div><![endif]-->
+<!--[if IE 6]></div><![endif]-->
+<!--[if IE 7]></div><![endif]-->
+<script type="text/javascript">
+var pageTracker = _gat._getTracker("UA-32013-37");
+pageTracker._setDomainName(".sourceforge.net");
+pageTracker._trackPageview();
+</script>
+</body>
+</html>
+
+
Added: trunk/components-core/src/etc/overview.html
===================================================================
--- trunk/components-core/src/etc/overview.html (rev 0)
+++ trunk/components-core/src/etc/overview.html 2011-08-22 11:08:02 UTC (rev 3085)
@@ -0,0 +1,17 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+<head></head>
+<body>
+<p>DL-Learner is a tool for supervised Machine Learning in OWL and Description Logics.</p>
+
+<p><img src="http://aksw.org/Projects/DLLearner/files?get=dllearner.gif" alt="DL-Learner logo" /></p>
+
+<p>
+Project Homepage: <a href="http://dl-learner.org">http://dl-learner.org</a> <br />
+Sourceforge.net Website: <a href="http://sourceforge.net/projects/dl-learner">http://sf.net/projects/dl-learner</a>
+</p>
+
+<p><img src="http://sflogo.sourceforge.net/sflogo.php?group_id=203619&type=1" width="88" height="31" border="0" alt="SourceForge.net Logo" /></p>
+
+</body>
+</html>
\ No newline at end of file
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|
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![http://aksw.org/Projects/DLLearner/files?get=dllearner.gif"](http://aksw.org/Projects/DLLearner/files?get=dllearner.gif"){kind=link}
|
From: <lor...@us...> - 2012-03-26 12:10:58
|
Revision: 3618
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3618&view=rev
Author: lorenz_b
Date: 2012-03-26 12:10:46 +0000 (Mon, 26 Mar 2012)
Log Message:
-----------
Updated pom.
Removed QueryEngineHTTP classes as timeout is now implemented in official JENA jar.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseFunctionalObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/refinementoperators/SynchronizedRhoDRDown.java
Removed Paths:
-------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtendedQueryEngineHTTP.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/HttpQuery.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/pom.xml 2012-03-26 12:10:46 UTC (rev 3618)
@@ -132,6 +132,7 @@
<artifactId>log4j</artifactId>
</dependency>
+ <!-- Latest JENA ARQ - we have to exclude XercesImpl and use an older version here because use version bei JENA leads to some errors -->
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
@@ -142,6 +143,11 @@
</exclusion>
</exclusions>
</dependency>
+ <dependency>
+ <groupId>xerces</groupId>
+ <artifactId>xercesImpl</artifactId>
+ <version>2.6.0</version>
+ </dependency>
<!--JSON is in Central -->
<dependency>
@@ -185,16 +191,6 @@
</dependency>
- <dependency>
- <groupId>org.apache.jena</groupId>
- <artifactId>jena-core</artifactId>
- <exclusions>
- <exclusion>
- <artifactId>xercesImpl</artifactId>
- <groupId>xerces</groupId>
- </exclusion>
- </exclusions>
- </dependency>
<dependency>
<groupId>junit</groupId>
@@ -253,5 +249,7 @@
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-core</artifactId>
</dependency>
+
+
</dependencies>
</project>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -66,6 +66,7 @@
import org.dllearner.refinementoperators.OperatorInverter;
import org.dllearner.refinementoperators.RefinementOperator;
import org.dllearner.refinementoperators.RhoDRDown;
+import org.dllearner.refinementoperators.SynchronizedRhoDRDown;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.Helper;
import org.dllearner.utilities.owl.ConceptComparator;
@@ -295,15 +296,15 @@
// variables to it
if(operator == null) {
// we use a default operator and inject the class hierarchy for now
- operator = new RhoDRDown();
- ((RhoDRDown)operator).setStartClass(startClass);
- ((RhoDRDown)operator).setReasoner(reasoner);
- ((RhoDRDown)operator).init();
+ operator = new SynchronizedRhoDRDown();
+ ((SynchronizedRhoDRDown)operator).setStartClass(startClass);
+ ((SynchronizedRhoDRDown)operator).setReasoner(reasoner);
+ ((SynchronizedRhoDRDown)operator).init();
}
// TODO: find a better solution as this is quite difficult to debug
- ((RhoDRDown)operator).setSubHierarchy(classHierarchy);
- ((RhoDRDown)operator).setObjectPropertyHierarchy(reasoner.getObjectPropertyHierarchy());
- ((RhoDRDown)operator).setDataPropertyHierarchy(reasoner.getDatatypePropertyHierarchy());
+ ((SynchronizedRhoDRDown)operator).setSubHierarchy(classHierarchy);
+ ((SynchronizedRhoDRDown)operator).setObjectPropertyHierarchy(reasoner.getObjectPropertyHierarchy());
+ ((SynchronizedRhoDRDown)operator).setDataPropertyHierarchy(reasoner.getDatatypePropertyHierarchy());
// operator = new RhoDRDown(reasoner, classHierarchy, startClass, configurator);
@@ -996,6 +997,7 @@
return heuristic;
}
+ @Autowired(required=false)
public void setHeuristic(OEHeuristicRuntime heuristic) {
this.heuristic = heuristic;
}
@@ -1052,12 +1054,18 @@
}
// chose best node according to heuristics
+ if(logger.isDebugEnabled()){
+ logger.debug("Get next node to expand...");
+ }
nextNode = getNextNodeToExpand();
if(nextNode != null){
int horizExp = nextNode.getHorizontalExpansion();
// apply operator
Monitor mon = MonitorFactory.start("refineNode");
+ if(logger.isDebugEnabled()){
+ logger.debug("Refining node...");
+ }
TreeSet<Description> refinements = refineNode(nextNode);
mon.stop();
@@ -1081,6 +1089,9 @@
// System.out.println("potentially adding " + refinement + " to search tree as child of " + nextNode + " " + new Date());
Monitor mon2 = MonitorFactory.start("addNode");
+ if(logger.isDebugEnabled()){
+ logger.debug("Add node...");
+ }
addNode(refinement, nextNode);
mon2.stop();
// adding nodes is potentially computationally expensive, so we have
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -215,10 +215,12 @@
public static void main(String[] args) throws Exception{
DisjointObjectPropertyAxiomLearner l = new DisjointObjectPropertyAxiomLearner(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/state"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/stateOfOrigin"));
l.setMaxExecutionTimeInSeconds(10);
l.init();
l.start();
- System.out.println(l.getCurrentlyBestEvaluatedAxioms(Integer.MAX_VALUE));
+ for(EvaluatedAxiom ax : l.getCurrentlyBestEvaluatedAxioms(Integer.MAX_VALUE)){
+ System.out.println(ax);
+ }
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseFunctionalObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseFunctionalObjectPropertyAxiomLearner.java 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseFunctionalObjectPropertyAxiomLearner.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -19,7 +19,9 @@
package org.dllearner.algorithms.properties;
+import java.net.URL;
import java.util.ArrayList;
+import java.util.Collections;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
import org.dllearner.core.ComponentAnn;
@@ -166,9 +168,10 @@
}
public static void main(String[] args) throws Exception{
- SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
+ SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(
+ new URL("http://dbpedia.aksw.org:8902/sparql"), Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList()));
InverseFunctionalObjectPropertyAxiomLearner l = new InverseFunctionalObjectPropertyAxiomLearner(ks);
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/starring"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/profession"));
l.setMaxExecutionTimeInSeconds(10);
l.init();
l.start();
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -38,7 +38,6 @@
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
import org.dllearner.kb.SparqlEndpointKS;
-import org.dllearner.kb.sparql.ExtendedQueryEngineHTTP;
import org.dllearner.kb.sparql.SPARQLTasks;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.learningproblems.AxiomScore;
@@ -220,7 +219,7 @@
logger.info("Sending query\n{} ...", query);
if(ks.isRemote()){
SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
- ExtendedQueryEngineHTTP queryExecution = new ExtendedQueryEngineHTTP(endpoint.getURL().toString(),
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
query);
queryExecution.setTimeout(maxExecutionTimeInSeconds * 1000);
queryExecution.setDefaultGraphURIs(endpoint.getDefaultGraphURIs());
@@ -236,7 +235,7 @@
logger.info("Sending query\n{} ...", query);
if(ks.isRemote()){
SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
- ExtendedQueryEngineHTTP queryExecution = new ExtendedQueryEngineHTTP(endpoint.getURL().toString(),
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
query);
queryExecution.setTimeout(maxExecutionTimeInSeconds * 1000);
queryExecution.setDefaultGraphURIs(endpoint.getDefaultGraphURIs());
Modified: trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/src/main/java/org/dllearner/core/AnnComponentManager.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -50,7 +50,7 @@
// components must be listed here if they should be supported in interfaces
// (CLI, GUI, Web Service) and scripts (HTML documentation generator)
private static List<String> componentClassNames = new ArrayList<String> ( Arrays.asList(new String[]{
- "org.dllearner.algorithms.celoe.CELOE",
+ "org.dllearner.algorithms.celoe.CELOE",
"org.dllearner.algorithms.celoe.PCELOE",
"org.dllearner.algorithms.el.ELLearningAlgorithm",
"org.dllearner.algorithms.el.ELLearningAlgorithmDisjunctive",
@@ -91,6 +91,7 @@
"org.dllearner.algorithms.ocel.MultiHeuristic",
"org.dllearner.algorithms.celoe.OEHeuristicRuntime",
"org.dllearner.refinementoperators.RhoDRDown",
+ "org.dllearner.refinementoperators.SynchronizedRhoDRDown",
} ));
private static Collection<Class<? extends Component>> components;
private static BidiMap<Class<? extends Component>, String> componentNames;
Deleted: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtendedQueryEngineHTTP.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtendedQueryEngineHTTP.java 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtendedQueryEngineHTTP.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -1,408 +0,0 @@
-/**
- * Copyright (C) 2007-2011, Jens Lehmann
- *
- * This file is part of DL-Learner.
- *
- * DL-Learner is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * DL-Learner is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-
-package org.dllearner.kb.sparql;
-
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.concurrent.TimeUnit;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.hp.hpl.jena.query.ARQ;
-import com.hp.hpl.jena.query.Dataset;
-import com.hp.hpl.jena.query.Query;
-import com.hp.hpl.jena.query.QueryExecution;
-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.query.ResultSetFactory;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.sparql.engine.http.HttpParams;
-import com.hp.hpl.jena.sparql.engine.http.Params;
-import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
-import com.hp.hpl.jena.sparql.graph.GraphFactory;
-import com.hp.hpl.jena.sparql.resultset.XMLInput;
-import com.hp.hpl.jena.sparql.util.Context;
-import com.hp.hpl.jena.util.FileManager;
-
-/**
- * Created by Claus Stadler
- * Date: Oct 25, 2010
- * Time: 10:15:31 PM
- */
-class DisconnectorThread
- extends Thread {
- private static final Logger logger = LoggerFactory.getLogger(DisconnectorThread.class);
-
- private HttpQuery connection;
-
- private long timeOut;
-
- private boolean canceled = false;
-
- public DisconnectorThread(HttpQuery connection, long timeOut) {
- this.connection = connection;
- this.timeOut = timeOut;
- }
-
- public void run() {
- synchronized (this) {
-
- while(!canceled && connection.getConnection() == null) {
- //logger.trace("Waiting for connection...");
-
- try {
- this.wait(500l);
- } catch (InterruptedException e) {
- }
- }
-
- long startTime = System.currentTimeMillis();
-
- long remaining;
- while (!canceled && (remaining = (timeOut - (System.currentTimeMillis() - startTime))) > 0) {
- logger.trace("Forced disconnect in " + remaining + "ms");
- try {
- this.wait(remaining);
- } catch (InterruptedException e) {
- }
- }
-
- if (!canceled && connection.getConnection() != null) {
- logger.warn("Disconnecting Http connection since a sparql query is taking too long");
- connection.getConnection().disconnect();
- canceled = true;
- }
- }
- }
-
- public void cancel() {
- synchronized (this) {
- if(!this.canceled) {
- logger.trace("Disconnect cancelled");
- }
-
- this.canceled = true;
- this.notify();
- }
- }
-}
-
-/**
- * A QueryEngineHTTP that is capable of closing connections after a given timeout.
- *
- * Jena now provides one on its own
- */
-public class ExtendedQueryEngineHTTP
- implements QueryExecution {
- private static Logger log = LoggerFactory.getLogger(QueryEngineHTTP.class);
-
- public static final String QUERY_MIME_TYPE = "application/sparql-query";
- String queryString;
- String service;
- Context context = null;
-
-
- long timeOut = 0l;
-
- public void setTimeOut(long timeOut) {
- this.timeOut = timeOut;
- }
-
- public long getTimeOut() {
- return timeOut;
- }
-
-
- //Params
- Params params = null;
-
- // Protocol
- List<String> defaultGraphURIs = new ArrayList<String>();
- List<String> namedGraphURIs = new ArrayList<String>();
- private String user = null;
- private char[] password = null;
-
- // Releasing HTTP input streams is important. We remember this for SELECT,
- // and will close when the engine is closed
- private InputStream retainedConnection = null;
-
- public ExtendedQueryEngineHTTP(String serviceURI, Query query) {
- this(serviceURI, query.toString());
- }
-
- public ExtendedQueryEngineHTTP(String serviceURI, String queryString) {
- this.queryString = queryString;
- service = serviceURI;
- // Copy the global context to freeze it.
- context = new Context(ARQ.getContext());
- }
-
-// public void setParams(Params params)
-// { this.params = params ; }
-
- // Meaning-less
-
- public void setFileManager(FileManager fm) {
- throw new UnsupportedOperationException("FileManagers do not apply to remote query execution");
- }
-
- public void setInitialBinding(QuerySolution binding) {
- throw new UnsupportedOperationException("Initial bindings not supported for remote queries");
- }
-
- public void setInitialBindings(ResultSet table) {
- throw new UnsupportedOperationException("Initial bindings not supported for remote queries");
- }
-
- /**
- * @param defaultGraphURIs The defaultGraphURIs to set.
- */
- public void setDefaultGraphURIs(List<String> defaultGraphURIs) {
- this.defaultGraphURIs = defaultGraphURIs;
- }
-
- /**
- * @param namedGraphURIs The namedGraphURIs to set.
- */
- public void setNamedGraphURIs(List<String> namedGraphURIs) {
- this.namedGraphURIs = namedGraphURIs;
- }
-
- public void addParam(String field, String value) {
- if (params == null)
- params = new Params();
- params.addParam(field, value);
- }
-
- /**
- * @param defaultGraph The defaultGraph to add.
- */
- public void addDefaultGraph(String defaultGraph) {
- if (defaultGraphURIs == null)
- defaultGraphURIs = new ArrayList<String>();
- defaultGraphURIs.add(defaultGraph);
- }
-
- /**
- * @param name The URI to add.
- */
- public void addNamedGraph(String name) {
- if (namedGraphURIs == null)
- namedGraphURIs = new ArrayList<String>();
- namedGraphURIs.add(name);
- }
-
- /**
- * Set user and password for basic authentication.
- * After the request is made (one of the exec calls), the application
- * can overwrite the password array to remove details of the secret.
- *
- * @param user
- * @param password
- */
- public void setBasicAuthentication(String user, char[] password) {
- this.user = user;
- this.password = password;
- }
-
- private InputStream doTimedExec(HttpQuery httpQuery) {
- DisconnectorThread stopTask = null;
- if (timeOut > 0) {
- stopTask = new DisconnectorThread(httpQuery, timeOut);
-// stopTask.start();
- }
-
- InputStream in;
- try {
- in = httpQuery.exec();
- }
- finally {
- if (stopTask != null) {
- stopTask.cancel();
- }
- }
-
- return in;
- }
-
-
- public ResultSet execSelect() {
- HttpQuery httpQuery = makeHttpQuery();
- // TODO Allow other content types.
- httpQuery.setAccept(HttpParams.contentTypeResultsXML);
-
- InputStream in = httpQuery.exec();
-
-
- ResultSet rs = ResultSetFactory.fromXML(in);
- retainedConnection = in; // This will be closed on close()
- return rs;
- }
-
- public Model execConstruct() {
- return execConstruct(GraphFactory.makeJenaDefaultModel());
- }
-
- public Model execConstruct(Model model) {
- return execModel(model);
- }
-
- public Model execDescribe() {
- return execDescribe(GraphFactory.makeJenaDefaultModel());
- }
-
- public Model execDescribe(Model model) {
- return execModel(model);
- }
-
- private Model execModel(Model model) {
- HttpQuery httpQuery = makeHttpQuery();
- httpQuery.setAccept(HttpParams.contentTypeRDFXML);
- InputStream in = doTimedExec(httpQuery);
- model.read(in, null);
- return model;
- }
-
- public boolean execAsk() {
- HttpQuery httpQuery = makeHttpQuery();
- httpQuery.setAccept(HttpParams.contentTypeResultsXML);
- InputStream in = doTimedExec(httpQuery);
- boolean result = XMLInput.booleanFromXML(in);
- // Ensure connection is released
- try {
- in.close();
- }
- catch (java.io.IOException e) {
- log.warn("Failed to close connection", e);
- }
- return result;
- }
-
- public Context getContext() {
- return context;
- }
-
- private HttpQuery makeHttpQuery() {
- HttpQuery httpQuery = new HttpQuery(service);
- httpQuery.setTimeOut((int)timeOut);
- httpQuery.addParam(HttpParams.pQuery, queryString);
-
- for (Iterator<String> iter = defaultGraphURIs.iterator(); iter.hasNext();) {
- String dft = iter.next();
- httpQuery.addParam(HttpParams.pDefaultGraph, dft);
- }
- for (Iterator<String> iter = namedGraphURIs.iterator(); iter.hasNext();) {
- String name = iter.next();
- httpQuery.addParam(HttpParams.pNamedGraph, name);
- }
-
- if (params != null)
- httpQuery.merge(params);
-
- httpQuery.setBasicAuthentication(user, password);
- return httpQuery;
- }
-
- public void abort() {
- }
-
- public void close() {
- if (retainedConnection != null) {
- try {
- retainedConnection.close();
- }
- catch (java.io.IOException e) {
- log.warn("Failed to close connection", e);
- }
- finally {
- retainedConnection = null;
- }
- }
- }
-
- @Override
- public void setTimeout(long timeout, TimeUnit timeoutUnits) {
- //To change body of implemented methods use File | Settings | File Templates.
- }
-
- @Override
- public void setTimeout(long timeout) {
- this.timeOut = timeout;
- }
-
- @Override
- public void setTimeout(long timeout1, TimeUnit timeUnit1, long timeout2, TimeUnit timeUnit2) {
- //To change body of implemented methods use File | Settings | File Templates.
- }
-
- @Override
- public void setTimeout(long timeout1, long timeout2) {
- //To change body of implemented methods use File | Settings | File Templates.
- }
-
-// public boolean isActive() { return false ; }
-
- @Override
- public String toString() {
- HttpQuery httpQuery = makeHttpQuery();
- return "GET " + httpQuery.toString();
- }
-
- public Dataset getDataset() {
- return null;
- }
-
- @Override
- public Query getQuery() {
- return QueryFactory.create(queryString);
- }
-}
-
-/*
- * (c) Copyright 2005, 2006, 2007, 2008, 2009 Hewlett-Packard Development Company, LP
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the distribution.
- * 3. The name of the author may not be used to endorse or promote products
- * derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
- * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
- * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
- * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -19,22 +19,29 @@
package org.dllearner.kb.sparql;
+import java.io.ByteArrayOutputStream;
+import java.io.StringReader;
+import java.io.UnsupportedEncodingException;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.sql.Clob;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Statement;
+
+import org.dllearner.utilities.Helper;
+
import com.hp.hpl.jena.query.ResultSetFactory;
import com.hp.hpl.jena.query.ResultSetRewindable;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
-import org.aksw.commons.jena.ExtendedQueryEngineHTTP;
-import org.dllearner.utilities.Helper;
-import java.io.ByteArrayOutputStream;
-import java.io.StringReader;
-import java.io.UnsupportedEncodingException;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
-import java.sql.*;
-
/**
* The class is used to cache information about resources to a database.
* Provides the connection to an H2 database in a light weight, configuration free
@@ -127,8 +134,8 @@
// System.out.println("Posing new query");
// String endpoint = "http://139.18.2.37:8890/sparql";
- ExtendedQueryEngineHTTP queryExecution = new ExtendedQueryEngineHTTP(endpoint.getURL().toString(), query);
- queryExecution.setTimeOut(maxExecutionTimeInSeconds * 1000);
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(), query);
+ queryExecution.setTimeout(maxExecutionTimeInSeconds * 1000);
for (String dgu : endpoint.getDefaultGraphURIs()) {
queryExecution.addDefaultGraph(dgu);
}
@@ -187,8 +194,8 @@
} else {
mon.start();
// System.out.println("no-cache");
- ExtendedQueryEngineHTTP queryExecution = new ExtendedQueryEngineHTTP(endpoint.getURL().toString(), query);
- queryExecution.setTimeOut(maxExecutionTimeInSeconds * 1000);
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(), query);
+ queryExecution.setTimeout(maxExecutionTimeInSeconds * 1000);
for (String dgu : endpoint.getDefaultGraphURIs()) {
queryExecution.addDefaultGraph(dgu);
}
Deleted: trunk/components-core/src/main/java/org/dllearner/kb/sparql/HttpQuery.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/HttpQuery.java 2012-03-23 14:53:07 UTC (rev 3617)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/HttpQuery.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -1,419 +0,0 @@
-/**
- * Copyright (C) 2007-2011, Jens Lehmann
- *
- * This file is part of DL-Learner.
- *
- * DL-Learner is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * DL-Learner is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-
-package org.dllearner.kb.sparql;
-
-/*
- * (c) Copyright 2003, 2004, 2005, 2006, 2007, 2008, 2009 Hewlett-Packard Development Company, LP
- * [See end of file]
- */
-
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.UnsupportedEncodingException;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.codec.binary.Base64;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.hp.hpl.jena.query.ARQ;
-import com.hp.hpl.jena.shared.JenaException;
-import com.hp.hpl.jena.sparql.ARQInternalErrorException;
-import com.hp.hpl.jena.sparql.engine.http.HttpParams;
-import com.hp.hpl.jena.sparql.engine.http.Params;
-import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
-import com.hp.hpl.jena.sparql.util.Convert;
-import com.hp.hpl.jena.util.FileUtils;
-
-/** Create an execution object for performing a query on a model
- * over HTTP. This is the main protocol engine for HTTP query.
- * There are higher level classes for doing a query and presenting
- * the results in an API fashion.
- *
- * If the query string is large, then HTTP POST is used. */
-public class HttpQuery extends Params
-{
- static final Logger log = LoggerFactory.getLogger(HttpQuery.class.getName()) ;
-
- /** The definition of "large" queries */
- // Not final so that other code can change it.
- static public /*final*/ int urlLimit = 2*1024 ;
-
- String serviceURL ;
-
- String contentTypeResult = HttpParams.contentTypeResultsXML ;
- HttpURLConnection httpConnection = null ;
-
- // An object indicate no value associated with parameter name
- final static Object noValue = new Object() ;
- String user = null ;
- char[] password = null ;
-
- int responseCode = 0;
- String responseMessage = null ;
- boolean forcePOST = false ;
- String queryString = null ;
-
- private int timeOut = 0;
-
- public void setTimeOut(int timeOut){
- this.timeOut = timeOut;
- }
-
- //static final String ENC_UTF8 = "UTF-8" ;
-
- /** Create a execution object for a whole model GET
- * @param serviceURL The model
- */
-
- public HttpQuery(String serviceURL)
- {
- init(serviceURL) ;
- }
-
-
- /** Create a execution object for a whole model GET
- * @param url The model
- */
-
- public HttpQuery(URL url)
- {
- init(url.toString()) ;
- }
-
-
- private void init(String serviceURL)
- {
- if ( log.isTraceEnabled())
- log.trace("URL: "+serviceURL) ;
-
- if ( serviceURL.indexOf('?') >= 0 )
- throw new QueryExceptionHTTP(-1, "URL already has a query string ("+serviceURL+")") ;
-
- this.serviceURL = serviceURL ;
- }
-
- private String getQueryString()
- {
- if ( queryString == null )
- queryString = super.httpString() ;
- return queryString ;
- }
-
- public HttpURLConnection getConnection() { return httpConnection ; }
-
- /** Set the content type (Accept header) for the results
- */
-
- public void setAccept(String contentType)
- {
- contentTypeResult = contentType ;
- }
-
- public void setBasicAuthentication(String user, char[] password)
- {
- this.user = user ;
- this.password = password ;
- }
-
- /** Return whether this request will go by GET or POST
- * @return boolean
- */
- public boolean usesPOST()
- {
- if ( forcePOST )
- return true ;
- String s = getQueryString() ;
-
- return serviceURL.length()+s.length() >= urlLimit ;
- }
-
- /** Force the use of HTTP POST for the query operation
- */
-
- public void setForcePOST()
- {
- forcePOST = true ;
- }
-
- /** Execute the operation
- * @return Model The resulting model
- * @throws QueryExceptionHTTP
- */
- public InputStream exec() throws QueryExceptionHTTP
- {
- try {
- if (usesPOST())
- return execPost();
- return execGet();
- } catch (QueryExceptionHTTP httpEx)
- {
- log.trace("Exception in exec", httpEx);
- throw httpEx;
- }
- catch (JenaException jEx)
- {
- log.trace("JenaException in exec", jEx);
- throw jEx ;
- }
- }
-
- private InputStream execGet() throws QueryExceptionHTTP
- {
- URL target = null ;
- String qs = getQueryString() ;
-
- ARQ.getHttpRequestLogger().trace(qs) ;
-
- try {
- if ( count() == 0 )
- target = new URL(serviceURL) ;
- else
- target = new URL(serviceURL+"?"+qs) ;
- }
- catch (MalformedURLException malEx)
- { throw new QueryExceptionHTTP(0, "Malformed URL: "+malEx) ; }
- log.trace("GET "+target.toExternalForm()) ;
-
- try
- {
- httpConnection = (HttpURLConnection) target.openConnection();
- httpConnection.setRequestProperty("Accept", contentTypeResult) ;
- httpConnection.setReadTimeout(timeOut);
- int x = httpConnection.getReadTimeout() ;
-
- // By default, following 3xx redirects is true
- //conn.setFollowRedirects(true) ;
- basicAuthentication(httpConnection) ;
-
- httpConnection.setDoInput(true);
- httpConnection.connect();
- try
- {
- return execCommon();
- }
- catch (QueryExceptionHTTP qEx)
- {
- // Back-off and try POST if something complain about long URIs
- // Broken
- if (qEx.getResponseCode() == 414 /*HttpServletResponse.SC_REQUEST_URI_TOO_LONG*/ )
- return execPost();
- throw qEx;
- }
- }
- catch (java.net.ConnectException connEx)
- { throw new QueryExceptionHTTP(QueryExceptionHTTP.NoServer, "Failed to connect to remote server"); }
- catch (IOException ioEx)
- { throw new QueryExceptionHTTP(ioEx); }
- }
-
- private InputStream execPost() throws QueryExceptionHTTP
- {
- URL target = null;
- try { target = new URL(serviceURL); }
- catch (MalformedURLException malEx)
- { throw new QueryExceptionHTTP(0, "Malformed URL: " + malEx); }
- log.trace("POST "+target.toExternalForm()) ;
-
- ARQ.getHttpRequestLogger().trace(target.toExternalForm()) ;
-
- try
- {
- httpConnection = (HttpURLConnection) target.openConnection();
- httpConnection.setRequestMethod("POST") ;
- httpConnection.setRequestProperty("Accept", contentTypeResult) ;
- httpConnection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded") ;
- basicAuthentication(httpConnection) ;
- httpConnection.setDoOutput(true) ;
-
- boolean first = true ;
- OutputStream out = httpConnection.getOutputStream() ;
- for ( Iterator<Pair> iter = pairs().listIterator() ; iter.hasNext() ; )
- {
- if ( ! first )
- out.write('&') ;
- first = false ;
- Pair p = iter.next() ;
- out.write(p.getName().getBytes()) ;
- out.write('=') ;
- String x = p.getValue() ;
- x = Convert.encWWWForm(x) ;
- out.write(x.getBytes()) ;
- ARQ.getHttpRequestLogger().trace("Param: "+x) ;
- }
- out.flush() ;
- httpConnection.connect() ;
- return execCommon() ;
- }
- catch (java.net.ConnectException connEx)
- { throw new QueryExceptionHTTP(-1, "Failed to connect to remote server"); }
- catch (IOException ioEx)
- { throw new QueryExceptionHTTP(ioEx); }
- }
-
- private void basicAuthentication(HttpURLConnection httpConnection2)
- {
- // Do basic authentication : do directly, not via an Authenticator, because it
- // avoids an extra round trip (Java normally does the request without authetication,
- // then reties with)
-
- if ( user != null || password != null)
- {
- try
- {
- if ( user == null || password == null )
- log.warn("Only one of user/password is set") ;
- // We want: "Basic user:password" except user:password is base 64 encoded.
- // Build string, get as UTF-8, bytes, translate to base 64.
- StringBuffer x = new StringBuffer() ;
- byte b[] = x.append(user).append(":").append(password).toString().getBytes("UTF-8") ;
- String y = Base64.encodeBase64String(b);
- httpConnection.setRequestProperty("Authorization", "Basic "+y) ;
- // Overwrite any password details we copied.
- // Still leaves the copy in the HTTP connection. But this only basic auth.
- for ( int i = 0 ; i < x.length() ; i++ ) x.setCharAt(i, '*') ;
- for ( int i = 0 ; i < b.length ; i++ ) b[i] = (byte)0 ;
- } catch (UnsupportedEncodingException ex)
- {
- // Can't happen - UTF-8 is required of all Java platforms.
- throw new ARQInternalErrorException("UTF-8 is broken on this platform", ex) ;
- }
- }
- }
-
-
- private InputStream execCommon() throws QueryExceptionHTTP
- {
- try {
- responseCode = httpConnection.getResponseCode() ;
- responseMessage = Convert.decWWWForm(httpConnection.getResponseMessage()) ;
-
- // 1xx: Informational
- // 2xx: Success
- // 3xx: Redirection
- // 4xx: Client Error
- // 5xx: Server Error
-
- if ( 300 <= responseCode && responseCode < 400 )
- throw new QueryExceptionHTTP(responseCode, responseMessage) ;
-
- // Other 400 and 500 - errors
-
- if ( responseCode >= 400 )
- throw new QueryExceptionHTTP(responseCode, responseMessage) ;
-
- // Request suceeded
- //httpConnection.setReadTimeout(10) ;
- InputStream in = httpConnection.getInputStream() ;
-
- if ( false )
- {
- // Dump the header
- Map<String,List<String>> map = httpConnection.getHeaderFields() ;
- for ( Iterator<String> iter = map.keySet().iterator() ; iter.hasNext() ; )
- {
- String k = iter.next();
- List<String> v = map.get(k) ;
- System.out.println(k+" = "+v) ;
- }
- }
-
- // Dump response body
- if ( false )
- {
- StringBuffer b = new StringBuffer(1000) ;
- byte[] chars = new byte[1000] ;
- while(true)
- {
- int x = in.read(chars) ;
- if ( x < 0 ) break ;
- b.append(new String(chars, 0, x, FileUtils.encodingUTF8)) ;
- }
- System.out.println(b.toString()) ;
- System.out.flush() ;
- // Reset
- in = new ByteArrayInputStream(b.toString().getBytes(FileUtils.encodingUTF8)) ;
- }
-
-
- // +++ WORKAROUND for badly behaved apps.
- // Apps sometimes call QueryExecution.close straight after .execSelect.
- // that results in some resuls being seen, not all of them => XMl parse errors.
-// byte[] bytes = IO.readWholeFile(in) ;
-// in = new ByteArrayInputStream(bytes) ;
- // +++
-
- return in ;
- }
- catch (IOException ioEx)
- {
- throw new QueryExceptionHTTP(ioEx) ;
- }
- catch (JenaException rdfEx)
- {
- throw new QueryExceptionHTTP(rdfEx) ;
- }
- }
-
- @Override
- public String toString()
- {
- String s = httpString() ;
- if ( s != null && s.length() > 0 )
- return serviceURL+"?"+s ;
- return serviceURL ;
- }
-}
-
-/*
- * (c) Copyright 2003, 2004, 2005, 2006, 2007, 2008, 2009 Hewlett-Packard Development Company, LP
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the distribution.
- * 3. The name of the author may not be used to endorse or promote products
- * derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
- * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
- * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
- * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
Added: trunk/components-core/src/main/java/org/dllearner/refinementoperators/SynchronizedRhoDRDown.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/refinementoperators/SynchronizedRhoDRDown.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/refinementoperators/SynchronizedRhoDRDown.java 2012-03-26 12:10:46 UTC (rev 3618)
@@ -0,0 +1,1713 @@
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.dllearner.refinementoperators;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.Component;
+import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.config.BooleanEditor;
+import org.dllearner.core.config.ConfigOption;
+import org.dllearner.core.options.CommonConfigOptions;
+import org.dllearner.core.owl.BooleanValueRestriction;
+import org.dllearner.core.owl.ClassHierarchy;
+import org.dllearner.core.owl.Constant;
+import org.dllearner.core.owl.DataRange;
+import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.DatatypePropertyHierarchy;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DoubleMaxValue;
+import org.dllearner.core.owl.DoubleMinValue;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.Negation;
+import org.dllearner.core.owl.Nothing;
+import org.dllearner.core.owl.ObjectAllRestriction;
+import org.dllearner.core.owl.ObjectCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMaxCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyExpression;
+import org.dllearner.core.owl.ObjectPropertyHierarchy;
+import org.dllearner.core.owl.ObjectQuantorRestriction;
+import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.core.owl.ObjectValueRestriction;
+import org.dllearner.core.owl.StringValueRestriction;
+import org.dllearner.core.owl.Thing;
+import org.dllearner.core.owl.Union;
+import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.owl.ConceptComparator;
+import org.dllearner.utilities.owl.ConceptTransformation;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * A downward refinement operator, which makes use of domains
+ * and ranges of properties. The operator is currently under
+ * development. Its aim is to span a much "cleaner" and smaller search
+ * tree compared to RhoDown by omitting many class descriptions,
+ * which are obviously too weak, because they violate
+ * domain/range restrictions. Furthermore, it makes use of disjoint
+ * classes in the knowledge base.
+ *
+ * TODO Some of the code has moved to {@link Utility} in a modified
+ * form to make it accessible for implementations of other refinement
+ * operators. These utility methods may be completed and carefully
+ * integrated back later.
+ *
+ * @author Jens Lehmann
+ *
+ */
+@ComponentAnn(name = "synchronized rho refinement operator", shortName = "syncrho", version = 0.8)
+public class SynchronizedRhoDRDown extends RefinementOperatorAdapter implements Component {
+
+ private static Logger logger = Logger
+ .getLogger(SynchronizedRhoDRDown.class);
+
+ private AbstractReasonerComponent reasoner;
+
+ // hierarchies
+ private ClassHierarchy subHierarchy;
+ private ObjectPropertyHierarchy objectPropertyHierarchy;
+ private DatatypePropertyHierarchy dataPropertyHierarchy;
+
+ // domains and ranges
+ private Map<ObjectProperty,Description> opDomains = new TreeMap<ObjectProperty,Description>();
+ private Map<DatatypeProperty,Description> dpDomains = new TreeMap<DatatypeProperty,Description>();
+ private Map<ObjectProperty,Description> opRanges = new TreeMap<ObjectProperty,Description>();
+
+ // maximum number of fillers for eeach role
+ private Map<ObjectProperty,Integer> maxNrOfFillers = new TreeMap<ObjectProperty,Integer>();
+ // limit for cardinality restrictions (this makes sense if we e.g. have compounds with up to
+ // more than 200 atoms but we are only interested in atoms with certain characteristics and do
+ // not want something like e.g. >= 204 hasAtom.NOT Carbon-87; which blows up the search space
+ private int cardinalityLimit = 5;
+
+ // start concept (can be used to start from an arbitrary concept, needs
+ // to be Thing or NamedClass), note that when you use e.g. Compound as
+ // start class, then the algorithm should start the search with class
+ // Compound (and not with Thing), because otherwise concepts like
+ // NOT Carbon-87 will be returned which itself is not a subclass of Compound
+ private Description startClass = new Thing();
+
+ // the length of concepts of top refinements, the first values is
+ // for refinements of \rho_\top(\top), the second one for \rho_A(\top)
+ private int topRefinementsLength = 0;
+ private Map<NamedClass, Integer> topARefinementsLength = new TreeMap<NamedClass, Integer>();
+ // M is finite and this value is the maximum length of any value in M
+ private static int mMaxLength = 4;
+
+ // the sets M_\top and M_A
+ private Map<Integer,SortedSet<Description>> m = new TreeMap<Integer,SortedSet<Description>>();
+ private Map<NamedClass,Map<Integer,SortedSet<Description>>> mA = new TreeMap<NamedClass,Map<Integer,SortedSet<Description>>>();
+
+ // @see MathOperations.getCombos
+ private Map<Integer, List<List<Integer>>> combos = new HashMap<Integer, List<List<Integer>>>();
+
+ // refinements of the top concept ordered by length
+ private Map<Integer, SortedSet<Description>> topRefinements = Collections.synchronizedSortedMap(new TreeMap<Integer, SortedSet<Description>>());
+ private Map<NamedClass,Map<Integer, SortedSet<Description>>> topARefinements = Collections.synchronizedSortedMap(new TreeMap<NamedClass,Map<Integer, SortedSet<Description>>>());
+
+ // cumulated refinements of top (all from length one to the specified length)
+ private Map<Integer, TreeSet<Description>> topRefinementsCumulative = Collections.synchronizedMap(new HashMap<Integer, TreeSet<Description>>());
+ private Map<NamedClass,Map<Integer, TreeSet<Description>>> topARefinementsCumulative = Collections.synchronizedSortedMap(new TreeMap<NamedClass,Map<Integer, TreeSet<Description>>>());
+
+ // app_A set of applicable properties for a given class (separate for
+ // object properties, boolean datatypes, and double datatypes)
+ private Map<NamedClass, Set<ObjectProperty>> appOP = new TreeMap<NamedClass, Set<ObjectProperty>>();
+ private Map<NamedClass, Set<DatatypeProperty>> appBD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
+ private Map<NamedClass, Set<DatatypeProperty>> appDD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
+ private Map<NamedClass, Set<DatatypeProperty>> appSD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
+
+ // most general applicable properties
+ private Map<NamedClass,Set<ObjectProperty>> mgr = new TreeMap<NamedClass,Set<ObjectProperty>>();
+ private Map<NamedClass,Set<DatatypeProperty>> mgbd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
+ private Map<NamedClass,Set<DatatypeProperty>> mgdd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
+ private Map<NamedClass,Set<DatatypeProperty>> mgsd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
+
+ // concept comparator
+ private ConceptComparator conceptComparator = new ConceptComparator();
+
+ // splits for double datatype properties in ascening order
+ private Map<DatatypeProperty,List<Double>> splits = new TreeMap<DatatypeProperty,List<Double>>();
+ private int maxNrOfSplits = 10;
+
+ // data structure for a simple frequent pattern matching preprocessing phase
+ private int frequencyThreshold = CommonConfigOptions.valueFrequencyThresholdDefault;
+ private Map<ObjectProperty, Map<Individual, Integer>> valueFrequency = new HashMap<ObjectProperty, Map<Individual, Integer>>();
+ // data structure with identified frequent values
+ private Map<ObjectProperty, Set<Individual>> frequentValues = new HashMap<ObjectProperty, Set<Individual>>();
+ // frequent data values
+ private Map<DatatypeProperty, Set<Constant>> frequentDataValues = new HashMap<DatatypeProperty, Set<Constant>>();
+ private Map<DatatypeProperty, Map<Constant, Integer>> dataValueFrequency = new HashMap<DatatypeProperty, Map<Constant, Integer>>();
+ private boolean useDataHasValueConstructor = false;
+
+ // statistics
+ public long mComputationTimeNs = 0;
+ public long topComputationTimeNs = 0;
+
+ @ConfigOption(name = "applyAllFilter", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean applyAllFilter = true;
+
+ @ConfigOption(name = "applyExistsFilter", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean applyExistsFilter = true;
+
+ @ConfigOption(name = "useAllConstructor", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean useAllConstructor = true;
+
+ @ConfigOption(name = "useExistsConstructor", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean useExistsConstructor = true;
+
+ @ConfigOption(name = "useHasValueConstructor", defaultValue="false", propertyEditorClass = BooleanEditor.class)
+ private boolean useHasValueConstructor = false;
+
+ @ConfigOption(name = "useCardinalityRestrictions", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean useCardinalityRestrictions = true;
+
+ @ConfigOption(name = "useNegation", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean useNegation = true;
+
+ @ConfigOption(name = "useBooleanDatatypes", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean useBooleanDatatypes = true;
+
+ @ConfigOption(name = "useDoubleDatatypes", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean useDoubleDatatypes = true;
+
+ @ConfigOption(name = "useStringDatatypes", defaultValue="false", propertyEditorClass = BooleanEditor.class)
+ private boolean useStringDatatypes = false;
+
+ @ConfigOption(name = "disjointChecks", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean disjointChecks = true;
+
+ @ConfigOption(name = "instanceBasedDisjoints", defaultValue="true", propertyEditorClass = BooleanEditor.class)
+ private boolean instanceBasedDisjoints = true;
+
+ @ConfigOption(name = "dropDisjuncts", defaultValue="false", propertyEditorClass = BooleanEditor.class)
+ private boolean dropDisjuncts = false;
+
+ // caches for reasoner queries
+ private Map<Description,Map<Description,Boolean>> cachedDisjoints = new TreeMap<Description,Map<Description,Boolean>>(conceptComparator);
+
+// private Map<NamedClass,Map<NamedClass,Boolean>> abDisjoint = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
+// private Map<NamedClass,Map<NamedClass,Boolean>> notABDisjoint = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
+// private Map<NamedClass,Map<NamedClass,Boolean>> notABMeaningful = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
+
+ private boolean isInitialised = false;
+
+ public SynchronizedRhoDRDown() {
+
+ }
+
+// public RhoDRDown(AbstractReasonerComponent reasoningService) {
+//// this(reasoningService, reasoningService.getClassHierarchy(), null, true, true, true, true, true, 3, true, true, true, true, null);
+// this.reasoner = reasoningService;
+// this.subHierarchy = reasoner.getClassHierarchy();
+// init();
+// }
+
+ // TODO constructor which takes a RhoDRDownConfigurator object;
+ // this should be an interface implemented e.g. by ExampleBasedROLComponentConfigurator;
+ // the goal is to use the configurator system while still being flexible enough to
+ // use one refinement operator in several learning algorithms
+// public RhoDRDown(AbstractReasonerComponent reasoningService, ClassHierarchy subHierarchy, boolean applyAllFilter, boolean applyExistsFilter, boolean useAllConstructor,
+// boolean useExistsConstructor, boolean useHasValueConstructor, int valueFrequencyThreshold, boolean useCardinalityRestrictions,boolean useNegation, boolean useBooleanDatatypes, boolean useDoubleDatatypes, NamedClass startClass,
+// int cardinalityLimit, boolean useStringDatatypes, boolean instanceBasedDisjoints) {
+// this.reasoner = reasoningService;
+// this.subHierarchy = subHierarchy;
+// this.applyAllFilter = applyAllFilter;
+// this.applyExistsFilter = applyExistsFilter;
+// this.useAllConstructor = useAllConstructor;
+// this.useExistsConstructor = useExistsConstructor;
+// this.useHasValueConstructor = useHasValueConstructor;
+// this.frequencyThreshold = valueFrequencyThreshold;
+// this.useCardinalityRestrictions = useCardinalityRestrictions;
+// this.cardinalityLimit = cardinalityLimit;
+// this.useNegation = useNegation;
+// this.useBooleanDatatypes = useBooleanDatatypes;
+// this.useDoubleDatatypes = useDoubleDatatypes;
+// this.useStringDatatypes = useStringDatatypes;
+// this.instanceBasedDisjoints = instanceBasedDisjoints;
+// if(startClass != null) {
+// this.startClass = startClass;
+// }
+// init();
+// }
+
+// subHierarchy = rs.getClassHierarchy();
+ public void init() throws ComponentInitException {
+ if(isInitialised) {
+ throw new ComponentInitException("Refinement operator cannot be nitialised twice.");
+ }
+// System.out.println("subHierarchy: " + subHierarchy);
+// System.out.println("object properties: " + );
+
+ // query reasoner for domains and ranges
+ // (because they are used often in the operator)
+ for(ObjectProperty op : reasoner.getObjectProperties()) {
+ opDomains.put(op, reasoner.getDomain(op));
+ opRanges.put(op, reasoner.getRange(op));
+
+ if(useHasValueConstructor) {
+ // init
+ Map<Individual, Integer> opMap = new TreeMap<Individual, Integer>();
+ valueFrequency.put(op, opMap);
+
+ // sets ordered by corresponding individual (which we ignore)
+ Collection<SortedSet<Individual>> fillerSets = reasoner.getPropertyMembers(op).values();
+ for(SortedSet<Individual> fillerSet : fillerSets) {
+ for(Individual i : fillerSet) {
+// System.out.println("op " + op + " i " + i);
+ Integer value = opMap.get(i);
+
+ if(value != null) {
+ opMap.put(i, value+1);
+ } else {
+ opMap.put(i, 1);
+ }
+ }
+ }
+
+ // keep only frequent patterns
+ Set<Individual> frequentInds = new TreeSet<Individual>();
+ for(Individual i : opMap.keySet()) {
+ if(opMap.get(i) >= frequencyThreshold) {
+ frequentInds.add(i);
+// break;
+ }
+ }
+ frequentValues.put(op, frequentInds);
+
+ }
+
+ }
+
+ for(DatatypeProperty dp : reasoner.getDatatypeProperties()) {
+ dpDomains.put(dp, reasoner.getDomain(dp));
+
+ if(useDataHasValueConstructor) {
+ Map<Constant, Integer> dpMap = new TreeMap<Constant, Integer>();
+ dataValueFrequency.put(dp, dpMap);
+
+ // sets ordered by corresponding individual (which we ignore)
+ Collection<SortedSet<Constant>> fillerSets = reasoner.getDatatypeMembers(dp).values();
+ for(SortedSet<Constant> fillerSet : fillerSets) {
+ for(Constant i : fillerSet) {
+// System.out.println("op " + op + " i " + i);
+ Integer value = dpMap.get(i);
+
+ if(value != null) {
+ dpMap.put(i, value+1);
+ } else {
+ dpMap.put(i, 1);
+ }
+ }
+ }
+
+ // keep only frequent patterns
+ Set<Constant> frequentInds = new TreeSet<Constant>();
+ for(Constant i : dpMap.keySet()) {
+ if(dpMap.get(i) >= frequencyThreshold) {
+ logger.trace("adding value "+i+", because "+dpMap.get(i) +">="+frequencyThreshold);
+ frequentInds.add(i);
+ }
+ }
+ frequentDataValues.put(dp, frequentInds);
+ }
+ }
+
+ // we do not need the temporary set anymore and let the
+ // garbage collector take c...
[truncated message content] |
|
From: <tc...@us...> - 2012-05-11 05:49:31
|
Revision: 3702
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3702&view=rev
Author: tcanvn
Date: 2012-05-11 05:49:23 +0000 (Fri, 11 May 2012)
Log Message:
-----------
Changes:
1. add Apache Common Pool library into the build path (pom)
2. change visibility of some of the properties on OENode from private to protected
3. add RhoDRDown used in Dl-Learner version 2008 back to refinement operators package (for ParCEL)
4. modify KBFile.class to fix the bug that causes file-separate redundancy when loading a KB file by a relative path (in Windows)
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java
trunk/components-core/src/main/java/org/dllearner/kb/KBFile.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown2008.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2012-05-10 13:31:25 UTC (rev 3701)
+++ trunk/components-core/pom.xml 2012-05-11 05:49:23 UTC (rev 3702)
@@ -211,7 +211,6 @@
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
-
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
@@ -229,7 +228,18 @@
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
</dependency>
-
-
- </dependencies>
+ <dependency>
+ <groupId>commons-pool</groupId>
+ <artifactId>commons-pool</artifactId>
+ </dependency>
+ </dependencies>
+ <dependencyManagement>
+ <dependencies>
+ <dependency>
+ <groupId>commons-pool</groupId>
+ <artifactId>commons-pool</artifactId>
+ <version>1.6</version>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
</project>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java 2012-05-10 13:31:25 UTC (rev 3701)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/OENode.java 2012-05-11 05:49:23 UTC (rev 3702)
@@ -43,14 +43,14 @@
*/
public class OENode implements SearchTreeNode {
- private Description description;
+ protected Description description;
- private double accuracy;
+ protected double accuracy;
- private int horizontalExpansion;
+ protected int horizontalExpansion;
- private OENode parent;
- private List<OENode> children = new LinkedList<OENode>();
+ protected OENode parent;
+ protected List<OENode> children = new LinkedList<OENode>();
// the refinement count corresponds to the number of refinements of the
// description in this node - it is a better heuristic indicator than child count
Modified: trunk/components-core/src/main/java/org/dllearner/kb/KBFile.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/KBFile.java 2012-05-10 13:31:25 UTC (rev 3701)
+++ trunk/components-core/src/main/java/org/dllearner/kb/KBFile.java 2012-05-11 05:49:23 UTC (rev 3702)
@@ -37,7 +37,6 @@
import org.dllearner.parser.ParseException;
import org.dllearner.reasoning.DIGConverter;
import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
-import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -106,7 +105,16 @@
/** Leave it as is */
kb = KBParser.parseKBFile(getUrl());
} else {
- File f = new File(new URI(baseDir + File.separator + getUrl()));
+
+ //this check is for eliminating the redundancy
+ //if the baseDir has separator at the end, do not add one more between baseDir and KB filename (or url)
+ String fullFilepath;
+ if (baseDir.endsWith("\\") || baseDir.endsWith("/"))
+ fullFilepath = baseDir + getUrl();
+ else
+ fullFilepath = baseDir + File.separator + getUrl();
+
+ File f = new File(new URI(fullFilepath));
setUrl(f.toURI().toString());
kb = KBParser.parseKBFile(f);
}
Added: trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown2008.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown2008.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown2008.java 2012-05-11 05:49:23 UTC (rev 3702)
@@ -0,0 +1,1520 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.refinementoperators;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+import java.util.Map.Entry;
+
+import org.apache.log4j.Logger;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.options.CommonConfigOptions;
+import org.dllearner.core.owl.BooleanValueRestriction;
+import org.dllearner.core.owl.ClassHierarchy;
+import org.dllearner.core.owl.Constant;
+import org.dllearner.core.owl.DataRange;
+import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.DatatypeSomeRestriction;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.DoubleMaxValue;
+import org.dllearner.core.owl.DoubleMinValue;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.Negation;
+import org.dllearner.core.owl.Nothing;
+import org.dllearner.core.owl.ObjectAllRestriction;
+import org.dllearner.core.owl.ObjectCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMaxCardinalityRestriction;
+import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyExpression;
+import org.dllearner.core.owl.ObjectQuantorRestriction;
+import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.core.owl.ObjectValueRestriction;
+import org.dllearner.core.owl.StringValueRestriction;
+import org.dllearner.core.owl.Thing;
+import org.dllearner.core.owl.Union;
+import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.owl.ConceptComparator;
+import org.dllearner.utilities.owl.ConceptTransformation;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * A downward refinement operator, which makes use of domains
+ * and ranges of properties. The operator is currently under
+ * development. Its aim is to span a much "cleaner" and smaller search
+ * tree compared to RhoDown by omitting many class descriptions,
+ * which are obviously too weak, because they violate
+ * domain/range restrictions. Furthermore, it makes use of disjoint
+ * classes in the knowledge base.
+ *
+ * TODO Some of the code has moved to {@link Utility} in a modified
+ * form to make it accessible for implementations of other refinement
+ * operators. These utility methods may be completed and carefully
+ * integrated back later.
+ *
+ * @author Jens Lehmann
+ *
+ */
+
+@ComponentAnn(name = "rho refinement operator 2008", shortName = "rho2008", version = 0.08)
+public class RhoDRDown2008 extends RefinementOperatorAdapter {
+
+ private static Logger logger = Logger.getLogger(RhoDRDown2008.class);
+
+ private AbstractReasonerComponent rs;
+
+ // hierarchies
+ private ClassHierarchy subHierarchy;
+
+ // domains and ranges
+ private Map<ObjectProperty,Description> opDomains = new TreeMap<ObjectProperty,Description>();
+ private Map<DatatypeProperty,Description> dpDomains = new TreeMap<DatatypeProperty,Description>();
+ private Map<ObjectProperty,Description> opRanges = new TreeMap<ObjectProperty,Description>();
+
+ // maximum number of fillers for eeach role
+ private Map<ObjectProperty,Integer> maxNrOfFillers = new TreeMap<ObjectProperty,Integer>();
+ // limit for cardinality restrictions (this makes sense if we e.g. have compounds with up to
+ // more than 200 atoms but we are only interested in atoms with certain characteristics and do
+ // not want something like e.g. >= 204 hasAtom.NOT Carbon-87; which blows up the search space
+ private int cardinalityLimit = 5;
+
+ // start concept (can be used to start from an arbitrary concept, needs
+ // to be Thing or NamedClass), note that when you use e.g. Compound as
+ // start class, then the algorithm should start the search with class
+ // Compound (and not with Thing), because otherwise concepts like
+ // NOT Carbon-87 will be returned which itself is not a subclass of Compound
+ private Description startClass = new Thing();
+
+ // the length of concepts of top refinements, the first values is
+ // for refinements of \rho_\top(\top), the second one for \rho_A(\top)
+ private int topRefinementsLength = 0;
+ private Map<NamedClass, Integer> topARefinementsLength = new TreeMap<NamedClass, Integer>();
+ // M is finite and this value is the maximum length of any value in M
+ private static int mMaxLength = 4;
+
+ // the sets M_\top and M_A
+ private Map<Integer,SortedSet<Description>> m = new TreeMap<Integer,SortedSet<Description>>();
+ private Map<NamedClass,Map<Integer,SortedSet<Description>>> mA = new TreeMap<NamedClass,Map<Integer,SortedSet<Description>>>();
+
+ // @see MathOperations.getCombos
+ private Map<Integer, List<List<Integer>>> combos = new HashMap<Integer, List<List<Integer>>>();
+
+ // refinements of the top concept ordered by length
+ private Map<Integer, SortedSet<Description>> topRefinements = new TreeMap<Integer, SortedSet<Description>>();
+ private Map<NamedClass,Map<Integer, SortedSet<Description>>> topARefinements = new TreeMap<NamedClass,Map<Integer, SortedSet<Description>>>();
+
+ // cumulated refinements of top (all from length one to the specified length)
+ private Map<Integer, TreeSet<Description>> topRefinementsCumulative = new HashMap<Integer, TreeSet<Description>>();
+ private Map<NamedClass,Map<Integer, TreeSet<Description>>> topARefinementsCumulative = new TreeMap<NamedClass,Map<Integer, TreeSet<Description>>>();
+
+ // app_A set of applicable properties for a given class (separate for
+ // object properties, boolean datatypes, and double datatypes)
+ private Map<NamedClass, Set<ObjectProperty>> appOP = new TreeMap<NamedClass, Set<ObjectProperty>>();
+ private Map<NamedClass, Set<DatatypeProperty>> appBD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
+ private Map<NamedClass, Set<DatatypeProperty>> appDD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
+
+ // most general applicable properties
+ private Map<NamedClass,Set<ObjectProperty>> mgr = new TreeMap<NamedClass,Set<ObjectProperty>>();
+ private Map<NamedClass,Set<DatatypeProperty>> mgbd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
+ private Map<NamedClass,Set<DatatypeProperty>> mgdd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
+ private Map<NamedClass,Set<DatatypeProperty>> mgsd = new TreeMap<NamedClass,Set<DatatypeProperty>>();
+
+ // concept comparator
+ private ConceptComparator conceptComparator = new ConceptComparator();
+
+ // splits for double datatype properties in ascening order
+ private Map<DatatypeProperty,List<Double>> splits = null; //new TreeMap<DatatypeProperty,List<Double>>();
+
+ /**
+ * how many splits will be made for double data properties
+ */
+ private int maxNrOfSplits = 10;
+
+ // data structure for a simple frequent pattern matching preprocessing phase
+ private int frequencyThreshold = CommonConfigOptions.valueFrequencyThresholdDefault;
+ private Map<ObjectProperty, Map<Individual, Integer>> valueFrequency = new HashMap<ObjectProperty, Map<Individual, Integer>>();
+ // data structure with identified frequent values
+ private Map<ObjectProperty, Set<Individual>> frequentValues = new HashMap<ObjectProperty, Set<Individual>>();
+ // frequent data values
+ private Map<DatatypeProperty, Set<Constant>> frequentDataValues = new HashMap<DatatypeProperty, Set<Constant>>();
+ private Map<DatatypeProperty, Map<Constant, Integer>> dataValueFrequency = new HashMap<DatatypeProperty, Map<Constant, Integer>>();
+ private boolean useDataHasValueConstructor = false;
+
+ // staistics
+ public long mComputationTimeNs = 0;
+ public long topComputationTimeNs = 0;
+
+ private boolean applyAllFilter = true;
+ private boolean applyExistsFilter = true;
+ private boolean useAllConstructor = true;
+ private boolean useExistsConstructor = true;
+ private boolean useHasValueConstructor = false;
+ private boolean useCardinalityRestrictions = true;
+ private boolean useNegation = true;
+ private boolean useBooleanDatatypes = true;
+ private boolean useDoubleDatatypes = true;
+ @SuppressWarnings("unused")
+ private boolean useStringDatatypes = false;
+ private boolean disjointChecks = true;
+ private boolean instanceBasedDisjoints = true;
+
+ private boolean dropDisjuncts = false;
+
+ private boolean isDisjunctionAllowed = true;
+
+ // caches for reasoner queries
+ private Map<Description,Map<Description,Boolean>> cachedDisjoints = new TreeMap<Description,Map<Description,Boolean>>(conceptComparator);
+
+
+ public RhoDRDown2008(AbstractReasonerComponent reasoningService) {
+ this.rs = reasoningService;
+ this.subHierarchy = rs.getClassHierarchy();
+ }
+
+ public RhoDRDown2008(AbstractReasonerComponent reasoner, ClassHierarchy subHierarchy, Description startClass) {
+ this.rs = reasoner;
+ this.subHierarchy = subHierarchy;
+ this.startClass = startClass;
+ }
+
+ public void init() {
+ // query reasoner for domains and ranges
+ // (because they are used often in the operator)
+
+ if (logger.isDebugEnabled())
+ logger.debug("[Refinement operator] " + this.getClass().getSimpleName() + " created (splits: " + (splits!=null?"using Splitter":"fix split="+maxNrOfSplits) + ")"); //actran
+
+
+ for(ObjectProperty op : rs.getObjectProperties()) {
+ opDomains.put(op, rs.getDomain(op));
+ opRanges.put(op, rs.getRange(op));
+
+ if(useHasValueConstructor) {
+ // init
+ Map<Individual, Integer> opMap = new TreeMap<Individual, Integer>();
+ valueFrequency.put(op, opMap);
+
+ // sets ordered by corresponding individual (which we ignore)
+ Collection<SortedSet<Individual>> fillerSets = rs.getPropertyMembers(op).values();
+ for(SortedSet<Individual> fillerSet : fillerSets) {
+ for(Individual i : fillerSet) {
+ // System.out.println("op " + op + " i " + i);
+ Integer value = opMap.get(i);
+
+ if(value != null) {
+ opMap.put(i, value+1);
+ } else {
+ opMap.put(i, 1);
+ }
+ }
+ }
+
+ // keep only frequent patterns
+ Set<Individual> frequentInds = new TreeSet<Individual>();
+ for(Individual i : opMap.keySet()) {
+ if(opMap.get(i) >= frequencyThreshold) {
+ frequentInds.add(i);
+ // break;
+ }
+ }
+ frequentValues.put(op, frequentInds);
+
+ }
+
+ }
+
+ //logger.trace("[rho] Init ObjectProperty: " + opDomains);
+ //logger.trace("[rho] Init ObjectProperty: " + opRanges);
+
+ for(DatatypeProperty dp : rs.getDatatypeProperties()) {
+ dpDomains.put(dp, rs.getDomain(dp));
+
+ if(useDataHasValueConstructor) {
+ Map<Constant, Integer> dpMap = new TreeMap<Constant, Integer>();
+ dataValueFrequency.put(dp, dpMap);
+
+ // sets ordered by corresponding individual (which we ignore)
+ Collection<SortedSet<Constant>> fillerSets = rs.getDatatypeMembers(dp).values();
+ for(SortedSet<Constant> fillerSet : fillerSets) {
+ for(Constant i : fillerSet) {
+ // System.out.println("op " + op + " i " + i);
+ Integer value = dpMap.get(i);
+
+ if(value != null) {
+ dpMap.put(i, value+1);
+ } else {
+ dpMap.put(i, 1);
+ }
+ }
+ }
+
+ // keep only frequent patterns
+ Set<Constant> frequentInds = new TreeSet<Constant>();
+ for(Constant i : dpMap.keySet()) {
+ if(dpMap.get(i) >= frequencyThreshold) {
+ logger.trace("adding value "+i+", because "+dpMap.get(i) +">="+frequencyThreshold);
+ frequentInds.add(i);
+ }
+ }
+ frequentDataValues.put(dp, frequentInds);
+ }
+ }
+
+ // we do not need the temporary set anymore and let the
+ // garbage collector take care of it
+ valueFrequency = null;
+ dataValueFrequency = null;
+
+
+ // compute splits for double datatype properties
+ if (this.splits == null) {
+ splits = new TreeMap<DatatypeProperty,List<Double>>();
+ for(DatatypeProperty dp : rs.getDoubleDatatypeProperties())
+ computeSplits(dp);
+
+ if (logger.isDebugEnabled()) {
+ logger.debug("[RhoDRDown2008] Uses original split strategy: " + splits);
+ }
+ }
+
+
+
+ // determine the maximum number of fillers for each role
+ // (up to a specified cardinality maximum)
+ if(useCardinalityRestrictions) {
+ for(ObjectProperty op : rs.getObjectProperties()) {
+ int maxFillers = 0;
+ Map<Individual,SortedSet<Individual>> opMembers = rs.getPropertyMembers(op);
+ for(SortedSet<Individual> inds : opMembers.values()) {
+ if(inds.size()>maxFillers)
+ maxFillers = inds.size();
+ if(maxFillers >= cardinalityLimit) {
+ maxFillers = cardinalityLimit;
+ break;
+ }
+ }
+ maxNrOfFillers.put(op, maxFillers);
+ }
+ }
+
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.algorithms.refinement.RefinementOperator#refine(org.dllearner.core.owl.Description)
+ */
+ @Override
+ public Set<Description> refine(Description concept) {
+ throw new RuntimeException();
+ }
+
+ @Override
+ public Set<Description> refine(Description description, int maxLength) {
+ // check that maxLength is valid
+ if(maxLength < description.getLength()) {
+ throw new Error("length has to be at least description length (description: " + description + ", max length: " + maxLength + ")");
+ }
+ return refine(description, maxLength, null, startClass);
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.algorithms.refinement.RefinementOperator#refine(org.dllearner.core.owl.Description, int, java.util.List)
+ */
+ @Override
+ public Set<Description> refine(Description description, int maxLength,
+ List<Description> knownRefinements) {
+ return refine(description, maxLength, knownRefinements, startClass);
+ }
+
+ @SuppressWarnings({"unchecked"})
+ public Set<Description> refine(Description description, int maxLength,
+ List<Description> knownRefinements, Description currDomain) {
+
+ // System.out.println("|- " + description + " " + currDomain + " " + maxLength);
+
+ //logger.trace(" [rho-refine] Refine called for: " + description);
+ //logger.trace(" \t\tmaxLength: " + maxLength + "; knownRefinrements: " + knownRefinements +"; currDomain: " + currDomain);
+
+
+ // actions needing to be performed if this is the first time the
+ // current domain is used
+ if(!(currDomain instanceof Thing) && !topARefinementsLength.containsKey(currDomain))
+ topARefinementsLength.put((NamedClass)currDomain, 0);
+
+ // check whether using list or set makes more sense
+ // here; and whether HashSet or TreeSet should be used
+ // => TreeSet because duplicates are possible
+ Set<Description> refinements = new TreeSet<Description>(conceptComparator);
+
+ // used as temporary variable
+ Set<Description> tmp = new HashSet<Description>();
+
+ if(description instanceof Thing) {
+ // extends top refinements if necessary
+ if(currDomain instanceof Thing) {
+ if(maxLength>topRefinementsLength)
+ computeTopRefinements(maxLength);
+ refinements = (TreeSet<Description>) topRefinementsCumulative.get(maxLength).clone();
+ } else {
+ if(maxLength>topARefinementsLength.get(currDomain)) {
+ computeTopRefinements(maxLength, (NamedClass) currDomain);
+ }
+ refinements = (TreeSet<Description>) topARefinementsCumulative.get(currDomain).get(maxLength).clone();
+ }
+ // refinements.addAll(subHierarchy.getMoreSpecialConcepts(description));
+ } else if(description instanceof Nothing) {
+ // cannot be further refined
+ } else if(description instanceof NamedClass) {
+ refinements.addAll(subHierarchy.getSubClasses(description));
+ refinements.remove(new Nothing());
+ } else if (description instanceof Negation && description.getChild(0) instanceof NamedClass) {
+
+ tmp = subHierarchy.getSuperClasses(description.getChild(0));
+
+ for(Description c : tmp) {
+ if(!(c instanceof Thing))
+ refinements.add(new Negation(c));
+ }
+ } else if (description instanceof Intersection) {
+
+ // refine one of the elements
+ for(Description child : description.getChildren()) {
+
+ // refine the child; the new max length is the current max length minus
+ // the currently considered concept plus the length of the child
+ // TODO: add better explanation
+ tmp = refine(child, maxLength - description.getLength()+child.getLength(),null,currDomain);
+
+ // create new intersection
+ for(Description c : tmp) {
+ List<Description> newChildren = (List<Description>)((LinkedList<Description>)description.getChildren()).clone();
+ newChildren.add(c);
+ newChildren.remove(child);
+ Intersection mc = new Intersection(newChildren);
+
+ // clean concept and transform it to ordered negation normal form
+ // (non-recursive variant because only depth 1 was modified)
+ ConceptTransformation.cleanConceptNonRecursive(mc);
+ ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(mc, conceptComparator);
+
+ // check whether the intersection is OK (sanity checks), then add it
+ if(checkIntersection(mc))
+ refinements.add(mc);
+ }
+
+ }
+
+ } else if (description instanceof Union) {
+ // refine one of the elements
+ for(Description child : description.getChildren()) {
+
+ // System.out.println("union child: " + child + " " + maxLength + " " + description.getLength() + " " + child.getLength());
+
+ // refine child
+ tmp = refine(child, maxLength - description.getLength()+child.getLength(),null,currDomain);
+
+ // construct intersection (see above)
+ for(Description c : tmp) {
+ List<Description> newChildren = new LinkedList<Description>(description.getChildren());
+ newChildren.remove(child);
+ newChildren.add(c);
+ Union md = new Union(newChildren);
+
+ // transform to ordered negation normal form
+ ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(md, conceptComparator);
+ // note that we do not have to call clean here because a disjunction will
+ // never be nested in another disjunction in this operator
+
+ refinements.add(md);
+ }
+
+ }
+
+ // if enabled, we can remove elements of the disjunction
+ if(dropDisjuncts) {
+ // A1 OR A2 => {A1,A2}
+ if(description.getChildren().size() == 2) {
+ refinements.add(description.getChild(0));
+ refinements.add(description.getChild(1));
+ } else {
+ // copy children list and remove a different element in each turn
+ for(int i=0; i<description.getChildren().size(); i++) {
+ List<Description> newChildren = new LinkedList<Description>(description.getChildren());
+ newChildren.remove(i);
+ Union md = new Union(newChildren);
+ refinements.add(md);
+ }
+ }
+ }
+
+ } else if (description instanceof ObjectSomeRestriction) {
+ ObjectPropertyExpression role = ((ObjectQuantorRestriction)description).getRole();
+ Description range = opRanges.get(role);
+
+ // rule 1: EXISTS r.D => EXISTS r.E
+ tmp = refine(description.getChild(0), maxLength-2, null, range);
+
+ for(Description c : tmp)
+ refinements.add(new ObjectSomeRestriction(((ObjectQuantorRestriction)description).getRole(),c));
+
+ // rule 2: EXISTS r.D => EXISTS s.D or EXISTS r^-1.D => EXISTS s^-1.D
+ // currently inverse roles are not supported
+ ObjectProperty ar = (ObjectProperty) role;
+ Set<ObjectProperty> moreSpecialRoles = rs.getSubProperties(ar);
+ for(ObjectProperty moreSpecialRole : moreSpecialRoles)
+ refinements.add(new ObjectSomeRestriction(moreSpecialRole, description.getChild(0)));
+
+ // rule 3: EXISTS r.D => >= 2 r.D
+ // (length increases by 1 so we have to check whether max length is sufficient)
+ if(useCardinalityRestrictions) {
+ if(maxLength > description.getLength() && maxNrOfFillers.get(ar)>1) {
+ ObjectMinCardinalityRestriction min = new ObjectMinCardinalityRestriction(2,role,description.getChild(0));
+ refinements.add(min);
+ }
+ }
+
+ // rule 4: EXISTS r.TOP => EXISTS r.{value}
+ if(useHasValueConstructor && description.getChild(0) instanceof Thing) {
+ // watch out for frequent patterns
+ Set<Individual> frequentInds = frequentValues.get(role);
+ if(frequentInds != null) {
+ for(Individual ind : frequentInds) {
+ ObjectValueRestriction ovr = new ObjectValueRestriction((ObjectProperty)role, ind);
+ refinements.add(ovr);
+ }
+ }
+ }
+
+ } else if (description instanceof ObjectAllRestriction) {
+ ObjectPropertyExpression role = ((ObjectQuantorRestriction)description).getRole();
+ Description range = opRanges.get(role);
+
+ // rule 1: ALL r.D => ALL r.E
+ tmp = refine(description.getChild(0), maxLength-2, null, range);
+
+ for(Description c : tmp) {
+ refinements.add(new ObjectAllRestriction(((ObjectQuantorRestriction)description).getRole(),c));
+ }
+
+ // rule 2: ALL r.D => ALL r.BOTTOM if D is a most specific atomic concept
+ if(description.getChild(0) instanceof NamedClass && tmp.size()==0) {
+ refinements.add(new ObjectAllRestriction(((ObjectQuantorRestriction)description).getRole(),new Nothing()));
+ }
+
+ // rule 3: ALL r.D => ALL s.D or ALL r^-1.D => ALL s^-1.D
+ // currently inverse roles are not supported
+ ObjectProperty ar = (ObjectProperty) role;
+ Set<ObjectProperty> moreSpecialRoles = rs.getSubProperties(ar);
+ for(ObjectProperty moreSpecialRole : moreSpecialRoles) {
+ refinements.add(new ObjectAllRestriction(moreSpecialRole, description.getChild(0)));
+ }
+
+ // rule 4: ALL r.D => <= (maxFillers-1) r.D
+ // (length increases by 1 so we have to check whether max length is sufficient)
+ // => commented out because this is acutally not a downward refinement
+ // if(useCardinalityRestrictions) {
+ // if(maxLength > description.getLength() && maxNrOfFillers.get(ar)>1) {
+ // ObjectMaxCardinalityRestriction max = new ObjectMaxCardinalityRestriction(maxNrOfFillers.get(ar)-1,role,description.getChild(0));
+ // refinements.add(max);
+ // }
+ // }
+ } else if (description instanceof ObjectCardinalityRestriction) {
+ ObjectPropertyExpression role = ((ObjectCardinalityRestriction)description).getRole();
+ Description range = opRanges.get(role);
+ int number = ((ObjectCardinalityRestriction)description).getCardinality();
+ if(description instanceof ObjectMaxCardinalityRestriction) {
+ // rule 1: <= x r.C => <= x r.D
+ tmp = refine(description.getChild(0), maxLength-3, null, range);
+
+ for(Description d : tmp) {
+ refinements.add(new ObjectMaxCardinalityRestriction(number,role,d));
+ }
+
+ // rule 2: <= x r.C => <= (x-1) r.C
+ ObjectMaxCardinalityRestriction max = (ObjectMaxCardinalityRestriction) description;
+ // int number = max.getNumber();
+ if(number > 1)
+ refinements.add(new ObjectMaxCardinalityRestriction(number-1,max.getRole(),max.getChild(0)));
+
+ } else if(description instanceof ObjectMinCardinalityRestriction) {
+ tmp = refine(description.getChild(0), maxLength-3, null, range);
+
+ for(Description d : tmp) {
+ refinements.add(new ObjectMinCardinalityRestriction(number,role,d));
+ }
+
+ // >= x r.C => >= (x+1) r.C
+ ObjectMinCardinalityRestriction min = (ObjectMinCardinalityRestriction) description;
+ // int number = min.getNumber();
+ if(number < maxNrOfFillers.get(min.getRole()))
+ refinements.add(new ObjectMinCardinalityRestriction(number+1,min.getRole(),min.getChild(0)));
+ }
+ } else if (description instanceof DatatypeSomeRestriction) {
+
+ DatatypeSomeRestriction dsr = (DatatypeSomeRestriction) description;
+ DatatypeProperty dp = (DatatypeProperty) dsr.getRestrictedPropertyExpression();
+ DataRange dr = dsr.getDataRange();
+ if(dr instanceof DoubleMaxValue) {
+ double value = ((DoubleMaxValue)dr).getValue();
+ // find out which split value was used
+ int splitIndex = splits.get(dp).lastIndexOf(value);
+ if(splitIndex == -1)
+ throw new Error("split error");
+ int newSplitIndex = splitIndex - 1;
+ if(newSplitIndex >= 0) {
+ DoubleMaxValue max = new DoubleMaxValue(splits.get(dp).get(newSplitIndex));
+ DatatypeSomeRestriction newDSR = new DatatypeSomeRestriction(dp,max);
+ refinements.add(newDSR);
+ // System.out.println(description + " => " + newDSR);
+ }
+ } else if(dr instanceof DoubleMinValue) {
+ double value = ((DoubleMinValue)dr).getValue();
+ // find out which split value was used
+ int splitIndex = splits.get(dp).lastIndexOf(value);
+ if(splitIndex == -1)
+ throw new Error("split error");
+ int newSplitIndex = splitIndex + 1;
+ if(newSplitIndex < splits.get(dp).size()) {
+ DoubleMinValue min = new DoubleMinValue(splits.get(dp).get(newSplitIndex));
+ DatatypeSomeRestriction newDSR = new DatatypeSomeRestriction(dp,min);
+ refinements.add(newDSR);
+ }
+ }
+ } else if (description instanceof StringValueRestriction) {
+ StringValueRestriction svr = (StringValueRestriction) description;
+ DatatypeProperty dp = svr.getRestrictedPropertyExpression();
+ Set<DatatypeProperty> subDPs = rs.getSubProperties(dp);
+ for(DatatypeProperty subDP : subDPs) {
+ refinements.add(new StringValueRestriction(subDP, svr.getStringValue()));
+ }
+ }
+
+ // if a refinement is not Bottom, Top, ALL r.Bottom a refinement of top can be appended
+ if(!(description instanceof Thing) && !(description instanceof Nothing)
+ && !(description instanceof ObjectAllRestriction && description.getChild(0) instanceof Nothing)) {
+ // -1 because of the AND symbol which is appended
+ int topRefLength = maxLength - description.getLength() - 1;
+
+ // maybe we have to compute new top refinements here
+ if(currDomain instanceof Thing) {
+ if(topRefLength > topRefinementsLength)
+ computeTopRefinements(topRefLength);
+ } else if(topRefLength > topARefinementsLength.get(currDomain))
+ computeTopRefinements(topRefLength,(NamedClass)currDomain);
+
+ if(topRefLength>0) {
+ Set<Description> topRefs;
+ if(currDomain instanceof Thing)
+ topRefs = topRefinementsCumulative.get(topRefLength);
+ else
+ topRefs = topARefinementsCumulative.get(currDomain).get(topRefLength);
+
+ for(Description c : topRefs) {
+ // true if refinement should be skipped due to filters,
+ // false otherwise
+ boolean skip = false;
+
+ // if a refinement of of the form ALL r, we check whether ALL r
+ // does not occur already
+ if(applyAllFilter) {
+ if(c instanceof ObjectAllRestriction) {
+ for(Description child : description.getChildren()) {
+ if(child instanceof ObjectAllRestriction) {
+ ObjectPropertyExpression r1 = ((ObjectAllRestriction)c).getRole();
+ ObjectPropertyExpression r2 = ((ObjectAllRestriction)child).getRole();
+ if(r1.toString().equals(r2.toString()))
+ skip = true;
+ }
+ }
+ }
+ }
+
+ // check for double datatype properties
+ /*
+ if(c instanceof DatatypeSomeRestriction &&
+ description instanceof DatatypeSomeRestriction) {
+ DataRange dr = ((DatatypeSomeRestriction)c).getDataRange();
+ DataRange dr2 = ((DatatypeSomeRestriction)description).getDataRange();
+ // it does not make sense to have statements like height >= 1.8 AND height >= 1.7
+ if((dr instanceof DoubleMaxValue && dr2 instanceof DoubleMaxValue)
+ ||(dr instanceof DoubleMinValue && dr2 instanceof DoubleMinValue))
+ skip = true;
+ }*/
+
+ // perform a disjointness check when named classes are added;
+ // this can avoid a lot of superfluous computation in the algorithm e.g.
+ // when A1 looks good, so many refinements of the form (A1 OR (A2 AND A3))
+ // are generated which are all equal to A1 due to disjointness of A2 and A3
+ if(disjointChecks && c instanceof NamedClass && description instanceof NamedClass && isDisjoint(description, c)) {
+ skip = true;
+ // System.out.println(c + " ignored when refining " + description);
+ }
+
+ if(!skip) {
+ Intersection mc = new Intersection();
+ mc.addChild(description);
+ mc.addChild(c);
+
+ // clean and transform to ordered negation normal form
+ ConceptTransformation.cleanConceptNonRecursive(mc);
+ ConceptTransformation.transformToOrderedNegationNormalFormNonRecursive(mc, conceptComparator);
+
+ // last check before intersection is added
+ if(checkIntersection(mc))
+ refinements.add(mc);
+ }
+ }
+ }
+ }
+
+ // for(Description refinement : refinements) {
+ // if((refinement instanceof Intersection || refinement instanceof Union) && refinement.getChildren().size()<2) {
+ // System.out.println(description + " " + refinement + " " + currDomain + " " + maxLength);
+ // System.exit(0);
+ // }
+ // }
+
+
+
+ return refinements;
+ }
+
+ // when a child of an intersection is refined and reintegrated into the
+ // intersection, we can perform some sanity checks;
+ // method returns true if everything is OK and false otherwise
+ // TODO: can be implemented more efficiently if the newly added child
+ // is given as parameter
+ public static boolean checkIntersection(Intersection intersection) {
+ // rule 1: max. restrictions at most once
+ boolean maxDoubleOccurence = false;
+ // rule 2: min restrictions at most once
+ boolean minDoubleOccurence = false;
+ // rule 3: no double occurences of boolean datatypes
+ TreeSet<DatatypeProperty> occuredDP = new TreeSet<DatatypeProperty>();
+ // rule 4: no double occurences of hasValue restrictions
+ TreeSet<ObjectProperty> occuredVR = new TreeSet<ObjectProperty>();
+
+ for(Description child : intersection.getChildren()) {
+ if(child instanceof DatatypeSomeRestriction) {
+ DataRange dr = ((DatatypeSomeRestriction)child).getDataRange();
+ if(dr instanceof DoubleMaxValue) {
+ if(maxDoubleOccurence)
+ return false;
+ else
+ maxDoubleOccurence = true;
+ } else if(dr instanceof DoubleMinValue) {
+ if(minDoubleOccurence)
+ return false;
+ else
+ minDoubleOccurence = true;
+ }
+ } else if(child instanceof BooleanValueRestriction) {
+ DatatypeProperty dp = (DatatypeProperty) ((BooleanValueRestriction)child).getRestrictedPropertyExpression();
+ // System.out.println("dp: " + dp);
+ // return false if the boolean property exists already
+ if(!occuredDP.add(dp))
+ return false;
+ } else if(child instanceof ObjectValueRestriction) {
+ ObjectProperty op = (ObjectProperty) ((ObjectValueRestriction)child).getRestrictedPropertyExpression();
+ if(!occuredVR.add(op))
+ return false;
+ }
+ // System.out.println(child.getClass());
+ }
+ return true;
+ }
+
+ /**
+ * By default, the operator does not specialize e.g. (A or B) to A, because
+ * it only guarantees weak completeness. Under certain circumstances, e.g.
+ * refinement of a fixed given concept, it can be useful to allow such
+ * refinements, which can be done by passing the parameter true to this method.
+ * @param dropDisjuncts Whether to remove disjuncts in refinement process.
+ */
+ public void setDropDisjuncts(boolean dropDisjuncts) {
+ this.dropDisjuncts = dropDisjuncts;
+ }
+
+ private void computeTopRefinements(int maxLength) {
+ computeTopRefinements(maxLength, null);
+ }
+
+ private void computeTopRefinements(int maxLength, NamedClass domain) {
+ long topComputationTimeStartNs = System.nanoTime();
+
+ if(domain == null && m.size() == 0)
+ computeM();
+
+ if(domain != null && !mA.containsKey(domain))
+ computeM(domain);
+
+ int refinementsLength;
+
+ if(domain == null) {
+ refinementsLength = topRefinementsLength;
+ } else {
+ if(!topARefinementsLength.containsKey(domain))
+ topARefinementsLength.put(domain,0);
+
+ refinementsLength = topARefinementsLength.get(domain);
+ }
+
+
+ // compute all possible combinations of the disjunction
+ for(int i = refinementsLength+1; i <= maxLength; i++) {
+ combos.put(i,MathOperations.getCombos(i, mMaxLength));
+
+ // initialise the refinements with empty sets
+ if(domain == null) {
+ topRefinements.put(i, new TreeSet<Description>(conceptComparator));
+ } else {
+ if(!topARefinements.containsKey(domain))
+ topARefinements.put(domain, new TreeMap<Integer,SortedSet<Description>>());
+ topARefinements.get(domain).put(i, new TreeSet<Description>(conceptComparator));
+ }
+
+ for(List<Integer> combo : combos.get(i)) {
+
+ // combination is a single number => try to use M
+ if(combo.size()==1) {
+ // note we cannot use "put" instead of "addAll" because there
+ // can be several combos for one length
+ if(domain == null)
+ topRefinements.get(i).addAll(m.get(i));
+ else
+ topARefinements.get(domain).get(i).addAll(mA.get(domain).get(i));
+ // combinations has several numbers => generate disjunct
+ } else if (isDisjunctionAllowed) {
+
+ // check whether the combination makes sense, i.e. whether
+ // all lengths mentioned in it have corresponding elements
+ // e.g. when negation is deactivated there won't be elements of
+ // length 2 in M
+ boolean validCombo = true;
+ for(Integer j : combo) {
+ if((domain == null && m.get(j).size()==0) ||
+ (domain != null && mA.get(domain).get(j).size()==0))
+ validCombo = false;
+ }
+
+
+ if(validCombo) {
+
+ SortedSet<Union> baseSet = new TreeSet<Union>(conceptComparator);
+ for(Integer j : combo) {
+ if(domain == null)
+ baseSet = MathOperations.incCrossProduct(baseSet, m.get(j));
+ else
+ baseSet = MathOperations.incCrossProduct(baseSet, mA.get(domain).get(j));
+ }
+
+ // convert all concepts in ordered negation normal form
+ for(Description concept : baseSet) {
+ ConceptTransformation.transformToOrderedForm(concept, conceptComparator);
+ }
+
+ // apply the exists filter (throwing out all refinements with
+ // double \exists r for any r)
+ // TODO: similar filtering can be done for boolean datatype
+ // properties
+ if(applyExistsFilter) {
+ Iterator<Union> it = baseSet.iterator();
+ while(it.hasNext()) {
+ if(MathOperations.containsDoubleObjectSomeRestriction(it.next()))
+ it.remove();
+ }
+ }
+
+ // add computed refinements
+ if(domain == null)
+ topRefinements.get(i).addAll(baseSet);
+ else
+ topARefinements.get(domain).get(i).addAll(baseSet);
+
+ }
+ }
+ } //for loop
+
+ // create cumulative versions of refinements such that they can
+ // be accessed easily
+ TreeSet<Description> cumulativeRefinements = new TreeSet<Description>(conceptComparator);
+ for(int j=1; j<=i; j++) {
+ if(domain == null) {
+ cumulativeRefinements.addAll(topRefinements.get(j));
+ } else {
+ cumulativeRefinements.addAll(topARefinements.get(domain).get(j));
+ }
+ }
+
+ if(domain == null) {
+ topRefinementsCumulative.put(i, cumulativeRefinements);
+ } else {
+ if(!topARefinementsCumulative.containsKey(domain))
+ topARefinementsCumulative.put(domain, new TreeMap<Integer, TreeSet<Description>>());
+ topARefinementsCumulative.get(domain).put(i, cumulativeRefinements);
+ }
+ } //for loop for disjunction
+
+
+ // register new top refinements length
+ if(domain == null)
+ topRefinementsLength = maxLength;
+ else
+ topARefinementsLength.put(domain,maxLength);
+
+ topComputationTimeNs += System.nanoTime() - topComputationTimeStartNs;
+ }
+
+ // compute M_\top
+ private void computeM() {
+ long mComputationTimeStartNs = System.nanoTime();
+
+ // initialise all possible lengths (1 to 3) //actran: 3 or 4?
+ for(int i=1; i<=mMaxLength; i++) {
+ m.put(i, new TreeSet<Description>(conceptComparator));
+ }
+
+
+ //actran: computes the most general atomic concepts (subclasses of Thing)
+ SortedSet<Description> m1 = subHierarchy.getSubClasses(new Thing());
+ m.put(1,m1);
+
+
+ //actran: computes negated most specific atomic concepts
+ SortedSet<Description> m2 = new TreeSet<Description>(conceptComparator);
+ if(useNegation) {
+ Set<Description> m2tmp = subHierarchy.getSuperClasses(new Nothing());
+ for(Description c : m2tmp) {
+ if(!(c instanceof Thing)) {
+ m2.add(new Negation(c));
+ }
+ }
+ }
+
+ // boolean datatypes, e.g. testPositive = true
+ if(useBooleanDatatypes) {
+ Set<DatatypeProperty> booleanDPs = rs.getBooleanDatatypeProperties();
+ for(DatatypeProperty dp : booleanDPs) {
+ m2.add(new BooleanValueRestriction(dp,true));
+ m2.add(new BooleanValueRestriction(dp,false));
+ }
+ }
+ m.put(2,m2);
+
+ SortedSet<Description> m3 = new TreeSet<Description>(conceptComparator);
+ if(useExistsConstructor) {
+ // only uses most general roles
+ for(ObjectProperty r : rs.getMostGeneralProperties()) {
+ m3.add(new ObjectSomeRestriction(r, new Thing()));
+ }
+ }
+
+ if(useAllConstructor) {
+ // we allow \forall r.\top here because otherwise the operator
+ // becomes too difficult to manage due to dependencies between
+ // M_A and M_A' where A'=ran(r)
+ for(ObjectProperty r : rs.getMostGeneralProperties()) {
+ m3.add(new ObjectAllRestriction(r, new Thing()));
+ }
+ }
+
+ if(useDoubleDatatypes) {
+ Set<DatatypeProperty> doubleDPs = rs.getDoubleDatatypeProperties();
+ for(DatatypeProperty dp : doubleDPs) {
+ if ((splits.get(dp) != null) && (splits.get(dp).size() > 0)) {
+ DoubleMaxValue max = new DoubleMaxValue(splits.get(dp).get(splits.get(dp).size()-1));
+ DoubleMinValue min = new DoubleMinValue(splits.get(dp).get(0));
+ m3.add(new DatatypeSomeRestriction(dp,max));
+ m3.add(new DatatypeSomeRestriction(dp,min));
+ }
+ }
+ }
+
+ if(useDataHasValueConstructor) {
+ Set<DatatypeProperty> stringDPs = rs.getStringDatatypeProperties();
+ for(DatatypeProperty dp : stringDPs) {
+ // loop over frequent values
+ Set<Constant> freqValues = frequentDataValues.get(dp);
+ for(Constant c : freqValues) {
+ m3.add(new StringValueRestriction(dp, c.getLiteral()));
+ }
+ }
+ }
+
+ m.put(3,m3);
+
+ SortedSet<Description> m4 = new TreeSet<Description>(conceptComparator);
+ if(useCardinalityRestrictions) {
+ for(ObjectProperty r : rs.getMostGeneralProperties()) {
+ int maxFillers = maxNrOfFillers.get(r);
+ // zero fillers: <= -1 r.C does not make sense
+ // one filler: <= 0 r.C is equivalent to NOT EXISTS r.C,
+ // but we still keep it, because ALL r.NOT C may be difficult to reach
+ if(maxFillers > 0)
+ m4.add(new ObjectMaxCardinalityRestriction(maxFillers-1, r, new Thing()));
+ }
+ }
+ m.put(4,m4);
+
+ mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
+ }
+
+ // computation of the set M_A
+ // a major difference compared to the ILP 2007 \rho operator is that
+ // M is finite and contains elements of length (currently) at most 3
+ private void computeM(NamedClass nc) {
+ long mComputationTimeStartNs = System.nanoTime();
+
+ // System.out.println(nc);
+
+ mA.put(nc, new TreeMap<Integer,SortedSet<Description>>());
+ // initialise all possible lengths (1 to 3)
+ for(int i=1; i<=mMaxLength; i++) {
+ mA.get(nc).put(i, new TreeSet<Description>(conceptComparator));
+ }
+
+ // incomplete, prior implementation
+ // SortedSet<Description> m1 = subHierarchy.getSubClasses(nc);
+ // mA.get(nc).put(1,m1);
+
+ // most general classes, which are not disjoint with nc and provide real refinement
+ SortedSet<Description> m1 = getClassCandidates(nc);
+ mA.get(nc).put(1,m1);
+
+ // most specific negated classes, which are not disjoint with nc
+ SortedSet<Description> m2 = new TreeSet<Description>();
+ if(useNegation) {
+ m2 = getNegClassCandidates(nc);
+ mA.get(nc).put(2,m2);
+ }
+
+ // System.out.println("m1 " + "(" + nc + "): " + m1);
+ // System.out.println("m2 " + "(" + nc + "): " + m2);
+
+ /*
+ SortedSet<Description> m2 = new TreeSet<Description>(conceptComparator);
+ if(useNegation) {
+ // the definition in the paper is more complex, but actually
+ // we only have to insert the most specific concepts satisfying
+ // the mentioned restrictions; there is no need to implement a
+ // recursive method because for A subClassOf A' we have not A'
+ // subClassOf A and thus: if A and B are disjoint then also A'
+ // and B; if not A AND B = B then also not A' AND B = B
+ // 2010/03: the latter is not correct => a recursive method is needed
+ SortedSet<Description> m2tmp = subHierarchy.getSuperClasses(new Nothing());
+
+ for(Description c : m2tmp) {
+// if(c instanceof Thing)
+// m2.add(c);
+// else {
+ // we obviously do not add \top (\top refines \top does not make sense)
+ if(!(c instanceof Thing)) {
+ NamedClass a = (NamedClass) c;
+ if(!isNotADisjoint(a, nc) && isNotAMeaningful(a, nc))
+ m2.add(new Negation(a));
+ }
+ }
+ }
+ */
+
+ // compute applicable properties
+ computeMg(nc);
+
+ // boolean datatypes, e.g. testPositive = true
+ if(useBooleanDatatypes) {
+ Set<DatatypeProperty> booleanDPs = mgbd.get(nc);
+ for(DatatypeProperty dp : booleanDPs) {
+ m2.add(new BooleanValueRestriction(dp,true));
+ m2.add(new BooleanValueRestriction(dp,false));
+ }
+ }
+
+ mA.get(nc).put(2,m2);
+
+ SortedSet<Description> m3 = new TreeSet<Description>(conceptComparator);
+ if(useExistsConstructor) {
+ for(ObjectProperty r : mgr.get(nc)) {
+ m3.add(new ObjectSomeRestriction(r, new Thing()));
+ }
+ }
+
+ if(useAllConstructor) {
+ // we allow \forall r.\top here because otherwise the operator
+ // becomes too difficult to manage due to dependencies between
+ // M_A and M_A' where A'=ran(r)
+ for(ObjectProperty r : mgr.get(nc)) {
+ m3.add(new ObjectAllRestriction(r, new Thing()));
+ }
+ }
+
+ if(useDoubleDatatypes) {
+ Set<DatatypeProperty> doubleDPs = mgdd.get(nc);
+ // System.out.println("cached disjoints " + cachedDisjoints);
+ // System.out.println("appOP " + appOP);
+ // System.out.println("appBD " + appBD);
+ // System.out.println("appDD " + appDD);
+ // System.out.println("mgr " + mgr);
+ // System.out.println("mgbd " + mgbd);
+ // System.out.println("mgdd " + mgdd);
+
+ for(DatatypeProperty dp : doubleDPs) {
+ if((splits.get(dp) != null) && (splits.get(dp).size() > 0)) {
+ DoubleMaxValue max = new DoubleMaxValue(splits.get(dp).get(splits.get(dp).size()-1));
+ DoubleMinValue min = new DoubleMinValue(splits.get(dp).get(0));
+ m3.add(new DatatypeSomeRestriction(dp,max));
+ m3.add(new DatatypeSomeRestriction(dp,min));
+ }
+ }
+ }
+
+ if(useDataHasValueConstructor) {
+ Set<DatatypeProperty> stringDPs = mgsd.get(nc);
+ for(DatatypeProperty dp : stringDPs) {
+ // loop over frequent values
+ Set<Constant> freqValues = frequentDataValues.get(dp);
+ for(Constant c : freqValues) {
+ m3.add(new StringValueRestriction(dp, c.getLiteral()));
+ }
+ }
+ }
+
+ mA.get(nc).put(3,m3);
+
+ SortedSet<Description> m4 = new TreeSet<Description>(conceptComparator);
+ if(useCardinalityRestrictions) {
+ for(ObjectProperty r : mgr.get(nc)) {
+ int maxFillers = maxNrOfFillers.get(r);
+ // zero fillers: <= -1 r.C does not make sense
+ // one filler: <= 0 r.C is equivalent to NOT EXISTS r.C,
+ // but we still keep it, because ALL r.NOT C may be difficult to reach
+ if(maxFillers > 0)
+ m4.add(new ObjectMaxCardinalityRestriction(maxFillers-1, r, new Thing()));
+ }
+ }
+ mA.get(nc).put(4,m4);
+
+ // System.out.println(mA.get(nc));
+
+ mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
+ }
+
+ // get candidates for a refinement of \top restricted to a class B
+ public SortedSet<Description> getClassCandidates(NamedClass index) {
+ return getClassCandidatesRecursive(index, Thing.instance);
+ }
+
+ private SortedSet<Description> getClassCandidatesRecursive(Description index, Description upperClass) {
+ SortedSet<Description> candidates = new TreeSet<Description>();
+ // System.out.println("index " + index + " upper class " + upperClass);
+
+ // we descend the subsumption hierarchy to ensure that we get
+ // the most general concepts satisfying the criteria
+ for(Description candidate : subHierarchy.getSubClasses(upperClass)) {
+ // System.out.println("testing " + candidate + " ... ");
+
+ // NamedClass candidate = (NamedClass) d;
+ // check disjointness with index (if not no further traversal downwards is necessary)
+ if(!isDisjoint(candidate,index)) {
+ // System.out.println( " passed disjointness test ... ");
+ // check whether the class is meaningful, i.e. adds something to the index
+ // to do this, we need to make sure that the class is not a superclass of the
+ // index (otherwise we get nothing new) - for instance based disjoints, we
+ // make sure that there is at least one individual, which is not already in the
+ // upper class
+ boolean meaningful;
+ if(instanceBasedDisjoints) {
+ // bug: tests should be performed against the index, not the upper class
+ // SortedSet<Individual> tmp = rs.getIndividuals(upperClass);
+ SortedSet<Individual> tmp = rs.getIndividuals(index);
+ tmp.removeAll(rs.getIndividuals(candidate));
+ // System.out.println(" instances of " + index + " and not " + candidate + ": " + tmp.size());
+ meaningful = tmp.size() != 0;
+ } else {
+ meaningful = !isDisjoint(new Negation(candidate),index);
+ }
+
+ if(meaningful) {
+ // candidate went successfully through all checks
+ candidates.add(candidate);
+ // System.out.println(" real refinement");
+ } else {
+ // descend subsumption hierarchy to find candidates
+ // System.out.println(" enter recursion");
+ candidates.addAll(getClassCandidatesRecursive(index, candidate));
+ }
+ }
+ // else {
+ // System.out.println(" ruled out, because it is disjoint");
+ // }
+ }
+ // System.out.println("cc method exit");
+ return candidates;
+ }
+
+ // get candidates for a refinement of \top restricted to a class B
+ public SortedSet<Description> getNegClassCandidates(NamedClass index) {
+ return getNegClassCandidatesRecursive(index, Nothing.instance);
+ }
+
+ private SortedSet<Description> getNegClassCandidatesRecursive(Description index, Description lowerClass) {
+ SortedSet<Description> candidates = new TreeSet<Description>(conceptComparator);
+ // System.out.println("index " + index + " lower class " + lowerClass);
+
+ for(Description candidate : subHierarchy.getSuperClasses(lowerClass)) {
+ if(!(candidate instanceof Thing)) {
+ // System.out.println("candidate: " + candidate);
+ // check disjointness with index/range (should not be disjoint otherwise not useful)
+ if(!isDisjoint(new Negation(candidate),index)) {
+ boolean meaningful;
+ // System.out.println("not disjoint");
+ if(instanceBasedDisjoints) {
+ SortedSet<Individual> tmp = rs.getIndividuals(index);
+ tmp.removeAll(rs.getIndividuals(new Negation(candidate)));
+ meaningful = tmp.size() != 0;
+ // System.out.println("instances " + tmp.size());
+ } else {
+ meaningful = !isDisjoint(candidate,index);
+ }
+
+ if(meaningful) {
+ candidates.add(new Negation(candidate));
+ } else {
+ candidates.addAll(getNegClassCandidatesRecursive(index, candidate));
+ }
+ }
+ }
+ }
+ return candidates;
+ }
+
+ private void computeMg(NamedClass domain) {
+ // compute the applicable properties if this has not been done yet
+ if(appOP.get(domain) == null)
+ computeApp(domain);
+
+ // initialise mgr, mgbd, mgdd, mgsd
+ mgr.put(domain, new TreeSet<ObjectProperty>());
+ mgbd.put(domain, new TreeSet<DatatypeProperty>());
+ mgdd.put(domain, new TreeSet<DatatypeProperty>());
+ mgsd.put(domain, new TreeSet<DatatypeProperty>());
+
+ SortedSet<ObjectProperty> mostGeneral = rs.getMostGeneralProperties();
+ computeMgrRecursive(domain, mostGeneral, mgr.get(domain));
+ SortedSet<DatatypeProperty> mostGeneralDP = rs.getMostGeneralDatatypeProperties();
+ // we make the (reasonable) assumption here that all sub and super
+ // datatype properties have the same type (e.g. boolean, integer, double)
+ Set<DatatypeProperty> mostGeneralBDP = Helper.intersection(mostGeneralDP, rs.getBooleanDatatypeProperties());
+ Set<DatatypeProperty> mostGeneralDDP = Helper.intersection(mostGeneralDP, rs.getDoubleDatatypeProperties());
+ Set<DatatypeProperty> mostGeneralSDP = Helper.intersection(mostGeneralDP, rs.getStringDatatypeProperties());
+ computeMgbdRecursive(domain, mostGeneralBDP, mgbd.get(domain));
+ computeMgddRecursive(domain, mostGeneralDDP, mgdd.get(domain));
+ computeMgsdRecursive(domain, mostGeneralSDP, mgsd.get(domain));
+ }
+
+ private void computeMgrRecursive(NamedClass domain, Set<ObjectProperty> currProperties, Set<ObjectProperty> mgrTmp) {
+ for(ObjectProperty prop : currProperties) {
+ if(appOP.get(domain).contains(prop))
+ mgrTmp.add(prop);
+ else
+ computeMgrRecursive(domain, rs.getSubProperties(prop), mgrTmp);
+ }
+ }
+
+ private void computeMgbdRecursive(NamedClass domain, Set<DatatypeProperty> currProperties, Set<DatatypeProperty> mgbdTmp) {
+ for(DatatypeProperty prop : currProperties) {
+ if(appBD.get(domain).contains(prop))
+ mgbdTmp.add(prop);
+ else
+ computeMgbdRecursive(domain, rs.getSubProperties(prop), mgbdTmp);
+ }
+ }
+
+ private void computeMgddRecursive(NamedClass domain, Set<DatatypeProperty> currProperties, Set<DatatypeProperty> mgddTmp) {
+ for(DatatypeProperty prop : currProperties) {
+ if(appDD.get(domain).contains(prop))
+ mgddTmp.add(prop);
+ else
+ computeMgddRecursive(domain, rs.getSubProperties(prop), mgddTmp);
+ }
+ }
+
+ private void computeMgsdRecursive(NamedClass domain, Set<DatatypeProperty> currProperties, Set<DatatypeProperty> mgsdTmp) {
+ for(DatatypeProperty prop : currProperties) {
+ if(appDD.get(domain).contains(prop))
+ mgsdTmp.add(prop);
+ else
+ computeMgsdRecursive(domain, rs.getSubProperties(prop), mgsdTmp);
+ }
+ }
+
+ // computes the set of applicable properties for a given class
+ private void computeApp(NamedClass domain) {
+ // object properties
+ Set<ObjectProperty> mostGeneral = rs.getObjectProperties();
+ Set<ObjectProperty> applicableRoles = new TreeSet<ObjectProperty>();
+ for(ObjectProperty role : mostGeneral) {
+ // TODO: currently we just rely on named classes as roles,
+ // instead of computing dom(r) and ran(r)
+ Description d = rs.getDomain(role);
+ if(!isDisjoint(domain,d))
+ applicableRoles.add(role);
+ }
+ appOP.put(domain, applicableRoles);
+
+ // boolean datatype properties
+ Set<DatatypeProperty> mostGeneralBDPs = rs.getBooleanDatatypeProperties();
+ Set<DatatypeProperty> applicableBDPs = new TreeSet<DatatypeProperty>();
+ for(DatatypeProperty role : mostGeneralBDPs) {
+ // Description d = (NamedClass) rs.getDomain(role);
+ Description d = rs.getDomain(role);
+ if(!isDisjoint(domain,d))
+ applicableBDPs.add(role);
+ }
+ appBD.put(domain, applicableBDPs);
+
+ // double datatype properties
+ Set<DatatypeProperty> mostGeneralDDPs = rs.getDoubleDatatypeProperties();
+ Set<DatatypeProperty> applicableDDPs = new TreeSet<DatatypeProperty>();
+ for(DatatypeProperty role : mostGeneralDDPs) {
+ // Description d = (NamedClass) rs.getDomain(role);
+ Description d = rs.getDomain(role);
+ // System.out.println("domain: " + d);
+ if(!isDisjoint(domain,d))
+ applicableDDPs.add(role);
+ }
+ appDD.put(domain, applicableDDPs);
+ }
+
+ // returns true of the intersection contains elements disjoint
+ // to the given description (if true adding the description to
+ // the intersection results in a description equivalent to bottom)
+ // e.g. OldPerson AND YoungPerson; Nitrogen-34 AND Tin-113
+ // Note: currently we only check named classes in the intersection,
+ // it would be interesting to see whether it makes sense to extend this
+ // (advantage: less refinements, drawback: operator will need infinitely many
+ // reasoner queries in the long run)
+ @SuppressWarnings({"unused"})
+ private boolean containsDisjoints(Intersection intersection, Description d) {
+ List<Description> children = intersection.getChildren();
+ for(Description child : children) {
+ if(d instanceof Nothing)
+ return true;
+ else if(child instanceof NamedClass) {
+ if(isDisjoint((NamedClass)child, d))
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private boolean isDisjoint(Description d1, Description d2) {
+
+ // System.out.println("| " + d1 + " " + d2);
+ // System.out.println("| " + cachedDisjoints);
+
+ // check whether we have cached this query
+ Map<Description,Boolean> tmp = cachedDisjoints.get(d1);
+ Boolean tmp2 = null;
+ if(tmp != null)
+ tmp2 = tmp.get(d2);
+
+ // System.out.println("| " + tmp + " " + tmp2);
+
+ if(tmp2==null) {
+ Boolean result;
+ if(instanceBasedDisjoints) {
+ result = isDisjointInstanceBased(d1,d2);
+ } else {
+ Description d = new Intersection(d1, d2);
+ result = rs.isSuperClassOf(new Nothing(), d);
+ }
+ // add the result to the cache (we add it twice such that
+ // the order of access does not matter)
+
+ // System.out.println("| result: " + result);
+
+ // create new entries if necessary
+ Map<Description,Boolean> map1 = new TreeMap<Description,Boolean>(conceptComparator);
+ Map<Description,Boolean> map2 = new TreeMap<Description,Boolean>(conceptComparator);
+ if(tmp == null)
+ cachedDisjoints.put(d1, map1);
+ if(!cachedDisjoints.containsKey(d2))
+ cachedDisjoints.put(d2, map2);
+
+ // add result symmetrically in the description matrix
+ cachedDisjoints.get(d1).put(d2, result);
+ cachedDisjoints.get(d2).put(d1, result);
+ // System.out.println("---");
+ return result;
+ } else {
+ // System.out.println("===");
+ return tmp2;
+ }
+ }
+
+ private boolean isDisjointInstanceBased(Description d1, Description d2) {
+ SortedSet<Individual> d1Instances = rs.getIndividuals(d1);
+ SortedSet<Individual> d2Instances = rs.getIndividuals(d2);
+ // System.out.println(d1 + " " + d2);
+ // System.out.println(d1 + " " + d1Instances);
+ // System.out.println(d2 + " " + d2Instances);
+ for(Individual d1Instance : d1Instances) {
+ if(d2Instances.contains(d1Instance))
+ return false;
+ }
+ return true;
+ }
+
+ /*
+ // computes whether two classes are disjoint; this should be computed
+ // by the reasoner on...
[truncated message content] |
|
From: <lor...@us...> - 2012-07-20 12:43:13
|
Revision: 3800
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3800&view=rev
Author: lorenz_b
Date: 2012-07-20 12:43:03 +0000 (Fri, 20 Jul 2012)
Log Message:
-----------
Updated ELK dependency. Fixed problem in SPARQL reasoner.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2012-07-19 08:12:17 UTC (rev 3799)
+++ trunk/components-core/pom.xml 2012-07-20 12:43:03 UTC (rev 3800)
@@ -230,7 +230,7 @@
<dependency>
<groupId>org.semanticweb.elk</groupId>
<artifactId>elk-owlapi</artifactId>
- <version>0.2.0</version>
+ <version>0.3.0</version>
</dependency>
<dependency>
<groupId>de.tudresden.inf.lat.cel</groupId>
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 2012-07-19 08:12:17 UTC (rev 3799)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java 2012-07-20 12:43:03 UTC (rev 3800)
@@ -190,7 +190,7 @@
ObjectPropertyDomainAxiomLearner l = new ObjectPropertyDomainAxiomLearner(ks);
l.setReasoner(reasoner);
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/creator"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/grammyAward"));
l.setMaxExecutionTimeInSeconds(40);
l.addFilterNamespace("http://dbpedia.org/ontology/");
// l.setReturnOnlyNewAxioms(true);
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2012-07-19 08:12:17 UTC (rev 3799)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2012-07-20 12:43:03 UTC (rev 3800)
@@ -108,15 +108,20 @@
if(useCache){
cache = new ExtractionDBCache("cache");
}
+ classPopularityMap = new HashMap<NamedClass, Integer>();
}
public SPARQLReasoner(SparqlEndpointKS ks, ExtractionDBCache cache) {
this.ks = ks;
this.cache = cache;
+
+ classPopularityMap = new HashMap<NamedClass, Integer>();
}
public SPARQLReasoner(OntModel model) {
this.model = model;
+
+ classPopularityMap = new HashMap<NamedClass, Integer>();
}
public void precomputePopularity(){
@@ -127,7 +132,6 @@
public void precomputeClassPopularity(){
logger.info("Precomputing class popularity ...");
- classPopularityMap = new HashMap<NamedClass, Integer>();
Set<NamedClass> classes = new SPARQLTasks(ks.getEndpoint()).getAllClasses();
String queryTemplate = "SELECT (COUNT(*) AS ?cnt) WHERE {?s a <%s>}";
@@ -197,7 +201,7 @@
}
public int getPopularity(NamedClass nc){
- if(classPopularityMap.containsKey(nc)){
+ if(classPopularityMap != null && classPopularityMap.containsKey(nc)){
return classPopularityMap.get(nc);
} else {
System.out.println("Cache miss: " + nc);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-08-23 13:19:14
|
Revision: 3834
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3834&view=rev
Author: lorenz_b
Date: 2012-08-23 13:19:03 +0000 (Thu, 23 Aug 2012)
Log Message:
-----------
Started feature to explain score in enrichment algorithms and return pos and neg examples.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner2.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2012-08-23 13:13:39 UTC (rev 3833)
+++ trunk/components-core/pom.xml 2012-08-23 13:19:03 UTC (rev 3834)
@@ -242,7 +242,12 @@
<artifactId>jsexp</artifactId>
<version>0.1.0</version>
</dependency>
-
+
+ <dependency>
+ <groupId>xerces</groupId>
+ <artifactId>xercesImpl</artifactId>
+ <version>2.8.0</version>
+ </dependency>
</dependencies>
<dependencyManagement>
<dependencies>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2012-08-23 13:13:39 UTC (rev 3833)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2012-08-23 13:19:03 UTC (rev 3834)
@@ -20,6 +20,11 @@
package org.dllearner.algorithms.properties;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
import org.dllearner.core.ComponentAnn;
@@ -27,12 +32,14 @@
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.config.ObjectPropertyEditor;
import org.dllearner.core.owl.FunctionalObjectPropertyAxiom;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Model;
@@ -51,6 +58,8 @@
public FunctionalObjectPropertyAxiomLearner(SparqlEndpointKS ks){
this.ks = ks;
+ posExamplesQueryTemplate = new ParameterizedSparqlString("SELECT ?s WHERE {?s ?p ?o1. FILTER NOT EXISTS {?s ?p ?o2. FILTER(?o1 != ?o2)} }");
+ negExamplesQueryTemplate = new ParameterizedSparqlString("SELECT ?s WHERE {?s ?p ?o1. ?s ?p ?o2. FILTER(?o1 != ?o2)}");
}
public ObjectProperty getPropertyToDescribe() {
@@ -59,6 +68,8 @@
public void setPropertyToDescribe(ObjectProperty propertyToDescribe) {
this.propertyToDescribe = propertyToDescribe;
+ posExamplesQueryTemplate.setIri("p", propertyToDescribe.getURI().toString());
+ negExamplesQueryTemplate.setIri("p", propertyToDescribe.getURI().toString());
}
@Override
@@ -86,36 +97,36 @@
}
private void runSPARQL1_0_Mode() {
- Model model = ModelFactory.createDefaultModel();
+ workingModel = ModelFactory.createDefaultModel();
int limit = 1000;
int offset = 0;
String baseQuery = "CONSTRUCT {?s <%s> ?o.} WHERE {?s <%s> ?o} LIMIT %d OFFSET %d";
String query = String.format(baseQuery, propertyToDescribe.getName(), propertyToDescribe.getName(), limit, offset);
Model newModel = executeConstructQuery(query);
while(!terminationCriteriaSatisfied() && newModel.size() != 0){System.out.println(query);
- model.add(newModel);
+ workingModel.add(newModel);
// get number of instances of s with <s p o>
query = String.format(
"SELECT (COUNT(DISTINCT ?s) AS ?all) WHERE {?s <%s> ?o.}",
propertyToDescribe.getName());
- ResultSet rs = executeSelectQuery(query, model);
+ ResultSet rs = executeSelectQuery(query, workingModel);
QuerySolution qs;
int all = 1;
while (rs.hasNext()) {
qs = rs.next();
all = qs.getLiteral("all").getInt();
}
- System.out.println(all);
+
// 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 != ?o2)} }";
query = query.replace("%s", propertyToDescribe.getURI().toString());
- rs = executeSelectQuery(query, model);
+ rs = executeSelectQuery(query, workingModel);
int functional = 1;
while (rs.hasNext()) {
qs = rs.next();
functional = qs.getLiteral("functional").getInt();
}
- System.out.println(functional);
+
if (all > 0) {
currentlyBestAxioms.clear();
currentlyBestAxioms.add(new EvaluatedAxiom(
@@ -155,13 +166,21 @@
}
public static void main(String[] args) throws Exception{
- FunctionalObjectPropertyAxiomLearner l = new FunctionalObjectPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW()));
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/wikiPageExternalLink"));
- l.setMaxExecutionTimeInSeconds(10);
-// l.setForceSPARQL_1_0_Mode(true);
+ FunctionalObjectPropertyAxiomLearner l = new FunctionalObjectPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia()));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/league"));
+ l.setMaxExecutionTimeInSeconds(20);
+ l.setForceSPARQL_1_0_Mode(true);
l.init();
l.start();
- System.out.println(l.getCurrentlyBestEvaluatedAxioms(5));
+ 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);
+ }
+
}
}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner2.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner2.java 2012-08-23 13:19:03 UTC (rev 3834)
@@ -0,0 +1,221 @@
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.dllearner.algorithms.properties;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedSet;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.core.AbstractAxiomLearningAlgorithm;
+import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.EvaluatedAxiom;
+import org.dllearner.core.config.ConfigOption;
+import org.dllearner.core.config.ObjectPropertyEditor;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyDomainAxiom;
+import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.hp.hpl.jena.query.ParameterizedSparqlString;
+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.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.RDFS;
+
+@ComponentAnn(name="objectproperty domain axiom learner", shortName="opldomain", version=0.1)
+public class ObjectPropertyDomainAxiomLearner2 extends AbstractAxiomLearningAlgorithm {
+
+ private static final Logger logger = LoggerFactory.getLogger(ObjectPropertyDomainAxiomLearner2.class);
+
+ private Map<Individual, SortedSet<Description>> individual2Types;
+
+
+ @ConfigOption(name="propertyToDescribe", description="", propertyEditorClass=ObjectPropertyEditor.class)
+ private ObjectProperty propertyToDescribe;
+
+ public ObjectPropertyDomainAxiomLearner2(SparqlEndpointKS ks){
+ this.ks = ks;
+ super.posExamplesQueryTemplate = new ParameterizedSparqlString("SELECT DISTINCT ?s WHERE {?s a ?type}");
+ super.negExamplesQueryTemplate = new ParameterizedSparqlString("SELECT DISTINCT ?s WHERE {?s ?p ?o. FILTER NOT EXISTS{?s a ?type}}");
+
+ }
+
+ public ObjectProperty getPropertyToDescribe() {
+ return propertyToDescribe;
+ }
+
+ public void setPropertyToDescribe(ObjectProperty propertyToDescribe) {
+ this.propertyToDescribe = propertyToDescribe;
+// negExamplesQueryTemplate.clearParams();
+// posExamplesQueryTemplate.clearParams();
+ }
+
+ @Override
+ public void start() {
+ iterativeQueryTemplate.setIri("p", propertyToDescribe.getName());
+ logger.info("Start learning...");
+ startTime = System.currentTimeMillis();
+ fetchedRows = 0;
+ currentlyBestAxioms = new ArrayList<EvaluatedAxiom>();
+
+ if(returnOnlyNewAxioms){
+ //get existing domains
+ Description existingDomain = reasoner.getDomain(propertyToDescribe);
+ if(existingDomain != null){
+ existingAxioms.add(new ObjectPropertyDomainAxiom(propertyToDescribe, existingDomain));
+ if(reasoner.isPrepared()){
+ if(reasoner.getClassHierarchy().contains(existingDomain)){
+ for(Description sup : reasoner.getClassHierarchy().getSuperClasses(existingDomain)){
+ existingAxioms.add(new ObjectPropertyDomainAxiom(propertyToDescribe, existingDomain));
+ logger.info("Existing domain(inferred): " + sup);
+ }
+ }
+
+ }
+ }
+ }
+
+ runSPARQL1_0_Mode();
+ logger.info("...finished in {}ms.", (System.currentTimeMillis()-startTime));
+ }
+
+ private void runSPARQL1_0_Mode() {
+ workingModel = ModelFactory.createDefaultModel();
+ int limit = 1000;
+ int offset = 0;
+ String baseQuery = "CONSTRUCT {?s a ?type.} WHERE {?s <%s> ?o. ?s a ?type.} LIMIT %d OFFSET %d";
+ String query = String.format(baseQuery, propertyToDescribe.getName(), limit, offset);
+ Model newModel = executeConstructQuery(query);
+ while(!terminationCriteriaSatisfied() && newModel.size() != 0){
+ workingModel.add(newModel);
+ // get number of distinct subjects
+ query = "SELECT (COUNT(DISTINCT ?s) AS ?all) WHERE {?s a ?type.}";
+ ResultSet rs = executeSelectQuery(query, workingModel);
+ QuerySolution qs;
+ int all = 1;
+ while (rs.hasNext()) {
+ qs = rs.next();
+ all = qs.getLiteral("all").getInt();
+ }
+
+ // get class and number of instances
+ query = "SELECT ?type (COUNT(DISTINCT ?s) AS ?cnt) WHERE {?s a ?type.} GROUP BY ?type";
+ rs = executeSelectQuery(query, workingModel);
+
+ if (all > 0) {
+ currentlyBestAxioms.clear();
+ while(rs.hasNext()){
+ qs = rs.next();
+ Resource type = qs.get("type").asResource();
+ //omit owl:Thing as trivial domain
+ if(type.equals(OWL.Thing)){
+ continue;
+ }
+ currentlyBestAxioms.add(new EvaluatedAxiom(
+ new ObjectPropertyDomainAxiom(propertyToDescribe, new NamedClass(type.getURI())),
+ computeScore(all, qs.get("cnt").asLiteral().getInt())));
+ }
+
+ }
+ offset += limit;
+ query = String.format(baseQuery, propertyToDescribe.getName(), limit, offset);
+ newModel = executeConstructQuery(query);
+ fillWithInference(newModel);
+ }
+ }
+
+ private void fillWithInference(Model model){
+ Model additionalModel = ModelFactory.createDefaultModel();
+ if(reasoner.isPrepared()){
+ for(StmtIterator iter = model.listStatements(null, RDF.type, (RDFNode)null); iter.hasNext();){
+ Statement st = iter.next();
+ Description cls = new NamedClass(st.getObject().asResource().getURI());
+ if(reasoner.getClassHierarchy().contains(cls)){
+ for(Description sup : reasoner.getClassHierarchy().getSuperClasses(cls)){
+ additionalModel.add(st.getSubject(), st.getPredicate(), model.createResource(sup.toString()));
+ }
+ }
+ }
+ }
+ model.add(additionalModel);
+ }
+
+ @Override
+ protected SortedSet<Individual> getPositiveExamples(EvaluatedAxiom evAxiom) {
+ ObjectPropertyDomainAxiom axiom = (ObjectPropertyDomainAxiom) evAxiom.getAxiom();
+ posExamplesQueryTemplate.setIri("type", axiom.getDomain().toString());
+ return super.getPositiveExamples(evAxiom);
+ }
+
+ @Override
+ protected SortedSet<Individual> getNegativeExamples(EvaluatedAxiom evAxiom) {
+ ObjectPropertyDomainAxiom axiom = (ObjectPropertyDomainAxiom) evAxiom.getAxiom();
+ negExamplesQueryTemplate.setIri("type", axiom.getDomain().toString());
+ return super.getNegativeExamples(evAxiom);
+ }
+
+ public static void main(String[] args) throws Exception{
+ org.apache.log4j.Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
+ org.apache.log4j.Logger.getRootLogger().setLevel(Level.INFO);
+ org.apache.log4j.Logger.getLogger(DataPropertyDomainAxiomLearner.class).setLevel(Level.INFO);
+
+ SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
+
+ SPARQLReasoner reasoner = new SPARQLReasoner(ks);
+ reasoner.prepareSubsumptionHierarchy();
+
+
+ ObjectPropertyDomainAxiomLearner2 l = new ObjectPropertyDomainAxiomLearner2(ks);
+ l.setReasoner(reasoner);
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/league"));
+ l.setMaxFetchedRows(20000);
+ l.setMaxExecutionTimeInSeconds(20);
+ l.addFilterNamespace("http://dbpedia.org/ontology/");
+// l.setReturnOnlyNewAxioms(true);
+ l.init();
+ l.start();
+
+ List<EvaluatedAxiom> axioms = l.getCurrentlyBestEvaluatedAxioms(10, 0.3);
+ System.out.println(axioms);
+ for(EvaluatedAxiom axiom : axioms){
+ printSubset(l.getPositiveExamples(axiom), 10);
+ printSubset(l.getNegativeExamples(axiom), 10);
+ l.explainScore(axiom);
+ }
+ }
+
+}
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-08-23 13:13:39 UTC (rev 3833)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-08-23 13:19:03 UTC (rev 3834)
@@ -24,6 +24,7 @@
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -37,6 +38,7 @@
import org.dllearner.core.owl.Axiom;
import org.dllearner.core.owl.ClassHierarchy;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
import org.dllearner.kb.SparqlEndpointKS;
@@ -116,6 +118,11 @@
protected ParameterizedSparqlString iterativeQueryTemplate;
+ protected Model workingModel;
+ protected ParameterizedSparqlString posExamplesQueryTemplate;
+ protected ParameterizedSparqlString negExamplesQueryTemplate;
+
+
public AbstractAxiomLearningAlgorithm() {
existingAxioms = new TreeSet<Axiom>(new AxiomComparator());
}
@@ -255,7 +262,7 @@
}
- protected Model executeConstructQuery(String query) {
+ protected Model executeConstructQuery(String query) {System.out.println(query);
logger.debug("Sending query\n{} ...", query);
if(ks.isRemote()){
SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
@@ -266,7 +273,12 @@
queryExecution.setNamedGraphURIs(endpoint.getNamedGraphURIs());
try {
Model model = queryExecution.execConstruct();
+ fetchedRows += model.size();
timeout = false;
+ if(model.size() == 0){
+ fullDataLoaded = true;
+ }
+
return model;
} catch (QueryExceptionHTTP e) {
if(e.getCause() instanceof SocketTimeoutException){
@@ -277,8 +289,13 @@
return ModelFactory.createDefaultModel();
}
} else {
- QueryExecution qexec = QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
- return qexec.execConstruct();
+ QueryExecution queryExecution = QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
+ Model model = queryExecution.execConstruct();
+ fetchedRows += model.size();
+ if(model.size() == 0){
+ fullDataLoaded = true;
+ }
+ return model;
}
}
@@ -456,6 +473,67 @@
filterNamespaces.add(namespace);
}
+ protected SortedSet<Individual> getPositiveExamples(EvaluatedAxiom axiom){
+ if(workingModel != null){
+ SortedSet<Individual> posExamples = new TreeSet<Individual>();
+
+ ResultSet rs = executeSelectQuery(posExamplesQueryTemplate.toString(), workingModel);
+ while(rs.hasNext()){
+ posExamples.add(new Individual(rs.next().get("s").asResource().getURI()));
+ }
+
+ return posExamples;
+ } else {
+ throw new UnsupportedOperationException("Getting positive examples is not possible.");
+ }
+ }
+
+ protected SortedSet<Individual> getNegativeExamples(EvaluatedAxiom axiom){
+ if(workingModel != null){
+ SortedSet<Individual> negExamples = new TreeSet<Individual>();
+
+ ResultSet rs = executeSelectQuery(negExamplesQueryTemplate.toString(), workingModel);
+ while(rs.hasNext()){
+ negExamples.add(new Individual(rs.next().get("s").asResource().getURI()));
+ }
+
+ return negExamples;
+ } else {
+ throw new UnsupportedOperationException("Getting negative examples is not possible.");
+ }
+ }
+
+ protected void explainScore(EvaluatedAxiom evAxiom){
+ int posExampleCnt = getPositiveExamples(evAxiom).size();
+ int negExampleCnt = getNegativeExamples(evAxiom).size();
+ int total = posExampleCnt + negExampleCnt;
+ StringBuilder sb = new StringBuilder();
+ String lb = "\n";
+ sb.append("######################################").append(lb);
+ sb.append("Explanation:").append(lb);
+ sb.append("Score(").append(evAxiom.getAxiom()).append(") = ").append(evAxiom.getScore().getAccuracy()).append(lb);
+ sb.append("Total number of resources:\t").append(total).append(lb);
+ sb.append("Number of positive examples:\t").append(posExampleCnt).append(lb);
+ sb.append("Number of negative examples:\t").append(negExampleCnt).append(lb);
+ sb.append("Complete data processed:\t").append(fullDataLoaded).append(lb);
+ sb.append("######################################");
+ System.out.println(sb.toString());
+ }
+
+ protected static <E> void printSubset(Collection<E> collection, int maxSize){
+ StringBuffer sb = new StringBuffer();
+ int i = 0;
+ Iterator<E> iter = collection.iterator();
+ while(iter.hasNext() && i < maxSize){
+ sb.append(iter.next().toString()).append(", ");
+ i++;
+ }
+ if(iter.hasNext()){
+ sb.append("...(").append(collection.size()-i).append(" more)");
+ }
+ System.out.println(sb.toString());
+ }
+
protected <K,T extends Set<V>, V> void addToMap(Map<K, T> map, K key, V value ){
T values = map.get(key);
if(values == null){
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-12-25 13:19:20
|
Revision: 3881
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3881&view=rev
Author: lorenz_b
Date: 2012-12-25 13:19:09 +0000 (Tue, 25 Dec 2012)
Log Message:
-----------
Added equals+hashcode for literals.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/core/owl/Datatype.java
trunk/components-core/src/main/java/org/dllearner/core/owl/TypedConstant.java
trunk/components-core/src/main/java/org/dllearner/core/owl/UntypedConstant.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2012-12-11 19:34:37 UTC (rev 3880)
+++ trunk/components-core/pom.xml 2012-12-25 13:19:09 UTC (rev 3881)
@@ -169,6 +169,11 @@
<groupId>org.semanticweb.hermit</groupId>
<artifactId>hermit</artifactId>
</dependency>
+
+ <dependency>
+ <groupId>eu.trowl</groupId>
+ <artifactId>trowl-core</artifactId>
+ </dependency>
<dependency>
<groupId>com.jamonapi</groupId>
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/Datatype.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/Datatype.java 2012-12-11 19:34:37 UTC (rev 3880)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/Datatype.java 2012-12-25 13:19:09 UTC (rev 3881)
@@ -22,6 +22,9 @@
import java.net.URI;
import java.util.Map;
+import org.semanticweb.owlapi.model.IRI;
+
+
/**
* @author Jens Lehmann
*
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/TypedConstant.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/TypedConstant.java 2012-12-11 19:34:37 UTC (rev 3880)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/TypedConstant.java 2012-12-25 13:19:09 UTC (rev 3881)
@@ -120,6 +120,35 @@
String str = literal + datatype;
String str2 = o.literal + ((TypedConstant)o).datatype;
return str.compareTo(str2);
+ }
+
+ @Override
+ public int hashCode() {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + ((datatype == null) ? 0 : datatype.hashCode());
+ result = prime * result + ((getLiteral() == null) ? 0 : getLiteral().hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ TypedConstant other = (TypedConstant) obj;
+ if (datatype == null) {
+ if (other.datatype != null)
+ return false;
+ } else if (!datatype.equals(other.datatype))
+ return false;
+ if(!getLiteral().equals(other.getLiteral())){
+ return false;
+ }
+ return true;
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/UntypedConstant.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/UntypedConstant.java 2012-12-11 19:34:37 UTC (rev 3880)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/UntypedConstant.java 2012-12-25 13:19:09 UTC (rev 3881)
@@ -124,4 +124,36 @@
return str.compareTo(str2);
}
+ @Override
+ public int hashCode() {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + (hasLang ? 1231 : 1237);
+ result = prime * result + ((lang == null) ? 0 : lang.hashCode());
+ result = prime * result + ((getLiteral() == null) ? 0 : getLiteral().hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ UntypedConstant other = (UntypedConstant) obj;
+ if (hasLang != other.hasLang)
+ return false;
+ if (lang == null) {
+ if (other.lang != null)
+ return false;
+ } else if (!lang.equals(other.lang))
+ return false;
+ if(!getLiteral().equals(other.getLiteral())){
+ return false;
+ }
+ return true;
+ }
+
}
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 2012-12-11 19:34:37 UTC (rev 3880)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2012-12-25 13:19:09 UTC (rev 3881)
@@ -2,28 +2,22 @@
import java.io.UnsupportedEncodingException;
import java.sql.SQLException;
-import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
-import java.util.Set;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
-import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
-import com.hp.hpl.jena.vocabulary.RDF;
-import com.hp.hpl.jena.vocabulary.RDFS;
public class ConciseBoundedDescriptionGeneratorImpl implements ConciseBoundedDescriptionGenerator{
private static final Logger logger = Logger.getLogger(ConciseBoundedDescriptionGeneratorImpl.class);
- private static final int CHUNK_SIZE = 1000;
+ private int chunkSize = 0;
private ExtractionDBCache cache;
private SparqlEndpoint endpoint;
@@ -37,6 +31,12 @@
this.cache = cache;
}
+ public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache, int maxRecursionDepth) {
+ this.endpoint = endpoint;
+ this.cache = cache;
+ this.maxRecursionDepth = maxRecursionDepth;
+ }
+
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint) {
this(endpoint, null);
}
@@ -53,8 +53,12 @@
return getModelChunked(resourceURI, depth);
}
+ public void setChunkSize(int chunkSize) {
+ this.chunkSize = chunkSize;
+ }
+
private Model getModelChunked(String resource, int depth){
- String query = makeConstructQueryOptional(resource, CHUNK_SIZE, 0, depth);
+ String query = makeConstructQueryOptional(resource, chunkSize, 0, depth);
Model all = ModelFactory.createDefaultModel();
try {
Model model;
@@ -65,9 +69,9 @@
}
all.add(model);
int i = 1;
- while(model.size() != 0){
+ do{
// while(model.size() == CHUNK_SIZE){
- query = makeConstructQueryOptional(resource, CHUNK_SIZE, i * CHUNK_SIZE, depth);
+ query = makeConstructQueryOptional(resource, chunkSize, i * chunkSize, depth);
if(cache == null){
model = getModel(query);
} else {
@@ -75,7 +79,7 @@
}
all.add(model);
i++;
- }
+ } while(chunkSize > 0 && model.size() != 0);
} catch (UnsupportedEncodingException e) {
logger.error(e);
} catch (SQLException e) {
@@ -124,8 +128,10 @@
sb.append("}");
}
sb.append("}\n");
- sb.append("LIMIT ").append(limit).append("\n");
- sb.append("OFFSET ").append(offset);
+ if(chunkSize > 0){
+ sb.append("LIMIT ").append(limit).append("\n");
+ sb.append("OFFSET ").append(offset);
+ }
return sb.toString();
}
@@ -179,8 +185,8 @@
Logger.getRootLogger().setLevel(Level.DEBUG);
ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint.getEndpointDBpedia());
cbdGen = new CachingConciseBoundedDescriptionGenerator(cbdGen);
- cbdGen.setRestrictToNamespaces(Arrays.asList(new String[]{"http://dbpedia.org/ontology/", RDF.getURI(), RDFS.getURI()}));
- Model cbd = cbdGen.getConciseBoundedDescription("http://dbpedia.org/resource/Leipzig", 2);
+// cbdGen.setRestrictToNamespaces(Arrays.asList(new String[]{"http://dbpedia.org/ontology/", RDF.getURI(), RDFS.getURI()}));
+ Model cbd = cbdGen.getConciseBoundedDescription("http://dbpedia.org/resource/Leipzig", 3);
System.out.println(cbd.size());
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2012-12-11 19:34:37 UTC (rev 3880)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2012-12-25 13:19:09 UTC (rev 3881)
@@ -23,6 +23,7 @@
import java.net.URI;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
@@ -99,7 +100,9 @@
import org.semanticweb.owlapi.model.UnknownOWLOntologyException;
import org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory;
import org.semanticweb.owlapi.owllink.OWLlinkReasonerConfiguration;
+import org.semanticweb.owlapi.reasoner.FreshEntitiesException;
import org.semanticweb.owlapi.reasoner.FreshEntityPolicy;
+import org.semanticweb.owlapi.reasoner.InconsistentOntologyException;
import org.semanticweb.owlapi.reasoner.IndividualNodeSetPolicy;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.reasoner.Node;
@@ -107,8 +110,10 @@
import org.semanticweb.owlapi.reasoner.NullReasonerProgressMonitor;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
+import org.semanticweb.owlapi.reasoner.ReasonerInterruptedException;
import org.semanticweb.owlapi.reasoner.ReasonerProgressMonitor;
import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
+import org.semanticweb.owlapi.reasoner.TimeOutException;
import org.semanticweb.owlapi.util.SimpleIRIMapper;
import org.semanticweb.owlapi.vocab.PrefixOWLOntologyFormat;
import org.springframework.beans.propertyeditors.StringTrimmerEditor;
@@ -119,1103 +124,1000 @@
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import de.tudresden.inf.lat.cel.owlapi.CelReasoner;
+import eu.trowl.owlapi3.rel.reasoner.dl.RELReasonerFactory;
/**
- * Mapping to OWL API reasoner interface. The OWL API currently supports three
- * reasoners: FaCT++, HermiT and Pellet. FaCT++ is connected using JNI and
- * native libraries, while HermiT and Pellet are pure Java libraries.
- *
+ * Mapping to OWL API reasoner interface. The OWL API currently
+ * supports three reasoners: FaCT++, HermiT and Pellet. FaCT++ is connected
+ * using JNI and native libraries, while HermiT and Pellet are pure Java
+ * libraries.
+ *
* @author Jens Lehmann
*/
@ComponentAnn(name = "OWL API Reasoner", shortName = "oar", version = 0.8)
public class OWLAPIReasoner extends AbstractReasonerComponent {
- // private static Logger logger = Logger
- // .getLogger(OWLAPIReasoner.class);
+// private static Logger logger = Logger
+// .getLogger(OWLAPIReasoner.class);
- // private String reasonerType = "pellet";
- private OWLReasoner reasoner;
- private OWLOntologyManager manager;
+ //private String reasonerType = "pellet";
+ private OWLReasoner reasoner;
+ private OWLOntologyManager manager;
- private OWLOntology ontology;
- // the data factory is used to generate OWL API objects
- private OWLDataFactory factory;
- // static factory
- // private static OWLDataFactory staticFactory =
- // OWLManager.createOWLOntologyManager().getOWLDataFactory();
+ private OWLOntology ontology;
+ // the data factory is used to generate OWL API objects
+ private OWLDataFactory factory;
+ // static factory
+// private static OWLDataFactory staticFactory = OWLManager.createOWLOntologyManager().getOWLDataFactory();
- private ConceptComparator conceptComparator = new ConceptComparator();
- private RoleComparator roleComparator = new RoleComparator();
- // private ClassHierarchy subsumptionHierarchy;
- // private ObjectPropertyHierarchy roleHierarchy;
- // private DatatypePropertyHierarchy datatypePropertyHierarchy;
- // private Set<Description> allowedConceptsInSubsumptionHierarchy;
+ private ConceptComparator conceptComparator = new ConceptComparator();
+ private RoleComparator roleComparator = new RoleComparator();
+// private ClassHierarchy subsumptionHierarchy;
+// private ObjectPropertyHierarchy roleHierarchy;
+// private DatatypePropertyHierarchy datatypePropertyHierarchy;
+// private Set<Description> allowedConceptsInSubsumptionHierarchy;
- // primitives
- Set<NamedClass> atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
- Set<ObjectProperty> atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
- SortedSet<DatatypeProperty> datatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<DatatypeProperty> stringDatatypeProperties = new TreeSet<DatatypeProperty>();
- SortedSet<Individual> individuals = new TreeSet<Individual>();
+ // primitives
+ Set<NamedClass> atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
+ Set<ObjectProperty> atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
+ SortedSet<DatatypeProperty> datatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> intDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<DatatypeProperty> stringDatatypeProperties = new TreeSet<DatatypeProperty>();
+ SortedSet<Individual> individuals = new TreeSet<Individual>();
- // namespaces
- private Map<String, String> prefixes = new TreeMap<String, String>();
- private String baseURI;
+ // namespaces
+ private Map<String, String> prefixes = new TreeMap<String, String>();
+ private String baseURI;
- // references to OWL API ontologies
- private List<OWLOntology> owlAPIOntologies = new LinkedList<OWLOntology>();
- @ConfigOption(name = "reasonerType", description = "The name of the OWL APIReasoner to use {\"fact\", \"hermit\", \"owllink\", \"pellet\", \"elk\", \"cel\"}", defaultValue = "pellet", required = false, propertyEditorClass = StringTrimmerEditor.class)
- private String reasonerTypeString = "pellet";
- @ConfigOption(name = "owlLinkURL", description = "The URL to the owl server", defaultValue = "", required = false, propertyEditorClass = StringTrimmerEditor.class)
- private String owlLinkURL;
+ // references to OWL API ontologies
+ private List<OWLOntology> owlAPIOntologies = new LinkedList<OWLOntology>();
+ @ConfigOption(name = "reasonerType", description = "The name of the OWL APIReasoner to use {\"fact\", \"hermit\", \"owllink\", \"pellet\", \"elk\", \"cel\"}", defaultValue = "pellet", required = false, propertyEditorClass = StringTrimmerEditor.class)
+ private String reasonerTypeString = "pellet";
+ @ConfigOption(name = "owlLinkURL", description = "The URL to the owl server", defaultValue = "", required = false, propertyEditorClass = StringTrimmerEditor.class)
+ private String owlLinkURL;
- public OWLAPIReasoner() {
- }
+ public OWLAPIReasoner() {
- public OWLAPIReasoner(Set<KnowledgeSource> sources) {
- super(sources);
- }
+ }
+
+ public OWLAPIReasoner(KnowledgeSource... sources) {
+ super(new HashSet<KnowledgeSource>(Arrays.asList(sources)));
+ }
- public static String getName() {
- return "OWL API reasoner";
- }
+ public OWLAPIReasoner(Set<KnowledgeSource> sources) {
+ super(sources);
+ }
- @Override
- public void init() throws ComponentInitException {
- // reset variables (otherwise subsequent initialisation with
- // different knowledge sources will merge both)
- atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
- atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
- datatypeProperties = new TreeSet<DatatypeProperty>();
- booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
- doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
- intDatatypeProperties = new TreeSet<DatatypeProperty>();
- stringDatatypeProperties = new TreeSet<DatatypeProperty>();
- individuals = new TreeSet<Individual>();
+ public static String getName() {
+ return "OWL API reasoner";
+ }
- // create OWL API ontology manager - make sure we use a new data factory
- // so that we don't default to the static one which can cause problems
- // in a multi threaded environment.
- manager = OWLManager.createOWLOntologyManager(new OWLDataFactoryImpl());
+ @Override
+ public void init() throws ComponentInitException {
+ // reset variables (otherwise subsequent initialisation with
+ // different knowledge sources will merge both)
+ atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
+ atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
+ datatypeProperties = new TreeSet<DatatypeProperty>();
+ booleanDatatypeProperties = new TreeSet<DatatypeProperty>();
+ doubleDatatypeProperties = new TreeSet<DatatypeProperty>();
+ intDatatypeProperties = new TreeSet<DatatypeProperty>();
+ stringDatatypeProperties = new TreeSet<DatatypeProperty>();
+ individuals = new TreeSet<Individual>();
- // it is a bit cumbersome to obtain all classes, because there
- // are no reasoner queries to obtain them => hence we query them
- // for each ontology and add them to a set; a comparator avoids
- // duplicates by checking URIs
- Comparator<OWLNamedObject> namedObjectComparator = new Comparator<OWLNamedObject>() {
- public int compare(OWLNamedObject o1, OWLNamedObject o2) {
- return o1.getIRI().compareTo(o2.getIRI());
- }
- };
- Set<OWLClass> classes = new TreeSet<OWLClass>(namedObjectComparator);
- Set<OWLObjectProperty> owlObjectProperties = new TreeSet<OWLObjectProperty>(
- namedObjectComparator);
- Set<OWLDataProperty> owlDatatypeProperties = new TreeSet<OWLDataProperty>(
- namedObjectComparator);
- Set<OWLNamedIndividual> owlIndividuals = new TreeSet<OWLNamedIndividual>(
- namedObjectComparator);
+ // create OWL API ontology manager - make sure we use a new data factory so that we don't default to the static one which can cause problems in a multi threaded environment.
+ manager = OWLManager.createOWLOntologyManager(new OWLDataFactoryImpl());
- Set<OWLOntology> allImports = new HashSet<OWLOntology>();
- prefixes = new TreeMap<String, String>();
+ // it is a bit cumbersome to obtain all classes, because there
+ // are no reasoner queries to obtain them => hence we query them
+ // for each ontology and add them to a set; a comparator avoids
+ // duplicates by checking URIs
+ Comparator<OWLNamedObject> namedObjectComparator = new Comparator<OWLNamedObject>() {
+ public int compare(OWLNamedObject o1, OWLNamedObject o2) {
+ return o1.getIRI().compareTo(o2.getIRI());
+ }
+ };
+ Set<OWLClass> classes = new TreeSet<OWLClass>(namedObjectComparator);
+ Set<OWLObjectProperty> owlObjectProperties = new TreeSet<OWLObjectProperty>(namedObjectComparator);
+ Set<OWLDataProperty> owlDatatypeProperties = new TreeSet<OWLDataProperty>(namedObjectComparator);
+ Set<OWLNamedIndividual> owlIndividuals = new TreeSet<OWLNamedIndividual>(namedObjectComparator);
- Set<OWLImportsDeclaration> directImports = new HashSet<OWLImportsDeclaration>();
+ Set<OWLOntology> allImports = new HashSet<OWLOntology>();
+ prefixes = new TreeMap<String, String>();
- for (KnowledgeSource source : sources) {
+ Set<OWLImportsDeclaration> directImports = new HashSet<OWLImportsDeclaration>();
- if (source instanceof OWLOntologyKnowledgeSource) {
- ontology = ((OWLOntologyKnowledgeSource) source).createOWLOntology(manager);
- owlAPIOntologies.add(ontology);
- } else {
- // This reasoner requires an ontology to process
- throw new ComponentInitException(
- "OWL API Reasoner Requires an OWLKnowledgeSource. Received a KS of type: "
- + source.getClass().getName());
- }
+ for (KnowledgeSource source : sources) {
- directImports.addAll(ontology.getImportsDeclarations());
+ if (source instanceof OWLOntologyKnowledgeSource) {
+ ontology = ((OWLOntologyKnowledgeSource) source).createOWLOntology(manager);
+ owlAPIOntologies.add(ontology);
+ }else{
+ //This reasoner requires an ontology to process
+ throw new ComponentInitException("OWL API Reasoner Requires an OWLKnowledgeSource. Received a KS of type: " + source.getClass().getName());
+ }
- try {
- // imports includes the ontology itself
- // FIXME this line throws the strange error
- Set<OWLOntology> imports = manager.getImportsClosure(ontology);
- allImports.addAll(imports);
+ directImports.addAll(ontology.getImportsDeclarations());
- // System.out.println(imports);
- for (OWLOntology ont : imports) {
- classes.addAll(ont.getClassesInSignature());
- owlObjectProperties.addAll(ont.getObjectPropertiesInSignature());
- owlDatatypeProperties.addAll(ont.getDataPropertiesInSignature());
- owlIndividuals.addAll(ont.getIndividualsInSignature());
- }
+ try {
+ // imports includes the ontology itself
+ //FIXME this line throws the strange error
+ Set<OWLOntology> imports = manager.getImportsClosure(ontology);
+ allImports.addAll(imports);
- } catch (UnknownOWLOntologyException uooe) {
- logger.error("UnknownOWLOntologyException occured, imports were not loaded! This is a bug, which has not been fixed yet.");
- }
+// System.out.println(imports);
+ for (OWLOntology ont : imports) {
+ classes.addAll(ont.getClassesInSignature());
+ owlObjectProperties.addAll(ont.getObjectPropertiesInSignature());
+ owlDatatypeProperties.addAll(ont.getDataPropertiesInSignature());
+ owlIndividuals.addAll(ont.getIndividualsInSignature());
+ }
- // if several knowledge sources are included, then we can only
- // guarantee that the base URI is from one of those sources (there
- // can't be more than one); but we will take care that all prefixes
- // are
- // correctly imported
- OWLOntologyFormat format = manager.getOntologyFormat(ontology);
- if (format instanceof PrefixOWLOntologyFormat) {
- prefixes.putAll(((PrefixOWLOntologyFormat) format).getPrefixName2PrefixMap());
- baseURI = ((PrefixOWLOntologyFormat) format).getDefaultPrefix();
- prefixes.remove("");
- }
+ } catch (UnknownOWLOntologyException uooe) {
+ logger.error("UnknownOWLOntologyException occured, imports were not loaded! This is a bug, which has not been fixed yet.");
+ }
- }
+ // if several knowledge sources are included, then we can only
+ // guarantee that the base URI is from one of those sources (there
+ // can't be more than one); but we will take care that all prefixes are
+ // correctly imported
+ OWLOntologyFormat format = manager.getOntologyFormat(ontology);
+ if (format instanceof PrefixOWLOntologyFormat) {
+ prefixes.putAll(((PrefixOWLOntologyFormat) format).getPrefixName2PrefixMap());
+ baseURI = ((PrefixOWLOntologyFormat) format).getDefaultPrefix();
+ prefixes.remove("");
+ }
- // Now merge all of the knowledge sources into one ontology instance.
- try {
- // The following line illustrates a problem with using different
- // OWLOntologyManagers. This can manifest itself if we have multiple
- // sources who were created with different manager instances.
- // ontology =
- // OWLManager.createOWLOntologyManager().createOntology(IRI.create("http://dl-learner/all"),
- // new HashSet<OWLOntology>(owlAPIOntologies));
- ontology = manager.createOntology(IRI.create("http://dl-learner/all"),
- new HashSet<OWLOntology>(owlAPIOntologies));
- // we have to add all import declarations manually here, because
- // this are no axioms
- List<OWLOntologyChange> addImports = new ArrayList<OWLOntologyChange>();
- for (OWLImportsDeclaration i : directImports) {
- addImports.add(new AddImport(ontology, i));
- }
- manager.applyChanges(addImports);
- } catch (OWLOntologyCreationException e1) {
- e1.printStackTrace();
- }
+ }
- // configure reasoner
- ReasonerProgressMonitor progressMonitor = new NullReasonerProgressMonitor();
- FreshEntityPolicy freshEntityPolicy = FreshEntityPolicy.ALLOW;
- long timeOut = Integer.MAX_VALUE;
- IndividualNodeSetPolicy individualNodeSetPolicy = IndividualNodeSetPolicy.BY_NAME;
- OWLReasonerConfiguration conf = new SimpleConfiguration(progressMonitor, freshEntityPolicy,
- timeOut, individualNodeSetPolicy);
+ //Now merge all of the knowledge sources into one ontology instance.
+ try {
+ //The following line illustrates a problem with using different OWLOntologyManagers. This can manifest itself if we have multiple sources who were created with different manager instances.
+ //ontology = OWLManager.createOWLOntologyManager().createOntology(IRI.create("http://dl-learner/all"), new HashSet<OWLOntology>(owlAPIOntologies));
+ ontology = manager.createOntology(IRI.create("http://dl-learner/all"), new HashSet<OWLOntology>(owlAPIOntologies));
+ //we have to add all import declarations manually here, because this are no axioms
+ List<OWLOntologyChange> addImports = new ArrayList<OWLOntologyChange>();
+ for (OWLImportsDeclaration i : directImports) {
+ addImports.add(new AddImport(ontology, i));
+ }
+ manager.applyChanges(addImports);
+ } catch (OWLOntologyCreationException e1) {
+ e1.printStackTrace();
+ }
- // create actual reasoner
- if (getReasonerTypeString().equals("fact")) {
- try {
- reasoner = new FaCTPlusPlusReasonerFactory().createNonBufferingReasoner(ontology,
- conf);
+ //configure reasoner
+ ReasonerProgressMonitor progressMonitor = new NullReasonerProgressMonitor();
+ FreshEntityPolicy freshEntityPolicy = FreshEntityPolicy.ALLOW;
+ long timeOut = Integer.MAX_VALUE;
+ IndividualNodeSetPolicy individualNodeSetPolicy = IndividualNodeSetPolicy.BY_NAME;
+ OWLReasonerConfiguration conf = new SimpleConfiguration(progressMonitor, freshEntityPolicy, timeOut, individualNodeSetPolicy);
- } catch (Exception e) {
- throw new RuntimeException(e);
- }
- System.out.println("Using FaCT++.");
- } else if (getReasonerTypeString().equals("hermit")) {
- // instantiate HermiT reasoner
- reasoner = new ReasonerFactory().createNonBufferingReasoner(ontology, conf);
- } else if (getReasonerTypeString().equals("pellet")) {
- // instantiate Pellet reasoner
- reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(ontology,
- conf);
- // change log level to WARN for Pellet, because otherwise log
- // output will be very large
- Logger pelletLogger = Logger.getLogger("org.mindswap.pellet");
- pelletLogger.setLevel(Level.WARN);
- } else if (getReasonerTypeString().equals("elk")) {
- // instantiate ELK reasoner
- reasoner = new ElkReasonerFactory().createNonBufferingReasoner(ontology, conf);
- // reasoner = new
- // MyElkReasonerFactory().createNonBufferingReasoner(ontology,
- // conf);
- } else if (getReasonerTypeString().equals("cel")) {
- // instantiate CEL reasoner
- reasoner = new CelReasoner(ontology, conf);
- } else {
- try {
- OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
- URL url = new URL(getOwlLinkURL());// Configure the server
- // end-point
- OWLlinkReasonerConfiguration config = new OWLlinkReasonerConfiguration(url);
- reasoner = factory.createNonBufferingReasoner(ontology, config);
- System.out.println(reasoner.getReasonerName());
- } catch (Exception e) {
- // e.printStackTrace();
- throw new ComponentInitException(e);
- }
- }
+ // create actual reasoner
+ if (getReasonerTypeString().equals("fact")) {
+ try {
+ reasoner = new FaCTPlusPlusReasonerFactory().createNonBufferingReasoner(ontology, conf);
+ } catch (Exception e) {
+ throw new RuntimeException(e);
+ }
+ System.out.println("Using FaCT++.");
+ } else if (getReasonerTypeString().equals("hermit")) {
+ // instantiate HermiT reasoner
+ reasoner = new ReasonerFactory().createNonBufferingReasoner(ontology, conf);
+ } else if (getReasonerTypeString().equals("pellet")) {
+ // instantiate Pellet reasoner
+ reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(ontology, conf);
+ // change log level to WARN for Pellet, because otherwise log
+ // output will be very large
+ Logger pelletLogger = Logger.getLogger("org.mindswap.pellet");
+ pelletLogger.setLevel(Level.WARN);
+ } else if (getReasonerTypeString().equals("elk")) {
+ // instantiate ELK reasoner
+ reasoner = new ElkReasonerFactory().createNonBufferingReasoner(ontology, conf);
+ } else if (getReasonerTypeString().equals("cel")) {
+ // instantiate CEL reasoner
+ reasoner = new CelReasoner(ontology, conf);
+ } else if (getReasonerTypeString().equals("trowl")) {
+ // instantiate TrOWL reasoner
+ reasoner = new RELReasonerFactory().createNonBufferingReasoner(ontology, conf);
+ } else {
+ try {
+ OWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();
+ URL url = new URL(getOwlLinkURL());//Configure the server end-point
+ OWLlinkReasonerConfiguration config = new OWLlinkReasonerConfiguration(url);
+ reasoner = factory.createNonBufferingReasoner(ontology, config);
+ System.out.println(reasoner.getReasonerName());
+ } catch (Exception e) {
+// e.printStackTrace();
+ throw new ComponentInitException(e);
+ }
+ }
- /*
- * Set<OWLOntology> importsClosure =
- * manager.getImportsClosure(ontology);
- * System.out.println("imports closure : " + importsClosure); try {
- * reasoner.loadOntologies(importsClosure); } catch
- * (OWLReasonerException e1) { // TODO Auto-generated catch block
- * e1.printStackTrace(); }
- */
+ /*
+ Set<OWLOntology> importsClosure = manager.getImportsClosure(ontology);
+ System.out.println("imports closure : " + importsClosure);
+ try {
+ reasoner.loadOntologies(importsClosure);
+ } catch (OWLReasonerException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }*/
- // System.out.println(classes);
- // System.out.println(properties);
- // System.out.println(individuals);
+// System.out.println(classes);
+// System.out.println(properties);
+// System.out.println(individuals);
- // compute class hierarchy and types of individuals
- // (done here to speed up later reasoner calls)
- boolean inconsistentOntology = !reasoner.isConsistent();
+ // compute class hierarchy and types of individuals
+ // (done here to speed up later reasoner calls)
+ boolean inconsistentOntology = !reasoner.isConsistent();
- if (!inconsistentOntology) {
- reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY,
- InferenceType.CLASS_ASSERTIONS);
- } else {
- throw new ComponentInitException("Inconsistent ontologies.");
- }
+ if (!inconsistentOntology) {
+ reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY, InferenceType.CLASS_ASSERTIONS);
+ } else {
+ throw new ComponentInitException("Inconsistent ontologies.");
+ }
- factory = manager.getOWLDataFactory();
+ factory = manager.getOWLDataFactory();
- // try {
- // if(reasoner.isDefined(factory.getOWLIndividual(URI.create("http://example.com/father#female"))))
- // System.out.println("DEFINED.");
- // else
- // System.out.println("NOT DEFINED.");
- // } catch (OWLReasonerException e) {
- // // TODO Auto-generated catch block
- // e.printStackTrace();
- // }
+// try {
+// if(reasoner.isDefined(factory.getOWLIndividual(URI.create("http://example.com/father#female"))))
+// System.out.println("DEFINED.");
+// else
+// System.out.println("NOT DEFINED.");
+// } catch (OWLReasonerException e) {
+// // TODO Auto-generated catch block
+// e.printStackTrace();
+// }
- // read in primitives
- for (OWLClass owlClass : classes)
- atomicConcepts.add(new NamedClass(owlClass.toStringID()));
- for (OWLObjectProperty owlProperty : owlObjectProperties)
- atomicRoles.add(new ObjectProperty(owlProperty.toStringID()));
- for (OWLDataProperty owlProperty : owlDatatypeProperties) {
- DatatypeProperty dtp = new DatatypeProperty(owlProperty.toStringID());
- Set<OWLDataRange> ranges = owlProperty.getRanges(allImports);
- Iterator<OWLDataRange> it = ranges.iterator();
- if (it.hasNext()) {
- OWLDataRange range = it.next();
- if (range.isDatatype()) {
- URI uri = ((OWLDatatype) range).getIRI().toURI();
- if (uri.equals(OWL2Datatype.BOOLEAN.getURI()))
- booleanDatatypeProperties.add(dtp);
- else if (uri.equals(OWL2Datatype.DOUBLE.getURI()))
- doubleDatatypeProperties.add(dtp);
- else if (uri.equals(OWL2Datatype.INT.getURI()))
- intDatatypeProperties.add(dtp);
- else if (uri.equals(OWL2Datatype.STRING.getURI()))
- stringDatatypeProperties.add(dtp);
- }
- } else {
- stringDatatypeProperties.add(dtp);
- }
- datatypeProperties.add(dtp);
- }
- for (OWLNamedIndividual owlIndividual : owlIndividuals) {
- individuals.add(new Individual(owlIndividual.toStringID()));
- }
+ // read in primitives
+ for (OWLClass owlClass : classes)
+ atomicConcepts.add(new NamedClass(owlClass.toStringID()));
+ for (OWLObjectProperty owlProperty : owlObjectProperties)
+ atomicRoles.add(new ObjectProperty(owlProperty.toStringID()));
+ for (OWLDataProperty owlProperty : owlDatatypeProperties) {
+ DatatypeProperty dtp = new DatatypeProperty(owlProperty.toStringID());
+ Set<OWLDataRange> ranges = owlProperty.getRanges(allImports);
+ Iterator<OWLDataRange> it = ranges.iterator();
+ if (it.hasNext()) {
+ OWLDataRange range = it.next();
+ if (range.isDatatype()) {
+ URI uri = ((OWLDatatype) range).getIRI().toURI();
+ if (uri.equals(OWL2Datatype.BOOLEAN.getURI())) booleanDatatypeProperties.add(dtp);
+ else if (uri.equals(OWL2Datatype.DOUBLE.getURI())) doubleDatatypeProperties.add(dtp);
+ else if (uri.equals(OWL2Datatype.INT.getURI())) intDatatypeProperties.add(dtp);
+ else if (uri.equals(OWL2Datatype.STRING.getURI())) stringDatatypeProperties.add(dtp);
+ }
+ } else {
+ stringDatatypeProperties.add(dtp);
+ }
+ datatypeProperties.add(dtp);
+ }
+ for (OWLNamedIndividual owlIndividual : owlIndividuals) {
+ individuals.add(new Individual(owlIndividual.toStringID()));
+ }
- // remove top and bottom properties (for backwards compatibility)
- // atomicRoles.remove(new
- // ObjectProperty("http://www.w3.org/2002/07/owl#bottomObjectProperty"));
- // atomicRoles.remove(new
- // ObjectProperty("http://www.w3.org/2002/07/owl#topObjectProperty"));
- }
+ // remove top and bottom properties (for backwards compatibility)
+// atomicRoles.remove(new ObjectProperty("http://www.w3.org/2002/07/owl#bottomObjectProperty"));
+// atomicRoles.remove(new ObjectProperty("http://www.w3.org/2002/07/owl#topObjectProperty"));
+ }
- /*
- * (non-Javadoc)
- *
- * @see org.dllearner.core.Reasoner#getAtomicConcepts()
- */
- public Set<NamedClass> getNamedClasses() {
- return Collections.unmodifiableSet(atomicConcepts);
- }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#getAtomicConcepts()
+ */
+ public Set<NamedClass> getNamedClasses() {
+ return Collections.unmodifiableSet(atomicConcepts);
+ }
- /*
- * (non-Javadoc)
- *
- * @see org.dllearner.core.Reasoner#getAtomicRoles()
- */
- public Set<ObjectProperty> getObjectProperties() {
- return Collections.unmodifiableSet(atomicRoles);
- }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#getAtomicRoles()
+ */
+ public Set<ObjectProperty> getObjectProperties() {
+ return Collections.unmodifiableSet(atomicRoles);
+ }
- @Override
- public SortedSet<DatatypeProperty> getDatatypePropertiesImpl() {
- return datatypeProperties;
- }
+ @Override
+ public SortedSet<DatatypeProperty> getDatatypePropertiesImpl() {
+ return datatypeProperties;
+ }
- /*
- * (non-Javadoc)
- *
- * @see org.dllearner.core.Reasoner#getIndividuals()
- */
- public SortedSet<Individual> getIndividuals() {
- return individuals;
- }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#getIndividuals()
+ */
+ public SortedSet<Individual> getIndividuals() {
+ return individuals;
+ }
- /*
- * (non-Javadoc)
- *
- * @see org.dllearner.core.Reasoner#getReasonerType()
- */
- @Override
- public ReasonerType getReasonerType() {
- if (getReasonerTypeString().equals("fact")) {
- return ReasonerType.OWLAPI_FACT;
- } else if (getReasonerTypeString().equals("hermit")) {
- return ReasonerType.OWLAPI_HERMIT;
- } else {
- return ReasonerType.OWLAPI_PELLET;
- }
- }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#getReasonerType()
+ */
+ @Override
+ public ReasonerType getReasonerType() {
+ if (getReasonerTypeString().equals("fact")) {
+ return ReasonerType.OWLAPI_FACT;
+ } else if (getReasonerTypeString().equals("hermit")) {
+ return ReasonerType.OWLAPI_HERMIT;
+ } else {
+ return ReasonerType.OWLAPI_PELLET;
+ }
+ }
- // @Override
- // public ObjectPropertyHierarchy prepareRoleHierarchy() {
- // // code copied from DIG reasoner
- //
- // TreeMap<ObjectProperty, TreeSet<ObjectProperty>> roleHierarchyUp = new
- // TreeMap<ObjectProperty, TreeSet<ObjectProperty>>(
- // roleComparator);
- // TreeMap<ObjectProperty, TreeSet<ObjectProperty>> roleHierarchyDown = new
- // TreeMap<ObjectProperty, TreeSet<ObjectProperty>>(
- // roleComparator);
- //
- // // refinement of atomic concepts
- // for (ObjectProperty role : atomicRoles) {
- // roleHierarchyDown.put(role, getMoreSpecialRolesImpl(role));
- // roleHierarchyUp.put(role, getMoreGeneralRolesImpl(role));
- // }
- //
- // roleHierarchy = new ObjectPropertyHierarchy(atomicRoles, roleHierarchyUp,
- // roleHierarchyDown);
- // return roleHierarchy;
- // }
+// @Override
+// public ObjectPropertyHierarchy prepareRoleHierarchy() {
+// // code copied from DIG reasoner
+//
+// TreeMap<ObjectProperty, TreeSet<ObjectProperty>> roleHierarchyUp = new TreeMap<ObjectProperty, TreeSet<ObjectProperty>>(
+// roleComparator);
+// TreeMap<ObjectProperty, TreeSet<ObjectProperty>> roleHierarchyDown = new TreeMap<ObjectProperty, TreeSet<ObjectProperty>>(
+// roleComparator);
+//
+// // refinement of atomic concepts
+// for (ObjectProperty role : atomicRoles) {
+// roleHierarchyDown.put(role, getMoreSpecialRolesImpl(role));
+// roleHierarchyUp.put(role, getMoreGeneralRolesImpl(role));
+// }
+//
+// roleHierarchy = new ObjectPropertyHierarchy(atomicRoles, roleHierarchyUp,
+// roleHierarchyDown);
+// return roleHierarchy;
+// }
- /*
- * (non-Javadoc)
- *
- * @see org.dllearner.core.Reasoner#prepareRoleHierarchy(java.util.Set)
- */
- // public void prepareRoleHierarchy(Set<ObjectProperty> allowedRoles) {
- // // code copied from DIG reasoner
- //
- // TreeMap<ObjectProperty, TreeSet<ObjectProperty>> roleHierarchyUp = new
- // TreeMap<ObjectProperty, TreeSet<ObjectProperty>>(
- // roleComparator);
- // TreeMap<ObjectProperty, TreeSet<ObjectProperty>> roleHierarchyDown = new
- // TreeMap<ObjectProperty, TreeSet<ObjectProperty>>(
- // roleComparator);
- //
- // // refinement of atomic concepts
- // for (ObjectProperty role : atomicRoles) {
- // roleHierarchyDown.put(role, getMoreSpecialRolesImpl(role));
- // roleHierarchyUp.put(role, getMoreGeneralRolesImpl(role));
- // }
- //
- // roleHierarchy = new ObjectPropertyHierarchy(allowedRoles,
- // roleHierarchyUp,
- // roleHierarchyDown);
- // }
+ /* (non-Javadoc)
+ * @see org.dllearner.core.Reasoner#prepareRoleHierarchy(java.util.Set)
+ */
+// public void prepareRoleHierarchy(Set<ObjectProperty> allowedRoles) {
+// // code copied from DIG reasoner
+//
+// TreeMap<ObjectProperty, TreeSet<ObjectProperty>> roleHierarchyUp = new TreeMap<ObjectProperty, TreeSet<ObjectProperty>>(
+// roleComparator);
+// TreeMap<ObjectProperty, TreeSet<ObjectProperty>> roleHierarchyDown = new TreeMap<ObjectProperty, TreeSet<ObjectProperty>>(
+// roleComparator);
+//
+// // refinement of atomic concepts
+// for (ObjectProperty role : atomicRoles) {
+// roleHierarchyDown.put(role, getMoreSpecialRolesImpl(role));
+// roleHierarchyUp.put(role, getMoreGeneralRolesImpl(role));
+// }
+//
+// roleHierarchy = new ObjectPropertyHierarchy(allowedRoles, roleHierarchyUp,
+// roleHierarchyDown);
+// }
- // @Override
- // public ObjectPropertyHierarchy getRoleHierarchy() {
- // return roleHierarchy;
- // }
+// @Override
+// public ObjectPropertyHierarchy getRoleHierarchy() {
+// return roleHierarchy;
+// }
- // public void prepareDatatypePropertyHierarchyImpl(Set<DatatypeProperty>
- // allowedRoles) {
- // // code copied from DIG reasoner
- //
- // TreeMap<DatatypeProperty, TreeSet<DatatypeProperty>>
- // datatypePropertyHierarchyUp = new TreeMap<DatatypeProperty,
- // TreeSet<DatatypeProperty>>(
- // roleComparator);
- // TreeMap<DatatypeProperty, TreeSet<DatatypeProperty>>
- // datatypePropertyHierarchyDown = new TreeMap<DatatypeProperty,
- // TreeSet<DatatypeProperty>>(
- // roleComparator);
- //
- // // refinement of atomic concepts
- // for (DatatypeProperty role : datatypeProperties) {
- // datatypePropertyHierarchyDown.put(role,
- // getMoreSpecialDatatypePropertiesImpl(role));
- // datatypePropertyHierarchyUp.put(role,
- // getMoreGeneralDatatypePropertiesImpl(role));
- // }
- //
- // datatypePropertyHierarchy = new DatatypePropertyHierarchy(allowedRoles,
- // datatypePropertyHierarchyUp,
- // datatypePropertyHierarchyDown);
- // }
+// public void prepareDatatypePropertyHierarchyImpl(Set<DatatypeProperty> allowedRoles) {
+// // code copied from DIG reasoner
+//
+// TreeMap<DatatypeProperty, TreeSet<DatatypeProperty>> datatypePropertyHierarchyUp = new TreeMap<DatatypeProperty, TreeSet<DatatypeProperty>>(
+// roleComparator);
+// TreeMap<DatatypeProperty, TreeSet<DatatypeProperty>> datatypePropertyHierarchyDown = new TreeMap<DatatypeProperty, TreeSet<DatatypeProperty>>(
+// roleComparator);
+//
+// // refinement of atomic concepts
+// for (DatatypeProperty role : datatypeProperties) {
+// datatypePropertyHierarchyDown.put(role, getMoreSpecialDatatypePropertiesImpl(role));
+// datatypePropertyHierarchyUp.put(role, getMoreGeneralDatatypePropertiesImpl(role));
+// }
+//
+// datatypePropertyHierarchy = new DatatypePropertyHierarchy(allowedRoles, datatypePropertyHierarchyUp,
+// datatypePropertyHierarchyDown);
+// }
- // @Override
- // public DatatypePropertyHierarchy getDatatypePropertyHierarchy() {
- // return datatypePropertyHierarchy;
- // }
+// @Override
+// public DatatypePropertyHierarchy getDatatypePropertyHierarchy() {
+// return datatypePropertyHierarchy;
+// }
- @Override
- public boolean isSuperClassOfImpl(Description superConcept, Description subConcept) {
- return reasoner.isEntailed(factory.getOWLSubClassOfAxiom(
- OWLAPIDescriptionConvertVisitor.getOWLClassExpression(subConcept),
- OWLAPIDescriptionConvertVisitor.getOWLClassExpression(superConcept)));
- }
+ @Override
+ public boolean isSuperClassOfImpl(Description superConcept, Description subConcept) {
+ return reasoner.isEntailed(factory.getOWLSubClassOfAxiom(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(subConcept), OWLAPIDescriptionConvertVisitor.getOWLClassExpression(superConcept)));
+ }
- @Override
- protected boolean isEquivalentClassImpl(Description class1, Description class2) {
- return reasoner.isEntailed(factory.getOWLEquivalentClassesAxiom(
- OWLAPIDescriptionConvertVisitor.getOWLClassExpression(class1),
- OWLAPIDescriptionConvertVisitor.getOWLClassExpression(class2)));
- }
+ @Override
+ protected boolean isEquivalentClassImpl(Description class1, Description class2) {
+ return reasoner.isEntailed(factory.getOWLEquivalentClassesAxiom(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(class1), OWLAPIDescriptionConvertVisitor.getOWLClassExpression(class2)));
+ }
- @Override
- protected TreeSet<Description> getSuperClassesImpl(Description concept) {
- NodeSet<OWLClass> classes = null;
+ @Override
+ protected TreeSet<Description> getSuperClassesImpl(Description concept) {
+ NodeSet<OWLClass> classes = null;
- classes = reasoner.getSuperClasses(
- OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept), true);
+ classes = reasoner.getSuperClasses(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept), true);
- return getFirstClasses(classes);
- }
+ return getFirstClasses(classes);
+ }
- @Override
- protected TreeSet<Description> getSubClassesImpl(Description concept) {
- NodeSet<OWLClass> classes = null;
+ @Override
+ protected TreeSet<Description> getSubClassesImpl(Description concept) {
+ NodeSet<OWLClass> classes = null;
- classes = reasoner.getSubClasses(
- OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept), true);
+ classes = reasoner.getSubClasses(OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept), true);
- return getFirstClasses(classes);
- }
+ return getFirstClasses(classes);
+ }
- @Override
- protected TreeSet<ObjectProperty> getSuperPropertiesImpl(ObjectProperty role) {
- NodeSet<OWLObjectPropertyExpression> properties = null;
+ @Override
+ protected TreeSet<ObjectProperty> getSuperPropertiesImpl(ObjectProperty role) {
+ NodeSet<OWLObjectPropertyExpression> properties = null;
- try {
- properties = reasoner.getSuperObjectProperties(
- OWLAPIConverter.getOWLAPIObjectProperty(role), true);
- return getFirstObjectProperties(properties);
- } catch (Exception e) {
- TreeSet<ObjectProperty> roles = new TreeSet<ObjectProperty>(roleComparator);
- return roles;
- }
- }
+ properties = reasoner.getSuperObjectProperties(OWLAPIConverter.getOWLAPIObjectProperty(role), true);
- @Override
- protected TreeSet<ObjectProperty> getSubPropertiesImpl(ObjectProperty role) {
- NodeSet<OWLObjectPropertyExpression> properties = null;
+ return getFirstObjectProperties(properties);
+ }
- try {
- properties = reasoner.getSubObjectProperties(
- OWLAPIConverter.getOWLAPIObjectProperty(role), true);
- return getFirstObjectProperties(properties);
- } catch (Exception e) {
- TreeSet<ObjectProperty> roles = new TreeSet<ObjectProperty>(roleComparator);
- return roles;
- }
+ @Override
+ protected TreeSet<ObjectProperty> getSubPropertiesImpl(ObjectProperty role) {
+ NodeSet<OWLObjectPropertyExpression> properties = null;
- }
+ properties = reasoner.getSubObjectProperties(OWLAPIConverter.getOWLAPIObjectProperty(role), true);
- @Override
- protected TreeSet<DatatypeProperty> getSuperPropertiesImpl(DatatypeProperty role) {
- NodeSet<OWLDataProperty> properties = null;
+ return getFirstObjectProperties(properties);
+ }
- properties = reasoner.getSuperDataProperties(OWLAPIConverter.getOWLAPIDataProperty(role),
- true);
+ @Override
+ protected TreeSet<DatatypeProperty> getSuperPropertiesImpl(DatatypeProperty role) {
+ NodeSet<OWLDataProperty> properties = null;
- return getFirstDatatypeProperties(properties);
- }
+ properties = reasoner.getSuperDataProperties(OWLAPIConverter.getOWLAPIDataProperty(role), true);
- @Override
- protected TreeSet<DatatypeProperty> getSubPropertiesImpl(DatatypeProperty role) {
- NodeSet<OWLDataProperty> properties = null;
+ return getFirstDatatypeProperties(properties);
+ }
- properties = reasoner.getSubDataProperties(OWLAPIConverter.getOWLAPIDataProperty(role),
- true);
+ @Override
+ protected TreeSet<DatatypeProperty> getSubPropertiesImpl(DatatypeProperty role) {
+ NodeSet<OWLDataProperty> properties = null;
- return getFirstDatatypeProperties(properties);
- }
+ properties = reasoner.getSubDataProperties(OWLAPIConverter.getOWLAPIDataProperty(role), true);
- @Override
- public boolean hasTypeImpl(Description concept, Individual individual) {
- boolean test = false;
- OWLClassExpression d = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept);
- OWLNamedIndividual i = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
-// try {
-// test = reasoner.isEntailed(factory.getOWLClassAssertionAxiom(d, i));
-// } catch (Exception e) {
-// test = true;
-// }
- if(d.isAnonymous()){
- throw new UnsupportedOperationException("Can not do type checking for complex class expressions.");
- }
- for(OWLClass type : reasoner.getTypes(i, false).getFlattened()){
- if(type.equals(d.asOWLClass())){
- return true;
- }
- }
- return test;
- }
+ return getFirstDatatypeProperties(properties);
+ }
- @Override
- public SortedSet<Individual> getIndividualsImpl(Description concept) {
- // OWLDescription d = getOWLAPIDescription(concept);
- OWLClassExpression d = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept);
- Set<OWLNamedIndividual> individuals = reasoner.getInstances(d, false).getFlattened();
- SortedSet<Individual> inds = new TreeSet<Individual>();
- for (OWLNamedIndividual ind : individuals)
- // ugly code
- if (ind != null)
- inds.add(new Individual(ind.toStringID()));
- return inds;
- }
+ @Override
+ public boolean hasTypeImpl(Description concept, Individual individual) {
+ OWLClassExpression d = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept);
+ OWLIndividual i = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
+ if(concept instanceof Thing) return true;
+ if(concept instanceof NamedClass && ((NamedClass)concept).getName().contains("Error"))return false;
+ return reasoner.isEntailed(factory.getOWLClassAssertionAxiom(d, i));
+ }
- @Override
- public Set<NamedClass> getTypesImpl(Individual individual) {
- Set<Node<OWLClass>> result = null;
+ @Override
+ public SortedSet<Individual> getIndividualsImpl(Description concept) {
+// OWLDescription d = getOWLAPIDescription(concept);
+ OWLClassExpression d = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(concept);
+ Set<OWLNamedIndividual> individuals = reasoner.getInstances(d, false).getFlattened();
+ SortedSet<Individual> inds = new TreeSet<Individual>();
+ for (OWLNamedIndividual ind : individuals)
+ //ugly code
+ if (ind != null) inds.add(new Individual(ind.toStringID()));
+ return inds;
+ }
- result = reasoner.getTypes(factory.getOWLNamedIndividual(IRI.create(individual.getName())),
- false).getNodes();
+ @Override
+ public Set<NamedClass> getTypesImpl(Individual individual) {
+ Set<Node<OWLClass>> result = null;
- return getFirstClassesNoTopBottom(result);
- }
+ result = reasoner.getTypes(factory.getOWLNamedIndividual(IRI.create(individual.getName())), false).getNodes();
- @Override
- public boolean isSatisfiableImpl() {
- return reasoner.isSatisfiable(factory.getOWLThing());
- }
+ return getFirstClassesNoTopBottom(result);
+ }
- @Override
- public Description getDomainImpl(ObjectProperty objectProperty) {
- OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
+ @Override
+ public boolean isSatisfiableImpl() {
+ return reasoner.isSatisfiable(factory.getOWLThing());
+ }
- // Pellet returns a set of nodes of named classes, which are more
- // general than the actual domain/range
- NodeSet<OWLClass> set;
+ @Override
+ public Description getDomainImpl(ObjectProperty objectProperty) {
+ OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
+
+ // Pellet returns a set of nodes of named classes, which are more
+ // general than the actual domain/range
+ NodeSet<OWLClass> set;
try {
set = reasoner.getObjectPropertyDomains(prop, false);
return getDescriptionFromReturnedDomain(set);
- } catch (Exception e) {
- return getDescriptionFromReturnedDomain(null);
+ } catch (InconsistentOntologyException e) {
+ e.printStackTrace();
+ } catch (FreshEntitiesException e) {
+ e.printStackTrace();
+ } catch (TimeOutException e) {
+ e.printStackTrace();
+ } catch (ReasonerInterruptedException e) {
+ e.printStackTrace();
+ } catch(de.tudresden.inf.lat.cel.owlapi.UnsupportedReasonerOperationInCelException e){
+ e.printStackTrace();
}
- }
+ return Thing.instance;
- @Override
- public Description getDomainImpl(DatatypeProperty datatypeProperty) {
- OWLDataProperty prop = OWLAPIConverter.getOWLAPIDataProperty(datatypeProperty);
+ }
- NodeSet<OWLClass> set = reasoner.getDataPropertyDomains(prop, true);
- return getDescriptionFromReturnedDomain(set);
+ @Override
+ public Description getDomainImpl(DatatypeProperty datatypeProperty) {
+ OWLDataProperty prop = OWLAPIConverter.getOWLAPIDataProperty(datatypeProperty);
- }
+ NodeSet<OWLClass> set = reasoner.getDataPropertyDomains(prop, true);
+ return getDescriptionFromReturnedDomain(set);
- @Override
- public Description getRangeImpl(ObjectProperty objectProperty) {
- OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
+ }
- NodeSet<OWLClass> set;
+ @Override
+ public Description getRangeImpl(ObjectProperty objectProperty) {
+ OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(objectProperty);
+
+ NodeSet<OWLClass> set;
try {
set = reasoner.getObjectPropertyRanges(prop, true);
- if (set.isEmpty())
- return new Thing();
- OWLClass oc = set.iterator().next().getRepresentativeElement();
- if (oc.isOWLThing()) {
- return Thing.instance;
- }
- return new NamedClass(oc.toStringID());
- } catch (Exception e) {
- return Thing.instance;
+ if (set.isEmpty()) return new Thing();
+ OWLClass oc = set.iterator().next().getRepresentativeElement();
+ if (oc.isOWLThing()) {
+ return Thing.instance;
+ }
+ return new NamedClass(oc.toStringID());
+ } catch (InconsistentOntologyException e) {
+ e.printStackTrace();
+ } catch (FreshEntitiesException e) {
+ e.printStackTrace();
+ } catch (TimeOutException e) {
+ e.printStackTrace();
+ } catch (ReasonerInterruptedException e) {
+ e.printStackTrace();
+ } catch(de.tudresden.inf.lat.cel.owlapi.UnsupportedReasonerOperationInCelException e){
+ e.printStackTrace();
}
- }
+ return Thing.instance;
- private Description getDescriptionFromReturnedDomain(NodeSet<OWLClass> set) {
- if (set.isEmpty())
- return new Thing();
+ }
- Set<OWLClassExpression> union = new HashSet<OWLClassExpression>();
- Set<OWLClassExpression> domains = new HashSet<OWLClassExpression>();
+ private Description getDescriptionFromReturnedDomain(NodeSet<OWLClass> set) {
+ if (set.isEmpty()) return new Thing();
- for (Node<OWLClass> descs : set) {
- for (OWLClassExpression desc : descs) {
- union.add(desc);
- }
- }
- for (OWLClassExpression desc : union) {
- boolean isSuperClass = false;
- for (Description d : getClassHierarchy().getSubClasses(
- OWLAPIConverter.convertClass(desc.asOWLClass()))) {
- if (union.contains(OWLAPIConverter.getOWLAPIDescription(d))) {
- isSuperClass = true;
- break;
- }
- }
- if (!isSuperClass) {
- domains.add(desc);
- }
- }
+ Set<OWLClassExpression> union = new HashSet<OWLClassExpression>();
+ Set<OWLClassExpression> domains = new HashSet<OWLClassExpression>();
- OWLClass oc = (OWLClass) domains.iterator().next();
- if (oc.isOWLThing()) {
- return new Thing();
- } else {
- return new NamedClass(oc.toStringID());
- }
- }
+ for (Node<OWLClass> descs : set) {
+ for (OWLClassExpression desc : descs) {
+ union.add(desc);
+ }
+ }
+ for (OWLClassExpression desc : union) {
+ boolean isSuperClass = false;
+ for (Description d : getClassHierarchy().getSubClasses(OWLAPIConverter.convertClass(desc.asOWLClass()))) {
+ if (union.contains(OWLAPIConverter.getOWLAPIDescription(d))) {
+ isSuperClass = true;
+ break;
+ }
+ }
+ if (!isSuperClass) {
+ domains.add(desc);
+ }
+ }
- @Override
- public Map<Individual, SortedSet<Individual>> getPropertyMembersImpl(ObjectProperty atomicRole) {
- OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(atomicRole);
- Map<Individual, SortedSet<Individual>> map = new TreeMap<Individual, SortedSet<Individual>>();
- for (Individual i : individuals) {
- OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(i.getName()));
+ OWLClass oc = (OWLClass) domains.iterator().next();
+ if (oc.isOWLThing()) {
+ return new Thing();
+ } else {
+ return new NamedClass(oc.toStringID());
+ }
+ }
- // get all related individuals via OWL API
- Set<OWLNamedIndividual> inds;
- try {
- inds = reasoner.getObjectPropertyValues(ind, prop).getFlattened();
- } catch (Exception e) {
- inds = null;
- }
+ @Override
+ public Map<Individual, SortedSet<Individual>> getPropertyMembersImpl(ObjectProperty atomicRole) {
+ OWLObjectProperty prop = OWLAPIConverter.getOWLAPIObjectProperty(atomicRole);
+ Map<Individual, SortedSet<Individual>> map = new TreeMap<Individual, SortedSet<Individual>>();
+ for (Individual i : individuals) {
+ OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(i.getName()));
- // convert data back to DL-Learner structures
- SortedSet<Individual> is = new TreeSet<Individual>();
- try {
- for (OWLNamedIndividual oi : inds)
- is.add(new Individual(oi.toStringID()));
- map.put(i, is);
- } catch (Exception e) {
- map = null;
- }
- }
- return map;
- }
+ // get all related individuals via OWL API
+ Set<OWLNamedIndividual> inds = reasoner.getObjectPropertyValues(ind, prop).getFlattened();
- @Override
- protected Map<ObjectProperty, Set<Individual>> getObjectPropertyRelationshipsImpl(
- Individual individual) {
- OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(individual.getName()));
- Map<OWLObjectPropertyExpression, Set<OWLNamedIndividual>> mapAPI = new HashMap<OWLObjectPropertyExpression, Set<OWLNamedIndividual>>();
+ // convert data back to DL-Learner structures
+ SortedSet<Individual> is = new TreeSet<Individual>();
+ for (OWLNamedIndividual oi : inds)
+ ...
[truncated message content] |
|
From: <lor...@us...> - 2013-01-22 09:47:32
|
Revision: 3884
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3884&view=rev
Author: lorenz_b
Date: 2013-01-22 09:47:20 +0000 (Tue, 22 Jan 2013)
Log Message:
-----------
Moving QTL algorithm to core module.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.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/reasoning/SPARQLReasoner.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeFactory.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/cache/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/cache/QueryTreeCache.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/NodeRenderer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/GeneralisedQueryTree.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeChange.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/examples/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/examples/DBpediaExample.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/examples/LinkedGeoDataExample.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/exception/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/exception/EmptyLGGException.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/exception/NBRException.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/exception/NegativeTreeCoverageExecption.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/exception/QTLException.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/exception/TimeOutException.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/ExactMatchFilter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/Filter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/Filters.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/I_Sub.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QueryTreeFilter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedQueryTreeFilter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedQueryTreeFilterAggressive.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedStatementFilter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedStatementFilter2.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedStatementSelector.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/ZeroFilter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/QueryTreeFactoryImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/QueryTreeFactoryImpl2.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/FilterVisitor.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/Generalisation.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/NBR.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/PostLGG.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGenerator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/nbr/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/nbr/NBRGenerator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/nbr/NBRGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/nbr/strategy/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/nbr/strategy/BruteForceNBRStrategy.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/nbr/strategy/GreedyNBRStrategy.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/nbr/strategy/NBRStrategy.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/nbr/strategy/TagNonSubsumingPartsNBRStrategy.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/Prefixes.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/SPARQLEndpointEx.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/util/TreeHelper.java
trunk/components-core/src/test/java/org/dllearner/algorithms/
trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/
trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/GeneralisationTest.java
trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/LGGTest.java
trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/NBRTest.java
trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/QTLTest.java
trunk/components-core/src/test/java/org/dllearner/algorithms/qtl/TreeSubsumptionTest.java
Property Changed:
----------------
trunk/components-core/
Property changes on: trunk/components-core
___________________________________________________________________
Modified: svn:ignore
- components-core.iml
target
log
.classpath
.project
.settings
+ components-core.iml
target
log
.classpath
.project
.settings
cache
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-01-22 09:43:25 UTC (rev 3883)
+++ trunk/components-core/pom.xml 2013-01-22 09:47:20 UTC (rev 3884)
@@ -113,11 +113,18 @@
</exclusions>
</dependency>
- <!-- THIS IS FROM THE UNIBAS REPO -->
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi</artifactId>
+ <artifactId>owlapi-distribution</artifactId>
</dependency>
+ <dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-reasoner</artifactId>
+</dependency>
+<dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-util</artifactId>
+ </dependency>
<!-- THIS IS FROM THE UNIBAS REPO -->
<dependency>
@@ -253,6 +260,12 @@
<artifactId>xercesImpl</artifactId>
<version>2.8.0</version>
</dependency>
+
+ <dependency>
+ <groupId>uk.ac.shef.wit</groupId>
+ <artifactId>simmetrics</artifactId>
+ <version>1.6.2</version>
+ </dependency>
</dependencies>
<dependencyManagement>
<dependencies>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java 2013-01-22 09:43:25 UTC (rev 3883)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -178,12 +178,12 @@
class2Overlap.put(cls, cnt);
}
//for each property in knowledge base
- for(NamedClass cls : allClasses){
+ for(NamedClass cls : allClasses){if(!cls.toString().equals("http://dbpedia.org/ontology/MotorcycleRider"))continue;
//get the popularity
int otherPopularity = reasoner.getPopularity(cls);
if(otherPopularity == 0){//skip empty properties
continue;
- }
+ }System.out.println(cls);
//get the overlap
int overlap = class2Overlap.containsKey(cls) ? class2Overlap.get(cls) : 0;
//compute the estimated precision
@@ -455,7 +455,8 @@
ks = new LocalModelBasedSparqlEndpointKS(new URL("http://dl-learner.svn.sourceforge.net/viewvc/dl-learner/trunk/examples/swore/swore.rdf?revision=2217"));
ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
DisjointClassesLearner l = new DisjointClassesLearner(ks);
- l.setClassToDescribe(new NamedClass("http://dbpedia.org/ontology/Book"));
+ l.setClassToDescribe(new NamedClass("http://dbpedia.org/ontology/Agent"));
+ l.setMaxExecutionTimeInSeconds(60);
l.init();
l.getReasoner().prepareSubsumptionHierarchy();
l.getReasoner().precomputeClassPopularity();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2013-01-22 09:43:25 UTC (rev 3883)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -164,7 +164,7 @@
public static void main(String[] args) throws Exception{
FunctionalObjectPropertyAxiomLearner l = new FunctionalObjectPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia()));
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/league"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/currency"));
l.setMaxExecutionTimeInSeconds(20);
l.setForceSPARQL_1_0_Mode(true);
l.init();
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 2013-01-22 09:43:25 UTC (rev 3883)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -206,14 +206,14 @@
ObjectPropertyDomainAxiomLearner l = new ObjectPropertyDomainAxiomLearner(ks);
l.setReasoner(reasoner);
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/grammyAward"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/anthem"));
l.setMaxExecutionTimeInSeconds(40);
- l.addFilterNamespace("http://dbpedia.org/ontology/");
+// l.addFilterNamespace("http://dbpedia.org/ontology/");
// l.setReturnOnlyNewAxioms(true);
l.init();
l.start();
- System.out.println(l.getCurrentlyBestEvaluatedAxioms(10, 0.3));
+ System.out.println(l.getCurrentlyBestEvaluatedAxioms());
}
}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -0,0 +1,387 @@
+/**
+ * Copyright (C) 2007-2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.algorithms.qtl;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.commons.collections15.ListUtils;
+import org.apache.log4j.Logger;
+import org.dllearner.algorithms.qtl.cache.QueryTreeCache;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.exception.EmptyLGGException;
+import org.dllearner.algorithms.qtl.exception.NegativeTreeCoverageExecption;
+import org.dllearner.algorithms.qtl.exception.TimeOutException;
+import org.dllearner.algorithms.qtl.filters.QueryTreeFilter;
+import org.dllearner.algorithms.qtl.operations.NBR;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
+import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
+import org.dllearner.algorithms.qtl.util.SPARQLEndpointEx;
+import org.dllearner.core.AbstractComponent;
+import org.dllearner.core.AbstractLearningProblem;
+import org.dllearner.core.ComponentAnn;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.SparqlQueryLearningAlgorithm;
+import org.dllearner.core.options.CommonConfigOptions;
+import org.dllearner.core.options.ConfigOption;
+import org.dllearner.core.options.IntegerConfigOption;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.CachingConciseBoundedDescriptionGenerator;
+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;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.learningproblems.PosOnlyLP;
+import org.dllearner.utilities.Helper;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSetRewindable;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.util.iterator.Filter;
+
+/**
+ *
+ * Learning algorithm for SPARQL queries based on so called query trees.
+ *
+ * @author Lorenz Bühmann
+ * @author Jens Lehmann
+ *
+ *
+ */
+@ComponentAnn(name="query tree learner", shortName="qtl", version=0.8)
+public class QTL extends AbstractComponent implements SparqlQueryLearningAlgorithm {
+
+ private static final Logger logger = Logger.getLogger(QTL.class);
+
+ private LearningProblem learningProblem;
+ private SparqlEndpointKS endpointKS;
+// private QTLConfigurator configurator;
+
+ private SparqlEndpoint endpoint;
+ private ExtractionDBCache cache;
+
+ private QueryTreeCache treeCache;
+
+ private LGGGenerator<String> lggGenerator;
+ private NBR<String> nbr;
+
+ private List<String> posExamples;
+ private List<String> negExamples;
+
+ private List<QueryTree<String>> posExampleTrees;
+ private List<QueryTree<String>> negExampleTrees;
+
+ private QueryTreeFilter queryTreeFilter;
+
+ private ConciseBoundedDescriptionGenerator cbdGenerator;
+
+ private int maxExecutionTimeInSeconds = 60;
+ private int maxQueryTreeDepth = 2;
+
+ private QueryTree<String> lgg;
+ private SortedSet<String> lggInstances;
+
+ public static Collection<ConfigOption<?>> createConfigOptions() {
+ Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
+ options.add(CommonConfigOptions.maxExecutionTimeInSeconds(10));
+ options.add(new IntegerConfigOption("maxQueryTreeDepth", "recursion depth of query tree extraction", 2));
+ return options;
+ }
+
+ public QTL() {
+
+ }
+
+ public QTL(AbstractLearningProblem learningProblem, SparqlEndpointKS endpointKS) throws LearningProblemUnsupportedException{
+ if(!(learningProblem instanceof PosOnlyLP || learningProblem instanceof PosNegLP)){
+ throw new LearningProblemUnsupportedException(learningProblem.getClass(), getClass());
+ }
+ this.learningProblem = learningProblem;
+ this.endpointKS = endpointKS;
+
+// this.configurator = new QTLConfigurator(this);
+ }
+
+ public QTL(SPARQLEndpointEx endpoint, ExtractionDBCache cache) {
+ this.endpoint = endpoint;
+ this.cache = cache;
+
+ treeCache = new QueryTreeCache();
+ cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(endpoint, cache));
+ cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
+
+ lggGenerator = new LGGGeneratorImpl<String>();
+ nbr = new NBR<String>(endpoint, cache);
+ nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+
+ posExampleTrees = new ArrayList<QueryTree<String>>();
+ negExampleTrees = new ArrayList<QueryTree<String>>();
+ }
+
+ public String getQuestion(List<String> posExamples, List<String> negExamples) throws EmptyLGGException, NegativeTreeCoverageExecption, TimeOutException {
+ this.posExamples = posExamples;
+ this.negExamples = negExamples;
+
+ generatePositiveExampleTrees();
+ generateNegativeExampleTrees();
+
+ if(negExamples.isEmpty()){
+ QueryTree<String> dummyNegTree = new QueryTreeImpl<String>("?");
+ dummyNegTree.addChild(new QueryTreeImpl<String>("?"), "dummy");
+ negExampleTrees.add(dummyNegTree);
+ }
+
+ lgg = lggGenerator.getLGG(posExampleTrees);
+
+ if(queryTreeFilter != null){
+ lgg = queryTreeFilter.getFilteredQueryTree(lgg);
+ }
+ if(logger.isDebugEnabled()){
+ logger.debug("LGG: \n" + lgg.getStringRepresentation());
+ }
+ if(lgg.isEmpty()){
+ throw new EmptyLGGException();
+ }
+
+ int index = coversNegativeQueryTree(lgg);
+ if(index != -1){
+ throw new NegativeTreeCoverageExecption(negExamples.get(index));
+ }
+
+ lggInstances = getResources(lgg);
+ nbr.setLGGInstances(lggInstances);
+
+ String question = nbr.getQuestion(lgg, negExampleTrees, getKnownResources());
+
+ return question;
+ }
+
+ public void setExamples(List<String> posExamples, List<String> negExamples){
+ this.posExamples = posExamples;
+ this.negExamples = negExamples;
+ }
+
+ public void addStatementFilter(Filter<Statement> filter){
+ treeCache.setStatementFilter(filter);
+ }
+
+ public void addQueryTreeFilter(QueryTreeFilter queryTreeFilter){
+ this.queryTreeFilter = queryTreeFilter;
+ }
+
+ public void setMaxExecutionTimeInSeconds(int maxExecutionTimeInSeconds){
+ this.maxExecutionTimeInSeconds = maxExecutionTimeInSeconds;
+ nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+ }
+
+ public void setMaxQueryTreeDepth(int maxQueryTreeDepth){
+ this.maxQueryTreeDepth = maxQueryTreeDepth;
+ cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
+ }
+
+ public String getSPARQLQuery(){
+ if(lgg == null){
+ lgg = lggGenerator.getLGG(getQueryTrees(posExamples));
+ }
+ return lgg.toSPARQLQueryString();
+ }
+
+ public void setRestrictToNamespaces(List<String> namespaces){
+ cbdGenerator.setRestrictToNamespaces(namespaces);
+ }
+
+ private void generatePositiveExampleTrees(){
+ posExampleTrees.clear();
+ posExampleTrees.addAll(getQueryTrees(posExamples));
+ }
+
+ private void generateNegativeExampleTrees(){
+ negExampleTrees.clear();
+ negExampleTrees.addAll(getQueryTrees(negExamples));
+ }
+
+ private List<QueryTree<String>> getQueryTrees(List<String> resources){
+ List<QueryTree<String>> trees = new ArrayList<QueryTree<String>>();
+ Model model;
+ QueryTree<String> tree;
+ for(String resource : resources){
+ if(logger.isDebugEnabled()){
+ logger.debug("Tree for resource " + resource);
+ }
+ model = cbdGenerator.getConciseBoundedDescription(resource);
+ tree = treeCache.getQueryTree(resource, model);
+ if(logger.isDebugEnabled()){
+ logger.debug(tree.getStringRepresentation());
+ }
+ trees.add(tree);
+ }
+ return trees;
+ }
+
+ private List<String> getKnownResources(){
+ return ListUtils.union(posExamples, negExamples);
+ }
+
+// private boolean coversNegativeQueryTree(QueryTree<String> tree){
+// for(QueryTree<String> negTree : negExampleTrees){
+// if(negTree.isSubsumedBy(tree)){
+// return true;
+// }
+// }
+// return false;
+// }
+
+ private int coversNegativeQueryTree(QueryTree<String> tree){
+ for(int i = 0; i < negExampleTrees.size(); i++){
+ if(negExampleTrees.get(i).isSubsumedBy(tree)){
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ private SortedSet<String> getResources(QueryTree<String> tree){
+ SortedSet<String> resources = new TreeSet<String>();
+ String query = getDistinctSPARQLQuery(tree);
+ String result = cache.executeSelectQuery(endpoint, query);
+ ResultSetRewindable rs = SparqlQuery.convertJSONtoResultSet(result);
+ String uri;
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ uri = qs.getResource("x0").getURI();
+ resources.add(uri);
+ }
+ return resources;
+ }
+
+ private String getDistinctSPARQLQuery(QueryTree<String> tree){
+ String query = tree.toSPARQLQueryString();
+// query = "SELECT DISTINCT " + query.substring(7);
+ return query;
+ }
+
+ @Override
+ public void start(){
+ generatePositiveExampleTrees();
+
+ lgg = lggGenerator.getLGG(posExampleTrees);
+
+ if(queryTreeFilter != null){
+ lgg = queryTreeFilter.getFilteredQueryTree(lgg);
+ }
+ if(logger.isDebugEnabled()){
+ logger.debug("LGG: \n" + lgg.getStringRepresentation());
+ }
+
+ }
+
+ @Override
+ public List<String> getCurrentlyBestSPARQLQueries(int nrOfSPARQLQueries) {
+ return Collections.singletonList(getBestSPARQLQuery());
+ }
+
+ @Override
+ public String getBestSPARQLQuery() {
+ return lgg.toSPARQLQueryString();
+ }
+
+ public void init() {
+ if(learningProblem instanceof PosOnlyLP){
+ this.posExamples = convert(((PosOnlyLP)learningProblem).getPositiveExamples());
+ } else if(learningProblem instanceof PosNegLP){
+ this.posExamples = convert(((PosNegLP)learningProblem).getPositiveExamples());
+ this.negExamples = convert(((PosNegLP)learningProblem).getNegativeExamples());
+ }
+ endpoint = endpointKS.getEndpoint();
+
+ treeCache = new QueryTreeCache();
+ cbdGenerator = new CachingConciseBoundedDescriptionGenerator(new ConciseBoundedDescriptionGeneratorImpl(endpoint, cache));
+ cbdGenerator.setRecursionDepth(maxQueryTreeDepth);
+
+ lggGenerator = new LGGGeneratorImpl<String>();
+ nbr = new NBR<String>(endpoint);
+ nbr.setMaxExecutionTimeInSeconds(maxExecutionTimeInSeconds);
+
+ posExampleTrees = new ArrayList<QueryTree<String>>();
+ negExampleTrees = new ArrayList<QueryTree<String>>();
+ }
+
+ private List<String> convert(Set<Individual> individuals){
+ List<String> list = new ArrayList<String>();
+ for(Individual ind : individuals){
+ list.add(ind.toString());
+ }
+ return list;
+ }
+
+ public static void main(String[] args) throws Exception {
+ Set<String> positiveExamples = new HashSet<String>();
+ positiveExamples.add("http://dbpedia.org/resource/Liverpool_F.C.");
+ positiveExamples.add("http://dbpedia.org/resource/Chelsea_F.C.");
+
+ ComponentManager cm = ComponentManager.getInstance();
+ SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
+ ks.init();
+ PosOnlyLP lp = new PosOnlyLP();
+ cm.getPool().registerComponent(lp);
+ lp.setPositiveExamples(Helper.getIndividualSet(positiveExamples));
+ QTL qtl = new QTL(lp, ks);
+ qtl.init();
+ qtl.start();
+ String query = qtl.getBestSPARQLQuery();
+ System.out.println(query);
+ }
+
+ public LearningProblem getLearningProblem() {
+ return learningProblem;
+ }
+
+ @Autowired
+ public void setLearningProblem(LearningProblem learningProblem) {
+ this.learningProblem = learningProblem;
+ }
+
+ public SparqlEndpointKS getEndpointKS() {
+ return endpointKS;
+ }
+
+ @Autowired
+ public void setEndpointKS(SparqlEndpointKS endpointKS) {
+ this.endpointKS = endpointKS;
+ }
+
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeFactory.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeFactory.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeFactory.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -0,0 +1,53 @@
+/**
+ * Copyright (C) 2007-2010, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.algorithms.qtl;
+
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.dllearner.algorithms.qtl.filters.Filter;
+
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Selector;
+import com.hp.hpl.jena.rdf.model.Statement;
+
+/**
+ *
+ * @author Lorenz Bühmann
+ *
+ */
+public interface QueryTreeFactory<N> {
+
+ QueryTreeImpl<N> getQueryTree(String example, Model model);
+
+ QueryTreeImpl<N> getQueryTree(String example, Model model, int maxEdges);
+
+ QueryTreeImpl<N> getQueryTree(Resource example, Model model);
+
+ QueryTreeImpl<N> getQueryTree(String example);
+
+ void setPredicateFilter(Filter filter);
+
+ void setObjectFilter(Filter filter);
+
+ void setStatementSelector(Selector selector);
+
+ void setStatementFilter(com.hp.hpl.jena.util.iterator.Filter<Statement> filter);
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/cache/QueryTreeCache.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/cache/QueryTreeCache.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/cache/QueryTreeCache.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -0,0 +1,65 @@
+package org.dllearner.algorithms.qtl.cache;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.dllearner.algorithms.qtl.QueryTreeFactory;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.filters.Filter;
+import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Selector;
+import com.hp.hpl.jena.rdf.model.Statement;
+
+public class QueryTreeCache {
+
+ private Map<Model, QueryTree<String>> cache;
+ private QueryTreeFactory<String> factory;
+
+ public QueryTreeCache(){
+ cache = new HashMap<Model, QueryTree<String>>();
+ factory = new QueryTreeFactoryImpl();
+ }
+
+ public QueryTree<String> getQueryTree(String root, Model model){
+ QueryTree<String> tree = cache.get(model);
+ if(tree == null){
+ tree = factory.getQueryTree(root, model);
+ }
+ return tree;
+ }
+
+ public QueryTree<String> getQueryTree(Resource root, Model model){
+ QueryTree<String> tree = cache.get(model);
+ if(tree == null){
+ tree = factory.getQueryTree(root, model);
+ }
+ return tree;
+ }
+
+ public void setPredicateFilter(Filter filter){
+ factory.setPredicateFilter(filter);
+ }
+
+ public void setObjectFilter(Filter filter){
+ factory.setObjectFilter(filter);
+ }
+
+ public void setStatementFilter(com.hp.hpl.jena.util.iterator.Filter<Statement> filter){
+ factory.setStatementFilter(filter);
+ }
+
+ public void setStatementSelector(Selector selector){
+ factory.setStatementSelector(selector);
+ }
+
+ public void clear(){
+ cache.clear();
+ }
+
+ public void dispose(){
+ cache = null;
+ }
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/NodeRenderer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/NodeRenderer.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/NodeRenderer.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -0,0 +1,32 @@
+/**
+ * Copyright (C) 2007-2010, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.algorithms.qtl.datastructures;
+
+
+/**
+ *
+ * @author Lorenz Bühmann
+ *
+ */
+public interface NodeRenderer<N> {
+
+ String render(QueryTree<N> node);
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -0,0 +1,144 @@
+/**
+ * Copyright (C) 2007-2010, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.algorithms.qtl.datastructures;
+
+import java.io.PrintWriter;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
+
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+
+import com.hp.hpl.jena.datatypes.RDFDatatype;
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.rdf.model.Literal;
+
+/**
+ *
+ * @author Lorenz Bühmann
+ *
+ */
+public interface QueryTree<N> {
+
+ /**
+ * Gets the "content" of this tree node.
+ * @return The user content of this node.
+ */
+ N getUserObject();
+
+ void setUserObject(N userObject);
+
+ void setId(int id);
+
+ int getId();
+
+ boolean isEmpty();
+
+ QueryTree<N> getNodeById(int nodeId);
+
+ boolean isLiteralNode();
+
+ void setLiteralNode(boolean isLiteralNode);
+
+ boolean isResourceNode();
+
+ void setResourceNode(boolean isResourceNode);
+
+ boolean isVarNode();
+
+ void setVarNode(boolean isVarNode);
+
+ QueryTree<N> getParent();
+
+ List<QueryTree<N>> getChildren();
+
+ List<QueryTree<N>> getChildren(Object edge);
+
+ List<QueryTree<N>> getChildrenClosure();
+
+ Object getEdge(QueryTree<N> child);
+
+ void addChild(QueryTreeImpl<N> child);
+
+ void addChild(QueryTreeImpl<N> child, int position);
+
+ void addChild(QueryTreeImpl<N> child, Object edge);
+
+ void addChild(QueryTreeImpl<N> child, Object edge, int position);
+
+ int removeChild(QueryTreeImpl<N> child);
+
+ Set<Object> getEdges();
+
+ void sortChildren(Comparator<QueryTree<N>> comparator);
+
+ int getChildCount();
+
+ int getMaxDepth();
+
+ boolean isRoot();
+
+ boolean isLeaf();
+
+ boolean isSubsumedBy(QueryTree<N> tree);
+
+ boolean isSubsumedBy(QueryTree<N> tree, boolean stopAfterError);
+
+ boolean isSameTreeAs(QueryTree<N> tree);
+
+ void tag();
+
+ boolean isTagged();
+
+ QueryTree<N> getRoot();
+
+ List<QueryTree<N>> getLeafs();
+
+ List<QueryTree<N>> getPathToRoot();
+
+ List<N> getUserObjectPathToRoot();
+
+ void dump();
+
+ public String getStringRepresentation();
+
+ void dump(PrintWriter writer);
+
+ void dump(PrintWriter writer, int indent);
+
+ Set<N> getUserObjectClosure();
+
+ List<N> fillDepthFirst();
+
+ String toSPARQLQueryString();
+
+ String toSPARQLQueryString(boolean filtered);
+
+ Query toSPARQLQuery();
+
+ int getTriplePatternCount();
+
+ Query toQuery();
+
+ RDFDatatype getDatatype();
+
+ List<Literal> getLiterals();
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/GeneralisedQueryTree.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/GeneralisedQueryTree.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/GeneralisedQueryTree.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -0,0 +1,51 @@
+package org.dllearner.algorithms.qtl.datastructures.impl;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeChange.ChangeType;
+
+public class GeneralisedQueryTree<N> {
+
+ private QueryTree<N> tree;
+ private List<QueryTreeChange> changes;
+
+ public GeneralisedQueryTree(QueryTree<N> tree){
+ this.tree = tree;
+ changes = new ArrayList<QueryTreeChange>();
+ }
+
+ public GeneralisedQueryTree(QueryTree<N> tree, List<QueryTreeChange> changes){
+ this.tree = tree;
+ this.changes = changes;
+ }
+
+ public void setQueryTree(QueryTree<N> tree){
+ this.tree = tree;
+ }
+
+ public QueryTree<N> getQueryTree(){
+ return tree;
+ }
+
+ public void addChange(QueryTreeChange change){
+ changes.add(change);
+ }
+
+ public void addChanges(List<QueryTreeChange> changes){
+ this.changes.addAll(changes);
+ }
+
+ public List<QueryTreeChange> getChanges(){
+ return changes;
+ }
+
+ public QueryTreeChange getLastChange(){
+ if(changes.isEmpty()){
+ return new QueryTreeChange(0, ChangeType.REPLACE_LABEL);
+ }
+ return changes.get(changes.size()-1);
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeChange.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeChange.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeChange.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -0,0 +1,72 @@
+package org.dllearner.algorithms.qtl.datastructures.impl;
+
+
+
+public class QueryTreeChange {
+
+ public enum ChangeType{
+ REPLACE_LABEL,
+ REMOVE_NODE;
+ }
+
+ private int nodeId;
+
+ private ChangeType type;
+
+ private String object;
+ private String edge;
+
+ public QueryTreeChange(int nodeId, ChangeType type){
+ this.nodeId = nodeId;
+ this.type = type;
+ }
+
+ public int getNodeId() {
+ return nodeId;
+ }
+
+ public ChangeType getType() {
+ return type;
+ }
+
+ public String getObject() {
+ return object;
+ }
+
+ public void setObject(String object) {
+ this.object = object;
+ }
+
+ public String getEdge() {
+ return edge;
+ }
+
+ public void setEdge(String edge) {
+ this.edge = edge;
+ }
+
+ @Override
+ public String toString() {
+// return "nodeId" + (type==ChangeType.REPLACE_LABEL ? "Replace" : "Remove");
+ return nodeId + (type==ChangeType.REPLACE_LABEL ? "a" : "b");
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if(obj == this){
+ return true;
+ }
+ if(obj == null || !(obj instanceof QueryTreeChange)){
+ return false;
+ }
+ QueryTreeChange other = (QueryTreeChange)obj;
+ return nodeId == other.getNodeId() && type == other.getType();
+ }
+
+ @Override
+ public int hashCode() {
+ return nodeId + type.hashCode() + 37;
+ }
+
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java 2013-01-22 09:47:20 UTC (rev 3884)
@@ -0,0 +1,905 @@
+/**
+ * Copyright (C) 2007-2010, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.algorithms.qtl.datastructures.impl;
+
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.regex.Pattern;
+
+import javax.xml.bind.DatatypeConverter;
+
+import org.dllearner.algorithms.qtl.datastructures.NodeRenderer;
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.algorithms.qtl.filters.Filters;
+
+import com.hp.hpl.jena.datatypes.BaseDatatype;
+import com.hp.hpl.jena.datatypes.RDFDatatype;
+import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
+import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.graph.Triple;
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.Syntax;
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.sparql.syntax.ElementGroup;
+import com.hp.hpl.jena.sparql.syntax.ElementTriplesBlock;
+
+/**
+ *
+ * @author Lorenz Bühmann
+ *
+ */
+public class QueryTreeImpl<N> implements QueryTree<N>{
+
+ private N userObject;
+
+ private QueryTreeImpl<N> parent;
+
+ private List<QueryTreeImpl<N>> children;
+
+ private Map<QueryTree<N>, Object> child2EdgeMap;
+ private Map<String, List<QueryTree<N>>> edge2ChildrenMap;
+
+ private NodeRenderer<N> toStringRenderer;
+
+ private boolean tagged = false;
+
+ private int cnt;
+
+ private int id;
+
+ private boolean isLiteralNode = false;
+ private boolean isResourceNode = false;
+
+ private List<Literal> literals = new ArrayList<Literal>();
+
+
+ public QueryTreeImpl(N userObject) {
+ this.userObject = userObject;
+ children = new ArrayList<QueryTreeImpl<N>>();
+ child2EdgeMap = new HashMap<QueryTree<N>, Object>();
+ edge2ChildrenMap = new HashMap<String, List<QueryTree<N>>>();
+ toStringRenderer = new NodeRenderer<N>() {
+ public String render(QueryTree<N> object) {
+ String label = object.toString() + "(" + object.getId() + ")";
+ if(object.isLiteralNode()){
+ if(!object.getLiterals().isEmpty()){
+ label += "Values: " + object.getLiterals();
+ }
+ }
+ return label;
+ }
+ };
+ }
+
+ public QueryTreeImpl(QueryTree<N> tree){
+ this(tree.getUserObject());
+ setId(tree.getId());
+ QueryTreeImpl<N> subTree;
+ for(QueryTree<N> child : tree.getChildren()){
+ subTree = new QueryTreeImpl<N>(child);
+ subTree.setId(child.getId());
+ subTree.setLiteralNode(child.isLiteralNode());
+ subTree.setResourceNode(child.isResourceNode());
+ addChild(subTree, tree.getEdge(child));
+ }
+ }
+
+ public N getUserObject() {
+ return userObject;
+ }
+
+ public void setUserObject(N userObject) {
+ this.userObject = userObject;
+ }
+
+ @Override
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ @Override
+ public int getId() {
+ return id;
+ }
+
+ @Override
+ public boolean isEmpty(){
+ return this.children.isEmpty();
+ }
+
+ public QueryTree<N> getNodeById(int nodeId){
+ QueryTree<N> node = null;
+ if(this.id == nodeId){
+ node = this;
+ } else {
+ for(QueryTree<N> child : children){
+ node = child.getNodeById(nodeId);
+ if(node != null){
+ return node;
+ }
+ }
+ }
+ return node;
+ }
+
+ @Override
+ public boolean isLiteralNode() {
+ return isLiteralNode;
+ }
+
+ @Override
+ public void setLiteralNode(boolean isLiteralNode) {
+ this.isLiteralNode = isLiteralNode;
+ }
+
+ @Override
+ public boolean isResourceNode() {
+ return isResourceNode;
+ }
+
+ @Override
+ public void setResourceNode(boolean isResourceNode) {
+ this.isResourceNode = isResourceNode;
+ }
+
+ @Override
+ public boolean isVarNode() {
+ return !isLiteralNode && !isResourceNode;
+ }
+
+ @Override
+ public void setVarNode(boolean isVarNode) {
+ isLiteralNode = false;
+ isResourceNode = false;
+ }
+
+
+ public void setParent(QueryTreeImpl<N> parent) {
+ if (this.parent != null) {
+ this.parent.children.remove(this);
+ }
+ this.parent = parent;
+ this.parent.children.add(this);
+ }
+
+
+ public void addChild(QueryTreeImpl<N> child) {
+ children.add(child);
+ child.parent = this;
+ }
+
+ @Override
+ public void addChild(QueryTreeImpl<N> child, int position) {
+ children.add(position, child);
+ child.parent = this;
+ }
+
+ public void addChild(QueryTreeImpl<N> child, Object edge) {
+ addChild(child);
+ child2EdgeMap.put(child, edge);
+
+ List<QueryTree<N>> children = edge2ChildrenMap.get(edge);
+ if(children == null){
+ children = new ArrayList<QueryTree<N>>();
+ edge2ChildrenMap.put((String)edge, children);
+ }
+ children.add(child);
+ }
+
+ @Override
+ public void addChild(QueryTreeImpl<N> child, Object edge, int position) {
+ addChild(child, position);
+ child2EdgeMap.put(child, edge);
+
+ List<QueryTree<N>> children = edge2ChildrenMap.get(edge);
+ if(children == null){
+ children = new ArrayList<QueryTree<N>>();
+ edge2ChildrenMap.put((String)edge, children);
+ }
+ children.add(child);
+
+ }
+
+
+ public int removeChild(QueryTreeImpl<N> child) {
+ int pos = children.indexOf(child);
+ children.remove(child);
+ edge2ChildrenMap.get(child2EdgeMap.get(child)).remove(child);
+ child.parent = null;
+ return pos;
+ }
+
+ public void removeChildren(Set<QueryTreeImpl<N>> children) {
+ for(QueryTreeImpl<N> child : children){
+ this.children.remove(child);
+ child.parent = null;
+ }
+ }
+
+
+ public Object getEdge(QueryTree<N> child) {
+ return child2EdgeMap.get(child);
+ }
+
+ public Set<Object> getEdges(){
+ return new TreeSet<Object>(child2EdgeMap.values());
+ }
+
+
+ public void sortChildren(Comparator<QueryTree<N>> comparator) {
+ Collections.sort(children, comparator);
+ }
+
+
+ public void clearChildren() {
+ for (QueryTreeImpl<N> child : new ArrayList<QueryTreeImpl<N>>(children)) {
+ removeChild(child);
+ }
+ }
+
+
+ public QueryTree<N> getParent() {
+ return parent;
+ }
+
+
+ public List<QueryTree<N>> getChildren() {
+ return new ArrayList<QueryTree<N>>(children);
+ }
+
+ public List<QueryTree<N>> getChildren(Object edge) {
+// List<QueryTree<N>> children = new ArrayList<QueryTree<N>>();
+// for(Entry<QueryTree<N>, Object> entry : child2EdgeMap.entrySet()){
+// if(entry.getValue().equals(edge)){
+// children.add(entry.getKey());
+// }
+// }
+// return children;
+ List<QueryTree<N>> children = edge2ChildrenMap.get(edge);
+ if(children == null){
+ children = new ArrayList<QueryTree<N>>();
+ }
+ return new ArrayList<QueryTree<N>>(children);
+ }
+
+ public int getChildCount() {
+ return children.size();
+ }
+
+
+ public boolean isRoot() {
+ return parent == null;
+ }
+
+
+ public boolean isLeaf() {
+ return children.isEmpty();
+ }
+
+ @Override
+ public boolean isSubsumedBy(QueryTree<N> tree) {
+ if(!(tree.getUserObject().equals("?") || tree.getUserObject().equals(this.userObject))){
+ return false;
+ }
+
+ Object edge;
+ for(QueryTree<N> child : tree.getChildren()){
+ boolean isSubsumed = false;
+ edge = tree.getEdge(child);
+ for(QueryTree<N> child2 : this.getChildren(edge)){
+ if(child2.isSubsumedBy(child)){
+ isSubsumed = true;
+ break;
+ }
+ }
+ if(!isSubsumed){
+ return false;
+ }
+ }
+ return true;
+ }
+
+ @Override
+ public boolean isSubsumedBy(QueryTree<N> tree, boolean stopAfterError) {
+ if(!(tree.getUserObject().equals("?") || tree.getUserObject().equals(this.userObject))){
+ return false;
+ }
+
+ Object edge;
+ for(QueryTree<N> child : tree.getChildren()){
+ boolean isSubsumed = false;
+ edge = tree.getEdge(child);
+ for(QueryTree<N> child2 : this.getChildren(edge)){
+ if(child2.isSubsumedBy(child, true)){
+ isSubsumed = true;
+ break;
+ }
+ }
+ if(!isSubsumed){
+ child.tag();
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public void tag(){
+ tagged = true;
+ }
+
+ public boolean isTagged(){
+ return tagged;
+ }
+
+
+ public QueryTree<N> getRoot() {
+ if (parent == null) {
+ return this;
+ }
+ return parent.getRoot();
+ }
+
+ public List<QueryTree<N>> getLeafs(){
+ List<QueryTree<N>> leafs = new LinkedList<QueryTree<N>>();
+ if(isLeaf()){
+ leafs.add(this);
+ } else {
+ for(QueryTree<N> child : children){
+ leafs.addAll(child.getLeafs());
+ }
+ }
+ return leafs;
+ }
+
+
+ public List<QueryTree<N>> getPathToRoot() {
+ List<QueryTree<N>> path = new ArrayList<QueryTree<N>>();
+ path.add(0, this);
+ QueryTree<N> par = parent;
+ while (par != null) {
+ path.add(0, par);
+ par = par.getParent();
+ }
+ return path;
+ }
+
+
+
+
+ public List<N> getUserObjectPathToRoot() {
+ List<N> path = new ArrayList<N>();
+ path.add(0, this.getUserObject());
+ QueryTree<N> par = parent;
+ while (par != null) {
+ path.add(0, par.getUserObject());
+ par = par.getParent();
+ }
+ return path;
+ }
+
+ public List<QueryTree<N>> getChildrenClosure() {
+ List<QueryTree<N>> children = new ArrayList<QueryTree<N>>();
+ getChildrenClosure(this, children);
+ return children;
+ }
+
+ private void getChildrenClosure(QueryTree<N> tree, List<QueryTree<N>> bin) {
+ bin.add(tree);
+ for (QueryTree<N> child : tree.getChildren()) {
+ getChildrenClosure(child, bin);
+ }
+ }
+
+
+ public Set<N> getUserObjectClosure() {
+ Set<N> objects = new HashSet<N>();
+ getUserObjectClosure(this, objects);
+ return objects;
+ }
+
+ public int getTriplePatternCount(){
+ return countTriplePattern(this);
+ }
+
+ private int countTriplePattern(QueryTree<N> tree){
+ int cnt = 0;
+ Object object;
+ if(!tree.isLeaf()){
+ for(QueryTree<N> child : tree.getChildren()){
+ object = child.getUserObject();
+ boolean objectIsResource = !object.equals("?");
+ cnt++;
+ if(!objectIsResource){
+ cnt+=countTriplePattern(child);
+ }
+ }
+ }
+ return cnt;
+ }
+
+ public QueryTree<N> getSPARQLQueryTree(){
+ return createSPARQLQueryTree(this);
+ }
+
+ private QueryTree<N> createSPARQLQueryTree(QueryTree<N> tree){
+ QueryTree<N> copy = new QueryTreeImpl<N>(tree.getUserObject());
+ if(tree.getUserObject().equals("?")){
+ for(QueryTree<N> child : tree.getChildren()){
+ copy.addChild((QueryTreeImpl<N>) createSPARQLQueryTree(child), tree.getEdge(child));
+ }
+ }
+// for(QueryTree<N> child : tree.getChildren()){
+// if(child.getUserObject().equals("?")){
+// copy.addChild((QueryTreeImpl<N>) createSPARQLQueryTree(child), tree.getEdge(child));
+// } else {
+// copy.addChild((QueryTreeImpl<N>) child, tree.getEdge(child));
+// }
+//
+// }
+
+ return copy;
+ }
+
+ private void getUserObjectClosure(QueryTree<N> tree, Set<N> bin) {
+ bin.add(tree.getUserObject());
+ for (QueryTree<N> child : tree.getChildren()) {
+ getUserObjectClosure(child, bin);
+ }
+ }
+
+ public String getStringRepresentation(){
+ int depth = getPathToRoot().size();
+ StringBuilder sb = new StringBuilder();
+ if(isRoot()){
+ sb.append("TREE\n\n");
+ }
+ String ren = toStringRenderer.render(this);
+ ren = ren.replace("\n", "\n" + sb);
+ sb.append(ren);
+ sb.append("\n");
+ for (QueryTree<N> child : getChildren()) {
+ for (int i = 0; i < depth; i++) {
+ sb.append("\t");
+ }
+ Object edge = getEdge(child);
+ if (edge != null) {
+ sb.append(" ");
+ sb.append(edge);
+ sb.append(" ---> ");
+ }
+ sb.append(((QueryTreeImpl<N>)child).getStringRepresentation());
+ }
+ return sb.toString();
+ }
+
+ public String getStringRepresentation(int indent){
+ int depth = getPathToRoot().size();
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < depth + indent; i++) {
+ sb.append("\t");
+ }
+ String ren = toStringRenderer.render(this);
+ ren = ren.replace("\n", "\n" + sb);
+ sb.append(ren);
+ sb.append("\n");
+ for (QueryTree<N> child : getChildren()) {
+ Object edge = getEdge(child);
+ if (edge != null) {
+ sb.append("--- ");
+ sb.append(edge);
+ sb.append(" ---\n");
+ }
+ sb.append(((QueryTreeImpl<N>)child).getStringRepresentation(indent));
+ }
+ return sb.toString();
+ }
+
+ public void dump() {
+ dump(new PrintWriter(System.out), 0);
+ }
+
+ public void dump(PrintWriter writer) {
+ dump(writer, 0);
+ }
+
+ public void dump(PrintWriter writer, int indent) {
+ int depth = getPathToRoot().size();
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < depth + indent; i++) {
+ sb.append("\t");
+ }
+ writer.print(sb.toString());
+ String ren = toStringRenderer.render(this);
+ ren = ren.replace("\n", "\n" + sb);
+ writer.println(ren);
+ for (QueryTree<N> child : getChildren()) {
+ Object edge = getEdge(child);
+ if (edge != null) {
+ writer.print(sb.toString());
+ writer.print("--- ");
+ writer.print(edge);
+ writer.print(" ---\n");
+ }
+ child.dump(writer, indent);
+ }
+ writer.flush();
+// int depth = getPathToRoot().size();
+// StringBuilder sb = new StringBuilder();
+// for (int i = 0; i < depth + indent; i++) {
+// sb.append("\t");
+// }
+// writer.print(sb.toString());
+// String ren = toStringRenderer.render(this);
+// ren = ren.replace("\n", "\n" + sb);
+// writer.println(ren);
+// for (QueryTree<N> child : getChildren()) {
+// Object edge = getEdge(child);
+// if (edge != null) {
+// writer.print(sb.toString());
+// writer.print("--- ");
+// writer.print(edge);
+// writer.print(" ---\n");
+// }
+// child.dump(writer, indent);
+// }
+// writer.flush();
+ }
+
+
+ public List<N> fillDepthFirst() {
+ List<N> results = new ArrayList<N>();
+ fillDepthFirst(this, results);
+ return results;
+ }
+
+ private void fillDepthFirst(QueryTree<N> tree, List<N> bin) {
+ bin.add(tree.getUserObject());
+ for (QueryTree<N> child : tree.getChildren()) {
+ fillDepthFirst(child, bin);
+ }
+ }
+
+ public void replace(QueryTreeImpl<N> tree) {
+ parent.children.remove(this);
+ parent.children.add(tree);
+ parent = null;
+ tree.children.clear();
+ tree.children.addAll(children);
+ children.clear();
+ }
+
+ public String toString() {
+ if (userObject != null) {
+ return userObject.toString();
+ } else {
+ return "";
+ }
+ }
+
+
+ public int getSize() {
+ return getUserObjectClosure().size();
+ }
+
+
+
+ public int getMaxDepth() {
+ return getMaxDepth(this);
+ }
+
+ private int getMaxDepth(QueryTree<N> tree) {
+ int maxChildDepth = tree.getPathToRoot().size();
+ for (QueryTree<N> child : tree.getChildren()) {
+ int childDepth = getMaxDepth(child);
+ if(childDepth > maxChildDepth) {
+ maxChildDepth = childDepth;
+ }
+ }
+ return maxChildDepth;
+ }
+
+ @Override
+ public Object clone() throws CloneNotSupportedException {
+ QueryTreeImpl<N> copy = new QueryTreeImpl<N>(this.userObject);
+ for(QueryTreeImpl<N> child : children){
+ copy.addChild((QueryTreeImpl<N>)child.clone(), getEdge(child));
+ }
+
+ return copy;
+ }
+
+// @Override
+// public boolean equals(Object obj) {
+// if(obj == this){
+// return true;
+// }
+// if(!(obj instanceof QueryTreeImpl<?>)){
+// return false;
+// }
+// QueryTreeImpl<N> other = (QueryTreeImpl<N>)obj;
+// if(!this.userObject.equals(other.getUserObject())){
+// return false;
+// }
+// Object edge;
+// for(QueryTreeImpl<N> child : this.children){
+// boolean existsEqualChild = false;
+// edge = child2EdgeMap.get(child);
+// for(QueryTree<N> child2 : other.getChildren(edge)){
+// if(child.equals(child2)){
+// existsEqualChild = true;
+// break;
+// }
+// }
+// if(!existsEqualChild){
+// return false;
+// }
+// }
+// return true;
+// }
+
+ public boolean isSameTreeAs(QueryTree<N> tree){
+ if(!this.userObject.equals(tree.getUserObject())){
+ return false;
+ }
+ Object edge;
+ for(QueryTreeImpl<N> child : this.children){
+ boolean existsEqualChild = false;
+ edge = child2EdgeMap.get(child);
+ for(QueryTree<N> child2 : tree.getChildren(edge)){
+ if(child.isSameTreeAs(child2)){
+ existsEqualChild = true;
+ break;
+ }
+ }
+ if(!existsEqualChild){
+ return false;
+ }
+ }
+ return true;
+ }
+
+ @Override
+ public Query toSPARQLQuery() {
+ return QueryFactory.create(toSPARQLQueryString(), Syntax.syntaxARQ);
+ }
+
+ @Override
+ public String toSPARQLQueryString() {
+ if(children.isEmpty()){
+ return "SELECT ?x0 WHERE {?x0 ?y ?z.}";
+ }
+ cnt = 0;
+ StringBuilder sb = new StringBuilder();
+ sb.append("SELECT DISTINCT ?x0 WHERE {\n");
+ List<String> filters = new ArrayList<String>();
+ buildSPARQLQueryString(this, sb, false, filters);
+ for(String filter : filters){
+ sb.append(filter).append("\n");
+ }
+ sb.append("}");
+ return sb.toString();
+ }
+
+ @Override
+ public String toSPARQLQueryString(boolean filtered) {
+ if(children.isEmpty()){
+ return "SELECT ?x0 WHERE {?x0 ?y ?z.}";
+ }
+ cnt = 0;
+ StringBuilder sb = new StringBuilder();
+ List<String> filters = new ArrayList<String>();
+ sb.append("SELECT DISTINCT ?x0 WHERE {\n");
+ buildSPARQLQueryString(this, sb, filtered, filters);
+ for(String filter : filters){
+ sb.append(filter).append("\n");
+ }
+ sb.append("}");
+ return sb.toString();
+ }
+
+ private void buildSPARQLQueryString(QueryTree<N> tree, StringBuilder sb, boolean filtered, List<String> filters){
+ Object subject = null;
+ if(tree.getUserObject().equals("?")){
+ subject = "?x" + cnt++;
+ if(tree.isLiteralNode() && !tree.getLiterals().isEmpty()){
+ filters.add(getFilter(subject.toString(), tree.getLiterals()));
+ }
+ } else {
+ subject = "<" + tree.getUserObject() + ">";
+ }
+ Object predicate;
+ Object object;
+ if(!tree.isLeaf()){
+ for(QueryTree<N> child : tree.getChildren()){
+ predicate = tree.getEdge(child);
+ if(filtered){
+ if(Filters.getAllFilterProperties().contains(predicate.toString())){
+ continue;
+ }
+ }
+ object = child.getUserObject();
+ boolean objectIsResource = !object.equals("?");
+ if(!objectIsResource){
+ object = "?x" + cnt;
+ } else if(((String)object).startsWith("http://")){
+ object = "<" + object + ">";
+ ...
[truncated message content] |
|
From: <lor...@us...> - 2013-03-18 12:24:48
|
Revision: 3912
http://sourceforge.net/p/dl-learner/code/3912
Author: lorenz_b
Date: 2013-03-18 12:24:44 +0000 (Mon, 18 Mar 2013)
Log Message:
-----------
Some updates.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGenerator.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-03-12 09:29:04 UTC (rev 3911)
+++ trunk/components-core/pom.xml 2013-03-18 12:24:44 UTC (rev 3912)
@@ -116,12 +116,23 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
+ <version>3.4.4</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-reasoner</artifactId>
</dependency>
<dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-debugging</artifactId>
+ <version>3.3</version>
+</dependency>
+<dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-modularity</artifactId>
+ <version>3.3</version>
+</dependency>
+<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-util</artifactId>
</dependency>
@@ -135,6 +146,10 @@
<groupId>org.mortbay.jetty</groupId>
<artifactId>org.mortbay.jetty</artifactId>
</exclusion>
+ <exclusion>
+ <artifactId>owlapi</artifactId>
+ <groupId>net.sourceforge.owlapi</groupId>
+ </exclusion>
</exclusions>
</dependency>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2013-03-12 09:29:04 UTC (rev 3911)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2013-03-18 12:24:44 UTC (rev 3912)
@@ -116,7 +116,7 @@
//compute the overlap if exist
Map<ObjectProperty, Integer> property2Overlap = new HashMap<ObjectProperty, Integer>();
String query = String.format("SELECT ?p (COUNT(*) AS ?cnt) WHERE {?s <%s> ?o. ?s ?p ?o.} GROUP BY ?p", propertyToDescribe.getName());
- ResultSet rs = executeSelectQuery(query);
+ System.out.println(query);ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
qs = rs.next();
@@ -336,13 +336,13 @@
}
public static void main(String[] args) throws Exception{
- SparqlEndpoint endpoint = SparqlEndpoint.getEndpointDBpedia();
+ SparqlEndpoint endpoint = SparqlEndpoint.getEndpointDBpediaLiveAKSW();
// endpoint = new SparqlEndpoint(new URL("http://dbpedia.aksw.org:8902/sparql"), Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList()));
DisjointObjectPropertyAxiomLearner l = new DisjointObjectPropertyAxiomLearner(new SparqlEndpointKS(endpoint));//.getEndpointDBpediaLiveAKSW()));
l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/league"));
l.setMaxExecutionTimeInSeconds(10);
l.init();
- l.getReasoner().precomputeObjectPropertyPopularity();
+// l.getReasoner().precomputeObjectPropertyPopularity();
l.start();
for(EvaluatedAxiom ax : l.getCurrentlyBestEvaluatedAxioms(Integer.MAX_VALUE)){
System.out.println(ax);
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGenerator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGenerator.java 2013-03-12 09:29:04 UTC (rev 3911)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGenerator.java 2013-03-18 12:24:44 UTC (rev 3912)
@@ -13,4 +13,5 @@
public void setRestrictToNamespaces(List<String> namespaces);
public void setRecursionDepth(int maxRecursionDepth);
+
}
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2013-03-12 09:29:04 UTC (rev 3911)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2013-03-18 12:24:44 UTC (rev 3912)
@@ -38,9 +38,9 @@
import com.hp.hpl.jena.query.ResultSetRewindable;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
+//import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
/**
* The class is used to cache information about resources to a database.
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java 2013-03-12 09:29:04 UTC (rev 3911)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlEndpoint.java 2013-03-18 12:24:44 UTC (rev 3912)
@@ -20,6 +20,7 @@
package org.dllearner.kb.sparql;
import java.net.URL;
+import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
@@ -49,6 +50,10 @@
this.namedGraphURIs=namedGraphURIs;
}
+ public SparqlEndpoint(URL url, String defaultGraphURI) {
+ this(url, Collections.singletonList(defaultGraphURI), Collections.<String>emptyList());
+ }
+
public URL getURL() {
return this.url;
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-03-12 09:29:04 UTC (rev 3911)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-03-18 12:24:44 UTC (rev 3912)
@@ -783,12 +783,34 @@
return isObjectProperty;
}
- public boolean isDataProperty(String propertyURI){
- String query = String.format("ASK {<%s> a <%s>}", propertyURI, OWL.DatatypeProperty.getURI());
+ public boolean isObjectProperty(String propertyURI, boolean analyzeData){
+ String query = String.format("ASK {<%s> a <%s>}", propertyURI, OWL.ObjectProperty.getURI());
boolean isObjectProperty = executeAskQuery(query);
+ if(!isObjectProperty && analyzeData){
+ query = String.format("ASK {?s <%s> ?o.FILTER(isURI(?o))}", propertyURI);
+ isObjectProperty = executeAskQuery(query);
+ }
return isObjectProperty;
}
+ public boolean isDataProperty(String propertyURI){
+ if(propertyURI.equals("http://www.w3.org/2000/01/rdf-schema#label")) return true;
+ String query = String.format("ASK {<%s> a <%s>}", propertyURI, OWL.DatatypeProperty.getURI());
+ boolean isDataProperty = executeAskQuery(query);
+ return isDataProperty;
+ }
+
+ public boolean isDataProperty(String propertyURI, boolean analyzeData){
+ if(propertyURI.equals("http://www.w3.org/2000/01/rdf-schema#label")) return true;
+ String query = String.format("ASK {<%s> a <%s>}", propertyURI, OWL.DatatypeProperty.getURI());
+ boolean isDataProperty = executeAskQuery(query);
+ if(!isDataProperty && analyzeData){
+ query = String.format("ASK {?s <%s> ?o.FILTER(isLITERAL(?o))}", propertyURI);
+ isDataProperty = executeAskQuery(query);
+ }
+ return isDataProperty;
+ }
+
public int getIndividualsCount(NamedClass nc){
String query = String.format("SELECT (COUNT(?s) AS ?cnt) WHERE {" +
"?s a <%s>." +
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-04-15 20:52:45
|
Revision: 3922
http://sourceforge.net/p/dl-learner/code/3922
Author: lorenz_b
Date: 2013-04-15 20:52:41 +0000 (Mon, 15 Apr 2013)
Log Message:
-----------
Continued pattern learning algorithm. Added classes for remote ontology repositories and local datasets.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionRenamer.java
trunk/components-core/src/main/java/org/dllearner/kb/SparqlEndpointKS.java
trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLAxiomRenamerTest.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/kb/dataset/
trunk/components-core/src/main/java/org/dllearner/kb/dataset/AbstractOWLOntologyDataset.java
trunk/components-core/src/main/java/org/dllearner/kb/dataset/BioPortalDataset.java
trunk/components-core/src/main/java/org/dllearner/kb/dataset/OWLOntologyDataset.java
trunk/components-core/src/main/java/org/dllearner/kb/dataset/TONESDataset.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/
trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepository.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepositoryEntry.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepositoryManager.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/Data.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/OntologyAclEntry.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/OntologyBean.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/Success.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/UserAcl.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/UserEntry.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/
trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java
trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-04-12 10:57:03 UTC (rev 3921)
+++ trunk/components-core/pom.xml 2013-04-15 20:52:41 UTC (rev 3922)
@@ -281,6 +281,26 @@
<artifactId>simmetrics</artifactId>
<version>1.6.2</version>
</dependency>
+ <dependency>
+ <groupId>com.thoughtworks.xstream</groupId>
+ <artifactId>xstream</artifactId>
+ <version>1.4.3</version>
+ </dependency>
+ <dependency>
+ <groupId>xpp3</groupId>
+ <artifactId>xpp3_min</artifactId>
+ <version>1.1.4c</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.kxml</groupId>
+ <artifactId>kxml2-min</artifactId>
+ <version>2.3.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>com.google.guava</groupId>
+ <artifactId>guava</artifactId>
+ </dependency>
</dependencies>
<dependencyManagement>
<dependencies>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-04-12 10:57:03 UTC (rev 3921)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -1,55 +1,27 @@
package org.dllearner.algorithms.pattern;
-import java.util.ArrayList;
-import java.util.Arrays;
+import java.net.URI;
import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
import java.util.Queue;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
+import org.dllearner.kb.dataset.OWLOntologyDataset;
+import org.dllearner.kb.repository.OntologyRepository;
+import org.dllearner.kb.repository.OntologyRepositoryEntry;
import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.expression.OWLEntityChecker;
-import org.semanticweb.owlapi.expression.ParserException;
-import org.semanticweb.owlapi.io.ToStringRenderer;
-import org.semanticweb.owlapi.model.EntityType;
import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAxiom;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
-import org.semanticweb.owlapi.model.OWLDataProperty;
-import org.semanticweb.owlapi.model.OWLDatatype;
-import org.semanticweb.owlapi.model.OWLEntity;
-import org.semanticweb.owlapi.model.OWLNamedIndividual;
-import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
-import org.semanticweb.owlapi.model.OWLObjectUnionOf;
+import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
-import org.semanticweb.owlapi.reasoner.OWLReasoner;
-import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
-import org.semanticweb.owlapi.util.IRIShortFormProvider;
-import org.semanticweb.owlapi.util.OWLAxiomVisitorAdapter;
-import org.semanticweb.owlapi.util.OWLClassExpressionVisitorAdapter;
-import org.semanticweb.owlapi.util.SimpleIRIShortFormProvider;
-import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
-import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
-
-import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
+import com.google.common.collect.Multisets;
+
public class OWLAxiomPatternFinder {
private static Queue<String> classVarQueue = new LinkedList<String>();
@@ -69,133 +41,46 @@
}
};
+
+ private OntologyRepository repository;
+ private OWLOntologyManager manager;
+ private OWLDataFactory dataFactory;
- public OWLAxiomPatternFinder(OWLOntology ontology) {
- generalizeAxioms(ontology.getLogicalAxioms());
+ public OWLAxiomPatternFinder(OWLOntologyDataset dataset) {
+
}
- private void generalizeAxioms(Collection<? extends OWLAxiom> axioms){
- ManchesterOWLSyntaxOWLObjectRendererImpl renderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
- String NS = "http://dl-learner.org/pattern/";
- IRIShortFormProvider sfp = new SimpleIRIShortFormProvider();
-// renderer.setShortFormProvider(new FullIRIEntityShortFromProvider());
- for(OWLAxiom axiom : axioms){
- OWLAxiom nnfAxiom = axiom.getNNF();
- String renderedAxiom = renderer.render(nnfAxiom);
- final OWLDataFactory dataFactory = new OWLDataFactoryImpl();
- Map<OWLEntity, OWLEntity> map = new HashMap<OWLEntity, OWLEntity>();
- Queue<String> classVarQueue = new LinkedList<String>(this.classVarQueue);
- Queue<String> propertyVarQueue = new LinkedList<String>(this.propertyVarQueue);
- Queue<String> individualVarQueue = new LinkedList<String>(this.individualVarQueue);
- Queue<String> datatypeVarQueue = new LinkedList<String>(this.datatypeVarQueue);
- final Set<String> classNames = new HashSet<String>();
- final Set<String> objectPropertyNames = new HashSet<String>();
- final Set<String> dataPropertyNames = new HashSet<String>();
- final Set<String> individualNames = new HashSet<String>();
- final Set<String> datatypeNames = new HashSet<String>();
- for(OWLEntity entity : axiom.getSignature()){
- if(entity.isOWLClass()){
- if(entity.asOWLClass().isBuiltIn()){
-
- } else {
- OWLEntity newEntity = dataFactory.getOWLEntity(EntityType.CLASS, IRI.create(NS + classVarQueue.poll()));
- map.put(entity, newEntity);
- classNames.add(newEntity.toStringID());
- }
- } else if(entity.isOWLObjectProperty()){
- OWLEntity newEntity = dataFactory.getOWLEntity(EntityType.OBJECT_PROPERTY, IRI.create(NS + propertyVarQueue.poll()));
- map.put(entity, newEntity);
- objectPropertyNames.add(newEntity.toStringID());
- } else if(entity.isOWLDataProperty()){
- OWLEntity newEntity = dataFactory.getOWLEntity(EntityType.DATA_PROPERTY, IRI.create(NS + propertyVarQueue.poll()));
- map.put(entity, newEntity);
- dataPropertyNames.add(newEntity.toStringID());
- } else if(entity.isOWLNamedIndividual()){
- OWLEntity newEntity = dataFactory.getOWLEntity(EntityType.NAMED_INDIVIDUAL, IRI.create(NS + individualVarQueue.poll()));
- map.put(entity, newEntity);
- individualNames.add(newEntity.toStringID());
- } else if(entity.isOWLDatatype()){
-// OWLEntity newEntity = dataFactory.getOWLEntity(EntityType.DATATYPE, IRI.create(datatypeVarQueue.poll()));
- OWLEntity newEntity = dataFactory.getOWLEntity(EntityType.DATATYPE, IRI.create(sfp.getShortForm(entity.getIRI())));
-// OWLEntity newEntity = entity;
- map.put(entity, newEntity);
- datatypeNames.add(newEntity.toStringID());
+ public OWLAxiomPatternFinder(OntologyRepository repository) {
+ this.repository = repository;
+ manager = OWLManager.createOWLOntologyManager();
+ dataFactory = manager.getOWLDataFactory();
+ }
+
+ public void start(){
+ OWLAxiomRenamer renamer = new OWLAxiomRenamer(dataFactory);
+ Collection<OntologyRepositoryEntry> entries = repository.getEntries();
+ Multiset<OWLAxiom> multiset = HashMultiset.create();
+ for (OntologyRepositoryEntry entry : entries) {
+ try {
+ URI uri = entry.getPhysicalURI();
+ OWLOntology ontology = manager.loadOntology(IRI.create(uri));
+ for(OWLLogicalAxiom axiom : ontology.getLogicalAxioms()){
+ OWLAxiom renamedAxiom = renamer.rename(axiom);
+ multiset.add(renamedAxiom);
}
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
}
-// System.out.println(renderedAxiom);
- for (Entry<OWLEntity, OWLEntity> entry : map.entrySet()) {
- OWLEntity key = entry.getKey();
- OWLEntity value = entry.getValue();
- renderedAxiom = renderedAxiom.replaceAll("\\b" + sfp.getShortForm(key.getIRI()) + "\\b", value.toStringID());
+ for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(multiset).elementSet()) {
+ System.out.println(owlAxiom + ": " + multiset.count(owlAxiom));
}
- ManchesterOWLSyntaxEditorParser parser = new ManchesterOWLSyntaxEditorParser(dataFactory, renderedAxiom);
- parser.setOWLEntityChecker(new OWLEntityChecker() {
-
- @Override
- public OWLObjectProperty getOWLObjectProperty(String iri) {
- return objectPropertyNames.contains(iri) ? dataFactory.getOWLObjectProperty(IRI.create(iri)) : null;
- }
-
- @Override
- public OWLNamedIndividual getOWLIndividual(String iri) {
- return individualNames.contains(iri) ? dataFactory.getOWLNamedIndividual(IRI.create(iri)) : null;
- }
-
- @Override
- public OWLDatatype getOWLDatatype(String iri) {
- return datatypeNames.contains(iri) ? dataFactory.getOWLDatatype(IRI.create(iri)) : null;
- }
-
- @Override
- public OWLDataProperty getOWLDataProperty(String iri) {
- return dataPropertyNames.contains(iri) ? dataFactory.getOWLDataProperty(IRI.create(iri)) : null;
- }
-
- @Override
- public OWLClass getOWLClass(String iri) {
- if(iri.equals("Thing")){
- return dataFactory.getOWLThing();
- } else if(iri.equals("Nothing")){
- return dataFactory.getOWLNothing();
- } else {
- return classNames.contains(iri) ? dataFactory.getOWLClass(IRI.create(iri)) : null;
- }
- }
-
- @Override
- public OWLAnnotationProperty getOWLAnnotationProperty(String iri) {
- return null;
- }
- });
- try {
- OWLAxiom parsedAxiom = parser.parseAxiom();
- System.out.println(parsedAxiom);
- } catch (ParserException e) {
- e.printStackTrace();
- }
}
+ for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(multiset).elementSet()) {
+ System.out.println(owlAxiom + ": " + multiset.count(owlAxiom));
+ }
}
public static void main(String[] args) throws Exception {
- ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
- String ontologyURL = "http://protege.stanford.edu/plugins/owl/owl-library/koala.owl";
- OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- OWLDataFactory dataFactory = man.getOWLDataFactory();
- OWLOntology ontology = man.loadOntology(IRI.create(ontologyURL));
- OWLAxiomRenamer renamer = new OWLAxiomRenamer(dataFactory);
- Multiset<OWLAxiom> multiset = HashMultiset.create();
- for (OWLAxiom axiom : ontology.getLogicalAxioms()) {
- OWLAxiom renamedAxiom = renamer.rename(axiom);
- multiset.add(renamedAxiom);
-// System.out.println(axiom + "-->" + renamedAxiom);
- }
- for (OWLAxiom owlAxiom : multiset.elementSet()) {
- System.out.println(owlAxiom + ": " + multiset.count(owlAxiom));
- }
-
-
-// OWLAxiomPatternFinder pf = new OWLAxiomPatternFinder(ontology);
}
-
}
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 2013-04-12 10:57:03 UTC (rev 3921)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -38,6 +38,7 @@
import org.semanticweb.owlapi.model.OWLInverseFunctionalObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLInverseObjectPropertiesAxiom;
import org.semanticweb.owlapi.model.OWLIrreflexiveObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLNegativeDataPropertyAssertionAxiom;
import org.semanticweb.owlapi.model.OWLNegativeObjectPropertyAssertionAxiom;
import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
@@ -166,6 +167,13 @@
@Override
public void visit(OWLObjectPropertyAssertionAxiom axiom) {
+ OWLObjectPropertyExpression property = axiom.getProperty();
+ property = expressionRenamer.rename(property);
+ OWLIndividual subject = axiom.getSubject();
+ subject = expressionRenamer.rename(subject);
+ OWLIndividual object = axiom.getObject();
+ object = expressionRenamer.rename(object);
+ renamedAxiom = df.getOWLObjectPropertyAssertionAxiom(property, subject, object);
}
@Override
@@ -177,6 +185,11 @@
@Override
public void visit(OWLSubObjectPropertyOfAxiom axiom) {
+ OWLObjectPropertyExpression subProperty = axiom.getSubProperty();
+ subProperty = expressionRenamer.rename(subProperty);
+ OWLObjectPropertyExpression superProperty = axiom.getSuperProperty();
+ superProperty = expressionRenamer.rename(superProperty);
+ renamedAxiom = df.getOWLSubObjectPropertyOfAxiom(subProperty, superProperty);
}
@Override
@@ -231,6 +244,13 @@
@Override
public void visit(OWLDataPropertyAssertionAxiom axiom) {
+ OWLDataPropertyExpression property = axiom.getProperty();
+ property = expressionRenamer.rename(property);
+ OWLIndividual subject = axiom.getSubject();
+ subject = expressionRenamer.rename(subject);
+ OWLLiteral object = axiom.getObject();
+ object = expressionRenamer.rename(object);
+ renamedAxiom = df.getOWLDataPropertyAssertionAxiom(property, subject, object);
}
@Override
@@ -249,6 +269,11 @@
@Override
public void visit(OWLSubDataPropertyOfAxiom axiom) {
+ OWLDataPropertyExpression subProperty = axiom.getSubProperty();
+ subProperty = expressionRenamer.rename(subProperty);
+ OWLDataPropertyExpression superProperty = axiom.getSuperProperty();
+ superProperty = expressionRenamer.rename(superProperty);
+ renamedAxiom = df.getOWLSubDataPropertyOfAxiom(subProperty, superProperty);
}
@Override
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionRenamer.java 2013-04-12 10:57:03 UTC (rev 3921)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionRenamer.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -64,9 +64,9 @@
private static final String NS = "http://dl-learner.org/pattern/";
- private Queue<String> classVarQueue = new LinkedList<String>(Arrays.asList("A", "B", "C" , "D"));
- private Queue<String> propertyVarQueue = new LinkedList<String>(Arrays.asList("p", "q", "r" , "s"));
- private Queue<String> individualVarQueue = new LinkedList<String>(Arrays.asList("a", "b", "c" , "d"));
+ private Queue<String> classVarQueue = new LinkedList<String>(Arrays.asList("A", "B", "C" , "D", "E", "F", "G"));
+ private Queue<String> propertyVarQueue = new LinkedList<String>(Arrays.asList("p", "q", "r" , "s", "t"));
+ private Queue<String> individualVarQueue = new LinkedList<String>(Arrays.asList("a", "b", "c" , "d", "e", "f", "g"));
private OWLDataFactory df;
private Map<OWLEntity, OWLEntity> renaming;
private OWLObject renamedOWLObject;
@@ -101,6 +101,12 @@
return (OWLDataRange) renamedOWLObject;
}
+ public OWLLiteral rename(OWLLiteral lit){
+ renamedOWLObject = null;
+ renamedOWLObject = lit;
+ return (OWLLiteral) renamedOWLObject;
+ }
+
@Override
public void visit(OWLObjectIntersectionOf desc) {
List<OWLClassExpression> operands = desc.getOperandsAsList();
@@ -325,6 +331,12 @@
@Override
public void visit(OWLAnonymousIndividual ind) {
+ OWLEntity newEntity = renaming.get(ind);
+ if(newEntity == null){
+ newEntity = df.getOWLNamedIndividual(getIRI(individualVarQueue.poll()));
+// renaming.put(ind, newEntity);
+ }
+ renamedOWLObject = (OWLNamedIndividual)newEntity;
}
@Override
@@ -333,7 +345,13 @@
}
@Override
- public void visit(OWLDataOneOf arg0) {
+ public void visit(OWLDataOneOf desc) {
+ Set<OWLLiteral> literals = desc.getValues();
+ Set<OWLLiteral> renamedLiterals = new TreeSet<OWLLiteral>();
+ for (OWLLiteral lit : literals) {
+ renamedLiterals.add(rename(lit));
+ }
+ renamedOWLObject = df.getOWLDataOneOf(renamedLiterals);
}
@Override
Modified: trunk/components-core/src/main/java/org/dllearner/kb/SparqlEndpointKS.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/SparqlEndpointKS.java 2013-04-12 10:57:03 UTC (rev 3921)
+++ trunk/components-core/src/main/java/org/dllearner/kb/SparqlEndpointKS.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -28,6 +28,7 @@
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.config.ListStringEditor;
+import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SPARQLTasks;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.springframework.beans.propertyeditors.URLEditor;
@@ -44,6 +45,7 @@
public class SparqlEndpointKS implements KnowledgeSource {
private SparqlEndpoint endpoint;
+ private ExtractionDBCache cache;
private boolean supportsSPARQL_1_1 = false;
private boolean isRemote = true;
private boolean initialized = false;
@@ -64,9 +66,18 @@
}
public SparqlEndpointKS(SparqlEndpoint endpoint) {
+ this(endpoint, null);
+ }
+
+ public SparqlEndpointKS(SparqlEndpoint endpoint, ExtractionDBCache cache) {
this.endpoint = endpoint;
+ this.cache = cache;
}
+ public ExtractionDBCache getCache() {
+ return cache;
+ }
+
@Override
public void init() throws ComponentInitException {
if(!initialized){
Added: trunk/components-core/src/main/java/org/dllearner/kb/dataset/AbstractOWLOntologyDataset.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/dataset/AbstractOWLOntologyDataset.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/dataset/AbstractOWLOntologyDataset.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,342 @@
+package org.dllearner.kb.dataset;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
+
+import org.semanticweb.HermiT.Configuration;
+import org.semanticweb.HermiT.Reasoner;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.reasoner.ConsoleProgressMonitor;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.semanticweb.owlapi.reasoner.SimpleConfiguration;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.google.common.io.Files;
+
+public abstract class AbstractOWLOntologyDataset implements OWLOntologyDataset{
+
+ protected Collection<OWLOntology> ontologies = new TreeSet<OWLOntology>();
+ protected Collection<OWLOntology> correctOntologies = new TreeSet<OWLOntology>();
+ protected Collection<OWLOntology> incoherentOntologies = new TreeSet<OWLOntology>();
+ protected Collection<OWLOntology> inconsistentOntologies = new TreeSet<OWLOntology>();
+
+ protected String name;
+
+ protected File directory;
+ protected File correctSubdirectory;
+ protected File inconsistentSubdirectory;
+ protected File incoherentSubdirectory;
+ protected File errorSubdirectory;
+ protected File tooLargeSubdirectory;
+
+ protected OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance();
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+
+ protected Map<URL, String> ontologyURLs = new HashMap<URL, String>();
+
+ private final int nrOfThreads = 1;
+ private boolean analyze = false;
+
+ public AbstractOWLOntologyDataset(String name, boolean analyze) {
+ this.name = name;
+ this.analyze = analyze;
+ //create file structure
+ directory = new File(datasetDirectory, name);
+ directory.mkdirs();
+ correctSubdirectory = new File(directory, "correct");
+ correctSubdirectory.mkdirs();
+ incoherentSubdirectory = new File(directory, "incoherent");
+ incoherentSubdirectory.mkdirs();
+ inconsistentSubdirectory = new File(directory, "inconsistent");
+ inconsistentSubdirectory.mkdirs();
+ tooLargeSubdirectory = new File(directory, "too_large");
+ tooLargeSubdirectory.mkdirs();
+ errorSubdirectory = new File(directory, "error");
+ errorSubdirectory.mkdirs();
+ addOntologyURLs();
+ initialize();
+ }
+
+ public AbstractOWLOntologyDataset(String name) {
+ this(name, false);
+ }
+
+ private boolean analyzed(URL url){
+ String filename = getFilename(url);
+ for(File parent : Arrays.asList(tooLargeSubdirectory, correctSubdirectory, incoherentSubdirectory, inconsistentSubdirectory, errorSubdirectory)){
+ File file = new File(parent, filename);
+ if(file.exists()){
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private Set<String> load403Errors(){
+ Set<String> errors = new HashSet<String>();
+ try {
+ if(new File(directory, "403.txt").exists()){
+ errors = new HashSet<String>(Files.readLines(new File(directory, "403.txt"), Charset.defaultCharset()));
+ }
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ return errors;
+ }
+
+ private boolean analyzedDataset(){
+ return new File(directory + "/" + "analyzed").exists();
+ }
+
+ public void initialize(){
+ //check if dataset was already analyzed
+ boolean analyzed = analyzedDataset();
+ if(!analyzed){
+ Set<String> errors = load403Errors();
+ ExecutorService threadPool = Executors.newFixedThreadPool(nrOfThreads);
+ List<Entry<URL, String>> urlList = new ArrayList<java.util.Map.Entry<URL, String>>(ontologyURLs.entrySet());
+ Collections.shuffle(urlList);
+ for (java.util.Map.Entry<URL, String> entry : urlList) {
+ URL url = entry.getKey();
+ if(!errors.contains(url.toString()) && !analyzed(url)){
+ threadPool.submit(new OntologyLoadingTask(url));
+ }
+ }
+ threadPool.shutdown();
+ try {
+ threadPool.awaitTermination(100, TimeUnit.MINUTES);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+ try {
+ new File(directory + "/" + "analyzed").createNewFile();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ } else {
+
+ }
+ }
+
+ protected abstract void addOntologyURLs();
+
+ private void analyzeAndCategorizeOntology(OWLOntology ontology, String filename){
+ System.out.println("Analyzing ontology " + filename + "...");
+ OWLReasoner reasoner;
+ File from = new File(man.getOntologyDocumentIRI(ontology).toURI());
+ try {
+ Configuration conf = new Configuration();
+ conf.reasonerProgressMonitor = new ConsoleProgressMonitor();
+ conf.ignoreUnsupportedDatatypes = true;
+ reasoner = new Reasoner(conf, ontology);
+ int logicalAxiomCount = ontology.getLogicalAxiomCount();
+ boolean consistent = reasoner.isConsistent();
+ Set<OWLClass> unsatisfiableClasses = null;
+
+ if(consistent){
+ unsatisfiableClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ if(!unsatisfiableClasses.isEmpty()){
+ File to = new File(incoherentSubdirectory, filename);
+ Files.move(from, to);
+ } else {
+ File to = new File(correctSubdirectory, filename);
+ Files.move(from, to);
+ }
+ } else {
+ File to = new File(inconsistentSubdirectory, filename);
+ Files.move(from, to);
+ }
+ System.out.println(consistent + "\t" + logicalAxiomCount + "\t" + ((unsatisfiableClasses != null) ? unsatisfiableClasses.size() : "n/a"));
+ reasoner.dispose();
+ } catch (Exception e){
+ e.printStackTrace();
+ try {
+ reasoner = reasonerFactory.createNonBufferingReasoner(ontology, new SimpleConfiguration(new ConsoleProgressMonitor()));
+ int logicalAxiomCount = ontology.getLogicalAxiomCount();
+ boolean consistent = reasoner.isConsistent();
+ Set<OWLClass> unsatisfiableClasses = null;
+ if(consistent){
+ unsatisfiableClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
+ if(!unsatisfiableClasses.isEmpty()){
+ File to = new File(incoherentSubdirectory, filename);
+ Files.move(from, to);
+ } else {
+ File to = new File(correctSubdirectory, filename);
+ Files.move(from, to);
+ }
+ } else {
+ File to = new File(inconsistentSubdirectory, filename);
+ Files.move(from, to);
+ }
+ System.out.println(consistent + "\t" + logicalAxiomCount + "\t" + ((unsatisfiableClasses != null) ? unsatisfiableClasses.size() : "n/a"));
+ reasoner.dispose();
+ } catch (Exception e1){
+ File to = new File(errorSubdirectory, filename);
+ try {
+ Files.move(from, to);
+ } catch (IOException e2) {
+ e2.printStackTrace();
+ }
+ }
+ }
+ }
+
+ protected OWLOntology loadOWLOntology(URL url) {
+ OWLOntology ontology = loadFromLocal(url);
+ if(ontology == null){
+ File file = null;
+ try {
+ file = downloadFile(url);
+ if(file != null){
+ ontology = man.loadOntologyFromOntologyDocument(file);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ String filename = getFilename(url);
+ File to = new File(errorSubdirectory, filename);
+ try {
+ Files.move(file, to);
+ } catch (IOException e2) {
+ e2.printStackTrace();
+ }
+ }
+ }
+ return ontology;
+ }
+
+ private OWLOntology loadFromLocal(URL url){
+ String filename = getFilename(url);
+ for(File parent : Arrays.asList(directory)){
+ File file = new File(parent, filename);
+ if(file.exists()){
+ try {
+ OWLOntology ontology = man.loadOntologyFromOntologyDocument(file);
+ return ontology;
+ } catch(Exception e){
+ e.printStackTrace();
+ File to = new File(errorSubdirectory, filename);
+ try {
+ Files.move(file, to);
+ } catch (IOException e2) {
+ e2.printStackTrace();
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+ private String getFilename(URL url){
+ return ontologyURLs.get(url);
+// String filename = url.toString().substring(url.toString().lastIndexOf("/"));
+// return filename;
+ }
+
+ /**
+ * Download the file such that later on we can load it from the local file system.
+ */
+ protected File downloadFile(URL url){
+
+ String filename = getFilename(url);
+ File file = new File(directory + "/" + filename);
+ if(!file.exists()){
+ System.out.print("Downloading file...");
+ try {
+ InputStream is = url.openConnection().getInputStream();
+ OutputStream out = new FileOutputStream(file);
+ int read = 0;
+ byte[] bytes = new byte[1024];
+
+ while ((read = is.read(bytes)) != -1) {
+ out.write(bytes, 0, read);
+ }
+
+ is.close();
+ out.flush();
+ out.close();
+ System.out.println("done.");
+ return file;
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ add403Error(url);
+ }
+ }
+ return null;
+ }
+
+ private void add403Error(URL url){
+ try {
+ Files.append(url.toString() + "\n", new File(directory, "403.txt"), Charset.defaultCharset());
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ @Override
+ public Collection<OWLOntology> loadOntologies() {
+ return ontologies;
+ }
+
+ @Override
+ public Collection<OWLOntology> loadIncoherentOntologies() {
+ return incoherentOntologies;
+ }
+
+ @Override
+ public Collection<OWLOntology> loadInconsistentOntologies() {
+ return inconsistentOntologies;
+ }
+
+ class OntologyLoadingTask implements Runnable{
+
+ private URL url;
+
+ public OntologyLoadingTask(URL url) {
+ this.url = url;
+ }
+
+ @Override
+ public void run() {
+ System.out.println("Processing " + ontologyURLs.get(url));
+ OWLOntology ontology = loadOWLOntology(url);
+ if(ontology != null){
+ if(analyze){
+ analyzeAndCategorizeOntology(ontology, getFilename(url));
+ } else {
+ ontologies.add(ontology);
+ }
+ }
+ }
+
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/dataset/BioPortalDataset.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/dataset/BioPortalDataset.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/dataset/BioPortalDataset.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,34 @@
+package org.dllearner.kb.dataset;
+
+import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
+import java.net.URLEncoder;
+
+import org.dllearner.kb.repository.OntologyRepositoryEntry;
+import org.dllearner.kb.repository.bioportal.BioPortalRepository;
+
+public class BioPortalDataset extends AbstractOWLOntologyDataset{
+
+ private static final String name = "BioPortal";
+
+ public BioPortalDataset() {
+ super(name);
+ }
+
+ @Override
+ protected void addOntologyURLs() {
+ BioPortalRepository bioportal = new BioPortalRepository();
+ bioportal.initialize();
+ for (OntologyRepositoryEntry entry : bioportal.getEntries()) {
+ try {
+ String name = URLEncoder.encode(entry.getOntologyShortName(), "UTF-8");
+ super.ontologyURLs.put(entry.getPhysicalURI().toURL(), name);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (UnsupportedEncodingException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/dataset/OWLOntologyDataset.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/dataset/OWLOntologyDataset.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/dataset/OWLOntologyDataset.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,16 @@
+package org.dllearner.kb.dataset;
+
+import java.io.File;
+import java.util.Collection;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+
+public interface OWLOntologyDataset {
+
+ static File datasetDirectory = new File("dataset");
+
+ Collection<OWLOntology> loadOntologies();
+ Collection<OWLOntology> loadIncoherentOntologies();
+ Collection<OWLOntology> loadInconsistentOntologies();
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/dataset/TONESDataset.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/dataset/TONESDataset.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/dataset/TONESDataset.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,36 @@
+package org.dllearner.kb.dataset;
+
+import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
+import java.net.URLEncoder;
+
+import org.dllearner.kb.repository.OntologyRepositoryEntry;
+import org.dllearner.kb.repository.tones.TONESRepository;
+
+public class TONESDataset extends AbstractOWLOntologyDataset{
+
+ private static final String name = "TONES";
+
+ public TONESDataset() {
+ super(name);
+ }
+
+ @Override
+ protected void addOntologyURLs() {
+ TONESRepository tones = new TONESRepository();
+ tones.initialize();
+ for (OntologyRepositoryEntry entry : tones.getEntries()) {
+ try {
+ String name = URLEncoder.encode(entry.getOntologyShortName(), "UTF-8");
+ ontologyURLs.put(entry.getPhysicalURI().toURL(), name);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (UnsupportedEncodingException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepository.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepository.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepository.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,32 @@
+package org.dllearner.kb.repository;
+
+import java.util.Collection;
+import java.util.List;
+
+public interface OntologyRepository {
+
+ /**
+ * Gets the name of the repository
+ * @return A short name for the repository
+ */
+ String getName();
+
+ /**
+ * Gets a description of the location of the repository
+ * @return A human readable description of the repository location
+ */
+ String getLocation();
+
+
+ /**
+ * Ensures the repository is up to date
+ */
+ void refresh();
+
+ void initialize();
+
+ Collection<OntologyRepositoryEntry> getEntries();
+
+ List<Object> getMetaDataKeys();
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepositoryEntry.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepositoryEntry.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepositoryEntry.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,33 @@
+package org.dllearner.kb.repository;
+
+import java.net.URI;
+
+public interface OntologyRepositoryEntry {
+ /**
+ * Gets a short human readable name for this entry
+ * @return A short human readable name
+ */
+ String getOntologyShortName();
+
+
+ /**
+ * Gets the URI of the ontology that is described by this entry.
+ * @return The ontology URI.
+ */
+ URI getOntologyURI();
+
+
+ /**
+ * Gets the physical URI of the ontology that is described by this entry.
+ * @return The physical URI.
+ */
+ URI getPhysicalURI();
+
+
+ /**
+ * Gets associated metadata.
+ * @param key The key that describes the metadata
+ * @return The metadata or <code>null</code> if there is no metadata associated with this key.
+ */
+ String getMetaData(Object key);
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepositoryManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepositoryManager.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/OntologyRepositoryManager.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,32 @@
+package org.dllearner.kb.repository;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+
+public class OntologyRepositoryManager {
+ private static OntologyRepositoryManager instance;
+
+ private List<OntologyRepository> repositories;
+
+ private OntologyRepositoryManager() {
+ repositories = new ArrayList<OntologyRepository>();
+ }
+
+ public static synchronized OntologyRepositoryManager getManager() {
+ if(instance == null) {
+ instance = new OntologyRepositoryManager();
+ }
+ return instance;
+ }
+
+
+ public void addRepository(OntologyRepository repository) {
+ repositories.add(repository);
+ }
+
+ public Collection<OntologyRepository> getOntologyRepositories() {
+ return Collections.unmodifiableList(repositories);
+ }
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,166 @@
+package org.dllearner.kb.repository.bioportal;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.dllearner.kb.repository.OntologyRepository;
+import org.dllearner.kb.repository.OntologyRepositoryEntry;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import com.thoughtworks.xstream.XStream;
+import com.thoughtworks.xstream.io.xml.KXml2Driver;
+
+public class BioPortalRepository implements OntologyRepository {
+
+ private static final Logger log = Logger.getLogger(BioPortalRepository.class);
+
+ private String apiKey = "8fadfa2c-47de-4487-a1f5-b7af7378d693";
+ private String serviceURL = "http://rest.bioontology.org/bioportal/ontologies";
+
+ private List<OntologyRepositoryEntry> entries = new ArrayList<OntologyRepositoryEntry>();
+
+ @Override
+ public String getName() {
+ return "BioPortal";
+ }
+
+ @Override
+ public String getLocation() {
+ return "http://www.bioontology.org/";
+ }
+
+ @Override
+ public void initialize() {
+ refresh();
+ }
+
+ @Override
+ public void refresh() {
+ fillRepository();
+ }
+
+ private void fillRepository(){
+ XStream xstream = new XStream(new KXml2Driver());
+ xstream.alias("success", Success.class);
+ xstream.alias("data", Data.class);
+ xstream.alias("ontologyBean", OntologyBean.class);
+// xstream.alias("userAcl", UserAcl.class);
+ xstream.alias("userEntry", UserEntry.class);
+
+ InputStream is = null;
+ try {
+ is = getInputStream(new URL(withAPIKey(serviceURL)));
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ if (is == null) {
+ return;
+ }
+ Success success = (Success) xstream.fromXML(is);
+ if (success == null) {
+ return;
+ }
+ List<OntologyBean> beans = success.getData().getOntologyBeans();
+ entries = new ArrayList<OntologyRepositoryEntry>();
+ for(OntologyBean bean : beans){
+ URI physicalURI = URI.create(withAPIKey(serviceURL + "/download/" + bean.getId()));
+ String shortName = bean.getDisplayLabel();
+ boolean add = false;
+ for(String filename : bean.getFilenames()){
+ if(filename.endsWith(".owl") || filename.endsWith("rdf") || filename.endsWith(".obo") || filename.endsWith(".nt") || filename.endsWith("*.ttl")){
+ add = true;
+ break;
+ }
+ }
+ if(add){
+ entries.add(new RepositoryEntry(physicalURI, physicalURI, shortName));
+ }
+ }
+ log.info("Loaded " + entries.size() + " ontology entries from BioPortal.");
+ }
+
+ @Override
+ public Collection<OntologyRepositoryEntry> getEntries() {
+ return entries;
+ }
+
+ @Override
+ public List<Object> getMetaDataKeys() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ private InputStream getInputStream(URL url) throws IOException {
+ if (url.getProtocol().equals("http")) {
+ URLConnection conn;
+ conn = url.openConnection();
+ conn.setRequestProperty("Accept", "application/rdf+xml");
+ conn.addRequestProperty("Accept", "text/xml");
+ conn.addRequestProperty("Accept", "*/*");
+ return conn.getInputStream();
+ } else {
+ return url.openStream();
+ }
+ }
+
+ private String withAPIKey(String url){
+ return url + "?apikey=" + apiKey;
+ }
+
+ public static void main(String[] args) throws Exception{
+ Collection<OntologyRepositoryEntry> entries = new BioPortalRepository().getEntries();
+ for(OntologyRepositoryEntry entry : entries){
+ System.out.println("Loading " + entry.getOntologyShortName());
+ System.out.println("From " + entry.getPhysicalURI());
+ OWLOntology ont = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(entry.getPhysicalURI()));
+ System.out.println(ont.getAxiomCount());
+ }
+
+ }
+
+ private class RepositoryEntry implements OntologyRepositoryEntry {
+
+ private String shortName;
+
+ private URI ontologyURI;
+
+ private URI physicalURI;
+
+ public RepositoryEntry(URI ontologyURI, URI physicalURI, String shortName) {
+ this.ontologyURI = ontologyURI;
+ this.physicalURI = physicalURI;
+ this.shortName = shortName;
+ }
+
+
+ public String getOntologyShortName() {
+ return shortName;
+ }
+
+
+ public URI getOntologyURI() {
+ return ontologyURI;
+ }
+
+
+ public URI getPhysicalURI() {
+ return physicalURI;
+ }
+
+
+ public String getMetaData(Object key) {
+ return null;
+ }
+
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/Data.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/Data.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/Data.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,16 @@
+package org.dllearner.kb.repository.bioportal;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class Data {
+ List<OntologyBean> list = new ArrayList<OntologyBean>();
+
+ public void setOntologyBeans(List<OntologyBean> list) {
+ this.list = list;
+ }
+
+ public List<OntologyBean> getOntologyBeans() {
+ return list;
+ }
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/OntologyAclEntry.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/OntologyAclEntry.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/OntologyAclEntry.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,45 @@
+package org.dllearner.kb.repository.bioportal;
+
+public class OntologyAclEntry {
+ private String ontologyId;
+ private String isOwner;
+
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ return "OntologyAclEntry [isOwner=" + isOwner + ", ontologyId="
+ + ontologyId + "]";
+ }
+
+ /**
+ * @return the ontologyId
+ */
+ public String getOntologyId() {
+ return ontologyId;
+ }
+
+ /**
+ * @param ontologyId
+ * the ontologyId to set
+ */
+ public void setOntologyId(String ontologyId) {
+ this.ontologyId = ontologyId;
+ }
+
+ /**
+ * @return the isOwner
+ */
+ public String getIsOwner() {
+ return isOwner;
+ }
+
+ /**
+ * @param isOwner
+ * the isOwner to set
+ */
+ public void setIsOwner(String isOwner) {
+ this.isOwner = isOwner;
+ }
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/OntologyBean.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/OntologyBean.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/OntologyBean.java 2013-04-15 20:52:41 UTC (rev 3922)
@@ -0,0 +1,564 @@
+package org.dllearner.kb.repository.bioportal;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+/**
+ * Simplified version of the
+ * <code>org.ncbo.stanford.bean.concept.OntologyBean</code> class used to decode
+ * the "ontologyBean" element from a successful REST call to a BioPortal
+ * ontology service
+ *
+ * @author csnyulas
+ *
+ */
+public class OntologyBean implements Comparable<OntologyBean> {
+
+ public static final String DEFAULT_SYNONYM_SLOT = "http://www.w3.org/2004/02/skos/core#altLabel";
+ public static final String DEFAULT_PREFERRED_NAME_SLOT = "http://www.w3.org/2004/02/skos/core#prefLabel";
+ public static final String DEFAULT_DEFINITION_SLOT = "http://www.w3.org/2004/02/skos/core#definition";
+ public static final String DEFAULT_AUTHOR_SLOT = "http://purl.org/dc/elements/1.1/creator";
+
+ private Integer id;
+ private Integer ontologyId;
+ // virtual view id(s) on the virtual ontology
+ private List<Integer> virtualViewIds = new ArrayList<Integer>(0);
+ private Integer internalVersionNumber;
+ private List<Integer> userIds;
+ private String versionNumber;
+ private String versionStatus;
+ private Byte isRemote;
+ private Byte isReviewed;
+ private Integer statusId;
+ private Date dateCreated;
+ private Date dateReleased;
+ private String oboFoundryId;
+ private Byte isManual;
+ private String displayLabel;
+ private String description;
+ private String abbreviation;
+ private String format;
+ private String contactName;
+ private String contactEmail;
+ private String homepage;
+ private String documentation;
+ private String publication;
+ private String urn;
+ private String codingScheme;
+ private String targetTerminologies;
+ private Byte isFlat;
+ private Byte isFoundry;
+ private Byte isMetadataOnly;
+ private String synonymSlot;
+ private String preferredNameSlot;
+ private String documentationSlot;
+ private String authorSlot;
+ private String slotWithUniqueValue;
+ private Integer preferredMaximumSubclassLimit;
+ private String obsoleteParent;
+ private String naturalLanguage;
+ private String obsoleteProperty;
+ private String licenseInformation;
+
+ private String viewingRestriction;
+
+ private List<UserEntry> userAcl = new ArrayList<UserEntry>(0);
+
+ private boolean isView = false;
+
+ // category id(s)
+ private List<Integer> categoryIds = new ArrayList<Integer>(0);
+
+ // group id(s)
+ private List<Integer> groupIds = new ArrayList<Integer>(0);
+
+ // file name(s)
+ private List<String> filenames = new ArrayList<String>(0);
+
+ // source fileItem
+ // private FileItem fileItem;
+
+ // destination directory
+ private String filePath;
+
+ // Download location of ontology
+ private String downloadLocation;
+
+ // views on this ontology version
+ private List<Integer> hasViews = new ArrayList<Integer>(0);
+
+ // view specific properties
+ private List<Integer> viewOnOntologyVersionId = new ArrayList<Integer>(0);
+ private String viewDefinition;
+ private String viewDefinitionLanguage;
+ private String viewGenerationEngine;
+
+ @Override
+ public String toString() {
+ final int max = 80;
+ String viewDef = this.getViewDefinition();
+
+ if (viewDef != null && viewDef.length() > max) {
+ viewDef = viewDef.substring(0, max) + "...";
+ }
+
+ String name = isView ? "OntologyView " : "Ontology ";
+
+ return name + "{Id: " + this.getId() + ", Ontology Id: " + this.getOntologyId() + ", Virtual View Ids: "
+ + this.getVirtualViewIds() + ", Remote: " + this.getIsRemote() + ", Obo Foundry Id: "
+ + this.getOboFoundryId() + ", Internal Version Number: " + this.getInternalVersionNumber()
+ + ", Date Created: " + this.getDateCreated() + ", User Ids: " + this.getUserIds()
+ + ", Version Number: " + this.getVersionNumber() + ", Version Status: " + this.getVersionStatus()
+ + ", Display Label: " + this.getDisplayLabel() + ", Description: " + this.getDescription()
+ + ", Abbreviation: " + this.getAbbreviation() + ", Format: " + this.getFormat() + ", Contact Name: "
+ + this.getContactName() + ", Contact Email: " + this.getContactEmail() + ", Foundry: "
+ + this.getIsFoundry() + " Coding Scheme: " + this.getCodingScheme() + ", Target Terminologies: "
+ + this.getTargetTerminologies() + ", Synonym Slot: " + this.getSynonymSlot()
+ + ", Preferred Name Slot: " + this.getPreferredNameSlot() + ", View Definition: " + viewDef
+ + ", View Definition Language: " + this.getViewDefinitionLanguage() + ", View Generation Engine: "
+ + this.getViewGenerationEngine() + ", View on Ontology Versions: " + this.getViewOnOntologyVersionId()
+ + "}";
+ }
+
+ public Integer getId() {
+ return id;
+ }
+
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ public Integer getOntologyId() {
+ return ontologyId;
+ }
+
+ public void setOntologyId(Integer ontologyId) {
+ this.ontologyId = ontologyId;
+ }
+
+ public List<Integer> getVirtualViewIds() {
+ return virtualViewIds;
+ }
+
+ public void setVirtualViewIds(List<Integer> virtualViewIds) {
+ this.virtualViewIds = virtualViewIds;
+ }
+
+ public Integer getInternalVersionNumber() {
+ return internalVersionNumber;
+ }
+
+ public void setInternalVersionNumber(Integer internalVersionNumber) {
+ this.internalVersionNumber = internalVersionNumber;
+ }
+
+ public List<Integer> getUserIds() {
+ return userIds;
+ }
+
+ public void setUserIds(List<Integer> userIds) {
+ this.userIds = userIds;
+ }
+
+ public String getVersionNumber() {
+ return versionNumber;
+ }
+
+ public void setVersionNumber(String versionNumber) {
+ this.versionNumber = versionNumber;
+ }
+
+ public String getVersionStatus() {
+ return versionStatus;
+ }
+
+ public void setVersionStatus(String versionStatus) {
+ this.versionStatus = versionStatus;
+ }
+
+ public Byte getIsRemote() {
+ return isRemote;
+ }
+
+ public void setIsRemote(Byte isRemote) {
+ this.isRemote = isRemote;
+ }
+
+ public Byte getIsReviewed() {
+ return isReviewed;
+ }
+
+ public void setIsReviewed(Byte isReviewed) {
+ this.isReviewed = isReviewed;
+ }
+
+ public Integer getStatusId() {
+ return statusId;
+ }
+
+ public void setStatusId(Integer statusId) {
+ this.statusId = statusId;
+ }
+
+ public Date getDateCreated() {
+ return dateCreated;
+ }
+
+ public void setDateCreated(Date dateCreated) {
+ this.dateCreated = dateCreated;
+ }
+
+ public Date getDateReleased() {
+ return dateReleased;
+ }
+
+ public void setDateReleased(Date dateReleased) {
+ this.dateReleased = dateReleased;
+ }
+
+ public String getOboFoundryId() {
+ return oboFoundryId;
+ }
+
+ public void setOboFoundryId(String oboFoundryId) {
+ this.oboFoundryId = oboFoundryId;
+ }
+
+ public Byte getIsManual() {
+ return isManual;
+ }
+
+ public void setIsManual(Byte isManual) {
+ this.isManual = isManual;
+ }
+
+ public String getDisplayLabel() {
+ return displayLabel;
+ }
+
+ public void setDisplayLabel(String displayLabel) {
+ this.displayLabel = displayLabel;
+ }
+
+ public String getDescription() {
+ return description;
+ }
+
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ public String getAbbreviation() {
+ return abbreviation;
+ }
+
+ public void setAbbreviation(String abbreviation) {
+ this.abbreviation = abbreviation;
+ }
+
+ public String getFormat() {
+ return format;
+ }
+
+ public void setFormat(String format) {
+ this.format = format;
+ }
+
+ public String getContactName() {
+ return contactName;
+ }
+
+ public void setContactName(String contactName) {
+ this.contactName = contactName;
+ }
+
+ public String getContactEmail() {
+ return contactEmail;
+ }
+
+ public void setContactEmail(String contactEmail) {
+ this.contactEmail = contactEmail;
+ }
+
+ public String getHomepage() {
+ return homepage;
+ }
+
+ public void setHomepage(String homepage) {
+ this.homepage = homepage;
+ }
+
+ public String getDocumentation() {
+ return documentation;
+ }
+
+ public void setDocumentation(String documentation) {
+ this.documentation = documentation;
+ }
+
+ public String getPublication() {
+ return publication;
+ }
+
+ public void setPublication(String publication) {
+ this.publication = publication;
+ }
+
+ public String getUrn() {
+ return urn;
+ }
+
+ public void setUrn(String urn) {
+ this.urn = urn;
+ }
+
+ public String getCodingScheme() {
+ return codingScheme;
+ }
+
+ public void setCodingScheme(String codingScheme) {
+ this.codingScheme = codingScheme;
+ }
+
+ public String getTargetTerminologies() {
+ return targetTerminologies;
+ }
+
+ public void setTargetTerminologies(String targetTerminologies) {
+ this.targetTerminologies = targetTerminologies;
+ }
+
+ public Byte getIsFlat() {
+ return isFlat;
+ }
+
+ public void setIsFlat(Byte isFlat) {
+ this.isFlat = isFlat;
+ }
+
+ public Byte getIsFoundry() {
+ return isFoundry;
+ }
+
+ public void setIsFoundry(Byte isFoundry) {
+ this.isFoundry = isFoundry;
+ }
+
+ public Byte getIsMetadataOnly() {
+ return isMetadataOnly;
+ }
+
+ public void setIsMetadataOnly(Byte isMetadataOnly) {
+ this.isMetadataOnly = isMetadataOnly;
+ }
+
+ public String getSynonymSlot() {
+ return synonymSlot;
+ }
+
+ public void setSynonymSlot(String synonymSlot) {
+ this.synonymSlot = synonymSlot;
+ }
+
+ public String getPreferredNameSlot() {
+ return preferredNameSlot;
+ }
+
+ public void setPreferredNameSlot(String preferredNameSlot) {
+ this.preferredNameSlot = preferredNameSlot;
+ }
+
+ public String getDocumentationSlot() {
+ return documentationSlot;
+ }
+
+ public void setDocumentationSlot(String documentationSlot) {
+ this.documentationSlot = documentationSlot;
+ }
+
+ public String getAuthorSlot() {
+ return authorSlot;
+ }
+
+ public void setAuthorSlot(String authorSlot) {
+ this.authorSlot = authorSlot;
+ }
+
+ public String getSlotWithUniqueValue() {
+ return slotWithUniqueValue;
+ }
+
+ public void setSlotWithUniqueValue(String slotWithUniqueValue) {
+ this.slotWithUniqueValue = slotWithUniqueValue;
+ }
+
+ public Integer getPreferredMaximumSubclassLimit() {
+ return preferredMaximumSubclassLimit;
+ }
+
+ public void setPreferredMaximumSubclassLimit(Integer preferredMaximumSubclassLimit) {
+ this.preferredMaximumSubclassLimit = preferredMaximumSubclassLimit;
+ }
+
+ public boolean isView() {
+ return isView;
+ }
+
+ public void setView(boolean isView) {
+ this.isView = isView;
+ }
+
+ public List<Integer> getCategoryIds() {
+ return categoryIds;
+ }
+
+ public void setCategoryIds(List<Integer> categoryIds) {
+ this.categoryIds = categoryIds;
+ }
+
+ public List<Integer> getGroupIds() {
+ return groupIds;
+ }
+
+ public void setGroupIds(List<Integer> groupIds) {
+ this.groupIds = groupIds;
+ }
+
+ public List<String> getFilenames() {
+ return filenames;
+ }
+
+ public void setFilenames(List<String> filenames) {
+ this.filenames = filenames;
+ }
+
+ public String getFilePath() {
+ return filePath;
+ }
+
+ public void setFilePath(String filePath) {
+ this.filePath = filePath;
+ }
+
+ public List<Integer> getHasViews() {
+ return hasViews;
+ }
+
+ public void setHasViews(List<Integer> hasViews) {
+ this.hasViews = hasViews;
+ }
+
+ public List<Integer> getViewOnOntologyVersionId() {
+ return viewOnOntologyVersionId;
+ }
+
+ public void setViewOnOntologyVersionId(List<Integer> viewOnOntologyVersionId) {
+ this.viewOnOntologyVersionId = viewOnOntologyVersionId;
+ }
+
+ public String getViewDefinition() {
+ return viewDefinition;
+ }
+
+ public void setViewDefinition(String viewDefinition) {
+ this.viewDefinition = viewDefinition;
+ }
+
+ public String getViewDefinitionLanguage() {
+ return viewDefinitionLanguage;
+ }
+
+ public void setViewDefinitionLanguage(String viewDefinitionLanguage) {
+ this.viewDefinitionLanguage = viewDefinitionLanguage;
+ }
+
+ public String getViewGenerationEngine() {
+ return viewGenerationEngine;
+ }
+
+ public void setViewGenerationEngine(String viewGenerationEngine) {
+ this.viewGenerationEngine = viewGenerationEngine;
+ }
+
+ public static String getDefaultPreferredNameSlot() {
+ return DEFAULT_PREFERRED_NAME_SLOT;
+ }
+
+ public static String getDefaultDefinitionSlot() {
+ return DEFAULT_DEFINITION_SLOT;
+ }
+
+ public static String getDefaultAuthorSlot() {
+ return DEFAULT_AUTHOR_SLOT;
+ }
+
+ public String getDownloadLocation() {
+ return downloadLocation;
+ }
+
+ public void setDownloadLocation(String downloadLocation) {
+ this.downloadLocation = downloadLocation;
+ }
+
+ /**
+ * @return the userAcl
+ */
+ public List<UserEntry> getUserAcl() {
+ return userAcl;
+ }
+
+ /**
+ * @param userAcl
+ * the userAcl to set
+ */
+ public void setUserAcl(List<UserEntry> userAcl) {
+ this.userAcl = userAcl;
+ }
+
+ public String getViewingRestriction() {
+ return viewingRestriction;
+ }
+
+ public void setViewingRestriction(String viewingRestriction) {
+ this.viewingRestriction = viewingRestriction;
+ }
+
+ public String getObsoleteParent() {
+ return obsoleteParent;
+ }
+
+ public void setObsoleteParent(String obsoleteParent) {
+ this.obsoleteParent = obsoleteParent;
+ }
+
+ public String getNaturalLanguage() {
+ return naturalLanguage;
+ }
+
+ public void setNaturalLanguage(String naturalLanguage) {
+ this.naturalLanguage = naturalLanguage;
+ }
+
+ public String getObsoleteProperty() {
+ return obsoleteProperty;
+ }
+
+ public void setObsoleteProperty(String obsoleteProperty) {
+ this.obsoleteProperty = obsoleteProperty;
+ }
+
+ public String getLicenseInformation() {
+ return licenseInformation;
+ }
+
+ public void setLicenseInformation(String licenseInformation) {
+ this.licenseInformation = licenseInformation;
+ }
+
+ @Override
+ public int compareTo(OntologyBean o) {
+ return this.displayLabel.compareTo(o.getDisplayLabel());
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/Success.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/Success.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/biopo...
[truncated message content] |
|
From: <lor...@us...> - 2013-04-19 14:04:25
|
Revision: 3924
http://sourceforge.net/p/dl-learner/code/3924
Author: lorenz_b
Date: 2013-04-19 14:04:20 +0000 (Fri, 19 Apr 2013)
Log Message:
-----------
Added class expression to SPARQL rewriter.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionOrderingComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionRenamer.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLLiteralRenamer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLObjectComparator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternAxiomToSPARQLConverter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternExpressionToSPARQLConverter.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
trunk/components-core/src/main/resources/db_settings.ini.dist
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-04-15 20:53:29 UTC (rev 3923)
+++ trunk/components-core/pom.xml 2013-04-19 14:04:20 UTC (rev 3924)
@@ -112,13 +112,32 @@
</exclusion>
</exclusions>
</dependency>
+ <dependency>
+ <groupId>org.ini4j</groupId>
+ <artifactId>ini4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>mysql</groupId>
+ <artifactId>mysql-connector-java</artifactId>
+ </dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
- <version>3.4.4</version>
+ <version>3.4</version>
</dependency>
<dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-dlsyntax</artifactId>
+ <version>3.3</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-functional</artifactId>
+ <version>3.3</version>
+ </dependency>
+
+ <dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-reasoner</artifactId>
</dependency>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-04-15 20:53:29 UTC (rev 3923)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -1,22 +1,46 @@
package org.dllearner.algorithms.pattern;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringWriter;
import java.net.URI;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Statement;
import java.util.Collection;
import java.util.LinkedList;
import java.util.Queue;
+import java.util.prefs.Preferences;
+import org.coode.owlapi.functionalrenderer.OWLFunctionalSyntaxRenderer;
import org.dllearner.kb.dataset.OWLOntologyDataset;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.OntologyRepositoryEntry;
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.AbstractOWLRenderer;
+import org.semanticweb.owlapi.io.OWLObjectRenderer;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
import com.google.common.collect.Multisets;
@@ -45,6 +69,15 @@
private OntologyRepository repository;
private OWLOntologyManager manager;
private OWLDataFactory dataFactory;
+
+ private Connection conn;
+ private PreparedStatement selectOntologyIdPs;
+ private PreparedStatement insertOntologyPs;
+ private PreparedStatement selectPatternIdPs;
+ private PreparedStatement insertPatternIdPs;
+ private PreparedStatement insertOntologyPatternPs;
+
+ private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
public OWLAxiomPatternFinder(OWLOntologyDataset dataset) {
@@ -54,33 +87,228 @@
this.repository = repository;
manager = OWLManager.createOWLOntologyManager();
dataFactory = manager.getOWLDataFactory();
+
+ initDBConnection();
+ createTables();
+ try {
+ selectOntologyIdPs = conn.prepareStatement("SELECT id FROM Ontology WHERE url=?");
+ insertOntologyPs = conn.prepareStatement("INSERT INTO Ontology (url, iri, repository) VALUES(?,?,?)");
+ selectPatternIdPs = conn.prepareStatement("SELECT id FROM Pattern WHERE pattern=?");
+ insertPatternIdPs = conn.prepareStatement("INSERT INTO Pattern (pattern,pattern_pretty) VALUES(?,?)");
+ insertOntologyPatternPs = conn.prepareStatement("INSERT INTO Ontology_Pattern (ontology_id, pattern_id, occurrences) VALUES(?,?,?)");
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
}
- public void start(){
+ private String render(OWLAxiom axiom){
+ try {
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology ontology = man.createOntology();
+ man.addAxiom(ontology, axiom);
+ StringWriter sw = new StringWriter();
+ org.coode.owlapi.functionalrenderer.OWLObjectRenderer r = new org.coode.owlapi.functionalrenderer.OWLObjectRenderer(man, ontology, sw);
+ axiom.accept(r);
+ return sw.toString();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ private void initDBConnection() {
+ try {
+ InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini");
+ Preferences prefs = new IniPreferences(is);
+ 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);
+ } 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 createTables(){
+ try {
+ Statement statement = conn.createStatement();
+
+ statement.execute("CREATE TABLE IF NOT EXISTS Pattern ("
+ + "id MEDIUMINT NOT NULL AUTO_INCREMENT,"
+ + "pattern VARCHAR(2000) NOT NULL,"
+ + "pattern_pretty VARCHAR(2000) NOT NULL,"
+ + "PRIMARY KEY(id),"
+ + "INDEX(pattern)) DEFAULT CHARSET=utf8");
+
+ statement.execute("CREATE TABLE IF NOT EXISTS Ontology ("
+ + "id MEDIUMINT NOT NULL AUTO_INCREMENT,"
+ + "url VARCHAR(2000) NOT NULL,"
+ + "iri VARCHAR(2000) NOT NULL,"
+ + "repository VARCHAR(200) NOT NULL,"
+ + "PRIMARY KEY(id),"
+ + "INDEX(url)) DEFAULT CHARSET=utf8");
+
+ statement.execute("CREATE TABLE IF NOT EXISTS Ontology_Pattern ("
+ + "ontology_id MEDIUMINT NOT NULL,"
+ + "pattern_id MEDIUMINT NOT NULL,"
+ + "occurrences INTEGER(8) NOT NULL,"
+ + "FOREIGN KEY (ontology_id) REFERENCES Ontology(id),"
+ + "FOREIGN KEY (pattern_id) REFERENCES Pattern(id),"
+ + "PRIMARY KEY(ontology_id, pattern_id)) DEFAULT CHARSET=utf8");
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+
+
+ private int addPattern(OWLAxiom axiom){
+ String axiomString = render(axiom);
+ //check for existing entry
+ try {
+ selectPatternIdPs.setString(1, axiomString);
+ ResultSet rs = selectPatternIdPs.executeQuery();
+ if(rs.next()){
+ return rs.getInt(1);
+ }
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ //add pattern entry
+ try {
+ insertPatternIdPs.setString(1, axiomString);
+ insertPatternIdPs.setString(2, axiomRenderer.render(axiom));
+ insertPatternIdPs.execute();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ //get the auto generated ID
+ try {
+ selectPatternIdPs.setString(1, axiomString);
+ ResultSet rs = selectPatternIdPs.executeQuery();
+ if(rs.next()){
+ return rs.getInt(1);
+ }
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ return -1;
+ }
+
+ private boolean ontologyProcessed(URI uri){
+ //check if ontology was already processed
+ try {
+ selectOntologyIdPs.setString(1, uri.toString());
+ ResultSet rs = selectOntologyIdPs.executeQuery();
+ return rs.next();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ return false;
+ }
+
+ private int addOntology(URI physicalURI, OWLOntology ontology){
+ String url = physicalURI.toString();
+ String ontologyIRI = ontology.getOntologyID().getOntologyIRI().toString();
+ //check for existing entry
+ try {
+ selectOntologyIdPs.setString(1, url);
+ ResultSet rs = selectOntologyIdPs.executeQuery();
+ if(rs.next()){
+ return rs.getInt(1);
+ }
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ //add ontology entry
+ try {
+ insertOntologyPs.setString(1, url);
+ insertOntologyPs.setString(2, ontologyIRI);
+ insertOntologyPs.setString(3, repository.getName());
+ insertOntologyPs.execute();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ //get the auto generated ID
+ try {
+ selectOntologyIdPs.setString(1, url);
+ ResultSet rs = selectOntologyIdPs.executeQuery();
+ if(rs.next()){
+ return rs.getInt(1);
+ }
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ return -1;
+ }
+
+ private void addOntologyPatterns(URI physicalURI, OWLOntology ontology, Multiset<OWLAxiom> patterns){
+ int ontologyId = addOntology(physicalURI, ontology);
+ for (OWLAxiom pattern : patterns.elementSet()) {
+ try {
+ int patternId = addPattern(pattern);
+ int occurrences = patterns.count(pattern);
+ insertOntologyPatternPs.setInt(1, ontologyId);
+ insertOntologyPatternPs.setInt(2, patternId);
+ insertOntologyPatternPs.setInt(3, occurrences);
+ insertOntologyPatternPs.execute();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ public void start() {
OWLAxiomRenamer renamer = new OWLAxiomRenamer(dataFactory);
Collection<OntologyRepositoryEntry> entries = repository.getEntries();
- Multiset<OWLAxiom> multiset = HashMultiset.create();
+ Multiset<OWLAxiom> allAxiomPatterns = HashMultiset.create();
for (OntologyRepositoryEntry entry : entries) {
- try {
- URI uri = entry.getPhysicalURI();
- OWLOntology ontology = manager.loadOntology(IRI.create(uri));
- for(OWLLogicalAxiom axiom : ontology.getLogicalAxioms()){
- OWLAxiom renamedAxiom = renamer.rename(axiom);
- multiset.add(renamedAxiom);
+ URI uri = entry.getPhysicalURI();
+ if (!ontologyProcessed(uri)) {
+ System.out.println("Loading " + uri);
+ try {
+ OWLOntology ontology = manager.loadOntology(IRI.create(uri));
+ Multiset<OWLAxiom> axiomPatterns = HashMultiset.create();
+ for (OWLLogicalAxiom axiom : ontology.getLogicalAxioms()) {
+ OWLAxiom renamedAxiom = renamer.rename(axiom);
+ axiomPatterns.add(renamedAxiom);
+ }
+ allAxiomPatterns.addAll(axiomPatterns);
+ addOntologyPatterns(uri, ontology, axiomPatterns);
+ for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(allAxiomPatterns).elementSet()) {
+// System.out.println(owlAxiom + ": " + allAxiomPatterns.count(owlAxiom));
+ }
+ manager.removeOntology(ontology);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
}
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
}
- for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(multiset).elementSet()) {
- System.out.println(owlAxiom + ": " + multiset.count(owlAxiom));
- }
+
}
- for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(multiset).elementSet()) {
- System.out.println(owlAxiom + ": " + multiset.count(owlAxiom));
- }
}
public static void main(String[] args) throws Exception {
+ String ontologyURL = "ontologyURL";
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLDataFactory dataFactory = man.getOWLDataFactory();
+ OWLFunctionalDataPropertyAxiom axiom = dataFactory.getOWLFunctionalDataPropertyAxiom(dataFactory.getOWLDataProperty(IRI.create("http://ex.org/p")));
+ OWLOntology ontology = man.createOntology();
+ man.addAxiom(ontology, axiom);
+ StringWriter sw = new StringWriter();
+ org.coode.owlapi.functionalrenderer.OWLObjectRenderer r = new org.coode.owlapi.functionalrenderer.OWLObjectRenderer(man, ontology, sw);
+ axiom.accept(r);
+ System.out.println(sw.toString());
}
}
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 2013-04-15 20:53:29 UTC (rev 3923)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -2,8 +2,10 @@
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.TreeSet;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
@@ -12,6 +14,7 @@
import org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLAxiomVisitor;
+import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
@@ -108,14 +111,26 @@
@Override
public void visit(OWLAsymmetricObjectPropertyAxiom axiom) {
+ OWLObjectPropertyExpression property = axiom.getProperty();
+ property = expressionRenamer.rename(property);
+ renamedAxiom = df.getOWLAsymmetricObjectPropertyAxiom(property);
}
@Override
public void visit(OWLReflexiveObjectPropertyAxiom axiom) {
+ OWLObjectPropertyExpression property = axiom.getProperty();
+ property = expressionRenamer.rename(property);
+ renamedAxiom = df.getOWLReflexiveObjectPropertyAxiom(property);
}
@Override
public void visit(OWLDisjointClassesAxiom axiom) {
+ Set<OWLClassExpression> classExpressions = axiom.getClassExpressions();
+ Set<OWLClassExpression> renamedClassExpressions = new HashSet<OWLClassExpression>();
+ for (OWLClassExpression classExpression : classExpressions) {
+ renamedClassExpressions.add(expressionRenamer.rename(classExpression));
+ }
+ renamedAxiom = df.getOWLDisjointClassesAxiom(renamedClassExpressions);
}
@Override
@@ -138,22 +153,46 @@
@Override
public void visit(OWLEquivalentObjectPropertiesAxiom axiom) {
+ Set<OWLObjectPropertyExpression> properties = axiom.getProperties();
+ Set<OWLObjectPropertyExpression> renamedProperties = new HashSet<OWLObjectPropertyExpression>();
+ for (OWLObjectPropertyExpression property : properties) {
+ renamedProperties.add(expressionRenamer.rename(property));
+ }
+ renamedAxiom = df.getOWLEquivalentObjectPropertiesAxiom(renamedProperties);
}
@Override
public void visit(OWLNegativeDataPropertyAssertionAxiom axiom) {
+// axiom.
}
@Override
public void visit(OWLDifferentIndividualsAxiom axiom) {
+ Set<OWLIndividual> renamedIndividuals = new HashSet<OWLIndividual>();
+ for(OWLIndividual ind : axiom.getIndividuals()){
+ renamedIndividuals.add(expressionRenamer.rename(ind));
+ }
+ renamedAxiom = df.getOWLDifferentIndividualsAxiom(renamedIndividuals);
}
@Override
public void visit(OWLDisjointDataPropertiesAxiom axiom) {
+ Set<OWLDataPropertyExpression> properties = axiom.getProperties();
+ Set<OWLDataPropertyExpression> renamedProperties = new HashSet<OWLDataPropertyExpression>();
+ for (OWLDataPropertyExpression property : properties) {
+ renamedProperties.add(expressionRenamer.rename(property));
+ }
+ renamedAxiom = df.getOWLDisjointDataPropertiesAxiom(renamedProperties);
}
@Override
public void visit(OWLDisjointObjectPropertiesAxiom axiom) {
+ Set<OWLObjectPropertyExpression> properties = axiom.getProperties();
+ Set<OWLObjectPropertyExpression> renamedProperties = new HashSet<OWLObjectPropertyExpression>();
+ for (OWLObjectPropertyExpression property : properties) {
+ renamedProperties.add(expressionRenamer.rename(property));
+ }
+ renamedAxiom = df.getOWLDisjointObjectPropertiesAxiom(renamedProperties);
}
@Override
@@ -194,6 +233,14 @@
@Override
public void visit(OWLDisjointUnionAxiom axiom) {
+ OWLClass cls = axiom.getOWLClass();
+ cls = expressionRenamer.rename(cls).asOWLClass();
+ Set<OWLClassExpression> classExpressions = axiom.getClassExpressions();
+ Set<OWLClassExpression> renamedClassExpressions = new HashSet<OWLClassExpression>();
+ for (OWLClassExpression classExpression : classExpressions) {
+ renamedClassExpressions.add(expressionRenamer.rename(classExpression));
+ }
+ renamedAxiom = df.getOWLDisjointUnionAxiom(cls, renamedClassExpressions);
}
@Override
@@ -221,6 +268,12 @@
@Override
public void visit(OWLEquivalentDataPropertiesAxiom axiom) {
+ Set<OWLDataPropertyExpression> properties = axiom.getProperties();
+ Set<OWLDataPropertyExpression> renamedProperties = new HashSet<OWLDataPropertyExpression>();
+ for (OWLDataPropertyExpression property : properties) {
+ renamedProperties.add(expressionRenamer.rename(property));
+ }
+ renamedAxiom = df.getOWLEquivalentDataPropertiesAxiom(renamedProperties);
}
@Override
@@ -278,10 +331,18 @@
@Override
public void visit(OWLInverseFunctionalObjectPropertyAxiom axiom) {
+ OWLObjectPropertyExpression property = axiom.getProperty();
+ property = expressionRenamer.rename(property);
+ renamedAxiom = df.getOWLInverseFunctionalObjectPropertyAxiom(property);
}
@Override
public void visit(OWLSameIndividualAxiom axiom) {
+ Set<OWLIndividual> renamedIndividuals = new HashSet<OWLIndividual>();
+ for(OWLIndividual ind : axiom.getIndividuals()){
+ renamedIndividuals.add(expressionRenamer.rename(ind));
+ }
+ renamedAxiom = df.getOWLSameIndividualAxiom(renamedIndividuals);
}
@Override
@@ -290,6 +351,11 @@
@Override
public void visit(OWLInverseObjectPropertiesAxiom axiom) {
+ OWLObjectPropertyExpression firstProperty = axiom.getFirstProperty();
+ firstProperty = expressionRenamer.rename(firstProperty);
+ OWLObjectPropertyExpression secondProperty = axiom.getSecondProperty();
+ secondProperty = expressionRenamer.rename(secondProperty);
+ renamedAxiom = df.getOWLInverseObjectPropertiesAxiom(firstProperty, secondProperty);
}
@Override
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionOrderingComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionOrderingComparator.java 2013-04-15 20:53:29 UTC (rev 3923)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionOrderingComparator.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -5,6 +5,7 @@
import java.util.List;
import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.util.OWLObjectTypeIndexProvider;
import uk.ac.manchester.cs.owl.owlapi.OWLClassExpressionImpl;
import uk.ac.manchester.cs.owl.owlapi.OWLClassImpl;
@@ -32,6 +33,8 @@
OWLObjectMaxCardinalityImpl.class,
OWLObjectExactCardinalityImpl.class
);
+
+ private final OWLObjectTypeIndexProvider indexProvider = new OWLObjectTypeIndexProvider();
@Override
public int compare(OWLClassExpression o1, OWLClassExpression o2) {
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionRenamer.java 2013-04-15 20:53:29 UTC (rev 3923)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLClassExpressionRenamer.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -1,10 +1,6 @@
package org.dllearner.algorithms.pattern;
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.Arrays;
+import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
@@ -58,23 +54,46 @@
import org.semanticweb.owlapi.model.OWLObjectUnionOf;
import org.semanticweb.owlapi.model.OWLPropertyExpression;
import org.semanticweb.owlapi.model.OWLPropertyExpressionVisitor;
-import org.semanticweb.owlapi.util.OWLClassExpressionVisitorAdapter;
public class OWLClassExpressionRenamer implements OWLClassExpressionVisitor, OWLPropertyExpressionVisitor, OWLIndividualVisitor, OWLDataRangeVisitor {
private static final String NS = "http://dl-learner.org/pattern/";
- private Queue<String> classVarQueue = new LinkedList<String>(Arrays.asList("A", "B", "C" , "D", "E", "F", "G"));
- private Queue<String> propertyVarQueue = new LinkedList<String>(Arrays.asList("p", "q", "r" , "s", "t"));
- private Queue<String> individualVarQueue = new LinkedList<String>(Arrays.asList("a", "b", "c" , "d", "e", "f", "g"));
private OWLDataFactory df;
private Map<OWLEntity, OWLEntity> renaming;
private OWLObject renamedOWLObject;
- private OWLClassExpressionOrderingComparator comparator = new OWLClassExpressionOrderingComparator();
+// private OWLClassExpressionOrderingComparator comparator = new OWLClassExpressionOrderingComparator();
+ private OWLObjectComparator comparator = new OWLObjectComparator();
+ private Queue<String> classVarQueue = new LinkedList<String>();
+ private Queue<String> propertyVarQueue = new LinkedList<String>();
+ private Queue<String> individualVarQueue = new LinkedList<String>();
+ private OWLLiteralRenamer literalRenamer;
+
+ private boolean normalizeCardinalities = true;
+ private boolean normalizeHasValue = true;
+ private boolean normalizeOneOf = true;
+
public OWLClassExpressionRenamer(OWLDataFactory df, Map<OWLEntity, OWLEntity> renaming) {
this.df = df;
this.renaming = renaming;
+
+ literalRenamer = new OWLLiteralRenamer(df);
+
+ for(int i = 65; i <= 90; i++){
+ classVarQueue.add(String.valueOf((char)i));
+ }
+ for(int j = 2; j <=5; j++){
+ for(int i = 65; i <= 90; i++){
+ classVarQueue.add(String.valueOf((char)i) + "_" + j);
+ }
+ }
+ for(int i = 97; i <= 111; i++){
+ individualVarQueue.add(String.valueOf((char)i));
+ }
+ for(int i = 112; i <= 122; i++){
+ propertyVarQueue.add(String.valueOf((char)i));
+ }
}
public OWLClassExpression rename(OWLClassExpression expr){
@@ -103,7 +122,7 @@
public OWLLiteral rename(OWLLiteral lit){
renamedOWLObject = null;
- renamedOWLObject = lit;
+ renamedOWLObject = literalRenamer.rename(lit);
return (OWLLiteral) renamedOWLObject;
}
@@ -134,6 +153,7 @@
OWLDataPropertyExpression property = desc.getProperty();
property = rename(property);
OWLLiteral value = desc.getValue();
+ value = rename(value);
renamedOWLObject = df.getOWLDataHasValue(property, value);
}
@@ -178,6 +198,9 @@
OWLClassExpression filler = desc.getFiller();
filler = rename(filler);
int cardinality = desc.getCardinality();
+ if(normalizeCardinalities){
+ cardinality = 1;
+ }
renamedOWLObject = df.getOWLObjectMinCardinality(cardinality, property, filler);
}
@@ -188,6 +211,9 @@
OWLClassExpression filler = desc.getFiller();
filler = rename(filler);
int cardinality = desc.getCardinality();
+ if(normalizeCardinalities){
+ cardinality = 1;
+ }
renamedOWLObject = df.getOWLObjectExactCardinality(cardinality, property, filler);
}
@@ -198,6 +224,9 @@
OWLClassExpression filler = desc.getFiller();
filler = rename(filler);
int cardinality = desc.getCardinality();
+ if(normalizeCardinalities){
+ cardinality = 1;
+ }
renamedOWLObject = df.getOWLObjectMaxCardinality(cardinality, property, filler);
}
@@ -243,6 +272,9 @@
OWLDataRange filler = desc.getFiller();
filler = rename(filler);
int cardinality = desc.getCardinality();
+ if(normalizeCardinalities){
+ cardinality = 1;
+ }
renamedOWLObject = df.getOWLDataMinCardinality(cardinality, property, filler);
}
@@ -253,6 +285,9 @@
OWLDataRange filler = desc.getFiller();
filler = rename(filler);
int cardinality = desc.getCardinality();
+ if(normalizeCardinalities){
+ cardinality = 1;
+ }
renamedOWLObject = df.getOWLDataExactCardinality(cardinality, property, filler);
}
@@ -263,6 +298,9 @@
OWLDataRange filler = desc.getFiller();
filler = rename(filler);
int cardinality = desc.getCardinality();
+ if(normalizeCardinalities){
+ cardinality = 1;
+ }
renamedOWLObject = df.getOWLDataMaxCardinality(cardinality, property, filler);
}
@@ -355,19 +393,37 @@
}
@Override
- public void visit(OWLDataComplementOf arg0) {
+ public void visit(OWLDataComplementOf desc) {
+ OWLDataRange dataRange = desc.getDataRange();
+ dataRange = rename(dataRange);
+ renamedOWLObject = df.getOWLDataComplementOf(dataRange);
}
@Override
- public void visit(OWLDataIntersectionOf arg0) {
+ public void visit(OWLDataIntersectionOf desc) {
+ List<OWLDataRange> operands = new ArrayList<OWLDataRange>(desc.getOperands());
+ Collections.sort(operands, comparator);
+ SortedSet<OWLDataRange> renamedOperands = new TreeSet<OWLDataRange>(comparator);
+ for(OWLDataRange expr : operands){
+ renamedOperands.add(rename(expr));
+ }
+ renamedOWLObject = df.getOWLDataIntersectionOf(renamedOperands);
}
@Override
- public void visit(OWLDataUnionOf arg0) {
+ public void visit(OWLDataUnionOf desc) {
+ List<OWLDataRange> operands = new ArrayList<OWLDataRange>(desc.getOperands());
+ Collections.sort(operands, comparator);
+ SortedSet<OWLDataRange> renamedOperands = new TreeSet<OWLDataRange>(comparator);
+ for(OWLDataRange expr : operands){
+ renamedOperands.add(rename(expr));
+ }
+ renamedOWLObject = df.getOWLDataUnionOf(renamedOperands);
}
@Override
- public void visit(OWLDatatypeRestriction arg0) {
+ public void visit(OWLDatatypeRestriction desc) {
+ renamedOWLObject = desc;
}
}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLLiteralRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLLiteralRenamer.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLLiteralRenamer.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -0,0 +1,44 @@
+package org.dllearner.algorithms.pattern;
+
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDatatype;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+
+public class OWLLiteralRenamer {
+
+ private OWLDataFactory dataFactory;
+
+ public OWLLiteralRenamer(OWLDataFactory dataFactory) {
+ this.dataFactory = dataFactory;
+ }
+
+ public OWLLiteral rename(OWLLiteral literal){
+ OWLLiteral renamedLiteral = literal;
+ OWLDatatype datatype = literal.getDatatype();
+ if(datatype.isRDFPlainLiteral()){
+ if(literal.hasLang()){
+ renamedLiteral = dataFactory.getOWLLiteral("plain", literal.getLang());
+ } else {
+ renamedLiteral = dataFactory.getOWLLiteral("plain");
+ }
+ } else {
+ if(datatype.getIRI().equals(OWL2Datatype.XSD_STRING.getIRI())){
+ renamedLiteral = dataFactory.getOWLLiteral("string", datatype);
+ } else if(datatype.getIRI().equals(OWL2Datatype.XSD_DOUBLE.getIRI()) ||
+ datatype.getIRI().equals(OWL2Datatype.XSD_DECIMAL.getIRI()) ||
+ datatype.getIRI().equals(OWL2Datatype.XSD_FLOAT.getIRI())){
+ renamedLiteral = dataFactory.getOWLLiteral("1.0", datatype);
+ } else if(datatype.getIRI().equals(OWL2Datatype.XSD_INT.getIRI()) ||
+ datatype.getIRI().equals(OWL2Datatype.XSD_INTEGER.getIRI()) ||
+ datatype.getIRI().equals(OWL2Datatype.XSD_LONG.getIRI()) ||
+ datatype.getIRI().equals(OWL2Datatype.XSD_BYTE.getIRI()) ||
+ datatype.getIRI().equals(OWL2Datatype.XSD_SHORT.getIRI())){
+ renamedLiteral = dataFactory.getOWLLiteral("1", datatype);
+ }
+ }
+ renamedLiteral = dataFactory.getOWLLiteral("", OWL2Datatype.RDF_PLAIN_LITERAL);
+ return renamedLiteral;
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLObjectComparator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLObjectComparator.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLObjectComparator.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -0,0 +1,21 @@
+package org.dllearner.algorithms.pattern;
+
+import java.util.Comparator;
+
+import org.semanticweb.owlapi.model.OWLObject;
+import org.semanticweb.owlapi.util.OWLObjectTypeIndexProvider;
+
+public class OWLObjectComparator implements Comparator<OWLObject> {
+
+ private final OWLObjectTypeIndexProvider indexProvider = new OWLObjectTypeIndexProvider();
+
+ @Override
+ public int compare(OWLObject o1, OWLObject o2) {
+ int diff = indexProvider.getTypeIndex(o1) - indexProvider.getTypeIndex(o2);
+ if(diff == 0){
+ return o1.compareTo(o2);
+ } else {
+ return diff;
+ }
+ }
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternAxiomToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternAxiomToSPARQLConverter.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternAxiomToSPARQLConverter.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -0,0 +1,286 @@
+package org.dllearner.algorithms.pattern;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLAnnotationPropertyDomainAxiom;
+import org.semanticweb.owlapi.model.OWLAnnotationPropertyRangeAxiom;
+import org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLAxiomVisitor;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLDataPropertyDomainAxiom;
+import org.semanticweb.owlapi.model.OWLDataPropertyRangeAxiom;
+import org.semanticweb.owlapi.model.OWLDatatypeDefinitionAxiom;
+import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
+import org.semanticweb.owlapi.model.OWLDifferentIndividualsAxiom;
+import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
+import org.semanticweb.owlapi.model.OWLDisjointDataPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLDisjointObjectPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLDisjointUnionAxiom;
+import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLEquivalentDataPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLEquivalentObjectPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLHasKeyAxiom;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLInverseFunctionalObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLInverseObjectPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLIrreflexiveObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLNegativeDataPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLNegativeObjectPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLObjectPropertyDomainAxiom;
+import org.semanticweb.owlapi.model.OWLObjectPropertyRangeAxiom;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLSameIndividualAxiom;
+import org.semanticweb.owlapi.model.OWLSubAnnotationPropertyOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubDataPropertyOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom;
+import org.semanticweb.owlapi.model.OWLSymmetricObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.PrefixManager;
+import org.semanticweb.owlapi.model.SWRLRule;
+import org.semanticweb.owlapi.util.DefaultPrefixManager;
+
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.Syntax;
+
+public class PatternAxiomToSPARQLConverter implements OWLAxiomVisitor {
+
+ private String root = "?x";
+ private PatternExpressionToSPARQLConverter expressionConverter;
+ private String sparql;
+
+ public PatternAxiomToSPARQLConverter() {
+ }
+
+ public Query convert(OWLAxiom axiom) {
+ expressionConverter = new PatternExpressionToSPARQLConverter();
+
+ sparql = "SELECT " + root + " WHERE {\n";
+ axiom.accept(this);
+ sparql += "}";
+
+ return QueryFactory.create(sparql, Syntax.syntaxARQ);
+ }
+
+ @Override
+ public void visit(OWLAnnotationAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubAnnotationPropertyOfAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLAnnotationPropertyDomainAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLAnnotationPropertyRangeAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDeclarationAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubClassOfAxiom axiom) {
+ OWLClassExpression subClass = axiom.getSubClass();
+ sparql += expressionConverter.convert(root, subClass);
+ OWLClassExpression superClass = axiom.getSuperClass();
+ sparql += expressionConverter.convert(root, superClass);
+ }
+
+ @Override
+ public void visit(OWLNegativeObjectPropertyAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLAsymmetricObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLReflexiveObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDisjointClassesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDataPropertyDomainAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLObjectPropertyDomainAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLEquivalentObjectPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLNegativeDataPropertyAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDifferentIndividualsAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDisjointDataPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDisjointObjectPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLObjectPropertyRangeAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLObjectPropertyAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLFunctionalObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubObjectPropertyOfAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDisjointUnionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSymmetricObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDataPropertyRangeAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLFunctionalDataPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLEquivalentDataPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLClassAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLEquivalentClassesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDataPropertyAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLTransitiveObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLIrreflexiveObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubDataPropertyOfAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLInverseFunctionalObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSameIndividualAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubPropertyChainOfAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLInverseObjectPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLHasKeyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDatatypeDefinitionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(SWRLRule axiom) {
+ }
+
+ public static void main(String[] args) throws Exception {
+ ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
+ PatternAxiomToSPARQLConverter converter = new PatternAxiomToSPARQLConverter();
+
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLDataFactory df = man.getOWLDataFactory();
+ PrefixManager pm = new DefaultPrefixManager("http://examples.org/ontology#");
+
+ OWLClass clsA = df.getOWLClass("A", pm);
+ OWLClass clsB = df.getOWLClass("B", pm);
+ OWLClass clsC = df.getOWLClass("C", pm);
+
+ OWLObjectProperty propR = df.getOWLObjectProperty("r", pm);
+ OWLObjectProperty propS = df.getOWLObjectProperty("s", pm);
+
+ OWLIndividual indA = df.getOWLNamedIndividual("a", pm);
+ OWLIndividual indB = df.getOWLNamedIndividual("b", pm);
+
+ OWLAxiom axiom = df.getOWLSubClassOfAxiom(
+ clsA,
+ clsB);
+ Query query = converter.convert(axiom);
+ System.out.println(axiom + "\n" + query);
+
+ axiom = df.getOWLSubClassOfAxiom(
+ clsA,
+ df.getOWLObjectSomeValuesFrom(propR, clsB));
+ query = converter.convert(axiom);
+ System.out.println(axiom + "\n" + query);
+
+ axiom = df.getOWLSubClassOfAxiom(
+ clsA,
+ df.getOWLObjectIntersectionOf(
+ df.getOWLObjectSomeValuesFrom(propR, clsB),
+ clsB));
+ query = converter.convert(axiom);
+ System.out.println(axiom + "\n" + query);
+
+ axiom = df.getOWLSubClassOfAxiom(
+ clsA,
+ df.getOWLObjectAllValuesFrom(propR, clsB));
+ query = converter.convert(axiom);
+ System.out.println(axiom + "\n" + query);
+
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternExpressionToSPARQLConverter.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternExpressionToSPARQLConverter.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -0,0 +1,207 @@
+package org.dllearner.algorithms.pattern;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.Stack;
+
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLClassExpressionVisitor;
+import org.semanticweb.owlapi.model.OWLDataAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLDataExactCardinality;
+import org.semanticweb.owlapi.model.OWLDataHasValue;
+import org.semanticweb.owlapi.model.OWLDataMaxCardinality;
+import org.semanticweb.owlapi.model.OWLDataMinCardinality;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLEntity;
+import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectComplementOf;
+import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
+import org.semanticweb.owlapi.model.OWLObjectHasSelf;
+import org.semanticweb.owlapi.model.OWLObjectHasValue;
+import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
+import org.semanticweb.owlapi.model.OWLObjectInverseOf;
+import org.semanticweb.owlapi.model.OWLObjectMaxCardinality;
+import org.semanticweb.owlapi.model.OWLObjectMinCardinality;
+import org.semanticweb.owlapi.model.OWLObjectOneOf;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
+import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectUnionOf;
+import org.semanticweb.owlapi.model.OWLPropertyExpressionVisitor;
+
+public class PatternExpressionToSPARQLConverter implements OWLClassExpressionVisitor, OWLPropertyExpressionVisitor{
+
+ private String sparql = "";
+ private Stack<String> variables = new Stack<String>();
+ private Map<OWLEntity, String> variablesMapping;
+
+ private int classCnt = 0;
+ private int propCnt = 0;
+ private int indCnt = 0;
+
+ public PatternExpressionToSPARQLConverter() {
+ variablesMapping = new HashMap<OWLEntity, String>();
+ }
+
+ public String convert(String root, OWLClassExpression expr){
+ sparql = "";
+ variables.push(root);
+ expr.accept(this);
+ return sparql;
+ }
+
+ private String getVariable(OWLEntity entity){
+ String var = variablesMapping.get(entity);
+ if(var == null){
+ if(entity.isOWLClass()){
+ var = "?cls" + classCnt++;
+ } else if(entity.isOWLObjectProperty() || entity.isOWLDataProperty()){
+ var = "?p" + propCnt++;
+ } else if(entity.isOWLNamedIndividual()){
+ var = buildIndividualVariable();
+ }
+ variablesMapping.put(entity, var);
+ }
+ return var;
+ }
+
+ private String buildIndividualVariable(){
+ return "?s" + indCnt++;
+ }
+
+ private String triple(String subject, String predicate, String object){
+ return subject + " " + predicate + " " + object + ".\n";
+ }
+
+ @Override
+ public void visit(OWLClass expr) {
+ sparql += variables.peek() + " a " + getVariable(expr) +".\n";
+ }
+
+ @Override
+ public void visit(OWLObjectProperty property) {
+
+ }
+
+ @Override
+ public void visit(OWLDataProperty property) {
+ }
+
+ @Override
+ public void visit(OWLObjectIntersectionOf expr) {
+ Set<OWLClassExpression> operands = expr.getOperands();
+ String variable = variables.peek();
+ for (OWLClassExpression operand : operands) {
+ sparql += convert(variable, operand);
+ }
+ }
+
+ @Override
+ public void visit(OWLObjectUnionOf expr) {
+ }
+
+ @Override
+ public void visit(OWLObjectComplementOf expr) {
+ }
+
+ @Override
+ public void visit(OWLObjectSomeValuesFrom expr) {
+ String variable = variables.peek();
+ OWLObjectPropertyExpression property = expr.getProperty();
+ if(!property.isAnonymous()){
+ String objectVariable = buildIndividualVariable();
+ variables.push(objectVariable);
+ //build the triple for the property
+ sparql += triple(variable, getVariable(property.asOWLObjectProperty()), objectVariable);
+ //build the rest according to the role filler
+ OWLClassExpression filler = expr.getFiller();
+ filler.accept(this);
+ variables.pop();
+
+ } else {
+ System.err.println("TODO: complex property expressions");
+ }
+
+ }
+
+ @Override
+ public void visit(OWLObjectAllValuesFrom expr) {
+ String variable = variables.peek();
+ OWLObjectPropertyExpression property = expr.getProperty();
+ if(!property.isAnonymous()){
+ String objectVariable = buildIndividualVariable();
+ variables.push(objectVariable);
+ //build the triple for the property
+ sparql += triple(variable, getVariable(property.asOWLObjectProperty()), objectVariable);
+ OWLClassExpression filler = expr.getFiller();
+ filler.accept(this);
+ //build the rest according to the role filler
+ sparql += "FILTER NOT EXISTS{";
+ objectVariable = buildIndividualVariable();
+ variables.push(objectVariable);
+ sparql += triple(variable, getVariable(property.asOWLObjectProperty()), objectVariable);
+ variables.pop();
+ sparql += "}";
+
+
+ } else {
+ System.err.println("TODO: complex property expressions");
+ }
+ }
+
+ @Override
+ public void visit(OWLObjectHasValue expr) {
+ }
+
+ @Override
+ public void visit(OWLObjectMinCardinality expr) {
+ }
+
+ @Override
+ public void visit(OWLObjectExactCardinality expr) {
+ }
+
+ @Override
+ public void visit(OWLObjectMaxCardinality expr) {
+ }
+
+ @Override
+ public void visit(OWLObjectHasSelf expr) {
+ }
+
+ @Override
+ public void visit(OWLObjectOneOf expr) {
+ }
+
+ @Override
+ public void visit(OWLDataSomeValuesFrom expr) {
+ }
+
+ @Override
+ public void visit(OWLDataAllValuesFrom expr) {
+ }
+
+ @Override
+ public void visit(OWLDataHasValue expr) {
+ }
+
+ @Override
+ public void visit(OWLDataMinCardinality expr) {
+ }
+
+ @Override
+ public void visit(OWLDataExactCardinality expr) {
+ }
+
+ @Override
+ public void visit(OWLDataMaxCardinality expr) {
+ }
+
+ @Override
+ public void visit(OWLObjectInverseOf property) {
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-04-19 14:04:20 UTC (rev 3924)
@@ -0,0 +1,568 @@
+package org.dllearner.utilities.owl;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Stack;
+
+import org.aksw.commons.collections.diff.ModelDiff;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLClassExpressionVisitor;
+import org.semanticweb.owlapi.model.OWLDataAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLDataComplementOf;
+import org.semanticweb.owlapi.model.OWLDataExactCardinality;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataHasValue;
+import org.semanticweb.owlapi.model.OWLDataIntersectionOf;
+import org.semanticweb.owlapi.model.OWLDataMaxCardinality;
+import org.semanticweb.owlapi.model.OWLDataMinCardinality;
+import org.semanticweb.owlapi.model.OWLDataOneOf;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLDataPropertyExpression;
+import org.semanticweb.owlapi.model.OWLDataRange;
+import org.semanticweb.owlapi.model.OWLDataRangeVisitor;
+import org.semanticweb.owlapi.model.OWLDataSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLDataUnionOf;
+import org.semanticweb.owlapi.model.OWLDatatype;
+import org.semanticweb.owlapi.model.OWLDatatypeRestriction;
+import org.semanticweb.owlapi.model.OWLEntity;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectComplementOf;
+import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
+import org.semanticweb.owlapi.model.OWLObjectHasSelf;
+import org.semanticweb.owlapi.model.OWLObjectHasValue;
+import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
+import org.semanticweb.owlapi.model.OWLObjectInverseOf;
+import org.semanticweb.owlapi.model.OWLObjectMaxCardinality;
+import org.semanticweb.owlapi.model.OWLObjectMinCardinality;
+import org.semanticweb.owlapi.model.OWLObjectOneOf;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
+import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
+import org.semanticweb.owlapi.model.OWLObjectUnionOf;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLPropertyExpression;
+import org.semanticweb.owlapi.model.OWLPropertyExpressionVisitor;
+import org.semanticweb.owlapi.model.PrefixManager;
+import org.semanticweb.owlapi.util.DefaultPrefixManager;
+
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.Syntax;
+
+public class OWLClassExpressionToSPARQLConverter implements OWLClassExpressionVisitor, OWLPropertyExpressionVisitor, OWLDataRangeVisitor{
+
+ private String sparql = "";
+ private Stack<String> variables = new Stack<String>();
+ private Map<OWLEntity, String> variablesMapping;
+
+ private int classCnt = 0;
+ private int propCnt = 0;
+ private int indCnt = 0;
+
+ private OWLDataFactory df = new OWLDataFactoryImpl();
+
+ public OWLClassExpressionToSPARQLConverter() {
+ }
+
+ public String convert(String rootVariable, OWLClassExpression expr){
+ reset();
+ variables.push(rootVariable);
+ expr.accept(this);
+ return sparql;
+ }
+
+ public String convert(String rootVariable, OWLPropertyExpression expr){
+ variables.push(rootVariable);
+ sparql = "";
+ expr.accept(this);
+ return sparql;
+ }
+
+ public Query asQuery(String rootVariable, OWLClassExpression expr){
+ String queryString = "SELECT " + rootVariable + " WHERE {";
+ queryString += convert(rootVariable, expr);
+ queryString += "}";System.out.println(queryString);
+ return QueryFactory.create(queryString, Syntax.syntaxARQ);
+ }
+
+ private void reset(){
+ variables.clear();
+ classCnt = 0;
+ propCnt = 0;
+ indCnt = 0;
+ sparql = "";
+ }
+
+ private String getVariable(OWLEntity entity){
+ String var = variablesMapping.get(entity);
+ if(var == null){
+ if(entity.isOWLClass()){
+ var = "?cls" + classCnt++;
+ } else if(entity.isOWLObjectProperty() || entity.isOWLDataProperty()){
+ var = "?p" + propCnt++;
+ } else if(entity.isOWLNamedIndividual()){
+ var = buildIndividualVariable();
+ }
+ variablesMapping.put(entity, var);
+ }
+ return var;
+ }
+
+ private String buildIndividualVariable(){
+ return "?s" + indCnt++;
+ }
+
+ private int modalDepth(){
+ return variables.size();
+ }
+
+ private String triple(String subject, String predicate, String object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ (predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
+ (object.startsWith("?") ? object : "<" + object + ">") + ".\n";
+ }
+
+ private String triple(String subject, String predicate, OWLLiteral object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ (predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
+ "\"" + object + "\"^^<" + object.getDatatype().toStringID() + ">.\n";
+ }
+
+ private String triple(String subject, String predicate, OWLIndividual object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ (predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
+ "<" + object.toStringID() + ">.\n";
+ }
+
+ @Override
+ public void visit(OWLObjectProperty property) {
+ }
+
+ @Override
+ public void visit(OWLObjectInverseOf property) {
+ }
+
+ @Override
+ public void visit(OWLDataProperty property) {
+ }
+
+ @Override
+ public void visit(OWLClass ce) {
+ sparql += triple(variables.peek(), "a", ce.toStringID());
+ }
+
+ @Override
+ public void visit(OWLObjectIntersectionOf ce) {
+ List<OWLClassExpression> operands = ce.getOperandsAsList();
+ for (OWLClassExpression operand : operands) {
+ operand.accept(this);
+ }
+ }
+
+ @Override
+ public void visit(OWLObjectUnionOf ce) {
+ List<OWLClassExpression> operands = ce.getOperandsAsList();
+ for (int i = 0; i < operands.size()-1; i++) {
+ sparql += "{";
+ operands.get(i).accept(this);
+ sparql += "}";
+ sparql += " UNION ";
+ }
+ sparql += "{";
+ operands.get(operands.size()-1).accept(this);
+ sparql += "}";
+ }
+
+ @Override
+ public void visit(OWLObjectComplementOf ce) {
+ }
+
+ @Override
+ public void visit(OWLObjectSomeValuesFrom ce) {
+ String objectVariable = buildIndividualVariable();
+ OWLObjectPropertyExpression propertyExpression = ce.getProperty();
+ if(propertyExpression.isAnonymous()){
+ //property expression is inverse of a property
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), variables.peek());
+ } else {
+ sparql += triple(variables.peek(), propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ }
+ OWLClassExpression filler = ce.getFiller();
+ if(filler.isAnonymous()){
+ if(filler instanceof OWLObjectOneOf){
+ variables.push(objectVariable);
+ filler.accept(this);
+ variables.pop();
+ } else {
+ String var = buildIndividualVariable();
+ variables.push(var);
+ sparql += triple(objectVariable, "a", var);
+ filler.accept(this);
+ variables.pop();
+ }
+ } else {
+ sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ }
+
+ }
+
+ @Override
+ public void visit(OWLObjectAllValuesFrom ce) {
+ String subject = variables.peek();
+ String objectVariable = buildIndividualVariable();
+ OWLObjectPropertyExpression propertyExpression = ce.getProperty();
+ String predicate = propertyExpression.getNamedProperty().toStringID();
+ OWLClassExpression filler = ce.getFiller();
+ if(propertyExpression.isAnonymous()){
+ //property expression is inverse of a property
+ sparql += triple(objectVariable, predicate, variables.peek());
+ } else {
+ sparql += triple(variables.peek(), predicate, objectVariable);
+ }
+
+ String var = buildIndividualVariable();
+ sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt1) WHERE {";
+ sparql += triple(subject, predicate, var);
+ variables.push(var);
+ filler.accept(this);
+ variables.pop();
+ sparql += "} GROUP BY " + subject + "}";
+
+ var = buildIndividualVariable();
+ sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt2) WHERE {";
+ sparql += triple(subject, predicate, var);
+ sparql += "} GROUP BY " + subject + "}";
+
+ sparql += "FILTER(?cnt1=?cnt2)";
+
+ }
+
+ @Override
+ public void visit(OWLObjectHasValue ce) {
+ OWLObjectPropertyExpression propertyExpression = ce.getProperty();
+ OWLIndividual value = ce.getValue();
+ if(propertyExpression.isAnonymous()){
+ //property expression is inverse of a property
+ sparql += triple(value.toStringID(), propertyExpression.getNamedProperty().toStringID(), variables.peek());
+ } else {
+ sparql += triple(variables.peek(), propertyExpression.getNamedProperty().toStringID(), value.toStringID());
+ }
+ }
+
+ @Override
+ public void visit(OWLObjectMinCardinality ce) {
+ String subjectVariable = variables.peek();
+ String objectVariable = buildIndividualVariable();
+ OWLObjectPropertyExpression propertyExpression = ce.getProperty();
+ int cardinality = ce.getCardinality();
+ sparql += "{SELECT " + subjectVariable + " WHERE {";
+ if(propertyExpression.isAnonymous()){
+ //property expression is inverse of a property
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ } else {
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ }
+ OWLClassExpression filler = ce.getFiller();
+ if(filler.isAnonymous()){
+ String var = buildIndividualVariable();
+ variables.push(var);
+ sparql += triple(objectVariable, "a", var);
+ filler.accept(this);
+ variables.pop();
+ } else {
+ sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ }
+
+ sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")>=" + cardinality + ")}";
+
+ }
+
+ @Override
+ public void visit(OWLObjectExactCardinality ce) {
+ String subjectVariable = variables.peek();
+ String objectVariable = buildIndividualVariable();
+ OWLObjectPropertyExpression propertyExpression = ce.getProperty();
+ int cardinality = ce.getCardinality();
+ sparql += "{SELECT " + subjectVariable + " WHERE {";
+ if(propertyExpression.isAnonymous()){
+ //property expression is inverse of a property
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ } else {
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ }
+ OWLClassExpression filler = ce.getFiller();
+ if(filler.isAnonymous()){
+ String var = buildIndividualVariable();
+ variables.push(var);
+ sparql += triple(objectVariable, "a", var);
+ filler.accept(this);
+ variables.pop();
+ } else {
+ sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ }
+
+ sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")=" + cardinality + ")}";
+ }
+
+ @Override
+ public void visit(OWLObjectMaxCardinality ce) {
+ String subjectVariable = variables.peek();
+ String objectVariable = buildIndividualVariable();
+ OWLObjectPropertyExpression propertyExpression = ce.getProperty();
+ int cardinality = ce.getCardinality();
+ sparql += "{SELECT " + subjectVariable + " WHERE {";
+ if(propertyExpression.isAnonymous()){
+ //property expression is inverse of a property
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ } else {
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ }
+ OWLClassExpression filler = ce.getFiller();
+ if(filler.isAnonymous()){
+ String var = buildIndividualVariable();
+ variables.push(var);
+ sparql += triple(objectVariable, "a", var);
+ filler.accept(this);
+ variables.pop();
+ } else {
+ sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ }
+
+ sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")<=" + cardinality + ")}";
+ }
+
+ @Override
+ public void visit(OWLObjectHasSelf ce) {
+ String subject = variables.peek();
+ OWLObjectPropertyExpression property = ce.getProperty();
+ sparql += triple(subject, property.getNamedProperty().toStringID(), subject);
+ }
+
+ @Override
+ public void visit(OWLObjectOneOf ce) {
+ String subject = variables.peek();
+ if(modalDepth() == 1){
+ sparql += triple(subject, "?p", "?o");
+ }
+ sparql += "FILTER(" + subject + " IN (";
+ String values = "";
+ for (OWLIndividual ind : ce.getIndividuals()) {
+ if(!values.isEmpty()){
+ values += ",";
+ }
+ values += "<" + ind.toStringID() + ">";
+ }
+ sparql += values;
+ sparql += ...
[truncated message content] |
|
From: <lor...@us...> - 2013-06-06 13:32:33
|
Revision: 3985
http://sourceforge.net/p/dl-learner/code/3985
Author: lorenz_b
Date: 2013-06-06 13:32:30 +0000 (Thu, 06 Jun 2013)
Log Message:
-----------
Updated LGG.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
trunk/components-core/src/main/resources/prefixes.csv
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/pom.xml 2013-06-06 13:32:30 UTC (rev 3985)
@@ -320,6 +320,11 @@
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.aksw.jena-sparql-api</groupId>
+ <artifactId>jena-sparql-api-core</artifactId>
+ <version>2.10.0-3</version>
+ </dependency>
</dependencies>
<dependencyManagement>
<dependencies>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -55,6 +55,8 @@
QueryTree<N> getNodeById(int nodeId);
+ boolean sameType(QueryTree<N> tree);
+
boolean isLiteralNode();
void setLiteralNode(boolean isLiteralNode);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -124,6 +124,12 @@
addChild(subTree, tree.getEdge(child));
}
}
+
+ public boolean sameType(QueryTree<N> tree){
+ return (isResourceNode && tree.isResourceNode()) ||
+ (isVarNode() && tree.isVarNode()) ||
+ (isLiteralNode && tree.isLiteralNode());
+ }
public N getUserObject() {
return userObject;
@@ -327,6 +333,9 @@
@Override
public boolean isSubsumedBy(QueryTree<N> tree) {
+// if(!sameType(tree)){
+// return false;
+// }
if(!(tree.getUserObject().equals("?") || tree.getUserObject().equals(this.userObject))){
return false;
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -145,7 +145,7 @@
// }
// }
// }
- if(!lgg.getUserObject().equals(tree2.getUserObject())){
+ if(!lgg.sameType(tree2) || !lgg.getUserObject().equals(tree2.getUserObject())){
lgg.setUserObject((N)"?");
lgg.setLiteralNode(false);
lgg.setResourceNode(false);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -2,7 +2,6 @@
import java.util.ArrayList;
import java.util.Collection;
-import java.util.HashSet;
import java.util.List;
import java.util.PriorityQueue;
import java.util.Queue;
@@ -11,6 +10,9 @@
import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
+
public class NoiseSensitiveLGG<N> {
private LGGGenerator<N> lggGenerator = new LGGGeneratorImpl<N>();
@@ -22,19 +24,25 @@
}
public List<EvaluatedQueryTree<N>> computeLGG(List<QueryTree<N>> trees){
+ Monitor subMon = MonitorFactory.getTimeMonitor("subsumption-mon");
+ Monitor lggMon = MonitorFactory.getTimeMonitor("lgg-mon");
init(trees);
EvaluatedQueryTree<N> currentElement;
- do{
+ do{System.out.println("TODO list size: " + todoList.size());
//pick best element from todo list
currentElement = todoList.poll();
for (QueryTree<N> example : currentElement.getUncoveredExamples()) {
QueryTree<N> tree = currentElement.getTree();
//compute the LGG
+ lggMon.start();
QueryTree<N> lgg = lggGenerator.getLGG(tree, example);
+ lggMon.stop();
//compute examples which are not covered by LGG
- Collection<QueryTree<N>> uncoveredExamples = new HashSet<QueryTree<N>>();
+ Collection<QueryTree<N>> uncoveredExamples = new ArrayList<QueryTree<N>>();
for (QueryTree<N> queryTree : trees) {
+ subMon.start();
boolean subsumed = queryTree.isSubsumedBy(lgg);
+ subMon.stop();
if(!subsumed){
uncoveredExamples.add(queryTree);
}
@@ -45,6 +53,12 @@
EvaluatedQueryTree<N> solution = new EvaluatedQueryTree<N>(lgg, uncoveredExamples, score);
todo(solution);
}
+ System.out.println("LGG time: " + lggMon.getTotal() + "ms");
+ System.out.println("Avg. LGG time: " + lggMon.getAvg() + "ms");
+ System.out.println("#LGG computations: " + lggMon.getHits());
+ System.out.println("Subsumption test time: " + subMon.getTotal() + "ms");
+ System.out.println("Avg. subsumption test time: " + subMon.getAvg() + "ms");
+ System.out.println("#Subsumption tests: " + subMon.getHits());
solutions.add(currentElement);
// todoList.remove(currentElement);
} while(!terminationCriteriaSatisfied());
@@ -57,8 +71,8 @@
// EvaluatedQueryTree<N> dummy = new EvaluatedQueryTree<N>(new QueryTreeImpl<N>((N)"TOP"), trees, 0d);
// todoList.add(dummy);
//compute distinct trees
- Collection<QueryTree<N>> distinctTrees = new HashSet<QueryTree<N>>();
- for (QueryTree<N> queryTree : trees) {
+ Collection<QueryTree<N>> distinctTrees = new ArrayList<QueryTree<N>>();
+ for (QueryTree<N> queryTree : trees) {//System.out.println(queryTree.getStringRepresentation());
boolean distinct = true;
for (QueryTree<N> otherTree : distinctTrees) {
if(queryTree.isSubsumedBy(otherTree)){
@@ -71,7 +85,7 @@
}
}
for (QueryTree<N> queryTree : distinctTrees) {
- Collection<QueryTree<N>> uncoveredExamples = new HashSet<QueryTree<N>>(distinctTrees);
+ Collection<QueryTree<N>> uncoveredExamples = new ArrayList<QueryTree<N>>(distinctTrees);
uncoveredExamples.remove(queryTree);
double score = (trees.size() - uncoveredExamples.size()) / (double)trees.size();
todoList.add(new EvaluatedQueryTree<N>(queryTree, uncoveredExamples, score));
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 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -1,16 +1,24 @@
package org.dllearner.kb.sparql;
-import java.io.UnsupportedEncodingException;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;
+import java.util.concurrent.TimeUnit;
+import org.aksw.jena_sparql_api.cache.core.QueryExecutionFactoryCacheEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheCoreEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheCoreH2;
+import org.aksw.jena_sparql_api.cache.extra.CacheEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
+import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
+import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
+import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
+import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
//import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
public class ConciseBoundedDescriptionGeneratorImpl implements ConciseBoundedDescriptionGenerator{
@@ -25,6 +33,7 @@
private List<String> namespaces;
private int maxRecursionDepth = 1;
+ private String cacheDir;
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache) {
this.endpoint = endpoint;
@@ -37,8 +46,19 @@
this.maxRecursionDepth = maxRecursionDepth;
}
+ public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir, int maxRecursionDepth) {
+ this.endpoint = endpoint;
+ this.cacheDir = cacheDir;
+ this.maxRecursionDepth = maxRecursionDepth;
+ }
+
+ public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir) {
+ this.endpoint = endpoint;
+ this.cacheDir = cacheDir;
+ }
+
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint) {
- this(endpoint, null);
+ this(endpoint, (String)null);
}
public ConciseBoundedDescriptionGeneratorImpl(Model model) {
@@ -59,34 +79,28 @@
private Model getModelChunked(String resource, int depth){
String query = makeConstructQueryOptional(resource, chunkSize, 0, depth);
- Model all = ModelFactory.createDefaultModel();
- try {
- Model model;
- if(cache == null){
- model = getModel(query);
- } else {
- model = cache.executeConstructQuery(endpoint, query);
+ QueryExecutionFactory qef;
+ if(endpoint != null){
+ qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+ if(cacheDir != null){
+ try {
+ long timeToLive = TimeUnit.DAYS.toMillis(30);
+ CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDir, timeToLive, true);
+ CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+ qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
}
- all.add(model);
- int i = 1;
- do{
-// while(model.size() == CHUNK_SIZE){
- query = makeConstructQueryOptional(resource, chunkSize, i * chunkSize, depth);
- if(cache == null){
- model = getModel(query);
- } else {
- model = cache.executeConstructQuery(endpoint, query);
- }
- all.add(model);
- i++;
- } while(chunkSize > 0 && model.size() != 0);
- } catch (UnsupportedEncodingException e) {
- logger.error(e);
- } catch (SQLException e) {
- logger.error(e);
+ qef = new QueryExecutionFactoryPaginated(qef, 10000);
+ } else {
+ qef = new QueryExecutionFactoryModel(baseModel);
}
-
- return all;
+ QueryExecution qe = qef.createQueryExecution(query);
+ Model model = qe.execConstruct();
+ return model;
}
@Override
@@ -151,36 +165,6 @@
return filter;
}
- private Model getModel(String query) throws UnsupportedEncodingException, SQLException{
- if(logger.isDebugEnabled()){
- logger.debug("Sending SPARQL query ...");
- logger.debug("Query:\n" + query.toString());
- }
-
- Model model;
- if(baseModel == null){
- if(cache == null){
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(), query);
- for (String dgu : endpoint.getDefaultGraphURIs()) {
- queryExecution.addDefaultGraph(dgu);
- }
- for (String ngu : endpoint.getNamedGraphURIs()) {
- queryExecution.addNamedGraph(ngu);
- }
- model = queryExecution.execConstruct();
- } else {
- model = cache.executeConstructQuery(endpoint, query);
- }
- } else {
- model = QueryExecutionFactory.create(query, baseModel).execConstruct();
- }
-
- if(logger.isDebugEnabled()){
- logger.debug("Got " + model.size() + " new triples in.");
- }
- return model;
- }
-
public static void main(String[] args) {
Logger.getRootLogger().setLevel(Level.DEBUG);
ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint.getEndpointDBpedia());
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -78,6 +78,10 @@
Statement stmt = conn.createStatement();
stmt.execute("CREATE TABLE IF NOT EXISTS QUERY_CACHE(QUERYHASH BINARY PRIMARY KEY,QUERY VARCHAR(20000), TRIPLES CLOB, STORE_TIME TIMESTAMP)");
}
+
+ public String getCacheDirectory() {
+ return databaseDirectory;
+ }
public ExtractionDBCache(String cacheDir) {
databaseDirectory = cacheDir;
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -73,6 +73,7 @@
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
@@ -494,7 +495,7 @@
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() + ">)) . }";
+ query += "FILTER( !SAMETERM(?sub, <" + cls.getName() + ">)) . }";System.out.println(query);
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -590,7 +591,6 @@
* @author sherif
*/
public SortedSet<Individual> getIndividualsExcluding(Description wantedClass, Description excludeClass, int limit) {
-
if(!(wantedClass instanceof NamedClass)){
throw new UnsupportedOperationException("Only named classes are supported.");
}
@@ -598,7 +598,7 @@
String query =
"SELECT DISTINCT ?ind WHERE {" +
"?ind a <"+((NamedClass)wantedClass).getName() + "> . " +
- "FILTER(NOT EXISTS { ?ind a <" + ((NamedClass)excludeClass).getName() + "> } )}";
+ "FILTER NOT EXISTS { ?ind a <" + ((NamedClass)excludeClass).getName() + "> } }";
if(limit != 0) {
query += " LIMIT " + limit;
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -19,10 +19,22 @@
package org.dllearner.utilities.examples;
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.RANDOM;
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SIBLING;
+import static org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2.Strategy.SUPERCLASS;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import org.dllearner.core.owl.ClassHierarchy;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.SPARQLTasks;
@@ -30,6 +42,10 @@
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.datastructures.Datastructures;
+import com.google.common.base.Predicate;
+import com.google.common.collect.HashMultiset;
+import com.google.common.collect.Multiset;
+import com.google.common.collect.Multisets;
/**
*
* Utility class for automatically retrieving negative examples from a
@@ -40,12 +56,18 @@
*
*/
public class AutomaticNegativeExampleFinderSPARQL2 {
+
+ public enum Strategy{
+ SUPERCLASS, SIBLING, RANDOM;
+ }
private SparqlEndpoint se;
// for re-using existing queries
private SPARQLReasoner sr;
private SPARQLTasks st;
+
+ private String namespace;
public AutomaticNegativeExampleFinderSPARQL2(SparqlEndpoint se) {
this.se = se;
@@ -54,6 +76,15 @@
st = new SPARQLTasks(se);
}
+ public AutomaticNegativeExampleFinderSPARQL2(SPARQLReasoner reasoner, String namespace) {
+ this.sr = reasoner;
+ this.namespace = namespace;
+ }
+
+ public AutomaticNegativeExampleFinderSPARQL2(SPARQLReasoner reasoner) {
+ this.sr = reasoner;
+ }
+
/**
* Get negative examples when learning the description of a class, i.e.
* all positives are from some known class.
@@ -82,4 +113,92 @@
return negEx;
}
+ public SortedSet<Individual> getNegativeExamples(Set<Individual> positiveExamples, int limit) {
+ return getNegativeExamples(positiveExamples, Arrays.asList(SUPERCLASS, SIBLING, RANDOM), limit);
+ }
+
+ public SortedSet<Individual> getNegativeExamples(Set<Individual> positiveExamples, Collection<Strategy> strategies, int limit) {
+ Map<Strategy, Double> strategiesWithWeight = new HashMap<Strategy, Double>();
+ double weight = 1d/strategies.size();
+ for (Strategy strategy : strategies) {
+ strategiesWithWeight.put(strategy, weight);
+ }
+ return getNegativeExamples(positiveExamples, strategiesWithWeight, limit);
+ }
+
+ public SortedSet<Individual> getNegativeExamples(Set<Individual> positiveExamples, Map<Strategy, Double> strategiesWithWeight, int maxNrOfReturnedInstances) {
+ SortedSet<Individual> negEx = new TreeSet<Individual>();
+
+ //get the types for each instance
+ Multiset<NamedClass> types = HashMultiset.create();
+ for (Individual ex : positiveExamples) {
+ types.addAll(sr.getTypes(ex));
+ }
+
+ //remove types that do not have the given namespace
+ if(namespace != null){
+ types = Multisets.filter(types, new Predicate<NamedClass>() {
+ public boolean apply(NamedClass input){
+ return input.getName().startsWith(namespace);
+ }
+ });
+ }
+
+ //keep the most specific types
+ keepMostSpecificClasses(types);
+
+ for (Entry<Strategy, Double> entry : strategiesWithWeight.entrySet()) {
+ Strategy strategy = entry.getKey();
+ Double weight = entry.getValue();
+ //the max number of instances returned by the current strategy
+ int limit = (int)(weight * maxNrOfReturnedInstances);
+ //the highest frequency value
+ int maxFrequency = types.entrySet().iterator().next().getCount();
+ if(strategy == SIBLING){
+ System.out.println("Sibling Classes Strategy");
+ for (NamedClass nc : types.elementSet()) {
+ int frequency = types.count(nc);
+ //get sibling classes
+ Set<NamedClass> siblingClasses = sr.getSiblingClasses(nc);
+ int nrOfSiblings = siblingClasses.size();
+ int v = (int)Math.ceil(((double)frequency / types.size()) / nrOfSiblings * limit); System.out.println(nc + ": " + v);
+ for (NamedClass siblingClass : siblingClasses) {
+ negEx.addAll(sr.getIndividualsExcluding(siblingClass, nc, v));
+ }
+
+ }
+ } else if(strategy == SUPERCLASS){
+ System.out.println("Super Classes Strategy");
+ for (NamedClass nc : types.elementSet()) {
+ int frequency = types.count(nc);
+ //get sibling classes
+ Set<Description> superClasses = sr.getSuperClasses(nc);System.out.println(superClasses);
+ int nrOfSuperClasses = superClasses.size();
+ int v = (int)Math.ceil(((double)frequency / types.size()) / nrOfSuperClasses * limit); System.out.println(nc + ": " + v);
+ for (Description superClass : superClasses) {
+ negEx.addAll(sr.getIndividualsExcluding(superClass, nc, v));
+ }
+ }
+ } else if(strategy == RANDOM){
+
+ }
+ }
+ return negEx;
+ }
+
+ private void keepMostSpecificClasses(Multiset<NamedClass> classes){
+ HashMultiset<NamedClass> copy = HashMultiset.create(classes);
+ final ClassHierarchy hierarchy = sr.getClassHierarchy();
+ for (NamedClass nc1 : copy.elementSet()) {
+ for (NamedClass nc2 : copy.elementSet()) {
+ if(!nc1.equals(nc2)){
+ //remove class nc1 if it is superclass of another class nc2
+ if(hierarchy.isSubclassOf(nc2, nc1)){
+ classes.remove(nc1, classes.count(nc1));
+ break;
+ }
+ }
+ }
+ }
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-06-06 13:32:30 UTC (rev 3985)
@@ -73,12 +73,7 @@
private String sparql = "";
private Stack<String> variables = new Stack<String>();
- private Map<OWLEntity, String> variablesMapping = new HashMap<OWLEntity, String>();
- private int classCnt = 0;
- private int propCnt = 0;
- private int indCnt = 0;
-
private OWLDataFactory df = new OWLDataFactoryImpl();
private Multimap<Integer, OWLEntity> properties = HashMultimap.create();
@@ -86,8 +81,19 @@
private Map<Integer, Boolean> intersection;
private Set<? extends OWLEntity> variableEntities = new HashSet<OWLEntity>();
+ private VariablesMapping mapping;
+
+ public OWLClassExpressionToSPARQLConverter(VariablesMapping mapping) {
+ this.mapping = mapping;
+ }
+
public OWLClassExpressionToSPARQLConverter() {
+ mapping = new VariablesMapping();
}
+
+ public VariablesMapping getVariablesMapping() {
+ return mapping;
+ }
public String convert(String rootVariable, OWLClassExpression expr){
reset();
@@ -132,7 +138,7 @@
queryString += rootVariable + " WHERE {";
} else {
for (OWLEntity owlEntity : variableEntities) {
- String var = variablesMapping.get(owlEntity);
+ String var = mapping.get(owlEntity);
queryString += var + " ";
}
if(count){
@@ -149,7 +155,7 @@
if(count){
queryString += "GROUP BY ";
for (OWLEntity owlEntity : variableEntities) {
- String var = variablesMapping.get(owlEntity);
+ String var = mapping.get(owlEntity);
queryString += var;
}
queryString += " ORDER BY DESC(?cnt)";
@@ -158,40 +164,14 @@
return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
- public Map<OWLEntity, String> getVariablesMapping() {
- return variablesMapping;
- }
-
private void reset(){
- variablesMapping.clear();
variables.clear();
properties.clear();
- classCnt = 0;
- propCnt = 0;
- indCnt = 0;
sparql = "";
intersection = new HashMap<Integer, Boolean>();
+ mapping.reset();
}
- private String getVariable(OWLEntity entity){
- String var = variablesMapping.get(entity);
- if(var == null){
- if(entity.isOWLClass()){
- var = "?cls" + classCnt++;
- } else if(entity.isOWLObjectProperty() || entity.isOWLDataProperty()){
- var = "?p" + propCnt++;
- } else if(entity.isOWLNamedIndividual()){
- var = buildIndividualVariable();
- }
- variablesMapping.put(entity, var);
- }
- return var;
- }
-
- private String buildIndividualVariable(){
- return "?s" + indCnt++;
- }
-
private int modalDepth(){
return variables.size();
}
@@ -253,7 +233,7 @@
private String render(OWLEntity entity){
String s;
if(variableEntities.contains(entity)){
- s = getVariable(entity);
+ s = mapping.getVariable(entity);
} else {
s = "<" + entity.toStringID() + ">";
}
@@ -295,8 +275,8 @@
if(props.size() > 1){
Collection<String> vars = new TreeSet<String>();
for (OWLEntity p : props) {
- if(variablesMapping.containsKey(p)){
- vars.add(variablesMapping.get(p));
+ if(mapping.containsKey(p)){
+ vars.add(mapping.get(p));
}
}
if(vars.size() == 2){
@@ -334,7 +314,7 @@
@Override
public void visit(OWLObjectSomeValuesFrom ce) {
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
@@ -356,7 +336,7 @@
@Override
public void visit(OWLObjectAllValuesFrom ce) {
String subject = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
OWLObjectProperty predicate = propertyExpression.getNamedProperty();
OWLClassExpression filler = ce.getFiller();
@@ -367,7 +347,7 @@
sparql += triple(variables.peek(), predicate, objectVariable);
}
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt1) WHERE {";
sparql += triple(subject, predicate, var);
variables.push(var);
@@ -375,7 +355,7 @@
variables.pop();
sparql += "} GROUP BY " + subject + "}";
- var = buildIndividualVariable();
+ var = mapping.newIndividualVariable();
sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt2) WHERE {";
sparql += triple(subject, predicate, var);
sparql += "} GROUP BY " + subject + "}";
@@ -399,7 +379,7 @@
@Override
public void visit(OWLObjectMinCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -411,7 +391,7 @@
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
variables.push(var);
sparql += triple(objectVariable, "a", var);
filler.accept(this);
@@ -427,7 +407,7 @@
@Override
public void visit(OWLObjectExactCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -439,7 +419,7 @@
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
variables.push(var);
sparql += triple(objectVariable, "a", var);
filler.accept(this);
@@ -454,7 +434,7 @@
@Override
public void visit(OWLObjectMaxCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -466,7 +446,7 @@
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
variables.push(var);
sparql += triple(objectVariable, "a", var);
filler.accept(this);
@@ -506,7 +486,7 @@
@Override
public void visit(OWLDataSomeValuesFrom ce) {
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
@@ -518,13 +498,13 @@
@Override
public void visit(OWLDataAllValuesFrom ce) {
String subject = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
String predicate = propertyExpression.asOWLDataProperty().toStringID();
OWLDataRange filler = ce.getFiller();
sparql += triple(variables.peek(), predicate, objectVariable);
- String var = buildIndividualVariable();
+ String var = mapping.newIndividualVariable();
sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt1) WHERE {";
sparql += triple(subject, predicate, var);
variables.push(var);
@@ -532,7 +512,7 @@
variables.pop();
sparql += "} GROUP BY " + subject + "}";
- var = buildIndividualVariable();
+ var = mapping.newIndividualVariable();
sparql += "{SELECT " + subject + " (COUNT(" + var + ") AS ?cnt2) WHERE {";
sparql += triple(subject, predicate, var);
sparql += "} GROUP BY " + subject + "}";
@@ -550,7 +530,7 @@
@Override
public void visit(OWLDataMinCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -566,7 +546,7 @@
@Override
public void visit(OWLDataExactCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -582,7 +562,7 @@
@Override
public void visit(OWLDataMaxCardinality ce) {
String subjectVariable = variables.peek();
- String objectVariable = buildIndividualVariable();
+ String objectVariable = mapping.newIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
@@ -774,7 +754,4 @@
System.out.println(expr + "\n" + query);
}
-
-
-
}
\ No newline at end of file
Modified: trunk/components-core/src/main/resources/prefixes.csv
===================================================================
--- trunk/components-core/src/main/resources/prefixes.csv 2013-05-24 09:16:41 UTC (rev 3984)
+++ trunk/components-core/src/main/resources/prefixes.csv 2013-06-06 13:32:30 UTC (rev 3985)
@@ -4,609 +4,963 @@
dbp,http://dbpedia.org/property/
owl,http://www.w3.org/2002/07/owl#
dc,http://purl.org/dc/elements/1.1/
+rdfs,http://www.w3.org/2000/01/rdf-schema#
dbo,http://dbpedia.org/ontology/
-rdfs,http://www.w3.org/2000/01/rdf-schema#
-sc,http://umbel.org/umbel/sc/
rss,http://purl.org/rss/1.0/
+sc,http://purl.org/science/owl/sciencecommons/
+skos,http://www.w3.org/2004/02/skos/core#
fb,http://rdf.freebase.com/ns/
geonames,http://www.geonames.org/ontology#
-skos,http://www.w3.org/2004/02/skos/core#
-cyc,http://sw.opencyc.org/concept/
geo,http://www.w3.org/2003/01/geo/wgs84_pos#
sioc,http://rdfs.org/sioc/ns#
+gr,http://purl.org/goodrelations/v1#
+gldp,http://www.w3.org/ns/people#
+cyc,http://sw.opencyc.org/concept/
akt,http://www.aktors.org/ontology/portal#
+xsd,http://www.w3.org/2001/XMLSchema#
dbpedia,http://dbpedia.org/resource/
+dcterms,http://purl.org/dc/terms/
+swrc,http://swrc.ontoware.org/ontology#
+commerce,http://search.yahoo.com/searchmonkey/commerce/
admin,http://webns.net/mvcb/
-gr,http://purl.org/goodrelations/v1#
-swrc,http://swrc.ontoware.org/ontology#
-xsd,http://www.w3.org/2001/XMLSchema#
-xhtml,http://www.w3.org/1999/xhtml/vocab#
+content,http://purl.org/rss/1.0/modules/content/
doap,http://usefulinc.com/ns/doap#
+void,http://rdfs.org/ns/void#
+xhtml,http://www.w3.org/1999/xhtml#
+bibo,http://purl.org/ontology/bibo/
+org,http://www.w3.org/ns/org#
vcard,http://www.w3.org/2006/vcard/ns#
-content,http://purl.org/rss/1.0/modules/content/
+gen,http://www.w3.org/2006/gen/ont#
bill,http://www.rdfabout.com/rdf/schema/usbill/
-dcterms,http://purl.org/dc/terms/
-mo,http://purl.org/ontology/mo/
+aiiso,http://purl.org/vocab/aiiso/schema#
wot,http://xmlns.com/wot/0.1/
-wn20schema,http://www.w3.org/2006/03/wn/wn20/schema/
-d2rq,http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#
-gen,http://www.w3.org/2006/gen/ont#
+qb,http://purl.org/linked-data/cube#
nie,http://www.semanticdesktop.org/ontologies/2007/01/19/nie#
-void,http://rdfs.org/ns/void#
test2,http://this.invalid/test2#
-org,http://www.w3.org/ns/org#
-movie,http://data.linkedmdb.org/resource/movie/
-ex,http://example.com/
+d2rq,http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#
rel,http://purl.org/vocab/relationship/
-bio,http://purl.org/vocab/bio/0.1/
+dcmit,http://purl.org/dc/dcmitype/
http,http://www.w3.org/2006/http#
-dcmit,http://purl.org/dc/dcmitype/
-reco,http://purl.org/reco#
cc,http://creativecommons.org/ns#
-nfo,http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#
-ac,http://umbel.org/umbel/ac/
-xfn,http://vocab.sindice.com/xfn#
+og,http://opengraphprotocol.org/schema/
+factbook,http://www4.wiwiss.fu-berlin.de/factbook/ns#
+vann,http://purl.org/vocab/vann/
+ex,http://example.com/
+bio,http://purl.org/vocab/bio/0.1/
+mo,http://purl.org/ontology/mo/
+ad,http://schemas.talis.com/2005/address/schema#
+media,http://purl.org/microformat/hmedia/
+event,http://purl.org/NET/c4dm/event.owl#
earl,http://www.w3.org/ns/earl#
-og,http://opengraphprotocol.org/schema/
+book,http://purl.org/NET/book/vocab#
+cv,http://purl.org/captsolo/resume-rdf/0.2/cv#
+ical,http://www.w3.org/2002/12/cal/ical#
+botany,http://purl.org/NET/biol/botany#
air,http://dig.csail.mit.edu/TAMI/2007/amord/air#
-ical,http://www.w3.org/2002/12/cal/ical#
-media,http://purl.org/media#
-rev,http://purl.org/stuff/rev#
-cv,http://rdfs.org/resume-rdf/
tag,http://www.holygoat.co.uk/owl/redwood/0.1/tags/
+dv,http://rdf.data-vocabulary.org/#
+cld,http://purl.org/cld/terms/
swc,http://data.semanticweb.org/ns/swc/ontology#
-botany,http://purl.org/NET/biol/botany#
-bibo,http://purl.org/ontology/bibo/
-xf,http://www.w3.org/2002/xforms/
-factbook,http://www4.wiwiss.fu-berlin.de/factbook/ns#
+drugbank,http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/
+musim,http://purl.org/ontology/similarity/
+dir,http://schemas.talis.com/2005/dir/schema#
+reco,http://purl.org/reco#
+rev,http://purl.org/stuff/rev#
+biblio,http://purl.org/net/biblio#
+ctag,http://commontag.org/ns#
+af,http://purl.org/ontology/af/
days,http://ontologi.es/days#
-cfp,http://sw.deri.org/2005/08/conf/cfp.owl#
-sism,http://purl.oclc.org/NET/sism/0.1/
-vann,http://purl.org/vocab/vann/
+log,http://www.w3.org/2000/10/swap/log#
+cs,http://purl.org/vocab/changeset/schema#
+sd,http://www.w3.org/ns/sparql-service-description#
osag,http://www.ordnancesurvey.co.uk/ontology/AdministrativeGeography/v2.0/AdministrativeGeography.rdf#
-owlim,http://www.ontotext.com/trree/owlim#
-dir,http://schemas.talis.com/2005/dir/schema#
-cld,http://purl.org/cld/terms/
-afn,http://jena.hpl.hp.com/ARQ/function#
-book,http://purl.org/NET/book/vocab#
+xhv,http://www.w3.org/1999/xhtml/vocab#
+rdfg,http://www.w3.org/2004/03/trix/rdfg-1/
+co,http://purl.org/ontology/co/core#
fn,http://www.w3.org/2005/xpath-functions#
-musim,http://purl.org/ontology/similarity/
-akts,http://www.aktors.org/ontology/support#
-cs,http://purl.org/vocab/changeset/schema#
-aiiso,http://purl.org/vocab/aiiso/schema#
-ad,http://schemas.talis.com/2005/address/schema#
+sism,http://purl.oclc.org/NET/sism/0.1/
mu,http://www.kanzaki.com/ns/music#
-sd,http://www.w3.org/ns/sparql-service-description#
-po,http://purl.org/ontology/po/
-biblio,http://purl.org/net/biblio#
-event,http://purl.org/NET/c4dm/event.owl#
-dv,http://rdf.data-vocabulary.org/#
-drugbank,http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/
-uniprot,http://purl.uniprot.org/core/
memo,http://ontologies.smile.deri.ie/2009/02/27/memo#
-dcn,http://www.w3.org/2007/uwa/context/deliverycontext.owl#
-rdfg,http://www.w3.org/2004/03/trix/rdfg-1/
-log,http://www.w3.org/2000/10/swap/log#
-co,http://purl.org/ontology/co/core#
-qb,http://purl.org/linked-data/cube#
ome,http://purl.org/ontomedia/core/expression#
-af,http://purl.org/ontology/af/
+daia,http://purl.org/ontology/daia/
+cmp,http://www.ontologydesignpatterns.org/cp/owl/componency.owl#
+owlim,http://www.ontotext.com/trree/owlim#
+cfp,http://sw.deri.org/2005/08/conf/cfp.owl#
+xfn,http://vocab.sindice.com/xfn#
+afn,http://jena.hpl.hp.com/ARQ/function#
+ok,http://okkam.org/terms#
giving,http://ontologi.es/giving#
+ir,http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl#
+xf,http://www.w3.org/2002/xforms/
+dcn,http://www.w3.org/2007/uwa/context/deliverycontext.owl#
swanq,http://purl.org/swan/1.2/qualifiers/
-cmp,http://www.ontologydesignpatterns.org/cp/owl/componency.owl#
lomvoc,http://ltsc.ieee.org/rdf/lomv1p0/vocabulary#
+math,http://www.w3.org/2000/10/swap/math#
+swande,http://purl.org/swan/1.2/discourse-elements/
rif,http://www.w3.org/2007/rif#
-ir,http://www.ontologydesignpatterns.org/cp/owl/informationrealization.owl#
-ctag,http://commontag.org/ns#
-ok,http://okkam.org/terms#
-swande,http://purl.org/swan/1.2/discourse-elements/
-math,http://www.w3.org/2000/10/swap/math#
-daia,http://purl.org/ontology/daia/
-sioct,http://rdfs.org/sioc/types#
+sr,http://www.openrdf.org/config/repository/sail#
jdbc,http://d2rq.org/terms/jdbc/
+tzont,http://www.w3.org/2006/timezone#
myspace,http://purl.org/ontology/myspace#
-sr,http://www.openrdf.org/config/repository/sail#
-tzont,http://www.w3.org/2006/timezone#
+con,http://www.w3.org/2000/10/swap/pim/contact#
+sider,http://www4.wiwiss.fu-berlin.de/sider/resource/sider/
+wn20schema,http://www.w3.org/2006/03/wn/wn20/schema/
+cert,http://www.w3.org/ns/auth/cert#
+pto,http://www.productontology.org/id/
+movie,http://data.linkedmdb.org/resource/movie/
+oo,http://purl.org/openorg/
+nfo,http://www.semanticdesktop.org/ontologies/nfo/#
+ac,http://umbel.org/umbel/ac/
+po,http://purl.org/ontology/po/
+akts,http://www.aktors.org/ontology/support#
+frbr,http://purl.org/vocab/frbr/core#
+uniprot,http://purl.uniprot.org/core/
+dcat,http://www.w3.org/ns/dcat#
+rsa,http://www.w3.org/ns/auth/rsa#
+ov,http://open.vocab.org/terms/
+sioct,http://rdfs.org/sioc/types#
+prv,http://purl.org/net/provenance/ns#
+prov,http://www.w3.org/ns/prov#
+granatum,http://chem.deri.ie/granatum/
+wo,http://purl.org/ontology/wo/
daml,http://www.daml.org/2001/03/daml+oil#
-wo,http://purl.org/ontology/wo/
-politico,http://www.rdfabout.com/rdf/schema/politico/
+spacerel,http://data.ordnancesurvey.co.uk/ontology/spatialrelations/
+pc,http://purl.org/procurement/public-contracts#
pmlj,http://inference-web.org/2.0/pml-justification.owl#
+vs,http://www.w3.org/2003/06/sw-vocab-status/ns#
usgov,http://www.rdfabout.com/rdf/schema/usgovt/
+acm,http://www.rkbexplorer.com/ontologies/acm#
taxo,http://purl.org/rss/1.0/modules/taxonomy/
-lfm,http://purl.org/ontology/last-fm/
-vote,http://www.rdfabout.com/rdf/schema/vote/
-frbr,http://purl.org/vocab/frbr/core#
-doac,http://ramonantonio.net/doac/0.1/#
wn,http://xmlns.com/wordnet/1.6/
-affy,http://www.affymetrix.com/community/publications/affymetrix/tmsplice#
-con,http://www.w3.org/2000/10/swap/pim/contact#
-prv,http://purl.org/net/provenance/ns#
-scot,http://scot-project.org/scot/ns#
-irrl,http://www.ontologydesignpatterns.org/cp/owl/informationobjectsandrepresentationlanguages.owl#
+wdrs,http://www.w3.org/2007/05/powder-s#
scovo,http://purl.org/NET/scovo#
-nco,http://www.semanticdesktop.org/ontologies/2007/03/22/nco#
+oauth,http://demiblog.org/vocab/oauth#
+politico,http://www.rdfabout.com/rdf/schema/politico/
lgd,http://linkedgeodata.org/ontology/
-wordmap,http://purl.org/net/ns/wordmap#
+lode,http://linkedevents.org/ontology/
+acl,http://www.w3.org/ns/auth/acl#
+ore,http://www.openarchives.org/ore/terms/
+abc,http://www.metadata.net/harmony/ABCSchemaV5Commented.rdf#
omt,http://purl.org/ontomedia/ext/common/trait#
-sider,http://www4.wiwiss.fu-berlin.de/sider/resource/sider/
+nao,http://www.semanticdesktop.org/ontologies/2007/08/15/nao#
+omb,http://purl.org/ontomedia/ext/common/being#
+loc,http://www.w3.org/2007/uwa/context/location.owl#
+mit,http://purl.org/ontology/mo/mit#
+skosxl,http://www.w3.org/2008/05/skos-xl#
+spc,http://purl.org/ontomedia/core/space#
+vote,http://www.rdfabout.com/rdf/schema/vote/
+lfm,http://purl.org/ontology/last-fm/
+irrl,http://www.ontologydesignpatterns.org/cp/owl/informationobjectsandrepresentationlanguages.owl#
+rep,http://www.openrdf.org/config/repository#
+chord,http://purl.org/ontology/chord/
+dcam,http://purl.org/dc/dcam/
user,http://schemas.talis.com/2005/user/schema#
-ore,http://www.openarchives.org/ore/terms/
-lode,http://linkedevents.org/ontology/
-ecs,http://rdf.ecs.soton.ac.uk/ontology/ecs#
-rep,http://www.openrdf.org/config/repository#
-nao,http://www.semanticdesktop.org/ontologies/2007/08/15/nao#
-spin,http://spinrdf.org/spin#
+resex,http://resex.rkbexplorer.com/ontologies/resex#
swrl,http://www.w3.org/2003/11/swrl#
-lx,http://purl.org/NET/lx#
+music,http://musicontology.com/
+doac,http://ramonantonio.net/doac/0.1/#
+scot,http://scot-project.org/scot/ns#
+irw,http://www.ontologydesignpatterns.org/ont/web/irw.owl#
ti,http://www.ontologydesignpatterns.org/cp/owl/timeinterval.owl#
-unit,http://qudt.org/vocab/unit#
-spc,http://purl.org/ontomedia/core/space#
-es,http://eulersharp.sourceforge.net/2003/03swap/log-rules#
-zoology,http://purl.org/NET/biol/zoology#
-swrlb,http://www.w3.org/2003/11/swrlb#
+affy,http://www.affymetrix.com/community/publications/affymetrix/tmsplice#
+lingvoj,http://www.lingvoj.org/ontology#
+courseware,http://courseware.rkbexplorer.com/ontologies/courseware#
+link,http://www.w3.org/2006/link#
+video,http://purl.org/media/video#
+tl,http://purl.org/NET/c4dm/timeline.owl#
+nco,http://www.semanticdesktop.org/ontologies/2007/03/22/nco#
fec,http://www.rdfabout.com/rdf/schema/usfec/
-lang,http://ontologi.es/lang/core#
-coref,http://www.rkbexplorer.com/ontologies/coref#
-doc,http://www.w3.org/2000/10/swap/pim/doc#
-os,http://www.w3.org/2000/10/swap/os#
-atomix,http://buzzword.org.uk/rdf/atomix#
-ne,http://umbel.org/umbel/ne/
-omb,http://purl.org/ontomedia/ext/common/being#
money,http://purl.org/net/rdf-money/
-hard,http://www.w3.org/2007/uwa/context/hardware.owl#
-ov,http://open.vocab.org/terms/
-java,http://www.w3.org/2007/uwa/context/java.owl#
-eztag,http://ontologies.ezweb.morfeo-project.org/eztag/ns#
-abc,http://www.metadata.net/harmony/ABCSchemaV5Commented.rdf#
-tmo,http://www.semanticdesktop.org/ontologies/2008/05/20/tmo#
-vs,http://www.w3.org/2003/06/sw-vocab-status/ns#
sede,http://eventography.org/sede/0.1/
+rec,http://purl.org/ontology/rec/core#
+atom,http://www.w3.org/2005/Atom/
+atomix,http://buzzword.org.uk/rdf/atomix#
+sit,http://www.ontologydesignpatterns.org/cp/owl/situation.owl#
+powder,http://www.w3.org/2007/05/powder#
+fresnel,http://www.w3.org/2004/09/fresnel#
+rei,http://www.w3.org/2004/06/rei#
+doc,http://www.w3.org/2000/10/swap/pim/doc#
+coref,http://www.rkbexplorer.com/ontologies/coref#
nrl,http://www.semanticdesktop.org/ontologies/2007/08/15/nrl#
-ibis,http://purl.org/ibis#
+spin,http://spinrdf.org/spin#
+umbel,http://umbel.org/umbel#
code,http://telegraphis.net/ontology/measurement/code#
-omp,http://purl.org/ontomedia/ext/common/profession#
-dcam,http://purl.org/dc/dcam/
+zoology,http://purl.org/NET/biol/zoology#
+wordmap,http://purl.org/net/ns/wordmap#
+lotico,http://www.lotico.com/resource/
+audio,http://purl.org/media/audio#
+meta,http://www.openrdf.org/rdf/2009/metadata#
+protege,http://protege.stanford.edu/system#
+time,http://www.w3.org/2006/time#
+sv,http://schemas.talis.com/2005/service/schema#
+ya,http://blogs.yandex.ru/schema/foaf/
+bio2rdf,http://bio2rdf.org/
+biol,http://purl.org/NET/biol/ns#
imm,http://schemas.microsoft.com/imm/
-xhe,http://buzzword.org.uk/rdf/xhtml-elements#
+sp,http://spinrdf.org/sp#
+exif,http://www.w3.org/2003/12/exif/ns#
+swrlb,http://www.w3.org/2003/11/swrlb#
+iswc,http://annotation.semanticweb.org/2004/iswc#
+ecs,http://rdf.ecs.soton.ac.uk/ontology/ecs#
+p3p,http://www.w3.org/2002/01/p3prdfv1#
kwijibo,http://kwijibo.talis.com/
-sv,http://schemas.talis.com/2005/service/schema#
-h5,http://buzzword.org.uk/rdf/h5#
-space,http://purl.org/net/schemas/space/
-wdrs,http://www.w3.org/2007/05/powder-s#
-video,http://purl.org/media/video#
-wnschema,http://www.cogsci.princeton.edu/~wn/schema/
+eztag,http://ontologies.ezweb.morfeo-project.org/eztag/ns#
+so,http://purl.org/ontology/symbolic-music/
+lang,http://ontologi.es/lang/core#
+tmo,http://www.semanticdesktop.org/ontologies/2008/05/20/tmo#
+airport,http://www.daml.org/2001/10/html/airport-ont#
+java,http://www.w3.org/2007/uwa/context/java.owl#
+acc,http://purl.org/NET/acc#
+os,http://www.w3.org/2000/10/swap/os#
+ne,http://umbel.org/umbel/ne/
+omp,http://purl.org/ontomedia/ext/common/profession#
+lx,http://purl.org/NET/lx#
+doclist,http://www.junkwork.net/xml/DocumentList#
+lifecycle,http://purl.org/vocab/lifecycle/schema#
+omc,http://purl.org/ontomedia/ext/common/bestiary#
+dailymed,http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/
+ibis,http://purl.org/ibis#
sail,http://www.openrdf.org/config/sail#
-custom,http://www.openrdf.org/config/sail/custom#
-acc,http://purl.org/NET/acc#
-rsa,http://www.w3.org/ns/auth/rsa#
-sit,http://www.ontologydesignpatterns.org/cp/owl/situation.owl#
-wdr,http://www.w3.org/2007/05/powder#
-airport,http://www.daml.org/2001/10/html/airport-ont#
-rei,http://www.w3.org/2004/06/rei#
-mit,http://purl.org/ontology/mo/mit#
-phss,http://ns.poundhill.com/phss/1.0/
-ncal,http://www.semanticdesktop.org/ontologies/2007/04/02/ncal#
osoc,http://web-semantics.org/ns/opensocial#
+hard,http://www.w3.org/2007/uwa/context/hardware.owl#
+grddl,http://www.w3.org/2003/g/data-view#
ptr,http://www.w3.org/2009/pointers#
-protege,http://protege.stanford.edu/system#
-irw,http://www.ontologydesignpatterns.org/ont/web/irw.owl#
-omc,http://purl.org/ontomedia/ext/common/bestiary#
-tdb,http://jena.hpl.hp.com/2008/tdb#
-meta,http://www.openrdf.org/rdf/2009/metadata#
-iswc,http://annotation.semanticweb.org/2004/iswc#
-lingvoj,http://www.lingvoj.org/ontology#
-resex,http://resex.rkbexplorer.com/ontologies/resex#
-chord,http://purl.org/ontology/chord/
-p3p,http://www.w3.org/2002/01/p3prdfv1#
-oauth,http://demiblog.org/vocab/oauth#
-acl,http://www.w3.org/ns/auth/acl#
-tl,http://purl.org/NET/c4dm/timeline.owl#
-xen,http://buzzword.org.uk/rdf/xen#
-acm,http://www.rkbexplorer.com/ontologies/acm#
-link,http://www.w3.org/2006/link#
-umbel,http://umbel.org/umbel#
-swh,http://plugin.org.uk/swh-plugins/
+spl,http://spinrdf.org/spl#
+wnschema,http://www.cogsci.princeton.edu/~wn/schema/
+es,http://eulersharp.sourceforge.net/2003/03swap/log-rules#
+unit,http://qudt.org/vocab/unit#
+label,http://purl.org/net/vocab/2004/03/label#
+moat,http://moat-project.org/ns#
+hlisting,http://sindice.com/hlisting/0.1/
+test,http://test2.example.com/
lom,http://ltsc.ieee.org/rdf/lomv1p0/lom#
-common,http://www.w3.org/2007/uwa/context/common.owl#
-ya,http://blogs.yandex.ru/schema/foaf/
-frbre,http://purl.org/vocab/frbr/extended#
+osgb,http://data.ordnancesurvey.co.uk/id/
+custom,http://www.openrdf.org/config/sail/custom#
prj,http://purl.org/stuff/project/
+resist,http://www.rkbexplorer.com/ontologies/resist#
+pmlp,http://inference-web.org/2.0/pml-provenance.owl#
+smiley,http://www.smileyontology.com/ns#
+formats,http://www.w3.org/ns/formats/
+h5,http://buzzword.org.uk/rdf/h5#
+sdl,http://purl.org/vocab/riro/sdl#
+space,http://purl.org/net/schemas/space/
+wv,http://vocab.org/waiver/terms/
+ncal,http://www.semanticdesktop.org/ontologies/2007/04/02/ncal#
+ping,http://purl.org/net/pingback/
+list,http://www.w3.org/2000/10/swap/list#
+sml,http://topbraid.org/sparqlmotionlib#
+phss,http://ns.poundhill.com/phss/1.0/
+omm,http://purl.org/ontomedia/core/media#
+meetup,http://www.lotico.com/meetup/
net,http://www.w3.org/2007/uwa/context/network.owl#
-hlisting,http://sindice.com/hlisting/0.1/
-sdl,http://purl.org/vocab/riro/sdl#
-trackback,http://madskills.com/public/xml/rss/module/trackback/
+qdoslf,http://foaf.qdos.com/lastfm/schema/
+xen,http://buzzword.org.uk/rdf/xen#
+tdb,http://jena.hpl.hp.com/2008/tdb#
+gold,http://purl.org/linguistics/gold/
nmo,http://www.semanticdesktop.org/ontologies/2007/03/22/nmo#
-cert,http://www.w3.org/ns/auth/cert#
-spl,http://spinrdf.org/spl#
-sp,http://spinrdf.org/sp#
-dailymed,http://www4.wiwiss.fu-berlin.de/dailymed/resource/dailymed/
-resist,http://www.rkbexplorer.com/ontologies/resist#
+xhe,http://buzzword.org.uk/rdf/xhtml-elements#
swp,http://www.w3.org/2004/03/trix/swp-2/
-fresnel,http://www.w3.org/2004/09/fresnel#
-lt,http://diplomski.nelakolundzija.org/LTontology.rdf#
-wv,http://vocab.org/waiver/terms/
product,http://purl.org/commerce/product#
-test,http://test2.example.com/
-gold,http://purl.org/linguistics/gold/
-smiley,http://www.smileyontology.com/ns#
+lfn,http://www.dotnetrdf.org/leviathan#
+whois,http://www.kanzaki.com/ns/whois#
+pr,http://ontologi.es/profiling#
+biocore,http://bio2rdf.org/core#
+cnt,http://www.w3.org/2008/content#
swandr,http://purl.org/swan/1.2/discourse-relationships/
-ddc,http://purl.org/NET/decimalised#
-soft,http://www.w3.org/2007/uwa/context/software.owl#
+frbre,http://purl.org/vocab/frbr/extended#
nexif,http://www.semanticdesktop.org/ontologies/2007/05/10/nexif#
-skosxl,http://www.w3.org/2008/05/skos-xl#
+sm,http://topbraid.org/sparqlmotion#
+fed,http://www.openrdf.org/config/sail/federation#
+oat,http://openlinksw.com/schemas/oat/
+c4n,http://vocab.deri.ie/c4n#
+smf,http://topbraid.org/sparqlmotionfunctions#
+trackback,http://madskills.com/public/xml/rss/module/trackback/
ire,http://www.ontologydesignpatterns.org/cpont/ire.owl#
-fed,http://www.openrdf.org/config/sail/federation#
-courseware,http://courseware.rkbexplorer.com/ontologies/courseware#
-biol,http://purl.org/NET/biol/ns#
+opm,http://openprovenance.org/ontology#
+common,http://www.w3.org/2007/uwa/context/common.owl#
gpt,http://purl.org/vocab/riro/gpt#
+soft,http://www.w3.org/2007/uwa/context/software.owl#
+bibtex,http://purl.oclc.org/NET/nknouf/ns/bibtex#
+climb,http://climb.dataincubator.org/vocabs/climb/
+wisski,http://wiss-ki.eu/
+pmt,http://tipsy.googlecode.com/svn/trunk/vocab/pmt#
+opensearch,http://a9.com/-/spec/opensearch/1.1/
+bsbm,http://www4.wiwiss.fu-berlin.de/bizer/bsbm/v01/vocabulary/
sesame,http://www.openrdf.org/schema/sesame#
-time,http://www.w3.org/2006/time#
-atom,http://www.w3.org/2005/Atom/
-omm,http://purl.org/ontomedia/core/media#
-lotico,http://www.lotico.com/resource/
+swh,http://plugin.org.uk/swh-plugins/
+mysql,http://web-semantics.org/ns/mysql/
+nid3,http://www.semanticdesktop.org/ontologies/2007/05/10/nid3#
+lt,http://diplomski.nelakolundzija.org/LTontology.rdf#
web,http://www.w3.org/2007/uwa/context/web.owl#
-sm,http://topbraid.org/sparqlmotion#
+like,http://ontologi.es/like#
states,http://www.w3.org/2005/07/aaa#
-moat,http://moat-project.org/ns#
-pimo,http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#
-push,http://www.w3.org/2007/uwa/context/push.owl#
-bio2rdf,http://bio2rdf.org/
-bsbm,http://www4.wiwiss.fu-berlin.de/bizer/bsbm/v01/vocabulary/
-bibtex,http://purl.oclc.org/NET/nknouf/ns/bibtex#
-music,http://musicontology.com/
+ddc,http://purl.org/NET/decimalised#
+imreg,http://www.w3.org/2004/02/image-regions#
+ddl,http://purl.org/vocab/riro/ddl#
+cycann,http://sw.cyc.com/CycAnnotations_v1#
dummy,http://hello.com/
-am,http://vocab.deri.ie/am#
-wairole,http://www.w3.org/2005/01/wai-rdf/GUIRoleTaxonomy#
-pmt,http://tipsy.googlecode.com/svn/trunk/vocab/pmt#
-loc,http://www.w3.org/2007/uwa/context/location.owl#
-doclist,http://www.junkwork.net/xml/DocumentList#
-pmlr,http://inference-web.org/2.0/pml-relation.owl#
-ddl,http://purl.org/vocab/riro/ddl#
-audio,http://purl.org/media/audio#
-qdoslf,http://foaf.qdos.com/lastfm/schema/
-uri,http://purl.org/NET/uri#
+obj,http://www.openrdf.org/rdf/2009/object#
+resource,http://purl.org/vocab/resourcelist/schema#
+compass,http://purl.org/net/compass#
+swanag,http://purl.org/swan/1.2/agents/
crypto,http://www.w3.org/2000/10/swap/crypto#
-like,http://ontologi.es/like#
-lfn,http://www.dotnetrdf.org/leviathan#
+push,http://www.w3.org/2007/uwa/context/push.owl#
+puc,http://purl.org/NET/puc#
+rdfa,http://www.w3.org/ns/rdfa#
xl,http://langegger.at/xlwrap/vocab#
+xhtmlvocab,http://www.w3.org/1999/xhtml/vocab/
dady,http://purl.org/NET/dady#
-sl,http://www.semanlink.net/2001/00/semanlink-schema#
-wisski,http://wiss-ki.eu/
-pr,http://ontologi.es/profiling#
-climb,http://climb.dataincubator.org/vocabs/climb/
+pmlr,http://inference-web.org/2.0/pml-relation.owl#
+psych,http://purl.org/vocab/psychometric-profile/
+pimo,http://www.semanticdesktop.org/ontologies/2007/11/01/pimo#
+string,http://www.w3.org/2000/10/swap/string#
+urn,http://fliqz.com/
+coin,http://purl.org/court/def/2009/coin#
+plink,http://buzzword.org.uk/rdf/personal-link-types#
conserv,http://conserv.deri.ie/ontology#
-sml,http://topbraid.org/sparqlmotionlib#
-dcat,http://www.w3.org/ns/dcat#
-formats,http://www.w3.org/ns/formats/
-label,http://purl.org/net/vocab/2004/03/label#
-puc,http://purl.org/NET/puc#
-list,http://www.w3.org/2000/10/swap/list#
-lifecycle,http://purl.org/vocab/lifecycle/schema#
-swanpav,http://purl.org/swan/1.2/pav/
-smf,http://topbraid.org/sparqlmotionfunctions#
-grddl,http://www.w3.org/2003/g/data-view#
-pmlp,http://inference-web.org/2.0/pml-provenance.owl#
-opm,http://openprovenance.org/ontology#
-cycann,http://sw.cyc.com/CycAnnotations_v1#
-obj,http://www.openrdf.org/rdf/2009/object#
-urn,http://fliqz.com/
+rooms,http://vocab.deri.ie/rooms#
+cco,http://purl.org/ontology/cco/core#
+xesam,http://freedesktop.org/standards/xesam/1.0/core#
+am,http://vocab.deri.ie/am#
play,http://uriplay.org/spec/ontology/#
-ping,http://purl.org/net/pingback/
-c4n,http://vocab.deri.ie/c4n#
-mysql,http://web-semantics.org/ns/mysql/
-rdfa,http://www.w3.org/ns/rdfa#
-osgb,http://data.ordnancesurvey.co.uk/id/
-resource,http://purl.org/vocab/resourcelist/schema#
-xesam,http://freedesktop.org/standards/xesam/1.0/core#
-plink,http://buzzword.org.uk/rdf/personal-link-types#
-so,http://purl.org/ontology/symbolic-music/
-commerce,http://purl.org/commerce#
-opensearch,http://a9.com/-/spec/opensearch/1.1/
-exif,http://www.w3.org/2003/12/exif/ns#
-psych,http://purl.org/vocab/psychometric-profile/
evset,http://dsnotify.org/vocab/eventset/0.1/
+mf,http://poshrdf.org/ns/mf#
+geographis,http://telegraphis.net/ontology/geography/geography#
sysont,http://ns.ontowiki.net/SysOnt/
-ldap,http://purl.org/net/ldap/
-string,http://www.w3.org/2000/10/swap/string#
-swanag,http://purl.org/swan/1.2/agents/
-nid3,http://www.semanticdesktop.org/ontologies/2007/05/10/nid3#
+sl,http://www.semanlink.net/2001/00/semanlink-schema#
+uri,http://purl.org/NET/uri#
+wairole,http://www.w3.org/2005/01/wai-rdf/GUIRoleTaxonomy#
ttl,http://www.w3.org/2008/turtle#
+swanpav,http://purl.org/swan/1.2/pav/
+bib,http://zeitkunst.org/bibtex/0.1/bibtex.owl#
+tripfs,http://purl.org/tripfs/2010/02#
swanco,http://purl.org/swan/1.2/swan-commons/
-tripfs,http://purl.org/tripfs/2010/02#
-imreg,http://www.w3.org/2004/02/image-regions#
-swanci,http://purl.org/swan/1.2/citations/
-meetup,http://www.lotico.com/meetup/
-cnt,http://www.w3.org/2008/content#
+opo,http://online-presence.net/opo/ns#
okkam,http://models.okkam.org/ENS-core-vocabulary#
-mf,http://poshrdf.org/ns/mf#
-rec,http://purl.org/ontology/rec/core#
-xhtmlvocab,http://www.w3.org/1999/xhtml/vocab/
-coin,http://purl.org/court/def/2009/coin#
-geographis,http://telegraphis.net/ontology/geography/geography#
-opo,http://online-presence.net/opo/ns#
+game,http://data.totl.net/game/
swivt,http://semantic-mediawiki.org/swivt/1.0#
-rooms,http://vocab.deri.ie/rooms#
-oat,http://openlinksw.com/schemas/oat/
-bib,http://zeitkunst.org/bibtex/0.1/bibtex.owl#
+status,http://ontologi.es/status#
+swanci,http://purl.org/swan/1.2/citations/
+olo,http://purl.org/ontology/olo/core#
+txn,http://lod.taxonconcept.org/ontology/txn.owl#
oc,http://opencoinage.org/rdf/
-status,http://ontologi.es/status#
ezcontext,http://ontologies.ezweb.morfeo-project.org/ezcontext/ns#
-swid,http://semanticweb.org/id/
-pmlt,http://inference-web.org/2.0/pml-trust.owl#
+geoes,http://geo.linkeddata.es/ontology/
+xtypes,http://purl.org/xtypes/
+meteo,http://purl.org/ns/meteo#
sparql,http://www.openrdf.org/config/repository/sparql#
-txn,http://lod.taxonconcept.org/ontology/txn.owl#
-oo,http://purl.org/openorg/
-ct,http://data.linkedct.org/resource/linkedct/
-wlp,http://weblab-project.org/core/model/property/processing/
-ufmedia,http://purl.org/microformat/hmedia/
-sioca,http://rdfs.org/sioc/actions#
awol,http://bblfish.net/work/atom-owl/2006-06-06/#
-pdo,http://ontologies.smile.deri.ie/pdo#
-pto,http://www.productontology.org/id/
+evopat,http://ns.aksw.org/Evolution/
+sdmx,http://purl.org/linked-data/sdmx#
+ldap,http://purl.org/net/ldap/
+isq,http://purl.org/ontology/is/quality/
+lark1,http://users.utcluj.ro/~raluca/ontology/Ontology1279614123500.owl#
aifb,http://www.aifb.kit.edu/id/
-prot,http://www.proteinontology.info/po.owl#
-evopat,http://ns.aksw.org/Evolution/
-meteo,http://purl.org/ns/meteo#
+isi,http://purl.org/ontology/is/inst/
+ao,http://purl.org/ontology/ao/core#
+wlp,http://weblab-project.org/core/model/property/processing/
+ct,http://data.linkedct.org/resource/linkedct/
tarot,http://data.totl.net/tarot/card/
+anca,http://users.utcluj.ro/~raluca/rdf_ontologies_ralu/ralu_modified_ontology_pizzas2_0#
+kb,http://deductions.sf.net/ontology/knowledge_base.owl#
+opmv,http://purl.org/net/opmv/ns#
+pmlt,http://inference-web.org/2.0/pml-trust.owl#
+xbrli,http://www.xbrl.org/2003/instance#
ist,http://purl.org/ontology/is/types/
-anca,http://users.utcluj.ro/~raluca/rdf_ontologies_ralu/ralu_modified_ontology_pizzas2_0#
-whois,http://www.kanzaki.com/ns/whois#
+xro,http://purl.org/xro/ns#
+postcode,http://data.ordnancesurvey.co.uk/id/postcodeunit/
+dayta,http://dayta.me/resource#
+swid,http://semanticweb.org/id/
+prot,http://www.proteinontology.info/po.owl#
+opus,http://lsdis.cs.uga.edu/projects/semdis/opus#
+core,http://vivoweb.org/ontology/core#
+geospecies,http://rdf.geospecies.org/ont/geospecies#
+go,http://www.geneontology.org/go#
sawsdl,http://www.w3.org/ns/sawsdl#
+pdo,http://ontologies.smil...
[truncated message content] |
|
From: <lor...@us...> - 2013-06-13 13:34:03
|
Revision: 3995
http://sourceforge.net/p/dl-learner/code/3995
Author: lorenz_b
Date: 2013-06-13 13:34:00 +0000 (Thu, 13 Jun 2013)
Log Message:
-----------
Cleaned up pom. Optimzed cache usage.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/pom.xml 2013-06-13 13:34:00 UTC (rev 3995)
@@ -102,37 +102,8 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
- <type>pom</type>
+ <version>3.4.4</version>
</dependency>
- <dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-dlsyntax</artifactId>
- <version>3.3</version>
- </dependency>
- <dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-functional</artifactId>
- <version>3.3</version>
- </dependency>
-
- <dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-reasoner</artifactId>
-</dependency>
-<dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-debugging</artifactId>
- <version>3.3</version>
-</dependency>
-<dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-modularity</artifactId>
- <version>3.3</version>
-</dependency>
-<dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-util</artifactId>
- </dependency>
<!-- THIS IS FROM THE UNIBAS REPO -->
<dependency>
Modified: trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java 2013-06-13 13:34:00 UTC (rev 3995)
@@ -21,6 +21,7 @@
import java.io.File;
import java.net.URI;
+import java.util.Collections;
import org.dllearner.core.AbstractKnowledgeSource;
import org.dllearner.core.OntologyFormat;
@@ -39,10 +40,12 @@
private byte[] ontologyBytes;
private OntologyToByteConverter converter = new SimpleOntologyToByteConverter();
+ private OWLOntology ontology;
- public OWLAPIOntology(OWLOntology onto) {
- ontologyBytes = converter.convert(onto);
+ public OWLAPIOntology(OWLOntology ontology) {
+ this.ontology = ontology;
+// ontologyBytes = converter.convert(ontology);
}
public static String getName() {
@@ -51,7 +54,20 @@
@Override
public OWLOntology createOWLOntology(OWLOntologyManager manager) {
- return converter.convert(ontologyBytes, manager);
+ OWLOntology copy = null;
+ try {
+ IRI iri;
+ if(ontology.getOntologyID().isAnonymous()){
+ iri = IRI.generateDocumentIRI();
+ } else {
+ iri = ontology.getOntologyID().getOntologyIRI();
+ }
+ copy = manager.createOntology(iri, Collections.singleton(ontology));
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+// return converter.convert(ontologyBytes, manager);
+ return copy;
}
@Override
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 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-06-13 13:34:00 UTC (rev 3995)
@@ -11,7 +11,6 @@
import org.aksw.jena_sparql_api.cache.extra.CacheEx;
import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
-//import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
import org.apache.log4j.Level;
@@ -19,6 +18,7 @@
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.rdf.model.Model;
+//import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
//import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
public class ConciseBoundedDescriptionGeneratorImpl implements ConciseBoundedDescriptionGenerator{
@@ -27,34 +27,42 @@
private int chunkSize = 0;
- private ExtractionDBCache cache;
- private SparqlEndpoint endpoint;
private Model baseModel;
private List<String> namespaces;
+ private static final int MAX_RECURSION_DEPTH_DEFAULT = 1;
private int maxRecursionDepth = 1;
- private String cacheDir;
+ private QueryExecutionFactory qef;
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache) {
- this.endpoint = endpoint;
- this.cache = cache;
+ this(endpoint, cache, MAX_RECURSION_DEPTH_DEFAULT);
}
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache, int maxRecursionDepth) {
- this.endpoint = endpoint;
- this.cache = cache;
- this.maxRecursionDepth = maxRecursionDepth;
+ this(endpoint, cache.getCacheDirectory(), maxRecursionDepth);
}
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir, int maxRecursionDepth) {
- this.endpoint = endpoint;
- this.cacheDir = cacheDir;
this.maxRecursionDepth = maxRecursionDepth;
+
+ qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+ if(cacheDir != null){
+ try {
+ long timeToLive = TimeUnit.DAYS.toMillis(30);
+ CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDir, timeToLive, true);
+ CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+ qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+ qef = new QueryExecutionFactoryPaginated(qef, 10000);
}
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir) {
- this.endpoint = endpoint;
- this.cacheDir = cacheDir;
+ this(endpoint, cacheDir, MAX_RECURSION_DEPTH_DEFAULT);
}
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint) {
@@ -63,6 +71,8 @@
public ConciseBoundedDescriptionGeneratorImpl(Model model) {
this.baseModel = model;
+
+ qef = new QueryExecutionFactoryModel(baseModel);
}
public Model getConciseBoundedDescription(String resourceURI){
@@ -79,25 +89,6 @@
private Model getModelChunked(String resource, int depth){
String query = makeConstructQueryOptional(resource, chunkSize, 0, depth);
- QueryExecutionFactory qef;
- if(endpoint != null){
- qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
- if(cacheDir != null){
- try {
- long timeToLive = TimeUnit.DAYS.toMillis(30);
- CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDir, timeToLive, true);
- CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
- qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (SQLException e) {
- e.printStackTrace();
- }
- }
- qef = new QueryExecutionFactoryPaginated(qef, 10000);
- } else {
- qef = new QueryExecutionFactoryModel(baseModel);
- }
QueryExecution qe = qef.createQueryExecution(query);
Model model = qe.execConstruct();
return model;
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-13 13:34:00 UTC (rev 3995)
@@ -19,7 +19,6 @@
package org.dllearner.reasoning;
-import java.net.SocketTimeoutException;
import java.net.URL;
import java.sql.SQLException;
import java.util.ArrayList;
@@ -41,6 +40,7 @@
import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
+import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
import org.dllearner.core.ComponentAnn;
import org.dllearner.core.IndividualReasoner;
@@ -81,9 +81,6 @@
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.sparql.engine.http.QueryEngineHTTP;
-import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
-import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.OWL2;
import com.hp.hpl.jena.vocabulary.RDF;
@@ -98,6 +95,7 @@
private boolean useCache = true;
private ExtractionDBCache cache;
+ private QueryExecutionFactory qef;
private SparqlEndpointKS ks;
private ClassHierarchy hierarchy;
@@ -128,6 +126,27 @@
classPopularityMap = new HashMap<NamedClass, Integer>();
objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
+
+ if(ks.isRemote()){
+ SparqlEndpoint endpoint = ks.getEndpoint();
+ qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+ if(cache != null){
+ try {
+ long timeToLive = TimeUnit.DAYS.toMillis(30);
+ CacheCoreEx cacheBackend = CacheCoreH2.create(cache.getCacheDirectory(), timeToLive, true);
+ CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+ qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+ qef = new QueryExecutionFactoryPaginated(qef, 10000);
+
+ } else {
+ qef = new QueryExecutionFactoryModel(((LocalModelBasedSparqlEndpointKS)ks).getModel());
+ }
}
public SPARQLReasoner(OntModel model) {
@@ -1362,58 +1381,25 @@
private ResultSet executeSelectQuery(String query){
logger.debug("Sending query \n {}", query);
- ResultSet rs = null;
- if(ks.isRemote()){
- SparqlEndpoint endpoint = ks.getEndpoint();
- QueryExecutionFactory qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
- if(cache != null){
- try {
- long timeToLive = TimeUnit.DAYS.toMillis(30);
- CacheCoreEx cacheBackend = CacheCoreH2.create(cache.getCacheDirectory(), timeToLive, true);
- CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
- qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (SQLException e) {
- e.printStackTrace();
- }
- }
- qef = new QueryExecutionFactoryPaginated(qef, 10000);
- QueryExecution qe = qef.createQueryExecution(query);
- rs = qe.execSelect();
- } else {
- QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
- rs = qExec.execSelect();
- }
+ QueryExecution qe = qef.createQueryExecution(query);
+ ResultSet rs = qe.execSelect();
return rs;
}
private ResultSet executeSelectQuery(String query, long timeout){
logger.debug("Sending query \n {}", query);
- ResultSet rs = null;
- if(ks.isRemote()){
- SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
- query);
- queryExecution.setTimeout(timeout);
- queryExecution.setDefaultGraphURIs(endpoint.getDefaultGraphURIs());
- queryExecution.setNamedGraphURIs(endpoint.getNamedGraphURIs());
- try {
- rs = queryExecution.execSelect();
- } catch (QueryExceptionHTTP e) {
- if(e.getCause() instanceof SocketTimeoutException){
- logger.warn("Got timeout");
- } else {
- logger.error("Exception executing query", e);
- }
- rs = new ResultSetMem();
- }
- } else {
- QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
- rs = qExec.execSelect();
- }
+ QueryExecution qe = qef.createQueryExecution(query);
+ qe.setTimeout(timeout);
+ ResultSet rs = qe.execSelect();
return rs;
}
+
+ private boolean executeAskQuery(String query){
+ logger.debug("Sending query \n {}", query);
+ QueryExecution qe = qef.createQueryExecution(query);
+ boolean ret = qe.execAsk();
+ return ret;
+ }
/**
* Returns TRUE if the class hierarchy was computed before.
@@ -1431,27 +1417,6 @@
this.useCache = useCache;
}
- private boolean executeAskQuery(String query){
- boolean ret;
- if(ks.isRemote()){
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(ks.getEndpoint().getURL().toString(), query);
- for (String dgu : ks.getEndpoint().getDefaultGraphURIs()) {
- queryExecution.addDefaultGraph(dgu);
- }
- for (String ngu : ks.getEndpoint().getNamedGraphURIs()) {
- queryExecution.addNamedGraph(ngu);
- }
- ret = queryExecution.execAsk();
-
- } else {
- QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
- ret = qExec.execAsk();
- }
-
- return ret;
- }
-
-
public static void main(String[] args) throws Exception{
// QueryEngineHTTP e = new QueryEngineHTTP("http://bibleontology.com/sparql/index.jsp",
// "SELECT DISTINCT ?type WHERE {?s a ?type) LIMIT 10");
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java 2013-06-13 13:34:00 UTC (rev 3995)
@@ -1,5 +1,8 @@
package org.dllearner.utilities.owl;
+import org.coode.owlapi.turtle.TurtleOntologyFormat;
+import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
@@ -7,7 +10,9 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
+import java.io.FileOutputStream;
import java.io.IOException;
+import java.util.Set;
/**
* Created by IntelliJ IDEA.
@@ -26,7 +31,7 @@
OWLOntologyManager manager = ontology.getOWLOntologyManager();
try {
- manager.saveOntology(ontology,baos);
+ manager.saveOntology(ontology, baos);
baos.close();
} catch (OWLOntologyStorageException e) {
throw new RuntimeException(e);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-07-01 19:05:53
|
Revision: 4013
http://sourceforge.net/p/dl-learner/code/4013
Author: lorenz_b
Date: 2013-07-01 19:05:50 +0000 (Mon, 01 Jul 2013)
Log Message:
-----------
Minor changes in SPARQL reasonr. Updated LUCENE libs for ISLE:
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/EntityTextRetriever.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneIndexer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneSearcher.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/OxfordRepository.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/simple/SparqlSimpleExtractor.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/pom.xml 2013-07-01 19:05:50 UTC (rev 4013)
@@ -215,6 +215,14 @@
<artifactId>lucene-core</artifactId>
</dependency>
<dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-analyzers-common</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-queryparser</artifactId>
+ </dependency>
+ <dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
</dependency>
@@ -272,7 +280,7 @@
<dependency>
<groupId>org.aksw.jena-sparql-api</groupId>
<artifactId>jena-sparql-api-core</artifactId>
- <version>2.10.0-4-SNAPSHOT</version>
+ <version>2.10.0-5-SNAPSHOT</version>
</dependency>
</dependencies>
<dependencyManagement>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/EntityTextRetriever.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/EntityTextRetriever.java 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/EntityTextRetriever.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -43,6 +43,6 @@
* @param entity The entity to handle.
* @return A weighted set of strings. For a value x, we need to have 0 <= x <= 1.
*/
- public Map<String, Integer> getRelevantText(Entity entity);
+ public Map<String, Double> getRelevantText(Entity entity);
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneIndexer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneIndexer.java 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneIndexer.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -25,8 +25,10 @@
import java.io.IOException;
import java.util.Date;
+import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.analysis.standard.StandardAnalyzer;
import org.apache.lucene.index.IndexWriter;
+import org.apache.lucene.index.IndexWriterConfig;
import org.apache.lucene.store.FSDirectory;
import org.apache.lucene.util.Version;
@@ -51,12 +53,12 @@
Date start = new Date();
try {
- IndexWriter writer = new IndexWriter( FSDirectory.open( INDEX ),
- new StandardAnalyzer( Version.LUCENE_CURRENT ), true, IndexWriter.MaxFieldLength.LIMITED );
+ Analyzer analyzer = new StandardAnalyzer(Version.LUCENE_43);
+ IndexWriterConfig indexWriterConfig = new IndexWriterConfig(Version.LUCENE_43, analyzer);
+ IndexWriter writer = new IndexWriter( FSDirectory.open( INDEX ), indexWriterConfig);
System.out.println( "Creating index ..." );
index( writer, docDir );
System.out.println( "Optimizing index ..." );
- writer.optimize();
writer.close();
Date end = new Date();
System.out.println( end.getTime() - start.getTime() + " total milliseconds" );
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneSearcher.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneSearcher.java 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/LuceneSearcher.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -32,13 +32,14 @@
import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.analysis.standard.StandardAnalyzer;
import org.apache.lucene.document.Document;
+import org.apache.lucene.index.AtomicReaderContext;
+import org.apache.lucene.index.DirectoryReader;
import org.apache.lucene.index.IndexReader;
-import org.apache.lucene.queryParser.QueryParser;
+import org.apache.lucene.queryparser.classic.QueryParser;
import org.apache.lucene.search.Collector;
import org.apache.lucene.search.IndexSearcher;
import org.apache.lucene.search.Query;
import org.apache.lucene.search.Scorer;
-import org.apache.lucene.search.Searcher;
import org.apache.lucene.store.FSDirectory;
import org.apache.lucene.util.Version;
@@ -48,7 +49,7 @@
private String FIELD = "contents";
private IndexReader m_reader = null;
- private Searcher m_searcher = null;
+ private IndexSearcher m_searcher = null;
private Analyzer m_analyzer = null;
private QueryParser m_parser = null;
@@ -70,10 +71,10 @@
@SuppressWarnings("deprecation")
public LuceneSearcher() throws Exception {
- m_reader = IndexReader.open( FSDirectory.open( new File( INDEX ) ), true );
+ m_reader = DirectoryReader.open( FSDirectory.open( new File( INDEX ) ));
m_searcher = new IndexSearcher( m_reader );
- m_analyzer = new StandardAnalyzer( Version.LUCENE_CURRENT );
- m_parser = new QueryParser( Version.LUCENE_CURRENT, FIELD, m_analyzer );
+ m_analyzer = new StandardAnalyzer( Version.LUCENE_43);
+ m_parser = new QueryParser( Version.LUCENE_43, FIELD, m_analyzer );
}
public void close() throws Exception {
@@ -139,13 +140,13 @@
return true;
}
@Override
- public void setNextReader( IndexReader reader, int docBase ) throws IOException {
- this.docBase = docBase;
- }
- @Override
public void setScorer(Scorer scorer) throws IOException {
this.scorer = scorer;
}
+ @Override
+ public void setNextReader(AtomicReaderContext context) throws IOException {
+ this.docBase = context.docBase;
+ }
};
m_searcher.search( query, collector );
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -364,7 +364,7 @@
System.out.print(i++ + ": ");
URI uri = entry.getPhysicalURI();
// if(uri.toString().startsWith("http://rest.bioontology.org/bioportal/ontologies/download/42764")){
- if (!ontologyProcessed(uri)) {
+ if (!ontologyProcessed(uri)) {//if(entry.getOntologyShortName().equals("00698"))continue;
System.out.print("Loading \"" + entry.getOntologyShortName() + "\" from "+ uri);
try {
manager = OWLManager.createOWLOntologyManager();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -116,7 +116,7 @@
//compute the overlap if exist
Map<ObjectProperty, Integer> property2Overlap = new HashMap<ObjectProperty, Integer>();
String query = String.format("SELECT ?p (COUNT(*) AS ?cnt) WHERE {?s <%s> ?o. ?s ?p ?o.} GROUP BY ?p", propertyToDescribe.getName());
- System.out.println(query);ResultSet rs = executeSelectQuery(query);
+ ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
qs = rs.next();
Modified: trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/OxfordRepository.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/OxfordRepository.java 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/OxfordRepository.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -90,7 +90,7 @@
private URI physicalURI;
public RepositoryEntry(URI ontologyIRI) {
- this.ontologyURI = ontologyIRI;System.out.println(ontologyIRI);
+ this.ontologyURI = ontologyIRI;
OntologyIRIShortFormProvider sfp = new OntologyIRIShortFormProvider();
shortName = sfp.getShortForm(IRI.create(ontologyIRI));
physicalURI = ontologyIRI;
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 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -268,7 +268,7 @@
private Model execModel(Model model)
{
HttpQuery httpQuery = makeHttpQuery() ;
- httpQuery.setAccept(WebContent.contentTypeNTriplesAlt) ;
+ httpQuery.setAccept(WebContent.contentTypeTurtleAlt1) ;
InputStream in = httpQuery.exec() ;
//Don't assume the endpoint actually gives back the content type we asked for
@@ -284,7 +284,7 @@
//Try to select language appropriately here based on the model content type
Lang lang = WebContent.contentTypeToLang(actualContentType);
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") ;
+ model.read(in, null, "TURTLE") ;
return model ;
}
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/simple/SparqlSimpleExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/simple/SparqlSimpleExtractor.java 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/simple/SparqlSimpleExtractor.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -11,7 +11,6 @@
import org.dllearner.core.AbstractKnowledgeSource;
import org.dllearner.core.ComponentAnn;
import org.dllearner.core.ComponentInitException;
-import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.OntologyFormat;
import org.dllearner.core.OntologyFormatUnsupportedException;
import org.dllearner.core.config.ConfigOption;
@@ -36,7 +35,6 @@
import com.jamonapi.MonitorFactory;
@ComponentAnn(name = "efficient SPARQL fragment extractor", shortName = "sparqls", version = 0.1)
-
public class SparqlSimpleExtractor extends AbstractKnowledgeSource implements OWLOntologyKnowledgeSource{
@@ -334,5 +332,10 @@
JenaToOwlapiConverter converter = new JenaToOwlapiConverter();
return converter.convert(this.model,manager);
}
+
+ public static String getName(){
+ return "efficient SPARQL fragment extractor";
+ }
+
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-07-01 18:51:19 UTC (rev 4012)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-07-01 19:05:50 UTC (rev 4013)
@@ -22,10 +22,12 @@
import java.net.URL;
import java.sql.SQLException;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeMap;
@@ -73,6 +75,8 @@
import org.slf4j.LoggerFactory;
import com.clarkparsia.owlapiv3.XSD;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Multimap;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.query.QueryExecution;
@@ -80,6 +84,7 @@
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.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.OWL2;
@@ -134,7 +139,7 @@
e.printStackTrace();
}
}
- qef = new QueryExecutionFactoryPaginated(qef, 10000);
+// qef = new QueryExecutionFactoryPaginated(qef, 10000);
} else {
qef = new QueryExecutionFactoryModel(((LocalModelBasedSparqlEndpointKS)ks).getModel());
@@ -518,6 +523,100 @@
}
return types;
}
+
+ public Set<Property> getProperties(boolean inferType, String namespace) {
+ Set<Property> properties = new HashSet<Property>();
+ String query = "SELECT DISTINCT ?p ?type WHERE {?s ?p ?o."
+ + (namespace != null ? ("FILTER(REGEX(?p,'^" + namespace + "'))") : "")
+ + "OPTIONAL{?p a ?type.}}";
+ ResultSet rs = executeSelectQuery(query);
+ Multimap<String, String> uri2Types = HashMultimap.create();
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ String uri = qs.getResource("p").getURI();
+ String type = "";
+ if(qs.getResource("type") != null){
+ type = qs.getResource("type").getURI();
+ }
+ uri2Types.put(uri, type);
+ }
+ for (Entry<String, Collection<String>> entry : uri2Types.asMap().entrySet()) {
+ String uri = entry.getKey();
+ Collection<String> types = entry.getValue();
+ if(types.contains(OWL.ObjectProperty.getURI()) && !types.contains(OWL.DatatypeProperty.getURI())){
+ properties.add(new ObjectProperty(uri));
+ } else if(!types.contains(OWL.ObjectProperty.getURI()) && types.contains(OWL.DatatypeProperty.getURI())){
+ properties.add(new DatatypeProperty(uri));
+ } else {
+ //infer the type by values
+ query = "SELECT ?o WHERE {?s <" + uri + "> ?o. } LIMIT 100";
+ rs = executeSelectQuery(query);
+ boolean op = true;
+ boolean dp = true;
+ RDFNode node;
+ while(rs.hasNext()){
+ node = rs.next().get("o");
+ op = node.isResource();
+ dp = node.isLiteral();
+ }
+ if(op && !dp){
+ properties.add(new ObjectProperty(uri));
+ } else if(!op && dp){
+ properties.add(new DatatypeProperty(uri));
+ } else {
+ //not possible to decide
+ }
+ }
+ }
+ return properties;
+ }
+
+ public Set<Property> getProperties(boolean inferType) {
+ Set<Property> properties = new TreeSet<Property>();
+ String query = "SELECT DISTINCT ?p ?type WHERE {?s ?p ?o. OPTIONAL{?p a ?type.}}";
+ ResultSet rs = executeSelectQuery(query);
+ Multimap<String, String> uri2Types = HashMultimap.create();
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ String uri = qs.getResource("p").getURI();
+ String type = "";
+ if(qs.getResource("type") != null){
+ type = qs.getResource("type").getURI();
+ }
+ uri2Types.put(uri, type);
+ }
+ for (Entry<String, Collection<String>> entry : uri2Types.asMap().entrySet()) {
+ String uri = entry.getKey();
+ Collection<String> types = entry.getValue();
+ if(types.contains(OWL.ObjectProperty.getURI()) && !types.contains(OWL.DatatypeProperty.getURI())){
+ properties.add(new ObjectProperty(uri));
+ } else if(!types.contains(OWL.ObjectProperty.getURI()) && types.contains(OWL.DatatypeProperty.getURI())){
+ properties.add(new DatatypeProperty(uri));
+ } else {
+ //infer the type by values
+ query = "SELECT ?o WHERE {?s <" + uri + "> ?o. } LIMIT 100";
+ rs = executeSelectQuery(query);
+ boolean op = true;
+ boolean dp = true;
+ RDFNode node;
+ while(rs.hasNext()){
+ node = rs.next().get("o");
+ op = node.isResource();
+ dp = node.isLiteral();
+ }
+ if(op && !dp){
+ properties.add(new ObjectProperty(uri));
+ } else if(!op && dp){
+ properties.add(new DatatypeProperty(uri));
+ } else {
+ //not possible to decide
+ }
+ }
+ }
+ return properties;
+ }
public Set<NamedClass> getOWLClasses() {
Set<NamedClass> types = new HashSet<NamedClass>();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-09-04 13:18:24
|
Revision: 4056
http://sourceforge.net/p/dl-learner/code/4056
Author: lorenz_b
Date: 2013-09-04 13:18:17 +0000 (Wed, 04 Sep 2013)
Log Message:
-----------
Added wordnet+stanford.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/StopWordFilter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/Annotation.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/SemanticAnnotation.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/SemanticAnnotator.java
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/semantic/simple/SimpleSemanticIndex.java
trunk/components-core/src/main/resources/wordnet_properties.xml
trunk/components-core/src/test/java/org/dllearner/algorithms/isle/ISLETest.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/algorithms/isle/SimpleWordSenseDisambiguation.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-09-04 10:04:14 UTC (rev 4055)
+++ trunk/components-core/pom.xml 2013-09-04 13:18:17 UTC (rev 4056)
@@ -282,6 +282,32 @@
<artifactId>jena-sparql-api-core</artifactId>
<version>2.10.0-5-SNAPSHOT</version>
</dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-lang3</artifactId>
+ <version>3.1</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.stanford.nlp</groupId>
+ <artifactId>stanford-corenlp</artifactId>
+ <version>1.3.4</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.stanford.nlp</groupId>
+ <artifactId>stanford-corenlp</artifactId>
+ <version>1.3.4</version>
+ </dependency>
+ <dependency>
+ <groupId>edu.stanford.nlp</groupId>
+ <artifactId>stanford-corenlp</artifactId>
+ <version>1.3.4</version>
+ <classifier>models</classifier>
+ </dependency>
+ <dependency>
+ <groupId>net.didion.jwnl</groupId>
+ <artifactId>jwnl</artifactId>
+ <version>1.4.1.RC2</version>
+ </dependency>
</dependencies>
<dependencyManagement>
<dependencies>
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/SimpleWordSenseDisambiguation.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/SimpleWordSenseDisambiguation.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/SimpleWordSenseDisambiguation.java 2013-09-04 13:18:17 UTC (rev 4056)
@@ -0,0 +1,79 @@
+/**
+ *
+ */
+package org.dllearner.algorithms.isle;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.dllearner.algorithms.isle.index.Annotation;
+import org.dllearner.algorithms.isle.index.SemanticAnnotation;
+import org.dllearner.core.owl.Entity;
+import org.dllearner.utilities.owl.OWLAPIConverter;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLEntity;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.util.IRIShortFormProvider;
+import org.semanticweb.owlapi.util.SimpleIRIShortFormProvider;
+
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
+/**
+ * @author Lorenz Buehmann
+ *
+ */
+public class SimpleWordSenseDisambiguation extends WordSenseDisambiguation{
+
+ private IRIShortFormProvider sfp = new SimpleIRIShortFormProvider();
+ private OWLDataFactory df = new OWLDataFactoryImpl();
+ private OWLAnnotationProperty annotationProperty = df.getRDFSLabel();
+
+ /**
+ * @param ontology
+ */
+ public SimpleWordSenseDisambiguation(OWLOntology ontology) {
+ super(ontology);
+ }
+
+ /* (non-Javadoc)
+ * @see org.dllearner.algorithms.isle.WordSenseDisambiguation#disambiguate(org.dllearner.algorithms.isle.index.Annotation, java.util.Set)
+ */
+ @Override
+ public SemanticAnnotation disambiguate(Annotation annotation, Set<Entity> candidateEntities) {
+ String token = annotation.getToken();
+ //check if annotation token matches label of entity or the part behind #(resp. /)
+ for (Entity entity : candidateEntities) {
+ Set<String> labels = getLabels(entity);
+ for (String label : labels) {
+ if(label.equals(token)){
+ return new SemanticAnnotation(annotation, entity);
+ }
+ }
+ String shortForm = sfp.getShortForm(IRI.create(entity.getURI()));
+ if(annotation.equals(shortForm)){
+ return new SemanticAnnotation(annotation, entity);
+ }
+ }
+ return null;
+ }
+
+ private Set<String> getLabels(Entity entity){
+ Set<String> labels = new HashSet<String>();
+ OWLEntity owlEntity = OWLAPIConverter.getOWLAPIEntity(entity);
+ Set<OWLAnnotationAssertionAxiom> axioms = ontology.getAnnotationAssertionAxioms(owlEntity.getIRI());
+ for (OWLAnnotationAssertionAxiom annotation : axioms) {
+ if(annotation.getProperty().equals(annotationProperty)){
+ if (annotation.getValue() instanceof OWLLiteral) {
+ OWLLiteral val = (OWLLiteral) annotation.getValue();
+ labels.add(val.getLiteral());
+ }
+ }
+ }
+ return labels;
+ }
+
+}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/StopWordFilter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/StopWordFilter.java 2013-09-04 10:04:14 UTC (rev 4055)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/StopWordFilter.java 2013-09-04 13:18:17 UTC (rev 4056)
@@ -45,7 +45,7 @@
public void removeStopWordAnnotations(Set<Annotation> annotations) {
for (Iterator<Annotation> iter = annotations.iterator(); iter.hasNext();) {
Annotation annotation = iter.next();
- String content = annotation.getGetReferencedDocument().getContent();
+ String content = annotation.getReferencedDocument().getContent();
String token = content.substring(annotation.getOffset(), annotation.getOffset()+annotation.getLength());
if(stopWords.contains(token)){
iter.remove();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/Annotation.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/Annotation.java 2013-09-04 10:04:14 UTC (rev 4055)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/Annotation.java 2013-09-04 13:18:17 UTC (rev 4056)
@@ -10,18 +10,18 @@
*/
public class Annotation {
- private Document getReferencedDocument;
+ private Document referencedDocument;
private int offset;
private int length;
- public Annotation(Document getReferencedDocument, int offset, int length) {
- this.getReferencedDocument = getReferencedDocument;
+ public Annotation(Document referencedDocument, int offset, int length) {
+ this.referencedDocument = referencedDocument;
this.offset = offset;
this.length = length;
}
- public Document getGetReferencedDocument() {
- return getReferencedDocument;
+ public Document getReferencedDocument() {
+ return referencedDocument;
}
public int getOffset() {
@@ -31,12 +31,16 @@
public int getLength() {
return length;
}
+
+ public String getToken(){
+ return referencedDocument.getContent().substring(offset, offset + length);
+ }
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
- result = prime * result + ((getReferencedDocument == null) ? 0 : getReferencedDocument.hashCode());
+ result = prime * result + ((referencedDocument == null) ? 0 : referencedDocument.hashCode());
result = prime * result + length;
result = prime * result + offset;
return result;
@@ -51,10 +55,10 @@
if (getClass() != obj.getClass())
return false;
Annotation other = (Annotation) obj;
- if (getReferencedDocument == null) {
- if (other.getReferencedDocument != null)
+ if (referencedDocument == null) {
+ if (other.referencedDocument != null)
return false;
- } else if (!getReferencedDocument.equals(other.getReferencedDocument))
+ } else if (!referencedDocument.equals(other.referencedDocument))
return false;
if (length != other.length)
return false;
@@ -68,6 +72,6 @@
*/
@Override
public String toString() {
- return "\"" + getReferencedDocument.getContent().substring(offset, offset+length) + "\" at position " + offset;
+ return "\"" + referencedDocument.getContent().substring(offset, offset+length) + "\" at position " + offset;
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/SemanticAnnotation.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/SemanticAnnotation.java 2013-09-04 10:04:14 UTC (rev 4055)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/SemanticAnnotation.java 2013-09-04 13:18:17 UTC (rev 4056)
@@ -14,7 +14,7 @@
private Entity entity;
public SemanticAnnotation(Annotation annotation, Entity entity) {
- super(annotation.getGetReferencedDocument(), annotation.getOffset(), annotation.getLength());
+ super(annotation.getReferencedDocument(), annotation.getOffset(), annotation.getLength());
this.entity = entity;
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/SemanticAnnotator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/SemanticAnnotator.java 2013-09-04 10:04:14 UTC (rev 4055)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/SemanticAnnotator.java 2013-09-04 13:18:17 UTC (rev 4056)
@@ -43,8 +43,9 @@
for (Annotation annotation : annotations) {
Set<Entity> candidateEntities = entityCandidateGenerator.getCandidates(annotation);
SemanticAnnotation semanticAnnotation = wordSenseDisambiguation.disambiguate(annotation, candidateEntities);
- semanticAnnotations.add(semanticAnnotation);
-
+ if(semanticAnnotation != null){
+ semanticAnnotations.add(semanticAnnotation);
+ }
}
AnnotatedDocument annotatedDocument = new AnnotatedTextDocument(document, semanticAnnotations);
return annotatedDocument;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/semantic/simple/SimpleSemanticIndex.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/semantic/simple/SimpleSemanticIndex.java 2013-09-04 10:04:14 UTC (rev 4055)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/isle/index/semantic/simple/SimpleSemanticIndex.java 2013-09-04 13:18:17 UTC (rev 4056)
@@ -4,6 +4,7 @@
package org.dllearner.algorithms.isle.index.semantic.simple;
import org.dllearner.algorithms.isle.RandomWordSenseDisambiguation;
+import org.dllearner.algorithms.isle.SimpleWordSenseDisambiguation;
import org.dllearner.algorithms.isle.index.SimpleEntityCandidateGenerator;
import org.dllearner.algorithms.isle.index.SimpleLinguisticAnnotator;
import org.dllearner.algorithms.isle.index.semantic.SemanticIndex;
@@ -28,7 +29,7 @@
public SimpleSemanticIndex(OWLOntology ontology, SyntacticIndex syntacticIndex) {
super(ontology,
syntacticIndex,
- new RandomWordSenseDisambiguation(ontology),
+ new SimpleWordSenseDisambiguation(ontology),
new SimpleEntityCandidateGenerator(ontology),
new SimpleLinguisticAnnotator());
}
Modified: trunk/components-core/src/main/resources/wordnet_properties.xml
===================================================================
--- trunk/components-core/src/main/resources/wordnet_properties.xml 2013-09-04 10:04:14 UTC (rev 4055)
+++ trunk/components-core/src/main/resources/wordnet_properties.xml 2013-09-04 13:18:17 UTC (rev 4056)
@@ -38,7 +38,7 @@
<param name="dictionary_element_factory" value="net.didion.jwnl.princeton.data.PrincetonWN17FileDictionaryElementFactory"/>
<param name="file_manager" value="net.didion.jwnl.dictionary.file_manager.FileManagerImpl">
<param name="file_type" value="net.didion.jwnl.princeton.file.PrincetonRandomAccessDictionaryFile"/>
- <param name="dictionary_path" value="/opt/wordnet/dict"/>
+ <param name="dictionary_path" value="/opt/wordnet"/>
</param>
</dictionary>
<resource class="PrincetonResource"/>
Modified: trunk/components-core/src/test/java/org/dllearner/algorithms/isle/ISLETest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/algorithms/isle/ISLETest.java 2013-09-04 10:04:14 UTC (rev 4055)
+++ trunk/components-core/src/test/java/org/dllearner/algorithms/isle/ISLETest.java 2013-09-04 13:18:17 UTC (rev 4056)
@@ -118,8 +118,14 @@
public void testSemanticIndexAnnotationProperty(){
semanticIndex = new SimpleSemanticIndex(ontology, syntacticIndex);
semanticIndex.buildIndex(df.getRDFSLabel(), null);
- Set<AnnotatedDocument> documents = semanticIndex.getDocuments(new NamedClass("http://example.com/father#father"));
- System.out.println(documents);
+
+ NamedClass nc = new NamedClass("http://example.com/father#father");
+ Set<AnnotatedDocument> documents = semanticIndex.getDocuments(nc);
+ System.out.println("Documents for " + nc + ":\n" + documents);
+
+ nc = new NamedClass("http://example.com/father#person");
+ documents = semanticIndex.getDocuments(nc);
+ System.out.println("Documents for " + nc + ":\n" + documents);
}
@Test
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