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From: <dc...@us...> - 2013-05-02 10:57:45
|
Revision: 3935
http://sourceforge.net/p/dl-learner/code/3935
Author: dcherix
Date: 2013-05-02 10:57:42 +0000 (Thu, 02 May 2013)
Log Message:
-----------
Added profile to create a standalone executable war
Modified Paths:
--------------
trunk/interfaces/pom.xml
Modified: trunk/interfaces/pom.xml
===================================================================
--- trunk/interfaces/pom.xml 2013-05-02 10:29:57 UTC (rev 3934)
+++ trunk/interfaces/pom.xml 2013-05-02 10:57:42 UTC (rev 3935)
@@ -4,7 +4,7 @@
<artifactId>interfaces</artifactId>
- <packaging>jar</packaging>
+ <packaging>${packaging.type}</packaging>
<name>Interfaces: GUI, CLI, Web Service</name>
<url>http://aksw.org/Projects/DLLearner</url>
@@ -19,11 +19,81 @@
<release.name>1.0-beta-2</release.name>
<dist-dir>dl-learner-dist</dist-dir>
<install-dir>share/dl-learner</install-dir>
+ <packaging.type>jar</packaging.type>
</properties>
<profiles>
<profile>
+ <id>jetty</id>
+ <properties>
+ <packaging.type>war</packaging.type>
+ </properties>
+ <build>
+ <plugins>
+ <!-- <plugin> <groupId>org.simplericity.jettyconsole</groupId> <artifactId>jetty-console-maven-plugin</artifactId>
+ <version>1.50</version> <executions> <execution> <goals> <goal>createconsole</goal>
+ </goals> <configuration> <backgroundImage>${basedir}/src/main/resources/dl.gif</backgroundImage>
+ <additionalDependencies> <additionalDependency> <artifactId>jetty-console-log4j-plugin</artifactId>
+ </additionalDependency> </additionalDependencies> </configuration> </execution>
+ </executions> </plugin> -->
+ <plugin>
+ <groupId>org.apache.tomcat.maven</groupId>
+ <artifactId>tomcat7-maven-plugin</artifactId>
+ <version>2.1</version>
+ <executions>
+ <execution>
+ <id>tomcat-run</id>
+ <goals>
+ <goal>exec-war-only</goal>
+ </goals>
+ <phase>package</phase>
+ <configuration>
+ <path>/interfaces</path>
+ <enableNaming>false</enableNaming>
+ <finalName>dl-learner-standalone.jar</finalName>
+ <charset>utf-8</charset>
+ <extraDependencies>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ <version>${slf4j.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>jul-to-slf4j</artifactId>
+ <version>${slf4j.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-log4j12</artifactId>
+ <version>${slf4j.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>${log4j.version}</version>
+ </dependency>
+ </extraDependencies>
+ <extraResources>
+ <extraRexource>
+ <directory>${basedir}/src/main/resources/</directory>
+ <includes>
+ <include>log4j.properties</include>
+ </includes>
+ </extraRexource>
+ </extraResources>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
+ <profile>
<id>release</id>
+ <properties>
+ <packaging.type>jar</packaging.type>
+ </properties>
<build>
<finalName>interfaces</finalName>
<plugins>
@@ -128,6 +198,9 @@
</profile>
<profile>
<id>debpackage</id>
+ <properties>
+ <packaging.type>jar</packaging.type>
+ </properties>
<build>
<finalName>dl-learner</finalName>
<plugins>
@@ -345,12 +418,12 @@
<logTimeZone>GMT</logTimeZone>
</requestLog>
<connectors>
- <connector implementation="org.mortbay.jetty.nio.SelectChannelConnector">
- <port>9099</port>
- <maxIdleTime>60000</maxIdleTime>
- </connector>
- </connectors>
-
+ <connector implementation="org.mortbay.jetty.nio.SelectChannelConnector">
+ <port>9099</port>
+ <maxIdleTime>60000</maxIdleTime>
+ </connector>
+ </connectors>
+
</configuration>
<!--execution is used for testing -->
<!--executions> <execution> <id>start-jetty</id> <phase>pre-integration-test</phase>
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|
|
From: <lor...@us...> - 2013-05-02 10:30:01
|
Revision: 3934
http://sourceforge.net/p/dl-learner/code/3934
Author: lorenz_b
Date: 2013-05-02 10:29:57 +0000 (Thu, 02 May 2013)
Log Message:
-----------
Updated pattern script.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
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 2013-05-02 09:46:14 UTC (rev 3933)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-02 10:29:57 UTC (rev 3934)
@@ -242,7 +242,9 @@
if(!(ex instanceof UnparsableOntologyException)){
errorMessage += (ex.getMessage() != null ? ("->" + ex.getMessage()) : "");
}
- errorMessage = errorMessage.substring(0, 1900);
+ if(errorMessage.length() > 1900){
+ errorMessage = errorMessage.substring(0, 1900);
+ }
insertOntologyErrorPs.setString(2, errorMessage);
insertOntologyErrorPs.setString(3, repository.getName());
insertOntologyErrorPs.execute();
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|
|
From: <lor...@us...> - 2013-05-02 09:46:18
|
Revision: 3933
http://sourceforge.net/p/dl-learner/code/3933
Author: lorenz_b
Date: 2013-05-02 09:46:14 +0000 (Thu, 02 May 2013)
Log Message:
-----------
Limited length of error message to avoid SQL errors.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
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 2013-05-02 08:43:07 UTC (rev 3932)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-02 09:46:14 UTC (rev 3933)
@@ -28,6 +28,7 @@
import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.io.UnparsableOntologyException;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
@@ -237,7 +238,12 @@
//add ontology loading/parsing/... error entry
try {
insertOntologyErrorPs.setString(1, url);
- insertOntologyErrorPs.setString(2, "ERROR:" + ex.getClass().getSimpleName() + (ex.getMessage() != null ? ("->" + ex.getMessage()) : ""));
+ String errorMessage = "ERROR:" + ex.getClass().getSimpleName();
+ if(!(ex instanceof UnparsableOntologyException)){
+ errorMessage += (ex.getMessage() != null ? ("->" + ex.getMessage()) : "");
+ }
+ errorMessage = errorMessage.substring(0, 1900);
+ insertOntologyErrorPs.setString(2, errorMessage);
insertOntologyErrorPs.setString(3, repository.getName());
insertOntologyErrorPs.execute();
} catch (SQLException e) {
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|
|
From: <lor...@us...> - 2013-05-02 08:43:10
|
Revision: 3932
http://sourceforge.net/p/dl-learner/code/3932
Author: lorenz_b
Date: 2013-05-02 08:43:07 +0000 (Thu, 02 May 2013)
Log Message:
-----------
Added noise aware LGG generator.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java 2013-05-02 08:43:07 UTC (rev 3932)
@@ -0,0 +1,42 @@
+package org.dllearner.algorithms.qtl.operations.lgg;
+
+import java.util.Collection;
+
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+
+public class EvaluatedQueryTree<N> implements Comparable<EvaluatedQueryTree<N>>{
+
+ private QueryTree<N> tree;
+ private Collection<QueryTree<N>> uncoveredExamples;
+ private double score;
+
+ public EvaluatedQueryTree(QueryTree<N> tree, Collection<QueryTree<N>> uncoveredExamples, double score) {
+ this.tree = tree;
+ this.uncoveredExamples = uncoveredExamples;
+ this.score = score;
+ }
+
+ public QueryTree<N> getTree() {
+ return tree;
+ }
+
+ public Collection<QueryTree<N>> getUncoveredExamples() {
+ return uncoveredExamples;
+ }
+
+ public double getScore() {
+ return score;
+ }
+
+ @Override
+ public int compareTo(EvaluatedQueryTree<N> other) {
+ double diff = score - other.getScore();
+ if(diff == 0){
+ return -1;
+ } else if(diff > 0){
+ return -1;
+ } else {
+ return 1;
+ }
+ }
+}
\ No newline at end of file
Added: 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 (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java 2013-05-02 08:43:07 UTC (rev 3932)
@@ -0,0 +1,111 @@
+package org.dllearner.algorithms.qtl.operations.lgg;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.PriorityQueue;
+import java.util.Queue;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+
+public class NoiseSensitiveLGG<N> {
+
+ private LGGGenerator<N> lggGenerator = new LGGGeneratorImpl<N>();
+
+ private Queue<EvaluatedQueryTree<N>> todoList;
+ private SortedSet<EvaluatedQueryTree<N>> solutions;
+
+ public NoiseSensitiveLGG() {
+ }
+
+ public List<EvaluatedQueryTree<N>> computeLGG(List<QueryTree<N>> trees){
+ init(trees);
+ EvaluatedQueryTree<N> currentElement;
+ do{
+ //pick best element from todo list
+ currentElement = todoList.poll();
+ for (QueryTree<N> example : currentElement.getUncoveredExamples()) {
+ QueryTree<N> tree = currentElement.getTree();
+ //compute the LGG
+ QueryTree<N> lgg = lggGenerator.getLGG(tree, example);
+ //compute examples which are not covered by LGG
+ Collection<QueryTree<N>> uncoveredExamples = new HashSet<QueryTree<N>>();
+ for (QueryTree<N> queryTree : trees) {
+ boolean subsumed = queryTree.isSubsumedBy(lgg);
+ if(!subsumed){
+ uncoveredExamples.add(queryTree);
+ }
+ }
+ //compute score
+ double score = (trees.size() - uncoveredExamples.size()) / (double)trees.size();
+ //add to todo list, if not already contained in todo list or solution list
+ EvaluatedQueryTree<N> solution = new EvaluatedQueryTree<N>(lgg, uncoveredExamples, score);
+ todo(solution);
+ }
+ solutions.add(currentElement);
+// todoList.remove(currentElement);
+ } while(!terminationCriteriaSatisfied());
+ return new ArrayList<EvaluatedQueryTree<N>>(solutions);
+ }
+
+ private void init(List<QueryTree<N>> trees){
+ todoList = new PriorityQueue<EvaluatedQueryTree<N>>();
+ solutions = new TreeSet<EvaluatedQueryTree<N>>();
+// 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) {
+ boolean distinct = true;
+ for (QueryTree<N> otherTree : distinctTrees) {
+ if(queryTree.isSubsumedBy(otherTree)){
+ distinct = false;
+ break;
+ }
+ }
+ if(distinct){
+ distinctTrees.add(queryTree);
+ }
+ }
+ for (QueryTree<N> queryTree : distinctTrees) {
+ Collection<QueryTree<N>> uncoveredExamples = new HashSet<QueryTree<N>>(distinctTrees);
+ uncoveredExamples.remove(queryTree);
+ double score = (trees.size() - uncoveredExamples.size()) / (double)trees.size();
+ todoList.add(new EvaluatedQueryTree<N>(queryTree, uncoveredExamples, score));
+ }
+ }
+
+ /**
+ * Add tree to todo list if not already contained in that list or the solutions.
+ * @param solution
+ */
+ private void todo(EvaluatedQueryTree<N> solution){
+ //check if not already contained in todo list
+ for (EvaluatedQueryTree<N> evTree : todoList) {
+ if(sameTrees(solution.getTree(), evTree.getTree())){
+ return;
+ }
+ }
+ //check if not already contained in solutions
+ for (EvaluatedQueryTree<N> evTree : solutions) {
+ if(sameTrees(solution.getTree(), evTree.getTree())){
+ return;
+ }
+ }
+ todoList.add(solution);
+ }
+
+ private boolean sameTrees(QueryTree<N> tree1, QueryTree<N> tree2){
+ return tree1.isSubsumedBy(tree2) && tree2.isSubsumedBy(tree1);
+ }
+
+ private boolean terminationCriteriaSatisfied(){
+ return todoList.isEmpty();
+ }
+
+
+
+}
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 2013-05-02 07:35:58 UTC (rev 3931)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-02 08:43:07 UTC (rev 3932)
@@ -119,7 +119,7 @@
String var = variablesMapping.get(owlEntity);
queryString += var;
}
- }System.out.println(queryString);
+ }
return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
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|
|
From: <lor...@us...> - 2013-05-02 07:36:03
|
Revision: 3931
http://sourceforge.net/p/dl-learner/code/3931
Author: lorenz_b
Date: 2013-05-02 07:35:58 +0000 (Thu, 02 May 2013)
Log Message:
-----------
Some improvements in pattern detection workflow.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
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 2013-04-30 11:06:03 UTC (rev 3930)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-02 07:35:58 UTC (rev 3931)
@@ -14,9 +14,11 @@
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.Queue;
+import java.util.Set;
import java.util.prefs.Preferences;
import org.dllearner.kb.dataset.OWLOntologyDataset;
@@ -26,6 +28,7 @@
import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
@@ -70,6 +73,7 @@
private Connection conn;
private PreparedStatement selectOntologyIdPs;
private PreparedStatement insertOntologyPs;
+ private PreparedStatement insertOntologyErrorPs;
private PreparedStatement selectPatternIdPs;
private PreparedStatement insertPatternIdPs;
private PreparedStatement insertOntologyPatternPs;
@@ -91,7 +95,9 @@
createTables();
try {
selectOntologyIdPs = conn.prepareStatement("SELECT id FROM Ontology WHERE url=?");
- insertOntologyPs = conn.prepareStatement("INSERT INTO Ontology (url, iri, repository) VALUES(?,?,?)");
+ insertOntologyPs = conn.prepareStatement("INSERT INTO Ontology (url, iri, repository, logical_axioms, tbox_axioms, rbox_axioms" +
+ ", abox_axioms, classes, object_properties, data_properties, individuals) VALUES(?,?,?,?,?,?,?,?,?,?,?)");
+ insertOntologyErrorPs = 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(?,?,?)");
@@ -156,6 +162,14 @@
+ "url VARCHAR(2000) NOT NULL,"
+ "iri VARCHAR(2000) NOT NULL,"
+ "repository VARCHAR(200) NOT NULL,"
+ + "logical_axioms MEDIUMINT DEFAULT 0,"
+ + "tbox_axioms MEDIUMINT DEFAULT 0,"
+ + "rbox_axioms MEDIUMINT DEFAULT 0,"
+ + "abox_axioms MEDIUMINT DEFAULT 0,"
+ + "classes MEDIUMINT DEFAULT 0,"
+ + "object_properties MEDIUMINT DEFAULT 0,"
+ + "data_properties MEDIUMINT DEFAULT 0,"
+ + "individuals MEDIUMINT DEFAULT 0,"
+ "PRIMARY KEY(id),"
+ "INDEX(url)) DEFAULT CHARSET=utf8");
@@ -222,10 +236,10 @@
String url = physicalURI.toString();
//add ontology loading/parsing/... error entry
try {
- insertOntologyPs.setString(1, url);
- insertOntologyPs.setString(2, "ERROR:" + ex.getClass().getSimpleName() + "->" + ex.getMessage());
- insertOntologyPs.setString(3, repository.getName());
- insertOntologyPs.execute();
+ insertOntologyErrorPs.setString(1, url);
+ insertOntologyErrorPs.setString(2, "ERROR:" + ex.getClass().getSimpleName() + (ex.getMessage() != null ? ("->" + ex.getMessage()) : ""));
+ insertOntologyErrorPs.setString(3, repository.getName());
+ insertOntologyErrorPs.execute();
} catch (SQLException e) {
e.printStackTrace();
}
@@ -233,7 +247,10 @@
private int addOntology(URI physicalURI, OWLOntology ontology){
String url = physicalURI.toString();
- String ontologyIRI = ontology.getOntologyID().getOntologyIRI().toString();
+ String ontologyIRI = "Anonymous";
+ if(!ontology.getOntologyID().isAnonymous()){
+ ontologyIRI = ontology.getOntologyID().getOntologyIRI().toString();
+ }
//check for existing entry
try {
selectOntologyIdPs.setString(1, url);
@@ -249,6 +266,20 @@
insertOntologyPs.setString(1, url);
insertOntologyPs.setString(2, ontologyIRI);
insertOntologyPs.setString(3, repository.getName());
+ Set<OWLAxiom> logicalAxioms = new HashSet<OWLAxiom>();
+ logicalAxioms.addAll(ontology.getLogicalAxioms());
+ Set<OWLAxiom> tbox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.TBoxAxiomTypes).toArray(new AxiomType[AxiomType.TBoxAxiomTypes.size()]));
+ Set<OWLAxiom> rbox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.RBoxAxiomTypes).toArray(new AxiomType[AxiomType.RBoxAxiomTypes.size()]));
+ Set<OWLAxiom> abox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.ABoxAxiomTypes).toArray(new AxiomType[AxiomType.ABoxAxiomTypes.size()]));
+
+ insertOntologyPs.setInt(4, ontology.getLogicalAxiomCount());
+ insertOntologyPs.setInt(5, tbox.size());
+ insertOntologyPs.setInt(6, rbox.size());
+ insertOntologyPs.setInt(7, abox.size());
+ insertOntologyPs.setInt(8, ontology.getClassesInSignature(true).size());
+ insertOntologyPs.setInt(9, ontology.getObjectPropertiesInSignature(true).size());
+ insertOntologyPs.setInt(10, ontology.getDataPropertiesInSignature(true).size());
+ insertOntologyPs.setInt(11, ontology.getIndividualsInSignature(true).size());
insertOntologyPs.execute();
} catch (SQLException e) {
e.printStackTrace();
@@ -293,9 +324,11 @@
Multiset<OWLAxiom> allAxiomPatterns = HashMultiset.create();
for (OntologyRepositoryEntry entry : entries) {
URI uri = entry.getPhysicalURI();
+// if(uri.toString().startsWith("http://rest.bioontology.org/bioportal/ontologies/download/42764")){
if (!ontologyProcessed(uri)) {
System.out.println("Loading \"" + entry.getOntologyShortName() + "\" from "+ uri);
try {
+ manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntology(IRI.create(uri));
Multiset<OWLAxiom> axiomPatterns = HashMultiset.create();
for (OWLLogicalAxiom axiom : ontology.getLogicalAxioms()) {
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 2013-04-30 11:06:03 UTC (rev 3930)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-02 07:35:58 UTC (rev 3931)
@@ -1,8 +1,10 @@
package org.dllearner.utilities.owl;
+import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.Stack;
import org.aksw.commons.collections.diff.ModelDiff;
@@ -31,6 +33,7 @@
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
import org.semanticweb.owlapi.model.OWLObjectComplementOf;
import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
@@ -62,7 +65,7 @@
private String sparql = "";
private Stack<String> variables = new Stack<String>();
- private Map<OWLEntity, String> variablesMapping;
+ private Map<OWLEntity, String> variablesMapping = new HashMap<OWLEntity, String>();
private int classCnt = 0;
private int propCnt = 0;
@@ -71,6 +74,7 @@
private OWLDataFactory df = new OWLDataFactoryImpl();
private Map<Integer, Boolean> intersection;
+ private Set<? extends OWLEntity> variableEntities;
public OWLClassExpressionToSPARQLConverter() {
}
@@ -90,13 +94,37 @@
}
public Query asQuery(String rootVariable, OWLClassExpression expr){
- String queryString = "SELECT DISTINCT " + rootVariable + " WHERE {";
- queryString += convert(rootVariable, expr);
+ return asQuery(rootVariable, expr, Collections.<OWLEntity>emptySet());
+ }
+
+ public Query asQuery(String rootVariable, OWLClassExpression expr, Set<? extends OWLEntity> variableEntities){
+ this.variableEntities = variableEntities;
+ String queryString = "SELECT DISTINCT ";
+ String triplePattern = convert(rootVariable, expr);
+ if(variableEntities.isEmpty()){
+ queryString += rootVariable + " WHERE {";
+ } else {
+ for (OWLEntity owlEntity : variableEntities) {
+ String var = variablesMapping.get(owlEntity);
+ queryString += var + " ";
+ }
+ queryString += "COUNT(" + rootVariable + ") WHERE {";
+ }
+
+ queryString += triplePattern;
queryString += "}";
+ if(!variableEntities.isEmpty()){
+ queryString += "GROUP BY ";
+ for (OWLEntity owlEntity : variableEntities) {
+ String var = variablesMapping.get(owlEntity);
+ queryString += var;
+ }
+ }System.out.println(queryString);
return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
private void reset(){
+ variablesMapping.clear();
variables.clear();
classCnt = 0;
propCnt = 0;
@@ -143,7 +171,7 @@
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";
+ (object.startsWith("?") ? object : object) + ".\n";
}
private String triple(String subject, String predicate, OWLLiteral object){
@@ -152,12 +180,46 @@
render(object) + ".\n";
}
+ private String triple(String subject, String predicate, OWLEntity object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ (predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
+ render(object) + ".\n";
+ }
+
+ private String triple(String subject, OWLEntity predicate, OWLEntity object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ render(predicate) + " " +
+ render(object) + ".\n";
+ }
+
+ private String triple(String subject, OWLEntity predicate, String object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ render(predicate) + " " +
+ object + ".\n";
+ }
+
+ private String triple(String subject, OWLEntity predicate, OWLLiteral object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ render(predicate) + " " +
+ render(object) + ".\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";
}
+ private String render(OWLEntity entity){
+ String s;
+ if(variableEntities.contains(entity)){
+ s = getVariable(entity);
+ } else {
+ s = "<" + entity.toStringID() + ">";
+ }
+ return s;
+ }
+
private String render(OWLLiteral literal){
return "\"" + literal + "\"^^<" + literal.getDatatype().toStringID() + ">";
}
@@ -176,7 +238,7 @@
@Override
public void visit(OWLClass ce) {
- sparql += triple(variables.peek(), "a", ce.toStringID());
+ sparql += triple(variables.peek(), "a", render(ce));
}
@Override
@@ -220,9 +282,9 @@
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), variables.peek());
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty(), variables.peek());
} else {
- sparql += triple(variables.peek(), propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ sparql += triple(variables.peek(), propertyExpression.getNamedProperty(), objectVariable);
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
@@ -230,7 +292,7 @@
filler.accept(this);
variables.pop();
} else {
- sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ sparql += triple(objectVariable, "a", filler.asOWLClass());
}
}
@@ -240,7 +302,7 @@
String subject = variables.peek();
String objectVariable = buildIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
- String predicate = propertyExpression.getNamedProperty().toStringID();
+ OWLObjectProperty predicate = propertyExpression.getNamedProperty();
OWLClassExpression filler = ce.getFiller();
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
@@ -269,12 +331,12 @@
@Override
public void visit(OWLObjectHasValue ce) {
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
- OWLIndividual value = ce.getValue();
+ OWLNamedIndividual value = ce.getValue().asOWLNamedIndividual();
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(value.toStringID(), propertyExpression.getNamedProperty().toStringID(), variables.peek());
+ sparql += triple(value.toStringID(), propertyExpression.getNamedProperty(), variables.peek());
} else {
- sparql += triple(variables.peek(), propertyExpression.getNamedProperty().toStringID(), value.toStringID());
+ sparql += triple(variables.peek(), propertyExpression.getNamedProperty(), value);
}
}
@@ -287,9 +349,9 @@
sparql += "{SELECT " + subjectVariable + " WHERE {";
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty(), subjectVariable);
} else {
- sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty(), objectVariable);
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
@@ -299,7 +361,7 @@
filler.accept(this);
variables.pop();
} else {
- sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ sparql += triple(objectVariable, "a", filler.asOWLClass());
}
sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")>=" + cardinality + ")}";
@@ -315,9 +377,9 @@
sparql += "{SELECT " + subjectVariable + " WHERE {";
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty(), subjectVariable);
} else {
- sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty(), objectVariable);
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
@@ -327,7 +389,7 @@
filler.accept(this);
variables.pop();
} else {
- sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ sparql += triple(objectVariable, "a", filler.asOWLClass());
}
sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")=" + cardinality + ")}";
@@ -342,9 +404,9 @@
sparql += "{SELECT " + subjectVariable + " WHERE {";
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty(), subjectVariable);
} else {
- sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty(), objectVariable);
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
@@ -354,7 +416,7 @@
filler.accept(this);
variables.pop();
} else {
- sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ sparql += triple(objectVariable, "a", filler.asOWLClass());
}
sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")<=" + cardinality + ")}";
@@ -364,7 +426,7 @@
public void visit(OWLObjectHasSelf ce) {
String subject = variables.peek();
OWLObjectPropertyExpression property = ce.getProperty();
- sparql += triple(subject, property.getNamedProperty().toStringID(), subject);
+ sparql += triple(subject, property.getNamedProperty(), subject);
}
@Override
@@ -390,7 +452,7 @@
public void visit(OWLDataSomeValuesFrom ce) {
String objectVariable = buildIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
- sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty().toStringID(), objectVariable);
+ sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
variables.push(objectVariable);
filler.accept(this);
@@ -426,7 +488,7 @@
public void visit(OWLDataHasValue ce) {
OWLDataPropertyExpression propertyExpression = ce.getProperty();
OWLLiteral value = ce.getValue();
- sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty().toStringID(), value);
+ sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty(), value);
}
@Override
@@ -436,7 +498,7 @@
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
- sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
variables.push(objectVariable);
filler.accept(this);
@@ -452,7 +514,7 @@
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
- sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
variables.push(objectVariable);
filler.accept(this);
@@ -468,7 +530,7 @@
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
- sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
variables.push(objectVariable);
filler.accept(this);
@@ -642,6 +704,13 @@
query = converter.asQuery(rootVar, expr).toString();
System.out.println(expr + "\n" + query);
+ //variable entity
+ expr = df.getOWLObjectIntersectionOf(
+ df.getOWLObjectSomeValuesFrom(propR, clsB),
+ clsB);
+ query = converter.asQuery(rootVar, expr, Collections.singleton(propR)).toString();
+ System.out.println(expr + "\n" + query);
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-04-30 11:06:06
|
Revision: 3930
http://sourceforge.net/p/dl-learner/code/3930
Author: lorenz_b
Date: 2013-04-30 11:06:03 +0000 (Tue, 30 Apr 2013)
Log Message:
-----------
Added class which fills JENA model with explicit type statements for entities.
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java
Added: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java 2013-04-30 11:06:03 UTC (rev 3930)
@@ -0,0 +1,50 @@
+package org.dllearner.utilities.owl;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import com.google.common.collect.Sets;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+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;
+
+public class OWLEntityTypeAdder {
+
+ /**
+ * Infers the type of predicates p_i by analyzing the object of the triples using p_i and adds the
+ * entity type assertion to the model, i.e. for a data property dp <dp a owl:DatatypeProperty>
+ * will be added.
+ * @param model
+ */
+ public static void addEntityTypes(Model model){
+ StmtIterator iterator = model.listStatements();
+ Set<Property> objectPropertyPredicates = new HashSet<Property>();
+ Set<Property> dataPropertyPredicates = new HashSet<Property>();
+ while(iterator.hasNext()){
+ Statement st = iterator.next();
+ Property predicate = st.getPredicate();
+ if(!predicate.getURI().startsWith(RDF.getURI()) && !predicate.getURI().startsWith(RDFS.getURI())){
+ RDFNode object = st.getObject();
+ if(object.isLiteral()){
+ dataPropertyPredicates.add(predicate);
+ } else if(object.isResource()){
+ objectPropertyPredicates.add(predicate);
+ }
+ }
+ }
+ iterator.close();
+
+ for (Property property : Sets.difference(objectPropertyPredicates, dataPropertyPredicates)) {
+ model.add(property, RDF.type, OWL.ObjectProperty);
+ }
+ for (Property property : Sets.difference(dataPropertyPredicates, objectPropertyPredicates)) {
+ model.add(property, RDF.type, OWL.DatatypeProperty);
+ }
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-04-30 11:05:16
|
Revision: 3929
http://sourceforge.net/p/dl-learner/code/3929
Author: lorenz_b
Date: 2013-04-30 11:05:12 +0000 (Tue, 30 Apr 2013)
Log Message:
-----------
Removed experimental classes.Updated LGG.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.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/QueryTreeImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/QueryTreeFactoryImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java
trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIConverter.java
Removed Paths:
-------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternAxiomToSPARQLConverter.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternExpressionToSPARQLConverter.java
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternAxiomToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternAxiomToSPARQLConverter.java 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternAxiomToSPARQLConverter.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -1,286 +0,0 @@
-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);
-
- }
-
-}
Deleted: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternExpressionToSPARQLConverter.java 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/PatternExpressionToSPARQLConverter.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -1,207 +0,0 @@
-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) {
- }
-
-}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -146,6 +146,17 @@
// this.configurator = new QTLConfigurator(this);
}
+ public QTL(AbstractLearningProblem learningProblem, SparqlEndpointKS endpointKS, ExtractionDBCache cache) throws LearningProblemUnsupportedException{
+ if(!(learningProblem instanceof PosOnlyLP || learningProblem instanceof PosNegLP)){
+ throw new LearningProblemUnsupportedException(learningProblem.getClass(), getClass());
+ }
+ this.learningProblem = learningProblem;
+ this.endpointKS = endpointKS;
+ this.cache = cache;
+
+// this.configurator = new QTLConfigurator(this);
+ }
+
public QTL(SPARQLEndpointEx endpoint, ExtractionDBCache cache) {
this.endpoint = endpoint;
this.cache = cache;
@@ -162,6 +173,22 @@
negExampleTrees = new ArrayList<QueryTree<String>>();
}
+ public QTL(SparqlEndpointKS endpointKS, ExtractionDBCache cache) {
+ this.endpointKS = endpointKS;
+ 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 QTL(Model model) {
this.model = model;
@@ -280,16 +307,20 @@
Model model;
QueryTree<String> tree;
for(String resource : resources){
- logger.info("Generating tree for " + resource);
- model = cbdGenerator.getConciseBoundedDescription(resource);
- applyFilters(model);
- tree = treeCache.getQueryTree(resource, model);
- if(logger.isDebugEnabled()){
- logger.debug("Tree for resource " + resource);
- logger.debug(tree.getStringRepresentation());
-
+ try {
+ logger.debug("Generating tree for " + resource);
+ model = cbdGenerator.getConciseBoundedDescription(resource);
+ applyFilters(model);
+ tree = treeCache.getQueryTree(resource, model);
+ if(logger.isDebugEnabled()){
+ logger.debug("Tree for resource " + resource);
+ logger.debug(tree.getStringRepresentation());
+
+ }
+ trees.add(tree);
+ } catch (Exception e) {
+ logger.error("Failed to create tree for resource " + resource + ".", e);
}
- trees.add(tree);
}
return trees;
}
@@ -367,7 +398,9 @@
if(logger.isDebugEnabled()){
logger.debug("LGG: \n" + lgg.getStringRepresentation());
}
- logger.info(lgg.toSPARQLQueryString(true, enableNumericLiteralFilters, prefixes));
+ if(logger.isInfoEnabled()){
+ logger.info(lgg.toSPARQLQueryString(true, enableNumericLiteralFilters, prefixes));
+ }
}
public void setEnableNumericLiteralFilters(boolean enableNumericLiteralFilters) {
@@ -421,6 +454,10 @@
return list;
}
+ public QueryTree<String> getLgg() {
+ return lgg;
+ }
+
public static void main(String[] args) throws Exception {
Set<String> positiveExamples = new HashSet<String>();
positiveExamples.add("http://dbpedia.org/resource/Liverpool_F.C.");
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 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -26,6 +26,7 @@
import java.util.Set;
import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
+import org.semanticweb.owlapi.model.OWLClassExpression;
import com.hp.hpl.jena.datatypes.RDFDatatype;
import com.hp.hpl.jena.query.Query;
@@ -136,6 +137,8 @@
Query toSPARQLQuery();
+ OWLClassExpression asOWLClassExpression();
+
int getTriplePatternCount();
Query toQuery();
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 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -21,7 +21,6 @@
import java.io.PrintWriter;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
@@ -41,7 +40,16 @@
import org.dllearner.algorithms.qtl.datastructures.NodeRenderer;
import org.dllearner.algorithms.qtl.datastructures.QueryTree;
import org.dllearner.algorithms.qtl.filters.Filters;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
import com.hp.hpl.jena.datatypes.BaseDatatype;
import com.hp.hpl.jena.datatypes.RDFDatatype;
import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
@@ -53,6 +61,7 @@
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.sparql.syntax.ElementGroup;
import com.hp.hpl.jena.sparql.syntax.ElementTriplesBlock;
+import com.hp.hpl.jena.vocabulary.RDF;
/**
*
@@ -80,6 +89,7 @@
private boolean isLiteralNode = false;
private boolean isResourceNode = false;
+ private boolean isBlankNode = false;
private List<Literal> literals = new ArrayList<Literal>();
@@ -163,6 +173,14 @@
this.isLiteralNode = isLiteralNode;
}
+ public void setBlankNode(boolean isBlankNode) {
+ this.isBlankNode = isBlankNode;
+ }
+
+ public boolean isBlankNode() {
+ return isBlankNode;
+ }
+
@Override
public boolean isResourceNode() {
return isResourceNode;
@@ -728,7 +746,7 @@
for(String filter : filters){
sb.append(filter).append("\n");
}
- sb.append("}");System.out.println(sb.toString());
+ sb.append("}");
Query query = QueryFactory.create(sb.toString(), Syntax.syntaxARQ);
query.setPrefix("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
query.setPrefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
@@ -869,9 +887,9 @@
} else if(objectLabel.startsWith("http:")){
object = Node.createURI(objectLabel);
} else {
- System.out.println(objectLabel);
+// System.out.println(objectLabel);
String[] split = objectLabel.split("@");
- System.out.println(Arrays.toString(split));
+// System.out.println(Arrays.toString(split));
if(split.length == 2){
object = Node.createLiteral(split[0], split[1], null);
} else {
@@ -917,5 +935,73 @@
}
}
+ public OWLClassExpression asOWLClassExpression(){
+ OWLDataFactory df = new OWLDataFactoryImpl();
+ QueryTree<N> root = getRoot();
+ Set<OWLClassExpression> classExpressions = buildOWLClassExpressions(df, root);
+ if(classExpressions.size() == 1){
+ return classExpressions.iterator().next();
+ } else {
+ return df.getOWLObjectIntersectionOf(classExpressions);
+ }
+ }
+
+ private Set<OWLClassExpression> buildOWLClassExpressions(OWLDataFactory df, QueryTree<N> tree){
+ Set<OWLClassExpression> classExpressions = new HashSet<OWLClassExpression>();
+
+ List<QueryTree<N>> children = tree.getChildren();
+ for(QueryTree<N> child : children){
+ String childLabel = (String) child.getUserObject();
+ String predicateString = (String) tree.getEdge(child);
+ if(predicateString.equals(RDF.type.getURI())){
+ classExpressions.add(df.getOWLClass(IRI.create(childLabel)));
+ } else {
+ if(child.isLiteralNode()){
+ OWLDataProperty p = df.getOWLDataProperty(IRI.create((String) tree.getEdge(child)));
+ if(childLabel.equals("?")){
+ List<Literal> literals = child.getLiterals();
+ Literal lit = literals.iterator().next();
+ RDFDatatype datatype = lit.getDatatype();
+ String datatypeURI;
+ if(datatype == null){
+ datatypeURI = OWL2Datatype.RDF_PLAIN_LITERAL.getURI().toString();
+ } else {
+ datatypeURI = datatype.getURI();
+ }
+ classExpressions.add(df.getOWLDataSomeValuesFrom(p, df.getOWLDatatype(IRI.create(datatypeURI))));
+ } else {
+ List<Literal> literals = child.getLiterals();
+ Literal lit = literals.iterator().next();
+ RDFDatatype datatype = lit.getDatatype();
+ OWLLiteral owlLiteral;
+ if(datatype == null){
+ owlLiteral = df.getOWLLiteral(lit.getLexicalForm(), lit.getLanguage());
+ } else {
+ owlLiteral = df.getOWLLiteral(lit.getLexicalForm(), df.getOWLDatatype(IRI.create(datatype.getURI())));
+ }
+ classExpressions.add(df.getOWLDataHasValue(p, owlLiteral));
+ }
+ } else {
+ OWLObjectProperty p = df.getOWLObjectProperty(IRI.create((String) tree.getEdge(child)));
+ OWLClassExpression filler;
+ if(child.isVarNode()){
+ Set<OWLClassExpression> fillerClassExpressions = buildOWLClassExpressions(df, child);
+ if(fillerClassExpressions.isEmpty()){
+ filler = df.getOWLThing();
+ } else if(fillerClassExpressions.size() == 1){
+ filler = fillerClassExpressions.iterator().next();
+ } else {
+ filler = df.getOWLObjectIntersectionOf(fillerClassExpressions);
+ }
+ classExpressions.add(df.getOWLObjectSomeValuesFrom(p, filler));
+ } else {
+ classExpressions.add(df.getOWLObjectHasValue(p, df.getOWLNamedIndividual(IRI.create(childLabel))));
+ }
+ }
+ }
+ }
+ return classExpressions;
+ }
+
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/QueryTreeFactoryImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/QueryTreeFactoryImpl.java 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/impl/QueryTreeFactoryImpl.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -250,12 +250,12 @@
|| lit.getDatatype() == XSDDatatype.XSDint
|| lit.getDatatype() == XSDDatatype.XSDdecimal){
subTree.addLiteral(lit);
+ } else {
+ subTree.addLiteral(lit);
}
+
tree.addChild(subTree, st.getPredicate().toString());
} else if(objectFilter.isRelevantResource(object.asResource().getURI())){
- if(object.asResource().isAnon()){
- System.out.println(object);
- }
if(!tree.getUserObjectPathToRoot().contains(st.getObject().toString())){
subTree = new QueryTreeImpl<String>(st.getObject().toString());
subTree.setResourceNode(true);
@@ -263,6 +263,9 @@
if(depth < maxDepth){
fillTree(subTree, resource2Statements, depth);
}
+ if(object.isAnon()){
+ subTree.setBlankNode(true);
+ }
}
} else if(object.isAnon()){
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 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorImpl.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -121,7 +121,10 @@
}
QueryTree<N> lgg = new QueryTreeImpl<N>(tree1.getUserObject());
- lgg.setLiteralNode(tree1.isLiteralNode());
+ if(tree1.isResourceNode() && tree2.isResourceNode()){
+ lgg.setResourceNode(true);
+
+ }
// if(!lgg.getUserObject().equals(tree2.getUserObject())){
// lgg.setUserObject((N)"?");
@@ -144,15 +147,19 @@
// }
if(!lgg.getUserObject().equals(tree2.getUserObject())){
lgg.setUserObject((N)"?");
+ lgg.setLiteralNode(false);
+ lgg.setResourceNode(false);
}
if(tree1.isLiteralNode() && tree2.isLiteralNode()){
RDFDatatype d1 = tree1.getDatatype();
RDFDatatype d2 = tree2.getDatatype();
- if(d1 != null && d2 != null && d1 == d2){
+// if(d1 != null && d2 != null && d1 == d2){
+ if(d1 == d2){
((QueryTreeImpl<N>)lgg).addLiterals(((QueryTreeImpl<N>)tree1).getLiterals());
((QueryTreeImpl<N>)lgg).addLiterals(((QueryTreeImpl<N>)tree2).getLiterals());
}
+ lgg.setLiteralNode(true);
}
Set<QueryTreeImpl<N>> addedChildren;
Modified: trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -21,8 +21,8 @@
import java.io.PrintWriter;
import java.io.StringWriter;
+import java.text.DecimalFormat;
import java.util.ArrayList;
-import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -30,8 +30,8 @@
import org.apache.commons.codec.digest.DigestUtils;
import org.dllearner.core.owl.Axiom;
import org.dllearner.utilities.EnrichmentVocabulary;
+import org.dllearner.utilities.PrefixCCMap;
import org.dllearner.utilities.owl.OWLAPIConverter;
-import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAxiom;
@@ -46,6 +46,8 @@
public class EvaluatedAxiom {
+ private static DecimalFormat df = new DecimalFormat("##0.0");
+
private Axiom axiom;
private Score score;
@@ -113,5 +115,26 @@
return ind2Axioms;
}
+ public static String prettyPrint(List<EvaluatedAxiom> learnedAxioms) {
+ String str = "suggested axioms and their score in percent:\n";
+ if(learnedAxioms.isEmpty()) {
+ return " no axiom suggested\n";
+ } else {
+ for (EvaluatedAxiom learnedAxiom : learnedAxioms) {
+ str += " " + prettyPrint(learnedAxiom) + "\n";
+ }
+ }
+ return str;
+ }
+
+ public static String prettyPrint(EvaluatedAxiom axiom) {
+ double acc = axiom.getScore().getAccuracy() * 100;
+ String accs = df.format(acc);
+ if(accs.length()==3) { accs = " " + accs; }
+ if(accs.length()==4) { accs = " " + accs; }
+ String str = accs + "%\t" + axiom.getAxiom().toManchesterSyntaxString(null, PrefixCCMap.getInstance());
+ return str;
+ }
+
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -720,8 +720,11 @@
// convert data back to DL-Learner structures
SortedSet<Individual> is = new TreeSet<Individual>();
- for (OWLNamedIndividual oi : inds)
- is.add(new Individual(oi.toStringID()));
+ for (OWLNamedIndividual oi : inds){
+ if(oi != null){
+ is.add(new Individual(oi.toStringID()));
+ }
+ }
map.put(i, is);
}
return map;
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -84,7 +84,7 @@
import com.hp.hpl.jena.vocabulary.RDFS;
@ComponentAnn(name = "SPARQL Reasoner", shortName = "spr", version = 0.1)
-public class SPARQLReasoner implements SchemaReasoner, IndividualReasoner{
+public class SPARQLReasoner implements SchemaReasoner, IndividualReasoner {
private static final Logger logger = LoggerFactory.getLogger(SPARQLReasoner.class);
@@ -450,7 +450,7 @@
}
public Set<NamedClass> getTypes() {
- Set<NamedClass> types = new HashSet<NamedClass>();
+ Set<NamedClass> types = new TreeSet<NamedClass>();
String query = String.format("SELECT DISTINCT ?class WHERE {[] a ?class.}");
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
@@ -519,7 +519,7 @@
throw new UnsupportedOperationException("Only named classes are supported.");
}
SortedSet<Individual> individuals = new TreeSet<Individual>();
- String query = String.format("SELECT ?ind WHERE {?ind a <%s>}", ((NamedClass)description).getName());
+ String query = String.format("SELECT DISTINCT ?ind WHERE {?ind a <%s>}", ((NamedClass)description).getName());
if(limit != 0) {
query += " LIMIT " + limit;
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIConverter.java 2013-04-25 08:12:24 UTC (rev 3928)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAPIConverter.java 2013-04-30 11:05:12 UTC (rev 3929)
@@ -51,6 +51,8 @@
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObjectProperty;
+import eu.trowl.vocab.RDF;
+
/**
* A collection of methods for exchanging objects between OWL API and
* DL-Learner.
@@ -191,7 +193,9 @@
return OWL2Datatype.DATE.getDatatype();
else if(iri.equals(OWL2Datatype.DATETIME.getIRI()))
return OWL2Datatype.DATETIME.getDatatype();
- throw new Error("Unsupported datatype " + dataType + ". Please inform a DL-Learner developer to add it.");
+ else
+ return new Datatype(dataType.getIRI().toString());
+// throw new Error("Unsupported datatype " + dataType + ". Please inform a DL-Learner developer to add it.");
}
}
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|
|
From: <lor...@us...> - 2013-04-25 08:12:31
|
Revision: 3928
http://sourceforge.net/p/dl-learner/code/3928
Author: lorenz_b
Date: 2013-04-25 08:12:24 +0000 (Thu, 25 Apr 2013)
Log Message:
-----------
Improved script.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
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 2013-04-24 12:41:48 UTC (rev 3927)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-04-25 08:12:24 UTC (rev 3928)
@@ -146,10 +146,10 @@
statement.execute("CREATE TABLE IF NOT EXISTS Pattern ("
+ "id MEDIUMINT NOT NULL AUTO_INCREMENT,"
- + "pattern VARCHAR(20000) NOT NULL,"
- + "pattern_pretty VARCHAR(20000) NOT NULL,"
+ + "pattern TEXT NOT NULL,"
+ + "pattern_pretty TEXT NOT NULL,"
+ "PRIMARY KEY(id),"
- + "INDEX(pattern)) DEFAULT CHARSET=utf8");
+ + "INDEX(pattern(8000))) DEFAULT CHARSET=utf8");
statement.execute("CREATE TABLE IF NOT EXISTS Ontology ("
+ "id MEDIUMINT NOT NULL AUTO_INCREMENT,"
@@ -294,7 +294,7 @@
for (OntologyRepositoryEntry entry : entries) {
URI uri = entry.getPhysicalURI();
if (!ontologyProcessed(uri)) {
- System.out.println("Loading " + uri);
+ System.out.println("Loading \"" + entry.getOntologyShortName() + "\" from "+ uri);
try {
OWLOntology ontology = manager.loadOntology(IRI.create(uri));
Multiset<OWLAxiom> axiomPatterns = HashMultiset.create();
@@ -311,6 +311,7 @@
} catch (OWLOntologyAlreadyExistsException e) {
e.printStackTrace();
} catch (Exception e){
+ e.printStackTrace();
addOntologyError(uri, e);
}
}
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|
|
From: <lor...@us...> - 2013-04-24 12:41:52
|
Revision: 3927
http://sourceforge.net/p/dl-learner/code/3927
Author: lorenz_b
Date: 2013-04-24 12:41:48 +0000 (Wed, 24 Apr 2013)
Log Message:
-----------
Updated Surefire plugin.
Modified Paths:
--------------
trunk/pom.xml
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2013-04-24 12:12:51 UTC (rev 3926)
+++ trunk/pom.xml 2013-04-24 12:41:48 UTC (rev 3927)
@@ -53,7 +53,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
- <version>2.4.3</version>
+ <version>2.14.1</version>
</plugin>
<!--Maven Compiler Plugin -->
<plugin>
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|
|
From: <lor...@us...> - 2013-04-24 12:12:55
|
Revision: 3926
http://sourceforge.net/p/dl-learner/code/3926
Author: lorenz_b
Date: 2013-04-24 12:12:51 +0000 (Wed, 24 Apr 2013)
Log Message:
-----------
Modified pattern analyzing class.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java
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 2013-04-21 11:20:26 UTC (rev 3925)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-04-24 12:12:51 UTC (rev 3926)
@@ -11,19 +11,20 @@
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
+import java.util.ArrayList;
import java.util.Collection;
+import java.util.Collections;
import java.util.LinkedList;
+import java.util.List;
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;
@@ -31,16 +32,12 @@
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.OWLOntologyAlreadyExistsException;
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;
@@ -78,6 +75,8 @@
private PreparedStatement insertOntologyPatternPs;
private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
+
+ private boolean randomOrder = true;
public OWLAxiomPatternFinder(OWLOntologyDataset dataset) {
@@ -147,8 +146,8 @@
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,"
+ + "pattern VARCHAR(20000) NOT NULL,"
+ + "pattern_pretty VARCHAR(20000) NOT NULL,"
+ "PRIMARY KEY(id),"
+ "INDEX(pattern)) DEFAULT CHARSET=utf8");
@@ -164,8 +163,8 @@
+ "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),"
+ + "FOREIGN KEY (ontology_id) REFERENCES Ontology(id) ON DELETE CASCADE,"
+ + "FOREIGN KEY (pattern_id) REFERENCES Pattern(id) ON DELETE CASCADE,"
+ "PRIMARY KEY(ontology_id, pattern_id)) DEFAULT CHARSET=utf8");
} catch (SQLException e) {
e.printStackTrace();
@@ -191,6 +190,7 @@
insertPatternIdPs.setString(2, axiomRenderer.render(axiom));
insertPatternIdPs.execute();
} catch (SQLException e) {
+ System.out.println(axiomString.length());
e.printStackTrace();
}
//get the auto generated ID
@@ -218,6 +218,19 @@
return false;
}
+ private void addOntologyError(URI physicalURI, Exception ex){
+ String url = physicalURI.toString();
+ //add ontology loading/parsing/... error entry
+ try {
+ insertOntologyPs.setString(1, url);
+ insertOntologyPs.setString(2, "ERROR:" + ex.getClass().getSimpleName() + "->" + ex.getMessage());
+ insertOntologyPs.setString(3, repository.getName());
+ insertOntologyPs.execute();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+
private int addOntology(URI physicalURI, OWLOntology ontology){
String url = physicalURI.toString();
String ontologyIRI = ontology.getOntologyID().getOntologyIRI().toString();
@@ -264,7 +277,7 @@
insertOntologyPatternPs.setInt(3, occurrences);
insertOntologyPatternPs.execute();
} catch (SQLException e) {
- e.printStackTrace();
+ System.err.println("Adding pattern\n" + pattern + "\nfailed." + e.getMessage());
}
}
}
@@ -272,6 +285,11 @@
public void start() {
OWLAxiomRenamer renamer = new OWLAxiomRenamer(dataFactory);
Collection<OntologyRepositoryEntry> entries = repository.getEntries();
+ if(randomOrder){
+ List<OntologyRepositoryEntry> entryList = new ArrayList<OntologyRepositoryEntry>(repository.getEntries());
+ Collections.shuffle(entryList);
+ entries = entryList;
+ }
Multiset<OWLAxiom> allAxiomPatterns = HashMultiset.create();
for (OntologyRepositoryEntry entry : entries) {
URI uri = entry.getPhysicalURI();
@@ -290,8 +308,10 @@
// System.out.println(owlAxiom + ": " + allAxiomPatterns.count(owlAxiom));
}
manager.removeOntology(ontology);
- } catch (OWLOntologyCreationException e) {
+ } catch (OWLOntologyAlreadyExistsException e) {
e.printStackTrace();
+ } catch (Exception e){
+ addOntologyError(uri, e);
}
}
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 2013-04-21 11:20:26 UTC (rev 3925)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-04-24 12:12:51 UTC (rev 3926)
@@ -90,7 +90,7 @@
}
public Query asQuery(String rootVariable, OWLClassExpression expr){
- String queryString = "SELECT " + rootVariable + " WHERE {";
+ String queryString = "SELECT DISTINCT " + rootVariable + " WHERE {";
queryString += convert(rootVariable, expr);
queryString += "}";
return QueryFactory.create(queryString, Syntax.syntaxARQ);
@@ -149,7 +149,7 @@
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";
+ render(object) + ".\n";
}
private String triple(String subject, String predicate, OWLIndividual object){
@@ -157,6 +157,10 @@
(predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
"<" + object.toStringID() + ">.\n";
}
+
+ private String render(OWLLiteral literal){
+ return "\"" + literal + "\"^^<" + literal.getDatatype().toStringID() + ">";
+ }
@Override
public void visit(OWLObjectProperty property) {
@@ -480,6 +484,20 @@
@Override
public void visit(OWLDataOneOf node) {
+ String subject = variables.peek();
+ if(modalDepth() == 1){
+ sparql += triple(subject, "?p", "?o");
+ }
+ sparql += "FILTER(" + subject + " IN (";
+ String values = "";
+ for (OWLLiteral value : node.getValues()) {
+ if(!values.isEmpty()){
+ values += ",";
+ }
+ values += render(value);
+ }
+ sparql += values;
+ sparql += "))";
}
@Override
@@ -620,6 +638,10 @@
query = converter.asQuery(rootVar, expr).toString();
System.out.println(expr + "\n" + query);
+ expr = df.getOWLDataAllValuesFrom(dpT,df.getOWLDataOneOf(lit));
+ query = converter.asQuery(rootVar, expr).toString();
+ System.out.println(expr + "\n" + query);
+
}
Modified: trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java 2013-04-21 11:20:26 UTC (rev 3925)
+++ trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java 2013-04-24 12:12:51 UTC (rev 3926)
@@ -1,6 +1,7 @@
package org.dllearner.algorithms.pattern;
import org.dllearner.kb.repository.OntologyRepository;
+import org.dllearner.kb.repository.bioportal.BioPortalRepository;
import org.dllearner.kb.repository.tones.TONESRepository;
import org.junit.Before;
import org.junit.Test;
@@ -23,5 +24,13 @@
OWLAxiomPatternFinder patternFinder = new OWLAxiomPatternFinder(repository);
patternFinder.start();
}
+
+ @Test
+ public void testBioPortalRepository(){
+ OntologyRepository repository = new BioPortalRepository();
+ repository.initialize();
+ OWLAxiomPatternFinder patternFinder = new OWLAxiomPatternFinder(repository);
+ patternFinder.start();
+ }
}
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|
|
From: <lor...@us...> - 2013-04-21 11:20:29
|
Revision: 3925
http://sourceforge.net/p/dl-learner/code/3925
Author: lorenz_b
Date: 2013-04-21 11:20:26 +0000 (Sun, 21 Apr 2013)
Log Message:
-----------
Continued OWL class expression to SPARQL converter.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-04-19 14:04:20 UTC (rev 3924)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-04-21 11:20:26 UTC (rev 3925)
@@ -523,7 +523,6 @@
if(limit != 0) {
query += " LIMIT " + limit;
}
- System.out.println(query);
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
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 2013-04-19 14:04:20 UTC (rev 3924)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-04-21 11:20:26 UTC (rev 3925)
@@ -1,5 +1,6 @@
package org.dllearner.utilities.owl;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Stack;
@@ -69,6 +70,8 @@
private OWLDataFactory df = new OWLDataFactoryImpl();
+ private Map<Integer, Boolean> intersection;
+
public OWLClassExpressionToSPARQLConverter() {
}
@@ -89,7 +92,7 @@
public Query asQuery(String rootVariable, OWLClassExpression expr){
String queryString = "SELECT " + rootVariable + " WHERE {";
queryString += convert(rootVariable, expr);
- queryString += "}";System.out.println(queryString);
+ queryString += "}";
return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
@@ -99,6 +102,7 @@
propCnt = 0;
indCnt = 0;
sparql = "";
+ intersection = new HashMap<Integer, Boolean>();
}
private String getVariable(OWLEntity entity){
@@ -124,6 +128,18 @@
return variables.size();
}
+ private boolean inIntersection(){
+ return intersection.containsKey(modalDepth()) ? intersection.get(modalDepth()) : false;
+ }
+
+ private void enterIntersection(){
+ intersection.put(modalDepth(), true);
+ }
+
+ private void leaveIntersection(){
+ intersection.remove(modalDepth());
+ }
+
private String triple(String subject, String predicate, String object){
return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
(predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
@@ -161,10 +177,12 @@
@Override
public void visit(OWLObjectIntersectionOf ce) {
+ enterIntersection();
List<OWLClassExpression> operands = ce.getOperandsAsList();
for (OWLClassExpression operand : operands) {
operand.accept(this);
}
+ leaveIntersection();
}
@Override
@@ -183,6 +201,13 @@
@Override
public void visit(OWLObjectComplementOf ce) {
+ String subject = variables.peek();
+ if(!inIntersection() && modalDepth() == 1){
+ sparql += triple(subject, "?p", "?o");
+ }
+ sparql += "FILTER NOT EXISTS {";
+ ce.getOperand().accept(this);
+ sparql += "}";
}
@Override
@@ -197,17 +222,9 @@
}
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();
- }
+ variables.push(objectVariable);
+ filler.accept(this);
+ variables.pop();
} else {
sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
}
@@ -378,6 +395,27 @@
@Override
public void visit(OWLDataAllValuesFrom ce) {
+ String subject = variables.peek();
+ String objectVariable = buildIndividualVariable();
+ OWLDataPropertyExpression propertyExpression = ce.getProperty();
+ String predicate = propertyExpression.asOWLDataProperty().toStringID();
+ OWLDataRange filler = ce.getFiller();
+ 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
@@ -561,6 +599,27 @@
query = converter.asQuery(rootVar, expr).toString();
System.out.println(expr + "\n" + query);
+ expr = df.getOWLObjectComplementOf(clsB);
+ query = converter.asQuery(rootVar, expr).toString();
+ System.out.println(expr + "\n" + query);
+
+ expr = df.getOWLObjectIntersectionOf(
+ clsA,
+ df.getOWLObjectComplementOf(clsB));
+ query = converter.asQuery(rootVar, expr).toString();
+ System.out.println(expr + "\n" + query);
+
+ expr = df.getOWLObjectSomeValuesFrom(propR,
+ df.getOWLObjectIntersectionOf(
+ clsA,
+ df.getOWLObjectComplementOf(clsB)));
+ query = converter.asQuery(rootVar, expr).toString();
+ System.out.println(expr + "\n" + query);
+
+ expr = df.getOWLDataAllValuesFrom(dpT, booleanRange);
+ query = converter.asQuery(rootVar, expr).toString();
+ System.out.println(expr + "\n" + query);
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
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...> - 2013-04-15 20:53:34
|
Revision: 3923
http://sourceforge.net/p/dl-learner/code/3923
Author: lorenz_b
Date: 2013-04-15 20:53:29 +0000 (Mon, 15 Apr 2013)
Log Message:
-----------
Updated Guava lib.
Modified Paths:
--------------
trunk/pom.xml
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2013-04-15 20:52:41 UTC (rev 3922)
+++ trunk/pom.xml 2013-04-15 20:53:29 UTC (rev 3923)
@@ -392,7 +392,7 @@
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
- <version>r07</version>
+ <version>14.0</version>
</dependency>
<dependency>
<groupId>com.dumontierlab</groupId>
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...> - 2013-04-12 10:57:06
|
Revision: 3921
http://sourceforge.net/p/dl-learner/code/3921
Author: lorenz_b
Date: 2013-04-12 10:57:03 +0000 (Fri, 12 Apr 2013)
Log Message:
-----------
Updated QTL.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.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/QueryTreeImpl.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/QuestionBasedQueryTreeFilter.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-04-12 10:21:20 UTC (rev 3920)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-04-12 10:57:03 UTC (rev 3921)
@@ -20,6 +20,7 @@
package org.dllearner.algorithms.qtl;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
@@ -40,6 +41,7 @@
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.filters.QuestionBasedQueryTreeFilter;
import org.dllearner.algorithms.qtl.operations.NBR;
import org.dllearner.algorithms.qtl.operations.lgg.LGGGenerator;
import org.dllearner.algorithms.qtl.operations.lgg.LGGGeneratorImpl;
@@ -365,7 +367,7 @@
if(logger.isDebugEnabled()){
logger.debug("LGG: \n" + lgg.getStringRepresentation());
}
- logger.info(lgg.toSPARQLQueryString(enableNumericLiteralFilters, prefixes));
+ logger.info(lgg.toSPARQLQueryString(true, enableNumericLiteralFilters, prefixes));
}
public void setEnableNumericLiteralFilters(boolean enableNumericLiteralFilters) {
@@ -429,6 +431,7 @@
PosOnlyLP lp = new PosOnlyLP();
lp.setPositiveExamples(Helper.getIndividualSet(positiveExamples));
QTL qtl = new QTL(lp, ks);
+ qtl.addQueryTreeFilter(new QuestionBasedQueryTreeFilter(Arrays.asList("soccer club", "Premier League")));
qtl.init();
qtl.start();
String query = qtl.getBestSPARQLQuery();
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 2013-04-12 10:21:20 UTC (rev 3920)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/QueryTree.java 2013-04-12 10:57:03 UTC (rev 3921)
@@ -130,9 +130,9 @@
String toSPARQLQueryString();
- String toSPARQLQueryString(boolean filtered);
+ String toSPARQLQueryString(boolean filterMeaninglessProperties, boolean useNumericalFilters);
- String toSPARQLQueryString(boolean filtered, Map<String, String> prefixMap);
+ String toSPARQLQueryString(boolean filterMeaninglessProperties, boolean useNumericalFilters, Map<String, String> prefixMap);
Query toSPARQLQuery();
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 2013-04-12 10:21:20 UTC (rev 3920)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/impl/QueryTreeImpl.java 2013-04-12 10:57:03 UTC (rev 3921)
@@ -703,7 +703,7 @@
StringBuilder sb = new StringBuilder();
sb.append("SELECT DISTINCT ?x0 WHERE {\n");
List<String> filters = new ArrayList<String>();
- buildSPARQLQueryString(this, sb, false, filters);
+ buildSPARQLQueryString(this, sb, true, false, filters);
for(String filter : filters){
sb.append(filter).append("\n");
}
@@ -711,13 +711,12 @@
return sb.toString();
}
- @Override
- public String toSPARQLQueryString(boolean filtered) {
- return toSPARQLQueryString(filtered, Collections.<String, String>emptyMap());
+ public String toSPARQLQueryString(boolean filterMeaninglessProperties, boolean useNumericalFilters) {
+ return toSPARQLQueryString(filterMeaninglessProperties, useNumericalFilters, Collections.<String, String>emptyMap());
}
@Override
- public String toSPARQLQueryString(boolean filtered, Map<String, String> prefixMap) {
+ public String toSPARQLQueryString(boolean filterMeaninglessProperties, boolean useNumericalFilters, Map<String, String> prefixMap) {
if(children.isEmpty()){
return "SELECT ?x0 WHERE {?x0 ?y ?z.}";
}
@@ -725,11 +724,11 @@
StringBuilder sb = new StringBuilder();
List<String> filters = new ArrayList<String>();
sb.append("SELECT DISTINCT ?x0 WHERE {\n");
- buildSPARQLQueryString(this, sb, filtered, filters);
+ buildSPARQLQueryString(this, sb, filterMeaninglessProperties, useNumericalFilters, filters);
for(String filter : filters){
sb.append(filter).append("\n");
}
- sb.append("}");
+ sb.append("}");System.out.println(sb.toString());
Query query = QueryFactory.create(sb.toString(), Syntax.syntaxARQ);
query.setPrefix("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
query.setPrefix("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
@@ -742,12 +741,14 @@
return query.toString();
}
- private void buildSPARQLQueryString(QueryTree<N> tree, StringBuilder sb, boolean filtered, List<String> filters){
+ private void buildSPARQLQueryString(QueryTree<N> tree, StringBuilder sb, boolean filterMeaninglessProperties, boolean useNumericalFilters, 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()));
+ if(useNumericalFilters){
+ if(tree.isLiteralNode() && !tree.getLiterals().isEmpty()){
+ filters.add(getFilter(subject.toString(), tree.getLiterals()));
+ }
}
} else {
subject = "<" + tree.getUserObject() + ">";
@@ -757,7 +758,7 @@
if(!tree.isLeaf()){
for(QueryTree<N> child : tree.getChildren()){
predicate = tree.getEdge(child);
- if(filtered){
+ if(filterMeaninglessProperties){
if(Filters.getAllFilterProperties().contains(predicate.toString())){
continue;
}
@@ -771,7 +772,7 @@
}
sb.append(subject).append(" <").append(predicate).append("> ").append(object).append(".\n");
if(!objectIsResource){
- buildSPARQLQueryString(child, sb, filtered, filters);
+ buildSPARQLQueryString(child, sb, filterMeaninglessProperties, useNumericalFilters, filters);
}
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/Filters.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/Filters.java 2013-04-12 10:21:20 UTC (rev 3920)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/Filters.java 2013-04-12 10:57:03 UTC (rev 3921)
@@ -57,6 +57,7 @@
filters.add(FOAF.name.toString());
filters.add(FOAF.firstName.toString());
// filters.add(FOAF.givenname.toString());
+ filters.add(FOAF.primaryTopic.toString());
return filters;
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedQueryTreeFilter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedQueryTreeFilter.java 2013-04-12 10:21:20 UTC (rev 3920)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedQueryTreeFilter.java 2013-04-12 10:57:03 UTC (rev 3921)
@@ -1,5 +1,6 @@
package org.dllearner.algorithms.qtl.filters;
+import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
@@ -15,7 +16,7 @@
public class QuestionBasedQueryTreeFilter implements QueryTreeFilter{
-private Set<String> questionWords;
+ private Collection<String> questionWords;
private AbstractStringMetric qGramMetric;
private AbstractStringMetric levensteinMetric;
@@ -25,7 +26,7 @@
private int topK = 3;
private double topKSumThreshold = 0.8;
- public QuestionBasedQueryTreeFilter(Set<String> questionWords){
+ public QuestionBasedQueryTreeFilter(Collection<String> questionWords){
this.questionWords = questionWords;
qGramMetric = new QGramsDistance();
levensteinMetric = new Levenshtein();
@@ -39,7 +40,7 @@
return copy;
}
- public Set<String> getQuestionWords(){
+ public Collection<String> getQuestionWords(){
return questionWords;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2013-04-12 10:21:23
|
Revision: 3920
http://sourceforge.net/p/dl-learner/code/3920
Author: jenslehmann
Date: 2013-04-12 10:21:20 +0000 (Fri, 12 Apr 2013)
Log Message:
-----------
minor QTL change
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-04-12 09:59:53 UTC (rev 3919)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-04-12 10:21:20 UTC (rev 3920)
@@ -424,11 +424,9 @@
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.getEndpointDBpedia());
ks.init();
PosOnlyLP lp = new PosOnlyLP();
- cm.getPool().registerComponent(lp);
lp.setPositiveExamples(Helper.getIndividualSet(positiveExamples));
QTL qtl = new QTL(lp, ks);
qtl.init();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2013-04-12 09:59:56
|
Revision: 3919
http://sourceforge.net/p/dl-learner/code/3919
Author: jenslehmann
Date: 2013-04-12 09:59:53 +0000 (Fri, 12 Apr 2013)
Log Message:
-----------
changed endpoint
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-04-11 08:03:30 UTC (rev 3918)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL.java 2013-04-12 09:59:53 UTC (rev 3919)
@@ -425,7 +425,7 @@
positiveExamples.add("http://dbpedia.org/resource/Chelsea_F.C.");
ComponentManager cm = ComponentManager.getInstance();
- SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
+ SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia());
ks.init();
PosOnlyLP lp = new PosOnlyLP();
cm.getPool().registerComponent(lp);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <chr...@us...> - 2013-04-11 08:03:35
|
Revision: 3918
http://sourceforge.net/p/dl-learner/code/3918
Author: christinaunger
Date: 2013-04-11 08:03:30 +0000 (Thu, 11 Apr 2013)
Log Message:
-----------
German lexicon
Modified Paths:
--------------
trunk/components-ext/src/main/resources/tbsl/lexicon/english.lex
Added Paths:
-----------
trunk/components-ext/src/main/resources/tbsl/lexicon/german.lex
Modified: trunk/components-ext/src/main/resources/tbsl/lexicon/english.lex
===================================================================
--- trunk/components-ext/src/main/resources/tbsl/lexicon/english.lex 2013-04-10 10:07:59 UTC (rev 3917)
+++ trunk/components-ext/src/main/resources/tbsl/lexicon/english.lex 2013-04-11 08:03:30 UTC (rev 3918)
@@ -166,7 +166,7 @@
there || (DP (NP EX:'there')) || <x,l1,<<e,t>,t>,[l1:[|]],[],[],[]>
-// NUMBERS (1-10)
+// NUMBERS (1-20)
// ---------------------
one || (NP NUM:'one' NP*) || <x,l1,<e,t>,[l1:[x|count(x,1)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,1)]],[],[],[ SLOT_arg/LITERAL/x ]>
@@ -179,8 +179,8 @@
eight || (NP NUM:'eight' NP*) || <x,l1,<e,t>,[l1:[x|count(x,8)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,8)]],[],[],[ SLOT_arg/LITERAL/x ]>
nine || (NP NUM:'nine' NP*) || <x,l1,<e,t>,[l1:[x|count(x,9)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,9)]],[],[],[ SLOT_arg/LITERAL/x ]>
ten || (NP NUM:'ten' NP*) || <x,l1,<e,t>,[l1:[x|count(x,10)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,10)]],[],[],[ SLOT_arg/LITERAL/x ]>
- eleven || (NP NUM:'one' NP*) || <x,l1,<e,t>,[l1:[x|count(x,11)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,11)]],[],[],[ SLOT_arg/LITERAL/x ]>
- twelve || (NP NUM:'two' NP*) || <x,l1,<e,t>,[l1:[x|count(x,12)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,12)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ eleven || (NP NUM:'eleven' NP*) || <x,l1,<e,t>,[l1:[x|count(x,11)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,11)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ twelve || (NP NUM:'twelve' NP*) || <x,l1,<e,t>,[l1:[x|count(x,12)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,12)]],[],[],[ SLOT_arg/LITERAL/x ]>
thirteen || (NP NUM:'thirteen' NP*) || <x,l1,<e,t>,[l1:[x|count(x,13)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,13)]],[],[],[ SLOT_arg/LITERAL/x ]>
fourteen || (NP NUM:'fourteen' NP*) || <x,l1,<e,t>,[l1:[x|count(x,14)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,14)]],[],[],[ SLOT_arg/LITERAL/x ]>
fifteen || (NP NUM:'fifteen' NP*) || <x,l1,<e,t>,[l1:[x|count(x,15)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,15)]],[],[],[ SLOT_arg/LITERAL/x ]>
@@ -210,3 +210,4 @@
eighteen || (NUM NUM:'eighteen') || <x,l1,e,[l1:[x|count(x,18)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,18)]],[],[],[ SLOT_arg/LITERAL/x ]>
nineteen || (NUM NUM:'nineteen') || <x,l1,e,[l1:[x|count(x,19)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,19)]],[],[],[ SLOT_arg/LITERAL/x ]>
twenty || (NUM NUM:'twenty') || <x,l1,e,[l1:[x|count(x,20)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,20)]],[],[],[ SLOT_arg/LITERAL/x ]>
+
Added: trunk/components-ext/src/main/resources/tbsl/lexicon/german.lex
===================================================================
--- trunk/components-ext/src/main/resources/tbsl/lexicon/german.lex (rev 0)
+++ trunk/components-ext/src/main/resources/tbsl/lexicon/german.lex 2013-04-11 08:03:30 UTC (rev 3918)
@@ -0,0 +1,275 @@
+
+// SEIN
+// ----
+
+ ist || (S DP[subject] (VP V:'ist' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | x=y ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ ist || (S DP[subject] (VP V:'ist' ADJ[comp])) || <x, l1, t, [ l1:[ | x=y ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+ war || (S DP[subject] (VP V:'war' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | x=y ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ war || (S DP[subject] (VP V:'war' ADJ[comp])) || <x, l1, t, [ l1:[ | x=y ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+
+ sind || (S DP[subject] (VP V:'sind' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | x=y ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ sind || (S DP[subject] (VP V:'sind' ADJ[comp])) || <x, l1, t, [ l1:[ | x=y ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+ waren || (S DP[subject] (VP V:'waren' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | x=y ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ waren || (S DP[subject] (VP V:'waren' ADJ[comp])) || <x, l1, t, [ l1:[ | x=y ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+
+ die .+ ist || (NP NP* (S C:'die' (VP DP[object] V:'ist'))) || <x, l1, t, [ l1:[ | x=y ] ], [ (l2,y,object,<<e,t>,t>) ], [ l2=l1 ],[]>
+ der .+ ist || (NP NP* (S C:'der' (VP DP[object] V:'ist'))) || <x, l1, t, [ l1:[ | x=y ] ], [ (l2,y,object,<<e,t>,t>) ], [ l2=l1 ],[]>
+ das .+ ist || (NP NP* (S C:'das' (VP DP[object] V:'ist'))) || <x, l1, t, [ l1:[ | x=y ] ], [ (l2,y,object,<<e,t>,t>) ], [ l2=l1 ],[]>
+ die .+ war || (NP NP* (S C:'die' (VP DP[object] V:'war'))) || <x, l1, t, [ l1:[ | x=y ] ], [ (l2,y,object,<<e,t>,t>) ], [ l2=l1 ],[]>
+ der .+ war || (NP NP* (S C:'der' (VP DP[object] V:'war'))) || <x, l1, t, [ l1:[ | x=y ] ], [ (l2,y,object,<<e,t>,t>) ], [ l2=l1 ],[]>
+ das .+ war || (NP NP* (S C:'das' (VP DP[object] V:'war'))) || <x, l1, t, [ l1:[ | x=y ] ], [ (l2,y,object,<<e,t>,t>) ], [ l2=l1 ],[]>
+ die .+ sind || (NP NP* (S C:'die' (VP DP[object] V:'sind'))) || <x, l1, t, [ l1:[ | x=y ] ], [ (l2,y,object,<<e,t>,t>) ], [ l2=l1 ],[]>
+ die .+ waren || (NP NP* (S C:'die' (VP DP[object] V:'waren'))) || <x, l1, t, [ l1:[ | x=y ] ], [ (l2,y,object,<<e,t>,t>) ], [ l2=l1 ],[]>
+
+ gibt es || (S V:'gibt' DP:'es' DP[dp]) || <x, l1, t, [ l1:[ | ] ], [ (l2,x,dp,<<e,t>,t>) ], [ l2=l1 ],[]>
+ gibt es || (S DP[dp] (VP V:'gibt' DP:'es')) || <x, l1, t, [ l1:[ | ] ], [ (l2,x,dp,<<e,t>,t>) ], [ l2=l1 ],[]>
+
+
+// SEIN: YES/NO QUESTIONS
+
+ ist || (S (VP V:'ist' DP[subject] DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | x=y ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ ist || (S (VP V:'ist' DP[subject] ADJ[comp])) || <x, l1, t, [ l1:[ | x=y ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+ war || (S V:'was' DP[subject] DP[object]) || <x, l1, t, [ l1:[ | ], l2:[ | x=y ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ war || (S V:'was' DP[subject] ADJ[comp]) || <x, l1, t, [ l1:[ | x=y ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+ sind || (S V:'sind' DP[subject] DP[object]) || <x, l1, t, [ l1:[ | ], l2:[ | x=y ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ sind || (S V:'sind' DP[subject] ADJ[comp]) || <x, l1, t, [ l1:[ | x=y ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+ waren || (S V:'waren' DP[subject] DP[object]) || <x, l1, t, [ l1:[ | ], l2:[ | x=y ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ waren || (S V:'waren' DP[subject] ADJ[comp]) || <x, l1, t, [ l1:[ | x=y ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+
+ did || (S V:'did' S*) || <x,l1,t,[ l1:[|] ],[],[],[]>
+
+// IMPERATIVES
+// ------------
+
+ gib mir || (S (VP V:'gib' (DP N:'mir') DP[object])) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ zeige mir || (S (VP V:'zeige' (DP N:'mir') DP[object])) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ zeig mir || (S (VP V:'zeig' (DP N:'mir') DP[object])) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ zeige || (S (VP V:'zeige' DP[object])) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ zeig || (S (VP V:'zeig' DP[object])) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ liste .+ auf || (S (VP V:'liste' DP[object] V:'auf')) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ finde || (S (VP V:'finde' DP[object])) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ suche || (S (VP V:'suche' DP[object])) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ suche .+ raus || (S (VP V:'suche' DP[object] V:'raus')) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+ suche .+ zusammen || (S (VP V:'suche' DP[object] V:'zusammen')) || <x,l1,t,[ l1:[ ?x | x=y ] ],[ (l2,y,object,<<e,t>,t>) ],[ l1=l2 ],[]>
+
+
+
+// DETERMINER
+// ----------
+
+ ein || (DP DET:'ein' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] SOME y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ eine || (DP DET:'eine' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] SOME y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ einen || (DP DET:'einen' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] SOME y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ einem || (DP DET:'einem' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] SOME y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ einige || (DP DET:'einige' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] SOME y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ einigen || (DP DET:'einigen' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] SOME y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ alle || (DP DET:'alle' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] EVERY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ allen || (DP DET:'allen' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] EVERY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ all die || (DP DET:'all' DET:'die' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ all den || (DP DET:'all' DET:'den' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ jede || (DP DET:'jede' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] EVERY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ jeder || (DP DET:'jeder' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] EVERY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ jedes || (DP DET:'jedes' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] EVERY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ jedem || (DP DET:'jedem' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] EVERY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ jeden || (DP DET:'jeden' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] EVERY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ kein || (DP DET:'kein' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] NO y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ keine || (DP DET:'keine' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] NO y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ keinem || (DP DET:'keinem' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] NO y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ keinen || (DP DET:'keinen' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] NO y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ die meisten || (DP DET:'die' ADJ:'meisten' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] THEMOST y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ den meisten || (DP DET:'den' ADJ:'meisten' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] THEMOST y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ die wenigsten || (DP DET:'die' ADJ:'wenigsten' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] THELEAST y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ den wenigsten || (DP DET:'den' ADJ:'wenigsten' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] THELEAST y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ wenige || (DP DET:'wenig' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] AFEW y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ wenig || (DP DET:'wenig' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] AFEW y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ manche || (DP DET:'manche' NP[noun]) || <x, l1, <<e,t>,t>, [ l1:[ x | ] ], [ (l2,x,noun,<e,t>) ], [ l2=l1 ],[]>
+ welche || (DP DET:'welche' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ ?y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ welcher || (DP DET:'welcher' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ ?y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ welches || (DP DET:'welches' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ ?y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ welchen || (DP DET:'welchen' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ ?y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ welchem || (DP DET:'welchem' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ ?y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ was fuer || (DP DET:'was' DET:'fuer' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ ?y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ was fuer ein || (DP DET:'was' DET:'fuer' DET:'ein' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ ?y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ was fuer eine || (DP DET:'was' DET:'fuer' DET:'eine' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ ?y | ] ], [ (l2,y,noun,<e,t>) ], [ l2=l1 ],[]>
+ viele || (DP DET:'viele' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] MANY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ vielen || (DP DET:'vielen' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] MANY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ viel || (DP DET:'viel' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] MANY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[]>
+ der || (DP DET:'der' NP[noun]) || <x, l1, <<e,t>,t>, [ l1:[x|] ], [ (l2,x,noun,<e,t>) ], [ l2=l1 ],[]>
+ die || (DP DET:'die' NP[noun]) || <x, l1, <<e,t>,t>, [ l1:[x|] ], [ (l2,x,noun,<e,t>) ], [ l2=l1 ],[]>
+ das || (DP DET:'das' NP[noun]) || <x, l1, <<e,t>,t>, [ l1:[x|] ], [ (l2,x,noun,<e,t>) ], [ l2=l1 ],[]>
+ dem || (DP DET:'dem' NP[noun]) || <x, l1, <<e,t>,t>, [ l1:[x|] ], [ (l2,x,noun,<e,t>) ], [ l2=l1 ],[]>
+ den || (DP DET:'den' NP[noun]) || <x, l1, <<e,t>,t>, [ l1:[x|] ], [ (l2,x,noun,<e,t>) ], [ l2=l1 ],[]>
+ mindestens || (DP DET:'mindestens' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[ l1:[ y,c | count(y,c), greaterorequal(c,x) ] ],[(l2,y,noun,<e,t>),(l3,x,num,e)],[l2=l1,l3=l1],[ SLOT_arg/RESOURCE/y ]> ;; <y,l1,<<e,t>,t>,[l1:[ y | greaterorequal(y,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[ SLOT_arg/LITERAL/y ]>
+ hoechstens || (DP DET:'hoechstens' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[ l1:[ y,c | count(y,c), lessorequal(c,x) ] ],[(l2,y,noun,<e,t>),(l3,x,num,e)],[l2=l1,l3=l1],[ SLOT_arg/RESOURCE/y ]> ;; <y,l1,<<e,t>,t>,[l1:[ y | lessorequal(y,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[ SLOT_arg/LITERAL/y ]>
+ mehr als || (DP DET:'mehr' DET:'als' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[ l1:[ y,c | count(y,c), greater(c,x) ] ],[(l2,y,noun,<e,t>),(l3,x,num,e)],[l2=l1,l3=l1],[ SLOT_arg/RESOURCE/y ]> ;; <y,l1,<<e,t>,t>,[l1:[ y | greater(y,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[ SLOT_arg/LITERAL/y ]>
+ weniger als || (DP DET:'weniger' DET:'als' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[ l1:[ y,c | count(y,c), less(c,x) ] ],[(l2,y,noun,<e,t>),(l3,x,num,e)],[l2=l1,l3=l1],[ SLOT_arg/RESOURCE/y ]> ;; <y,l1,<<e,t>,t>,[l1:[ y | less(y,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[ SLOT_arg/LITERAL/y ]>
+ genau || (DP DET:'genau' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[ l1:[ y,c | count(y,c), equal(c,x) ] ],[(l2,y,noun,<e,t>),(l3,x,num,e)],[l2=l1,l3=l1],[ SLOT_arg/RESOURCE/y ]> ;; <y,l1,<<e,t>,t>,[l1:[ y | equal(y,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[ SLOT_arg/LITERAL/y ]>
+ insgesamt || (DP DET:'insgesamt' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[ l1:[ y,c | count(y,c), equal(c,x) ] ],[(l2,y,noun,<e,t>),(l3,x,num,e)],[l2=l1,l3=l1],[ SLOT_arg/RESOURCE/y ]> ;; <y,l1,<<e,t>,t>,[l1:[ y | equal(y,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[ SLOT_arg/LITERAL/y ]>
+ // also sum(a,x,s) ?
+
+ andere || (NP ADJ:'other' NP*) || <x,l1,<e,t>,[ l1:[ | ] ], [],[],[]>
+ andere || (NP ADJ:'other' NP*) || <x,l1,<e,t>,[ l1:[ | ] ], [],[],[]>
+ andere || (NP ADJ:'other' NP*) || <x,l1,<e,t>,[ l1:[ | ] ], [],[],[]>
+
+ die wenigsten || (ADJ DET:'die' DET:'wenigsten' ADJ*) || <x,l1,<e,t>,[ l1:[ | minimum(a,x,x) ] ], [],[],[]>
+ den wenigsten || (ADJ DET:'den' DET:'wenigsten' ADJ*) || <x,l1,<e,t>,[ l1:[ | minimum(a,x,x) ] ], [],[],[]>
+
+ wieviele || (DET DET:'wieviele') || <x,l1,e, [ l1:[ ?x | ] ], [],[],[ SLOT_arg/DATATYPEPROPERTY/x ]>
+ wieviel || (DET DET:'wieviel') || <x,l1,e, [ l1:[ ?c,x | count(a,x,c) ] ], [],[],[ SLOT_arg/OBJECTPROPERTY_CLASS/x ]>
+ ein || (DET DET:'ein') || <x,l1,e, [ l1:[ x |] ], [],[],[]>
+ eine || (DET DET:'eine') || <x,l1,e, [ l1:[ x |] ], [],[],[]>
+ welche || (DET DET:'welche') || <x,l1,e, [ l1:[ ?x |] ], [],[],[]>
+ welcher || (DET DET:'welcher') || <x,l1,e, [ l1:[ ?x |] ], [],[],[]>
+ welches || (DET DET:'welches') || <x,l1,e, [ l1:[ ?x |] ], [],[],[]>
+
+ der || (DET DET:'der') || <x,l1,e, [ l1:[ x |] ], [],[],[]>
+ die || (DET DET:'die') || <x,l1,e, [ l1:[ x |] ], [],[],[]>
+ das || (DET DET:'das') || <x,l1,e, [ l1:[ x |] ], [],[],[]>
+ den || (DET DET:'den') || <x,l1,e, [ l1:[ x |] ], [],[],[]>
+ dam || (DET DET:'dem') || <x,l1,e, [ l1:[ x |] ], [],[],[]>
+ die meisten || (DET DET:'die' DET:'meisten') || <y, l1, e, [ l1:[ | l2:[ y | ] THEMOST y l3:[|] ] ], [], [],[]>
+ den meisten || (DET DET:'den' DET:'meisten') || <y, l1, e, [ l1:[ | l2:[ y | ] THEMOST y l3:[|] ] ], [], [],[]>
+ die wenigsten || (DET DET:'die' DET:'wenigsten') || <y, l1, e, [ l1:[ | l2:[ y | ] THELEAST y l3:[|] ] ], [], [],[]>
+ den wenigsten || (DET DET:'den' DET:'wenigsten') || <y, l1, e, [ l1:[ | l2:[ y | ] THELEAST y l3:[|] ] ], [], [],[]>
+
+
+ // NECESSARY "CHEAT"
+ hoechste || (NP ADJ:'hoechste' NP*) || <x, l1, e, [ l1:[ | maximum(x) ] ], [], [],[]> ;; <x, l1, e, [ l1:[ j | SLOT_high(x,j), maximum(j) ] ],[],[],[ SLOT_high/DATATYPEPROPERTY/height ]>
+ hoechsten || (NP ADJ:'hoechsten' NP*) || <x, l1, e, [ l1:[ | maximum(x) ] ], [], [],[]> ;; <x, l1, e, [ l1:[ j | SLOT_high(x,j), maximum(j) ] ],[],[],[ SLOT_high/DATATYPEPROPERTY/height ]>
+
+ // WIE
+ // wie || (DP DET:'wie' ADJ[adj]) || <x,l1,<<e,t>,t>,[ l1:[?x,|] ],[ (x,l2,adj,<e,t>) ],[l2=l1],[]>
+
+
+// EMPTY STUFF
+// ------------
+
+ auch || (VP ADV:'auch' VP*) || <x,l1,t,[ l1:[|] ],[],[],[]>
+ auch || (DP ADV:'auch' DP*) || <x,l1,<<e,t>,t>,[ l1:[|] ],[],[],[]>
+
+ hat || (S DP[subject] (VP V:'hat' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | empty(x,y) ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ haben || (S DP[subject] (VP V:'haben' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | empty(x,y) ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ hatte || (S DP[subject] (VP V:'hatte' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | empty(x,y) ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ hatten || (S DP[subject] (VP V:'hatten' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | empty(x,y) ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+
+// mit || (NP NP* (PP P:'mit' DP[dp])) || <x,l1,<e,t>,[ l1:[| empty(x,y) ] ],[(l2,y,dp,<<e,t>,t>)],[l2=l1],[]>
+
+// people || (NP N:'people') || <x,l1,<e,t>,[ l1:[|] ],[],[],[]>
+
+
+// WH WORDS
+// --------
+
+ was || (DP WH:'was') || <x, l1, <<e,t>,t>, [ l1:[ ?x | ] ], [], [], []>
+ wer || (DP WH:'wer') || <x, l1, <<e,t>,t>, [ l1:[ ?x | ] ], [], [], []>
+ wen || (DP WH:'wen') || <x, l1, <<e,t>,t>, [ l1:[ ?x | ] ], [], [], []>
+ wem || (DP WH:'wem') || <x, l1, <<e,t>,t>, [ l1:[ ?x | ] ], [], [], []>
+
+// welche || (DP WH:'welche') || <x, l1, <<e,t>,t>, [ l1:[ ?x | ] ], [], [], []>
+// welches || (DP WH:'welche') || <x, l1, <<e,t>,t>, [ l1:[ ?x | ] ], [], [], []>
+// welcher || (DP WH:'welche') || <x, l1, <<e,t>,t>, [ l1:[ ?x | ] ], [], [], []>
+
+ wieviel || (DP WH:'wieviel' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] HOWMANY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[ SLOT_arg/RESOURCE/y ]>
+ wieviele || (DP WH:'wieviele' NP[noun]) || <y, l1, <<e,t>,t>, [ l1:[ | l2:[ y | ] HOWMANY y l3:[|] ] ], [ (l4,y,noun,<e,t>) ], [ l4=l2 ],[ SLOT_arg/RESOURCE/y ]>
+
+ wann || (S WH:'wann' S[s]) || <x, l1, t, [ l1:[ ?x | SLOT_p(y,x) ] ], [(l2,y,s,t)], [l2=l1], [ SLOT_p/PROPERTY/date ]>
+ wann || (DP WH:'wann') || <y, l1, <<e,t>,t>, [ l1:[ ?x | SLOT_p(y,x) ] ], [], [], [ SLOT_p/PROPERTY/date ]>
+ wo || (S WH:'wo' S[s]) || <x, l1, t, [ l1:[ ?x | SLOT_p(y,x) ] ], [(l2,y,s,t)], [l2=l1], [ SLOT_p/PROPERTY/place ]>
+ wo || (DP WH:'wo') || <y, l1, <<e,t>,t>, [ l1:[ ?x | SLOT_p(y,x) ] ], [], [], [ SLOT_p/PROPERTY/place ]>
+ wo in || (DP WH:'wo' (PP P:'in' DP[dp])) || <y, l1, <<e,t>,t>, [ l1:[ ?x | SLOT_p(y,x), SLOT_in(x,z) ] ], [(l2,z,dp,<<e,t>,t>)], [l2=l1], [ SLOT_p/PROPERTY/place ]>
+
+
+// NEGATION
+// --------
+
+ nicht || (ADJ NEG:'nicht' ADJ*) || <x,l2,t,[ l1:[ | NOT l2:[|] ] ],[],[],[]>
+ nicht || (VP NEG:'nicht' VP*) || <x,l2,t,[ l1:[ | NOT l2:[|] ] ],[],[],[]>
+ hat nicht || (VP V:'hat' NEG:'nicht' VP*) || <x,l2,t,[ l1:[ | NOT l2:[|] ] ],[],[],[]>
+ haben nicht || (VP V:'haben' NEG:'nicht' VP*) || <x,l2,t,[ l1:[ | NOT l2:[|] ] ],[],[],[]>
+ hatte nicht || (VP V:'hatte' NEG:'nicht' VP*) || <x,l2,t,[ l1:[ | NOT l2:[|] ] ],[],[],[]>
+ hatten nicht || (VP V:'hatten' NEG:'nicht' VP*) || <x,l2,t,[ l1:[ | NOT l2:[|] ] ],[],[],[]>
+
+ ist nicht || (S DP[subject] (VP V:'ist' NEG:'nicht' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | NOT [ | x=y ] ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ ist nicht || (S DP[subject] (VP V:'ist' NEG:'nicht' ADJ[comp])) || <x, l1, t, [ l1:[ | NOT [ | x=y ] ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+ war nicht || (S DP[subject] (VP V:'war' NEG:'nicht' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | NOT [ | x=y ] ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ war nicht || (S DP[subject] (VP V:'war' NEG:'nicht' ADJ[comp])) || <x, l1, t, [ l1:[ | NOT [ | x=y ] ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+ sind nicht || (S DP[subject] (VP V:'sind' NEG:'nicht' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | NOT [ | x=y ] ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ sind nicht || (S DP[subject] (VP V:'sind' NEG:'nicht' ADJ[comp])) || <x, l1, t, [ l1:[ | NOT [ | x=y ] ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+ waren nicht || (S DP[subject] (VP V:'waren' NEG:'nicht' DP[object])) || <x, l1, t, [ l1:[ | ], l2:[ | NOT [ | x=y ] ] ], [ (l3,x,subject,<<e,t>,t>), (l4,y,object,<<e,t>,t>) ], [ l3<l1, l4<l1, l2<scope(l3), l2<scope(l4) ],[]>
+ waren nicht || (S DP[subject] (VP V:'waren' NEG:'nicht' ADJ[comp])) || <x, l1, t, [ l1:[ | NOT [ | x=y ] ]], [ (l2,x,subject,<<e,t>,t>), (l3,y,comp,<e,t>) ], [ l2=l1, l3=l2 ],[]>
+
+
+// COORDINATION
+// ------------
+
+ und || (S S* CC:'und' S[s]) || <x,l1,t,[l1:[|]],[(l2,y,s,t)],[l1=l2],[]>
+ und || (DP DP* CC:'und' DP[dp]) || <x,l1,<<e,t>,t>,[l1:[|]],[(l2,y,dp,<<e,t>,t>)],[l1=l2],[]>
+ und || (NP NP* CC:'und' NP[np]) || <x,l1,<e,t>,[l1:[|x=y]],[(l2,y,np,<e,t>)],[l1=l2],[]>
+ und || (PP PP* CC:'und' PP[pp]) || <x,l1,<e,t>,[l1:[|x=y]],[(l2,y,pp,<e,t>)],[l1=l2],[]>
+ und || (ADJ ADJ* CC:'und' ADJ[adj]) || <x,l1,<e,t>,[l1:[|]],[(l2,y,adj,<e,t>)],[l1=l2],[]>
+
+ aber || (S S* CC:'aber' S[s]) || <x,l1,t,[l1:[|]],[(l2,y,s,t)],[l1=l2],[]>
+ aber || (DP DP* CC:'aber' DP[dp]) || <x,l1,<<e,t>,t>,[l1:[|]],[(l2,y,dp,<<e,t>,t>)],[l1=l2],[]>
+ aber || (NP NP* CC:'aber' NP[np]) || <x,l1,<e,t>,[l1:[|x=y]],[(l2,y,np,<e,t>)],[l1=l2],[]>
+ aber || (PP PP* CC:'aber' PP[pp]) || <x,l1,<e,t>,[l1:[|x=y]],[(l2,y,pp,<e,t>)],[l1=l2],[]>
+ aber || (ADJ ADJ* CC:'aber' ADJ[adj]) || <x,l1,<e,t>,[l1:[|]],[(l2,y,adj,<e,t>)],[l1=l2],[]>
+
+ sowohl .+ als auch || (NP CC:'sowohl' NP* CC:'als' CC:'auch' NP[np]) || <x,l1,<e,t>,[l1:[|]],[(l2,y,np,<e,t>)],[l1=l2],[]>
+
+ oder || (S S[cc1] CC:'oder' S[cc2]) || <x, l1, t, [ l1:[ | l2:[|] OR l3:[|] ] ], [ (l5,x,cc1,t),(l4,y,cc2,t) ], [ l5=l2,l4=l3 ],[]>
+ oder || (DP DP[cc1] CC:'oder' DP[cc2]) || <x, l1, <<e,t>,t>, [ l1:[ | l2:[|] OR l3:[|], x=y ] ], [ (l5,x,cc1,<<e,t>,t>),(l4,y,cc2,<<e,t>,t>) ], [ l5=l2,l4=l3 ],[]>
+ oder || (NP NP[cc1] CC:'oder' NP[cc2]) || <x, l1, <e,t>, [ l1:[ | l2:[|] OR l3:[|], x=y ] ], [ (l5,x,cc1,<e,t>),(l4,y,cc2,<e,t>) ], [ l5=l2,l4=l3 ],[]>
+ oder || (ADJ ADJ* CC:'oder' ADJ[cc]) || -
+
+
+// EXPLETIVE
+// ----------
+
+ es || (DP NP:'es') || <x,l1,<<e,t>,t>,[l1:[|]],[],[],[]>
+
+
+// NUMBERS (1-20)
+// ---------------
+
+ eins || (NP NUM:'eins' NP*) || <x,l1,<e,t>,[l1:[x|count(x,1)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,1)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ zwei || (NP NUM:'zwei' NP*) || <x,l1,<e,t>,[l1:[x|count(x,2)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,2)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ drei || (NP NUM:'drei' NP*) || <x,l1,<e,t>,[l1:[x|count(x,3)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,3)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ vier || (NP NUM:'vier' NP*) || <x,l1,<e,t>,[l1:[x|count(x,4)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,4)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ fuenf || (NP NUM:'fuenf' NP*) || <x,l1,<e,t>,[l1:[x|count(x,5)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,5)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ sechs || (NP NUM:'sechs' NP*) || <x,l1,<e,t>,[l1:[x|count(x,6)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,6)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ sieben || (NP NUM:'sieben' NP*) || <x,l1,<e,t>,[l1:[x|count(x,7)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,7)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ acht || (NP NUM:'acht' NP*) || <x,l1,<e,t>,[l1:[x|count(x,8)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,8)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ neun || (NP NUM:'neun' NP*) || <x,l1,<e,t>,[l1:[x|count(x,9)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,9)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ zehn || (NP NUM:'zehn' NP*) || <x,l1,<e,t>,[l1:[x|count(x,10)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,10)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ elf || (NP NUM:'elf' NP*) || <x,l1,<e,t>,[l1:[x|count(x,11)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,11)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ zwoelf || (NP NUM:'zwoelf' NP*) || <x,l1,<e,t>,[l1:[x|count(x,12)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,12)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ dreizehn || (NP NUM:'dreizehn' NP*) || <x,l1,<e,t>,[l1:[x|count(x,13)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,13)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ vierzehn || (NP NUM:'vierzehn' NP*) || <x,l1,<e,t>,[l1:[x|count(x,14)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,14)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ fuenfzehn || (NP NUM:'fuenfzehn' NP*) || <x,l1,<e,t>,[l1:[x|count(x,15)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,15)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ sechzehn || (NP NUM:'sechzehn' NP*) || <x,l1,<e,t>,[l1:[x|count(x,16)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,16)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ siebzehn || (NP NUM:'siebzehn' NP*) || <x,l1,<e,t>,[l1:[x|count(x,17)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,17)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ achtzehn || (NP NUM:'achtzehn' NP*) || <x,l1,<e,t>,[l1:[x|count(x,18)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,18)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ neunzehn || (NP NUM:'neunzehn' NP*) || <x,l1,<e,t>,[l1:[x|count(x,19)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,19)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ zwanzig || (NP NUM:'zwanzig' NP*) || <x,l1,<e,t>,[l1:[x|count(x,20)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,<e,t>,[l1:[x|equal(x,10)]],[],[],[ SLOT_arg/LITERAL/x ]>
+
+ eins || (NUM NUM:'eins') || <x,l1,e,[l1:[x|count(x,1)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,1)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ zwei || (NUM NUM:'zwei') || <x,l1,e,[l1:[x|count(x,2)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,2)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ drei || (NUM NUM:'drei') || <x,l1,e,[l1:[x|count(x,3)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,3)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ vier || (NUM NUM:'vier') || <x,l1,e,[l1:[x|count(x,4)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,4)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ fuenf || (NUM NUM:'fuenf') || <x,l1,e,[l1:[x|count(x,5)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,5)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ sechs || (NUM NUM:'sechs') || <x,l1,e,[l1:[x|count(x,6)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,6)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ sieben || (NUM NUM:'sieben') || <x,l1,e,[l1:[x|count(x,7)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,7)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ acht || (NUM NUM:'acht') || <x,l1,e,[l1:[x|count(x,8)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,8)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ neun || (NUM NUM:'neun') || <x,l1,e,[l1:[x|count(x,9)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,9)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ zehn || (NUM NUM:'zehn') || <x,l1,e,[l1:[x|count(x,10)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,10)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ elf || (NUM NUM:'elf') || <x,l1,e,[l1:[x|count(x,11)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,11)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ zwoelf || (NUM NUM:'zwoelf') || <x,l1,e,[l1:[x|count(x,12)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,12)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ dreizehn || (NUM NUM:'dreizehn') || <x,l1,e,[l1:[x|count(x,13)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,13)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ vierzehn || (NUM NUM:'vierzehn') || <x,l1,e,[l1:[x|count(x,14)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,14)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ fuenfzehn || (NUM NUM:'fuenfzehn') || <x,l1,e,[l1:[x|count(x,15)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,15)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ sechzehn || (NUM NUM:'sechzehn') || <x,l1,e,[l1:[x|count(x,16)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,16)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ siebzehn || (NUM NUM:'siebzehn') || <x,l1,e,[l1:[x|count(x,17)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,17)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ achtzehn || (NUM NUM:'achtzehn') || <x,l1,e,[l1:[x|count(x,18)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,18)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ neunzehn || (NUM NUM:'neunzehn') || <x,l1,e,[l1:[x|count(x,19)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,19)]],[],[],[ SLOT_arg/LITERAL/x ]>
+ zwanzig || (NUM NUM:'zwanzig') || <x,l1,e,[l1:[x|count(x,20)]],[],[],[ SLOT_arg/RESOURCE/x ]> ;; <x,l1,e,[l1:[x|equal(x,20)]],[],[],[ SLOT_arg/LITERAL/x ]>
+
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|
|
From: <lor...@us...> - 2013-04-10 10:08:02
|
Revision: 3917
http://sourceforge.net/p/dl-learner/code/3917
Author: lorenz_b
Date: 2013-04-10 10:07:59 +0000 (Wed, 10 Apr 2013)
Log Message:
-----------
Added JUNIT test for pattern detection.
Added Paths:
-----------
trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/
trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLAxiomRenamerTest.java
Added: trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLAxiomRenamerTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLAxiomRenamerTest.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLAxiomRenamerTest.java 2013-04-10 10:07:59 UTC (rev 3917)
@@ -0,0 +1,95 @@
+package org.dllearner.algorithms.pattern;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+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;
+
+public class OWLAxiomRenamerTest {
+ private OWLDataFactory df;
+
+ private OWLClass clsA;
+ private OWLClass clsB;
+ private OWLClass clsC;
+ private OWLObjectProperty propR;
+ private OWLObjectProperty propS;
+ private OWLIndividual indA;
+ private OWLIndividual indB;
+
+ private OWLAxiomRenamer renamer;
+
+ @Before
+ public void setUp() throws Exception {
+ df = new OWLDataFactoryImpl();
+ PrefixManager pm = new DefaultPrefixManager("http://examples.org/ontology#");
+
+ clsA = df.getOWLClass("A", pm);
+ clsB = df.getOWLClass("B", pm);
+ clsC = df.getOWLClass("C", pm);
+
+ propR = df.getOWLObjectProperty("r", pm);
+ propS = df.getOWLObjectProperty("s", pm);
+
+ indA = df.getOWLNamedIndividual("a", pm);
+ indB = df.getOWLNamedIndividual("b", pm);
+
+ renamer = new OWLAxiomRenamer(df);
+ }
+
+ @Test
+ public void testRename() {
+ ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
+ OWLAxiom ax1 = df.getOWLSubClassOfAxiom(clsA, clsB);
+ OWLAxiom ax2 = df.getOWLSubClassOfAxiom(clsB, clsC);
+
+ System.out.print(ax1 + "->");ax1 = renamer.rename(ax1);System.out.println(ax1);
+ System.out.print(ax2 + "->");ax2 = renamer.rename(ax2);System.out.println(ax1);
+ assertEquals(ax1, ax2);
+
+ ax1 = df.getOWLSubClassOfAxiom(
+ clsA,
+ df.getOWLObjectIntersectionOf(
+ clsB,
+ df.getOWLObjectSomeValuesFrom(propR, clsC)));
+ ax2 = df.getOWLSubClassOfAxiom(
+ clsA,
+ df.getOWLObjectIntersectionOf(
+ df.getOWLObjectSomeValuesFrom(propS, clsB),
+ clsC));
+ System.out.print(ax1 + "->");ax1 = renamer.rename(ax1);System.out.println(ax1);
+ System.out.print(ax2 + "->");ax2 = renamer.rename(ax2);System.out.println(ax2);
+ assertEquals(ax1, ax2);
+
+ ax1 = df.getOWLSubClassOfAxiom(
+ clsA,
+ df.getOWLObjectIntersectionOf(
+ clsB,
+ df.getOWLObjectSomeValuesFrom(
+ propR,
+ df.getOWLObjectUnionOf(clsB, clsA))));
+ ax2 = df.getOWLSubClassOfAxiom(
+ clsA,
+ df.getOWLObjectIntersectionOf(
+ df.getOWLObjectSomeValuesFrom(
+ propS,
+ df.getOWLObjectUnionOf(clsB, clsA)),
+ clsB));
+ System.out.print(ax1 + "->");ax1 = renamer.rename(ax1);System.out.println(ax1);
+ System.out.print(ax2 + "->");ax2 = renamer.rename(ax2);System.out.println(ax2);
+ assertEquals(ax1, ax2);
+
+
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-04-10 10:07:14
|
Revision: 3916
http://sourceforge.net/p/dl-learner/code/3916
Author: lorenz_b
Date: 2013-04-10 10:07:10 +0000 (Wed, 10 Apr 2013)
Log Message:
-----------
Updated JENA.
Modified Paths:
--------------
trunk/pom.xml
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2013-04-10 10:06:38 UTC (rev 3915)
+++ trunk/pom.xml 2013-04-10 10:07:10 UTC (rev 3916)
@@ -257,7 +257,7 @@
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
- <version>2.9.2</version>
+ <version>2.10.0</version>
</dependency>
<!--Junits -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-04-10 10:06:41
|
Revision: 3915
http://sourceforge.net/p/dl-learner/code/3915
Author: lorenz_b
Date: 2013-04-10 10:06:38 +0000 (Wed, 10 Apr 2013)
Log Message:
-----------
Fixed bug.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java
trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/LabelShortFormProvider.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -58,7 +58,7 @@
public class OWLAxiomRenamer implements OWLAxiomVisitor {
private OWLDataFactory df;
- private OWLClassExpressionRenamer renamer;
+ private OWLClassExpressionRenamer expressionRenamer;
private OWLAxiom renamedAxiom;
public OWLAxiomRenamer(OWLDataFactory df) {
@@ -67,7 +67,7 @@
public OWLAxiom rename(OWLAxiom axiom){
Map<OWLEntity, OWLEntity> renaming = new HashMap<OWLEntity, OWLEntity>();
- renamer = new OWLClassExpressionRenamer(df, renaming);
+ expressionRenamer = new OWLClassExpressionRenamer(df, renaming);
axiom.accept(this);
return renamedAxiom;
}
@@ -75,9 +75,9 @@
@Override
public void visit(OWLSubClassOfAxiom axiom) {
OWLClassExpression subClass = axiom.getSubClass();
- subClass = renamer.rename(subClass);
+ subClass = expressionRenamer.rename(subClass);
OWLClassExpression superClass = axiom.getSuperClass();
- superClass = renamer.rename(superClass);
+ superClass = expressionRenamer.rename(superClass);
renamedAxiom = df.getOWLSubClassOfAxiom(subClass, superClass);
}
@@ -120,18 +120,18 @@
@Override
public void visit(OWLDataPropertyDomainAxiom axiom) {
OWLDataPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
OWLClassExpression domain = axiom.getDomain();
- domain = renamer.rename(domain);
+ domain = expressionRenamer.rename(domain);
renamedAxiom = df.getOWLDataPropertyDomainAxiom(property, domain);
}
@Override
public void visit(OWLObjectPropertyDomainAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
OWLClassExpression domain = axiom.getDomain();
- domain = renamer.rename(domain);
+ domain = expressionRenamer.rename(domain);
renamedAxiom = df.getOWLObjectPropertyDomainAxiom(property, domain);
}
@@ -158,9 +158,9 @@
@Override
public void visit(OWLObjectPropertyRangeAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
OWLClassExpression range = axiom.getRange();
- range = renamer.rename(range);
+ range = expressionRenamer.rename(range);
renamedAxiom = df.getOWLObjectPropertyDomainAxiom(property, range);
}
@@ -171,7 +171,7 @@
@Override
public void visit(OWLFunctionalObjectPropertyAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLFunctionalObjectPropertyAxiom(property);
}
@@ -186,23 +186,23 @@
@Override
public void visit(OWLSymmetricObjectPropertyAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLSymmetricObjectPropertyAxiom(property);
}
@Override
public void visit(OWLDataPropertyRangeAxiom axiom) {
OWLDataPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
OWLDataRange range = axiom.getRange();
- range = renamer.rename(range);
+ range = expressionRenamer.rename(range);
renamedAxiom = df.getOWLDataPropertyRangeAxiom(property, range);
}
@Override
public void visit(OWLFunctionalDataPropertyAxiom axiom) {
OWLDataPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLFunctionalDataPropertyAxiom(property);
}
@@ -213,9 +213,9 @@
@Override
public void visit(OWLClassAssertionAxiom axiom) {
OWLClassExpression classExpression = axiom.getClassExpression();
- classExpression = renamer.rename(classExpression);
+ classExpression = expressionRenamer.rename(classExpression);
OWLIndividual individual = axiom.getIndividual();
- individual = renamer.rename(individual);
+ individual = expressionRenamer.rename(individual);
renamedAxiom = df.getOWLClassAssertionAxiom(classExpression, individual);
}
@@ -224,7 +224,7 @@
List<OWLClassExpression> classExpressions = axiom.getClassExpressionsAsList();
List<OWLClassExpression> renamedClassExpressions = new ArrayList<OWLClassExpression>();
for (OWLClassExpression expr : classExpressions) {
- renamedClassExpressions.add(renamer.rename(expr));
+ renamedClassExpressions.add(expressionRenamer.rename(expr));
}
renamedAxiom = df.getOWLEquivalentClassesAxiom(new TreeSet<OWLClassExpression>(renamedClassExpressions));
}
@@ -236,14 +236,14 @@
@Override
public void visit(OWLTransitiveObjectPropertyAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLTransitiveObjectPropertyAxiom(property);
}
@Override
public void visit(OWLIrreflexiveObjectPropertyAxiom axiom) {
OWLObjectPropertyExpression property = axiom.getProperty();
- property = renamer.rename(property);
+ property = expressionRenamer.rename(property);
renamedAxiom = df.getOWLIrreflexiveObjectPropertyAxiom(property);
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -20,6 +20,7 @@
package org.dllearner.algorithms.properties;
import java.util.ArrayList;
+import java.util.List;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
import org.dllearner.core.ComponentAnn;
@@ -29,6 +30,8 @@
import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.FunctionalDatatypePropertyAxiom;
import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.learningproblems.AxiomScore;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -109,7 +112,7 @@
all = qs.getLiteral("all").getInt();
}
// get number of instances of s with <s p o> <s p o1> where o != o1
- query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o1)} }";
+ query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o2)} }";
query = query.replace("%s", propertyToDescribe.getURI().toString());
rs = executeSelectQuery(query, workingModel);
int functional = 1;
@@ -140,7 +143,7 @@
if (numberOfSubjects > 0) {
int functional = 0;
- String query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o1)} }";
+ String query = "SELECT (COUNT(DISTINCT ?s) AS ?functional) WHERE {?s <%s> ?o1. FILTER NOT EXISTS {?s <%s> ?o2. FILTER(?o1 != ?o2)} }";
query = query.replace("%s", propertyToDescribe.getURI().toString());
ResultSet rs = executeSelectQuery(query);
if (rs.hasNext()) {
@@ -153,4 +156,23 @@
declaredAsFunctional));
}
}
+
+ public static void main(String[] args) throws Exception {
+ FunctionalDataPropertyAxiomLearner l = new FunctionalDataPropertyAxiomLearner(new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia()));
+ l.setPropertyToDescribe(new DatatypeProperty("http://dbpedia.org/ontology/birthDate"));
+ l.setMaxExecutionTimeInSeconds(10);
+ l.setForceSPARQL_1_0_Mode(true);
+ l.init();
+ l.start();
+ List<EvaluatedAxiom> axioms = l.getCurrentlyBestEvaluatedAxioms(5);
+ System.out.println(axioms);
+
+ for(EvaluatedAxiom axiom : axioms){
+ printSubset(l.getPositiveExamples(axiom), 10);
+ printSubset(l.getNegativeExamples(axiom), 10);
+ l.explainScore(axiom);
+ System.out.println(((AxiomScore)axiom.getScore()).getTotalNrOfExamples());
+ System.out.println(((AxiomScore)axiom.getScore()).getNrOfPositiveExamples());
+ }
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/ObjectPropertyDomainAxiomLearner.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -198,22 +198,24 @@
org.apache.log4j.Logger.getRootLogger().setLevel(Level.INFO);
org.apache.log4j.Logger.getLogger(DataPropertyDomainAxiomLearner.class).setLevel(Level.INFO);
- SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
+ SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia());
+
SPARQLReasoner reasoner = new SPARQLReasoner(ks);
reasoner.prepareSubsumptionHierarchy();
ObjectPropertyDomainAxiomLearner l = new ObjectPropertyDomainAxiomLearner(ks);
l.setReasoner(reasoner);
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/anthem"));
- l.setMaxExecutionTimeInSeconds(40);
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/birthPlace"));
+ l.setMaxExecutionTimeInSeconds(10);
// l.addFilterNamespace("http://dbpedia.org/ontology/");
// l.setReturnOnlyNewAxioms(true);
+ l.setForceSPARQL_1_0_Mode(true);
l.init();
l.start();
- System.out.println(l.getCurrentlyBestEvaluatedAxioms());
+ System.out.println(l.getCurrentlyBestEvaluatedAxioms(0.7));
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -307,7 +307,7 @@
}
protected ResultSet executeSelectQuery(String query) {
- logger.debug("Sending query\n{} ...", query);
+ logger.info("Sending query\n{} ...", query);
if(ks.isRemote()){
SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryEngineHTTP.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -27,10 +27,11 @@
import java.util.Map;
import java.util.concurrent.TimeUnit;
-import org.openjena.atlas.io.IO;
-import org.openjena.riot.Lang;
-import org.openjena.riot.RiotReader;
-import org.openjena.riot.WebContent;
+import org.apache.jena.atlas.io.IO;
+import org.apache.jena.riot.Lang;
+import org.apache.jena.riot.RDFLanguages;
+import org.apache.jena.riot.RiotReader;
+import org.apache.jena.riot.WebContent;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -267,7 +268,7 @@
private Model execModel(Model model)
{
HttpQuery httpQuery = makeHttpQuery() ;
- httpQuery.setAccept(WebContent.contentTypeNTriples) ;
+ httpQuery.setAccept(WebContent.contentTypeNTriplesAlt) ;
InputStream in = httpQuery.exec() ;
//Don't assume the endpoint actually gives back the content type we asked for
@@ -282,7 +283,7 @@
//Try to select language appropriately here based on the model content type
Lang lang = WebContent.contentTypeToLang(actualContentType);
- if (!lang.isTriples()) throw new QueryException("Endpoint returned Content Type: " + actualContentType + " which is not a valid RDF Graph syntax");
+ if (! RDFLanguages.isTriples(lang)) throw new QueryException("Endpoint returned Content Type: " + actualContentType + " which is not a valid RDF Graph syntax");
model.read(in, null, "N-TRIPLES") ;
return model ;
@@ -306,7 +307,7 @@
//Try to select language appropriately here based on the model content type
Lang lang = WebContent.contentTypeToLang(actualContentType);
- if (!lang.isTriples()) throw new QueryException("Endpoint returned Content Type: " + actualContentType + " which is not a valid RDF Graph syntax");
+ if (! RDFLanguages.isTriples(lang)) throw new QueryException("Endpoint returned Content Type: " + actualContentType + " which is not a valid RDF Graph syntax");
return RiotReader.createIteratorTriples(in, lang, null);
}
@@ -527,9 +528,20 @@
//Check that this is a valid setting
Lang lang = WebContent.contentTypeToLang(contentType);
if (lang == null) throw new IllegalArgumentException("Given Content Type '" + contentType + "' is not supported by RIOT");
- if (!lang.isTriples()) throw new IllegalArgumentException("Given Content Type '" + contentType + " is not a RDF Graph format");
+ if (! RDFLanguages.isTriples(lang)) throw new IllegalArgumentException("Given Content Type '" + contentType + " is not a RDF Graph format");
modelContentType = contentType;
}
+
+ @Override
+ public long getTimeout1() { return asMillis(readTimeout, readTimeoutUnit) ; }
+
+ @Override
+ public long getTimeout2() { return asMillis(connectTimeout, connectTimeoutUnit) ; }
+
+ private static long asMillis(long duration, TimeUnit timeUnit)
+ {
+ return (duration < 0 ) ? duration : timeUnit.toMillis(duration) ;
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/AxiomScore.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -61,7 +61,7 @@
return totalNrOfExamples;
}
- public int getNrOfpositiveExamples() {
+ public int getNrOfPositiveExamples() {
return nrOfpositiveExamples;
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -451,7 +451,7 @@
//
Comparator<OWLNamedObject> namedObjectComparator = new Comparator<OWLNamedObject>() {
public int compare(OWLNamedObject o1, OWLNamedObject o2) {
- return o1.getIRI().compareTo(o2.getIRI());
+ return o1.compareTo(o2);
}
};
Set<OWLClass> classes = new TreeSet<OWLClass>(namedObjectComparator);
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -460,6 +460,39 @@
}
return types;
}
+
+ public Set<NamedClass> getOWLClasses() {
+ Set<NamedClass> types = new HashSet<NamedClass>();
+ String query = String.format("SELECT DISTINCT ?class WHERE {?class a <%s>.}",OWL.Class.getURI());
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ types.add(new NamedClass(qs.getResource("class").getURI()));
+ }
+ return types;
+ }
+
+ /**
+ * Returns a set of classes which are siblings, i.e. on the same level
+ * in the class hierarchy.
+ * @param cls
+ * @param limit
+ * @return
+ */
+ public Set<NamedClass> getSiblingClasses(NamedClass cls) {
+ Set<NamedClass> siblings = new HashSet<NamedClass>();
+ String query = "SELECT ?sub WHERE { <" + cls.getName() + "> <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
+ query += "?sub <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
+ query += "FILTER( !SAMETERM(?sub, <" + cls.getName() + ">)) . }";
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ siblings.add(new NamedClass(qs.getResource("sub").getURI()));
+ }
+ return siblings;
+ }
@Override
public boolean hasType(Description description, Individual individual) {
@@ -490,12 +523,14 @@
if(limit != 0) {
query += " LIMIT " + limit;
}
-
+ System.out.println(query);
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
qs = rs.next();
- individuals.add(new Individual(qs.getResource("ind").getURI()));
+ if(qs.get("ind").isURIResource()){
+ individuals.add(new Individual(qs.getResource("ind").getURI()));
+ }
}
return individuals;
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/LabelShortFormProvider.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/LabelShortFormProvider.java 2013-03-20 12:08:41 UTC (rev 3914)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/LabelShortFormProvider.java 2013-04-10 10:06:38 UTC (rev 3915)
@@ -9,7 +9,9 @@
import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.hp.hpl.jena.vocabulary.RDFS;
@@ -23,7 +25,12 @@
private ExtractionDBCache cache;
private SparqlEndpoint endpoint;
+ private Model model;
+ public LabelShortFormProvider(Model model) {
+ this.model = model;
+ }
+
public LabelShortFormProvider(SparqlEndpoint endpoint) {
this.endpoint = endpoint;
}
@@ -59,15 +66,20 @@
protected ResultSet executeSelect(Query query){
ResultSet rs = null;
- if(cache != null){
- rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query.toString()));
+ if(endpoint != null){
+ if(cache != null){
+ rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query.toString()));
+ } else {
+ QueryEngineHTTP qe = new QueryEngineHTTP(endpoint.getURL().toString(), query);
+ for(String uri : endpoint.getDefaultGraphURIs()){
+ qe.addDefaultGraph(uri);
+ }
+ rs = qe.execSelect();
+ }
} else {
- QueryEngineHTTP qe = new QueryEngineHTTP(endpoint.getURL().toString(), query);
- for(String uri : endpoint.getDefaultGraphURIs()){
- qe.addDefaultGraph(uri);
- }
- rs = qe.execSelect();
+ rs = QueryExecutionFactory.create(query, model).execSelect();
}
+
return rs;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-03-20 12:08:44
|
Revision: 3914
http://sourceforge.net/p/dl-learner/code/3914
Author: lorenz_b
Date: 2013-03-20 12:08:41 +0000 (Wed, 20 Mar 2013)
Log Message:
-----------
Started OWL axiom pattern detection.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/AbstractRenderer.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/FullIRIEntityShortFromProvider.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/ManchesterOWLSyntaxEditorParser.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/ManchesterOWLSyntaxOWLObjectRendererImpl.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/ManchesterOWLSyntaxObjectRenderer.java
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: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/AbstractRenderer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/AbstractRenderer.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/AbstractRenderer.java 2013-03-20 12:08:41 UTC (rev 3914)
@@ -0,0 +1,219 @@
+package org.dllearner.algorithms.pattern;
+
+/*
+ * This file is part of the OWL API.
+ *
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ *
+ * Copyright (C) 2011, The University of Manchester
+ *
+ * This program 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.
+ *
+ * This program 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/.
+ *
+ *
+ * Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0
+ * in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
+ *
+ * Copyright 2011, University of Manchester
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+import java.io.IOException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+
+import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntax;
+import org.semanticweb.owlapi.io.OWLRendererException;
+import org.semanticweb.owlapi.io.OWLRendererIOException;
+import org.semanticweb.owlapi.util.ShortFormProvider;
+
+/**
+ * Author: Matthew Horridge<br>
+ * The University Of Manchester<br>
+ * Bio-Health Informatics Group<br>
+ * Date: 25-Apr-2007<br><br>
+ */
+@SuppressWarnings("javadoc")
+public class AbstractRenderer {
+
+ private ShortFormProvider shortFormProvider;
+
+ private int lastNewLinePos = -1;
+
+ private int currentPos;
+
+ private Writer writer;
+
+ private List<Integer> tabs;
+
+ private boolean useTabbing = true;
+
+ private boolean useWrapping = true;
+
+ public AbstractRenderer(Writer writer, ShortFormProvider shortFormProvider) {
+ this.writer = writer;
+ this.shortFormProvider = shortFormProvider;
+ tabs = new ArrayList<Integer>();
+ pushTab(0);
+ }
+
+
+ public void setUseTabbing(boolean useTabbing) {
+ this.useTabbing = useTabbing;
+ }
+
+
+ public void setUseWrapping(boolean useWrapping) {
+ this.useWrapping = useWrapping;
+ }
+
+
+ public boolean isUseWrapping() {
+ return useWrapping;
+ }
+
+
+ public boolean isUseTabbing() {
+ return useTabbing;
+ }
+
+
+// public void setShortFormProvider(ShortFormProvider shortFormProvider) {
+// this.shortFormProvider = shortFormProvider;
+// }
+
+
+ public void flush() throws OWLRendererException {
+ try {
+ writer.flush();
+ }
+ catch (IOException e) {
+ throw new OWLRendererIOException(e);
+ }
+ }
+
+ protected void pushTab(int size) {
+ tabs.add(0, size);
+ }
+
+ protected void incrementTab(int increment) {
+ int base = 0;
+ if(!tabs.isEmpty()) {
+ base = tabs.get(0);
+ }
+ tabs.add(0, base + increment);
+ }
+
+ protected void popTab() {
+ tabs.remove(0);
+ }
+
+ protected void writeTab() {
+ int tab = tabs.get(0);
+ for(int i = 0; i < tab; i++) {
+ write(" ");
+ }
+ }
+
+ protected int getIndent() {
+ return currentPos - lastNewLinePos - 2;
+ }
+
+
+ protected void write(String s) {
+ if(s == null) {
+ return;
+ }
+ int indexOfNewLine = s.indexOf('\n');
+ if(indexOfNewLine != -1) {
+ lastNewLinePos = currentPos + indexOfNewLine;
+ }
+ currentPos += s.length();
+ try {
+ writer.write(s);
+ }
+ catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ protected void write(char ch) {
+ write(Character.toString(ch));
+ }
+
+ protected void write(String s, int lineLen) {
+ StringTokenizer tokenizer = new StringTokenizer(s, " \n\t-", true);
+ int currentLineLength = 0;
+ while(tokenizer.hasMoreTokens()) {
+ String curToken = tokenizer.nextToken();
+ write(curToken);
+ if(curToken.equals("\n")) {
+ writeTab();
+ }
+ currentLineLength += curToken.length();
+ if(currentLineLength > lineLen && curToken.trim().length() != 0 && tokenizer.hasMoreTokens()) {
+ writeNewLine();
+ currentLineLength = 0;
+ }
+ }
+ }
+
+ protected void writeSpace() {
+ write(" ");
+ }
+
+ protected void write(ManchesterOWLSyntax keyword) {
+ write(" ", keyword, keyword.isSectionKeyword() ? ": " : " ");
+ }
+
+ protected void writeFrameKeyword(ManchesterOWLSyntax keyword) {
+ write("", keyword, ": ");
+ }
+
+ protected void writeSectionKeyword(ManchesterOWLSyntax keyword) {
+ write(" ", keyword, ": ");
+ }
+
+ protected void writeNewLine() {
+ write("\n");
+ if (useTabbing) {
+ writeTab();
+ }
+ }
+
+ protected void write(String prefix, ManchesterOWLSyntax keyword, String suffix) {
+ write(prefix);
+ write(keyword.toString());
+ write(suffix);
+ }
+
+ protected ShortFormProvider getShortFormProvider() {
+ return shortFormProvider;
+ }
+
+}
+
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/FullIRIEntityShortFromProvider.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/FullIRIEntityShortFromProvider.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/FullIRIEntityShortFromProvider.java 2013-03-20 12:08:41 UTC (rev 3914)
@@ -0,0 +1,17 @@
+package org.dllearner.algorithms.pattern;
+
+import org.semanticweb.owlapi.model.OWLEntity;
+import org.semanticweb.owlapi.util.ShortFormProvider;
+
+public class FullIRIEntityShortFromProvider implements ShortFormProvider{
+
+ @Override
+ public void dispose() {
+ }
+
+ @Override
+ public String getShortForm(OWLEntity entity) {
+ return entity.toStringID();
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/ManchesterOWLSyntaxEditorParser.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/ManchesterOWLSyntaxEditorParser.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/ManchesterOWLSyntaxEditorParser.java 2013-03-20 12:08:41 UTC (rev 3914)
@@ -0,0 +1,4129 @@
+package org.dllearner.algorithms.pattern;
+
+/*
+ * This file is part of the OWL API.
+ *
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ *
+ * Copyright (C) 2011, The University of Manchester
+ *
+ * This program 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.
+ *
+ * This program 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/.
+ *
+ *
+ * Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0
+ * in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
+ *
+ * Copyright 2011, University of Manchester
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntax;
+import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat;
+import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyHeader;
+import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxTokenizer;
+import org.coode.owlapi.manchesterowlsyntax.OntologyAxiomPair;
+import org.semanticweb.owlapi.expression.OWLEntityChecker;
+import org.semanticweb.owlapi.expression.OWLOntologyChecker;
+import org.semanticweb.owlapi.expression.ParserException;
+import org.semanticweb.owlapi.model.AddAxiom;
+import org.semanticweb.owlapi.model.AddImport;
+import org.semanticweb.owlapi.model.AddOntologyAnnotation;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLAnnotationSubject;
+import org.semanticweb.owlapi.model.OWLAnnotationValue;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassAxiom;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLDataPropertyCharacteristicAxiom;
+import org.semanticweb.owlapi.model.OWLDataPropertyExpression;
+import org.semanticweb.owlapi.model.OWLDataRange;
+import org.semanticweb.owlapi.model.OWLDatatype;
+import org.semanticweb.owlapi.model.OWLEntity;
+import org.semanticweb.owlapi.model.OWLFacetRestriction;
+import org.semanticweb.owlapi.model.OWLImportsDeclaration;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLObjectPropertyCharacteristicAxiom;
+import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
+import org.semanticweb.owlapi.model.OWLOntologyID;
+import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLPropertyExpression;
+import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom;
+import org.semanticweb.owlapi.model.SWRLAtom;
+import org.semanticweb.owlapi.model.SWRLBuiltInAtom;
+import org.semanticweb.owlapi.model.SWRLDArgument;
+import org.semanticweb.owlapi.model.SWRLDifferentIndividualsAtom;
+import org.semanticweb.owlapi.model.SWRLIArgument;
+import org.semanticweb.owlapi.model.SWRLIndividualArgument;
+import org.semanticweb.owlapi.model.SWRLLiteralArgument;
+import org.semanticweb.owlapi.model.SWRLRule;
+import org.semanticweb.owlapi.model.SWRLSameIndividualAtom;
+import org.semanticweb.owlapi.model.SWRLVariable;
+import org.semanticweb.owlapi.model.SetOntologyID;
+import org.semanticweb.owlapi.model.UnloadableImportException;
+import org.semanticweb.owlapi.util.DefaultPrefixManager;
+import org.semanticweb.owlapi.util.NamespaceUtil;
+import org.semanticweb.owlapi.vocab.DublinCoreVocabulary;
+import org.semanticweb.owlapi.vocab.Namespaces;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+import org.semanticweb.owlapi.vocab.OWLFacet;
+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
+import org.semanticweb.owlapi.vocab.SWRLBuiltInsVocabulary;
+import org.semanticweb.owlapi.vocab.XSDVocabulary;
+
+
+/**
+ * Author: Matthew Horridge<br> The University Of Manchester<br> Bio-Health Informatics Group<br> Date:
+ * 10-Sep-2007<br><br>
+ * <p/>
+ * A parser for the Manchester OWL Syntax. All properties must be defined before they are used. For example, consider
+ * the restriction hasPart some Leg. The parser must know in advance whether or not hasPart is an object property or a
+ * data property so that Leg gets parsed correctly. In a tool, such as an editor, it is expected that hasPart will
+ * already exists as either a data property or an object property. If a complete ontology is being parsed, it is
+ * expected that hasPart will have been defined at the top of the file before it is used in any class expressions or
+ * property assertions (e.g. ObjectProperty: hasPart)
+ */
+@SuppressWarnings({"unused","javadoc"})
+public class ManchesterOWLSyntaxEditorParser {
+
+ // This parser was built by hand! After struggling with terrible
+ // error messages produced by ANTLR (or JavaCC) I decides to construct
+ // this parser by hand. The error messages that this parser generates
+ // are specific to the Manchester OWL Syntax and are such that it should
+ // be easy to use this parser in tools such as editors.
+
+ private OWLOntologyLoaderConfiguration configuration;
+
+ protected OWLDataFactory dataFactory;
+
+ private List<ManchesterOWLSyntaxTokenizer.Token> tokens;
+
+ private int tokenIndex;
+
+ private OWLEntityChecker owlEntityChecker;
+
+ private OWLOntologyChecker owlOntologyChecker = new OWLOntologyChecker() {
+ public OWLOntology getOntology(String name) {
+ return null;
+ }
+ };
+
+ private String base;
+
+ private Set<String> classNames;
+
+ private Set<String> objectPropertyNames;
+
+ private Set<String> dataPropertyNames;
+
+ private Set<String> individualNames;
+
+ private Set<String> dataTypeNames;
+
+ private Set<String> annotationPropertyNames;
+
+ private Map<String, SWRLBuiltInsVocabulary> ruleBuiltIns = new TreeMap<String, SWRLBuiltInsVocabulary>();
+
+ private DefaultPrefixManager pm = new DefaultPrefixManager();
+
+ public static final String AND = ManchesterOWLSyntax.AND.toString();
+
+ public static final String OR = ManchesterOWLSyntax.OR.toString();
+
+ public static final String INVERSE = ManchesterOWLSyntax.INVERSE.toString();
+
+ public static final String SOME = ManchesterOWLSyntax.SOME.toString();
+
+ public static final String SELF = ManchesterOWLSyntax.SELF.toString();
+
+ public static final String ONLY = ManchesterOWLSyntax.ONLY.toString();
+
+ public static final String VALUE = ManchesterOWLSyntax.VALUE.toString();
+
+ public static final String MIN = ManchesterOWLSyntax.MIN.toString();
+
+ public static final String MAX = ManchesterOWLSyntax.MAX.toString();
+
+ public static final String EXACTLY = ManchesterOWLSyntax.EXACTLY.toString();
+
+ public static final String ONLYSOME = ManchesterOWLSyntax.ONLYSOME.toString();
+
+ public static final String NOT = ManchesterOWLSyntax.NOT.toString();
+
+ public static final String CLASS = ManchesterOWLSyntax.CLASS.toString() + ":";
+
+ public static final String DATATYPE = ManchesterOWLSyntax.DATATYPE.toString() + ":";
+
+ public static final String SUB_CLASS_OF = ManchesterOWLSyntax.SUBCLASS_OF.toString() + ":";
+
+ public static final String SUPER_CLASS_OF = ManchesterOWLSyntax.SUPERCLASS_OF.toString() + ":";
+
+ public static final String INSTANCES = "Instances:";
+
+ public static final String EQUIVALENT_TO = ManchesterOWLSyntax.EQUIVALENT_TO.toString() + ":";
+
+ public static final String EQUIVALENT_CLASSES = ManchesterOWLSyntax.EQUIVALENT_CLASSES.toString() + ":";
+
+ public static final String EQUIVALENT_PROPERTIES = ManchesterOWLSyntax.EQUIVALENT_PROPERTIES.toString() + ":";
+
+ public static final String DISJOINT_WITH = ManchesterOWLSyntax.DISJOINT_WITH.toString() + ":";
+
+ public static final String DISJOINT_UNION_OF = ManchesterOWLSyntax.DISJOINT_UNION_OF.toString() + ":";
+
+ public static final String HAS_KEY = ManchesterOWLSyntax.HAS_KEY.toString() + ":";
+
+ public static final String DISJOINT_CLASSES = ManchesterOWLSyntax.DISJOINT_CLASSES.toString() + ":";
+
+ public static final String DISJOINT_PROPERTIES = ManchesterOWLSyntax.DISJOINT_PROPERTIES.toString() + ":";
+
+ public static final String OBJECT_PROPERTY = ManchesterOWLSyntax.OBJECT_PROPERTY.toString() + ":";
+
+ public static final String DATA_PROPERTY = ManchesterOWLSyntax.DATA_PROPERTY.toString() + ":";
+
+ public static final String ANNOTATION_PROPERTY = ManchesterOWLSyntax.ANNOTATION_PROPERTY.toString() + ":";
+
+ public static final String SUB_PROPERTY_OF = ManchesterOWLSyntax.SUB_PROPERTY_OF.toString() + ":";
+
+ public static final String SUPER_PROPERTY_OF = ManchesterOWLSyntax.SUPER_PROPERTY_OF.toString() + ":";
+
+ public static final String DOMAIN = ManchesterOWLSyntax.DOMAIN.toString() + ":";
+
+ public static final String RANGE = ManchesterOWLSyntax.RANGE.toString() + ":";
+
+ public static final String INVERSES = ManchesterOWLSyntax.INVERSES.toString() + ":";
+
+ public static final String CHARACTERISTICS = ManchesterOWLSyntax.CHARACTERISTICS.toString() + ":";
+
+ public static final String INDIVIDUAL = ManchesterOWLSyntax.INDIVIDUAL.toString() + ":";
+
+ public static final String INDIVIDUALS = ManchesterOWLSyntax.INDIVIDUALS.toString() + ":";
+
+ public static final String ANNOTATIONS = ManchesterOWLSyntax.ANNOTATIONS.toString() + ":";
+
+ public static final String TYPES = ManchesterOWLSyntax.TYPES.toString() + ":";
+
+ public static final String TYPE = ManchesterOWLSyntax.TYPE.toString() + ":";
+
+ public static final String FACTS = ManchesterOWLSyntax.FACTS.toString() + ":";
+
+ public static final String SAME_AS = ManchesterOWLSyntax.SAME_AS.toString() + ":";
+
+ public static final String SAME_INDIVIDUAL = ManchesterOWLSyntax.SAME_INDIVIDUAL.toString() + ":";
+
+ public static final String DIFFERENT_FROM = ManchesterOWLSyntax.DIFFERENT_FROM.toString() + ":";
+
+ public static final String DIFFERENT_INDIVIDUALS = ManchesterOWLSyntax.DIFFERENT_INDIVIDUALS.toString() + ":";
+
+ public static final String VALUE_PARTITION = "ValuePartition:";
+
+ public static final String ONTOLOGY = ManchesterOWLSyntax.ONTOLOGY.toString() + ":";
+
+ public static final String PREFIX = ManchesterOWLSyntax.PREFIX.toString() + ":";
+
+ public static final String IMPORT = ManchesterOWLSyntax.IMPORT.toString() + ":";
+
+ public static final String SUB_PROPERTY_CHAIN = ManchesterOWLSyntax.SUB_PROPERTY_CHAIN.toString() + ":";
+
+ public static final String FUNCTIONAL = ManchesterOWLSyntax.FUNCTIONAL.toString() + ":";
+
+ public static final String INVERSE_FUNCTIONAL = ManchesterOWLSyntax.INVERSE_FUNCTIONAL.toString() + ":";
+
+ public static final String SYMMETRIC = ManchesterOWLSyntax.SYMMETRIC.toString() + ":";
+
+ public static final String ANTI_SYMMETRIC = ManchesterOWLSyntax.ANTI_SYMMETRIC.toString() + ":";
+
+ public static final String ASYMMETRIC = ManchesterOWLSyntax.ASYMMETRIC.toString() + ":";
+
+ public static final String TRANSITIVE = ManchesterOWLSyntax.TRANSITIVE.toString() + ":";
+
+ public static final String REFLEXIVE = ManchesterOWLSyntax.REFLEXIVE.toString() + ":";
+
+ public static final String IRREFLEXIVE = ManchesterOWLSyntax.IRREFLEXIVE.toString() + ":";
+
+ public static final String INVERSE_OF = ManchesterOWLSyntax.INVERSE_OF + ":";
+
+ public static final String RULE = ManchesterOWLSyntax.RULE + ":";
+
+ private Set<String> potentialKeywords;
+
+ private OWLOntology defaultOntology = null;
+
+ private boolean allowEmptyFrameSections = false;
+
+
+ private Map<String, AnnotatedListItemParser<OWLDataProperty, ?>> dataPropertyFrameSections = new HashMap<String, AnnotatedListItemParser<OWLDataProperty, ?>>();
+
+
+ public ManchesterOWLSyntaxEditorParser(OWLDataFactory dataFactory, String s) {
+ this(new OWLOntologyLoaderConfiguration(), dataFactory, s);
+ }
+
+ public boolean isAllowEmptyFrameSections() {
+ return allowEmptyFrameSections;
+ }
+
+ public void setAllowEmptyFrameSections(boolean allowEmptyFrameSections) {
+ this.allowEmptyFrameSections = allowEmptyFrameSections;
+ }
+
+ public ManchesterOWLSyntaxEditorParser(OWLOntologyLoaderConfiguration configuration, OWLDataFactory dataFactory, String s) {
+ this.configuration = configuration;
+ this.dataFactory = dataFactory;
+ potentialKeywords = new HashSet<String>();
+
+ classNames = new HashSet<String>();
+ objectPropertyNames = new HashSet<String>();
+ dataPropertyNames = new HashSet<String>();
+ individualNames = new HashSet<String>();
+ dataTypeNames = new HashSet<String>();
+ annotationPropertyNames = new HashSet<String>();
+ pm.setPrefix("rdf:", Namespaces.RDF.toString());
+ pm.setPrefix("rdfs:", Namespaces.RDFS.toString());
+ pm.setPrefix("owl:", Namespaces.OWL.toString());
+ pm.setPrefix("dc:", DublinCoreVocabulary.NAME_SPACE);
+ NamespaceUtil u = new NamespaceUtil();
+
+ initialiseClassFrameSections();
+ initialiseObjectPropertyFrameSections();
+ initialiseDataPropertyFrameSections();
+ initialiseAnnotationPropertyFrameSections();
+ initialiseIndividualFrameSections();
+
+
+ for (XSDVocabulary v : XSDVocabulary.values()) {
+ dataTypeNames.add(v.getIRI().getFragment());
+ dataTypeNames.add("xsd:" + v.getIRI().getFragment());
+ }
+ dataTypeNames.add(OWLRDFVocabulary.RDF_XML_LITERAL.getIRI().getFragment());
+ dataTypeNames.add("rdf:" + OWLRDFVocabulary.RDF_XML_LITERAL.getIRI().getFragment());
+
+ dataTypeNames.add(dataFactory.getTopDatatype().getIRI().getFragment());
+
+ for (IRI iri : OWLRDFVocabulary.BUILT_IN_ANNOTATION_PROPERTY_IRIS) {
+ String[] res = u.split(iri.toString(), null);
+ annotationPropertyNames.add(u.getPrefix(res[0]) + ":" + res[1]);
+ }
+
+ base = "http://www.semanticweb.org#";
+ owlEntityChecker = new DefaultEntityChecker();
+ tokens = new ArrayList<ManchesterOWLSyntaxTokenizer.Token>();
+ tokens.addAll(getTokenizer(s).tokenize());
+ tokenIndex = 0;
+
+ for (SWRLBuiltInsVocabulary v : SWRLBuiltInsVocabulary.values()) {
+ ruleBuiltIns.put(v.getShortName(), v);
+ ruleBuiltIns.put(v.getIRI().toQuotedString(), v);
+ }
+ }
+
+ protected ManchesterOWLSyntaxTokenizer getTokenizer(String s) {
+ return new ManchesterOWLSyntaxTokenizer(s);
+ }
+
+ public OWLDataFactory getDataFactory() {
+ return dataFactory;
+ }
+
+ private Map<String, AnnotatedListItemParser<OWLClass, ?>> classFrameSections = new HashMap<String, AnnotatedListItemParser<OWLClass, ?>>();
+
+ public void initialiseClassFrameSections() {
+ initialiseSection(new EntityAnnotationsListItemParser<OWLClass>(), classFrameSections);
+ initialiseSection(new ClassSubClassOfListItemParser(), classFrameSections);
+ initialiseSection(new ClassEquivalentToListItemParser(), classFrameSections);
+ initialiseSection(new ClassDisjointWithListItemParser(), classFrameSections);
+ initialiseSection(new ClassHasKeyListItemParser(), classFrameSections);
+ // Extensions
+ initialiseSection(new ClassSuperClassOfListItemParser(), classFrameSections);
+ initialiseSection(new ClassDisjointClassesListItemParser(), classFrameSections);
+ initialiseSection(new ClassIndividualsListItemParser(), classFrameSections);
+ }
+
+ private Map<String, AnnotatedListItemParser<OWLObjectProperty, ?>> objectPropertyFrameSections = new HashMap<String, AnnotatedListItemParser<OWLObjectProperty, ?>>();
+
+ private void initialiseObjectPropertyFrameSections() {
+ initialiseSection(new EntityAnnotationsListItemParser<OWLObjectProperty>(), objectPropertyFrameSections);
+ initialiseSection(new ObjectPropertySubPropertyOfListItemParser(), objectPropertyFrameSections);
+ initialiseSection(new ObjectPropertyEquivalentToListItemParser(), objectPropertyFrameSections);
+ initialiseSection(new ObjectPropertyDisjointWithListItemParser(), objectPropertyFrameSections);
+ initialiseSection(new ObjectPropertyDomainListItemParser(), objectPropertyFrameSections);
+ initialiseSection(new ObjectPropertyRangeListItemParser(), objectPropertyFrameSections);
+ initialiseSection(new ObjectPropertyInverseOfListItemParser(), objectPropertyFrameSections);
+ initialiseSection(new ObjectPropertyCharacteristicsItemParser(), objectPropertyFrameSections);
+ initialiseSection(new ObjectPropertySubPropertyChainListItemParser(), objectPropertyFrameSections);
+ // Extensions
+ initialiseSection(new ObjectPropertySuperPropertyOfListItemParser(), objectPropertyFrameSections);
+ }
+
+ private void initialiseDataPropertyFrameSections() {
+ initialiseSection(new DataPropertySubPropertyOfListItemParser(), dataPropertyFrameSections);
+ initialiseSection(new DataPropertyEquivalentToListItemParser(), dataPropertyFrameSections);
+ initialiseSection(new DataPropertyDisjointWithListItemParser(), dataPropertyFrameSections);
+ initialiseSection(new DataPropertyDomainListItemParser(), dataPropertyFrameSections);
+ initialiseSection(new DataPropertyRangeListItemParser(), dataPropertyFrameSections);
+ initialiseSection(new DataPropertyCharacteristicsItemParser(), dataPropertyFrameSections);
+ initialiseSection(new EntityAnnotationsListItemParser<OWLDataProperty>(), dataPropertyFrameSections);
+ }
+
+
+ private Map<String, AnnotatedListItemParser<OWLAnnotationProperty, ?>> annotationPropertyFrameSections = new HashMap<String, AnnotatedListItemParser<OWLAnnotationProperty, ?>>();
+
+ private void initialiseAnnotationPropertyFrameSections() {
+ initialiseSection(new AnnotationPropertySubPropertyOfListItemParser(), annotationPropertyFrameSections);
+ initialiseSection(new AnnotationPropertyDomainListItemParser(), annotationPropertyFrameSections);
+ initialiseSection(new AnnotationPropertyRangeListItemParser(), annotationPropertyFrameSections);
+ initialiseSection(new EntityAnnotationsListItemParser<OWLAnnotationProperty>(), annotationPropertyFrameSections);
+ }
+
+ private Map<String, AnnotatedListItemParser<OWLIndividual, ?>> individualFrameSections = new HashMap<String, AnnotatedListItemParser<OWLIndividual, ?>>();
+
+ public void initialiseIndividualFrameSections() {
+ initialiseSection(new IndividualAnnotationItemParser(), individualFrameSections);
+ initialiseSection(new IndividualTypesItemParser(), individualFrameSections);
+ initialiseSection(new IndividualFactsItemParser(), individualFrameSections);
+ initialiseSection(new IndividualSameAsItemParser(), individualFrameSections);
+ initialiseSection(new IndividualDifferentFromItemParser(), individualFrameSections);
+ // Extensions
+ initialiseSection(new IndividualDifferentIndividualsItemParser(), individualFrameSections);
+ }
+
+
+
+ protected List<ManchesterOWLSyntaxTokenizer.Token> getTokens() {
+ return tokens;
+ }
+
+
+ protected void reset() {
+ tokenIndex = 0;
+ }
+
+
+ public String getBase() {
+ return base;
+ }
+
+
+ public void setBase(String base) {
+ this.base = base;
+ }
+
+
+ public OWLEntityChecker getOWLEntityChecker() {
+ return owlEntityChecker;
+ }
+
+
+ public void setOWLEntityChecker(OWLEntityChecker owlEntityChecker) {
+ this.owlEntityChecker = owlEntityChecker;
+ }
+
+
+ public boolean isOntologyName(String name) {
+ return owlOntologyChecker.getOntology(name) != null;
+ }
+
+
+ public boolean isClassName(String name) {
+ return classNames.contains(name) || owlEntityChecker != null && owlEntityChecker.getOWLClass(name) != null;
+ }
+
+
+ public OWLOntology getOntology(String name) {
+ return owlOntologyChecker.getOntology(name);
+ }
+
+
+ public void setOWLOntologyChecker(OWLOntologyChecker owlOntologyChecker) {
+ this.owlOntologyChecker = owlOntologyChecker;
+ }
+
+
+ public boolean isObjectPropertyName(String name) {
+ return objectPropertyNames.contains(name) || owlEntityChecker != null && owlEntityChecker.getOWLObjectProperty(name) != null;
+ }
+
+
+ public boolean isAnnotationPropertyName(String name) {
+ return annotationPropertyNames.contains(name) || owlEntityChecker != null && owlEntityChecker.getOWLAnnotationProperty(name) != null;
+ }
+
+
+ public boolean isDataPropertyName(String name) {
+ return dataPropertyNames.contains(name) || owlEntityChecker != null && owlEntityChecker.getOWLDataProperty(name) != null;
+ }
+
+
+ public boolean isIndividualName(String name) {
+ return individualNames.contains(name) || owlEntityChecker != null && owlEntityChecker.getOWLIndividual(name) != null;
+ }
+
+
+ public boolean isDatatypeName(String name) {
+ return dataTypeNames.contains(name) || owlEntityChecker != null && owlEntityChecker.getOWLDatatype(name) != null;
+ }
+
+
+ public boolean isSWRLBuiltin(String name) {
+ return ruleBuiltIns.containsKey(name);
+ }
+
+
+ public OWLClass getOWLClass(String name) {
+ OWLClass cls = owlEntityChecker.getOWLClass(name);
+ if (cls == null && classNames.contains(name)) {
+ cls = dataFactory.getOWLClass(getIRI(name));
+ }
+ return cls;
+ }
+
+
+ public OWLObjectProperty getOWLObjectProperty(String name) {
+ OWLObjectProperty prop = owlEntityChecker.getOWLObjectProperty(name);
+ if (prop == null && objectPropertyNames.contains(name)) {
+ prop = dataFactory.getOWLObjectProperty(getIRI(name));
+ }
+ return prop;
+ }
+
+
+ public OWLIndividual getOWLIndividual(String name) {
+ if (name.startsWith("_:")) {
+ return dataFactory.getOWLAnonymousIndividual(name);
+ }
+ return getOWLNamedIndividual(name);
+ }
+
+ private OWLNamedIndividual getOWLNamedIndividual(String name) {
+ OWLNamedIndividual ind = owlEntityChecker.getOWLIndividual(name);
+ if (ind == null && individualNames.contains(name)) {
+ ind = dataFactory.getOWLNamedIndividual(getIRI(name));
+ }
+ return ind;
+ }
+
+
+ public OWLDataProperty getOWLDataProperty(String name) {
+ OWLDataProperty prop = owlEntityChecker.getOWLDataProperty(name);
+ if (prop == null && dataPropertyNames.contains(name)) {
+ prop = dataFactory.getOWLDataProperty(getIRI(name));
+ }
+ return prop;
+ }
+
+
+ public OWLDatatype getOWLDatatype(String name) {
+ OWLDatatype dt = owlEntityChecker.getOWLDatatype(name);
+ if (dt == null && dataTypeNames.contains(name)) {
+ dt = dataFactory.getOWLDatatype(getIRI(name));
+ }
+ return dt;
+ }
+
+
+ public OWLAnnotationProperty getOWLAnnotationProperty(String name) {
+ OWLAnnotationProperty prop = owlEntityChecker.getOWLAnnotationProperty(name);
+ if (prop == null && annotationPropertyNames.contains(name)) {
+ prop = dataFactory.getOWLAnnotationProperty(getIRI(name));
+ }
+ return prop;
+ }
+
+
+ protected ManchesterOWLSyntaxTokenizer.Token getLastToken() {
+ if (tokenIndex - 1 > -1) {
+ return tokens.get(tokenIndex - 1);
+// return tokenIndex < tokens.size() ? tokens.get(tokenIndex) : tokens.get(tokens.size() - 1);
+ }
+ else {
+ return tokens.get(0);
+ }
+ }
+
+
+ protected String peekToken() {
+ return getToken().getToken();
+ }
+
+ ////////////////////////////////////////////////////////////////////////////////////////////////////
+ //
+ // Tokenizer
+ //
+ ////////////////////////////////////////////////////////////////////////////////////////////////////
+
+
+ protected String consumeToken() {
+ String token = getToken().getToken();
+ if (tokenIndex < tokens.size() - 1) {
+ tokenIndex++;
+ }
+
+ return token;
+ }
+
+
+ protected void consumeToken(String expected) throws ParserException {
+ String tok = consumeToken();
+ if (!tok.equals(expected)) {
+ throw createException(expected);
+ }
+ }
+
+
+ public ManchesterOWLSyntaxTokenizer.Token getToken() {
+ return tokens.get((tokenIndex < tokens.size()) ? tokenIndex : tokenIndex - 1);
+ }
+
+
+ public int getTokenPos() {
+ return getToken().getPos();
+ }
+
+
+ public int getTokenCol() {
+ return getToken().getCol();
+ }
+
+
+ public int getTokenRow() {
+ return getToken().getRow();
+ }
+
+ ////////////////////////////////////////////////////////////////////////////////////////////////////
+ //
+ // Parser
+ //
+ ////////////////////////////////////////////////////////////////////////////////////////////////////
+
+
+ /**
+ * Parses an OWL class expression that is represented in Manchester OWL Syntax
+ * @return The parsed class expression
+ * @throws ParserException If a class expression could not be parsed.
+ */
+ public OWLClassExpression parseClassExpression() throws ParserException {
+ OWLClassExpression desc = parseIntersection();
+ if (!consumeToken().equals(ManchesterOWLSyntaxTokenizer.EOF)) {
+ throw createException(ManchesterOWLSyntaxTokenizer.EOF);
+ }
+ return desc;
+ }
+
+
+ public OWLClassExpression parseIntersection() throws ParserException {
+ Set<OWLClassExpression> ops = new HashSet<OWLClassExpression>();
+ String kw = AND;
+ while (kw.equalsIgnoreCase(AND)) {
+ potentialKeywords.remove(AND);
+ ops.add(parseUnion());
+ potentialKeywords.add(AND);
+ kw = peekToken();
+ if (kw.equalsIgnoreCase(AND)) {
+ kw = consumeToken();
+ }
+ else if (kw.equalsIgnoreCase("that")) {
+ consumeToken();
+ kw = AND;
+ }
+ }
+ if (ops.size() == 1) {
+ return ops.iterator().next();
+ }
+ else {
+ return dataFactory.getOWLObjectIntersectionOf(ops);
+ }
+ }
+
+
+ public OWLClassExpression parseUnion() throws ParserException {
+ Set<OWLClassExpression> ops = new HashSet<OWLClassExpression>();
+ String kw = OR;
+ while (kw.equalsIgnoreCase(OR)) {
+ potentialKeywords.remove(OR);
+ ops.add(parseNonNaryClassExpression());
+ potentialKeywords.add(OR);
+ kw = peekToken();
+ if (kw.equalsIgnoreCase(OR)) {
+ kw = consumeToken();
+ }
+ }
+ if (ops.size() == 1) {
+ return ops.iterator().next();
+ }
+ else {
+ return dataFactory.getOWLObjectUnionOf(ops);
+ }
+ }
+
+
+ public OWLObjectPropertyExpression parseObjectPropertyExpression(boolean allowUndeclared) throws ParserException {
+ String tok = consumeToken();
+ if (tok.equalsIgnoreCase(INVERSE)) {
+ String open = peekToken();
+ boolean brackets = false;
+ if (open.equals("(")) {
+ consumeToken();
+ brackets = true;
+ }
+ OWLObjectPropertyExpression prop = parseObjectPropertyExpression();
+ if (brackets) {
+ String close = consumeToken();
+ if (!close.equals(")")) {
+ throw createException(")");
+ }
+ }
+ return dataFactory.getOWLObjectInverseOf(prop);
+ }
+ else {
+ if (!allowUndeclared && !isObjectPropertyName(tok)) {
+ throw createException(false, true, false, false, false, false, INVERSE);
+ }
+ return getOWLObjectProperty(tok);
+ }
+ }
+
+
+ public OWLObjectPropertyExpression parseObjectPropertyExpression() throws ParserException {
+ return parseObjectPropertyExpression(false);
+ }
+
+
+ public OWLPropertyExpression<?,?> parsePropertyExpression() throws ParserException {
+ String tok = peekToken();
+ if (isObjectPropertyName(tok)) {
+ return parseObjectPropertyExpression();
+ }
+ else if (tok.equalsIgnoreCase(INVERSE)) {
+ return parseObjectPropertyExpression();
+ }
+ else if (isDataPropertyName(tok)) {
+ return parseDataProperty();
+ }
+ else {
+ consumeToken();
+ throw createException(false, true, true, false, false, false, INVERSE);
+ }
+ }
+
+
+ public OWLClassExpression parseRestriction() throws ParserException {
+ String tok = peekToken();
+ if (isObjectPropertyName(tok) || tok.equalsIgnoreCase(INVERSE)) {
+ return parseObjectRestriction();
+ }
+ else if (isDataPropertyName(tok)) {
+ return parseDataRestriction();
+ }
+ else {
+ consumeToken();
+ throw createException(false, true, true, false);
+ }
+ }
+
+
+ /**
+ * Parses all class expressions except ObjectIntersectionOf and ObjectUnionOf
+ * @return The class expression which was parsed
+ * @throws ParserException if a non-nary class expression could not be parsed
+ */
+ public OWLClassExpression parseNonNaryClassExpression() throws ParserException {
+
+ String tok = peekToken();
+ if (tok.equalsIgnoreCase(NOT)) {
+ consumeToken();
+ OWLClassExpression complemented = parseNestedClassExpression(false);
+ return dataFactory.getOWLObjectComplementOf(complemented);
+ }
+ else if (isObjectPropertyName(tok) || tok.equalsIgnoreCase(INVERSE)) {
+ return parseObjectRestriction();
+ }
+ else if (isDataPropertyName(tok)) {
+ // Data restriction
+ return parseDataRestriction();
+ }
+ else if (tok.equals("{")) {
+ return parseObjectOneOf();
+ }
+ else if (tok.equals("(")) {
+ return parseNestedClassExpression(false);
+ }
+ else if (isClassName(tok)) {
+ consumeToken();
+ return getOWLClass(tok);
+ }
+ // Add option for strict class name checking
+ else {
+ consumeToken();
+ throw createException(true, true, true, false, false, false, "(", "{", NOT, INVERSE);
+ }
+ }
+
+
+ public OWLClassExpression parseObjectRestriction() throws ParserException {
+ OWLObjectPropertyExpression prop = parseObjectPropertyExpression();
+ String kw = consumeToken();
+ if (kw.equalsIgnoreCase(SOME)) {
+ String possSelfToken = peekToken();
+ if (possSelfToken.equalsIgnoreCase(SELF)) {
+ consumeToken();
+ return dataFactory.getOWLObjectHasSelf(prop);
+ }
+ else {
+ OWLClassExpression filler = null;
+ try {
+ filler = parseNestedClassExpression(false);
+ }
+ catch (ParserException e) {
+ Set<String> keywords = new HashSet<String>();
+ keywords.addAll(e.getExpectedKeywords());
+ keywords.add(SELF);
+ throw createException(e.isClassNameExpected(), e.isObjectPropertyNameExpected(), e.isDataPropertyNameExpected(), e.isIndividualNameExpected(), e.isDatatypeNameExpected(), e.isAnnotationPropertyNameExpected(), keywords.toArray(new String[keywords.size()]));
+ }
+ return dataFactory.getOWLObjectSomeValuesFrom(prop, filler);
+ }
+ }
+ else if (kw.equalsIgnoreCase(ONLY)) {
+ OWLClassExpression filler = parseNestedClassExpression(false);
+ return dataFactory.getOWLObjectAllValuesFrom(prop, filler);
+ }
+ else if (kw.equalsIgnoreCase(VALUE)) {
+ String indName = consumeToken();
+ if (!isIndividualName(indName)) {
+ throw createException(false, false, false, true);
+ }
+ return dataFactory.getOWLObjectHasValue(prop, getOWLIndividual(indName));
+ }
+ else if (kw.equalsIgnoreCase(MIN)) {
+ int card = parseInteger();
+ OWLClassExpression filler = parseNestedClassExpression(true);
+ if (filler != null) {
+ return dataFactory.getOWLObjectMinCardinality(card, prop, filler);
+ }
+ else {
+ return dataFactory.getOWLObjectMinCardinality(card, prop);
+ }
+ }
+ else if (kw.equalsIgnoreCase(MAX)) {
+ int card = parseInteger();
+ OWLClassExpression filler = parseNestedClassExpression(true);
+ if (filler != null) {
+ return dataFactory.getOWLObjectMaxCardinality(card, prop, filler);
+ }
+ else {
+ return dataFactory.getOWLObjectMaxCardinality(card, prop);
+ }
+ }
+ else if (kw.equalsIgnoreCase(EXACTLY)) {
+ int card = parseInteger();
+ OWLClassExpression filler = parseNestedClassExpression(true);
+ if (filler != null) {
+ return dataFactory.getOWLObjectExactCardinality(card, prop, filler);
+ }
+ else {
+ return dataFactory.getOWLObjectExactCardinality(card, prop);
+ }
+ }
+ else if (kw.equalsIgnoreCase(ONLYSOME)) {
+ String tok = peekToken();
+ Set<OWLClassExpression> descs = new HashSet<OWLClassExpression>();
+ if (!tok.equals("[")) {
+ descs.add(parseIntersection());
+ }
+ else {
+ descs.addAll(parseClassExpressionList("[", "]"));
+ }
+ Set<OWLClassExpression> ops = new HashSet<OWLClassExpression>();
+ for (OWLClassExpression desc : descs) {
+ ops.add(dataFactory.getOWLObjectSomeValuesFrom(prop, desc));
+ }
+ OWLClassExpression filler;
+ if (descs.size() == 1) {
+ filler = descs.iterator().next();
+ }
+ else {
+ filler = dataFactory.getOWLObjectUnionOf(descs);
+ }
+ ops.add(dataFactory.getOWLObjectAllValuesFrom(prop, filler));
+ return dataFactory.getOWLObjectIntersectionOf(ops);
+ }
+ else if (kw.equalsIgnoreCase(SELF)) {
+ return dataFactory.getOWLObjectHasSelf(prop);
+ }
+ else {
+ // Error!
+ throw createException(SOME, ONLY, VALUE, MIN, MAX, EXACTLY, SELF);
+ }
+ }
+
+
+ public OWLClassExpression parseDataRestriction() throws ParserException {
+ OWLDataPropertyExpression prop = parseDataProperty();
+ String kw = consumeToken();
+ if (kw.equalsIgnoreCase(SOME)) {
+ OWLDataRange rng = parseDataRange();
+ if(rng==null) {
+ throw new ParserException(getTokenSequence(), getTokenPos(), getTokenRow(), getTokenCol(), true, false, false, false, true, false, Collections.<String>emptySet());
+// return dataFactory.getOWLDataSomeValuesFrom(prop, rng)
+ }
+ return dataFactory.getOWLDataSomeValuesFrom(prop, rng);
+ }
+ else if (kw.equalsIgnoreCase(ONLY)) {
+ OWLDataRange rng = parseDataRange();
+ return dataFactory.getOWLDataAllValuesFrom(prop, rng);
+ }
+ else if (kw.equalsIgnoreCase(VALUE)) {
+ OWLLiteral con = parseConstant();
+ return dataFactory.getOWLDataHasValue(prop, con);
+ }
+ else if (kw.equalsIgnoreCase(MIN)) {
+ int card = parseInteger();
+ OWLDataRange rng = parseDataRange();
+ if (rng != null) {
+ return dataFactory.getOWLDataMinCardinality(card, prop, rng);
+ }
+ else {
+ return dataFactory.getOWLDataMinCardinality(card, prop);
+ }
+ }
+ else if (kw.equalsIgnoreCase(EXACTLY)) {
+ int card = parseInteger();
+ OWLDataRange rng = parseDataRange();
+ if (rng != null) {
+ return dataFactory.getOWLDataExactCardinality(card, prop, rng);
+ }
+ else {
+ return dataFactory.getOWLDataExactCardinality(card, prop);
+ }
+ }
+ else if (kw.equalsIgnoreCase(MAX)) {
+ int card = parseInteger();
+ OWLDataRange rng = parseDataRange();
+ if (rng != null) {
+ return dataFactory.getOWLDataMaxCardinality(card, prop, rng);
+ }
+ else {
+ return dataFactory.getOWLDataMaxCardinality(card, prop);
+ }
+ }
+ throw createException(SOME, ONLY, VALUE, MIN, EXACTLY, MAX);
+ }
+
+
+ public OWLFacet parseFacet() throws ParserException {
+ String facet = consumeToken();
+ if (facet.equals(">")) {
+ if (peekToken().equals("=")) {
+ consumeToken();
+ return OWLFacet.MIN_INCLUSIVE;
+ }
+ else {
+ return OWLFacet.MIN_EXCLUSIVE;
+ }
+ }
+ else if (facet.equals("<")) {
+ if (peekToken().equals("=")) {
+ consumeToken();
+ return OWLFacet.MAX_INCLUSIVE;
+ }
+ else {
+ return OWLFacet.MAX_EXCLUSIVE;
+ }
+ }
+ return OWLFacet.getFacetBySymbolicName(facet);
+ }
+
+
+ public OWLDatatype parseDatatype() throws ParserException {
+ String name = consumeToken();
+ return getOWLDatatype(name);
+ }
+
+
+ public OWLDataRange parseDataRange() throws ParserException {
+ return parseDataIntersectionOf();
+ }
+
+ public OWLDataRange parseDataIntersectionOf() throws ParserException {
+ String sep = AND;
+ Set<OWLDataRange> ranges = new HashSet<OWLDataRange>();
+ while (sep.equals(AND)) {
+ ranges.add(parseDataUnionOf());
+ sep = peekToken();
+ if (sep.equals(AND)) {
+ consumeToken();
+ }
+ }
+ if (ranges.size() == 1) {
+ return ranges.iterator().next();
+ }
+ else {
+ return dataFactory.getOWLDataIntersectionOf(ranges);
+ }
+ }
+
+ public OWLDataRange parseDataUnionOf() throws ParserException {
+ String sep = OR;
+ Set<OWLDataRange> ranges = new HashSet<OWLDataRange>();
+ while (sep.equals(OR)) {
+ ranges.add(parseDataRangePrimary());
+ sep = peekToken();
+ if (sep.equals(OR)) {
+ consumeToken();
+ }
+ }
+ if (ranges.size() == 1) {
+ return ranges.iterator().next();
+ }
+ else {
+ return dataFactory.getOWLDataUnionOf(ranges);
+ }
+ }
+
+ private OWLDataRange parseDataRangePrimary() throws ParserException {
+ String tok = peekToken();
+
+ if (isDatatypeName(tok)) {
+ consumeToken();
+ OWLDatatype datatype = getOWLDatatype(tok);
+ String next = peekToken();
+ if (next.equals("[")) {
+ // Restricted data range
+ consumeToken();
+ String sep = ",";
+ Set<OWLFacetRestriction> facetRestrictions = new HashSet<OWLFacetRestriction>();
+ while (sep.equals(",")) {
+ OWLFacet fv = parseFacet();
+ if (fv == null) {
+ throw createException(OWLFacet.getFacets().toArray(new String[OWLFacet.getFacetIRIs().size()]));
+ }
+ OWLLiteral con = parseConstant();
+ // if (!con.isRDFPlainLiteral()) {
+ // con = dataFactory.getOWLLiteral(con.getLiteral());
+ // }
+ facetRestrictions.add(dataFactory.getOWLFacetRestriction(fv, con));
+ sep = consumeToken();
+ }
+ if (!sep.equals("]")) {
+ throw createException("]");
+ }
+ return dataFactory.getOWLDatatypeRestriction(datatype, facetRestrictions);
+ }
+ else {
+ return datatype;
+ }
+ }
+ else if (tok.equalsIgnoreCase(NOT)) {
+ return parseDataComplementOf();
+ }
+ else if (tok.equals("{")) {
+ return parseDataOneOf();
+ }
+ else if (tok.equals("(")) {
+ consumeToken();
+ OWLDataRange rng = parseDataRange();
+ consumeToken(")");
+ return rng;
+ }
+ else if (!tok.equals(ManchesterOWLSyntaxTokenizer.EOF)) {
+ consumeToken();
+ throw createException(false, false, false, false, true, false, NOT, "{");
+ }
+ return null;
+ }
+
+
+ public Set<OWLDataRange> parseDataRangeList() throws ParserException {
+ String sep = ",";
+ Set<OWLDataRange> ranges = new HashSet<OWLDataRange>();
+ while (sep.equals(",")) {
+ potentialKeywords.remove(",");
+ OWLDataRange rng = parseDataRange();
+ ranges.add(rng);
+ potentialKeywords.add(",");
+ sep = peekToken();
+ if (sep.equals(",")) {
+ consumeToken();
+ }
+ }
+ return ranges;
+ }
+
+
+ private OWLDataRange parseDataOneOf() throws ParserException {
+ consumeToken();
+ Set<OWLLiteral> cons = new HashSet<OWLLiteral>();
+ String sep = ",";
+ while (sep.equals(",")) {
+ OWLLiteral con = parseConstant();
+ cons.add(con);
+ sep = consumeToken();
+ }
+ if (!sep.equals("}")) {
+ throw createException(",", "}");
+ }
+ return dataFactory.getOWLDataOneOf(cons);
+ }
+
+
+ private OWLDataRange parseDataComplementOf() throws ParserException {
+ String not = consumeToken();
+ if (!not.equalsIgnoreCase(NOT)) {
+ throw createException(NOT);
+ }
+ OWLDataRange complementedDataRange = parseDataRangePrimary();
+ return dataFactory.getOWLDataComplementOf(complementedDataRange);
+ }
+
+ public OWLLiteral parseLiteral() throws ParserException {
+ String tok = consumeToken();
+ if (tok.startsWith("\"")) {
+ String lit = "";
+ if (tok.length() > 2) {
+ lit = tok.substring(1, tok.length() - 1);
+ }
+ if (peekToken().equals("^")) {
+ consumeToken();
+ if (!peekToken().equals("^")) {
+ throw createException("^");
+ }
+ consumeToken();
+ return dataFactory.getOWLLiteral(lit, parseDatatype());
+ }
+ else if (peekToken().startsWith("@")) {
+ // Plain literal with a language tag
+ String lang = consumeToken().substring(1);
+ return dataFactory.getOWLLiteral(lit, lang);
+ }
+ else {
+ // Plain literal without a language tag
+ return dataFactory.getOWLLiteral(lit, "");
+ }
+ }
+ else {
+ try {
+ int i = Integer.parseInt(tok);
+ return dataFactory.getOWLLiteral(tok, OWL2Datatype.XSD_INTEGER);
+ }
+ catch (NumberFormatException e) {
+ // Ignore - not interested
+ }
+ if (tok.endsWith("f")||tok.endsWith("F")) {
+ try {
+ // XXX this extra F might qualify as Float a Double INF/-INF
+ float f = Float.parseFloat(tok.replace("INF", "Infinity").replace("inf", "Infinity"));
+ return dataFactory.getOWLLiteral(Float.toString(f).replace("Infinity", "INF"), OWL2Datatype.XSD_FLOAT);
+ }
+ catch (NumberFormatException e) {
+ // Ignore - not interested
+ }
+ }
+ try {
+ double d = Double.parseDouble(tok);
+ return dataFactory.getOWLLiteral(tok, OWL2Datatype.XSD_DOUBLE);
+ }
+ catch (NumberFormatException e) {
+ // Ignore - not interested
+ }
+
+ if (tok.equals("true")) {
+ return dataFactory.getOWLLiteral(true);
+ }
+ else if (tok.equals("false")) {
+ return dataFactory.getOWLLiteral(false);
+ }
+ }
+ throw createException(false, false, false, false, false, false, "true", "false", "$integer$", "$float$", "$double$", "\"$Literal$\"", "\"$Literal$\"^^<datatype>", "\"$Literal$\"@<lang>");
+ }
+
+ /**
+ * @deprecated Use {@link #parseLiteral()} instead
+ */
+ @Deprecated
+ public OWLLiteral parseConstant() throws ParserException {
+ return parseLiteral();
+ }
+
+
+ public int parseInteger() throws ParserException {
+ String i = consumeToken();
+ try {
+ return Integer.parseInt(i);
+ }
+ catch (NumberFormatException e) {
+ throw new ParserException(Arrays.asList(getToken().getToken()), getTokenPos(), getTokenRow(), true, getTokenCol());
+ }
+ }
+
+
+ public String getLineCol() {
+ return "Encountered " + getLastToken() + " at " + getTokenRow() + ":" + getTokenCol() + " ";
+ }
+
+
+ private OWLClassExpression parseNestedClassExpression(boolean lookaheadCheck) throws ParserException {
+ String tok = peekToken();
+ if (tok.equals("(")) {
+ consumeToken();
+ OWLClassExpression desc = parseIntersection();
+ String closeBracket = consumeToken();
+ if (!closeBracket.equals(")")) {
+ // Error!
+ throw createException(")");
+ }
+ return desc;
+ }
+ else if (tok.equals("{")) {
+ return parseObjectOneOf();
+ }
+ else if (isClassName(tok)) {
+ String name = consumeToken();
+ return getOWLClass(name);
+ }
+ else if (!tok.equals(ManchesterOWLSyntaxTokenizer.EOF) || !lookaheadCheck) {
+ consumeToken();
+ throw createException(true, false, false, false, false, false, "(", "{");
+ }
+ return null;
+ }
+
+
+ public OWLClassExpression parseObjectOneOf() throws ParserException {
+ String open = consumeToken();
+ if (!open.equals("{")) {
+ throw createException("{");
+ }
+ String sep = ",";
+ Set<OWLIndividual> inds = new HashSet<OWLIndividual>();
+ while (sep.equals(",")) {
+ OWLIndividual ind = parseIndividual();
+ inds.add(ind);
+ sep = peekToken();
+ if (sep.equals(",")) {
+ consumeToken();
+ }
+ }
+ String close = consumeToken();
+ if (!close.equals("}")) {
+ throw createException("}", ",");
+ }
+ return dataFactory.getOWLObjectOneOf(inds);
+ }
+
+
+
+ private <F> void initialiseSection(AnnotatedListItemParser<F, ?> parser, Map<String, AnnotatedListItemParser<F, ?>> map, String ... synonyms) {
+ map.put(parser.getFrameSectionKeyword(), parser);
+ for(String syn : synonyms) {
+ map.put(syn, parser);
+ }
+ }
+
+ public Set<OntologyAxiomPair> parseFrames() throws ParserException {
+ Set<OntologyAxiomPair> axioms = new HashSet<OntologyAxiomPair>();
+ Set<String> possible = new HashSet<String>();
+ resetPossible(possible);
+ while (true) {
+ String tok = peekToken();
+ if (tok.equalsIgnoreCase(CLASS)) {
+ potentialKeywords.clear();
+ resetPossible(possible);
+ axioms.addAll(parseClassFrame());
+ possible.addAll(classFrameSections.keySet());
+ }
+ else if (tok.equalsIgnoreCase(OBJECT_PROPERTY)) {
+ potentialKeywords.clear();
+ resetPossible(possible);
+ axioms.addAll(parseObjectPropertyFrame());
+ possible.addAll(objectPropertyFrameSections.keySet());
+ }
+ else if (tok.equalsIgnoreCase(DATA_PROPERTY)) {
+ potentialKeywords.clear();
+ resetPossible(possible);
+ axioms.addAll(parseDataPropertyFrame());
+ possible.ad...
[truncated message content] |
|
From: <lor...@us...> - 2013-03-19 13:41:06
|
Revision: 3913
http://sourceforge.net/p/dl-learner/code/3913
Author: lorenz_b
Date: 2013-03-19 13:40:46 +0000 (Tue, 19 Mar 2013)
Log Message:
-----------
Changed SPARQL kb constructors.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/LocalModelBasedSparqlEndpointKS.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-ext/src/main/java/org/dllearner/common/index/HierarchicalIndex.java
trunk/components-ext/src/main/java/org/dllearner/common/index/SOLRIndex.java
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
trunk/pom.xml
trunk/scripts/pom.xml
Modified: trunk/components-core/src/main/java/org/dllearner/kb/LocalModelBasedSparqlEndpointKS.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/LocalModelBasedSparqlEndpointKS.java 2013-03-18 12:24:44 UTC (rev 3912)
+++ trunk/components-core/src/main/java/org/dllearner/kb/LocalModelBasedSparqlEndpointKS.java 2013-03-19 13:40:46 UTC (rev 3913)
@@ -37,6 +37,10 @@
this.model = model;
}
+ public LocalModelBasedSparqlEndpointKS(Model model) {
+ this.model = ModelFactory.createOntologyModel(enableReasoning ? OntModelSpec.OWL_MEM : OntModelSpec.OWL_MEM_RDFS_INF, model);
+ }
+
@Override
public void init() throws ComponentInitException {
Model baseModel = ModelFactory.createDefaultModel();
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-03-18 12:24:44 UTC (rev 3912)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-03-19 13:40:46 UTC (rev 3913)
@@ -439,7 +439,7 @@
@Override
public Set<NamedClass> getTypes(Individual individual) {
Set<NamedClass> types = new HashSet<NamedClass>();
- String query = String.format("SELECT ?class WHERE {<%s> a ?class.}", individual.getName());
+ String query = String.format("SELECT DISTINCT ?class WHERE {<%s> a ?class.}", individual.getName());
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -448,6 +448,18 @@
}
return types;
}
+
+ public Set<NamedClass> getTypes() {
+ Set<NamedClass> types = new HashSet<NamedClass>();
+ String query = String.format("SELECT ?class WHERE {[] a ?class.}");
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ types.add(new NamedClass(qs.getResource("class").getURI()));
+ }
+ return types;
+ }
@Override
public boolean hasType(Description description, Individual individual) {
Modified: trunk/components-ext/src/main/java/org/dllearner/common/index/HierarchicalIndex.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/common/index/HierarchicalIndex.java 2013-03-18 12:24:44 UTC (rev 3912)
+++ trunk/components-ext/src/main/java/org/dllearner/common/index/HierarchicalIndex.java 2013-03-19 13:40:46 UTC (rev 3913)
@@ -15,6 +15,14 @@
this.primaryIndex = primaryIndex;
this.secondaryIndex = secondaryIndex;
}
+
+ public Index getPrimaryIndex() {
+ return primaryIndex;
+ }
+
+ public Index getSecondaryIndex() {
+ return secondaryIndex;
+ }
@Override
public List<String> getResources(String queryString) {
Modified: trunk/components-ext/src/main/java/org/dllearner/common/index/SOLRIndex.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/common/index/SOLRIndex.java 2013-03-18 12:24:44 UTC (rev 3912)
+++ trunk/components-ext/src/main/java/org/dllearner/common/index/SOLRIndex.java 2013-03-19 13:40:46 UTC (rev 3913)
@@ -115,6 +115,7 @@
SolrQuery query = new SolrQuery(solrString);
query.setRows(limit);
query.setStart(offset);
+ query.addField("uri");
if(sortField != null){
query.addSortField(sortField, ORDER.desc);
}
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-03-18 12:24:44 UTC (rev 3912)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-03-19 13:40:46 UTC (rev 3913)
@@ -25,6 +25,7 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
@@ -32,7 +33,9 @@
import java.io.UnsupportedEncodingException;
import java.lang.reflect.InvocationTargetException;
import java.math.BigInteger;
+import java.net.Authenticator;
import java.net.MalformedURLException;
+import java.net.PasswordAuthentication;
import java.net.SocketTimeoutException;
import java.net.URI;
import java.net.URISyntaxException;
@@ -41,19 +44,21 @@
import java.security.SecureRandom;
import java.text.DecimalFormat;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Collections;
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.TreeSet;
import joptsimple.OptionException;
import joptsimple.OptionParser;
import joptsimple.OptionSet;
+import joptsimple.OptionSpec;
import org.aksw.commons.jena_owlapi.Conversion;
import org.apache.log4j.ConsoleAppender;
@@ -61,8 +66,6 @@
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat;
-import org.dllearner.algorithms.DisjointClassesLearner;
-import org.dllearner.algorithms.SimpleSubclassLearner;
import org.dllearner.algorithms.celoe.CELOE;
import org.dllearner.algorithms.properties.AsymmetricObjectPropertyAxiomLearner;
import org.dllearner.algorithms.properties.DataPropertyDomainAxiomLearner;
@@ -91,9 +94,9 @@
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.EvaluatedAxiom;
import org.dllearner.core.EvaluatedDescription;
+import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblemUnsupportedException;
-import org.dllearner.core.OntologyFormat;
import org.dllearner.core.Score;
import org.dllearner.core.config.ConfigHelper;
import org.dllearner.core.config.ConfigOption;
@@ -105,11 +108,13 @@
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.SubClassAxiom;
+import org.dllearner.kb.OWLAPIOntology;
import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SPARQLTasks;
import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.learningproblems.ClassLearningProblem;
import org.dllearner.learningproblems.Heuristics.HeuristicType;
@@ -118,14 +123,10 @@
import org.dllearner.utilities.EnrichmentVocabulary;
import org.dllearner.utilities.Helper;
import org.dllearner.utilities.PrefixCCMap;
-import org.dllearner.utilities.datastructures.Datastructures;
import org.dllearner.utilities.datastructures.SetManipulation;
import org.dllearner.utilities.datastructures.SortedSetTuple;
import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2;
-import org.dllearner.utilities.owl.DLLearnerAxiomConvertVisitor;
import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
-import org.dllearner.utilities.owl.OWLAPIConverter;
-import org.dllearner.utilities.owl.OWLAPIDescriptionConvertVisitor;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
@@ -144,10 +145,18 @@
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+import com.clarkparsia.owlapiv3.XSD;
+import com.google.common.collect.Sets;
import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.rdf.model.Literal;
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.Statement;
import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.RDFS;
/**
* Command Line Interface for Enrichment.
@@ -210,6 +219,7 @@
private double threshold = 0.7;
private int chunksize = 1000;
private boolean omitExistingAxioms;
+ private List<String> allowedNamespaces = new ArrayList<String>();
private boolean useInference;
private SPARQLReasoner reasoner;
@@ -227,13 +237,15 @@
// private CommonPrefixMap prefixes = new CommonPrefixMap();
// cache for SparqKnowledgeSource
- SparqlKnowledgeSource ksCached;
+ KnowledgeSource ksCached;
AbstractReasonerComponent rcCached;
private Set<OWLAxiom> learnedOWLAxioms;
private Set<EvaluatedAxiom> learnedEvaluatedAxioms;
- public Enrichment(SparqlEndpoint se, Entity resource, double threshold, int nrOfAxiomsToLearn, boolean useInference, boolean verbose, int chunksize, int maxExecutionTimeInSeconds, boolean omitExistingAxioms) {
+ public Enrichment(SparqlEndpoint se, Entity resource, double threshold, int nrOfAxiomsToLearn,
+ boolean useInference, boolean verbose, int chunksize,
+ int maxExecutionTimeInSeconds, boolean omitExistingAxioms) {
this.se = se;
this.resource = resource;
this.verbose = verbose;
@@ -276,8 +288,8 @@
dataPropertyAlgorithms.add(SubDataPropertyOfAxiomLearner.class);
classAlgorithms = new LinkedList<Class<? extends LearningAlgorithm>>();
- classAlgorithms.add(DisjointClassesLearner.class);
- classAlgorithms.add(SimpleSubclassLearner.class);
+// classAlgorithms.add(DisjointClassesLearner.class);
+// classAlgorithms.add(SimpleSubclassLearner.class);
classAlgorithms.add(CELOE.class);
algorithmRuns = new LinkedList<AlgorithmRun>();
@@ -286,6 +298,10 @@
learnedEvaluatedAxioms = new HashSet<EvaluatedAxiom>();
}
+ public void setAllowedNamespaces(List<String> allowedNamespaces) {
+ this.allowedNamespaces = allowedNamespaces;
+ }
+
public void start() throws ComponentInitException, IllegalArgumentException, SecurityException, InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException, LearningProblemUnsupportedException, MalformedURLException {
// instantiate SPARQL endpoint wrapper component
@@ -310,7 +326,9 @@
if(resource == null) {
// loop over all entities and call appropriate algorithms
- Set<NamedClass> classes = st.getAllClasses();
+
+ Set<NamedClass> classes = reasoner.getTypes();//st.getAllClasses();
+ filterByNamespaces(classes);
int entities = 0;
for(NamedClass nc : classes) {
try {
@@ -323,24 +341,26 @@
break;
}
}
- entities = 0;
- Set<ObjectProperty> objectProperties = st.getAllObjectProperties();
- for(ObjectProperty property : objectProperties) {
- runObjectPropertyAlgorithms(ks, property);
- entities++;
- if(maxEntitiesPerType != -1 && entities > maxEntitiesPerType) {
- break;
- }
- }
- entities = 0;
- Set<DatatypeProperty> dataProperties = st.getAllDataProperties();
- for(DatatypeProperty property : dataProperties) {
- runDataPropertyAlgorithms(ks, property);
- entities++;
- if(maxEntitiesPerType != -1 && entities > maxEntitiesPerType) {
- break;
- }
- }
+// entities = 0;
+// Set<ObjectProperty> objectProperties = st.getAllObjectProperties();
+// filterByNamespaces(objectProperties);
+// for(ObjectProperty property : objectProperties) {
+// runObjectPropertyAlgorithms(ks, property);
+// entities++;
+// if(maxEntitiesPerType != -1 && entities > maxEntitiesPerType) {
+// break;
+// }
+// }
+// entities = 0;
+// Set<DatatypeProperty> dataProperties = st.getAllDataProperties();
+// filterByNamespaces(dataProperties);
+// for(DatatypeProperty property : dataProperties) {
+// runDataPropertyAlgorithms(ks, property);
+// entities++;
+// if(maxEntitiesPerType != -1 && entities > maxEntitiesPerType) {
+// break;
+// }
+// }
} else {
if(resource instanceof ObjectProperty) {
System.out.println(resource + " appears to be an object property. Running appropriate algorithms.\n");
@@ -363,13 +383,32 @@
}
}
+ private <T extends Entity> void filterByNamespaces(Collection<T> entities){
+ if(allowedNamespaces != null && !allowedNamespaces.isEmpty()){
+ for (Iterator<T> iterator = entities.iterator(); iterator.hasNext();) {
+ T entity = iterator.next();System.out.println(entity.getName());
+ boolean startsWithAllowedNamespace = false;
+ for (String ns : allowedNamespaces) {
+ if(entity.getName().startsWith(ns)){
+ startsWithAllowedNamespace = true;
+ break;
+ }
+ }
+ if(!startsWithAllowedNamespace){
+ iterator.remove();
+ }
+ }
+ }
+ }
+
@SuppressWarnings("unchecked")
private void runClassLearningAlgorithms(SparqlEndpointKS ks, NamedClass nc) throws ComponentInitException {
-// System.out.println("Running algorithms for class " + nc);
+ System.out.println("Running algorithms for class " + nc);
for (Class<? extends LearningAlgorithm> algorithmClass : classAlgorithms) {
if(algorithmClass == CELOE.class) {
- applyCELOE(ks, nc, false, false);
- applyCELOE(ks, nc, true, true);
+// applyCELOE(ks, nc, false, false);
+// applyCELOE(ks, nc, true, true);
+ applyCELOE(ks, nc, true, false);
} else {
applyLearningAlgorithm((Class<AxiomLearningAlgorithm>)algorithmClass, ks, nc);
}
@@ -377,14 +416,14 @@
}
private void runObjectPropertyAlgorithms(SparqlEndpointKS ks, ObjectProperty property) throws ComponentInitException {
-// System.out.println("Running algorithms for object property " + property);
+ System.out.println("Running algorithms for object property " + property);
for (Class<? extends AxiomLearningAlgorithm> algorithmClass : objectPropertyAlgorithms) {
applyLearningAlgorithm(algorithmClass, ks, property);
}
}
private void runDataPropertyAlgorithms(SparqlEndpointKS ks, DatatypeProperty property) throws ComponentInitException {
-// System.out.println("Running algorithms for data property " + property);
+ System.out.println("Running algorithms for data property " + property);
for (Class<? extends AxiomLearningAlgorithm> algorithmClass : dataPropertyAlgorithms) {
applyLearningAlgorithm(algorithmClass, ks, property);
}
@@ -394,24 +433,55 @@
// get instances of class as positive examples
SPARQLReasoner sr = new SPARQLReasoner(ks);
+ System.out.print("finding positives ... ");
+ long startTime = System.currentTimeMillis();
SortedSet<Individual> posExamples = sr.getIndividuals(nc, 20);
+ long runTime = System.currentTimeMillis() - startTime;
if(posExamples.isEmpty()){
System.out.println("Skipping CELOE because class " + nc.toString() + " is empty.");
return Collections.emptyList();
}
SortedSet<String> posExStr = Helper.getStringSet(posExamples);
+ System.out.println("done (" + posExStr.size()+ " examples found in " + runTime + " ms)");
// use own implementation of negative example finder
- long startTime = System.currentTimeMillis();
System.out.print("finding negatives ... ");
+ startTime = System.currentTimeMillis();
AutomaticNegativeExampleFinderSPARQL2 finder = new AutomaticNegativeExampleFinderSPARQL2(ks.getEndpoint());
SortedSet<String> negExStr = finder.getNegativeExamples(nc.getName(), posExStr);
- negExStr = SetManipulation.fuzzyShrink(negExStr, 20);
+ negExStr = SetManipulation.stableShrink(negExStr, 20);
SortedSet<Individual> negExamples = Helper.getIndividualSet(negExStr);
SortedSetTuple<Individual> examples = new SortedSetTuple<Individual>(posExamples, negExamples);
- long runTime = System.currentTimeMillis() - startTime;
- System.out.println("done (" + negExStr.size()+ " examples fround in " + runTime + " ms)");
+ runTime = System.currentTimeMillis() - startTime;
+ System.out.println("done (" + negExStr.size()+ " examples found in " + runTime + " ms)");
+ AbstractReasonerComponent rc;
+ KnowledgeSource ksFragment;
+ if(reuseKnowledgeSource){
+ ksFragment = ksCached;
+ rc = rcCached;
+ } else {
+ System.out.print("extracting fragment ... ");
+ startTime = System.currentTimeMillis();
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(ks.getEndpoint(), cache, 2);
+ Model model = ModelFactory.createDefaultModel();
+ for(Individual example : Sets.union(posExamples, negExamples)){
+ Model cbd = cbdGen.getConciseBoundedDescription(example.getName());
+ model.add(cbd);
+ }
+ filter(model);
+ runTime = System.currentTimeMillis() - startTime;
+ System.out.println("done (" + model.size()+ " triples found in " + runTime + " ms)");
+ OWLOntology ontology = asOWLOntology(model);
+ ksFragment = new OWLAPIOntology(ontology);
+// ksFragment.init();
+ rc = new FastInstanceChecker(ksFragment);
+ rc.init();
+ ksCached = ksFragment;
+ rcCached = rc;
+ }
+
+ /*//old way to get SPARQL fragment
SparqlKnowledgeSource ks2;
AbstractReasonerComponent rc;
if(reuseKnowledgeSource) {
@@ -439,7 +509,7 @@
rc.init();
ksCached = ks2;
rcCached = rc;
- }
+ }*/
ClassLearningProblem lp = new ClassLearningProblem(rc);
lp.setClassToDescribe(nc);
@@ -684,6 +754,50 @@
// return model;
// }
+ private OWLOntology asOWLOntology(Model model) {
+ try {
+ FileOutputStream fos = null;
+ try {
+ fos = new FileOutputStream("bug.ttl");
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ model.write(baos, "TURTLE", null);
+ model.write(fos, "TURTLE", null);
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology ontology = man.loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray()));
+ return ontology;
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ private void filter(Model model) {
+ // filter out triples with String literals, as there often occur are
+ // some syntax errors and they are not relevant for learning
+ List<Statement> statementsToRemove = new ArrayList<Statement>();
+ for (Iterator<Statement> iter = model.listStatements().toList().iterator(); iter.hasNext();) {
+ Statement st = iter.next();
+ RDFNode object = st.getObject();
+ if (object.isLiteral()) {
+ // statementsToRemove.add(st);
+ Literal lit = object.asLiteral();
+ if (lit.getDatatype() == null || lit.getDatatype().equals(XSD.STRING)) {
+ st.changeObject("shortened", "en");
+ }
+ }
+ //remove statements like <x a owl:Class>
+ if(st.getPredicate().equals(RDF.type)){
+ if(object.equals(RDFS.Class.asNode()) || object.equals(OWL.Class.asNode()) || object.equals(RDFS.Literal.asNode())){
+ statementsToRemove.add(st);
+ }
+ }
+ }
+ model.remove(statementsToRemove);
+ }
+
Model getModel(List<OWLAxiom> axioms) {
Model model = ModelFactory.createDefaultModel();
try {
@@ -793,7 +907,7 @@
"The resource for which enrichment axioms should be suggested.").withOptionalArg().ofType(URI.class);
parser.acceptsAll(asList("o", "output"), "Specify a file where the output can be written.")
.withOptionalArg().ofType(File.class);
- // TODO: other interestig formats: html, manchester, sparul
+ // TODO: other interesting formats: html, manchester, sparul
parser.acceptsAll(asList("f", "format"),
"Format of the generated output (plain, rdf/xml, turtle, n-triples).").withOptionalArg()
.ofType(String.class).defaultsTo("plain");
@@ -815,7 +929,16 @@
"Specifies the max execution time for each algorithm run and each entity.").withRequiredArg().ofType(Integer.class).defaultsTo(10);
parser.acceptsAll(asList("omitExistingAxioms"),
"Specifies whether return only axioms which not already exist in the knowlegde base.").withOptionalArg().ofType(Boolean.class).defaultsTo(false);
+ OptionSpec<String> allowedNamespacesOption = parser.accepts( "ns" ).withRequiredArg().ofType( String.class )
+ .withValuesSeparatedBy( ',' );
+
+ //username and password if endpoint is protected
+ parser.acceptsAll(asList("u", "username"), "Specify the username.")
+ .withOptionalArg().ofType(String.class);
+ parser.acceptsAll(asList("pw", "password"), "Specify the password.")
+ .withOptionalArg().ofType(String.class);
+
// parse options and display a message for the user in case of problems
OptionSet options = null;
try {
@@ -865,6 +988,19 @@
System.out.println("The specified resource appears not be a proper URI.");
System.exit(0);
}
+ //set credentials if needed
+ if(options.has("username") && options.has("password")){
+ final String username = (String) options.valueOf("username");
+ final String password = (String) options.valueOf("password");
+ Authenticator.setDefault (new Authenticator() {
+ @Override
+ protected PasswordAuthentication getPasswordAuthentication() {
+ return new PasswordAuthentication(username, password.toCharArray());
+ }
+ });
+ }
+
+
LinkedList<String> defaultGraphURIs = new LinkedList<String>();
if(graph != null) {
defaultGraphURIs.add(graph.toString());
@@ -912,9 +1048,13 @@
if(options.has("o") && (!options.has("f") || options.valueOf("f").equals("plain"))) {
PrintStream printStream = new PrintStream(new FileOutputStream(f));
System.setOut(printStream);
- }
+ }
+ //extract namespaces to which the analyzed entities will be restricted
+ List<String> allowedNamespaces = options.valuesOf(allowedNamespacesOption);
+
Enrichment e = new Enrichment(se, resource, threshold, maxNrOfResults, useInference, false, chunksize, maxExecutionTimeInSeconds, omitExistingAxioms);
+ e.setAllowedNamespaces(allowedNamespaces);
e.start();
SparqlEndpointKS ks = new SparqlEndpointKS(se);
@@ -927,6 +1067,8 @@
axioms.addAll(e.toRDF(run.getAxioms(), run.getAlgorithm(), run.getParameters(), ks));
}
Model model = e.getModel(axioms);
+ OutputStream os = options.has("o") ? new FileOutputStream((File)options.valueOf("o")) : System.out;
+
if(options.valueOf("f").equals("turtle")) {
if(options.has("o")) {
model.write(new FileOutputStream(f), "TURTLE");
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2013-03-18 12:24:44 UTC (rev 3912)
+++ trunk/pom.xml 2013-03-19 13:40:46 UTC (rev 3913)
@@ -123,7 +123,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
- <version>3.4</version>
+ <version>3.4.4</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
Modified: trunk/scripts/pom.xml
===================================================================
--- trunk/scripts/pom.xml 2013-03-18 12:24:44 UTC (rev 3912)
+++ trunk/scripts/pom.xml 2013-03-19 13:40:46 UTC (rev 3913)
@@ -116,7 +116,6 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
-<!-- <version>3.4.4-SNAPSHOT</version> -->
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
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|
|
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>." +
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|
|
From: <dc...@us...> - 2013-03-12 09:29:07
|
Revision: 3911
http://sourceforge.net/p/dl-learner/code/3911
Author: dcherix
Date: 2013-03-12 09:29:04 +0000 (Tue, 12 Mar 2013)
Log Message:
-----------
statics paths removed
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java
trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/NewSparqlCompDBpediaClassLearnerCELOE.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java 2013-03-04 15:00:36 UTC (rev 3910)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/DBpediaClassLearnerCELOE.java 2013-03-12 09:29:04 UTC (rev 3911)
@@ -88,369 +88,387 @@
* @author Sebastian Hellmann
*/
public class DBpediaClassLearnerCELOE {
-
- public static String endpointurl = "http://live.dbpedia.org/sparql";
- public static int examplesize = 30;
-
- private static org.apache.log4j.Logger logger = org.apache.log4j.Logger
- .getLogger(DBpediaClassLearnerCELOE.class);
-
- SparqlEndpoint sparqlEndpoint = null;
- private Cache cache;
-
- public DBpediaClassLearnerCELOE() {
- // OPTIONAL: if you want to do some case distinctions in the learnClass
- // method, you could add
- // parameters to the constructure e.g. YAGO_
- try {
- sparqlEndpoint = new SparqlEndpoint(new URL(endpointurl));
- } catch (MalformedURLException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- cache = new Cache("basCache");
- }
-
- public static void main(String args[])
- throws LearningProblemUnsupportedException, IOException, Exception {
- for (int i = 0; i < 4; i++) {
- DBpediaClassLearnerCELOE dcl = new DBpediaClassLearnerCELOE();
- Set<String> classesToLearn = dcl.getClasses();
- Monitor mon = MonitorFactory.start("Learn DBpedia");
- KB kb = dcl.learnAllClasses(classesToLearn);
- mon.stop();
- kb.export(new File("/home/dcherix/dllearner/old/result"+i+".owl"),
- OntologyFormat.RDF_XML);
- // Set<String> pos =
- // dcl.getPosEx("http://dbpedia.org/ontology/Person");
- // dcl.getNegEx("http://dbpedia.org/ontology/Person", pos);
- logger.info("Test" + i + ":\n"
- + JamonMonitorLogger.getStringForAllSortedByLabel());
- System.gc();
- }
- }
-
- public KB learnAllClasses(Set<String> classesToLearn) {
- KB kb = new KB();
- for (String classToLearn : classesToLearn) {
- logger.info("Leanring class: " + classToLearn);
- try {
- Description d = learnClass(classToLearn);
- if (d == null
- || d.toKBSyntaxString().equals(
- new Thing().toKBSyntaxString())) {
- logger.error("Description was " + d + ", continueing");
- continue;
- }
- kb.addAxiom(new EquivalentClassesAxiom(new NamedClass(
- classToLearn), d));
- kb.export(new File(
- "/home/dcherix/dllearner/old/result_partial.owl"),
- OntologyFormat.RDF_XML);
-
- } catch (Exception e) {
- logger.warn("", e);
- }
- this.dropCache();
- }
-
- return kb;
- }
-
- public Description learnClass(String classToLearn) throws Exception {
- // TODO: use aksw-commons-sparql instead of sparql-scala
- SortedSet<String> posEx = new TreeSet<String>(getPosEx(classToLearn));
- logger.info("Found " + posEx.size() + " positive examples");
- if (posEx.isEmpty()) {
- return null;
- }
- SortedSet<String> negEx = new TreeSet<String>(getNegEx(classToLearn,
- posEx));
-
- posEx = SetManipulation.fuzzyShrink(posEx, examplesize);
- negEx = SetManipulation.fuzzyShrink(negEx, examplesize);
-
- SortedSet<Individual> posExamples = Helper.getIndividualSet(posEx);
- SortedSet<Individual> negExamples = Helper.getIndividualSet(negEx);
- SortedSetTuple<Individual> examples = new SortedSetTuple<Individual>(
- posExamples, negExamples);
-
- ComponentManager cm = ComponentManager.getInstance();
-
- SparqlKnowledgeSource ks = cm
- .knowledgeSource(SparqlKnowledgeSource.class);
- ks.setInstances(Datastructures.individualSetToStringSet(examples
- .getCompleteSet()));
- // ks.getConfigurator().setPredefinedEndpoint("DBPEDIA"); // TODO:
- // probably the official endpoint is too slow?
- ks.setUrl(new URL(endpointurl));
- ks.setUseLits(false);
- ks.setUseCacheDatabase(true);
- ks.setUseCache(true);
- ks.setRecursionDepth(1);
- ks.setCloseAfterRecursion(true);
- ks.setSaveExtractedFragment(true);
- ks.setPredList(new HashSet<String>(Arrays.asList(new String[] {
- "http://dbpedia.org/property/wikiPageUsesTemplate",
- "http://dbpedia.org/ontology/wikiPageExternalLink",
- "http://dbpedia.org/property/wordnet_type",
- "http://www.w3.org/2002/07/owl#sameAs" })));
-
- ks.setObjList(new HashSet<String>(Arrays.asList(new String[] {
- "http://dbpedia.org/class/yago/",
- "http://dbpedia.org/resource/Category:" })));
-
- ks.init();
-
- AbstractReasonerComponent rc = cm.reasoner(FastInstanceChecker.class,
- ks);
- rc.init();
-
- PosNegLPStandard lp = cm.learningProblem(PosNegLPStandard.class, rc);
- lp.setPositiveExamples(posExamples);
- lp.setNegativeExamples(negExamples);
- lp.setAccuracyMethod("fmeasure");
- lp.setUseApproximations(false);
- lp.init();
-
- CELOE la = cm.learningAlgorithm(CELOE.class, lp, rc);
- // CELOEConfigurator cc = la.getConfigurator();
- la.setMaxExecutionTimeInSeconds(100);
- la.init();
- RhoDRDown op = (RhoDRDown) la.getOperator();
-
- op.setUseNegation(false);
- op.setUseAllConstructor(false);
- op.setUseCardinalityRestrictions(false);
- op.setUseHasValueConstructor(true);
- la.setNoisePercentage(20);
- la.setIgnoredConcepts(new HashSet<NamedClass>(Arrays
- .asList(new NamedClass[] { new NamedClass(classToLearn) })));
- la.init();
-
- // to write the above configuration in a conf file (optional)
- Config cf = new Config(cm, ks, rc, lp, la);
- new ConfigSave(cf).saveFile(new File("/dev/null"));
-
- la.start();
-
- cm.freeAllComponents();
- return la.getCurrentlyBestDescription();
- }
-
- public Set<String> getClasses() throws Exception {
- OntModel model = ModelFactory.createOntologyModel();
- model.read(new FileInputStream(
- "/home/dcherix/Downloads/dbpedia_3.6.owl"), null);
- Set<OntClass> classes = model.listClasses().toSet();
- Set<String> results = new HashSet<String>();
- for (OntClass ontClass : classes) {
- results.add(ontClass.getURI());
- }
- return results;
- }
-
- // gets all DBpedia Classes
- // public Set<String> getClasses() throws Exception {
- // SparqlTemplate st = SparqlTemplate.getInstance("allClasses.vm");
- // st.setLimit(0);
- // st.addFilter(sparqlEndpoint.like("classes", new
- // HashSet<String>(Arrays.asList(new
- // String[]{"http://dbpedia.org/ontology/"}))));
- // VelocityContext vc = st.putSgetVelocityContext();
- // String query = st.getQuery();
- // return new
- // HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)));
- // }
- //
- public Set<String> getPosEx(String clazz) throws Exception {
-// SparqlTemplate st = SparqlTemplate.getInstance("instancesOfClass.vm");
-// st.setLimit(0);
-// VelocityContext vc = st.getVelocityContext();
-// vc.put("class", clazz);
-// String queryString = st.getQuery();
- StringBuilder queryString = new StringBuilder();
- queryString.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>");
- queryString.append(" SELECT ?instances WHERE { ?instances rdf:type <");
- queryString.append(clazz);
- queryString.append("> }");
- System.out.println(queryString);
- return this.executeResourceQuery(queryString.toString());
- }
-
- /**
- * gets all direct classes of all instances and has a look, what the most
- * common is
- *
- * @param clazz
- * @param posEx
- * @return
- * @throws Exception
- */
- public String selectClass(String clazz, Set<String> posEx) throws Exception {
- Map<String, Integer> m = new HashMap<String, Integer>();
- // TODO: use aksw-commons-sparql instead of sparql-scala
- /*
- * for (String pos : posEx) { SparqlTemplate st =
- * SparqlTemplate.getInstance("directClassesOfInstance.vm");
- * st.setLimit(0); st.addFilter(sparqlEndpoint.like("direct", new
- * HashSet<String>(Arrays.asList(new
- * String[]{"http://dbpedia.org/ontology/"})))); VelocityContext vc =
- * st.getVelocityContext(); vc.put("instance", pos); String query =
- * st.getQuery(); Set<String> classes = new
- * HashSet<String>(ResultSetRenderer
- * .asStringSet(sparqlEndpoint.executeSelect(query)));
- * classes.remove(clazz); for (String s : classes) { if (m.get(s) ==
- * null) { m.put(s, 0); } m.put(s, m.get(s).intValue() + 1); } }
- */
-
- int max = 0;
- String maxClass = "";
- for (String key : m.keySet()) {
- if (m.get(key).intValue() > max) {
- maxClass = key;
- }
- }
-
- return maxClass;
- }
-
- /**
- * gets instances of a class or random instances
- *
- * @param clazz
- * @param posEx
- * @return
- * @throws Exception
- */
-
- public Set<String> getNegEx(String clazz, Set<String> posEx)
- throws Exception {
- Set<String> negEx = new HashSet<String>();
- // TODO: use aksw-commons-sparql instead of sparql-scala
- /*
- * String targetClass = getParallelClass(clazz);
- * logger.info("using class for negatives: " + targetClass); if
- * (targetClass != null) {
- *
- * SparqlTemplate st =
- * SparqlTemplate.getInstance("instancesOfClass.vm"); st.setLimit(0);
- * VelocityContext vc = st.getVelocityContext(); vc.put("class",
- * targetClass); // st.addFilter(sparqlEndpoint.like("class", new
- * HashSet<String>(Arrays.asList(new
- * String[]{"http://dbpedia.org/ontology/"})))); String query =
- * st.getQuery(); // negEx.addAll(new
- * HashSet<String>(ResultSetRenderer.asStringSet
- * (sparqlEndpoint.executeSelect(query)))); } else {
- *
- * SparqlTemplate st = SparqlTemplate.getInstance("someInstances.vm");
- * st.setLimit(posEx.size() + 100); VelocityContext vc =
- * st.getVelocityContext(); String query = st.getQuery(); //
- * negEx.addAll(new
- * HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint
- * .executeSelect(query)))); } negEx.removeAll(posEx);
- */
-
- String targetClass = getParallelClass(clazz);
- logger.info("using class for negatives: " + targetClass);
- if (targetClass != null) {
- SparqlTemplate st = SparqlTemplate
- .getInstance("instancesOfClass2.vm");
- st.setLimit(0);
- VelocityContext vc = st.getVelocityContext();
- vc.put("class", targetClass);
- st.addFilter("FILTER ( ?class LIKE (<http://dbpedia.org/ontology/%>");
-
- String query = st.getQuery();
- negEx.addAll(this.executeResourceQuery(query));
- } else {
- SparqlTemplate st = SparqlTemplate.getInstance("someInstances.vm");
- st.setLimit(posEx.size() + 100);
- VelocityContext vc = st.getVelocityContext();
- String query = st.getQuery();
- negEx.addAll(this.executeResourceQuery(query));
- }
- negEx.removeAll(posEx);
- return negEx;
-
- }
-
- public String getParallelClass(String clazz) throws Exception {
- // TODO: use aksw-commons-sparql instead of sparql-scala
- // SparqlTemplate st = SparqlTemplate.getInstance("parallelClass.vm");
- // st.setLimit(0);
- // VelocityContext vc = st.getVelocityContext();
- // vc.put("class", clazz);
- // String query = st.getQuery();
- // Set<String> parClasses = new
- // HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)));
- // for (String s : parClasses) {
- // return s;
- // }
- SparqlTemplate st = SparqlTemplate.getInstance("parallelClass.vm");
- st.setLimit(0);
- VelocityContext vc = st.getVelocityContext();
- vc.put("class", clazz);
- String query = st.getQuery();
- Set<String> parClasses = this.executeClassQuery(query);
- for (String s : parClasses) {
- if (s.startsWith("http://dbpedia.org/ontology")) {
- if (!s.endsWith("Unknown")) {
- return s;
- }
- }
- }
- return null;
- }
-
- public Set<String> executeResourceQuery(String queryString) {
-// Query query = QueryFactory.create(queryString);
-// QueryExecution qexec = QueryExecutionFactory.sparqlService(endpointurl,
-// query);
-// ResultSet resultSet = qexec.execSelect();
- ResultSetRewindable resultSet = SparqlQuery.convertJSONtoResultSet(cache.executeSparqlQuery(new SparqlQuery(queryString,sparqlEndpoint)));
- QuerySolution solution;
- Set<String> results = new HashSet<String>();
- while (resultSet.hasNext()) {
- solution = resultSet.next();
- results.add(solution.getResource("instances").getURI());
- }
- return results;
- }
-
- public Set<String> executeClassQuery(String queryString) {
-// Query query = QueryFactory.create(queryString);
-// QueryExecution qexec = QueryExecutionFactory.sparqlService(endpointurl,
-// query);
-// ResultSet resultSet = qexec.execSelect();
- ResultSetRewindable resultSet = SparqlQuery.convertJSONtoResultSet(cache.executeSparqlQuery(new SparqlQuery(queryString,sparqlEndpoint)));
- QuerySolution solution;
- Set<String> results = new HashSet<String>();
- while (resultSet.hasNext()) {
- solution = resultSet.next();
- results.add(solution.getResource("sub").getURI());
- }
- return results;
- }
-
- private void dropCache(){
- try {
- Class.forName("org.h2.Driver");
- String databaseName="extraction";
- String databaseDirectory="cache";
- Connection conn = DriverManager.getConnection("jdbc:h2:"+databaseDirectory+"/"+databaseName, "sa", "");
- Statement st = conn.createStatement();
- st.execute("DELETE FROM QUERY_CACHE");
- st.close();
- conn.close();
- System.gc();
- } catch (ClassNotFoundException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (SQLException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
+
+ public static String endpointurl = "http://live.dbpedia.org/sparql";
+ public static int examplesize = 30;
+
+ private static org.apache.log4j.Logger logger = org.apache.log4j.Logger
+ .getLogger(DBpediaClassLearnerCELOE.class);
+ private static String output;
+ private static String input;
+
+ SparqlEndpoint sparqlEndpoint = null;
+ private Cache cache;
+
+ public DBpediaClassLearnerCELOE() {
+ // OPTIONAL: if you want to do some case distinctions in the learnClass
+ // method, you could add
+ // parameters to the constructure e.g. YAGO_
+ try {
+ sparqlEndpoint = new SparqlEndpoint(new URL(endpointurl));
+ } catch (MalformedURLException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ cache = new Cache("basCache");
+ }
+
+ public static void main(String args[]) throws LearningProblemUnsupportedException, IOException,
+ Exception {
+ if (args.length < 3) {
+ usage();
+ return;
+ }
+ int iter;
+ try {
+ output = args[1];
+ input = args[0];
+ iter = Integer.parseInt(args[2]);
+ } catch (Exception e) {
+ usage();
+ return;
+ }
+ for (int i = 0; i < iter; i++) {
+ DBpediaClassLearnerCELOE dcl = new DBpediaClassLearnerCELOE();
+ Set<String> classesToLearn = dcl.getClasses();
+ Monitor mon = MonitorFactory.start("Learn DBpedia");
+ KB kb = dcl.learnAllClasses(classesToLearn);
+ mon.stop();
+ kb.export(new File(output + "/result" + i + ".owl"), OntologyFormat.RDF_XML);
+ // Set<String> pos =
+ // dcl.getPosEx("http://dbpedia.org/ontology/Person");
+ // dcl.getNegEx("http://dbpedia.org/ontology/Person", pos);
+ logger.info("Test" + i + ":\n" + JamonMonitorLogger.getStringForAllSortedByLabel());
+ System.gc();
+ }
+ }
+
+ /**
+ * Show the required parameters for usage
+ */
+ private static void usage() {
+ System.out.println("***************************************************************");
+ System.out.println("* Usage: java DBpediaClassLearnerCELOE input output iteration *");
+ System.out.println("* As input is the dbpedia schema as owl necessary *");
+ System.out.println("* As output is a directory for the owl results file expected *");
+ System.out.println("***************************************************************");
+ }
+
+ public KB learnAllClasses(Set<String> classesToLearn) {
+ KB kb = new KB();
+ for (String classToLearn : classesToLearn) {
+ logger.info("Learning class: " + classToLearn);
+ try {
+ Description d = learnClass(classToLearn);
+ if (d == null || d.toKBSyntaxString().equals(new Thing().toKBSyntaxString())) {
+ logger.error("Description was " + d + ", continueing");
+ continue;
+ }
+ kb.addAxiom(new EquivalentClassesAxiom(new NamedClass(classToLearn), d));
+ kb.export(new File(output+"/result_partial.owl"),
+ OntologyFormat.RDF_XML);
+
+ } catch (Exception e) {
+ logger.warn("", e);
+ }
+ this.dropCache();
+ }
+
+ return kb;
+ }
+
+ public Description learnClass(String classToLearn) throws Exception {
+ // TODO: use aksw-commons-sparql instead of sparql-scala
+ SortedSet<String> posEx = new TreeSet<String>(getPosEx(classToLearn));
+ logger.info("Found " + posEx.size() + " positive examples");
+ if (posEx.isEmpty()) {
+ return null;
+ }
+ SortedSet<String> negEx = new TreeSet<String>(getNegEx(classToLearn, posEx));
+
+ posEx = SetManipulation.fuzzyShrink(posEx, examplesize);
+ negEx = SetManipulation.fuzzyShrink(negEx, examplesize);
+
+ SortedSet<Individual> posExamples = Helper.getIndividualSet(posEx);
+ SortedSet<Individual> negExamples = Helper.getIndividualSet(negEx);
+ SortedSetTuple<Individual> examples = new SortedSetTuple<Individual>(posExamples,
+ negExamples);
+
+ ComponentManager cm = ComponentManager.getInstance();
+
+ SparqlKnowledgeSource ks = cm.knowledgeSource(SparqlKnowledgeSource.class);
+ ks.setInstances(Datastructures.individualSetToStringSet(examples.getCompleteSet()));
+ // ks.getConfigurator().setPredefinedEndpoint("DBPEDIA"); // TODO:
+ // probably the official endpoint is too slow?
+ ks.setUrl(new URL(endpointurl));
+ ks.setUseLits(false);
+ ks.setUseCacheDatabase(true);
+ ks.setUseCache(true);
+ ks.setRecursionDepth(1);
+ ks.setCloseAfterRecursion(true);
+ ks.setSaveExtractedFragment(true);
+ ks.setPredList(new HashSet<String>(Arrays
+ .asList(new String[] { "http://dbpedia.org/property/wikiPageUsesTemplate",
+ "http://dbpedia.org/ontology/wikiPageExternalLink",
+ "http://dbpedia.org/property/wordnet_type",
+ "http://www.w3.org/2002/07/owl#sameAs" })));
+
+ ks.setObjList(new HashSet<String>(Arrays.asList(new String[] {
+ "http://dbpedia.org/class/yago/", "http://dbpedia.org/resource/Category:" })));
+
+ ks.init();
+
+ AbstractReasonerComponent rc = cm.reasoner(FastInstanceChecker.class, ks);
+ rc.init();
+
+ PosNegLPStandard lp = cm.learningProblem(PosNegLPStandard.class, rc);
+ lp.setPositiveExamples(posExamples);
+ lp.setNegativeExamples(negExamples);
+ lp.setAccuracyMethod("fmeasure");
+ lp.setUseApproximations(false);
+ lp.init();
+
+ CELOE la = cm.learningAlgorithm(CELOE.class, lp, rc);
+ // CELOEConfigurator cc = la.getConfigurator();
+ la.setMaxExecutionTimeInSeconds(100);
+ la.init();
+ RhoDRDown op = (RhoDRDown) la.getOperator();
+
+ op.setUseNegation(false);
+ op.setUseAllConstructor(false);
+ op.setUseCardinalityRestrictions(false);
+ op.setUseHasValueConstructor(true);
+ la.setNoisePercentage(20);
+ la.setIgnoredConcepts(new HashSet<NamedClass>(Arrays
+ .asList(new NamedClass[] { new NamedClass(classToLearn) })));
+ la.init();
+
+ // to write the above configuration in a conf file (optional)
+ Config cf = new Config(cm, ks, rc, lp, la);
+ new ConfigSave(cf).saveFile(new File("/dev/null"));
+
+ la.start();
+
+ cm.freeAllComponents();
+ return la.getCurrentlyBestDescription();
+ }
+
+ public Set<String> getClasses() throws Exception {
+ OntModel model = ModelFactory.createOntologyModel();
+ model.read(new FileInputStream(input), null);
+ Set<OntClass> classes = model.listClasses().toSet();
+ Set<String> results = new HashSet<String>();
+ for (OntClass ontClass : classes) {
+ results.add(ontClass.getURI());
+ }
+ return results;
+ }
+
+ // gets all DBpedia Classes
+ // public Set<String> getClasses() throws Exception {
+ // SparqlTemplate st = SparqlTemplate.getInstance("allClasses.vm");
+ // st.setLimit(0);
+ // st.addFilter(sparqlEndpoint.like("classes", new
+ // HashSet<String>(Arrays.asList(new
+ // String[]{"http://dbpedia.org/ontology/"}))));
+ // VelocityContext vc = st.putSgetVelocityContext();
+ // String query = st.getQuery();
+ // return new
+ // HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)));
+ // }
+ //
+ public Set<String> getPosEx(String clazz) throws Exception {
+ // SparqlTemplate st =
+ // SparqlTemplate.getInstance("instancesOfClass.vm");
+ // st.setLimit(0);
+ // VelocityContext vc = st.getVelocityContext();
+ // vc.put("class", clazz);
+ // String queryString = st.getQuery();
+ StringBuilder queryString = new StringBuilder();
+ queryString.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>");
+ queryString.append(" SELECT ?instances WHERE { ?instances rdf:type <");
+ queryString.append(clazz);
+ queryString.append("> }");
+ System.out.println(queryString);
+ return this.executeResourceQuery(queryString.toString());
+ }
+
+ /**
+ * gets all direct classes of all instances and has a look, what the most
+ * common is
+ *
+ * @param clazz
+ * @param posEx
+ * @return
+ * @throws Exception
+ */
+ public String selectClass(String clazz, Set<String> posEx) throws Exception {
+ Map<String, Integer> m = new HashMap<String, Integer>();
+ // TODO: use aksw-commons-sparql instead of sparql-scala
+ /*
+ * for (String pos : posEx) { SparqlTemplate st =
+ * SparqlTemplate.getInstance("directClassesOfInstance.vm");
+ * st.setLimit(0); st.addFilter(sparqlEndpoint.like("direct", new
+ * HashSet<String>(Arrays.asList(new
+ * String[]{"http://dbpedia.org/ontology/"})))); VelocityContext vc =
+ * st.getVelocityContext(); vc.put("instance", pos); String query =
+ * st.getQuery(); Set<String> classes = new
+ * HashSet<String>(ResultSetRenderer
+ * .asStringSet(sparqlEndpoint.executeSelect(query)));
+ * classes.remove(clazz); for (String s : classes) { if (m.get(s) ==
+ * null) { m.put(s, 0); } m.put(s, m.get(s).intValue() + 1); } }
+ */
+
+ int max = 0;
+ String maxClass = "";
+ for (String key : m.keySet()) {
+ if (m.get(key).intValue() > max) {
+ maxClass = key;
+ }
+ }
+
+ return maxClass;
+ }
+
+ /**
+ * gets instances of a class or random instances
+ *
+ * @param clazz
+ * @param posEx
+ * @return
+ * @throws Exception
+ */
+
+ public Set<String> getNegEx(String clazz, Set<String> posEx) throws Exception {
+ Set<String> negEx = new HashSet<String>();
+ // TODO: use aksw-commons-sparql instead of sparql-scala
+ /*
+ * String targetClass = getParallelClass(clazz);
+ * logger.info("using class for negatives: " + targetClass); if
+ * (targetClass != null) {
+ *
+ * SparqlTemplate st =
+ * SparqlTemplate.getInstance("instancesOfClass.vm"); st.setLimit(0);
+ * VelocityContext vc = st.getVelocityContext(); vc.put("class",
+ * targetClass); // st.addFilter(sparqlEndpoint.like("class", new
+ * HashSet<String>(Arrays.asList(new
+ * String[]{"http://dbpedia.org/ontology/"})))); String query =
+ * st.getQuery(); // negEx.addAll(new
+ * HashSet<String>(ResultSetRenderer.asStringSet
+ * (sparqlEndpoint.executeSelect(query)))); } else {
+ *
+ * SparqlTemplate st = SparqlTemplate.getInstance("someInstances.vm");
+ * st.setLimit(posEx.size() + 100); VelocityContext vc =
+ * st.getVelocityContext(); String query = st.getQuery(); //
+ * negEx.addAll(new
+ * HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint
+ * .executeSelect(query)))); } negEx.removeAll(posEx);
+ */
+
+ String targetClass = getParallelClass(clazz);
+ logger.info("using class for negatives: " + targetClass);
+ if (targetClass != null) {
+ SparqlTemplate st = SparqlTemplate.getInstance("instancesOfClass2.vm");
+ st.setLimit(0);
+ VelocityContext vc = st.getVelocityContext();
+ vc.put("class", targetClass);
+ st.addFilter("FILTER ( ?class LIKE (<http://dbpedia.org/ontology/%>");
+
+ String query = st.getQuery();
+ negEx.addAll(this.executeResourceQuery(query));
+ } else {
+ SparqlTemplate st = SparqlTemplate.getInstance("someInstances.vm");
+ st.setLimit(posEx.size() + 100);
+ VelocityContext vc = st.getVelocityContext();
+ String query = st.getQuery();
+ negEx.addAll(this.executeResourceQuery(query));
+ }
+ negEx.removeAll(posEx);
+ return negEx;
+
+ }
+
+ public String getParallelClass(String clazz) throws Exception {
+ // TODO: use aksw-commons-sparql instead of sparql-scala
+ // SparqlTemplate st = SparqlTemplate.getInstance("parallelClass.vm");
+ // st.setLimit(0);
+ // VelocityContext vc = st.getVelocityContext();
+ // vc.put("class", clazz);
+ // String query = st.getQuery();
+ // Set<String> parClasses = new
+ // HashSet<String>(ResultSetRenderer.asStringSet(sparqlEndpoint.executeSelect(query)));
+ // for (String s : parClasses) {
+ // return s;
+ // }
+ SparqlTemplate st = SparqlTemplate.getInstance("parallelClass.vm");
+ st.setLimit(0);
+ VelocityContext vc = st.getVelocityContext();
+ vc.put("class", clazz);
+ String query = st.getQuery();
+ Set<String> parClasses = this.executeClassQuery(query);
+ for (String s : parClasses) {
+ if (s.startsWith("http://dbpedia.org/ontology")) {
+ if (!s.endsWith("Unknown")) {
+ return s;
+ }
+ }
+ }
+ return null;
+ }
+
+ public Set<String> executeResourceQuery(String queryString) {
+ // Query query = QueryFactory.create(queryString);
+ // QueryExecution qexec =
+ // QueryExecutionFactory.sparqlService(endpointurl,
+ // query);
+ // ResultSet resultSet = qexec.execSelect();
+ ResultSetRewindable resultSet = SparqlQuery.convertJSONtoResultSet(cache
+ .executeSparqlQuery(new SparqlQuery(queryString, sparqlEndpoint)));
+ QuerySolution solution;
+ Set<String> results = new HashSet<String>();
+ while (resultSet.hasNext()) {
+ solution = resultSet.next();
+ results.add(solution.getResource("instances").getURI());
+ }
+ return results;
+ }
+
+ public Set<String> executeClassQuery(String queryString) {
+ // Query query = QueryFactory.create(queryString);
+ // QueryExecution qexec =
+ // QueryExecutionFactory.sparqlService(endpointurl,
+ // query);
+ // ResultSet resultSet = qexec.execSelect();
+ ResultSetRewindable resultSet = SparqlQuery.convertJSONtoResultSet(cache
+ .executeSparqlQuery(new SparqlQuery(queryString, sparqlEndpoint)));
+ QuerySolution solution;
+ Set<String> results = new HashSet<String>();
+ while (resultSet.hasNext()) {
+ solution = resultSet.next();
+ results.add(solution.getResource("sub").getURI());
+ }
+ return results;
+ }
+
+ private void dropCache() {
+ try {
+ Class.forName("org.h2.Driver");
+ String databaseName = "extraction";
+ String databaseDirectory = "cache";
+ Connection conn = DriverManager.getConnection("jdbc:h2:" + databaseDirectory + "/"
+ + databaseName, "sa", "");
+ Statement st = conn.createStatement();
+ st.execute("DELETE FROM QUERY_CACHE");
+ st.close();
+ conn.close();
+ System.gc();
+ } catch (ClassNotFoundException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (SQLException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
}
\ No newline at end of file
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/NewSparqlCompDBpediaClassLearnerCELOE.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/NewSparqlCompDBpediaClassLearnerCELOE.java 2013-03-04 15:00:36 UTC (rev 3910)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/improveWikipedia/NewSparqlCompDBpediaClassLearnerCELOE.java 2013-03-12 09:29:04 UTC (rev 3911)
@@ -90,6 +90,8 @@
private static org.apache.log4j.Logger logger = org.apache.log4j.Logger
.getLogger(NewSparqlCompDBpediaClassLearnerCELOE.class);
+ private static String output;
+ private static String input;
SparqlEndpoint sparqlEndpoint = null;
@@ -107,6 +109,19 @@
public static void main(String args[])
throws LearningProblemUnsupportedException, IOException, Exception {
+ if (args.length < 3) {
+ usage();
+ return;
+ }
+ int iter;
+ try {
+ output = args[1];
+ input = args[0];
+ iter = Integer.parseInt(args[2]);
+ } catch (Exception e) {
+ usage();
+ return;
+ }
for (int i = 0; i < 4; i++) {
NewSparqlCompDBpediaClassLearnerCELOE dcl = new NewSparqlCompDBpediaClassLearnerCELOE();
Set<String> classesToLearn = dcl.getClasses();
@@ -114,7 +129,7 @@
Monitor mon = MonitorFactory.start("Learn DBpedia");
KB kb = dcl.learnAllClasses(classesToLearn);
mon.stop();
- kb.export(new File("/home/dcherix/dllearner/simple/result" + i
+ kb.export(new File(output+"/result" + i
+ ".owl"), OntologyFormat.RDF_XML);
// Set<String> pos =
// dcl.getPosEx("http://dbpedia.org/ontology/Person");
@@ -125,6 +140,17 @@
.getStringForAllSortedByLabel());
}
}
+
+ /**
+ * Show the required parameters for usage
+ */
+ private static void usage() {
+ System.out.println("***************************************************************");
+ System.out.println("* Usage: java DBpediaClassLearnerCELOE input output iteration *");
+ System.out.println("* As input is the dbpedia schema as owl necessary *");
+ System.out.println("* As output is a directory for the owl results file expected *");
+ System.out.println("***************************************************************");
+ }
public KB learnAllClasses(Set<String> classesToLearn) {
KB kb = new KB();
@@ -141,7 +167,7 @@
kb.addAxiom(new EquivalentClassesAxiom(new NamedClass(
classToLearn), d));
kb.export(new File(
- "/home/dcherix/dllearner/simple/result_partial.owl"),
+ output+"/result_partial.owl"),
OntologyFormat.RDF_XML);
} catch (Exception e) {
@@ -184,7 +210,7 @@
// ks.setUseCacheDatabase(true);
ks.setRecursionDepth(1);
ArrayList<String> ontologyUrls = new ArrayList<String>();
- ontologyUrls.add("http://downloads.dbpedia.org/3.6/dbpedia_3.6.owl");
+ ontologyUrls.add(new File(input).toURI().toURL().toString());
ks.setOntologySchemaUrls(ontologyUrls);
ks.setAboxfilter("FILTER (!regex(str(?p), '^http://dbpedia.org/property/wikiPageUsesTemplate') && "
+ "!regex(str(?p), '^http://dbpedia.org/ontology/wikiPageExternalLink') && "
@@ -247,7 +273,7 @@
public Set<String> getClasses() throws Exception {
OntModel model = ModelFactory.createOntologyModel();
model.read(new FileInputStream(
- "/home/dcherix/Downloads/dbpedia_3.6.owl"), null);
+ input), null);
Set<OntClass> classes = model.listClasses().toSet();
Set<String> results = new HashSet<String>();
int i = 0;
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