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[DL-Learner SVN] SF.net SVN: dl-learner:[3624] trunk
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From: <lor...@us...> - 2012-03-29 13:09:10
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Revision: 3624
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3624&view=rev
Author: lorenz_b
Date: 2012-03-29 13:09:03 +0000 (Thu, 29 Mar 2012)
Log Message:
-----------
Removed dependencies to SESAME.
Changed some examples by reducing execution time.
Fixed Unit test to ignore SPARQL examples correctly.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
trunk/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java
trunk/examples/carcinogenesis/train.conf
trunk/examples/family-benchmark/Aunt.conf
trunk/interfaces/src/test/java/org/dllearner/test/junit/ExampleTests.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2012-03-27 15:09:17 UTC (rev 3623)
+++ trunk/components-core/pom.xml 2012-03-29 13:09:03 UTC (rev 3624)
@@ -106,6 +106,10 @@
<artifactId>xercesImpl</artifactId>
<groupId>xerces</groupId>
</exclusion>
+ <exclusion>
+ <artifactId>any23-core</artifactId>
+ <groupId>org.deri.any23</groupId>
+ </exclusion>
</exclusions>
</dependency>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java 2012-03-27 15:09:17 UTC (rev 3623)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java 2012-03-29 13:09:03 UTC (rev 3624)
@@ -21,10 +21,8 @@
import java.net.URL;
import java.util.ArrayList;
-import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -46,11 +44,8 @@
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
import org.dllearner.kb.SparqlEndpointKS;
-import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.learningproblems.AxiomScore;
import org.dllearner.learningproblems.Heuristics;
-import org.openrdf.model.vocabulary.OWL;
-import org.openrdf.model.vocabulary.RDF;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -61,6 +56,8 @@
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.vocabulary.OWL2;
+import com.hp.hpl.jena.vocabulary.RDF;
/**
* Learns disjoint classes using SPARQL queries.
@@ -340,7 +337,7 @@
//secondly, create disjoint classexpressions with score 1 - (#occurence/#all)
for(Entry<NamedClass, Integer> entry : sortByValues(class2Count)){
//drop classes from OWL and RDF namespace
- if(entry.getKey().getName().startsWith(OWL.NAMESPACE) || entry.getKey().getName().startsWith(RDF.NAMESPACE))continue;
+ if(entry.getKey().getName().startsWith(OWL2.getURI()) || entry.getKey().getName().startsWith(RDF.getURI()))continue;
// evalDesc = new EvaluatedDescription(entry.getKey(),
// new AxiomScore(1 - (entry.getValue() / (double)all)));
double[] confidenceInterval = Heuristics.getConfidenceInterval95Wald(total, entry.getValue());
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-03-27 15:09:17 UTC (rev 3623)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-03-29 13:09:03 UTC (rev 3624)
@@ -44,9 +44,6 @@
import org.dllearner.learningproblems.Heuristics;
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.owl.AxiomComparator;
-import org.openrdf.model.vocabulary.OWL;
-import org.openrdf.model.vocabulary.RDF;
-import org.openrdf.model.vocabulary.RDFS;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@@ -58,6 +55,9 @@
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.hp.hpl.jena.util.iterator.Filter;
+import com.hp.hpl.jena.vocabulary.OWL2;
+import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.RDFS;
/**
* @author Lorenz Bühmann
@@ -334,7 +334,7 @@
@Override
public boolean accept(OntClass cls) {
if(!cls.isAnon()){
- return cls.getURI().startsWith(OWL.NAMESPACE);
+ return cls.getURI().startsWith(OWL2.getURI());
}
return false;
}
@@ -346,7 +346,7 @@
@Override
public boolean accept(OntClass cls) {
if(!cls.isAnon()){
- return cls.getURI().startsWith(RDFS.NAMESPACE);
+ return cls.getURI().startsWith(RDFS.getURI());
}
return false;
}
@@ -358,7 +358,7 @@
@Override
public boolean accept(OntClass cls) {
if(!cls.isAnon()){
- return cls.getURI().startsWith(RDF.NAMESPACE);
+ return cls.getURI().startsWith(RDF.getURI());
}
return false;
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java 2012-03-27 15:09:17 UTC (rev 3623)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java 2012-03-29 13:09:03 UTC (rev 3624)
@@ -8,7 +8,6 @@
import java.util.Map;
import java.util.Set;
-import org.apache.commons.httpclient.methods.GetMethod;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.AddAxiom;
import org.semanticweb.owlapi.model.AxiomType;
@@ -47,10 +46,6 @@
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
-import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
-
-import com.clarkparsia.modularity.ModularityUtils;
-import com.clarkparsia.owlapi.modularity.locality.LocalityClass;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
public class StructureBasedRootClassFinder implements RootClassFinder, OWLClassExpressionVisitor {
Modified: trunk/examples/carcinogenesis/train.conf
===================================================================
--- trunk/examples/carcinogenesis/train.conf 2012-03-27 15:09:17 UTC (rev 3623)
+++ trunk/examples/carcinogenesis/train.conf 2012-03-29 13:09:03 UTC (rev 3624)
@@ -355,7 +355,7 @@
"kb:d335"
}
-op.type = "syncrho"
+op.type = "rho"
op.cardinalityLimit = 5
// CELOE configuration
@@ -366,7 +366,7 @@
alg.writeSearchTree = false
alg.noisePercentage = 32
alg.startClass = "http://dl-learner.org/carcinogenesis#Compound"
-alg.maxExecutionTimeInSeconds = 1800
+alg.maxExecutionTimeInSeconds = 100
//alg.maxClassDescriptionTests = 10000000
// PCELOE configuration
Modified: trunk/examples/family-benchmark/Aunt.conf
===================================================================
--- trunk/examples/family-benchmark/Aunt.conf 2012-03-27 15:09:17 UTC (rev 3623)
+++ trunk/examples/family-benchmark/Aunt.conf 2012-03-29 13:09:03 UTC (rev 3624)
@@ -17,7 +17,7 @@
h.type ="celoe_heuristic"
h.expansionPenaltyFactor = 0.02
alg.type = "celoe"
-alg.maxExecutionTimeInSeconds = 200
+alg.maxExecutionTimeInSeconds = 100
alg.terminateOnNoiseReached = true
Modified: trunk/interfaces/src/test/java/org/dllearner/test/junit/ExampleTests.java
===================================================================
--- trunk/interfaces/src/test/java/org/dllearner/test/junit/ExampleTests.java 2012-03-27 15:09:17 UTC (rev 3623)
+++ trunk/interfaces/src/test/java/org/dllearner/test/junit/ExampleTests.java 2012-03-29 13:09:03 UTC (rev 3624)
@@ -163,13 +163,13 @@
// start example
CLI start = new CLI(new File(conf));
start.init();
- start.run();
// System.out.println("algorithm: " + start.getLearningAlgorithm());
boolean isSparql = start.getKnowledgeSource() instanceof SparqlKnowledgeSource;
// boolean isSparql = false;
LearningAlgorithm algorithm = start.getLearningAlgorithm();
if((testGP || !(algorithm instanceof GP)) &&
(sparql == 0 || (sparql == 1 && isSparql) || (sparql == 2 && !isSparql) ) ) {
+ start.run();
started = true;
// start.start(false);
// test is successful if a concept was learned
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