Removed dependencies to SESAME.

Changed some examples by reducing execution time. Fixed Unit test to ignore SPARQL examples correctly.
SmartDataAnalytics · Mar 29, 2012 · 133ee3d · 133ee3d
1 parent e642b33
commit 133ee3d
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Showing 7 changed files with 17 additions and 21 deletions.
diff --git a/components-core/pom.xml b/components-core/pom.xml
@@ -106,6 +106,10 @@
 					<artifactId>xercesImpl</artifactId>
 					<groupId>xerces</groupId>
 				</exclusion>
+				<exclusion>
+					<artifactId>any23-core</artifactId>
+					<groupId>org.deri.any23</groupId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 

diff --git a/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java b/components-core/src/main/java/org/dllearner/algorithms/DisjointClassesLearner.java
@@ -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 @@ private List<EvaluatedDescription> buildEvaluatedClassDescriptions(Map<NamedClas
 		//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());

diff --git a/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java b/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
@@ -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 @@ class OWLFilter extends Filter<OntClass>{
 		@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 @@ class RDFSFilter extends Filter<OntClass>{
 		@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 @@ class RDFFilter extends Filter<OntClass>{
 		@Override
 		public boolean accept(OntClass cls) {
 			if(!cls.isAnon()){
-				return cls.getURI().startsWith(RDF.NAMESPACE);
+				return cls.getURI().startsWith(RDF.getURI());
 			}
 			return false;
 		}

diff --git a/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java b/components-core/src/main/java/org/dllearner/utilities/StructureBasedRootClassFinder.java
@@ -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 {

diff --git a/examples/carcinogenesis/train.conf b/examples/carcinogenesis/train.conf
@@ -355,7 +355,7 @@ lp.negativeExamples = {
 "kb:d335"
 }
 
-op.type = "syncrho"
+op.type = "rho"
 op.cardinalityLimit = 5
 
 // CELOE configuration
@@ -366,7 +366,7 @@ alg.searchTreeFile = "log/carcinogenesis/searchTree.log"
 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

diff --git a/examples/family-benchmark/Aunt.conf b/examples/family-benchmark/Aunt.conf
@@ -17,7 +17,7 @@ op.useCardinalityRestrictions = false
 h.type ="celoe_heuristic"
 h.expansionPenaltyFactor = 0.02
 alg.type = "celoe"
-alg.maxExecutionTimeInSeconds = 200
+alg.maxExecutionTimeInSeconds = 100
 alg.terminateOnNoiseReached = true
 
 

diff --git a/interfaces/src/test/java/org/dllearner/test/junit/ExampleTests.java b/interfaces/src/test/java/org/dllearner/test/junit/ExampleTests.java
@@ -163,13 +163,13 @@ public void testAllConfFiles() throws ComponentInitException {
 					// 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