[DL-Learner SVN] SF.net SVN: dl-learner:[3922] trunk/components-core

[<lor...@us...>]

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...
 
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