[DL-Learner SVN] SF.net SVN: dl-learner: [912] trunk/src/dl-learner/org/dllearner

[<ku...@us...>]

Revision: 912
          http://dl-learner.svn.sourceforge.net/dl-learner/?rev=912&view=rev
Author:   kurzum
Date:     2008-05-21 07:59:31 -0700 (Wed, 21 May 2008)

Log Message:
-----------
cleanup

Modified Paths:
--------------
    trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
    trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
    trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
    trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
    trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
    trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
    trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java
    trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java
    trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java
    trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
    trunk/src/dl-learner/org/dllearner/utilities/learn/LearnSparql.java

Added Paths:
-----------
    trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java
    trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
    trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java

Removed Paths:
-------------
    trunk/src/dl-learner/org/dllearner/utilities/datastructures/JenaResultSetConvenience.java

Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -82,6 +82,18 @@
 		this("cache");
 	} */
 	
+	public static Cache getPersistentCache(){
+		Cache c = new Cache("cachePersistant"); 
+		c.setFreshnessInDays(365);
+		return c;
+	}
+	
+	public static Cache getDefaultCache(){
+		Cache c = new Cache("cache"); 
+		
+		return c;
+	}
+	
 	/**
 	 * Constructor for the cache itself.
 	 * 
@@ -242,5 +254,9 @@
 			return json;
 		}
 	}
+	
+	public void setFreshnessInDays(int days){
+		freshnessSeconds = days * 24 * 60 * 60;
+	}
 
 }

Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -112,6 +112,9 @@
 		return queryString;
 	}
 	
+	/**
+	 * @return String JSON
+	 */
 	public String getResult() {
 		return json;
 	}

Modified: trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/scripts/SKOS7030.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -1,7 +1,8 @@
 package org.dllearner.scripts;
 
-import java.util.LinkedList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
 
@@ -10,222 +11,198 @@
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
+import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
+import org.dllearner.core.ComponentManager;
 import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.ReasoningService;
 import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.NamedClass;
-import org.dllearner.core.owl.Union;
 import org.dllearner.kb.sparql.Cache;
 import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertRDFS;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.learningproblems.PosNegDefinitionLP;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.reasoning.FastInstanceChecker;
 import org.dllearner.utilities.datastructures.SetManipulation;
-import org.dllearner.utilities.examples.AutomaticExampleFinderSKOSSPARQL;
-import org.dllearner.utilities.learn.LearnSparql;
-import org.dllearner.utilities.statistics.SimpleClock;
+import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL;
+import org.dllearner.utilities.examples.AutomaticPositiveExampleFinderSPARQL;
+import org.dllearner.utilities.examples.SPARQLTasks;
 
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.sparql.core.ResultBinding;
-
 public class SKOS7030 {
 
-	static Cache c;
-	static SparqlEndpoint se;
+	private static SPARQLTasks sparqlTasks;
+	
 	private static Logger logger = Logger.getRootLogger();
+    static boolean local = true;
+    static String url = "";
 	
+	//LEARNING
+	static int recursiondepth=1;
+	static boolean closeAfterRecursion=true;
+	static boolean randomizeCache=false;
+	static double noise=15;
+	static int maxExecutionTimeInSeconds = 30;
+	static int guaranteeXgoodDescriptions = 40;
 	
+	//static int limit=200;
 	
 	
-	//vars
-	static boolean useRelated = false;
-	static boolean useSuperClasses = false;
-	static boolean useParallelClasses = true;
-	static int poslimit = 10;
-	static int neglimit = 20;
 	
-	static int recursiondepth=1;
-	static boolean closeAfterRecursion=true;
-	static boolean randomizeCache=false;
 	
-	static int resultsize=20;
-	static double noise=15;
-	static int limit=200;
-	static double percentage=0.3;
 	
+	//examples
+	static int sparqlResultSize=2000;
+	static double percentOfSKOSSet=0.7;
+	static double negfactor=0.3;
+	SortedSet<String> posExamples = new TreeSet<String>();
+	SortedSet<String> fullPositiveSet = new TreeSet<String>();
+	SortedSet<String> fullminusposRest = new TreeSet<String>();
+	SortedSet<String> negExamples = new TreeSet<String>();
+	
+	
+	
+	
+	
 	/**
 	 * @param args
 	 */
 	public static void main(String[] args) {
-		init();
-		//logger.setLevel(Level.TRACE);
-		Logger.getLogger(KnowledgeSource.class).setLevel(Level.WARN);
-		//System.out.println(Logger.getLogger(SparqlQuery.class).getLevel());
-		SimpleClock sc=new SimpleClock();
+		System.out.println("Start");
+		initLogger();
+		//parameters
 		
 		
-		se = SparqlEndpoint.EndpointLOCALDBpedia();
-//		String t="\"http://dbpedia.org/class/yago/Fiction106367107\"";
-//		t="(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))";
-//		//System.out.println(t);
-//		//t="\"http://www.w3.org/2004/02/skos/core#subject\"";
-//		//conceptRewrite(t);
-//		//getSubClasses(t);
-//		
-//		AutomaticExampleFinderSKOSSPARQL ae= new AutomaticExampleFinderSKOSSPARQL( se);	
-//			try{
-//			System.out.println("oneconcept: "+t);
-//			SortedSet<String> instances = ae.queryConceptAsStringSet(conceptRewrite(t), 200);
-//			if(instances.size()>=0)System.out.println("size of instances "+instances.size());
-//			if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
-//			}catch (Exception e) {
-//				e.printStackTrace();
-//			}
-		SortedSet<String> concepts = new TreeSet<String>();
+		if(local){
+			url = "http://139.18.2.37:8890/sparql";
+			sparqlTasks = new SPARQLTasks(Cache.getPersistentCache(),SparqlEndpoint.EndpointLOCALDBpedia());
+		}else{
+			url = "http://dbpedia.openlinksw.com:8890/sparql";
+			sparqlTasks = new SPARQLTasks(Cache.getPersistentCache(),SparqlEndpoint.EndpointDBpedia());
+		}
 		
 		String prim="http://dbpedia.org/resource/Category:Prime_Ministers_of_the_United_Kingdom";
 		
 		String award=("http://dbpedia.org/resource/Category:Best_Actor_Academy_Award_winners");
 		
-		System.out.println(DBpediaSKOS(prim));
-//		double acc1=0.0;
-//		for (int i = 0; i < 5; i++) {
-//			acc1+=DBpediaSKOS(prim);
-//		}
-//		System.out.println("accprim"+(acc1/5));
-//		
-//		double acc2=0.0;
-//		for (int i = 0; i < 5; i++) {
-//			acc2+=DBpediaSKOS(award);
-//		}
-//		System.out.println("accprim"+(acc2/5));
+		SKOS7030 s= new SKOS7030();
 		
-//		DBpediaSKOS(concepts.first());
-//		DBpediaSKOS(concepts.first());
-//		concepts.remove(concepts.first());
-//		DBpediaSKOS(concepts.first());
-//		DBpediaSKOS(concepts.first());
-//		concepts.remove(concepts.first());
-//		DBpediaSKOS(concepts.first());
-//		DBpediaSKOS(concepts.first());
-		//algorithm="refinement";
-		//roles();
+		s.makeExamples(prim, percentOfSKOSSet, negfactor, sparqlResultSize);
+		//QUALITY s.posExamples
+		List<Description> conceptresults = s.learn(s.posExamples, s.negExamples);
+		logger.debug("found nr of concepts: "+conceptresults.size());
 		
-		/*System.out.println(Level.DEBUG.getClass());
-			System.out.println(Level.toLevel("INFO"));
-			System.out.println(Level.INFO);*/
-			//System.exit(0);
+		for (Description oneConcept : conceptresults) {
+			s.evaluate(oneConcept, 1000);
 			
+		}
+		
+		
+		System.out.println("Finished");
+		
+	}	
 	
+	void evaluate(Description oneConcept, int sparqlResultLimit){
+		logger.debug("oneconcept: "+oneConcept);
+		SortedSet<String> instances = sparqlTasks.retrieveInstancesForConcept(oneConcept.toKBSyntaxString(), sparqlResultLimit);
 		
-			sc.printAndSet("Finished");
-
+		System.out.println(fullminusposRest.size());
+		System.out.println(instances.size());
+		
+		SortedSet<String> coveredInRest = new TreeSet<String>(fullminusposRest);
+		coveredInRest.retainAll(instances);
+		
+		System.out.println(fullminusposRest.size());
+		System.out.println(instances.size());
+		System.out.println(coveredInRest.size());
+		
+		
+		
+		//SortedSet<String> possibleNewCandidates = new TreeSet<String>();
+		//SortedSet<String> notCoveredInTotal = new TreeSet<String>();
+		
+		
 	}
 	
 	
-
-	static double DBpediaSKOS(String concept){
-		se = SparqlEndpoint.EndpointLOCALDBpedia();
-		//se = SparqlEndpoint.EndpointDBpedia();
-		String url = "http://dbpedia.openlinksw.com:8890/sparql";
-		url = "http://139.18.2.37:8890/sparql";
+	static void DBpediaSKOS(String SKOSConcept){
 		
+		
 		//concepts.add("http://dbpedia.org/resource/Category:Grammy_Award_winners");
 		//concepts.add("EXISTS \"http://dbpedia.org/property/grammyawards\".TOP");
 		
-		SortedSet<String> posExamples = new TreeSet<String>();
-		SortedSet<String> negExamples = new TreeSet<String>();
 		
+		
 		//HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
 		//HashMap<String, String> result2 = new HashMap<String, String>();
 		//System.out.println(concepts.first());
 		//logger.setLevel(Level.TRACE);
 		
 		
-			AutomaticExampleFinderSKOSSPARQL ae= new AutomaticExampleFinderSKOSSPARQL( se);	
+		
 			
-			ae.initDBpediaSKOS(concept,percentage , useRelated, useParallelClasses);
-			posExamples = ae.getPosExamples();
-			negExamples = ae.getNegExamples();
 			
-			for (String string2 : negExamples) {
-				logger.debug("-"+string2);
-			}
+//			LearnSparql ls = new LearnSparql();
+//	
+//			//igno.add(oneConcept.replaceAll("\"", ""));
+//			
+//			List<Description> conceptresults= ls.learnDBpediaSKOS(posExamples, negExamples, url,new TreeSet<String>(),recursiondepth, closeAfterRecursion,randomizeCache,resultsize,noise);
+//			
+//			System.out.println("concepts"+conceptresults);
+//			//System.exit(0);
+//			
+//			SortedSet<ResultCompare> res=new TreeSet<ResultCompare>();
+//			for (Description oneConcept : conceptresults) {
+//				try{
+//				
+//				
+//				int i=0;
+//				int a=0;
+//				for (String oneinst : instances) {
+//					boolean inRest=false;
+//					boolean inTotal=false;
+//					for (String onerest : rest) {
+//						if(onerest.equalsIgnoreCase(oneinst))
+//							{ i++; inRest=true; break;}
+//						
+//					}
+//					if (inRest){coveredInRest.add(oneinst);};
+//					
+//					for (String onetotal : totalSKOSset) {
+//						if(onetotal.equalsIgnoreCase(oneinst))
+//						{ a++; inTotal=true; break;}
+//					}
+//					if(!inRest && !inTotal){
+//						possibleNewCandidates.add(oneinst);
+//					}
+//				}
+//				
+//				for (String onetotal : totalSKOSset) {
+//					boolean mm=false;
+//					for (String oneinst : instances) {
+//						if(onetotal.equalsIgnoreCase(oneinst)){
+//							mm=true;break;
+//						}
+//							
+//					}
+//					if(!mm)notCoveredInTotal.add(onetotal);
+//					
+//				}
+//				
+//				
+//				
+//				double accuracy= (double)i/rest.size();
+//				double accuracy2= (double)a/totalSKOSset.size();
+//				
+//				logger.debug((new ResultCompare(oneConcept.toKBSyntaxString(),instances,accuracy,accuracy2,instances.size(),
+//						coveredInRest,possibleNewCandidates,notCoveredInTotal)).toStringFull());
+//				
+//				//if(instances.size()>=0)System.out.println("size of instances "+instances.size());
+//				//if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
+//				}catch (Exception e) {e.printStackTrace();}
+//			}
 			
-			for (String string2 : posExamples) {
-				logger.debug("+"+string2);
-			}
-			SortedSet<String> totalSKOSset= ae.totalSKOSset;
-			SortedSet<String> rest= ae.rest;
-			logger.debug(totalSKOSset);
-			logger.debug(rest);
-			
-			
-			LearnSparql ls = new LearnSparql();
-	
-			//igno.add(oneConcept.replaceAll("\"", ""));
-			
-			List<Description> conceptresults= ls.learnDBpediaSKOS(posExamples, negExamples, url,new TreeSet<String>(),recursiondepth, closeAfterRecursion,randomizeCache,resultsize,noise);
-			
-			System.out.println("concepts"+conceptresults);
-			//System.exit(0);
-			logger.debug("found nr of concepts:"+conceptresults.size());
-			SortedSet<ResultCompare> res=new TreeSet<ResultCompare>();
-			for (Description oneConcept : conceptresults) {
-				try{
-				System.out.println("oneconcept: "+oneConcept);
-				String rewritten = SparqlQueryDescriptionConvertRDFS.conceptRewrite(oneConcept.toKBSyntaxString(), se, c, true);
-				SortedSet<String> instances = ae.queryConceptAsStringSet(rewritten, 200);
-				SortedSet<String> coveredInRest = new TreeSet<String>();
-				SortedSet<String> possibleNewCandidates = new TreeSet<String>();
-				SortedSet<String> notCoveredInTotal = new TreeSet<String>();
-				
-				int i=0;
-				int a=0;
-				for (String oneinst : instances) {
-					boolean inRest=false;
-					boolean inTotal=false;
-					for (String onerest : rest) {
-						if(onerest.equalsIgnoreCase(oneinst))
-							{ i++; inRest=true; break;}
-						
-					}
-					if (inRest){coveredInRest.add(oneinst);};
-					
-					for (String onetotal : totalSKOSset) {
-						if(onetotal.equalsIgnoreCase(oneinst))
-						{ a++; inTotal=true; break;}
-					}
-					if(!inRest && !inTotal){
-						possibleNewCandidates.add(oneinst);
-					}
-				}
-				
-				for (String onetotal : totalSKOSset) {
-					boolean mm=false;
-					for (String oneinst : instances) {
-						if(onetotal.equalsIgnoreCase(oneinst)){
-							mm=true;break;
-						}
-							
-					}
-					if(!mm)notCoveredInTotal.add(onetotal);
-					
-				}
-				
-				
-				
-				double accuracy= (double)i/rest.size();
-				double accuracy2= (double)a/totalSKOSset.size();
-				
-				logger.debug((new ResultCompare(oneConcept.toKBSyntaxString(),instances,accuracy,accuracy2,instances.size(),
-						coveredInRest,possibleNewCandidates,notCoveredInTotal)).toStringFull());
-				
-				//if(instances.size()>=0)System.out.println("size of instances "+instances.size());
-				//if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
-				}catch (Exception e) {e.printStackTrace();}
-			}
-			
 //			System.out.println(res.last());
 //			res.remove(res.last());
 //			System.out.println(res.last());
@@ -250,7 +227,7 @@
 //				
 //			}
 //			
-			return 0.0;
+//			return 0.0;
 			
 			
 			//System.out.println("AAAAAAAA");
@@ -268,7 +245,7 @@
 
 	
 
-	public static void init() {
+	public static void initLogger() {
 		
 		SimpleLayout layout = new SimpleLayout();
 		// create logger (a simple logger which outputs
@@ -283,12 +260,11 @@
 		logger.addAppender(consoleAppender);
 		logger.addAppender(fileAppender);
 		logger.setLevel(Level.DEBUG);
-		c = new Cache("cachetemp");
-		
-
+		Logger.getLogger(KnowledgeSource.class).setLevel(Level.WARN);
+	
 	}
 	
-	public static SortedSet<String> selectDBpediaConcepts(int number){
+	/*public static SortedSet<String> selectDBpediaConcepts(int number){
 		String query = "SELECT DISTINCT ?concept WHERE { \n" + 
 		"[] a ?concept .FILTER (regex(str(?concept),'yago'))" +
 		" \n}  \n"; //LIMIT "+number+"
@@ -298,8 +274,181 @@
 		ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
 		JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
 		return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+	}*/
+	
+	public void makeExamples(String SKOSConcept, double percentOfSKOSSet , double negfactor, int sparqlResultSize){
+		
+		//POSITIVES
+		AutomaticPositiveExampleFinderSPARQL apos = new AutomaticPositiveExampleFinderSPARQL(sparqlTasks);
+		apos.makePositiveExamplesFromSKOSConcept(SKOSConcept);
+		fullPositiveSet =  apos.getPosExamples();
+		
+		int poslimit=(int)Math.round(percentOfSKOSSet*fullPositiveSet.size());
+		int neglimit=(int)Math.round(poslimit*negfactor);
+		
+		this.posExamples =  SetManipulation.fuzzyShrink(fullPositiveSet,poslimit);
+		
+		
+		
+		//NEGATIVES
+		
+		AutomaticNegativeExampleFinderSPARQL aneg = new AutomaticNegativeExampleFinderSPARQL(fullPositiveSet,sparqlTasks);
+		
+		aneg.makeNegativeExamplesFromParallelClasses(posExamples, sparqlResultSize);
+		SortedSet<String> negativeSet =  aneg.getNegativeExamples(neglimit);
+		
+		logger.debug("POSITIVE EXAMPLES");
+		for (String pos : posExamples) {
+			logger.debug("+"+pos);
+		}
+	
+		logger.debug("NEGATIVE EXAMPLES");
+		for (String negs : negativeSet) {
+			logger.debug("-"+negs);
+		}
+	
+		
+		
+		fullminusposRest = fullPositiveSet;
+		fullminusposRest.removeAll(posExamples);
+		
+		
+		logger.debug(fullPositiveSet);
+		logger.debug(fullminusposRest);
 	}
 	
+	public List<Description> learn(SortedSet<String> posExamples, SortedSet<String> negExamples){
+		
+		SortedSet<String> instances = new TreeSet<String>();
+		instances.addAll(posExamples);
+		instances.addAll(negExamples);
+		
+		
 	
+		ComponentManager cm = ComponentManager.getInstance();
+		LearningAlgorithm la = null;
+		ReasoningService rs = null;
+		LearningProblem lp = null; 
+		SparqlKnowledgeSource ks =null;
+		try {
+		Set<KnowledgeSource> sources = new HashSet<KnowledgeSource>();
+		ks = cm.knowledgeSource(SparqlKnowledgeSource.class);
+		ReasonerComponent r = new FastInstanceChecker(sources);
+		rs = new ReasoningService(r); 
+		//System.out.println("satisfy: "+rs.isSatisfiable());
+		lp = new PosNegDefinitionLP(rs);	
+		((PosNegLP) lp).setPositiveExamples(SetManipulation.stringToInd(posExamples));
+		((PosNegLP) lp).setNegativeExamples(SetManipulation.stringToInd(negExamples));
+		
+		la = cm.learningAlgorithm(ExampleBasedROLComponent.class, lp, rs);
+
+		logger.debug("start learning");
+		
+		
+		//KNOWLEDGESOURCE
+		cm.applyConfigEntry(ks, "instances",instances);
+		cm.applyConfigEntry(ks, "url",url);
+		cm.applyConfigEntry(ks, "recursionDepth",recursiondepth);
+		cm.applyConfigEntry(ks, "closeAfterRecursion",closeAfterRecursion);
+		cm.applyConfigEntry(ks, "predefinedFilter","YAGO");
+		if(local)
+			cm.applyConfigEntry(ks, "predefinedEndpoint","LOCALDBPEDIA");
+		else {
+			cm.applyConfigEntry(ks, "predefinedEndpoint","DBPEDIA");
+		}
+		if(randomizeCache)
+			cm.applyConfigEntry(ks, "cacheDir","cache/"+System.currentTimeMillis()+"");
+		else {cm.applyConfigEntry(ks, "cacheDir",Cache.getDefaultCache());}
+		
+		//LEARNINGALGORITHM
+		cm.applyConfigEntry(la,"useAllConstructor",false);
+		cm.applyConfigEntry(la,"useExistsConstructor",true);
+		cm.applyConfigEntry(la,"useCardinalityRestrictions",false);
+		cm.applyConfigEntry(la,"useNegation",false);
+		cm.applyConfigEntry(la,"minExecutionTimeInSeconds",0);
+		cm.applyConfigEntry(la,"maxExecutionTimeInSeconds",maxExecutionTimeInSeconds);
+		cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",guaranteeXgoodDescriptions);
+		cm.applyConfigEntry(la,"writeSearchTree",false);
+		cm.applyConfigEntry(la,"searchTreeFile","log/SKOS.txt");
+		cm.applyConfigEntry(la,"replaceSearchTree",true);
+		cm.applyConfigEntry(la,"noisePercentage",noise);
+		//cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",999999);
+		cm.applyConfigEntry(la,"logLevel","TRACE");
+		/*if(ignoredConcepts.size()>0)
+			cm.applyConfigEntry(la,"ignoredConcepts",ignoredConcepts);
+		*/
+		
+		ks.init();
+		sources.add(ks);
+		r.init();
+		lp.init();
+		la.init();	
+		
+		
+		la.start();
+		//Statistics.addTimeCollecting(sc.getTime());
+		//Statistics.addTimeLearning(sc.getTime());
+		
+		
+		return la.getGoodSolutions();
+		
+		}catch (Exception e) {e.printStackTrace();}
+		return null;
+		
+	}
+
 	
+//	String t="\"http://dbpedia.org/class/yago/Fiction106367107\"";
+//	t="(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))";
+//	//System.out.println(t);
+//	//t="\"http://www.w3.org/2004/02/skos/core#subject\"";
+//	//conceptRewrite(t);
+//	//getSubClasses(t);
+//	
+//	AutomaticExampleFinderSKOSSPARQL ae= new AutomaticExampleFinderSKOSSPARQL( se);	
+//		try{
+//		System.out.println("oneconcept: "+t);
+//		SortedSet<String> instances = ae.queryConceptAsStringSet(conceptRewrite(t), 200);
+//		if(instances.size()>=0)System.out.println("size of instances "+instances.size());
+//		if(instances.size()>=0 && instances.size()<100) System.out.println("instances"+instances);
+//		}catch (Exception e) {
+//			e.printStackTrace();
+//		}
+	//SortedSet<String> concepts = new TreeSet<String>();
+	
+	
+	
+	//System.out.println(DBpediaSKOS(prim));
+//	double acc1=0.0;
+//	for (int i = 0; i < 5; i++) {
+//		acc1+=DBpediaSKOS(prim);
+//	}
+//	System.out.println("accprim"+(acc1/5));
+//	
+//	double acc2=0.0;
+//	for (int i = 0; i < 5; i++) {
+//		acc2+=DBpediaSKOS(award);
+//	}
+//	System.out.println("accprim"+(acc2/5));
+	
+//	DBpediaSKOS(concepts.first());
+//	DBpediaSKOS(concepts.first());
+//	concepts.remove(concepts.first());
+//	DBpediaSKOS(concepts.first());
+//	DBpediaSKOS(concepts.first());
+//	concepts.remove(concepts.first());
+//	DBpediaSKOS(concepts.first());
+//	DBpediaSKOS(concepts.first());
+	//algorithm="refinement";
+	//roles();
+	
+	/*System.out.println(Level.DEBUG.getClass());
+		System.out.println(Level.toLevel("INFO"));
+		System.out.println(Level.INFO);*/
+		//System.exit(0);
+		
+
+	
+	
+	
 }

Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLExtractionEvaluation.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -14,8 +14,6 @@
 import org.dllearner.kb.sparql.Cache;
 import org.dllearner.kb.sparql.SparqlEndpoint;
 import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
 import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQLold;
 import org.dllearner.utilities.learn.LearnSparql;
 import org.dllearner.utilities.statistics.SimpleClock;
@@ -107,7 +105,7 @@
 			System.out.println(oneConcept);
 			AutomaticExampleFinderSPARQLold ae= new AutomaticExampleFinderSPARQLold( se);	
 			
-			ae.initDBpedia(oneConcept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
+			//ae.initDBpedia(oneConcept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
 			
 			posExamples = ae.getPosExamples();
 			negExamples = ae.getNegExamples();
@@ -183,6 +181,7 @@
 
 	}
 	
+	//FIXME
 	public static SortedSet<String> selectDBpediaConcepts(int number){
 		String query = "SELECT DISTINCT ?concept WHERE { \n" + 
 		"[] a ?concept .FILTER (regex(str(?concept),'yago'))" +
@@ -190,8 +189,9 @@
 
 		String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
 		ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
-		JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
-		return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+		//JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+		//return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+		return null;
 	}
 	
 	public static  SortedSet<String> initConcepts(){

Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -13,9 +13,6 @@
 import org.dllearner.kb.sparql.SparqlEndpoint;
 import org.dllearner.kb.sparql.SparqlKnowledgeSource;
 import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
-import org.dllearner.utilities.examples.AutomaticExampleFinderRolesSPARQL;
 import org.dllearner.utilities.examples.AutomaticExampleFinderSPARQLold;
 import org.dllearner.utilities.learn.ConfWriter;
 import org.dllearner.utilities.learn.LearnSparql;
@@ -114,12 +111,12 @@
 		//HashMap<String, String> result2 = new HashMap<String, String>();
 		//System.out.println(concepts.first());
 		//logger.setLevel(Level.TRACE);
-		AutomaticExampleFinderRolesSPARQL ae= new AutomaticExampleFinderRolesSPARQL( se);
+		//AutomaticExampleFinderRolesSPARQL ae= new AutomaticExampleFinderRolesSPARQL( se);
 		
-		ae.initDomainRange(roles.first(), poslimit, neglimit);
+		//ae.initDomainRange(roles.first(), poslimit, neglimit);
 	
-		posExamples = ae.getPosExamples();
-		negExamples = ae.getNegExamples();
+		//posExamples = ae.getPosExamples();
+		//negExamples = ae.getNegExamples();
 		
 		System.out.println(posExamples);
 		System.out.println(negExamples);
@@ -192,7 +189,7 @@
 			
 			poslimit=10;
 			neglimit=10;
-			ae.initDBpedia(concept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
+			//ae.initDBpedia(concept, useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
 			posExamples = ae.getPosExamples();
 			negExamples = ae.getNegExamples();
 		
@@ -286,8 +283,9 @@
 
 		String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
 		ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
-		JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
-		return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+		//JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+		//return SetManipulation.fuzzyShrink(rsc.getStringListForVariable("concept"),number);
+		return null;
 	}
 	
 	

Modified: trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -11,12 +11,9 @@
 import org.apache.log4j.SimpleLayout;
 import org.dllearner.kb.sparql.SparqlEndpoint;
 import org.dllearner.kb.sparql.SparqlKnowledgeSource;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
+import org.dllearner.utilities.examples.SPARQLTasks;
 import org.dllearner.utilities.statistics.SimpleClock;
 
-import com.hp.hpl.jena.query.ResultSet;
-
 public class SparqlEndpointTest {
 	private static Logger logger = Logger.getRootLogger();
 	static Set<String> working = new HashSet<String>();
@@ -65,22 +62,15 @@
 		SimpleClock sc =  new SimpleClock(); 
 		try{
 		
-		String query ="" +
+		String SPARQLquery ="" +
 			"SELECT DISTINCT ?c " +
 			"WHERE {[] a ?c }" +
 			"LIMIT 100";
 		
-		query ="SELECT DISTINCT ?c WHERE {[] a ?c }LIMIT 100";
-		
-		SparqlQuery s = new SparqlQuery(query,se);
+		SPARQLquery ="SELECT DISTINCT ?c WHERE {[] a ?c }LIMIT 100";
+		int i = new SPARQLTasks(se).queryAsSet(SPARQLquery, "c").size();
 	
-		s.send();
-		String result = s.getResult();
-		ResultSet rs = SparqlQuery.JSONtoResultSet(result);
 		
-		JenaResultSetConvenience jsr = new JenaResultSetConvenience(rs);
-		int i = jsr.getStringListForVariable("c").size();
-		
 		working.add(sc.getAndSet("endpoint working: "+se.getURL()+" ("+((i==100)?"more than 100 concepts":"about "+i+" concepts")+" )"));
 		}catch (Exception e) {notworking.add(sc.getAndSet("endpoint NOT working: "+se.getURL()));}
 	}

Added: trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java	                        (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/JamonTimeLogger.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -0,0 +1,9 @@
+package org.dllearner.utilities;
+
+/**
+ * provides convenience functions for timelogs
+ *
+ */
+public class JamonTimeLogger {
+
+}

Deleted: trunk/src/dl-learner/org/dllearner/utilities/datastructures/JenaResultSetConvenience.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/datastructures/JenaResultSetConvenience.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/datastructures/JenaResultSetConvenience.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -1,37 +0,0 @@
-package org.dllearner.utilities.datastructures;
-
-import java.util.List;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.sparql.core.ResultBinding;
-
-public class JenaResultSetConvenience {
-	ResultSet rs;
-
-	public JenaResultSetConvenience(ResultSet rs) {
-		super();
-		this.rs = rs;
-	}
-	
-	@SuppressWarnings("unchecked")
-	public SortedSet<String> getStringListForVariable(String var){
-		SortedSet<String> result = new TreeSet<String>();
-		
-		//String s=ResultSetFormatter.asXMLString(this.rs);
-		List<ResultBinding> l =  ResultSetFormatter.toList(this.rs);
-		
-		for (ResultBinding resultBinding : l) {
-				
-			result.add(resultBinding.get(var).toString());
-		
-		}
-		
-		return result;
-		
-	}
-	
-	
-}

Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderRolesSPARQL.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -1,18 +1,12 @@
 package org.dllearner.utilities.examples;
 
 import java.util.SortedSet;
-import java.util.TreeSet;
 
 import org.apache.log4j.Logger;
 import org.dllearner.core.ComponentManager;
 import org.dllearner.kb.sparql.Cache;
 import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
-
-import com.hp.hpl.jena.query.ResultSet;
-
+// keep this class it still needs to be worked in
 public class AutomaticExampleFinderRolesSPARQL {
 
 	private static Logger logger = Logger
@@ -24,7 +18,7 @@
 	private SortedSet<String> negExamples;
 	private int roleLimit=1000;
 	
-	
+	/*
 	public AutomaticExampleFinderRolesSPARQL(SparqlEndpoint se){
 		this.c=new Cache("cachetemp");
 		this.se=se;
@@ -119,7 +113,7 @@
 	
 	
 	
+	*/
 	
 	
-	
 }

Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSKOSSPARQL.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -7,13 +7,8 @@
 import org.dllearner.core.ComponentManager;
 import org.dllearner.kb.sparql.Cache;
 import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
 import org.dllearner.utilities.datastructures.SetManipulation;
 
-import com.hp.hpl.jena.query.ResultSet;
-
 public class AutomaticExampleFinderSKOSSPARQL {
 
 	private static Logger logger = Logger
@@ -35,8 +30,9 @@
 		negExamples = new TreeSet<String>();
 	}
 	
+	@Deprecated
 	public void initDBpediaSKOS(String concept, double percent, boolean useRelated,boolean useParallelClasses) { 
-		dbpediaMakePositiveExamplesFromConcept( concept);
+		//dbpediaMakePositiveExamplesFromConcept( concept);
 		SortedSet<String> keepForClean = new TreeSet<String>();
 		keepForClean.addAll(this.posExamples);
 		totalSKOSset.addAll(this.posExamples);
@@ -55,12 +51,12 @@
 		logger.debug("rest: "+rest.size());
 		
 		if(useRelated) {
-			dbpediaMakeNegativeExamplesFromRelatedInstances(this.posExamples);
+			//dbpediaMakeNegativeExamplesFromRelatedInstances(this.posExamples);
 		}
 		
 		if(useParallelClasses) {
 			int limit = this.posExamples.size();
-			 makeNegativeExamplesFromClassesOfInstances(limit);
+			 //makeNegativeExamplesFromClassesOfInstances(limit);
 		}
 		//clean
 		negExamples.removeAll(keepForClean);
@@ -98,16 +94,8 @@
 	
 	
 	
-	public SortedSet<String> dbpediaGetPosOnly(String concept, int limit){
-		dbpediaMakePositiveExamplesFromConcept( concept);
-		return SetManipulation.fuzzyShrink(this.posExamples, limit);
-	}
 	
-	public SortedSet<String> getPosOnly(String concept, int limit){
-		makePositiveExamplesFromConcept( concept);
-		return SetManipulation.fuzzyShrink(this.posExamples, limit);
-	}
-	
+	/*
 	private void dbpediaMakePositiveExamplesFromConcept(String concept){
 		logger.debug("making Positive Examples from Concept: "+concept);
 		if(concept.contains("http://dbpedia.org/resource/Category:")) {
@@ -118,14 +106,15 @@
 				.getStringListForVariable("subject");
 		}
 		logger.debug("pos Example size: "+posExamples.size());
-	}
+	}*/
 	
+	/*
 	private void makePositiveExamplesFromConcept(String concept){
 		logger.debug("making Positive Examples from Concept: "+concept);	
 		this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
 				.getStringListForVariable("subject");
 		logger.debug("   pos Example size: "+posExamples.size());
-	}
+	}*/
 	
 	
 	
@@ -145,60 +134,18 @@
 	
 	
 	
-	private void dbpediaMakeNegativeExamplesFromRelatedInstances(SortedSet<String> subject) {
-		logger.debug("making examples from related instances");
-		for (String string : subject) {
-			dbpediaMakeNegativeExamplesFromRelatedInstances(string);
-		}
-		logger.debug("  negExample size: "+negExamples.size());
-	}
 	
-	private void makeNegativeExamplesFromRelatedInstances(SortedSet<String> subject, String namespace) {
-		logger.debug("making examples from related instances");
-		for (String string : subject) {
-			makeNegativeExamplesFromRelatedInstances(string,namespace);
-		}
-		logger.debug("  negExample size: "+negExamples.size());
-	}
 	
-	
 	/**
 	 * 
 	 * @param subject
 	 * @return
 	 */
-	private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
-		// SortedSet<String> result = new TreeSet<String>();
 
-		String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
-				+ "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
-				+ "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
-				+ "}";
-		
-		String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
-		ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
-		JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
-		this.negExamples.addAll(rsc.getStringListForVariable("o"));
-		
-		
-	}
 	
-	private void makeNegativeExamplesFromRelatedInstances(String subject, String namespace) {
-		// SortedSet<String> result = new TreeSet<String>();
 
-		String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
-				+ "FILTER (REGEX(str(?o), '"+namespace+"')).\n"
-				+ "}";
-		
-		String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
-		ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
-		JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
-		this.negExamples.addAll(rsc.getStringListForVariable("o"));
-		
-		
-	}
 	
-	
+	/*
 	private void makeNegativeExamplesFromSuperClasses(String concept) {
 		
 		SortedSet<String> superClasses = new TreeSet<String>();
@@ -213,109 +160,14 @@
 			this.negExamples.addAll(rsc.getStringListForVariable("subject"));
 		}
 		logger.debug("   neg Example size: "+negExamples.size());
-	}
+	}*/
 	
 	
 	
-	private void makeNegativeExamplesFromClassesOfInstances(int limit) {
-		logger.debug("making neg Examples from parallel classes");
-		SortedSet<String> classes = new TreeSet<String>();
-		//superClasses.add(concept.replace("\"", ""));
-		//logger.debug("before"+superClasses);
-		//superClasses = dbpediaGetSuperClasses( superClasses, 4);
-		//logger.debug("getting negExamples from "+superClasses.size()+" superclasses");
-		JenaResultSetConvenience rsc;
-		ResultSet rs=null;
-		for (String instance : posExamples) {
-			//System.out.println(instance);
-			rs = getClassesForInstance(instance);
-			//System.out.println(ResultSetFormatter.asXMLString(rs));
-			rsc = new JenaResultSetConvenience(rs);
-			classes.addAll(rsc.getStringListForVariable("subject"));
-			//System.out.println(classes);
-		}
-		logger.debug("getting negExamples from "+classes.size()+" parallel classes");
-		for (String oneClass : classes) {
-			logger.debug(oneClass);
-			rsc = new JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit));
-			this.negExamples.addAll(rsc.getStringListForVariable("subject"));
-		}
-		logger.debug("neg Example size: "+negExamples.size());
-		
-	}
-
-	private SortedSet<String> getSuperClasses(SortedSet<String> superClasses, int depth) {
-		SortedSet<String> ret = new TreeSet<String>();
-		SortedSet<String> tmpset = new TreeSet<String>();
-		ret.addAll(superClasses);
-		//logger.debug(superClasses);
-		JenaResultSetConvenience rsc;
-		
-		String query = "";
-		for (; depth != 0 ; depth--) {
-			for (String oneSuperClass : superClasses) {
-				
-				//tmp = oneSuperClass.replace("\"", "");
-				query = "SELECT * WHERE { \n" + "<" + oneSuperClass  + "> " 
-					+ "<http://www.w3.org/2000/01/rdf-schema#subClassOf>  ?superclass. \n"
-					+ "}";
-				
-				String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
-				ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
-				rsc = new JenaResultSetConvenience(rs);
-				tmpset.addAll(rsc.getStringListForVariable("superclass"));
-				
-			}
-			ret.addAll(tmpset);
-			//logger.debug(ret);
-			superClasses.clear();
-			superClasses.addAll(tmpset);
-			tmpset.clear();
-		}
-		//logger.debug(concept);
-		//logger.debug(query);
-		return 	ret;
-	}
 	
-	
-	
-	public  ResultSet queryConcept(String concept,int limit) {
-		ResultSet rs = null;
-		try {
-			String query = SparqlQueryDescriptionConvertVisitor
-					.getSparqlQuery(concept,limit);
-			
-			SparqlQuery sq = new SparqlQuery(query, se);
-			String JSON = c.executeSparqlQuery(sq);
-			//System.out.println("JSON:\n"+JSON);
-			rs = SparqlQuery.JSONtoResultSet(JSON);
 
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-
-		return rs;
-	}
 	
-	public  SortedSet<String> queryConceptAsStringSet(String concept,int limit) {
-		ResultSet rs = null;
-		try {
-			String query = SparqlQueryDescriptionConvertVisitor
-					.getSparqlQuery(concept,limit);
-			
-			SparqlQuery sq = new SparqlQuery(query, se);
-			//System.out.println(query);
-			String JSON = c.executeSparqlQuery(sq);
-			//System.out.println("JSON:\n"+JSON);
-			rs = SparqlQuery.JSONtoResultSet(JSON);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-		return new JenaResultSetConvenience(rs).getStringListForVariable("subject");
-		
-	}
-	
+	/*
 	public  ResultSet dbpediaQuerySKOSConcept(String SKOSconcept,int limit) {
 		if(limit==0)limit=99999;
 		//
@@ -337,31 +189,10 @@
 		}
 
 		return rs;
-	}
+	}*/
 	
-	public  ResultSet getClassesForInstance(String instance) {
-		ResultSet rs = null;
-		try {
-			
-			String query = "SELECT ?subject WHERE { \n " + 
-			"<" + instance  + ">"+
-			" a " + 
-			"?subject " +
-			"\n" +
-			"} LIMIT 200";
-			SparqlQuery sq = new SparqlQuery(query, se);
-			//System.out.println(query);
-			String JSON = c.executeSparqlQuery(sq);
-			//System.out.println(JSON);
-			rs = SparqlQuery.JSONtoResultSet(JSON);
+	
 
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-
-		return rs;
-	}
-
 	public SortedSet<String> getPosExamples() {
 		return posExamples;
 	}

Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticExampleFinderSPARQLold.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -7,13 +7,7 @@
 import org.dllearner.core.ComponentManager;
 import org.dllearner.kb.sparql.Cache;
 import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
-import org.dllearner.utilities.datastructures.JenaResultSetConvenience;
-import org.dllearner.utilities.datastructures.SetManipulation;
 
-import com.hp.hpl.jena.query.ResultSet;
-
 public class AutomaticExampleFinderSPARQLold {
 
 	private static Logger logger = Logger
@@ -33,7 +27,7 @@
 		posExamples = new TreeSet<String>();
 		negExamples = new TreeSet<String>();
 	}
-	
+	/*
 	public void initDBpedia(String concept, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) { 
 		dbpediaMakePositiveExamplesFromConcept( concept);
 		SortedSet<String> keepForClean = new TreeSet<String>();
@@ -62,43 +56,21 @@
 		logger.debug("Finished examples for concept: "+concept);
 	}
 	
-	public void init(String concept, String namespace, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) { 
-		makePositiveExamplesFromConcept( concept);
-		SortedSet<String> keepForClean = new TreeSet<String>();
-		keepForClean.addAll(this.posExamples);
-		this.posExamples = SetManipulation.fuzzyShrink(this.posExamples, poslimit);
-		logger.trace("shrinking: pos Example size: "+posExamples.size());
-		
-		if(useRelated) {
-			makeNegativeExamplesFromRelatedInstances(this.posExamples,namespace);
-		}
-		if(useSuperclasses) {
-			 makeNegativeExamplesFromSuperClasses(concept);
-		}
-		if(useParallelClasses) {
-			makeNegativeExamplesFromClassesOfInstances();
-		}
-		//clean
-		negExamples.removeAll(keepForClean);
-		logger.trace("neg Example size after cleaning: "+negExamples.size());
-		this.negExamples = SetManipulation.fuzzyShrink(negExamples, neglimit);
-		logger.debug("pos Example size after shrinking: "+posExamples.size());
-		logger.debug("neg Example size after shrinking: "+negExamples.size());
-		logger.debug("Finished examples for concept: "+concept);
-	}
+	*/
 	
 	
-	
+	/*
 	public SortedSet<String> dbpediaGetPosOnly(String concept, int limit){
 		dbpediaMakePositiveExamplesFromConcept( concept);
 		return SetManipulation.fuzzyShrink(this.posExamples, limit);
-	}
+	}*/
 	
-	public SortedSet<String> getPosOnly(String concept, int limit){
+	/*public SortedSet<String> getPosOnly(String concept, int limit){
 		makePositiveExamplesFromConcept( concept);
 		return SetManipulation.fuzzyShrink(this.posExamples, limit);
-	}
+	}*/
 	
+	/*
 	private void dbpediaMakePositiveExamplesFromConcept(String concept){
 		logger.debug("making Positive Examples from Concept: "+concept);
 		if(concept.contains("http://dbpedia.org/resource/Category:")) {
@@ -110,16 +82,12 @@
 		}
 		logger.debug("   pos Example size: "+posExamples.size());
 	}
+	*/
 	
-	private void makePositiveExamplesFromConcept(String concept){
-		logger.debug("making Positive Examples from Concept: "+concept);	
-		this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
-				.getStringListForVariable("subject");
-		logger.debug("   pos Example size: "+posExamples.size());
-	}
 	
 	
 	
+	
 	/*private void makePositiveExamplesFromConcept(String concept){
 		logger.debug("making Positive Examples from Concept: "+concept);
 		if(concept.contains("http://dbpedia.org/resource/Category:")) {
@@ -136,29 +104,11 @@
 	
 	
 	
-	private void dbpediaMakeNegativeExamplesFromRelatedInstances(SortedSet<String> subject) {
-		logger.debug("making examples from related instances");
-		for (String string : subject) {
-			dbpediaMakeNegativeExamplesFromRelatedInstances(string);
-		}
-		logger.debug("  negExample size: "+negExamples.size());
-	}
 	
-	private void makeNegativeExamplesFromRelatedInstances(SortedSet<String> subject, String namespace) {
-		logger.debug("making examples from related instances");
-		for (String string : subject) {
-			makeNegativeExamplesFromRelatedInstances(string,namespace);
-		}
-		logger.debug("  negExample size: "+negExamples.size());
-	}
 	
 	
-	/**
-	 * 
-	 * @param subject
-	 * @return
-	 */
-	private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
+	
+	/*private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
 		// SortedSet<String> result = new TreeSet<String>();
 
 		String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
@@ -172,8 +122,8 @@
 		this.negExamples.addAll(rsc.getStringListForVariable("o"));
 		
 		
-	}
-	
+	}*/
+	/*
 	private void makeNegativeExamplesFromRelatedInstances(String subject, String namespace) {
 		// SortedSet<String> result = new TreeSet<String>();
 
@@ -187,27 +137,13 @@
 		this.negExamples.addAll(rsc.getStringListForVariable("o"));
 		
 		
-	}
+	}*/
 	
 	
-	private void makeNegativeExamplesFromSuperClasses(String concept) {
-		
-		SortedSet<String> superClasses = new TreeSet<String>();
-		superClasses.add(concept.replace("\"", ""));
-		//logger.debug("before"+superClasses);
-		superClasses = getSuperClasses( superClasses, 4);
-		logger.debug("making neg Examples from "+superClasses.size()+" superclasses");
-		JenaResultSetConvenience rsc;
-		for (String oneSuperClass : superClasses) {
-			logger.debug(oneSuperClass);
-			rsc = new JenaResultSetConvenience(queryConcept("\""+oneSuperClass+"\"", limit));
-			this.negExamples.addAll(rsc.getStringListForVariable("subject"));
-		}
-		logger.debug("   neg Example size: "+negExamples.size());
-	}
 	
 	
 	
+	/*
 	private void makeNegativeExamplesFromClassesOfInstances() {
 		logger.debug("making neg Examples from parallel classes");
 		SortedSet<String> classes = new TreeSet<String>();
@@ -233,107 +169,13 @@
 		}
 		logger.debug("neg Example size: "+negExamples.size());
 		
-	}
+	}*/
 
-	private SortedSet<String> getSuperClasses(SortedSet<String> superClasses, int depth) {
-		SortedSet<String> ret = new TreeSet<String>();
-		SortedSet<String> tmpset = new TreeSet<String>();
-		ret.addAll(superClasses);
-		//logger.debug(superClasses);
-		JenaResultSetConvenience rsc;
-		
-		String query = "";
-		for (; depth != 0 ; depth--) {
-			for (String oneSuperClass : superClasses) {
-				
-				//tmp = oneSuperClass.replace("\"", "");
-				query = "SELECT * WHERE { \n" + "<" + oneSuperClass  + "> " 
-					+ "<http://www.w3.org/2000/01/rdf-schema#subClassOf>  ?superclass. \n"
-					+ "}";
-				
-				String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
-				ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
-				rsc = new JenaResultSetConvenience(rs);
-				tmpset.addAll(rsc.getStringListForVariable("superclass"));
-				
-			}
-			ret.addAll(tmpset);
-			//logger.debug(ret);
-			superClasses.clear();
-			superClasses.addAll(tmpset);
-			tmpset.clear();
-		}
-		//logger.debug(concept);
-		//logger.debug(query);
-		return 	ret;
-	}
 	
 	
 	
-	public  ResultSet queryConcept(String concept,int limit) {
-		ResultSet rs = null;
-		try {
-			String query = SparqlQueryDescriptionConvertVisitor
-					.getSparqlQuery(concept,limit);
-			
-			SparqlQuery sq = new SparqlQuery(query, se);
-			String JSON = c.executeSparqlQuery(sq);
-			//System.out.println("JSON:\n"+JSON);
-			rs = SparqlQuery.JSONtoResultSet(JSON);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-
-		return rs;
-	}
 	
-	public  ResultSet dbpediaQuerySKOSConcept(String SKOSconcept,int limit) {
-		if(limit==0)limit=99999;
-		//
-		ResultSet rs = null;
-		try {
-			
-			String query = "SELECT * WHERE { \n " + 
-			"?subject " +
-			"<http://www.w3.org/2004/02/skos/core#subject> " + 
-			"<" + SKOSconcept  + "> \n" +
-			"} LIMIT "+limit;
-			SparqlQuery sq = new SparqlQuery(query, se);
-			String JSON = c.executeSparqlQuery(sq);
-			//System.out.println(JSON);
-			rs = SparqlQuery.JSONtoResultSet(JSON);
 
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-
-		return rs;
-	}
-	
-	public  ResultSet getClassesForInstance(String instance) {
-		ResultSet rs = null;
-		try {
-			
-			String query = "SELECT ?subject WHERE { \n " + 
-			"<" + instance  + ">"+
-			" a " + 
-			"?subject " +
-			"\n" +
-			"} LIMIT "+limit;
-			SparqlQuery sq = new SparqlQuery(query, se);
-			//System.out.println(query);
-			String JSON = c.executeSparqlQuery(sq);
-			//System.out.println(JSON);
-			rs = SparqlQuery.JSONtoResultSet(JSON);
-
-		} catch (Exception e) {
-			e.printStackTrace();
-		}
-
-		return rs;
-	}
-
 	public SortedSet<String> getPosExamples() {
 		return posExamples;
 	}

Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java	2008-05-21 13:53:46 UTC (rev 911)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -1,21 +1,145 @@
 package org.dllearner.utilities.examples;
 
 import java.util.SortedSet;
+import java.util.TreeSet;
 
+import org.apache.log4j.Logger;
+import org.dllearner.core.ComponentManager;
 import org.dllearner.kb.sparql.Cache;
 import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.utilities.datastructures.SetManipulation;
 
+import com.hp.hpl.jena.query.ResultSet;
+
 public class AutomaticNegativeExampleFinderSPARQL {
 
+	// CHECK
+	private static Logger logger = Logger.getLogger(ComponentManager.class);
+
+	private SPARQLTasks sparqltasks;
+
+	private SortedSet<String> fullPositiveSet;
 	
-	private Cache c;
-	private SparqlEndpoint se;
-	private SortedSet<String> posExamples;
-	private SortedSet<String> negExamples;
+	//static boolean useRelated = false;
+	private SortedSet<String> fromRelated;
+	//static boolean useSuperClasses = false;
+	private SortedSet<String> fromSuperclasses;
+	//static boolean useParallelClasses = true;
+	private SortedSet<String> fromParallelClasses;
 	
-	static boolean useRelated = false;
-	static boolean useSuperClasses = false;
-	static boolean useParallelClasses = true;
 	static int poslimit = 10;
 	static int neglimit = 20;
+
+	// CHECK all vars needed
+	public AutomaticNegativeExampleFinderSPARQL(
+			SortedSet<String> fullPositiveSet,
+			SPARQLTasks st) {
+		super();
+		this.fromParallelClasses = new TreeSet<String>();
+		this.fromRelated = new TreeSet<String>();
+		this.fromSuperclasses = new TreeSet<String>();
+		
+		this.fullPositiveSet = fullPositiveSet;
+		this.sparqltasks = st;
+
+	}
+	
+	
+
+	public SortedSet<String> getNegativeExamples(int neglimit ) {
+
+		SortedSet<String> negatives = new TreeSet<String>();
+		negatives.addAll(fromParallelClasses);
+		negatives.addAll(fromRelated);
+		negatives.addAll(fromSuperclasses);
+		logger.debug("neg Example size before shrinking: " + negatives.size());
+		negatives = SetManipulation.fuzzyShrink(negatives,neglimit);
+		logger.debug("neg Example size after shrinking: " + negatives.size());
+		return negatives;
+	}
+
+	// CHECK namespace
+	public void makeNegativeExamplesFromRelatedInstances(SortedSet<String> instances,
+			String namespace) {
+		logger.debug("making examples from related instances");
+		for (String oneInstance : instances) {
+			makeNegativeExamplesFromRelatedInstances(oneInstance, namespace);
+		}
+		logger.debug("|-negExample size from related: " + fromRelated.size());
+	}
+
+	private void makeNegativeExamplesFromRelatedInstances(String oneInstance, String objectnamespace) {
+		// SortedSet<String> result = new TreeSet<String>();
+
+		String SPARQLquery = "SELECT * WHERE { \n" + "<" + oneInstance + "> " + "?p ?object. \n"
+				+ "FILTER (REGEX(str(?object), '" + objectnamespace + "')).\n" + "}";
+
+		this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "object"));
+		this.fromRelated.removeAll(this.fullPositiveSet);
+
+	}
+
+	// QUALITY: weird function, best removed
+	public void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
+		// SortedSet<String> result = new TreeSet<String>();
+
+		String SPARQLquery = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
+				+ "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
+				+ "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n" + "}";
+
+		this.fromRelated.addAll(sparqltasks.queryAsSet(SPARQLquery, "o"));
+
+	}
+
+	public void makeNegativeExamplesFromParallelClasses(SortedSet<String> positiveSet, int resultLimit){
+		makeNegativeExamplesFromClassesOfInstances(positiveSet, resultLimit);
+	}
+	
+	public void makeNegativeExamplesFromClassesOfInstances(SortedSet<String> positiveSet,
+			int resultLimit) {
+		logger.debug("making neg Examples from parallel classes");
+		SortedSet<String> classes = new TreeSet<String>();
+		// superClasses.add(concept.replace("\"", ""));
+		// logger.debug("before"+superClasses);
+		// superClasses = dbpediaGetSuperClasses( superClasses, 4);
+		// logger.debug("getting negExamples from "+superClasses.size()+"
+		// superclasses");
+
+		for (String instance : positiveSet) {
+			classes.addAll(sparqltasks.getClassesForInstance(instance, resultLimit));
+		}
+		logger.debug("getting negExamples from " + classes.size() + " parallel classes");
+		for (String oneClass : classes) {
+			logger.debug(oneClass);
+			// rsc = new
+			// JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",limit));
+			this.fromParallelClasses.addAll(sparqltasks.retrieveInstancesForConcept("\"" + oneClass
+					+ "\"", resultLimit));
+
+		}
+		
+		this.fromParallelClasses.removeAll(this.fullPositiveSet);
+		logger.debug("|-neg Example size from parallelclass: " + fromParallelClasses.size());
+
+	}
+
+	public void makeNegativeExamplesFromSuperClasses(String concept, int resultLimit) {
+
+		concept = concept.replaceAll("\"", "");
+		// superClasses.add(concept.replace("\"", ""));
+		// logger.debug("before"+superClasses);
+		SortedSet<String> superClasses = sparqltasks.getSuperClasses(concept, 4);
+		logger.debug("making neg Examples from " + superClasses.size() + " superclasses");
+
+		for (String oneSuperClass : superClasses) {
+			logger.debug(oneSuperClass);
+			this.fromSuperclasses.addAll(sparqltasks.retrieveInstancesForConcept("\""
+					+ oneSuperClass + "\"", resultLimit));
+
+		}
+		this.fromSuperclasses.removeAll(this.fullPositiveSet);
+		logger.debug("|-neg Example from superclass: " + fromSuperclasses.size());
+	}
+
 }

Added: trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java	                        (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/AutomaticPositiveExampleFinderSPARQL.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -0,0 +1,59 @@
+package org.dllearner.utilities.examples;
+
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+
+public class AutomaticPositiveExampleFinderSPARQL {
+	
+	//CHECK
+	private static Logger logger = Logger
+	.getLogger(ComponentManager.class);
+
+	
+	private SPARQLTasks sparqltasks;
+	
+	private SortedSet<String> posExamples;
+	
+	public AutomaticPositiveExampleFinderSPARQL(SPARQLTasks st) {
+		super();
+		
+		this.posExamples = new TreeSet<String>();
+		this.sparqltasks = st;
+	}
+	
+	//QUALITY resultsize is not accounted for
+	public void makePositiveExamplesFromConcept(String conceptKBSyntax){
+		logger.debug("making Positive Examples from Concept: "+conceptKBSyntax);	
+		this.posExamples = sparqltasks.retrieveInstancesForConcept(conceptKBSyntax, 0);
+		logger.debug("   pos Example size: "+posExamples.size());
+	}
+	
+	
+	//QUALITY resultsize is not accounted for
+	public void makePositiveExamplesFromRoleAndObject(String role, String object){
+		logger.debug("making Positive Examples from role: "+role+" and object: "+object);	
+		this.posExamples = sparqltasks.retrieveDISTINCTSubjectsForRoleAndObject(role, object, 0);
+		logger.debug("   pos Example size: "+posExamples.size());
+	}
+	
+	//QUALITY resultsize is not accounted for
+	public void makePositiveExamplesFromSKOSConcept(String SKOSConcept){
+		logger.debug("making Positive Examples from SKOSConcept: "+SKOSConcept);	
+		this.posExamples = sparqltasks.retrieveInstancesForSKOSConcept(SKOSConcept, 0);
+		logger.debug("   pos Example size: "+posExamples.size());
+	}
+
+	public SortedSet<String> getPosExamples() {
+		return posExamples;
+	}
+
+
+
+
+	
+}

Added: trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java	                        (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/SPARQLTasks.java	2008-05-21 14:59:31 UTC (rev 912)
@@ -0,0 +1,216 @@
+package org.dllearner.utilities.examples;
+
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
+
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
+import com.hp.hpl.jena.sparql.core.ResultBinding;
+
+public class SPARQLTasks {
+	
+	private Cache c;
+	private SparqlEndpoint se;
+	
+	public SPARQLTasks(Cache c, SparqlEndpoint se) {
+		super();
+		this.c = c;
+		this.se = se;
+	}
+	
+	public SPARQLTasks( SparqlEndpoint se) {
+		super();
+		this.c = null;
+		this.se = se;
+	}
+	
+	
+	
+	
+	/**
+	 * QUALITY: doesn't seem optimal, check!
+	 * get all superclasses up to a certain depth
+	 * 1 means direct superclasses
+	 * depth 
+	 * @param superClasses
+	 * @param depth
+	 * @return
+	 */
+	public SortedSet<String> getSuperClasses(String oneClass, int depth) {
+		SortedSet<String> superClasses = new TreeSet<String>();
+		superClasses.add(oneClass);
+		SortedSet<String> ret = new TreeSet<String>();
+		SortedSet<String> tmpset = new TreeSet<String>();
+		//ret.addAll(superClasses);
+		//logger.debug(superClasses);
+		
+		
+		String SPARQLquery = "";
+		for (; depth != 0 ; depth--) {
+			for (String oneSuperClass : superClasses) {
+			...
 
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