[DL-Learner SVN] SF.net SVN: dl-learner:[3995] trunk/components-core

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

Revision: 3995
          http://sourceforge.net/p/dl-learner/code/3995
Author:   lorenz_b
Date:     2013-06-13 13:34:00 +0000 (Thu, 13 Jun 2013)
Log Message:
-----------
Cleaned up pom. Optimzed cache usage.

Modified Paths:
--------------
    trunk/components-core/pom.xml
    trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java
    trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
    trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
    trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java

Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml	2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/pom.xml	2013-06-13 13:34:00 UTC (rev 3995)
@@ -102,37 +102,8 @@
 		<dependency>
 			<groupId>net.sourceforge.owlapi</groupId>
 			<artifactId>owlapi-distribution</artifactId>
-			<type>pom</type>
+			<version>3.4.4</version>
 		</dependency>
-		<dependency>
-			<groupId>net.sourceforge.owlapi</groupId>
-			<artifactId>owlapi-dlsyntax</artifactId>
-			<version>3.3</version>
-		</dependency>
-		<dependency>
-			<groupId>net.sourceforge.owlapi</groupId>
-			<artifactId>owlapi-functional</artifactId>
-			<version>3.3</version>
-		</dependency>
-		
-		<dependency>
-	<groupId>net.sourceforge.owlapi</groupId>
-	<artifactId>owlapi-reasoner</artifactId>
-</dependency>
-<dependency>
-	<groupId>net.sourceforge.owlapi</groupId>
-	<artifactId>owlapi-debugging</artifactId>
-	<version>3.3</version>
-</dependency>
-<dependency>
-	<groupId>net.sourceforge.owlapi</groupId>
-	<artifactId>owlapi-modularity</artifactId>
-	<version>3.3</version>
-</dependency>
-<dependency>
-			<groupId>net.sourceforge.owlapi</groupId>
-			<artifactId>owlapi-util</artifactId>
-		</dependency>
 
 		<!-- THIS IS FROM THE UNIBAS REPO -->
 		<dependency>

Modified: trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java	2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java	2013-06-13 13:34:00 UTC (rev 3995)
@@ -21,6 +21,7 @@
 
 import java.io.File;
 import java.net.URI;
+import java.util.Collections;
 
 import org.dllearner.core.AbstractKnowledgeSource;
 import org.dllearner.core.OntologyFormat;
@@ -39,10 +40,12 @@
 	
     private byte[] ontologyBytes;
     private OntologyToByteConverter converter = new SimpleOntologyToByteConverter();
+	private OWLOntology ontology;
 
 	
-	public OWLAPIOntology(OWLOntology onto) {
-        ontologyBytes = converter.convert(onto);
+	public OWLAPIOntology(OWLOntology ontology) {
+        this.ontology = ontology;
+//		ontologyBytes = converter.convert(ontology);
     }
 	
 	public static String getName() {
@@ -51,7 +54,20 @@
 
     @Override
     public OWLOntology createOWLOntology(OWLOntologyManager manager) {
-        return converter.convert(ontologyBytes, manager);
+    	OWLOntology copy = null;
+    	try {
+    		IRI iri;
+    		if(ontology.getOntologyID().isAnonymous()){
+    			iri = IRI.generateDocumentIRI();
+    		} else {
+    			iri = ontology.getOntologyID().getOntologyIRI();
+    		}
+			copy = manager.createOntology(iri, Collections.singleton(ontology));
+		} catch (OWLOntologyCreationException e) {
+			e.printStackTrace();
+		}
+//        return converter.convert(ontologyBytes, manager);
+    	return copy;
     }
 
     @Override

Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java	2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java	2013-06-13 13:34:00 UTC (rev 3995)
@@ -11,7 +11,6 @@
 import org.aksw.jena_sparql_api.cache.extra.CacheEx;
 import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
 import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
-//import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
 import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
 import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
 import org.apache.log4j.Level;
@@ -19,6 +18,7 @@
 
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.rdf.model.Model;
+//import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
 //import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
 
 public class ConciseBoundedDescriptionGeneratorImpl implements ConciseBoundedDescriptionGenerator{
@@ -27,34 +27,42 @@
 	
 	private int chunkSize = 0;
 	
-	private ExtractionDBCache cache;
-	private SparqlEndpoint endpoint;
 	private Model baseModel;
 	
 	private List<String> namespaces;
+	private static final int MAX_RECURSION_DEPTH_DEFAULT = 1;
 	private int maxRecursionDepth = 1;
-	private String cacheDir;
+	private QueryExecutionFactory qef;
 	
 	public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache) {
-		this.endpoint = endpoint;
-		this.cache = cache;
+		this(endpoint, cache, MAX_RECURSION_DEPTH_DEFAULT);
 	}
 	
 	public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache, int maxRecursionDepth) {
-		this.endpoint = endpoint;
-		this.cache = cache;
-		this.maxRecursionDepth = maxRecursionDepth;
+		this(endpoint, cache.getCacheDirectory(), maxRecursionDepth);
 	}
 	
 	public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir, int maxRecursionDepth) {
-		this.endpoint = endpoint;
-		this.cacheDir = cacheDir;
 		this.maxRecursionDepth = maxRecursionDepth;
+		
+		qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+		if(cacheDir != null){
+			try {
+				long timeToLive = TimeUnit.DAYS.toMillis(30);
+				CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDir, timeToLive, true);
+				CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+				qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+			} catch (ClassNotFoundException e) {
+				e.printStackTrace();
+			} catch (SQLException e) {
+				e.printStackTrace();
+			}
+		}
+		qef = new QueryExecutionFactoryPaginated(qef, 10000);
 	}
 	
 	public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir) {
-		this.endpoint = endpoint;
-		this.cacheDir = cacheDir;
+		this(endpoint, cacheDir, MAX_RECURSION_DEPTH_DEFAULT);
 	}
 	
 	public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint) {
@@ -63,6 +71,8 @@
 	
 	public ConciseBoundedDescriptionGeneratorImpl(Model model) {
 		this.baseModel = model;
+		
+		qef = new QueryExecutionFactoryModel(baseModel);
 	}
 	
 	public Model getConciseBoundedDescription(String resourceURI){
@@ -79,25 +89,6 @@
 	
 	private Model getModelChunked(String resource, int depth){
 		String query = makeConstructQueryOptional(resource, chunkSize, 0, depth);
-		QueryExecutionFactory qef;
-		if(endpoint != null){
-			qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
-			if(cacheDir != null){
-				try {
-					long timeToLive = TimeUnit.DAYS.toMillis(30);
-					CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDir, timeToLive, true);
-					CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
-					qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
-				} catch (ClassNotFoundException e) {
-					e.printStackTrace();
-				} catch (SQLException e) {
-					e.printStackTrace();
-				}
-			}
-			qef = new QueryExecutionFactoryPaginated(qef, 10000);
-		} else {
-			qef = new QueryExecutionFactoryModel(baseModel);
-		}
 		QueryExecution qe = qef.createQueryExecution(query);
 		Model model = qe.execConstruct();
 		return model;

Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java	2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java	2013-06-13 13:34:00 UTC (rev 3995)
@@ -19,7 +19,6 @@
 
 package org.dllearner.reasoning;
 
-import java.net.SocketTimeoutException;
 import java.net.URL;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -41,6 +40,7 @@
 import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
 import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
 import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
+import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
 import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
 import org.dllearner.core.ComponentAnn;
 import org.dllearner.core.IndividualReasoner;
@@ -81,9 +81,6 @@
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
-import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
-import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.OWL2;
 import com.hp.hpl.jena.vocabulary.RDF;
@@ -98,6 +95,7 @@
 	private boolean useCache = true;
 
 	private ExtractionDBCache cache;
+	private QueryExecutionFactory qef;
 
 	private SparqlEndpointKS ks;
 	private ClassHierarchy hierarchy;
@@ -128,6 +126,27 @@
 
 		classPopularityMap = new HashMap<NamedClass, Integer>();
 		objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
+		
+		if(ks.isRemote()){
+			SparqlEndpoint endpoint = ks.getEndpoint();
+			qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+			if(cache != null){
+				try {
+					long timeToLive = TimeUnit.DAYS.toMillis(30);
+					CacheCoreEx cacheBackend = CacheCoreH2.create(cache.getCacheDirectory(), timeToLive, true);
+					CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+					qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+				} catch (ClassNotFoundException e) {
+					e.printStackTrace();
+				} catch (SQLException e) {
+					e.printStackTrace();
+				}
+			}
+			qef = new QueryExecutionFactoryPaginated(qef, 10000);
+			
+		} else {
+			qef = new QueryExecutionFactoryModel(((LocalModelBasedSparqlEndpointKS)ks).getModel());
+		}
 	}
 
 	public SPARQLReasoner(OntModel model) {
@@ -1362,58 +1381,25 @@
 
 	private ResultSet executeSelectQuery(String query){
 		logger.debug("Sending query \n {}", query);
-		ResultSet rs = null;
-		if(ks.isRemote()){
-			SparqlEndpoint endpoint = ks.getEndpoint();
-			QueryExecutionFactory qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
-			if(cache != null){
-				try {
-					long timeToLive = TimeUnit.DAYS.toMillis(30);
-					CacheCoreEx cacheBackend = CacheCoreH2.create(cache.getCacheDirectory(), timeToLive, true);
-					CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
-					qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
-				} catch (ClassNotFoundException e) {
-					e.printStackTrace();
-				} catch (SQLException e) {
-					e.printStackTrace();
-				}
-			}
-			qef = new QueryExecutionFactoryPaginated(qef, 10000);
-			QueryExecution qe = qef.createQueryExecution(query);
-			rs = qe.execSelect();
-		} else {
-			QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
-			rs = qExec.execSelect();
-		}
+		QueryExecution qe = qef.createQueryExecution(query);
+		ResultSet rs = qe.execSelect();
 		return rs;
 	}
 
 	private ResultSet executeSelectQuery(String query, long timeout){
 		logger.debug("Sending query \n {}", query);
-		ResultSet rs = null;
-		if(ks.isRemote()){
-			SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
-			QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
-					query);
-			queryExecution.setTimeout(timeout);
-			queryExecution.setDefaultGraphURIs(endpoint.getDefaultGraphURIs());
-			queryExecution.setNamedGraphURIs(endpoint.getNamedGraphURIs());
-			try {
-				rs = queryExecution.execSelect();
-			} catch (QueryExceptionHTTP e) {
-				if(e.getCause() instanceof SocketTimeoutException){
-					logger.warn("Got timeout");
-				} else {
-					logger.error("Exception executing query", e);
-				}
-				rs = new ResultSetMem();
-			}
-		} else {
-			QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
-			rs = qExec.execSelect();
-		}
+		QueryExecution qe = qef.createQueryExecution(query);
+		qe.setTimeout(timeout);
+		ResultSet rs = qe.execSelect();
 		return rs;
 	}
+	
+	private boolean executeAskQuery(String query){
+		logger.debug("Sending query \n {}", query);
+		QueryExecution qe = qef.createQueryExecution(query);
+		boolean ret = qe.execAsk();
+		return ret;
+	}
 
 	/**
 	 * Returns TRUE if the class hierarchy was computed before.
@@ -1431,27 +1417,6 @@
 		this.useCache = useCache;
 	}
 
-	private boolean executeAskQuery(String query){
-		boolean ret;
-		if(ks.isRemote()){
-			QueryEngineHTTP queryExecution = new QueryEngineHTTP(ks.getEndpoint().getURL().toString(), query);
-			for (String dgu : ks.getEndpoint().getDefaultGraphURIs()) {
-				queryExecution.addDefaultGraph(dgu);
-			}
-			for (String ngu : ks.getEndpoint().getNamedGraphURIs()) {
-				queryExecution.addNamedGraph(ngu);
-			}			
-			ret = queryExecution.execAsk();
-
-		} else {
-			QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query,  ((LocalModelBasedSparqlEndpointKS)ks).getModel());
-			ret = qExec.execAsk();
-		}
-
-		return ret;
-	}
-
-
 	public static void main(String[] args) throws Exception{
 		//		QueryEngineHTTP e = new QueryEngineHTTP("http://bibleontology.com/sparql/index.jsp",
 		//				"SELECT DISTINCT ?type WHERE {?s a ?type) LIMIT 10");

Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java	2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java	2013-06-13 13:34:00 UTC (rev 3995)
@@ -1,5 +1,8 @@
 package org.dllearner.utilities.owl;
 
+import org.coode.owlapi.turtle.TurtleOntologyFormat;
+import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
@@ -7,7 +10,9 @@
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.util.Set;
 
 /**
  * Created by IntelliJ IDEA.
@@ -26,7 +31,7 @@
 
         OWLOntologyManager manager = ontology.getOWLOntologyManager();
         try {
-            manager.saveOntology(ontology,baos);
+            manager.saveOntology(ontology, baos);
             baos.close();
         } catch (OWLOntologyStorageException e) {
             throw new RuntimeException(e);

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