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From: <lor...@us...> - 2010-07-21 17:27:35
|
Revision: 2213
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2213&view=rev
Author: lorenz_b
Date: 2010-07-21 17:27:28 +0000 (Wed, 21 Jul 2010)
Log Message:
-----------
Added main method to IncrementalInconsistencyFinder with 2 arguments SPARQL_ENDPOINT and DEFAULT_GRAPH_URI.
Added progress monitor class with no output.
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/tools/ore/sparql/SilentSPARQLProgressMonitor.java
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java 2010-07-21 16:44:12 UTC (rev 2212)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java 2010-07-21 17:27:28 UTC (rev 2213)
@@ -158,7 +158,7 @@
}
public boolean isSourceOWLAxiom(OWLAxiom ax){
- for(OWLOntology ont : reasoner.getLoadedOWLAPIOntologies()){System.out.println(ont.getLogicalAxiomCount());
+ for(OWLOntology ont : reasoner.getLoadedOWLAPIOntologies()){
if(ont.containsAxiom(ax)){
return true;
}
@@ -502,7 +502,6 @@
}
allIndividuals.remove(ind);
- System.out.println();
return allIndividuals;
}
@@ -526,7 +525,6 @@
for(OWLClassExpression domain : domains){
if(complements.contains(OWLAPIConverter.convertClass(domain.asOWLClass()))){
- System.out.println(domain);
return false;
}
}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java 2010-07-21 16:44:12 UTC (rev 2212)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java 2010-07-21 17:27:28 UTC (rev 2213)
@@ -82,7 +82,7 @@
private String endpointURI;
private String defaultGraphURI;
- private SPARQLProgressMonitor mon;
+ private SPARQLProgressMonitor mon = new SilentSPARQLProgressMonitor();
private boolean consistent = true;
private boolean useLinkedData;
@@ -107,7 +107,7 @@
ConsoleAppender consoleAppender = new ConsoleAppender(layout);
logger.removeAllAppenders();
logger.addAppender(consoleAppender);
- logger.setLevel(Level.OFF);
+ logger.setLevel(Level.INFO);
PelletOptions.USE_COMPLETION_QUEUE = true;
PelletOptions.USE_INCREMENTAL_CONSISTENCY = true;
@@ -1423,16 +1423,12 @@
public static void main(String[] args) throws OWLOntologyCreationException, IOException{
PelletExplanation.setup();
IncrementalInconsistencyFinder incFinder = new IncrementalInconsistencyFinder();
-// incFinder.checkForUnsatisfiableClasses(ENDPOINT_URL);
-// incFinder.checkForInconsistency(ENDPOINT_URL);
- incFinder.run(ENDPOINT_URL, DEFAULT_GRAPH_URI);
+ if(args.length == 1){
+ incFinder.run(args[0], "");
+ } else if(args.length == 2){
+ incFinder.run(args[0], args[1]);
+ }
-// String queryString = "CONSTRUCT { ?x <" + RDFS.subClassOf + "> ?y } WHERE { ?x <" + RDFS.subClassOf + "> ?y } ORDER BY ?x LIMIT 100 ";
-// Query query = QueryFactory.create(queryString) ;
-// QueryExecution qexec = QueryExecutionFactory.sparqlService(ENDPOINT_URL, query);
-// Model resultModel = qexec.execConstruct() ;
-// qexec.close() ;
-// resultModel.write(System.out);
}
Added: trunk/src/dl-learner/org/dllearner/tools/ore/sparql/SilentSPARQLProgressMonitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/sparql/SilentSPARQLProgressMonitor.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/sparql/SilentSPARQLProgressMonitor.java 2010-07-21 17:27:28 UTC (rev 2213)
@@ -0,0 +1,57 @@
+package org.dllearner.tools.ore.sparql;
+
+import java.util.Set;
+
+import org.semanticweb.owlapi.model.OWLAxiom;
+
+public class SilentSPARQLProgressMonitor implements SPARQLProgressMonitor{
+
+ @Override
+ public void inconsistencyFound(Set<OWLAxiom> explanation) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean isCancelled() {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public void setFinished() {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setIndeterminate(boolean b) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setMessage(String message) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setProgress(long progress) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setSize(long size) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setStarted() {
+ // TODO Auto-generated method stub
+
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java 2010-07-21 16:44:12 UTC (rev 2212)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java 2010-07-21 17:27:28 UTC (rev 2213)
@@ -349,12 +349,10 @@
*/
private static final long serialVersionUID = 6590889767286900162L;
-
protected void handleAdd() {
addURI();
}
-
protected void handleDelete() {
deleteSelectedBookmark();
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2010-07-26 13:23:21
|
Revision: 2217
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2217&view=rev
Author: lorenz_b
Date: 2010-07-26 13:23:14 +0000 (Mon, 26 Jul 2010)
Log Message:
-----------
Some changes in SPARQL debug UI.
Implemented new class MemoryWarningSystem to check if system is running out of memory.
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/tools/ore/MemoryWarningSystem.java
Added: trunk/src/dl-learner/org/dllearner/tools/ore/MemoryWarningSystem.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/MemoryWarningSystem.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/MemoryWarningSystem.java 2010-07-26 13:23:14 UTC (rev 2217)
@@ -0,0 +1,83 @@
+package org.dllearner.tools.ore;
+
+import javax.management.*;
+import java.lang.management.*;
+import java.util.*;
+
+/**
+ * This memory warning system will call the listener when we
+ * exceed the percentage of available memory specified. There
+ * should only be one instance of this object created, since the
+ * usage threshold can only be set to one number.
+ */
+public class MemoryWarningSystem {
+ private final Collection<MemoryWarningListener> listeners = new ArrayList<MemoryWarningListener>();
+
+ private static final MemoryPoolMXBean tenuredGenPool = findTenuredGenPool();
+
+ private static MemoryWarningSystem instance;
+
+ public interface MemoryWarningListener {
+ public void memoryUsageLow(long usedMemory, long maxMemory);
+ }
+
+ public static synchronized MemoryWarningSystem getInstance() {
+ if (instance == null) {
+ instance = new MemoryWarningSystem();
+ }
+ return instance;
+ }
+
+ private MemoryWarningSystem() {
+ MemoryMXBean mbean = ManagementFactory.getMemoryMXBean();
+
+ NotificationEmitter emitter = (NotificationEmitter) mbean;
+ emitter.addNotificationListener(new NotificationListener() {
+ public void handleNotification(Notification n, Object hb) {
+ if (n.getType().equals(
+ MemoryNotificationInfo.MEMORY_THRESHOLD_EXCEEDED)) {
+ long maxMemory = tenuredGenPool.getUsage().getMax();
+ long usedMemory = tenuredGenPool.getUsage().getUsed();
+ fireMemoryUsageLow(maxMemory, usedMemory);
+ }
+ }
+ }, null, null);
+ }
+
+ public boolean addListener(MemoryWarningListener listener) {
+ return listeners.add(listener);
+ }
+
+ public boolean removeListener(MemoryWarningListener listener) {
+ return listeners.remove(listener);
+ }
+
+ private void fireMemoryUsageLow(long maxMemory, long usedMemory){
+ for (MemoryWarningListener listener : listeners) {
+ listener.memoryUsageLow(usedMemory, maxMemory);
+ }
+ }
+
+ public static void setPercentageUsageThreshold(double percentage) {
+ if (percentage <= 0.0 || percentage > 1.0) {
+ throw new IllegalArgumentException("Percentage not in range");
+ }
+ long maxMemory = tenuredGenPool.getUsage().getMax();
+ long warningThreshold = (long) (maxMemory * percentage);
+ tenuredGenPool.setUsageThreshold(warningThreshold);
+ }
+
+ /**
+ * Tenured Space Pool can be determined by it being of type
+ * HEAP and by it being possible to set the usage threshold.
+ */
+ private static MemoryPoolMXBean findTenuredGenPool() {
+ for (MemoryPoolMXBean pool : ManagementFactory.getMemoryPoolMXBeans()) {
+ if (pool.getType() == MemoryType.HEAP && pool.isUsageThresholdSupported()) {
+ return pool;
+ }
+ }
+ throw new AssertionError("Could not find tenured space");
+ }
+}
+
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java 2010-07-26 11:27:07 UTC (rev 2216)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java 2010-07-26 13:23:14 UTC (rev 2217)
@@ -91,7 +91,7 @@
private boolean consistentOntology;
- public OREManager(){
+ private OREManager(){
cm = ComponentManager.getInstance();
listeners = new ArrayList<OREManagerListener>();
manchesterSyntaxRenderingCache = new ManchesterSyntaxRenderingCache(this);
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java 2010-07-26 11:27:07 UTC (rev 2216)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java 2010-07-26 13:23:14 UTC (rev 2217)
@@ -5,8 +5,11 @@
import java.net.URL;
import java.util.Collections;
import java.util.HashSet;
+import java.util.List;
import java.util.Set;
+import javax.xml.ws.http.HTTPException;
+
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
@@ -14,6 +17,7 @@
import org.dllearner.kb.extraction.ExtractionAlgorithm;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.scripts.SparqlEndpointFinder;
import org.dllearner.utilities.JamonMonitorLogger;
import org.mindswap.pellet.PelletOptions;
import org.semanticweb.owlapi.apibinding.OWLManager;
@@ -53,6 +57,8 @@
import com.hp.hpl.jena.rdf.model.RDFNode;
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.ResultSetException;
import com.hp.hpl.jena.sparql.resultset.ResultSetRewindable;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF;
@@ -63,8 +69,6 @@
private static Logger logger = Logger.getRootLogger();
- private static final String ENDPOINT_URL = "http://dbpedia-live.openlinksw.com/sparql";
- private static String DEFAULT_GRAPH_URI = "http://dbpedia.org";
private static String DBPEDIA_PREDICATE_FILTER = "!regex(?predicate, \"http://dbpedia.org/property\")";
private static String DBPEDIA_SUBJECT_FILTER = "!regex(?subject, \"http://dbpedia.org/property\")";
private static String OWL_THING_OBJECT_FILTER = "!regex(?object, \"http://www.w3.org/2002/07/owl#Thing\")";
@@ -102,12 +106,11 @@
public IncrementalInconsistencyFinder() throws OWLOntologyCreationException, IOException{
-
SimpleLayout layout = new SimpleLayout();
ConsoleAppender consoleAppender = new ConsoleAppender(layout);
logger.removeAllAppenders();
logger.addAppender(consoleAppender);
- logger.setLevel(Level.INFO);
+ logger.setLevel(Level.OFF);
PelletOptions.USE_COMPLETION_QUEUE = true;
PelletOptions.USE_INCREMENTAL_CONSISTENCY = true;
@@ -152,27 +155,51 @@
queryMonitor.reset();
overallMonitor.start();
- int disjointWithCount = getAxiomCountForPredicate(OWL.disjointWith);
- int equivalentClassCount = getAxiomCountForPredicate(OWL.equivalentClass);
- int subClassOfCount = getAxiomCountForPredicate(RDFS.subClassOf);
+ int disjointWithCount = Integer.MAX_VALUE;
+ int functionalCount = Integer.MAX_VALUE;
+ int inverseFunctionalCount = Integer.MAX_VALUE;
+ int equivalentClassCount = Integer.MAX_VALUE;
+ int subClassOfCount = Integer.MAX_VALUE;
+ int domainCount = Integer.MAX_VALUE;
+ int rangeCount = Integer.MAX_VALUE;
+ int subPropertyOfCount = Integer.MAX_VALUE;
+ int equivalentPropertyCount = Integer.MAX_VALUE;
+ int inverseOfCount = Integer.MAX_VALUE;
+ int transitiveCount = Integer.MAX_VALUE;
+ int classAssertionCount = Integer.MAX_VALUE;
+ int overallAxiomCount = Integer.MAX_VALUE;
- int domainCount = getAxiomCountForPredicate(RDFS.domain);
- int rangeCount = getAxiomCountForPredicate(RDFS.range);
+ if(canCountAxioms()){
+ disjointWithCount = getAxiomCountForPredicate(OWL.disjointWith);
+ functionalCount = getAxiomCountForObject(OWL.FunctionalProperty);
+ inverseFunctionalCount = getAxiomCountForObject(OWL.InverseFunctionalProperty);
+
+ if((disjointWithCount + functionalCount + inverseFunctionalCount) == 0){
+ return;
+ }
+
+ equivalentClassCount = getAxiomCountForPredicate(OWL.equivalentClass);
+ subClassOfCount = getAxiomCountForPredicate(RDFS.subClassOf);
+
+ domainCount = getAxiomCountForPredicate(RDFS.domain);
+ rangeCount = getAxiomCountForPredicate(RDFS.range);
+
+ subPropertyOfCount = getAxiomCountForPredicate(RDFS.subPropertyOf);
+ equivalentPropertyCount = getAxiomCountForPredicate(OWL.equivalentProperty);
+ inverseOfCount = getAxiomCountForPredicate(OWL.inverseOf);
+
+ transitiveCount = getAxiomCountForObject(OWL.TransitiveProperty);
+
+ classAssertionCount = getAxiomCountForPredicate(RDF.type);
+
+ overallAxiomCount = disjointWithCount + equivalentClassCount + subClassOfCount + domainCount + rangeCount
+ + subPropertyOfCount + equivalentPropertyCount + inverseOfCount + functionalCount
+ + inverseFunctionalCount + transitiveCount + classAssertionCount;
+
+ mon.setSize(overallAxiomCount);
+ }
- int subPropertyOfCount = getAxiomCountForPredicate(RDFS.subPropertyOf);
- int equivalentPropertyCount = getAxiomCountForPredicate(OWL.equivalentProperty);
- int inverseOfCount = getAxiomCountForPredicate(OWL.inverseOf);
- int functionalCount = getAxiomCountForObject(OWL.FunctionalProperty);
- int inverseFunctionalCount = getAxiomCountForObject(OWL.InverseFunctionalProperty);
- int transitiveCount = getAxiomCountForObject(OWL.TransitiveProperty);
- int classAssertionCount = getAxiomCountForPredicate(RDF.type);
-
- mon.setSize(disjointWithCount + equivalentClassCount + subClassOfCount + domainCount + rangeCount
- + subPropertyOfCount + equivalentPropertyCount + inverseOfCount + functionalCount
- + inverseFunctionalCount + transitiveCount + classAssertionCount);
-
-
Set<OWLClass> visitedClasses = new HashSet<OWLClass>();
Set<OWLNamedIndividual> visitedIndividuals = new HashSet<OWLNamedIndividual>();
Set<OWLObject> visitedLinkedDataResources = new HashSet<OWLObject>();
@@ -198,6 +225,23 @@
if(mon.isCancelled()){
break;
}
+ if(ontology.getAxiomCount(AxiomType.FUNCTIONAL_OBJECT_PROPERTY) + ontology.getAxiomCount(AxiomType.FUNCTIONAL_DATA_PROPERTY) < functionalCount){
+ manager.addAxioms(ontology, retrievePropertyCharacteristicAxioms(OWL.FunctionalProperty, AXIOM_COUNT, OFFSET * i));
+ }
+ mon.setProgress(ontology.getLogicalAxiomCount());
+ if(mon.isCancelled()){
+ break;
+ }
+ if(ontology.getAxiomCount(AxiomType.INVERSE_FUNCTIONAL_OBJECT_PROPERTY) < inverseFunctionalCount){
+ manager.addAxioms(ontology, retrievePropertyCharacteristicAxioms(OWL.InverseFunctionalProperty, AXIOM_COUNT, OFFSET * i));
+ }
+ mon.setProgress(ontology.getLogicalAxiomCount());
+ if(mon.isCancelled()){
+ break;
+ }
+ if(ontology.getLogicalAxiomCount() == 0){
+ return;
+ }
if(ontology.getAxiomCount(AxiomType.EQUIVALENT_CLASSES) < equivalentClassCount){
manager.addAxioms(ontology, retrieveClassExpressionsAxioms(OWL.equivalentClass, AXIOM_COUNT, OFFSET * i));
}
@@ -251,20 +295,6 @@
if(mon.isCancelled()){
break;
}
- if(ontology.getAxiomCount(AxiomType.FUNCTIONAL_OBJECT_PROPERTY) + ontology.getAxiomCount(AxiomType.FUNCTIONAL_DATA_PROPERTY) < functionalCount){
- manager.addAxioms(ontology, retrievePropertyCharacteristicAxioms(OWL.FunctionalProperty, AXIOM_COUNT, OFFSET * i));
- }
- mon.setProgress(ontology.getLogicalAxiomCount());
- if(mon.isCancelled()){
- break;
- }
- if(ontology.getAxiomCount(AxiomType.INVERSE_FUNCTIONAL_OBJECT_PROPERTY) < inverseFunctionalCount){
- manager.addAxioms(ontology, retrievePropertyCharacteristicAxioms(OWL.InverseFunctionalProperty, AXIOM_COUNT, OFFSET * i));
- }
- mon.setProgress(ontology.getLogicalAxiomCount());
- if(mon.isCancelled()){
- break;
- }
if(ontology.getAxiomCount(AxiomType.TRANSITIVE_OBJECT_PROPERTY) < transitiveCount){
manager.addAxioms(ontology, retrievePropertyCharacteristicAxioms(OWL.TransitiveProperty, AXIOM_COUNT, OFFSET * i));
}
@@ -559,7 +589,20 @@
this.linkedDataNamespaces = namespaces;
}
+ private boolean canCountAxioms() {
+ boolean canCount = true;
+ QueryEngineHTTP sparqlQueryExec = new QueryEngineHTTP(endpointURI,
+ "SELECT COUNT(*) WHERE {?s <http://test> ?o}");
+ sparqlQueryExec.addDefaultGraph(defaultGraphURI);
+ try {
+ sparqlQueryExec.execSelect();
+ } catch (QueryExceptionHTTP e) {
+ canCount = false;
+ }
+ return canCount;
+ }
+
private int getAxiomCountForPredicate(Property predicate){
StringBuilder sb = new StringBuilder();
sb.append("SELECT COUNT(*) WHERE {");
@@ -567,11 +610,15 @@
// sb.append("FILTER ").append("(").append(DBPEDIA_SUBJECT_FILTER).append(")");
sb.append("}");
+ logger.info(sb);
+
QueryEngineHTTP sparqlQueryExec = new QueryEngineHTTP(endpointURI, sb.toString());
sparqlQueryExec.addDefaultGraph(defaultGraphURI);
ResultSet sparqlResults = sparqlQueryExec.execSelect();
- return sparqlResults.nextSolution().getLiteral("?callret-0").getInt();
+ QuerySolution solution = sparqlResults.nextSolution();
+ return solution.getLiteral(solution.varNames().next().toString()).getInt();
+// return sparqlResults.nextSolution().getLiteral("?callret-0").getInt();
}
private int getAxiomCountForObject(Resource resource){
@@ -581,11 +628,15 @@
sb.append("FILTER ").append("(").append(DBPEDIA_SUBJECT_FILTER).append(")");
sb.append("}");
+ logger.info(sb);
+
QueryEngineHTTP sparqlQueryExec = new QueryEngineHTTP(endpointURI, sb.toString());
sparqlQueryExec.addDefaultGraph(defaultGraphURI);
ResultSet sparqlResults = sparqlQueryExec.execSelect();
- return sparqlResults.nextSolution().getLiteral("?callret-0").getInt();
+ QuerySolution solution = sparqlResults.nextSolution();
+ return solution.getLiteral(solution.varNames().next().toString()).getInt();
+// return sparqlResults.nextSolution().getLiteral("?callret-0").getInt();
}
private Set<OWLAxiom> retrieveClassExpressionsAxioms(Property property, int limit, int offset){
@@ -609,7 +660,6 @@
} else {
sparqlResults = query.send();
}
-
Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
QuerySolution solution;
@@ -622,7 +672,9 @@
rdfNodeSubject = solution.getResource("?subject");
rdfNodeObject = solution.getResource("?object");
-
+ if(rdfNodeObject == null || rdfNodeSubject == null){
+ continue;
+ }
//skip if solution contains blank node
if(rdfNodeSubject.isAnon() || rdfNodeObject.isAnon()){
continue;
@@ -681,7 +733,9 @@
rdfNodeSubject = solution.getResource("?subject");
rdfNodeObject = solution.getResource("?object");
-
+ if(rdfNodeObject == null || rdfNodeSubject == null){
+ continue;
+ }
//skip if solution contains blank node
if(rdfNodeSubject.isAnon() || rdfNodeObject.isAnon()){
continue;
@@ -777,7 +831,7 @@
rdfNodeSubject = solution.getResource("?subject");
//skip if solution contains blank node
- if(rdfNodeSubject.isAnon()){
+ if(rdfNodeSubject == null || rdfNodeSubject.isAnon()){
continue;
}
@@ -1421,13 +1475,25 @@
}
public static void main(String[] args) throws OWLOntologyCreationException, IOException{
- PelletExplanation.setup();
+// PelletExplanation.setup();
IncrementalInconsistencyFinder incFinder = new IncrementalInconsistencyFinder();
- if(args.length == 1){
- incFinder.run(args[0], "");
- } else if(args.length == 2){
- incFinder.run(args[0], args[1]);
+ List<String> endpoints = new SparqlEndpointFinder().find();
+ for(int i = 8; i < endpoints.size(); i++){
+ try{
+ incFinder.run(endpoints.get(i), "");
+ } catch (HTTPException e){
+ e.printStackTrace();
+ } catch (ResultSetException e){
+ e.printStackTrace();
+ } catch(Exception e){
+ e.printStackTrace();
+ }
}
+// if(args.length == 1){
+// incFinder.run(args[0], "");
+// } else if(args.length == 2){
+// incFinder.run(args[0], args[1]);
+// }
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java 2010-07-26 11:27:07 UTC (rev 2216)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java 2010-07-26 13:23:14 UTC (rev 2217)
@@ -1,9 +1,11 @@
package org.dllearner.tools.ore.ui;
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Component;
import java.awt.Cursor;
import java.awt.Dimension;
+import java.awt.FlowLayout;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
@@ -33,7 +35,6 @@
import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.DefaultListCellRenderer;
-import javax.swing.DefaultListModel;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
@@ -46,12 +47,14 @@
import javax.swing.JPanel;
import javax.swing.JProgressBar;
import javax.swing.JScrollPane;
+import javax.swing.JSeparator;
import javax.swing.JTextField;
+import javax.swing.JTextPane;
import javax.swing.JToggleButton;
import javax.swing.ProgressMonitor;
import javax.swing.SwingUtilities;
import javax.swing.SwingWorker;
-import javax.swing.Timer;
+import javax.swing.UIManager;
import javax.swing.border.TitledBorder;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
@@ -59,21 +62,23 @@
import javax.swing.text.Document;
import javax.swing.text.JTextComponent;
+import org.dllearner.tools.ore.MemoryWarningSystem;
+import org.dllearner.tools.ore.MemoryWarningSystem.MemoryWarningListener;
import org.dllearner.tools.ore.OREApplication;
import org.dllearner.tools.ore.sparql.IncrementalInconsistencyFinder;
import org.dllearner.tools.ore.sparql.SPARQLProgressMonitor;
import org.jdesktop.swingx.autocomplete.AutoCompleteDecorator;
+import org.protege.editor.core.ui.error.ErrorLogPanel;
import org.protege.editor.core.ui.list.MList;
import org.protege.editor.core.ui.list.MListItem;
import org.protege.editor.core.ui.list.MListSectionHeader;
-import org.protege.editor.core.ui.util.ComponentFactory;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
-public class DebugFromSparqlDialog extends JDialog implements ActionListener, PropertyChangeListener, DocumentListener, SPARQLProgressMonitor {
+public class DebugFromSparqlDialog extends JDialog implements ActionListener, PropertyChangeListener, DocumentListener, SPARQLProgressMonitor, MemoryWarningListener {
/**
*
@@ -93,8 +98,6 @@
private JTextField defaultGraphField;
private JButton searchStopButton;
- private JButton addNamespaceButton;
- private JButton deleteNamespaceButton;
private JLabel messageLabel;
private String progressMessage;
@@ -106,10 +109,6 @@
private JCheckBox useCacheCheckBox;
private JCheckBox restrictNamespacesCheckBox;
- private JList linkedDataNamespaceslist;
- private DefaultListModel linkedDataNamespaceslistModel;
- private JScrollPane linkedDataNamespaceslistScrollPane;
-
private MList namespacesList;
private IncrementalInconsistencyFinder inc;
@@ -131,9 +130,12 @@
"</tr> " +
"</table></html>";
- private OntologyExtractingTask extractTask;
+ private static final String warningMessage = "Searching " +
+ "inconsistencies can take several minutes or may even result in an " +
+ "out of memory exception, in particular for large knowledge bases.";
+
+ private SearchInconsistencyTask extractTask;
private ProgressMonitor mon;
- private Timer t;
private Map<URI, List<String>> endpointToDefaultGraph;
@@ -150,6 +152,11 @@
// addPredefinedEndpoints();
positionErrorDialog(owner);
addPredefinedEndpoints();
+
+ //add listener to warn if programm runs into OutOfMemoryError
+ MemoryWarningSystem.setPercentageUsageThreshold(0.8);
+ MemoryWarningSystem mws = MemoryWarningSystem.getInstance();
+ mws.addListener(this);
}
private void createControls() {
@@ -162,10 +169,14 @@
// Create a panel to hold a box with the buttons in it - to give it the
// right space around them
- JPanel buttonPanel = new JPanel();
- buttonPanel.add(buttonBox);
+ Box buttonPanel = Box.createVerticalBox();
+ JPanel b = new JPanel();b.add(buttonBox);
+
+ buttonPanel.add(b);
+ buttonPanel.add(createProgressPanel());
+
buttonPanel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
-
+
// Create the buttons and add them to the box (leading strut will give
// the dialog box its width)
buttonBox.add(okButton = createButton("Ok", 'o'));
@@ -178,6 +189,20 @@
// Add the button panel to the bottom of the BorderLayout
getContentPane().add(buttonPanel, BorderLayout.SOUTH);
}
+
+ private JPanel createProgressPanel(){
+ JPanel panel = new JPanel(new BorderLayout());
+ JPanel leftPanel = new JPanel(new FlowLayout());
+ progressBar = new JProgressBar();
+ leftPanel.add(progressBar);
+ leftPanel.add(new JSeparator(JSeparator.VERTICAL));
+ messageLabel = new JLabel();
+ leftPanel.add(messageLabel);
+ leftPanel.add(new JSeparator(JSeparator.VERTICAL));
+ leftPanel.setOpaque(false);
+ panel.add(leftPanel, BorderLayout.WEST);
+ return panel;
+ }
private void createSparqlPanel() {
JPanel panel = new JPanel();
@@ -208,17 +233,7 @@
endPointHelpPanel.setBorder(new TitledBorder("SPARQL endpoint"));
panel.add(endPointHelpPanel, c);
- searchStopButton = createButton("Search", 's');
- searchStopButton.setEnabled(false);
- c.fill = GridBagConstraints.NONE;
- panel.add(searchStopButton, c);
- progressBar = new JProgressBar();
- panel.add(progressBar, c);
-
- messageLabel = new JLabel("");
- panel.add(messageLabel, c);
-
optionsButton = new JToggleButton(new AbstractAction("Advanced options") {
/**
@@ -259,21 +274,42 @@
c.fill = GridBagConstraints.NONE;
c.anchor = GridBagConstraints.WEST;
panel.add(optionsButton, c);
-
+
c.anchor = GridBagConstraints.CENTER;
- c.fill = GridBagConstraints.HORIZONTAL;
+ c.fill = GridBagConstraints.BOTH;
+ c.weighty = 1.0;
optionsPanel = createSPARQLOptionsPanel();
panel.add(optionsPanel, c);
optionsPanel.setVisible(false);
+ c.weighty = 0.0;
+ searchStopButton = createButton("Search", 's');
+ searchStopButton.setEnabled(false);
+ searchStopButton.setMinimumSize(new Dimension(90, 30));
+ c.fill = GridBagConstraints.NONE;
+ panel.add(searchStopButton, c);
+
JLabel padding = new JLabel();
c.weighty = 1.0;
panel.add(padding, c);
+
+ c.weighty = 0.0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ JTextPane instructionsField = new JTextPane();
+ instructionsField.setContentType("text/html");
+ Color color = UIManager.getColor("Panel.background");
+ instructionsField.setBackground(new Color(color.getRed(), color.getGreen(), color.getBlue()));
+ instructionsField.setOpaque(true);
+ instructionsField.setEditable(false);
+ instructionsField.setText(warningMessage);
+ panel.add(instructionsField, c);
+
getContentPane().add(panel, BorderLayout.CENTER);
}
private JPanel createSPARQLOptionsPanel(){
JPanel panel = new JPanel();
+ panel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
panel.setLayout(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL;
@@ -289,9 +325,7 @@
@Override
public void actionPerformed(ActionEvent e) {
restrictNamespacesCheckBox.setEnabled(useLinkedDataCheckBox.isSelected());
-// linkedDataNamespaceslist.setEnabled(restrictNamespacesCheckBox.isSelected() && useLinkedDataCheckBox.isSelected());
-// addNamespaceButton.setEnabled(restrictNamespacesCheckBox.isSelected() && useLinkedDataCheckBox.isSelected());
-// deleteNamespaceButton.setEnabled(restrictNamespacesCheckBox.isSelected() && useLinkedDataCheckBox.isSelected());
+ namespacesList.setEnabled(restrictNamespacesCheckBox.isSelected() && useLinkedDataCheckBox.isSelected());
}
});
panel.add(useLinkedDataCheckBox, c);
@@ -303,66 +337,32 @@
@Override
public void actionPerformed(ActionEvent e) {
-// linkedDataNamespaceslist.setEnabled(restrictNamespacesCheckBox.isSelected() && useLinkedDataCheckBox.isSelected());
-// addNamespaceButton.setEnabled(restrictNamespacesCheckBox.isSelected() && useLinkedDataCheckBox.isSelected());
-// deleteNamespaceButton.setEnabled(restrictNamespacesCheckBox.isSelected() && useLinkedDataCheckBox.isSelected());
+ namespacesList.setEnabled(restrictNamespacesCheckBox.isSelected() && useLinkedDataCheckBox.isSelected());
}
});
panel.add(restrictNamespacesCheckBox, c);
c.weightx = 1.0;
c.gridx = 1;
-// linkedDataNamespaceslistModel = new DefaultListModel();
-// linkedDataNamespaceslist = new JList(linkedDataNamespaceslistModel);
-// linkedDataNamespaceslist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-// linkedDataNamespaceslist.setSelectedIndex(0);
-// linkedDataNamespaceslist.setVisibleRowCount(5);
-// linkedDataNamespaceslist.setEnabled(false);
-// linkedDataNamespaceslistScrollPane = new JScrollPane(linkedDataNamespaceslist);
-// linkedDataNamespaceslistScrollPane.setVisible(false);
-// c.fill = GridBagConstraints.HORIZONTAL;
-// panel.add(linkedDataNamespaceslistScrollPane, c);
-//
-// Box buttonBox = Box.createHorizontalBox();
-// addNamespaceButton = createButton("Add", 'a');
-// addNamespaceButton.setEnabled(false);
-// buttonBox.add(addNamespaceButton);
-//
-// buttonBox.add(Box.createHorizontalGlue());
-// buttonBox.add(Box.createHorizontalStrut(4));
-// deleteNamespaceButton = createButton("Delete", 'a');
-// deleteNamespaceButton.setEnabled(false);
-// buttonBox.add(deleteNamespaceButton);
-//
-// JPanel buttonPanel = new JPanel();
-// buttonPanel.add(buttonBox);
-// c.anchor = GridBagConstraints.WEST;
-// c.fill = GridBagConstraints.HORIZONTAL;
-// panel.add(buttonPanel, c);
-
-
- ///////////////////
- JPanel namespacesHolder = new JPanel(new BorderLayout());
- namespacesHolder.setBorder(ComponentFactory.createTitledBorder("Namespaces"));
+
namespacesList = new MList() {
- /**
- *
- */
private static final long serialVersionUID = 6590889767286900162L;
protected void handleAdd() {
- addURI();
+ addNamespace();
}
protected void handleDelete() {
- deleteSelectedBookmark();
+ deleteSelectedNamespace();
}
};
-
+ c.fill = GridBagConstraints.BOTH;
+ c.weighty = 1.0;
namespacesList.setCellRenderer(new NamespaceItemListRenderer());
- namespacesHolder.add(new JScrollPane(namespacesList));
+ namespacesList.setVisibleRowCount(5);
+ fillNamespacesList();
panel.add(new JScrollPane(namespacesList), c);
- fillList();
+
return panel;
}
@@ -413,7 +413,7 @@
}
public int showDialog(){
- setSize(700, 600);
+ setSize(700, 400);
setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
SwingUtilities.invokeLater(new Runnable() {
@@ -434,30 +434,9 @@
canceled = false;
messageLabel.setText("Checking SPARQL endpoint availability");
setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
- mon = new ProgressMonitor(this, "Extracting fragment", "", 0, 100);
- mon.setMillisToDecideToPopup(0);
- mon.setMillisToPopup(0);
- mon.getAccessibleContext().getLocale();
+ progressBar.setVisible(true);
-
- t = new Timer(1000,new ActionListener() {
-
-
- @Override
- public void actionPerformed(ActionEvent e) {
-
- if(mon.isCanceled()){
- extractTask.cancel(true);
- setCursor(null);
- t.stop();
-
- }
-
- }
- });
- t.start();
-
- extractTask = new OntologyExtractingTask(this, this);
+ extractTask = new SearchInconsistencyTask(this, this);
extractTask.addPropertyChangeListener(this);
extractTask.execute();
@@ -466,6 +445,7 @@
}
private void stopSearching() {
+ messageLabel.setText("Stopping ...");
canceled = true;
setCursor(Cursor.getDefaultCursor());
// extractTask.cancel(true);
@@ -550,12 +530,12 @@
return inc.getOntology();
}
- private class OntologyExtractingTask extends SwingWorker<Void, Void>{
+ private class SearchInconsistencyTask extends SwingWorker<Void, Void>{
private SPARQLProgressMonitor mon;
private JDialog dialog;
- public OntologyExtractingTask(JDialog dialog, SPARQLProgressMonitor mon) {
+ public SearchInconsistencyTask(JDialog dialog, SPARQLProgressMonitor mon) {
this.mon = mon;
this.dialog = dialog;
}
@@ -587,6 +567,8 @@
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
+ } catch (Exception e){
+ ErrorLogPanel.showErrorDialog(e);
}
@@ -624,29 +606,6 @@
canceled = true;
returnCode = CANCEL_RETURN_CODE;
closeDialog();
- } else if(e.getActionCommand().equals("Add")){
- String s = (String)JOptionPane.showInputDialog(
- this,
- "Enter linked data namespace",
- "Enter namespace",
- JOptionPane.PLAIN_MESSAGE,
- null,
- null,
- "");
- if(s != null){
- linkedDataNamespaceslistModel.addElement(s);
- linkedDataNamespaceslistScrollPane.setVisible(true);
- validate();
- }
- } else if(e.getActionCommand().equals("Delete")){
- if(linkedDataNamespaceslist.getSelectedValue() != null){
- linkedDataNamespaceslistModel.removeElement(linkedDataNamespaceslist.getSelectedValue());
- if(linkedDataNamespaceslistModel.isEmpty()){
- linkedDataNamespaceslistScrollPane.setVisible(false);
- validate();
- }
-
- }
} else if(e.getActionCommand().equals("endpoints")){
messageLabel.setText("");
JComboBox cb = (JComboBox)e.getSource();
@@ -757,15 +716,15 @@
dialog.showDialog();
}
- private void addURI() {
+ private void addNamespace() {
String namespace = JOptionPane.showInputDialog(this, "Please enter a namespace", "Namespace", JOptionPane.PLAIN_MESSAGE);
if (namespace != null) {
namespaces.add(namespace);
- fillList();
+ fillNamespacesList();
}
}
- private void fillList() {
+ private void fillNamespacesList() {
ArrayList<Object> data = new ArrayList<Object>();
data.add(new AddURIItem());
@@ -775,14 +734,14 @@
namespacesList.setListData(data.toArray());
}
- private void deleteSelectedBookmark() {
+ private void deleteSelectedNamespace() {
Object selObj = namespacesList.getSelectedValue();
if (!(selObj instanceof NamspaceListItem)) {
return;
}
NamspaceListItem item = (NamspaceListItem) selObj;
namespaces.remove(item.namespace);
- fillList();
+ fillNamespacesList();
}
private class NamespaceItemListRenderer extends DefaultListCellRenderer {
@@ -852,6 +811,17 @@
}
}
+ @Override
+ public void memoryUsageLow(long usedMemory, long maxMemory) {
+ double percentageUsed = ((double) usedMemory) / maxMemory;
+ StringBuilder message = new StringBuilder();
+ message.append("Memory usage low! \n\n");
+ message.append("Currently ").append((int)(percentageUsed * 100)).append(" % of the assigned memory is used.\n");
+ message.append("It is recommend to stop the task because otherwise the programm might crash.");
+ JOptionPane.showMessageDialog(this, message, "Memory usage low!", JOptionPane.WARNING_MESSAGE);
+
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2010-07-27 11:45:02
|
Revision: 2219
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2219&view=rev
Author: lorenz_b
Date: 2010-07-27 11:44:55 +0000 (Tue, 27 Jul 2010)
Log Message:
-----------
Some changes for release.
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/tools/ore/LearningManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExtractFromSparqlDialog.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/IntroductionPanel.java
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/LearningManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/LearningManager.java 2010-07-27 07:26:57 UTC (rev 2218)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/LearningManager.java 2010-07-27 11:44:55 UTC (rev 2219)
@@ -115,15 +115,15 @@
la.getConfigurator().setMaxNrOfResults(maxNrOfResults);
} catch (LearningProblemUnsupportedException e1) {
- // TODO Auto-generated catch block
e1.printStackTrace();
}
try {
la.init();
} catch (ComponentInitException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
+ } catch (Exception e){
+ e.printStackTrace();
}
}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java 2010-07-27 07:26:57 UTC (rev 2218)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/sparql/IncrementalInconsistencyFinder.java 2010-07-27 11:44:55 UTC (rev 2219)
@@ -42,9 +42,7 @@
import org.semanticweb.owlapi.model.OWLPropertyDomainAxiom;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
-import com.clarkparsia.owlapi.explanation.PelletExplanation;
import com.clarkparsia.owlapiv3.XSD;
-import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
@@ -69,9 +67,10 @@
private static Logger logger = Logger.getRootLogger();
- private static String DBPEDIA_PREDICATE_FILTER = "!regex(?predicate, \"http://dbpedia.org/property\")";
- private static String DBPEDIA_SUBJECT_FILTER = "!regex(?subject, \"http://dbpedia.org/property\")";
- private static String OWL_THING_OBJECT_FILTER = "!regex(?object, \"http://www.w3.org/2002/07/owl#Thing\")";
+ private static final String DBPEDIA_PREDICATE_FILTER = "!regex(?predicate, \"http://dbpedia.org/property\")";
+ private static final String DBPEDIA_SUBJECT_FILTER = "!regex(?subject, \"http://dbpedia.org/property\")";
+ private static final String OWL_OBJECT_FILTER = "!regex(?object, \"http://www.w3.org/2002/07/owl#\")";
+ private static final String OWL_SUBJECT_FILTER = "!regex(?subject, \"http://www.w3.org/2002/07/owl#\")";
// private static final String ENDPOINT_URL = "http://localhost:8890/sparql";
// private static String DEFAULT_GRAPH_URI = "http://opencyc2.org"; //(version 2.0)
@@ -92,10 +91,10 @@
private boolean useLinkedData;
private boolean useCache;
+ private volatile boolean stop;
+
private Set<String> linkedDataNamespaces;
- private PelletExplanation expGen;
-
private SparqlEndpoint endpoint;
private Cache cache;
@@ -104,6 +103,8 @@
private Monitor queryMonitor = JamonMonitorLogger.getTimeMonitor(ExtractionAlgorithm.class, "Query monitor");
private Monitor reasonerMonitor = JamonMonitorLogger.getTimeMonitor(ExtractionAlgorithm.class, "Reasoning monitor");
+ private SparqlQuery query;
+
public IncrementalInconsistencyFinder() throws OWLOntologyCreationException, IOException{
SimpleLayout layout = new SimpleLayout();
@@ -138,6 +139,8 @@
mon.setMessage("Searching...");
+ stop = false;
+
manager = OWLManager.createOWLOntologyManager();
try {
ontology = manager.createOntology(IRI.create(defaultGraphURI + "/" + "fragment"));
@@ -146,7 +149,6 @@
}
factory = manager.getOWLDataFactory();
reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(ontology);
- expGen = new PelletExplanation((PelletReasoner)reasoner);
consistent = true;
@@ -573,10 +575,6 @@
return ontology;
}
- public Set<OWLAxiom> getExplanation(){
- return expGen.getInconsistencyExplanation();
- }
-
public void setUseLinkedData(boolean useLinkedData){
this.useLinkedData = useLinkedData;
}
@@ -589,6 +587,17 @@
this.linkedDataNamespaces = namespaces;
}
+ public void dispose(){
+ reasoner.dispose();
+ }
+
+ public void stop(){
+ stop = true;
+ if(query != null){
+ query.stop();
+ }
+ }
+
private boolean canCountAxioms() {
boolean canCount = true;
QueryEngineHTTP sparqlQueryExec = new QueryEngineHTTP(endpointURI,
@@ -602,7 +611,6 @@
return canCount;
}
-
private int getAxiomCountForPredicate(Property predicate){
StringBuilder sb = new StringBuilder();
sb.append("SELECT COUNT(*) WHERE {");
@@ -612,9 +620,13 @@
logger.info(sb);
- QueryEngineHTTP sparqlQueryExec = new QueryEngineHTTP(endpointURI, sb.toString());
- sparqlQueryExec.addDefaultGraph(defaultGraphURI);
- ResultSet sparqlResults = sparqlQueryExec.execSelect();
+ query = new SparqlQuery(sb.toString(), endpoint);
+ ResultSetRewindable sparqlResults;
+ if(useCache){
+ sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
+ } else {
+ sparqlResults = query.send();
+ }
QuerySolution solution = sparqlResults.nextSolution();
return solution.getLiteral(solution.varNames().next().toString()).getInt();
@@ -630,9 +642,13 @@
logger.info(sb);
- QueryEngineHTTP sparqlQueryExec = new QueryEngineHTTP(endpointURI, sb.toString());
- sparqlQueryExec.addDefaultGraph(defaultGraphURI);
- ResultSet sparqlResults = sparqlQueryExec.execSelect();
+ query = new SparqlQuery(sb.toString(), endpoint);
+ ResultSetRewindable sparqlResults;
+ if(useCache){
+ sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
+ } else {
+ sparqlResults = query.send();
+ }
QuerySolution solution = sparqlResults.nextSolution();
return solution.getLiteral(solution.varNames().next().toString()).getInt();
@@ -648,12 +664,13 @@
sb.append("SELECT * WHERE {");
sb.append("?subject ").append("<").append(property).append(">").append(" ?object.");
sb.append("FILTER ").append("(").append(DBPEDIA_SUBJECT_FILTER).append(")");
+ sb.append("FILTER ").append("(").append(OWL_SUBJECT_FILTER).append(")");
sb.append("}");
sb.append(" ORDER BY ").append("?subject");
sb.append(" LIMIT ").append(limit);
sb.append(" OFFSET ").append(offset);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -706,12 +723,13 @@
sb.append("SELECT * WHERE {");
sb.append("?subject ").append("<").append(property).append(">").append(" ?object.");
sb.append("FILTER ").append("(").append(DBPEDIA_SUBJECT_FILTER).append(")");
+ sb.append("FILTER ").append("(").append(OWL_SUBJECT_FILTER).append(")");
sb.append("}");
sb.append(" ORDER BY ").append("?subject");
sb.append(" LIMIT ").append(limit);
sb.append(" OFFSET ").append(offset);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -809,7 +827,7 @@
sb.append(" LIMIT ").append(limit);
sb.append(" OFFSET ").append(offset);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -917,13 +935,12 @@
sb.append("ASK {");
sb.append("<").append(propertyURI).append("> ").append("<").append(RDF.type).append("> ").append("<").append(OWL.ObjectProperty).append(">");
sb.append("}");
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
if(useCache){
if(cache.executeSparqlAskQuery(query)){
logger.info("YES");
return true;
}
-
} else {
if(query.sendAsk()){
logger.info("YES");
@@ -942,7 +959,6 @@
logger.info("NO");
return false;
}
-
} else {
if(query.sendAsk()){
logger.info("NO");
@@ -987,7 +1003,7 @@
sb.append("}");
sb.append(" LIMIT ").append(limit);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -1025,7 +1041,7 @@
sb.append("}");
sb.append(" LIMIT ").append(limit);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -1067,7 +1083,7 @@
sb.append("}");
sb.append(" LIMIT ").append(limit);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -1132,7 +1148,7 @@
sb.append(" ORDER BY ").append("?subject");
sb.append(" LIMIT ").append(limit);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -1170,7 +1186,7 @@
sb.append(" HAVING COUNT(?o)>1");
sb.append(" LIMIT ").append(limit);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -1279,11 +1295,12 @@
StringBuilder sb = new StringBuilder();
sb.append("SELECT * WHERE {");
sb.append("<").append(ind.toStringID()).append("> ").append("?predicate").append(" ?object.");
- sb.append("FILTER ").append("(").append(DBPEDIA_PREDICATE_FILTER).append(" && ").append(OWL_THING_OBJECT_FILTER).append(")");
+ sb.append("FILTER ").append("(").append(DBPEDIA_PREDICATE_FILTER).append(")");
+// sb.append("FILTER ").append("(").append(OWL_OBJECT_FILTER).append(")");
sb.append("}");
sb.append(" LIMIT ").append(limit);
- SparqlQuery query = new SparqlQuery(sb.toString(), endpoint);
+ query = new SparqlQuery(sb.toString(), endpoint);
ResultSetRewindable sparqlResults;
if(useCache){
sparqlResults = cache.executeSparqlQuery(new SparqlQuery(sb.toString(), endpoint));
@@ -1478,7 +1495,7 @@
// PelletExplanation.setup();
IncrementalInconsistencyFinder incFinder = new IncrementalInconsistencyFinder();
List<String> endpoints = new SparqlEndpointFinder().find();
- for(int i = 8; i < endpoints.size(); i++){
+ for(int i = 1; i < endpoints.size(); i++){
try{
incFinder.run(endpoints.get(i), "");
} catch (HTTPException e){
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java 2010-07-27 07:26:57 UTC (rev 2218)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/DebugFromSparqlDialog.java 2010-07-27 11:44:55 UTC (rev 2219)
@@ -78,7 +78,7 @@
import com.clarkparsia.owlapi.explanation.PelletExplanation;
-public class DebugFromSparqlDialog extends JDialog implements ActionListener, PropertyChangeListener, DocumentListener, SPARQLProgressMonitor, MemoryWarningListener {
+public class DebugFromSparqlDialog extends JDialog implements ActionListener, PropertyChangeListener, DocumentListener, SPARQLProgressMonitor, MemoryWarningListener{
/**
*
@@ -100,7 +100,7 @@
private JButton searchStopButton;
private JLabel messageLabel;
- private String progressMessage;
+// private String progressMessage;
private int progress;
private boolean canceled;
private JProgressBar progressBar;
@@ -447,6 +447,7 @@
private void stopSearching() {
messageLabel.setText("Stopping ...");
canceled = true;
+ inc.stop();
setCursor(Cursor.getDefaultCursor());
// extractTask.cancel(true);
}
@@ -625,6 +626,10 @@
private void closeDialog(){
setVisible(false);
+ MemoryWarningSystem.getInstance().removeListener(this);
+ if(inc != null){
+ inc.dispose();
+ }
dispose();
}
@@ -672,13 +677,13 @@
@Override
public void setMessage(String message) {
- this.progressMessage = message;
- SwingUtilities.invokeLater(new Runnable() {
- @Override
- public void run() {
-// messageLabel.setText(progressMessage);
- }
- });
+// this.progressMessage = message;
+// SwingUtilities.invokeLater(new Runnable() {
+// @Override
+// public void run() {
+//// messageLabel.setText(progressMessage);
+// }
+// });
}
@Override
@@ -818,11 +823,19 @@
message.append("Memory usage low! \n\n");
message.append("Currently ").append((int)(percentageUsed * 100)).append(" % of the assigned memory is used.\n");
message.append("It is recommend to stop the task because otherwise the programm might crash.");
- JOptionPane.showMessageDialog(this, message, "Memory usage low!", JOptionPane.WARNING_MESSAGE);
+ final String m = message.toString();
+ SwingUtilities.invokeLater(new Runnable() {
+
+ @Override
+ public void run() {
+ JOptionPane.showMessageDialog(DebugFromSparqlDialog.this, m, "Memory usage low!", JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
}
-
+
}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExtractFromSparqlDialog.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExtractFromSparqlDialog.java 2010-07-27 07:26:57 UTC (rev 2218)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExtractFromSparqlDialog.java 2010-07-27 11:44:55 UTC (rev 2219)
@@ -18,7 +18,6 @@
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URI;
-import java.net.URISyntaxException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
@@ -126,7 +125,7 @@
//create main panel
createSparqlPanel();
//add predefined endpoints
-// addPredefinedEndpoints();
+ addPredefinedEndpoints();
positionErrorDialog(owner);
}
@@ -278,20 +277,29 @@
getContentPane().add(panel, BorderLayout.CENTER);
}
- @SuppressWarnings("unused")
- private void addPredefinedEndpoints(){
+ private void addPredefinedEndpoints() {
+ // endpointToDefaultGraph = new HashMap<URI, List<String>>();
+ // for(SparqlEndpoint endpoint : SparqlEndpoint.listEndpoints()){
+ // try {
+ // endpointToDefaultGraph.put(endpoint.getURL().toURI(),
+ // endpoint.getDefaultGraphURIs());
+ // } catch (URISyntaxException e) {
+ // // TODO Auto-generated catch block
+ // e.printStackTrace();
+ // }
+ // }
+ // for(URI url : endpointToDefaultGraph.keySet()){
+ // comboBox.addItem(url.toString());
+ // }
endpointToDefaultGraph = new HashMap<URI, List<String>>();
- for(SparqlEndpoint endpoint : SparqlEndpoint.listEndpoints()){
- try {
- endpointToDefaultGraph.put(endpoint.getURL().toURI(), endpoint.getDefaultGraphURIs());
- } catch (URISyntaxException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
- for(URI url : endpointToDefaultGraph.keySet()){
+ endpointToDefaultGraph.put(
+ URI.create("http://dbpedia-live.openlinksw.com/sparql/"),
+ Collections.singletonList("http://dbpedia.org"));
+ // endpointToDefaultGraph.put(URI.create("http://localhost:8890/sparql"),
+ // Collections.singletonList("http://opencyc2.org"));
+ for (URI url : endpointToDefaultGraph.keySet()) {
comboBox.addItem(url.toString());
- }
+ }
}
private void positionErrorDialog(JFrame owner) {
@@ -355,11 +363,11 @@
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
setLocation(screenSize.width / 2 - getWidth() / 2,
screenSize.height / 2 - getHeight() / 2);
- setVisible(true);
+
}
});
-
+ setVisible(true);
return returnCode;
}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/IntroductionPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/IntroductionPanel.java 2010-07-27 07:26:57 UTC (rev 2218)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/IntroductionPanel.java 2010-07-27 11:44:55 UTC (rev 2219)
@@ -60,7 +60,10 @@
"<p style=\"max-width:400px;\">ORE uses a wizard-style concept. On the left, you can see different steps in the wizard, where the current step is in bold. " +
"Each step contains an explanation of it in the main window. The wizard may omit steps if they are not necessary, e.g. " +
"if you load a consistent ontology, then the \"Debugging\" dialogue is skipped.</p>" +
- "<p>Please read the <a href=\"http://dl-learner.org/wiki/ORE\">the ORE wiki page</a> and view the <a href=\"http://dl-learner.org/files/screencast/ore/0.1/ore.htm\">screencast</a> to get started.</p></html>";
+ "<p>Please read the <a href=\"http://dl-learner.org/wiki/ORE\">the ORE wiki page</a> and view the screencasts " +
+ "[<a href=\"http://dl-learner.org/files/screencast/ore/0.2/ore.htm\">1</a>, " +
+ "<a href=\"http://dl-learner.org/files/screencast/ore/0.2/ore2.htm\">2</a>] " +
+ "to get started.</p></html>";
public IntroductionPanel() {
createUI();
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