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[DL-Learner SVN] SF.net SVN: dl-learner:[2219] trunk/src/dl-learner/org/dllearner/tools/ore
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From: <lor...@us...> - 2010-07-27 11:45:02
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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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