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[DL-Learner SVN] SF.net SVN: dl-learner:[1853] trunk/src/dl-learner/org/dllearner/tools/ore
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From: <lor...@us...> - 2009-09-20 14:45:51
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Revision: 1853
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1853&view=rev
Author: lorenz_b
Date: 2009-09-20 14:45:41 +0000 (Sun, 20 Sep 2009)
Log Message:
-----------
fixed bug in Sparql extraction - choosing predefined filter "YAGO" seems to fail into an exception when testing it for DPPEDIA endpoint
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/tools/ore/RecentManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/SPARQLTest.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExtractFromSparqlDialog.java
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/RecentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/RecentManager.java 2009-09-14 15:15:13 UTC (rev 1852)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/RecentManager.java 2009-09-20 14:45:41 UTC (rev 1853)
@@ -32,7 +32,7 @@
}
public void addURI(URI uri){
- if(!uriList.contains(uri)){
+ if(uri != null && !uriList.contains(uri)){
uriList.add(uri);
}
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/SPARQLTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/SPARQLTest.java 2009-09-14 15:15:13 UTC (rev 1852)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/SPARQLTest.java 2009-09-20 14:45:41 UTC (rev 1853)
@@ -96,13 +96,11 @@
SparqlKnowledgeSource ks = cm.knowledgeSource(SparqlKnowledgeSource.class);
cm.applyConfigEntry(ks, "predefinedEndpoint", "DBPEDIA");
ks.getConfigurator().setInstances(instances);
- ks.getConfigurator().setPredefinedFilter("YAGO");
-// ks.getConfigurator().setSaveExtractedFragment(true);
+// ks.getConfigurator().setPredefinedFilter("YAGO");
ks.init();
ReasonerComponent reasoner = cm.reasoner(FastInstanceChecker.class, ks);
reasoner.init();
ClassLearningProblem lp = cm.learningProblem(ClassLearningProblem.class, reasoner);
-// lp.getConfigurator().setPositiveExamples(posExamples);
lp.getConfigurator().setClassToDescribe(new URL(exampleClass));
lp.init();
LearningAlgorithm la = cm.learningAlgorithm(CELOE.class, lp, reasoner);
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java 2009-09-14 15:15:13 UTC (rev 1852)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java 2009-09-20 14:45:41 UTC (rev 1853)
@@ -32,12 +32,13 @@
public static void main(String[] args) {
-
- test();
- miniTest();
+
+// test();
+// miniTest();
miniEconomyTest();
- universityTest();
+// universityTest();
}
+
public static void test(){
String file = "file:/home/lorenz/neu.owl";
@@ -66,9 +67,6 @@
} catch (OWLOntologyCreationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
- } catch (OWLException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
}
}
@@ -78,61 +76,35 @@
try {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
- ManchesterSyntaxExplanationRenderer renderer = new ManchesterSyntaxExplanationRenderer();
- PrintWriter pw = new PrintWriter(System.out);
- renderer.startRendering(pw);
-
-
OWLOntology ontology = manager.loadOntologyFromPhysicalURI(URI
.create(file));
- Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
- ontologies.add(ontology);
+
PelletReasonerFactory resonerFact = new PelletReasonerFactory();
OWLDataFactory dataFactory = manager.getOWLDataFactory();
-
- ////////////////////HermiT test
-// HermiTReasonerFactory f = new HermiTReasonerFactory();
-// HermitReasoner re = (HermitReasoner) f.createReasoner(manager);
-// re.loadOntologies(ontologies);
-// Timer t1 = new Timer("classifying");
-// t1.start();
-// re.classify();
-// t1.stop();
-// re.realise();
-// System.out.println("HermiT" + re.getInconsistentClasses());
- //////////////////////////////
Reasoner reasoner = resonerFact.createReasoner(manager);
- reasoner.loadOntologies(ontologies);
- SwingProgressMonitor monitor = new SwingProgressMonitor();
- reasoner.getKB().getTaxonomyBuilder().setProgressMonitor(monitor);
+ reasoner.loadOntology(ontology);
+
reasoner.classify();
System.out.println(reasoner.getInconsistentClasses());
LaconicExplanationGenerator expGen = new LaconicExplanationGenerator(
- manager, resonerFact, ontologies);
+ manager, resonerFact, Collections.singleton(ontology));
-
-
-
-
Set<OWLClass> unsatClasses = reasoner.getInconsistentClasses();
OWLSubClassAxiom unsatAxiom;
- unsatAxiom = dataFactory.getOWLSubClassAxiom(dataFactory.getOWLClass(URI.create("http://reliant.teknowledge.com/DAML/Economy.owl#Cassava")),
- dataFactory.getOWLNothing());
-// for (OWLClass unsat : unsatClasses) {
-// unsatAxiom = dataFactory.getOWLSubClassAxiom(unsat, dataFactory
-// .getOWLNothing());
-// Set<Set<OWLAxiom>> preciseJusts = expGen
-// .getExplanations(unsatAxiom);
-// renderer.render(unsatAxiom, preciseJusts);
-// }
- Set<Explanation> preciseJusts = expGen.getExplanations(unsatAxiom);
-// renderer.render(unsatAxiom, preciseJusts);
- renderer.endRendering();
+ for (OWLClass unsat : unsatClasses) {
+ unsatAxiom = dataFactory.getOWLSubClassAxiom(unsat, dataFactory
+ .getOWLNothing());
+ Set<Explanation> explanations = expGen
+ .getExplanations(unsatAxiom);
+ System.out.println(explanations);
+ }
+
+
} catch (OWLOntologyCreationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExtractFromSparqlDialog.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExtractFromSparqlDialog.java 2009-09-14 15:15:13 UTC (rev 1852)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExtractFromSparqlDialog.java 2009-09-20 14:45:41 UTC (rev 1853)
@@ -1,6 +1,7 @@
package org.dllearner.tools.ore.ui;
import java.awt.BorderLayout;
+import java.awt.Cursor;
import java.awt.Dialog;
import java.awt.Dimension;
import java.awt.GridBagConstraints;
@@ -50,7 +51,6 @@
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.utilities.datastructures.SetManipulation;
-import org.dllearner.utilities.examples.AutomaticPositiveExampleFinderSPARQL;
import org.jdesktop.swingx.autocomplete.AutoCompleteDecorator;
public class ExtractFromSparqlDialog extends JDialog implements ActionListener, PropertyChangeListener, DocumentListener {
@@ -94,7 +94,7 @@
private Map<URL, List<String>> endpointToDefaultGraph;
public ExtractFromSparqlDialog(Dialog owner) {
- super(owner, "Extract fragment from Sparql-endpoint", true);
+ super(owner, "Extract fragment from SPARQL endpoint", true);
// Create the controls
createControls();
@@ -143,7 +143,7 @@
JPanel endPointHolderPanel = new JPanel();
endPointHolderPanel.setLayout(new GridLayout(0, 1));
- endPointHolderPanel.setBorder(new TitledBorder("Sparql endpoint"));
+ endPointHolderPanel.setBorder(new TitledBorder("SPARQL endpoint"));
comboBox = new JComboBox();
comboBox.setEditable(true);
comboBox.setActionCommand("endpoints");
@@ -160,7 +160,7 @@
JPanel classHolderPanel = new JPanel();
classHolderPanel.setLayout(new GridLayout(0, 1));
- classHolderPanel.setBorder(new TitledBorder("Class to learn"));
+ classHolderPanel.setBorder(new TitledBorder("Class to investigate"));
asLabelButton = new JRadioButton("label");
asURLButton = new JRadioButton("URI");
asURLButton.setSelected(true);
@@ -297,21 +297,27 @@
}
private void extract() {
- if(urlIsConnectable()){
- message.setText("");
- mon = new ProgressMonitor(this, "Extracting fragment", "", 0, 100);
- extractTask = new OntologyExtractingTask(mon);
- extractTask.addPropertyChangeListener(this);
- extractTask.execute();
- } else {
- message.setText("<html><font color=\"red\">Could not connect to endpoint</html>");
- }
+ message.setText("Checking SPARQL endpoint availability");
+ setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
+
+ mon = new ProgressMonitor(this, "Extracting fragment", "", 0, 100);
+
+ extractTask = new OntologyExtractingTask(this, mon);
+ extractTask.addPropertyChangeListener(this);
+ extractTask.execute();
+
}
private boolean urlIsConnectable()
- {
+ {
+
+
URL url = null;
try {
+// List<String> defaultGraphURIS = new ArrayList<String>(1);
+// defaultGraphURIS.add(defaultGraphField.getText());
+// SparqlEndpoint endpoint = new SparqlEndpoint(new URL(comboBox.getSelectedItem().toString()), defaultGraphURIS, Collections.<String>emptyList());
+// url = new URL(endpoint.getHTTPRequest() + "SELECT * WHERE {?s ?p ?o} LIMIT 1");
url = new URL((String)comboBox.getSelectedItem());
} catch (MalformedURLException e1) {
// TODO Auto-generated catch block
@@ -368,13 +374,23 @@
class OntologyExtractingTask extends SwingWorker<Void, Void>{
private ProgressMonitor mon;
+ private JDialog dialog;
- public OntologyExtractingTask(ProgressMonitor mon) {
- this.mon = mon;
+ public OntologyExtractingTask(JDialog dialog, ProgressMonitor mon) {
+ this.mon = mon;
+ this.dialog = dialog;
}
@Override
public Void doInBackground() {
+ if(urlIsConnectable()){
+ message.setText("Successfully connected to SPARQL endpoint");
+
+ } else {
+ message.setText("<html><font color=\"red\">Could not connect to SPARQL endpoint</html>");
+ cancel(true);
+ }
+
ComponentManager cm = ComponentManager.getInstance();
URL endpointURL = null;
try {
@@ -387,27 +403,33 @@
defaultGraphURIS.add(defaultGraphField.getText());
SparqlEndpoint endpoint = new SparqlEndpoint(endpointURL, defaultGraphURIS, Collections.<String>emptyList());
task = new SPARQLTasks(endpoint);
- String classKBString;
+ String concept;
if(asLabelButton.isSelected()){
- classKBString = "\"" + getClassFromLabel() + "\"";
+ concept = getClassFromLabel();
} else {
- classKBString = "\"" + classField.getText() +"\"";
+ concept = classField.getText();
}
+// String classKBString;
+// if(asLabelButton.isSelected()){
+// classKBString = "\"" + getClassFromLabel() + "\"";
+// } else {
+// classKBString = "\"" + classField.getText() +"\"";
+// }
- AutomaticPositiveExampleFinderSPARQL pos = new AutomaticPositiveExampleFinderSPARQL(
- task);
- pos.makePositiveExamplesFromConcept(classKBString);
+// AutomaticPositiveExampleFinderSPARQL pos = new AutomaticPositiveExampleFinderSPARQL(
+// task);
+// pos.makePositiveExamplesFromConcept(classKBString);
- SortedSet<String> allPosExamples = pos.getPosExamples();
+ SortedSet<String> allPosExamples = getPosExamples(concept);//pos.getPosExamples();
SortedSet<String> posExamples = SetManipulation.stableShrink(
allPosExamples, 20);
-
+ System.out.println(posExamples);
SortedSet<String> instances = new TreeSet<String>(posExamples);
ks = cm.knowledgeSource(SparqlKnowledgeSource.class);
- ks.getConfigurator().setUrl(SparqlEndpoint.getEndpointDBpedia().getURL());
+ ks.getConfigurator().setUrl(endpoint.getURL());
ks.getConfigurator().setInstances(instances);
- ks.getConfigurator().setPredefinedFilter("YAGO");
+// ks.getConfigurator().setPredefinedFilter("YAGO");
ks.getConfigurator().setBreakSuperClassRetrievalAfter(optionsPanel.getBreakSuperClassRetrievalAfterValue());
ks.getConfigurator().setRecursionDepth(optionsPanel.getRecursionDepthValue());
ks.getConfigurator().setUseCache(optionsPanel.isUseCache());
@@ -418,7 +440,7 @@
ks.getConfigurator().setGetPropertyInformation(optionsPanel.isGetPropertyInformation());
ks.getConfigurator().setCloseAfterRecursion(optionsPanel.isCloseAfterRecursion());
ks.addProgressMonitor(mon);
-
+ ks.getConfigurator().setSaveExtractedFragment(true);
ks.init();
return null;
@@ -426,12 +448,25 @@
@Override
public void done() {
-
+ dialog.setCursor(null);
if(!isCancelled() && ks != null){
okButton.setEnabled(true);
message.setText("<html><font color=\"green\">Fragment successfully extracted</html>");
+
}
}
+
+ private SortedSet<String> getPosExamples(String concept){
+ SortedSet<String> examples = new TreeSet<String>();
+ SortedSet<String> superClasses = task.getSuperClasses(concept, 2);
+
+ for (String sup : superClasses) {
+ examples.addAll(task.retrieveInstancesForClassDescription("\""
+ + sup + "\"", 20));
+
+ }
+ return examples;
+ }
}
@Override
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