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[DL-Learner SVN] SF.net SVN: dl-learner:[2144] trunk
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From: <lor...@us...> - 2010-05-04 20:36:58
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Revision: 2144
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2144&view=rev
Author: lorenz_b
Date: 2010-05-04 20:36:49 +0000 (Tue, 04 May 2010)
Log Message:
-----------
Refactoring to OWLAPI V3 almost finished.
Modified Paths:
--------------
trunk/lib/owlapi/owlapi-bin.jar
trunk/lib/pellet/pellet-core.jar
trunk/lib/pellet/pellet-datatypes.jar
trunk/lib/pellet/pellet-el.jar
trunk/lib/pellet/pellet-explanation.jar
trunk/lib/pellet/pellet-modularity.jar
trunk/lib/pellet/pellet-rules.jar
trunk/lib/protege/org.protege.editor.core.application.jar
trunk/lib/protege/org.protege.editor.owl.jar
trunk/src/dl-learner/org/dllearner/Info.java
trunk/src/dl-learner/org/dllearner/algorithms/gp/ADC.java
trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
trunk/src/dl-learner/org/dllearner/core/owl/KB.java
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/examples/Corpus.java
trunk/src/dl-learner/org/dllearner/examples/KRK.java
trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java
trunk/src/dl-learner/org/dllearner/examples/corpus/Sentence.java
trunk/src/dl-learner/org/dllearner/kb/OWLAPIOntology.java
trunk/src/dl-learner/org/dllearner/kb/extraction/BlankNode.java
trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java
trunk/src/dl-learner/org/dllearner/kb/extraction/DatatypePropertyNode.java
trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java
trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java
trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java
trunk/src/dl-learner/org/dllearner/kb/extraction/OWLAPIOntologyCollector.java
trunk/src/dl-learner/org/dllearner/kb/extraction/ObjectPropertyNode.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/learningproblems/EvaluatedDescriptionClass.java
trunk/src/dl-learner/org/dllearner/learningproblems/EvaluatedDescriptionPosNeg.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDIGConverter.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java
trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java
trunk/src/dl-learner/org/dllearner/scripts/evaluation/EvaluationGUI.java
trunk/src/dl-learner/org/dllearner/scripts/evaluation/OntologyChecker.java
trunk/src/dl-learner/org/dllearner/scripts/evaluation/StatsGenerator.java
trunk/src/dl-learner/org/dllearner/test/FaCTBugDemo.java
trunk/src/dl-learner/org/dllearner/test/JenaConstruct.java
trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java
trunk/src/dl-learner/org/dllearner/test/OWLAPIConsistency.java
trunk/src/dl-learner/org/dllearner/test/PelletBug.java
trunk/src/dl-learner/org/dllearner/test/PelletBug2.java
trunk/src/dl-learner/org/dllearner/test/PelletPerformanceProblem.java
trunk/src/dl-learner/org/dllearner/test/junit/OWLAPITests.java
trunk/src/dl-learner/org/dllearner/tools/evaluationplugin/EvaluationPlugin.java
trunk/src/dl-learner/org/dllearner/tools/evaluationplugin/EvaluationTable.java
trunk/src/dl-learner/org/dllearner/tools/evaluationplugin/EvaluationTableModel.java
trunk/src/dl-learner/org/dllearner/tools/evaluationplugin/GraphicalCoveragePanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ConcurrencyBug.java
trunk/src/dl-learner/org/dllearner/tools/ore/DescriptionParseTest.java
trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationTest.java
trunk/src/dl-learner/org/dllearner/tools/ore/ImpactManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/LearningManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/OntologyModifier.java
trunk/src/dl-learner/org/dllearner/tools/ore/PelletBug.java
trunk/src/dl-learner/org/dllearner/tools/ore/RepairManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/RepairManagerListener.java
trunk/src/dl-learner/org/dllearner/tools/ore/TaskManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/cache/DLSyntaxRenderingCache.java
trunk/src/dl-learner/org/dllearner/tools/ore/cache/ManchesterSyntaxRenderingCache.java
trunk/src/dl-learner/org/dllearner/tools/ore/cache/OWLEntityRenderingCache.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/AxiomSelector.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/AxiomUsageChecker.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/Explanation.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/ExplanationException.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/ExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/HSTExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LaconicTest.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/LostEntailmentsChecker.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/PelletExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/RemainingAxiomPartsGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/RootFinder.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/laconic/BaseDescriptionGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/laconic/Beta.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/laconic/BottomTester.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/laconic/LaconicExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/laconic/OPlus.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/laconic/Tau.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/laconic/TopTester.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/HittingSet.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/RelevanceBasedGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SimpleSelectionFunction.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SyntacticRelevanceBasedExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ChangesTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ClassesTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ClassesTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/DescriptionLabel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExplanationTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExplanationTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/GraphicalCoveragePanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ImpactTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ImpactTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/MarkableClassExpressionsTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/MarkableClassExpressionsTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/MetricsPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/MetricsTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/OverrideFileChooser.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RemainingAxiomsDialog.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RemainingAxiomsTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RemainingAxiomsTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RepairDialog.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RepairTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RepairTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ResultTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/SimpleExplanationTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/SimpleExplanationTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/StatsTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/StatsTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/StatusBar.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/StatusBar2.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/UndoLabel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/UnsatClassesTableCellRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/UnsatisfiableClassesTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/UnsatisfiableClassesTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/AutoCompleterMatcher.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/ExpressionEditor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/ManchesterOWLSyntaxParser.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OREOWLEntityChecker.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLAutoCompleter.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLAxiomChecker.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLAxiomsEditor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLClassAxiomChecker.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLClassAxiomEditor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLEntityFinder.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLExpressionChecker.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLExpressionParserException.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLObjectPropertyAxiomChecker.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/OWLObjectPropertyAxiomEditor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/editor/ParserUtil.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/item/RemoveAllPropertyAssertionsToMenuItem.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/DescriptionComparator.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/KeywordColorMap.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/ManchesterOWLSyntaxOWLObjectRendererImpl.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/ManchesterOWLSyntaxObjectRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/ManchesterSyntaxRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/ManchesterSyntaxTableCellRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/MultiLineTableCellRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/OWLEntityRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/TextAreaRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/WizardController.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/AutoLearnPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ClassChoosePanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/InconsistencyExplanationPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/KnowledgeSourcePanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ManualLearnPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/RepairPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/UnsatisfiableExplanationPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ClassChoosePanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/InconsistencyExplanationPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ManualLearnPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/UnsatisfiableExplanationPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/UnsatisfiableExplanationPanel2.java
trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerView.java
trunk/src/dl-learner/org/dllearner/tools/protege/GraphicalCoveragePanel.java
trunk/src/dl-learner/org/dllearner/tools/protege/GraphicalCoveragePanelHandler.java
trunk/src/dl-learner/org/dllearner/tools/protege/IndividualPoint.java
trunk/src/dl-learner/org/dllearner/tools/protege/ProtegePlugin.java
trunk/src/dl-learner/org/dllearner/tools/protege/ReadingOntologyThread.java
trunk/src/dl-learner/org/dllearner/tools/protege/StatusBar2.java
trunk/src/dl-learner/org/dllearner/tools/protege/SuggestionsTable.java
trunk/src/dl-learner/org/dllearner/tools/protege/SuggestionsTableModel.java
trunk/src/dl-learner/org/dllearner/utilities/owl/DLLearnerDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/utilities/owl/ManchesterOWLSyntaxParser.java
trunk/src/dl-learner/org/dllearner/utilities/owl/OWLAPIAxiomConvertVisitor.java
trunk/src/dl-learner/org/dllearner/utilities/owl/OWLAPIConverter.java
trunk/src/dl-learner/org/dllearner/utilities/owl/OWLAPIDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/utilities/owl/OWLAPIRenderers.java
trunk/src/dl-learner/org/dllearner/utilities/owl/OntologyClassRewriter.java
trunk/src/dl-learner/org/dllearner/utilities/owl/OntologyCloser.java
trunk/src/dl-learner/org/dllearner/utilities/owl/OntologyCloserOWLAPI.java
Added Paths:
-----------
trunk/lib/fact/factplusplus-1.3.1.jar
trunk/lib/pellet/pellet-owlapiv3.jar
trunk/lib/pellet/pellet-query.jar
trunk/src/dl-learner/org/dllearner/tools/evaluationplugin/SubsumptionTree.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/AddRoundButton.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/OWLEntityShortFormProvider.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/OWLTableCellRenderer.java
Removed Paths:
-------------
trunk/lib/fact/FaCTpp-OWLAPI-v1.1.11.jar
trunk/lib/owlapi/owlapiV3-bin.jar
trunk/lib/pellet/pellet-owlapi.jar
trunk/src/dl-learner/org/dllearner/tools/ore/ui/rendering/ManchesterRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/ManualLearnPanel2.java
Deleted: trunk/lib/fact/FaCTpp-OWLAPI-v1.1.11.jar
===================================================================
(Binary files differ)
Added: trunk/lib/fact/factplusplus-1.3.1.jar
===================================================================
(Binary files differ)
Property changes on: trunk/lib/fact/factplusplus-1.3.1.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/lib/owlapi/owlapi-bin.jar
===================================================================
(Binary files differ)
Deleted: trunk/lib/owlapi/owlapiV3-bin.jar
===================================================================
(Binary files differ)
Modified: trunk/lib/pellet/pellet-core.jar
===================================================================
(Binary files differ)
Modified: trunk/lib/pellet/pellet-datatypes.jar
===================================================================
(Binary files differ)
Modified: trunk/lib/pellet/pellet-el.jar
===================================================================
(Binary files differ)
Modified: trunk/lib/pellet/pellet-explanation.jar
===================================================================
(Binary files differ)
Modified: trunk/lib/pellet/pellet-modularity.jar
===================================================================
(Binary files differ)
Deleted: trunk/lib/pellet/pellet-owlapi.jar
===================================================================
(Binary files differ)
Added: trunk/lib/pellet/pellet-owlapiv3.jar
===================================================================
(Binary files differ)
Property changes on: trunk/lib/pellet/pellet-owlapiv3.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/lib/pellet/pellet-query.jar
===================================================================
(Binary files differ)
Property changes on: trunk/lib/pellet/pellet-query.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/lib/pellet/pellet-rules.jar
===================================================================
(Binary files differ)
Modified: trunk/lib/protege/org.protege.editor.core.application.jar
===================================================================
(Binary files differ)
Modified: trunk/lib/protege/org.protege.editor.owl.jar
===================================================================
(Binary files differ)
Modified: trunk/src/dl-learner/org/dllearner/Info.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/Info.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/Info.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -3,6 +3,6 @@
package org.dllearner;
public class Info {
- public static final String build = "2010-03-13";
+ public static final String build = "2010-03-15";
}
\ No newline at end of file
Modified: trunk/src/dl-learner/org/dllearner/algorithms/gp/ADC.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/gp/ADC.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/algorithms/gp/ADC.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -5,9 +5,9 @@
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.DescriptionVisitor;
import org.dllearner.core.owl.KBElementVisitor;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLDescriptionVisitor;
-import org.semanticweb.owl.model.OWLObjectVisitor;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpressionVisitor;
+import org.semanticweb.owlapi.model.OWLObjectVisitor;
/**
* ADC stand for "automatically defined concept". It is used for
@@ -73,7 +73,7 @@
/* (non-Javadoc)
* @see org.semanticweb.owl.model.OWLDescription#accept(org.semanticweb.owl.model.OWLDescriptionVisitor)
*/
- public void accept(OWLDescriptionVisitor arg0) {
+ public void accept(OWLClassExpressionVisitor arg0) {
// TODO Auto-generated method stub
}
Modified: trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -28,7 +28,7 @@
import org.dllearner.utilities.owl.OWLAPIRenderers;
import org.json.JSONException;
import org.json.JSONObject;
-import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owlapi.model.OWLClassExpression;
/**
* An evaluated description is a description and its score (with some
@@ -123,8 +123,8 @@
JSONObject object = new JSONObject();
try {
object.put("descriptionManchesterSyntax", description.toManchesterSyntaxString(null, null));
- OWLDescription d = OWLAPIDescriptionConvertVisitor.getOWLDescription(description);
- object.put("descriptionOWLXML", OWLAPIRenderers.toOWLXMLSyntax(d));
+ OWLClassExpression c = OWLAPIDescriptionConvertVisitor.getOWLClassExpression(description);
+ object.put("descriptionOWLXML", OWLAPIRenderers.toOWLXMLSyntax(c));
object.put("descriptionKBSyntax", description.toKBSyntaxString());
object.put("scoreValue", score.getAccuracy());
return object.toString(3);
Modified: trunk/src/dl-learner/org/dllearner/core/owl/KB.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/KB.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/core/owl/KB.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -1,7 +1,6 @@
package org.dllearner.core.owl;
import java.io.File;
-import java.net.URI;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
@@ -9,13 +8,14 @@
import java.util.TreeSet;
import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
-import org.semanticweb.owl.apibinding.OWLManager;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLOntologyCreationException;
-import org.semanticweb.owl.model.OWLOntologyManager;
-import org.semanticweb.owl.model.OWLOntologyStorageException;
-import org.semanticweb.owl.model.UnknownOWLOntologyException;
-import org.semanticweb.owl.util.SimpleURIMapper;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.UnknownOWLOntologyException;
+import org.semanticweb.owlapi.util.SimpleIRIMapper;
public class KB implements KBElement {
@@ -290,13 +290,13 @@
public void export(File file, org.dllearner.core.OntologyFormat format){
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
- URI ontologyURI = URI.create("http://example.com");
- URI physicalURI = file.toURI();
- SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
- manager.addURIMapper(mapper);
+ IRI ontologyIRI = IRI.create("http://example.com");
+ IRI physicalIRI = IRI.create(file.toURI());
+ SimpleIRIMapper mapper = new SimpleIRIMapper(ontologyIRI, physicalIRI);
+ manager.addIRIMapper(mapper);
OWLOntology ontology;
try {
- ontology = manager.createOntology(ontologyURI);
+ ontology = manager.createOntology(ontologyIRI);
// OWLAPIReasoner.fillOWLAPIOntology(manager,ontology,kb);
OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, this);
manager.saveOntology(ontology);
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -22,7 +22,6 @@
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
-import java.net.URI;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
@@ -33,18 +32,18 @@
import java.util.Set;
import java.util.TreeSet;
+import org.dllearner.core.owl.Axiom;
import org.dllearner.core.owl.BooleanDatatypePropertyAssertion;
+import org.dllearner.core.owl.ClassAssertionAxiom;
+import org.dllearner.core.owl.DatatypeProperty;
+import org.dllearner.core.owl.DatatypePropertyAssertion;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.DifferentIndividualsAxiom;
import org.dllearner.core.owl.DisjointClassesAxiom;
-import org.dllearner.core.owl.NamedClass;
-import org.dllearner.core.owl.Axiom;
-import org.dllearner.core.owl.ClassAssertionAxiom;
-import org.dllearner.core.owl.DatatypeProperty;
-import org.dllearner.core.owl.DatatypePropertyAssertion;
import org.dllearner.core.owl.DoubleDatatypePropertyAssertion;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.KB;
+import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.ObjectPropertyAssertion;
import org.dllearner.core.owl.SubClassAxiom;
@@ -57,6 +56,7 @@
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.Helper;
+import org.semanticweb.owlapi.model.IRI;
/**
* This class maps the carcinogenesis Prolog files to an OWL file. In a first
@@ -79,7 +79,7 @@
*/
public class Carcinogenesis {
- private static URI ontologyURI = URI.create("http://dl-learner.org/carcinogenesis");
+ private static IRI ontologyIRI = IRI.create("http://dl-learner.org/carcinogenesis");
// directory of Prolog files
private static final String prologDirectory = "examples/carcinogenesis/prolog/";
@@ -252,7 +252,7 @@
// writing generated knowledge base
System.out.print("Writing OWL file ... ");
startTime = System.nanoTime();
- OWLAPIReasoner.exportKBToOWL(owlFile, kb, ontologyURI);
+ OWLAPIReasoner.exportKBToOWL(owlFile, kb, ontologyIRI);
duration = System.nanoTime() - startTime;
time = Helper.prettyPrintNanoSeconds(duration, false, false);
System.out.println("OK (" + time + ").");
@@ -554,23 +554,23 @@
}
private static Individual getIndividual(String name) {
- return new Individual(ontologyURI + "#" + name);
+ return new Individual(ontologyIRI + "#" + name);
}
private static ObjectProperty getRole(String name) {
- return new ObjectProperty(ontologyURI + "#" + name);
+ return new ObjectProperty(ontologyIRI + "#" + name);
}
private static DatatypeProperty getDatatypeProperty(String name) {
- return new DatatypeProperty(ontologyURI + "#" + name);
+ return new DatatypeProperty(ontologyIRI + "#" + name);
}
private static NamedClass getAtomicConcept(String name) {
- return new NamedClass(ontologyURI + "#" + name);
+ return new NamedClass(ontologyIRI + "#" + name);
}
private static String getURI(String name) {
- return ontologyURI + "#" + name;
+ return ontologyIRI + "#" + name;
}
// returns URI including quotationsmark (need for KBparser)
Modified: trunk/src/dl-learner/org/dllearner/examples/Corpus.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Corpus.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/examples/Corpus.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -4,21 +4,21 @@
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
-import java.net.URI;
import java.util.ArrayList;
import java.util.List;
import java.util.StringTokenizer;
import org.dllearner.examples.corpus.Sentence;
-import org.semanticweb.owl.apibinding.OWLManager;
-import org.semanticweb.owl.model.AddAxiom;
-import org.semanticweb.owl.model.OWLAxiom;
-import org.semanticweb.owl.model.OWLDataFactory;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLOntologyChangeException;
-import org.semanticweb.owl.model.OWLOntologyCreationException;
-import org.semanticweb.owl.model.OWLOntologyManager;
-import org.semanticweb.owl.util.SimpleURIMapper;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.AddAxiom;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChangeException;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.util.SimpleIRIMapper;
public class Corpus {
@@ -85,11 +85,11 @@
public static void init(){
try{
br = new BufferedReader(new FileReader(file));
- URI ontologyURI = URI.create(namespace);
+ IRI ontologyURI = IRI.create(namespace);
//URI physicalURI = new File("cache/"+System.currentTimeMillis()+".owl").toURI();
- URI physicalURI = new File("cache/tiger.owl").toURI();
- SimpleURIMapper mapper = new SimpleURIMapper(ontologyURI, physicalURI);
- manager.addURIMapper(mapper);
+ IRI physicalURI = IRI.create(new File("cache/tiger.owl").toURI());
+ SimpleIRIMapper mapper = new SimpleIRIMapper(ontologyURI, physicalURI);
+ manager.addIRIMapper(mapper);
try{
currentOntology = manager.createOntology(ontologyURI);
}catch(OWLOntologyCreationException e){
@@ -109,7 +109,6 @@
try{
manager.applyChange(addAxiom);
}catch (OWLOntologyChangeException e) {
- //TODO
e.printStackTrace();
}
}
Modified: trunk/src/dl-learner/org/dllearner/examples/KRK.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRK.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/examples/KRK.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -7,7 +7,6 @@
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
-import java.net.URI;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
@@ -32,6 +31,7 @@
import org.dllearner.core.owl.TransitiveObjectPropertyAxiom;
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.owl.OntologyCloser;
+import org.semanticweb.owlapi.model.IRI;
/*
* Structure
@@ -75,7 +75,7 @@
static String owlfilename = "complete_nodraw.owl";
- static URI ontologyURI = URI.create("http://dl-learner.org/krk");
+ static IRI ontologyIRI = IRI.create("http://dl-learner.org/krk");
// static SortedSet<String> fileSet = new TreeSet<String>();
static SortedSet<String> allInstances = new TreeSet<String>();
static SortedSet<String> classSet = new TreeSet<String>();
@@ -682,7 +682,7 @@
File owlfile = new File(workingDir+"/" + filename);
// System.out.println(kb.toString("http://www.test.de/test", new
// HashMap<String, String>()));
- OWLAPIReasoner.exportKBToOWL(owlfile, kb, ontologyURI);
+ OWLAPIReasoner.exportKBToOWL(owlfile, kb, ontologyIRI);
}
@@ -691,7 +691,7 @@
System.out.println("Writing kb");
try{
FileWriter fw = new FileWriter(workingDir+"/" + filename,false);
- fw.write(kb.toKBSyntaxString(ontologyURI.toString(), null));
+ fw.write(kb.toKBSyntaxString(ontologyIRI.toString(), null));
fw.flush();
}catch (Exception e) {e.printStackTrace();}
System.out.println("done writing kb");
@@ -700,25 +700,25 @@
}
protected static Individual getIndividual(String name) {
- return new Individual(ontologyURI + "#" + name);
+ return new Individual(ontologyIRI + "#" + name);
}
protected static ObjectProperty getRole(String name) {
- return new ObjectProperty(ontologyURI + "#" + name);
+ return new ObjectProperty(ontologyIRI + "#" + name);
}
@SuppressWarnings("unused")
protected static DatatypeProperty getDatatypeProperty(String name) {
- return new DatatypeProperty(ontologyURI + "#" + name);
+ return new DatatypeProperty(ontologyIRI + "#" + name);
}
protected static NamedClass getAtomicConcept(String name) {
- return new NamedClass(ontologyURI + "#" + name);
+ return new NamedClass(ontologyIRI + "#" + name);
}
@SuppressWarnings("unused")
protected static String getURI(String name) {
- return ontologyURI + "#" + name;
+ return ontologyIRI + "#" + name;
}
@SuppressWarnings("unused")
Modified: trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -6,7 +6,6 @@
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
-import java.net.URI;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
@@ -36,6 +35,7 @@
import org.dllearner.reasoning.FastInstanceChecker;
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.statistics.SimpleClock;
+import org.semanticweb.owlapi.model.IRI;
/*
* Structure
@@ -74,7 +74,7 @@
static String allData = workingDir+"krkopt_no_draw.data";
//static String allData = workingDir+"krkopt_original_dataset.data";
- static URI ontologyURI = KRKOntologyTBox.ontologyURI;
+ static IRI ontologyURI = IRI.create(KRKOntologyTBox.ontologyURI);
// static SortedSet<String> fileSet = new TreeSet<String>();
//static SortedSet<String> allInstances = new TreeSet<String>();
Modified: trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -20,7 +20,6 @@
package org.dllearner.examples;
import java.io.File;
-import java.net.URI;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
@@ -45,6 +44,7 @@
import org.dllearner.utilities.Files;
import org.dllearner.utilities.Helper;
import org.ini4j.IniFile;
+import org.semanticweb.owlapi.model.IRI;
/**
* Converts SM2PH database to an OWL ontology. To run the script, please
@@ -55,7 +55,7 @@
*/
public class MonogenicDiseases {
- private static URI ontologyURI = URI.create("http://dl-learner.org/mutation");
+ private static IRI ontologyURI = IRI.create("http://dl-learner.org/mutation");
private static File owlFile = new File("examples/mutation/mutation.owl");
private static File confFile = new File("examples/mutation/mutation.conf");
Modified: trunk/src/dl-learner/org/dllearner/examples/corpus/Sentence.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/corpus/Sentence.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/examples/corpus/Sentence.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -1,16 +1,17 @@
package org.dllearner.examples.corpus;
-import java.net.URI;
import java.util.ArrayList;
import java.util.List;
import java.util.StringTokenizer;
import org.dllearner.examples.Corpus;
import org.dllearner.utilities.URLencodeUTF8;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLDescription;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
public class Sentence {
int id ;
@@ -34,22 +35,22 @@
super();
this.id = id;
this.sentence = sentence;
- this.sentenceURI = Corpus.factory.getOWLIndividual(URI.create(Corpus.namespace+"#"+"satz"+id));
+ this.sentenceURI = Corpus.factory.getOWLNamedIndividual(IRI.create(Corpus.namespace+"#"+"satz"+id));
this.urisInOrder = new ArrayList<String>();
this.wordsInOrder = new ArrayList<String>();
- element = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#Element"));
- structElement = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#StructureElement"));
- wordElement = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#WordElement"));
- sentenceClass = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#Sentence"));
- tagClass = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#Tag"));
- morphClass = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#Morph"));
- edgeClass = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#Edge"));
+ element = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#Element"));
+ structElement = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#StructureElement"));
+ wordElement = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#WordElement"));
+ sentenceClass = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#Sentence"));
+ tagClass = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#Tag"));
+ morphClass = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#Morph"));
+ edgeClass = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#Edge"));
- hasElement = Corpus.factory.getOWLObjectProperty(URI.create(Corpus.namespace+"#hasElement"));
+ hasElement = Corpus.factory.getOWLObjectProperty(IRI.create(Corpus.namespace+"#hasElement"));
- Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(this.sentenceURI,sentenceClass ));
+ Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(sentenceClass, this.sentenceURI));
}
public void processSentence(){
@@ -65,7 +66,7 @@
public void processLine(String line, int pos){
String elementURL = Corpus.namespace+"#";
- OWLIndividual lineElement;
+ OWLNamedIndividual lineElement;
StringTokenizer st = new StringTokenizer(line);
//%String %% word lemma tag morph edge parent secedge comment
@@ -78,20 +79,22 @@
//word
if(word.startsWith("#")){
elementURL+="s_"+id+"_"+word.substring(1);
- lineElement = Corpus.factory.getOWLIndividual(URI.create(elementURL));
- Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(lineElement, structElement));
+ lineElement = Corpus.factory.getOWLNamedIndividual(IRI.create(elementURL));
+ Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(structElement, lineElement));
}else{
elementURL+="s_"+id+"_"+pos+"_"+URLencodeUTF8.encode(word);
wordsInOrder.add(word);
urisInOrder.add(elementURL);
- lineElement = Corpus.factory.getOWLIndividual(URI.create(elementURL));
- Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(lineElement, wordElement));
- Corpus.addAxiom(Corpus.factory.getOWLEntityAnnotationAxiom(lineElement, Corpus.factory.getCommentAnnotation(line)));
- Corpus.addAxiom(Corpus.factory.getOWLEntityAnnotationAxiom(lineElement, Corpus.factory.getOWLLabelAnnotation(word)));
+ lineElement = Corpus.factory.getOWLNamedIndividual(IRI.create(elementURL));
+ Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(wordElement, lineElement));
+ Corpus.addAxiom(Corpus.factory.getOWLAnnotationAssertionAxiom(Corpus.factory.getRDFSComment(),
+ lineElement.getIRI(), Corpus.factory.getOWLStringLiteral(line)));
+ Corpus.addAxiom(Corpus.factory.getOWLAnnotationAssertionAxiom(Corpus.factory.getRDFSLabel(),
+ lineElement.getIRI(), Corpus.factory.getOWLStringLiteral(word)));
}
- Corpus.addAxiom(Corpus.factory.getOWLObjectPropertyAssertionAxiom(sentenceURI, hasElement, lineElement));
+ Corpus.addAxiom(Corpus.factory.getOWLObjectPropertyAssertionAxiom(hasElement, sentenceURI, lineElement));
//tag
tag = (tag.equals("$("))?"SentenceBoundary":tag;
@@ -103,20 +106,20 @@
void makeClasses(OWLIndividual lineElement, String tag, String morph, String edge){
if(!tag.equals("--")){
- OWLDescription d = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#"+tag));
- Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(lineElement,d ));
- Corpus.addAxiom(Corpus.factory.getOWLSubClassAxiom(d, tagClass));
+ OWLClassExpression d = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#"+tag));
+ Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(d, lineElement));
+ Corpus.addAxiom(Corpus.factory.getOWLSubClassOfAxiom(d, tagClass));
}
if(!morph.equals("m_--")){
- OWLDescription d = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#"+morph));
- Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(lineElement,d ));
- Corpus.addAxiom(Corpus.factory.getOWLSubClassAxiom(d, morphClass));
+ OWLClassExpression d = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#"+morph));
+ Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(d, lineElement));
+ Corpus.addAxiom(Corpus.factory.getOWLSubClassOfAxiom(d, morphClass));
}
if(!edge.equals("--")){
- OWLDescription d = Corpus.factory.getOWLClass(URI.create(Corpus.namespace+"#"+edge));
- Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(lineElement,d ));
- Corpus.addAxiom(Corpus.factory.getOWLSubClassAxiom(d, edgeClass));
+ OWLClassExpression d = Corpus.factory.getOWLClass(IRI.create(Corpus.namespace+"#"+edge));
+ Corpus.addAxiom(Corpus.factory.getOWLClassAssertionAxiom(d, lineElement));
+ Corpus.addAxiom(Corpus.factory.getOWLSubClassOfAxiom(d, edgeClass));
}
}
}
Modified: trunk/src/dl-learner/org/dllearner/kb/OWLAPIOntology.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/OWLAPIOntology.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/kb/OWLAPIOntology.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -11,11 +11,12 @@
import org.dllearner.core.options.ConfigEntry;
import org.dllearner.core.options.InvalidConfigOptionValueException;
import org.dllearner.core.owl.KB;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLDataProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLObjectProperty;
-import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLOntology;
public class OWLAPIOntology extends KnowledgeSource {
@@ -30,7 +31,7 @@
private Set<OWLClass> classes;
private Set<OWLObjectProperty> prop;
private Set<OWLDataProperty> dataProp;
- private Set<OWLIndividual> individuals;
+ private Set<OWLNamedIndividual> individuals;
public OWLAPIOntology() {
this(null);
@@ -39,10 +40,10 @@
public OWLAPIOntology(OWLOntology onto)
{
this.ontology = onto;
- classes = ontology.getReferencedClasses();
- prop = ontology.getReferencedObjectProperties();
- dataProp = ontology.getReferencedDataProperties();
- individuals = ontology.getReferencedIndividuals();
+ classes = ontology.getClassesInSignature();
+ prop = ontology.getObjectPropertiesInSignature();
+ dataProp = ontology.getDataPropertiesInSignature();
+ individuals = ontology.getIndividualsInSignature();
this.configurator = new OWLAPIOntologyConfigurator(this);
}
@@ -91,17 +92,17 @@
Iterator<OWLOntology> it = ontologies.iterator();
while(it.hasNext()) {
OWLOntology ont = it.next();
- if(ont.getReferencedClasses() != null) {
- classes.addAll(ont.getReferencedClasses());
+ if(ont.getClassesInSignature() != null) {
+ classes.addAll(ont.getClassesInSignature());
}
- if(ont.getReferencedObjectProperties() != null) {
- prop.addAll(ont.getReferencedObjectProperties());
+ if(ont.getObjectPropertiesInSignature() != null) {
+ prop.addAll(ont.getObjectPropertiesInSignature());
}
- if(ont.getReferencedDataProperties() != null) {
- dataProp.addAll(ont.getReferencedDataProperties());
+ if(ont.getDataPropertiesInSignature() != null) {
+ dataProp.addAll(ont.getDataPropertiesInSignature());
}
- if(ont.getReferencedIndividuals() != null) {
- individuals.addAll(ont.getReferencedIndividuals());
+ if(ont.getIndividualsInSignature() != null) {
+ individuals.addAll(ont.getIndividualsInSignature());
}
}
}
@@ -122,7 +123,7 @@
return dataProp;
}
- public Set<OWLIndividual> getOWLIndividuals() {
+ public Set<OWLNamedIndividual> getOWLIndividuals() {
return individuals;
}
}
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/BlankNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/BlankNode.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/BlankNode.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -1,6 +1,5 @@
package org.dllearner.kb.extraction;
-import java.net.URI;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
@@ -16,9 +15,10 @@
import org.dllearner.utilities.datastructures.RDFNodeTuple;
import org.dllearner.utilities.datastructures.StringTuple;
import org.dllearner.utilities.owl.OWLVocabulary;
-import org.semanticweb.owl.model.OWLDataFactory;
-import org.semanticweb.owl.model.OWLDescription;
-import org.semanticweb.owl.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
public class BlankNode extends Node {
private static Logger logger = Logger
@@ -107,8 +107,8 @@
}
@Override
- public URI getURI(){
- return URI.create("http://www.empty.org/empty#empty");
+ public IRI getIRI(){
+ return IRI.create("http://www.empty.org/empty#empty");
}
@Override
@@ -121,9 +121,9 @@
return inboundEdge;
}
- public OWLDescription getAnonymousClass(OWLAPIOntologyCollector owlAPIOntologyCollector){
+ public OWLClassExpression getAnonymousClass(OWLAPIOntologyCollector owlAPIOntologyCollector){
OWLDataFactory factory = owlAPIOntologyCollector.getFactory();
- OWLDescription ret = factory.getOWLClass(URI.create("http://dummy.org/dummy"));
+ OWLClassExpression ret = factory.getOWLClass(IRI.create("http://dummy.org/dummy"));
//System.out.println(inboundEdge);
@@ -132,7 +132,7 @@
(inboundEdge.equals(OWLVocabulary.OWL_complementOf))||
(inboundEdge.equals(OWLVocabulary.OWL_unionOf))
){
- Set<OWLDescription> target = new HashSet<OWLDescription>();
+ Set<OWLClassExpression> target = new HashSet<OWLClassExpression>();
List<BlankNode> tmp = new ArrayList<BlankNode>();
tmp.add(this);
while(!tmp.isEmpty()){
@@ -142,7 +142,7 @@
if(next.otherNodes.contains(new StringTuple(OWLVocabulary.RDF_REST, OWLVocabulary.RDF_NIL))){
for(StringTuple t : next.otherNodes){
if(t.a.equals(OWLVocabulary.RDF_FIRST)){
- target.add(factory.getOWLClass(URI.create(t.b)));
+ target.add(factory.getOWLClass(IRI.create(t.b)));
//System.out.println("added "+t.b);
}
}
@@ -153,7 +153,7 @@
try{
firstOtherNodes = next.otherNodes.first();
if(firstOtherNodes.a.equals(OWLVocabulary.RDF_FIRST)){
- target.add(factory.getOWLClass(URI.create(firstOtherNodes.b)));
+ target.add(factory.getOWLClass(IRI.create(firstOtherNodes.b)));
tmp.add(next.blankNodes.get(0));
//System.out.println("bnode added");
}else{
@@ -181,7 +181,7 @@
tail("more than one complement"+target);
}else{
- return factory.getOWLObjectComplementOf(new ArrayList<OWLDescription>(target).remove(0));
+ return factory.getOWLObjectComplementOf(new ArrayList<OWLClassExpression>(target).remove(0));
}
}else{
printAll();
@@ -226,11 +226,11 @@
}
- private OWLDescription getRestriction(OWLAPIOntologyCollector owlAPIOntologyCollector){
+ private OWLClassExpression getRestriction(OWLAPIOntologyCollector owlAPIOntologyCollector){
OWLDataFactory factory = owlAPIOntologyCollector.getFactory();
OWLObjectProperty property = null;
- OWLDescription concept = null;
- OWLDescription dummy = factory.getOWLClass(URI.create("http://dummy.org/dummy"));
+ OWLClassExpression concept = null;
+ OWLClassExpression dummy = factory.getOWLClass(IRI.create("http://dummy.org/dummy"));
int total = otherNodes.size()+blankNodes.size()+datatypeProperties.size();
if(total >=4 ){
@@ -240,7 +240,7 @@
// get Objectproperty
for(StringTuple n : otherNodes) {
if(n.a.equals(OWLVocabulary.OWL_ON_PROPERTY)){
- property = factory.getOWLObjectProperty(URI.create(n.b));
+ property = factory.getOWLObjectProperty(IRI.create(n.b));
}
}
@@ -249,11 +249,11 @@
DatatypePropertyNode d = datatypeProperties.get(0);
String p = d.getURIString();
if( p.equals(OWLVocabulary.OWL_cardinality)){
- return factory.getOWLObjectExactCardinalityRestriction(property, d.getBPart().getLiteral().getInt());
+ return factory.getOWLObjectExactCardinality(d.getBPart().getLiteral().getInt(), property);
}else if(p.equals(OWLVocabulary.OWL_maxCardinality)){
- return factory.getOWLObjectMaxCardinalityRestriction(property, d.getBPart().getLiteral().getInt());
+ return factory.getOWLObjectMaxCardinality(d.getBPart().getLiteral().getInt(), property);
}else if(p.equals(OWLVocabulary.OWL_minCardinality)){
- return factory.getOWLObjectMinCardinalityRestriction(property, d.getBPart().getLiteral().getInt());
+ return factory.getOWLObjectMinCardinality(d.getBPart().getLiteral().getInt(), property);
}else {
tail(p+d+" in "+this);
}
@@ -270,7 +270,7 @@
(p.equals(OWLVocabulary.OWL_SOME_VALUES_FROM)) ||
(p.equals(OWLVocabulary.OWL_HAS_VALUE))
){
- concept = factory.getOWLClass(URI.create(o));
+ concept = factory.getOWLClass(IRI.create(o));
}
}
}
@@ -278,9 +278,9 @@
for(StringTuple n : otherNodes) {
String p = n.a;
if(p.equals(OWLVocabulary.OWL_ALL_VALUES_FROM)){
- return factory.getOWLObjectAllRestriction(property, concept);
+ return factory.getOWLObjectAllValuesFrom(property, concept);
}else if(p.equals(OWLVocabulary.OWL_SOME_VALUES_FROM)){
- return factory.getOWLObjectSomeRestriction(property, concept);
+ return factory.getOWLObjectSomeValuesFrom(property, concept);
}else if(p.equals(OWLVocabulary.OWL_HAS_VALUE)){
logger.warn("OWL_hasValue not implemented yet");
return dummy;
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -30,11 +30,11 @@
import org.dllearner.kb.manipulator.Manipulator;
import org.dllearner.utilities.datastructures.RDFNodeTuple;
import org.dllearner.utilities.owl.OWLVocabulary;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLCommentAnnotation;
-import org.semanticweb.owl.model.OWLDataFactory;
-import org.semanticweb.owl.model.OWLDescription;
-import org.semanticweb.owl.model.OWLLabelAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
/**
* Is a node in the graph, that is a class.
@@ -149,11 +149,11 @@
try{
OWLDataFactory factory = owlAPIOntologyCollector.getFactory();
- OWLClass me =factory.getOWLClass(getURI());
+ OWLClass me =factory.getOWLClass(getIRI());
for (ObjectPropertyNode one : classProperties) {
- OWLClass c = factory.getOWLClass(one.getBPart().getURI());
+ OWLClass c = factory.getOWLClass(one.getBPart().getIRI());
if(OWLVocabulary.isStringSubClassVocab(one.getURIString())){
- owlAPIOntologyCollector.addAxiom(factory.getOWLSubClassAxiom(me, c));
+ owlAPIOntologyCollector.addAxiom(factory.getOWLSubClassOfAxiom(me, c));
}else if(one.getURIString().equals(OWLVocabulary.OWL_DISJOINT_WITH)){
owlAPIOntologyCollector.addAxiom(factory.getOWLDisjointClassesAxiom(me, c));
}else if(one.getURIString().equals(OWLVocabulary.OWL_EQUIVALENT_CLASS)){
@@ -171,12 +171,14 @@
//FIXME add languages
// watch for tail
if(one.getURIString().equals(OWLVocabulary.RDFS_COMMENT)){
- OWLCommentAnnotation comment = factory.getCommentAnnotation(one.getBPart().getLiteral().getString());
- owlAPIOntologyCollector.addAxiom(factory.getOWLEntityAnnotationAxiom(me, comment));
+ OWLAnnotation annoComment = factory.getOWLAnnotation(factory.getRDFSComment(), factory.getOWLStringLiteral(one.getBPart().getLiteral().getString()));
+ OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(me.getIRI(), annoComment);
+ owlAPIOntologyCollector.addAxiom(ax);
}else if(one.getURIString().equals(OWLVocabulary.RDFS_LABEL)) {
- OWLLabelAnnotation label = factory.getOWLLabelAnnotation(one.getBPart().getLiteral().getString());
- owlAPIOntologyCollector.addAxiom(factory.getOWLEntityAnnotationAxiom(me, label));
+ OWLAnnotation annoLabel = factory.getOWLAnnotation(factory.getRDFSLabel(), factory.getOWLStringLiteral(one.getBPart().getLiteral().getString()));
+ OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(me.getIRI(), annoLabel);
+ owlAPIOntologyCollector.addAxiom(ax);
}else {
tail(true, "in ontology conversion: no other datatypes, but annotation is allowed for classes."+" data property is: "+one.getURIString()+" connected with: "+one.getBPart().getNTripleForm());
@@ -184,10 +186,10 @@
}
for (BlankNode bn : blankNodes) {
- OWLDescription target = bn.getAnonymousClass(owlAPIOntologyCollector);
+ OWLClassExpression target = bn.getAnonymousClass(owlAPIOntologyCollector);
if(OWLVocabulary.isStringSubClassVocab(bn.getInBoundEdge())){
- owlAPIOntologyCollector.addAxiom(factory.getOWLSubClassAxiom(me, target));
+ owlAPIOntologyCollector.addAxiom(factory.getOWLSubClassOfAxiom(me, target));
}else if(bn.getInBoundEdge().equals(OWLVocabulary.OWL_DISJOINT_WITH)){
owlAPIOntologyCollector.addAxiom(factory.getOWLDisjointClassesAxiom(me, target));
}else if(bn.getInBoundEdge().equals(OWLVocabulary.OWL_EQUIVALENT_CLASS)){
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/DatatypePropertyNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/DatatypePropertyNode.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/DatatypePropertyNode.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -19,7 +19,6 @@
*/
package org.dllearner.kb.extraction;
-import java.net.URI;
import java.util.ArrayList;
import java.util.List;
import java.util.SortedSet;
@@ -30,12 +29,13 @@
import org.dllearner.kb.manipulator.Manipulator;
import org.dllearner.utilities.datastructures.RDFNodeTuple;
import org.dllearner.utilities.owl.OWLVocabulary;
-import org.semanticweb.owl.model.OWLAxiom;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLDataFactory;
-import org.semanticweb.owl.model.OWLDataProperty;
-import org.semanticweb.owl.model.OWLDataRange;
-import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLDataRange;
/**
* Property node, has connection to a and b part
@@ -122,28 +122,28 @@
OWLDataFactory factory = owlAPIOntologyCollector.getFactory();
- OWLDataProperty me =factory.getOWLDataProperty(getURI());
+ OWLDataProperty me =factory.getOWLDataProperty(getIRI());
for (RDFNodeTuple one : propertyInformation) {
if(one.aPartContains(OWLVocabulary.RDFS_range)){
//System.out.println(me + one.b.toString());
- OWLDataRange o = factory.getOWLDataType(URI.create(one.b.toString()));
+ OWLDataRange o = factory.getOWLDatatype(IRI.create(one.b.toString()));
OWLAxiom ax = factory.getOWLDataPropertyRangeAxiom(me, o);
owlAPIOntologyCollector.addAxiom(ax);
//XXX implement
//OWLClass c = factory.getOWLClass(URI.create(one.b.toString()));
//owlAPIOntologyCollector.addAxiom(factory.getOWLDataPropertyRangeAxiom(propery, owlDataRange)(me, c));
}else if(one.aPartContains(OWLVocabulary.RDFS_domain)){
- OWLClass c = factory.getOWLClass(URI.create(one.b.toString()));
+ OWLClass c = factory.getOWLClass(IRI.create(one.b.toString()));
owlAPIOntologyCollector.addAxiom(factory.getOWLDataPropertyDomainAxiom(me, c));
}
}
for (BlankNode bn : blankNodes) {
- OWLDescription target = bn.getAnonymousClass(owlAPIOntologyCollector);
+ OWLClassExpression target = bn.getAnonymousClass(owlAPIOntologyCollector);
if(bn.getInBoundEdge().equals(OWLVocabulary.RDFS_range)){
//XXX implement
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java 2010-04-22 17:09:08 UTC (rev 2143)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/InstanceNode.java 2010-05-04 20:36:49 UTC (rev 2144)
@@ -30,13 +30,14 @@
import org.dllearner.kb.manipulator.Manipulator;
import org.dllearner.utilities.datastructures.RDFNodeTuple;
import org.dllearner.utilities.owl.OWLVocabulary;
-import org.semanticweb.owl.model.OWLAxiom;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLDataFactory;
-import org.semanticweb.owl.model.OWLDataProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLLabelAnnotation;
-import org.semanticweb.owl.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
import com.hp.hpl.jena.rdf.model.Literal;
@@ -185,12 +186,12 @@
OWLDataFactory factory = owlAPIOntologyCollector.getFactory();
- OWLIndividual me = factory.getOWLIndividual(getURI());
+ OWLNamedIndividual me = factory.getOWLNamedIndividual(getIRI());
for (ClassNode one : classes) {
//create Axiom
- OWLClass c = factory.getOWLClass(one.getURI());
- OWLAxiom ax = factory.getOWLClassAssertionAxiom(me, c);
+ OWLClass c = factory.getOWLClass(one.getIRI());
+ OWLAxiom ax = factory.getOWLClassAssertionAxiom(c, me);
//collect
owlAPIOntologyCollector.addAxiom(ax);
//handover
@@ -199,15 +200,15 @@
for (ObjectPropertyNode one : objectProperties) {
OWLAxiom ax = null;
if(one.getURIString().equals(OWLVocabulary.OWL_DIFFERENT_FROM)){
- OWLIndividual o = factory.getOWLIndividual(one.getBPart().getURI());
+ OWLIndividual o = factory.getOWLNamedIndividual(one.getBPart().getIRI());
ax = factory.getOWLDifferentIndividualsAxiom(new OWLIndividual[]{me,o});
}else{
//create axiom
- OWLIndividual o = factory.getOWLIndividual(one.getBPart().getURI());
- OWLObjectProperty p = factory.getOWLObjectProperty(one.getURI());
- ax = factory.getOWLObjectPropertyAssertionAxiom(me, p, o);
+ OWLIndividual o = factory.getOWLNamedIndividual(one.getBPart().getIRI());
+ OWLObjectProperty p = factory.getOWLObjectProperty(one.getIRI());
+ ax = factory.getOWLObjectPropertyAssertionAxiom(p, me, o);
}
//collect
owlAPIOntologyCollector.addAxiom(ax);
@@ -218,7 +219,7 @@
}
for (DatatypePropertyNode one : datatypeProperties) {
- OWLDataProperty p = factory.getOWLDataProperty(one.getURI());
+ OWLDataProperty p = factory.getOWLDataProperty(one.getIRI());
Literal ln = one.getBPart().getLiteral();
if(one.getURIString().equals(OWLVocabulary.RDFS_COMMENT)){
@@ -226,28 +227,29 @@
//OWLCommentAnnotation comment = factory.getOWL(one.b.toString());
//owlAPIOntologyCollector.addAxiom(factory.getOWLEntityAnnotationAxiom(me, label));
}else if(one.getURIString().equals(OWLVocabulary.RDFS_LABEL)){
- OWLLabelAnnotation label = factory.getOWLLabelAnnotation(ln.getString());
- owlAPIOntologyCollector.addAxio...
[truncated message content] |
