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[DL-Learner SVN] SF.net SVN: dl-learner:[3612] trunk/components-core/src
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From: <sha...@us...> - 2012-03-15 03:17:19
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Revision: 3612
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3612&view=rev
Author: shadowtm
Date: 2012-03-15 03:17:12 +0000 (Thu, 15 Mar 2012)
Log Message:
-----------
Updated SparqlKnowledgeSource and SparqlSimpleExtractor to implement the OWLOntologyKnowledgeSource interface in clean up the code within the reasoners.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlSimpleExtractor.java
trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java
trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java
Added Paths:
-----------
trunk/components-core/src/test/java/org/dllearner/kb/sparql/
trunk/components-core/src/test/java/org/dllearner/kb/sparql/SparqlKnowledgeSourceTest.java
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2012-03-15 02:34:07 UTC (rev 3611)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2012-03-15 03:17:12 UTC (rev 3612)
@@ -47,6 +47,7 @@
import org.dllearner.core.options.StringTupleListConfigOption;
import org.dllearner.core.options.URLConfigOption;
import org.dllearner.core.owl.KB;
+import org.dllearner.kb.OWLOntologyKnowledgeSource;
import org.dllearner.kb.aquisitors.SparqlTupleAquisitor;
import org.dllearner.kb.aquisitors.SparqlTupleAquisitorImproved;
import org.dllearner.kb.aquisitors.TupleAquisitor;
@@ -60,11 +61,14 @@
import org.dllearner.utilities.Files;
import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.datastructures.StringTuple;
+import org.dllearner.utilities.owl.OntologyToByteConverter;
+import org.dllearner.utilities.owl.SimpleOntologyToByteConverter;
import org.dllearner.utilities.statistics.SimpleClock;
import org.semanticweb.owlapi.model.OWLOntology;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
/**
* Represents the SPARQL Endpoint Component.
@@ -74,12 +78,14 @@
* @author Sebastian Hellmann
*/
@ComponentAnn(name = "SPARQL endpoint fragment", shortName = "sparqlfrag", version = 0.5)
-public class SparqlKnowledgeSource extends AbstractKnowledgeSource {
+public class SparqlKnowledgeSource extends AbstractKnowledgeSource implements OWLOntologyKnowledgeSource{
private ProgressMonitor mon;
private static final boolean debugExitAfterExtraction = false; // switches
+ private byte[] ontologyBytes;
+ private OntologyToByteConverter converter = new SimpleOntologyToByteConverter();
// private SparqlKnowledgeSourceConfigurator configurator;
@@ -107,7 +113,6 @@
private URL ontologyFragmentURL;
- private OWLOntology fragment;
private Manipulator manipulator = null;
@@ -337,9 +342,10 @@
}*/
extractionTime.stop();
-
- fragment = m.getOWLAPIOntologyForNodes(seedNodes, saveExtractedFragment);
-
+ // Do this so that we can support the OWLOntologyKnowledgeSource
+ // and can be thread safe.
+ OWLOntology fragment = m.getOWLAPIOntologyForNodes(seedNodes, saveExtractedFragment);
+ ontologyBytes = getConverter().convert(fragment);
logger.info("Finished collecting fragment. needed "+extractionTime.getLastValue()+" ms");
@@ -362,8 +368,13 @@
System.exit(0);
}
}
-
- public List<Node> extractParallel(){
+
+ @Override
+ public OWLOntology createOWLOntology(OWLOntologyManager manager) {
+ return getConverter().convert(ontologyBytes, manager);
+ }
+
+ public List<Node> extractParallel(){
return null;
}
@@ -537,10 +548,6 @@
return ontologyFragmentURL;
}
- public OWLOntology getOWLAPIOntology() {
- return fragment;
- }
-
public boolean isUseCache() {
return useCache;
}
@@ -733,6 +740,39 @@
this.cacheDir = cacheDir;
}
-
+ /**
+ * Get the OntologyToByteConverter associated with this object.
+ *
+ * @return The OntologyToByteConverter associated with this object.
+ */
+ public OntologyToByteConverter getConverter() {
+ return converter;
+ }
+ /**
+ * Set the OntologyToByteConverter associated with this object.
+ *
+ * @param converter the OntologyToByteConverter to associate with this object.
+ */
+ public void setConverter(OntologyToByteConverter converter) {
+ this.converter = converter;
+ }
+
+ /**
+ * Accessor for getting the Ontology Bytes
+ *
+ * @return Get the underlying ontology bytes.
+ */
+ byte[] getOntologyBytes() {
+ return ontologyBytes;
+ }
+
+ /**
+ * Set the ontology bytes.
+ *
+ * @param ontologyBytes The byte array representation of the fragment.
+ */
+ void setOntologyBytes(byte[] ontologyBytes) {
+ this.ontologyBytes = ontologyBytes;
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlSimpleExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlSimpleExtractor.java 2012-03-15 02:34:07 UTC (rev 3611)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlSimpleExtractor.java 2012-03-15 03:17:12 UTC (rev 3612)
@@ -6,9 +6,12 @@
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.config.ConfigOption;
+import org.dllearner.kb.OWLOntologyKnowledgeSource;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
@ComponentAnn(name="efficient SPARQL fragment extractor", shortName="sparqls", version=0.1)
-public class SparqlSimpleExtractor implements KnowledgeSource {
+public class SparqlSimpleExtractor implements KnowledgeSource, OWLOntologyKnowledgeSource {
@ConfigOption(name="endpointURL", description="URL of the SPARQL endpoint", required=true)
private URL endpointURL = null;
@@ -38,5 +41,10 @@
public void setEndpointURL(URL endpointURL) {
this.endpointURL = endpointURL;
}
-
+
+ @Override
+ public OWLOntology createOWLOntology(OWLOntologyManager manager) {
+ //TODO Update this to return an ontology representation of what the reasoners should work with. Build with the passed in manager instance.
+ return null;
+ }
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2012-03-15 02:34:07 UTC (rev 3611)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2012-03-15 03:17:12 UTC (rev 3612)
@@ -161,14 +161,6 @@
if (source instanceof OWLFile || source instanceof SparqlKnowledgeSource || source instanceof SparqlSimpleExtractor || source instanceof OWLAPIOntology) {
- if (source instanceof SparqlKnowledgeSource) {
- ontology = ((SparqlKnowledgeSource) source).getOWLAPIOntology();
- manager = ontology.getOWLOntologyManager();
- owlAPIOntologies.add(ontology);
- } else if(source instanceof SparqlSimpleExtractor) {
- // TODO
- }
-
directImports.addAll(ontology.getImportsDeclarations());
try {
// imports includes the ontology itself
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java 2012-03-15 02:34:07 UTC (rev 3611)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/PelletReasoner.java 2012-03-15 03:17:12 UTC (rev 3612)
@@ -209,13 +209,6 @@
|| source instanceof SparqlKnowledgeSource
|| source instanceof OWLAPIOntology) {
- if (source instanceof SparqlKnowledgeSource) {
- ontology = ((SparqlKnowledgeSource) source)
- .getOWLAPIOntology();
- manager = ontology.getOWLOntologyManager();
- owlAPIOntologies.add(ontology);
- }
-
// imports includes the ontology itself
Set<OWLOntology> imports = manager
.getImportsClosure(ontology);
@@ -477,12 +470,6 @@
|| source instanceof SparqlKnowledgeSource
|| source instanceof OWLAPIOntology) {
- if (source instanceof SparqlKnowledgeSource) {
- ontology = ((SparqlKnowledgeSource) source).getOWLAPIOntology();
- manager = ontology.getOWLOntologyManager();
- owlAPIOntologies.add(ontology);
- }
-
// imports includes the ontology itself
Set<OWLOntology> imports = manager
.getImportsClosure(ontology);
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java 2012-03-15 02:34:07 UTC (rev 3611)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/ProtegeReasoner.java 2012-03-15 03:17:12 UTC (rev 3612)
@@ -258,12 +258,6 @@
|| source instanceof SparqlKnowledgeSource
|| source instanceof OWLAPIOntology) {
- if (source instanceof SparqlKnowledgeSource) {
- ontology = ((SparqlKnowledgeSource) source).getOWLAPIOntology();
- manager = ontology.getOWLOntologyManager();
- owlAPIOntologies.add(ontology);
- }
-
classes.addAll(ontology.getClassesInSignature(true));
owlObjectProperties.addAll(ontology.getObjectPropertiesInSignature(true));
owlDatatypeProperties.addAll(ontology.getDataPropertiesInSignature(true));
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java 2012-03-15 02:34:07 UTC (rev 3611)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/fuzzydll/FuzzyOWLAPIReasoner.java 2012-03-15 03:17:12 UTC (rev 3612)
@@ -253,12 +253,6 @@
if(source instanceof OWLFile || source instanceof SparqlKnowledgeSource || source instanceof OWLAPIOntology) {
- if (source instanceof SparqlKnowledgeSource) {
- ontology = ((SparqlKnowledgeSource) source).getOWLAPIOntology();
- manager = ontology.getOWLOntologyManager();
- owlAPIOntologies.add(ontology);
- }
-
// imports includes the ontology itself
Set<OWLOntology> imports = manager.getImportsClosure(ontology);
allImports.addAll(imports);
Added: trunk/components-core/src/test/java/org/dllearner/kb/sparql/SparqlKnowledgeSourceTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/kb/sparql/SparqlKnowledgeSourceTest.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/kb/sparql/SparqlKnowledgeSourceTest.java 2012-03-15 03:17:12 UTC (rev 3612)
@@ -0,0 +1,53 @@
+package org.dllearner.kb.sparql;
+
+import org.dllearner.utilities.owl.SimpleOntologyToByteConverter;
+import org.junit.Test;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.core.io.Resource;
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
+import java.io.IOException;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNotSame;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: Chris Shellenbarger
+ * Date: 3/14/12
+ * Time: 9:02 PM
+ *
+ * Basic test to test some components of the SparqlKnowledgeSource
+ */
+public class SparqlKnowledgeSourceTest {
+
+ private OWLOntology createOntology() throws OWLOntologyCreationException, IOException {
+ // Set up the ontology here and hide its manager - the test needs to use a different ontology manager on reconstitution
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager(new OWLDataFactoryImpl());
+ Resource owlFile = new ClassPathResource("/org/dllearner/kb/owl-api-ontology-data.owl");
+ return manager.loadOntologyFromOntologyDocument(owlFile.getInputStream());
+ }
+
+
+ @Test
+ public void testMethods() throws Exception {
+ OWLOntology ontology = createOntology();
+ assertNotNull(ontology);
+
+ SparqlKnowledgeSource testSubject = new SparqlKnowledgeSource();
+ testSubject.setOntologyBytes(new SimpleOntologyToByteConverter().convert(ontology));
+
+ OWLOntology result = testSubject.createOWLOntology(OWLManager.createOWLOntologyManager(new OWLDataFactoryImpl()));
+
+ assertNotNull(result);
+ assertNotSame(ontology,result);
+
+ // Basic Equality Check - for some reason axiom count is different - the result looks more complete than the original.
+ assertEquals(ontology.getIndividualsInSignature().size(), result.getIndividualsInSignature().size());
+ }
+}
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