From 11cfdaf9fb11a3560da83138fa8c8cb5e55dfa05 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20David?=
<Jerome.David@univ-grenoble-alpes.fr>
Date: Tue, 29 Apr 2008 08:32:08 +0000
Subject: [PATCH] In Ontlogy interface, Set<Object> have been replaced by
Set<?> Some corrections in JENAOntology API and in OWLAPIOntology concerning
the annotations methods
---
.../exmo/align/onto/LoadedOntology.java | 12 ++---
.../exmo/align/onto/jena25/JENAOntology.java | 44 +++++--------------
.../onto/jena25/JENAOntologyFactory.java | 11 ++++-
.../align/onto/owlapi10/OWLAPIOntology.java | 42 ++++++++----------
.../onto/owlapi10/OWLAPIOntologyFactory.java | 12 ++---
5 files changed, 52 insertions(+), 69 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/onto/LoadedOntology.java b/src/fr/inrialpes/exmo/align/onto/LoadedOntology.java
index 0d022729..6a690aa9 100644
--- a/src/fr/inrialpes/exmo/align/onto/LoadedOntology.java
+++ b/src/fr/inrialpes/exmo/align/onto/LoadedOntology.java
@@ -45,12 +45,12 @@ public interface LoadedOntology<O> extends Ontology<O> {
public boolean isObjectProperty( Object o );
public boolean isIndividual( Object o );
- public Set<Object> getEntities();
- public Set<Object> getClasses();
- public Set<Object> getProperties();
- public Set<Object> getObjectProperties();
- public Set<Object> getDataProperties();
- public Set<Object> getIndividuals();
+ public Set<?> getEntities();
+ public Set<?> getClasses();
+ public Set<?> getProperties();
+ public Set<?> getObjectProperties();
+ public Set<?> getDataProperties();
+ public Set<?> getIndividuals();
public int nbClasses();
public int nbProperties();
diff --git a/src/fr/inrialpes/exmo/align/onto/jena25/JENAOntology.java b/src/fr/inrialpes/exmo/align/onto/jena25/JENAOntology.java
index 626f8558..1ecfc676 100644
--- a/src/fr/inrialpes/exmo/align/onto/jena25/JENAOntology.java
+++ b/src/fr/inrialpes/exmo/align/onto/jena25/JENAOntology.java
@@ -1,9 +1,6 @@
package fr.inrialpes.exmo.align.onto.jena25;
import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.Collection;
-import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
@@ -17,7 +14,6 @@ import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.ontology.OntResource;
-import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.impl.LiteralImpl;
import fr.inrialpes.exmo.align.onto.BasicOntology;
@@ -26,12 +22,12 @@ import fr.inrialpes.exmo.align.onto.LoadedOntology;
public class JENAOntology extends BasicOntology<OntModel> implements LoadedOntology<OntModel>{
- protected Set<Object> listResources(Class<? extends OntResource> type) {
+ protected Set<?> listResources(Class<? extends OntResource> type) {
Set<Object> resources = new HashSet<Object>();
Iterator i = onto.listObjects();
while (i.hasNext()) {
Object r = i.next();
- if (type.isInstance(r))
+ if (type.isInstance(r) && ((OntResource)r).getURI()!=null)
resources.add(r);
}
return resources;
@@ -39,11 +35,11 @@ public class JENAOntology extends BasicOntology<OntModel> implements LoadedOntol
}
- public Set<Object> getClasses() {
+ public Set<?> getClasses() {
return onto.listNamedClasses().toSet();
}
- public Set<Object> getDataProperties() {
+ public Set<?> getDataProperties() {
return onto.listDatatypeProperties().toSet();
}
@@ -120,34 +116,18 @@ public class JENAOntology extends BasicOntology<OntModel> implements LoadedOntol
}
}
- public Set<Object> getIndividuals() {
- /*Set individuals = new HashSet();
- Iterator i = onto.listIndividuals();
- while (i.hasNext()) {
- Individual ind = (Individual) i.next();
- individuals.add(ind);
- Iterator j = ind.listProperties();
- while (j.hasNext()) {
- Statement s = (Statement) j.next();
- if (s.getPredicate().canAs(ObjectProperty.class)) {
- System.out.println(s.getObject());
- individuals.add(s.getObject());
- }
- }
- }
- return individuals;*/
- //return listResources(Individual.class);
- return onto.listIndividuals().toSet();
+ public Set<?> getIndividuals() {
+ return onto.listIndividuals().toSet();
}
- public Set<Object> getObjectProperties() {
- return onto.listObjectProperties().toSet();
+ public Set<?> getObjectProperties() {
+ return (Set<? extends Object>) onto.listObjectProperties().toSet();
}
- public Set<Object> getProperties() {
- Set properties = new HashSet();
- properties.addAll(onto.listDatatypeProperties().toSet());
- properties.addAll(onto.listObjectProperties().toSet());
+ public Set<?> getProperties() {
+ Set<Object> properties = new HashSet<Object>();
+ properties.addAll((Set<? extends Object>) onto.listDatatypeProperties().toSet());
+ properties.addAll((Set<? extends Object>) onto.listObjectProperties().toSet());
return properties;
}
diff --git a/src/fr/inrialpes/exmo/align/onto/jena25/JENAOntologyFactory.java b/src/fr/inrialpes/exmo/align/onto/jena25/JENAOntologyFactory.java
index dd844434..bce9791d 100644
--- a/src/fr/inrialpes/exmo/align/onto/jena25/JENAOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/align/onto/jena25/JENAOntologyFactory.java
@@ -1,7 +1,7 @@
package fr.inrialpes.exmo.align.onto.jena25;
import java.net.URI;
-import java.util.Iterator;
+import java.util.NoSuchElementException;
import org.semanticweb.owl.align.AlignmentException;
@@ -23,7 +23,14 @@ public class JENAOntologyFactory extends OntologyFactory{
JENAOntology onto = new JENAOntology();
onto.setFile(uri);
// to be checked : why several ontologies in a model ???
- onto.setURI(new URI(((Ontology)m.listOntologies().next()).getURI()));
+ // If no URI can be extracted from ontology, then we use the physical URI
+ try {
+ onto.setURI(new URI(((Ontology)m.listOntologies().next()).getURI()));
+ }
+ catch (NoSuchElementException nse) {
+ onto.setURI(new URI(m.getNsPrefixURI("")));
+ //onto.setFile(uri);
+ }
//onto.setURI(new URI(m.listOntologies()getOntology(null).getURI()));
onto.setOntology(m);
return onto;
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
index fd7d96dc..4509c678 100644
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
+++ b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
@@ -30,9 +30,6 @@ package fr.inrialpes.exmo.align.onto.owlapi10;
import java.net.URI;
import java.util.Set;
import java.util.HashSet;
-import java.util.Iterator;
-import java.util.NoSuchElementException;
-import java.lang.UnsupportedOperationException;
import org.semanticweb.owl.align.AlignmentException;
@@ -115,7 +112,8 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
protected Set<String> getAnnotations(OWLEntity e , String lang , String typeAnnot ) throws OWLException {
Set<String> annots = new HashSet<String>();
- for (OWLAnnotationInstance annot : (Set<OWLAnnotationInstance>) e.getAnnotations(onto)) {
+ for (Object objAnnot : e.getAnnotations(onto)) {
+ OWLAnnotationInstance annot = (OWLAnnotationInstance) objAnnot;
String annotUri = annot.getProperty().getURI().toString();
if (annotUri.equals(typeAnnot) || typeAnnot==null) {
if ( annot.getContent() instanceof OWLDataValue &&
@@ -197,12 +195,13 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
};
// JD: allows to retrieve some specific entities by giving their class
- protected Set<Object> getEntities(Class<? extends OWLEntity> c) throws OWLException{
+ protected Set<?> getEntities(Class<? extends OWLEntity> c) throws OWLException{
OWLEntityCollector ec = new OWLEntityCollector();
onto.accept(ec);
Set<Object> entities = new HashSet<Object>();
for (Object obj : ec.entities()) {
- if (c.isInstance(obj) ){
+ // JD: OWLEntitytCollector seems to return anonymous entities :&& ((OWLEntity)obj).getURI()!=null
+ if (c.isInstance(obj) ){
entities.add(obj);
}
}
@@ -211,18 +210,15 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
// Here it shoud be better to report exception
// JE: Onto this does not work at all, of course...!!!!
- public Set<Object> getEntities() {
- OWLEntityCollector ec = new OWLEntityCollector();
- try {
- onto.accept(ec);
- return ec.entities();
-
- } catch (OWLException e) {
- return null;
- }
+ public Set<?> getEntities() {
+ try {
+ return getEntities(OWLEntity.class);
+ } catch (OWLException ex) {
+ return null;
+ }
}
- public Set<Object> getClasses() {
+ public Set<?> getClasses() {
try {
return ((OWLOntology)onto).getClasses(); // [W:unchecked]
} catch (OWLException ex) {
@@ -230,7 +226,7 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
}
}
- public Set<Object> getProperties() {
+ public Set<?> getProperties() {
try {
//return ((OWLOntology)onto).getProperties(); // [W:unchecked]
return getEntities(OWLProperty.class);
@@ -242,7 +238,7 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
// The only point is if I should return OWLProperties or names...
// I guess that I will return names (ns+name) because otherwise I will need a full
// Abstract ontology interface and this is not the rule...
- public Set<Object> getObjectProperties() {
+ public Set<?> getObjectProperties() {
try {
// [Warning:unchecked] due to OWL API not serving generic types
return ((OWLOntology)onto).getObjectProperties(); // [W:unchecked]
@@ -251,7 +247,7 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
}
}
- public Set<Object> getDataProperties() {
+ public Set<?> getDataProperties() {
try {
return ((OWLOntology)onto).getDataProperties(); // [W:unchecked]
} catch (OWLException ex) {
@@ -259,7 +255,7 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
}
}
- public Set<Object> getIndividuals() {
+ public Set<?> getIndividuals() {
try {
return ((OWLOntology)onto).getIndividuals(); // [W:unchecked]
} catch (OWLException ex) {
@@ -372,7 +368,7 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
/* HeavyLoadedOntology specifics */
- public Set<Object> getProperties( OWLDescription desc ) {
+ public Set<?> getProperties( OWLDescription desc ) {
Set<Object> list = new HashSet<Object>();
try {
if ( desc instanceof OWLRestriction ){
@@ -381,13 +377,13 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
// JE: I suspect that this can be a cause for looping!!
for ( Object cl : ((OWLClass)desc).getEquivalentClasses((OWLOntology)onto) ){
// JE: strange casting
- Set<Object> res = getProperties( (OWLDescription)cl );
+ Set<?> res = getProperties( (OWLDescription)cl );
if ( res != null ) list.add( res );
}
} else if ( desc instanceof OWLNaryBooleanDescription ) {
for ( Object d : ((OWLNaryBooleanDescription)desc).getOperands() ){
// JE: strange casting
- Set<Object> res = getProperties( (OWLDescription)d );
+ Set<?> res = getProperties( (OWLDescription)d );
if ( res != null ) list.add( res );
}
}
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
index 8004be83..766a1394 100644
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
@@ -7,12 +7,12 @@
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 2.1 of the License, or
* (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
- *
+ *
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
@@ -66,8 +66,8 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
public LoadedOntology loadOntology( URI uri ) throws AlignmentException {
OWLConnection connection = null;
- Map parameters = new HashMap();
- parameters.put(OWLManager.OWL_CONNECTION, // [W:unchecked]
+ Map<Object,Object> parameters = new HashMap<Object, Object>();
+ parameters.put(OWLManager.OWL_CONNECTION,
"org.semanticweb.owl.impl.model.OWLConnectionImpl");
try {
connection = OWLManager.getOWLConnection(parameters);
@@ -88,7 +88,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
e.printStackTrace();
}
return onto;
- } catch (OWLException e) {
+ } catch (OWLException e) {
throw new AlignmentException("Cannot load "+uri, e );
}
}
@@ -104,7 +104,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
try {
OWLRDFParser parser = new OWLRDFParser();
OWLRDFErrorHandler handler = new OWLRDFErrorHandler(){
- public void owlFullConstruct( int code, String message )
+ public void owlFullConstruct( int code, String message )
throws SAXException {
}
public void owlFullConstruct(int code, String message, Object o)
--
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