From 3f0b6c8dabdc816b196f2fc7fb05b33d87f5296e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Fri, 28 Mar 2008 08:42:33 +0000
Subject: [PATCH] - Suppressed all entity representations
---
.../exmo/align/onto/LoadedOntology.java | 5 +-
.../exmo/align/onto/OntologyCache.java | 18 ++-
.../exmo/align/onto/OntologyFactory.java | 56 +++++++---
.../align/onto/owlapi10/OWLAPIOntology.java | 100 +++++++++++++++--
.../onto/owlapi10/OWLAPIOntologyFactory.java | 103 +++---------------
5 files changed, 161 insertions(+), 121 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/onto/LoadedOntology.java b/src/fr/inrialpes/exmo/align/onto/LoadedOntology.java
index 748a55bf..85ce0d0c 100644
--- a/src/fr/inrialpes/exmo/align/onto/LoadedOntology.java
+++ b/src/fr/inrialpes/exmo/align/onto/LoadedOntology.java
@@ -35,7 +35,7 @@ public interface LoadedOntology<O> extends Ontology<O> {
public boolean isEntity( Object o );
public boolean isClass( Object o );
public boolean isProperty( Object o );
- public boolean isDatatypeProperty( Object o );
+ public boolean isDataProperty( Object o );
public boolean isObjectProperty( Object o );
public boolean isIndividual( Object o );
@@ -43,10 +43,11 @@ public interface LoadedOntology<O> extends Ontology<O> {
public Set<Object> getClasses();
public Set<Object> getProperties();
public Set<Object> getObjectProperties();
- public Set<Object> getDatatypeProperties();
+ public Set<Object> getDataProperties();
public Set<Object> getIndividuals();
public int nbClasses();
+ public int nbProperties();
public int nbDataProperties();
public int nbObjectProperties();
public int nbInstances();
diff --git a/src/fr/inrialpes/exmo/align/onto/OntologyCache.java b/src/fr/inrialpes/exmo/align/onto/OntologyCache.java
index 5c8b2326..897fd147 100644
--- a/src/fr/inrialpes/exmo/align/onto/OntologyCache.java
+++ b/src/fr/inrialpes/exmo/align/onto/OntologyCache.java
@@ -43,32 +43,38 @@ public class OntologyCache {
* This is the ontology URI, NOT its filename
*/
Hashtable<URI,LoadedOntology> ontologies = null;
+ Hashtable<URI,LoadedOntology> ontologyUris = null;
public OntologyCache() {
ontologies = new Hashtable<URI,LoadedOntology>();
+ ontologyUris = new Hashtable<URI,LoadedOntology>();
}
public void recordOntology( URI uri, LoadedOntology ontology ){
- ontologies.put(uri,ontology);
+ ontologies.put( uri, ontology );
+ ontologyUris.put( ontology.getURI(), ontology );
}
- public Ontology getOntology( URI uri ){
+ public LoadedOntology getOntology( URI uri ){
return ontologies.get( uri );
}
+ public LoadedOntology getOntologyFromURI( URI uri ){
+ return ontologyUris.get( uri );
+ }
+
public void unloadOntology( URI uri, LoadedOntology ontology ){
- LoadedOntology o = ontologies.get(uri);
+ LoadedOntology o = ontologyUris.get(uri);
o.unload();
+ ontologyUris.remove( uri );
ontologies.remove( uri );
}
public void clear(){
- // JE: Onto [Is this correct ??]
- //for ( Enumeration e = ontologies.elements() ; e.hasMoreElements(); ){
- // Ontology o = (Ontology)e.nextElement();
for ( LoadedOntology o : ontologies.values() ){
o.unload();
}
+ ontologyUris.clear();
ontologies.clear();
}
diff --git a/src/fr/inrialpes/exmo/align/onto/OntologyFactory.java b/src/fr/inrialpes/exmo/align/onto/OntologyFactory.java
index 06a7f946..bcca9364 100644
--- a/src/fr/inrialpes/exmo/align/onto/OntologyFactory.java
+++ b/src/fr/inrialpes/exmo/align/onto/OntologyFactory.java
@@ -26,14 +26,22 @@ import java.util.Map;
import java.lang.reflect.InvocationTargetException;
+import org.semanticweb.owl.align.AlignmentException;
+
public abstract class OntologyFactory {
protected static OntologyFactory instance;
private static String API_NAME="fr.inrialpes.exmo.align.onto.owlapi10.OWLAPIOntologyFactory";
- protected static Map<URI,Ontology> loadedOntos= new HashMap<URI,Ontology>();
- protected static Map<URI,Ontology> loadedOntosLogical= new HashMap<URI,Ontology>();
+ public static String getDefaultFactory(){
+ return API_NAME;
+ }
+
+ public void setDefaultFactory( String className ){
+ API_NAME = className;
+ }
+
public static OntologyFactory newInstance() {
return newInstance(API_NAME);
}
@@ -59,23 +67,45 @@ public abstract class OntologyFactory {
return instance;
}
- public abstract LoadedOntology loadOntology( URI physicalURI );
+ /**
+ * Load an ontology, cache enabled
+ */
+ public abstract LoadedOntology loadOntology( URI uri ) throws AlignmentException;
+ /**
+ * Load an ontology, cache enabled if true, disabled otherwise
+ */
+ public LoadedOntology loadOntology( URI uri, OntologyCache ontologies ) throws AlignmentException {
+ LoadedOntology onto = null;
+ if ( ontologies != null ) {
+ onto = ontologies.getOntologyFromURI( uri );
+ if ( onto != null ) return onto;
+ onto = ontologies.getOntology( uri );
+ if ( onto != null ) return onto;
+ };
+ onto = loadOntology( uri );
+ if ( ontologies != null ) ontologies.recordOntology( uri, onto );
+ return onto;
+ };
- // JE: This is not really usefule since it doubles OntologyCache...
+ /* JE: this is a reimplementation of OntologyCache
+ // JE: This is not really useful since it doubles OntologyCache...
// This may be included as well...
- public Ontology getOntologyFromFile(URI physicalURI) {
- Ontology onto;
- if (loadedOntos.containsKey(physicalURI))
- onto = loadedOntos.get(physicalURI);
- else {
- onto = loadOntology( physicalURI );
- loadedOntos.put(physicalURI, onto);
- loadedOntosLogical.put(onto.getURI(), onto);
- }
+ protected static Map<URI,LoadedOntology> loadedOntos = new HashMap<URI,LoadedOntology>();
+ protected static Map<URI,LoadedOntology> loadedOntosLogical = new HashMap<URI,LoadedOntology>();
+ public LoadedOntology getOntologyFromCache( URI uri ) {
+ LoadedOntology onto;
+ if ( loadedOntos.containsKey( uri ) ) {
+ onto = loadedOntos.get( uri );
+ } else {
+ onto = loadOntology( uri );
+ loadedOntos.put( uri, onto );
+ loadedOntosLogical.put( onto.getURI(), onto);
+ }
return onto;
}
public static Ontology getOntologyFromURI(URI logicalURI) {
return loadedOntosLogical.get(logicalURI);
}
+ */
}
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
index 903478cc..d4093a9a 100644
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
+++ b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
@@ -40,16 +40,18 @@ import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLException;
+/*
+ * JE: BEWARE, THIS HAS NOT BEEN FULLY IMPLEMENTED SO FAR!!!!
+ * TO BE CHECKED
+ * getEntities() and getProperties() ARE INCORRECT
+ * nbXxxx() ARE INNEFICIENT
+ */
+
/**
* Store the information regarding ontologies in a specific structure
* Acts as an interface with regard to an ontology APY
*/
-//private class OWLAPIOntology extends OntologyAdapter<OWLOntology> {
-// private OWLAPIOntology() {super();}
-//}
-
-
public class OWLAPIOntology extends BasicOntology<OWLOntology> implements LoadedOntology<OWLOntology> {
public OWLAPIOntology() {
@@ -59,10 +61,12 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
} catch (Exception e) {}; // does not happen
};
+ // Ontology interface
public OWLOntology getOntology() { return onto; }
public void setOntology( OWLOntology o ) { this.onto = o; }
+ // LoadedOntology interface
public Object getEntity( URI uri ) throws AlignmentException {
try {
OWLEntity result = ((OWLOntology)onto).getClass( uri );
@@ -83,7 +87,14 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
}
}
public String getEntityName( Object o ) throws AlignmentException {
- return "Dummt";
+ try {
+ // Try to get labels first...
+ URI u = ((OWLEntity)o).getURI();
+ if ( u != null ) return u.getFragment();
+ else return "";
+ } catch (OWLException oex) {
+ return null;
+ }
};
public boolean isEntity( Object o ){
@@ -98,7 +109,7 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
if ( o instanceof OWLProperty ) return true;
else return false;
};
- public boolean isDatatypeProperty( Object o ){
+ public boolean isDataProperty( Object o ){
if ( o instanceof OWLDataProperty ) return true;
else return false;
};
@@ -145,17 +156,14 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
// [Warning:unchecked] due to OWL API not serving generic types
return ((OWLOntology)onto).getObjectProperties(); // [W:unchecked]
} catch (OWLException ex) {
- //throw new AlignmentException( "Cannot get object properties", ex );
return null;
}
}
- public Set<Object> getDatatypeProperties() {
+ public Set<Object> getDataProperties() {
try {
- // [Warning:unchecked] due to OWL API not serving generic types
return ((OWLOntology)onto).getDataProperties(); // [W:unchecked]
} catch (OWLException ex) {
- //throw new AlignmentException( "Cannot get object properties", ex );
return null;
}
}
@@ -168,6 +176,72 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
}
}
+ /*
+ private Set<Object> getEntities( Class<? extends OWLEntity> c ){
+ OWLEntityCollector ec = new OWLEntityCollector();
+ try {
+ getOntology().accept(ec);
+ Set<Object> entities = new HashSet<Object>();
+ for (Object obj : ec.entities()) {
+ if (c.isInstance(obj) && (((OWLEntity) obj).getURI() != null) &&
+ ((OWLEntity) obj).getURI().getSchemeSpecificPart().equals(ont.getURI().getSchemeSpecificPart())){
+ //System.out.println(((OWLEntity) obj).getURI().getSchemeSpecificPart()+" - "+ont.getURI().getSchemeSpecificPart());
+ //System.out.println(((OWLEntity) obj).getURI()+" : "+ont.getOntology().contains(obj));
+ entities.add(new OWLAPIEntity((OWLEntity)obj, ont, ((OWLEntity)obj).getURI() ));
+ }
+ }
+ return entities;
+ } catch (OWLException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+ */
+ /*
+ private void addAnnotations(OWLAPIEntity ent) {
+ for (String[] a : getAnnotations(ent.getObject(),(OWLOntology)ent.getOntology().getOntology())) {
+ ent.getAnnotations().add(a[0]);
+ if (a[1]!=null) {
+ ent.getLangToAnnot(EntityAdapter.LANGUAGES.valueOf(a[1])).add(a[0]);
+ }
+ if (a[2].equals(RDFSVocabularyAdapter.INSTANCE.getComment())) {
+ ent.getTypeToAnnot(EntityAdapter.TYPE.comment).add(a[0]);
+ }
+ else if (a[2].equals(RDFSVocabularyAdapter.INSTANCE.getLabel())) {
+ ent.getTypeToAnnot(EntityAdapter.TYPE.comment).add(a[0]);
+ }
+ }
+ }
+ */
+ /*
+ private Set<String[]> getAnnotations(OWLEntity e, OWLOntology o) {
+ Set<String[]> res = new HashSet<String[]>();
+ Set annots;
+ try {
+ annots = e.getAnnotations(o);
+ for (Object annot : annots) {
+ OWLAnnotationInstance annInst = ((OWLAnnotationInstance) annot);
+ String val;
+ String lang=null;
+ String annotUri = annInst.getProperty().getURI().toString();
+ if ( annInst.getContent() instanceof OWLDataValue ) {
+ OWLDataValue odv = (OWLDataValue) annInst.getContent();
+ val = odv.toString();
+ lang = odv.getLang();
+ }
+ else
+ val= (String) annInst.getContent();
+ res.add(new String[]{val,lang,annotUri});
+ }
+ }
+ catch (OWLException oe) {
+ oe.printStackTrace();
+ }
+ return Collections.unmodifiableSet(res);
+ }
+ */
+
// JE: particularly inefficient
public int nbClasses() {
try {
@@ -177,6 +251,10 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements Loaded
}
}
+ public int nbProperties() {
+ return nbObjectProperties()+nbDataProperties();
+ }
+
public int nbObjectProperties() {
try {
return ((OWLOntology)onto).getObjectProperties().size();
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
index e4886eab..deeb5cfd 100644
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
@@ -31,34 +31,22 @@ import java.util.Set;
import org.apache.log4j.Logger;
import org.apache.log4j.Level;
-import org.xml.sax.SAXException;
-
import org.semanticweb.owl.align.AlignmentException;
import fr.inrialpes.exmo.align.onto.OntologyCache;
import fr.inrialpes.exmo.align.onto.OntologyFactory;
-import fr.inrialpes.exmo.align.onto.EntityAdapter;
-import fr.inrialpes.exmo.align.onto.Entity;
-import fr.inrialpes.exmo.align.onto.EntityAdapter.TYPE;
import fr.inrialpes.exmo.align.onto.Ontology;
-import fr.inrialpes.exmo.align.onto.ConcreteOntology;
import fr.inrialpes.exmo.align.onto.LoadedOntology;
-import org.semanticweb.owl.io.vocabulary.RDFSVocabularyAdapter;
-import org.semanticweb.owl.model.OWLAnnotationInstance;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLDataValue;
-import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLException;
-import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.helper.OWLEntityCollector;
import org.semanticweb.owl.util.OWLConnection;
import org.semanticweb.owl.util.OWLManager;
-import org.semanticweb.owl.io.owl_rdf.OWLRDFParser;
-import org.semanticweb.owl.io.owl_rdf.OWLRDFErrorHandler;
+/*
+ * JE: everything should be asked to the Ontoogy, not to the factory...
+ * So I suppress many initial methods
+ */
public class OWLAPIOntologyFactory extends OntologyFactory {
private URI formalismUri = null;
@@ -76,7 +64,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
return instance;
}
- public LoadedOntology loadOntology( URI physicalURI ) {
+ public LoadedOntology loadOntology( URI uri ) throws AlignmentException {
OWLConnection connection = null;
Map parameters = new HashMap();
parameters.put(OWLManager.OWL_CONNECTION,
@@ -85,28 +73,27 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
connection = OWLManager.getOWLConnection(parameters);
Level lev = Logger.getLogger("org.semanticweb.owl").getLevel();
Logger.getLogger("org.semanticweb.owl").setLevel(Level.ERROR);
- OWLOntology ontology = connection.loadOntologyPhysical(physicalURI);
+ OWLOntology ontology = connection.loadOntologyPhysical(uri);
Logger.getLogger("org.semanticweb.owl").setLevel(lev);
OWLAPIOntology onto = new OWLAPIOntology();
// It may be possible to fill this as final in OWLAPIOntology...
onto.setFormalism( formalismId );
onto.setFormURI( formalismUri );
onto.setOntology( ontology );
- onto.setFile( physicalURI );
+ onto.setFile( uri );
try {
- onto.setURI( ontology.getLogicalURI() );//getURI();
+ onto.setURI( ontology.getLogicalURI() );
} catch (OWLException e) {
// Better put in the AlignmentException of loaded
e.printStackTrace();
}
return onto;
- } catch (OWLException e) {
- e.printStackTrace();
+ } catch (OWLException e) {
+ throw new AlignmentException("Cannot load "+uri, e );
}
- return null;
}
- /** Can be used for loading the ontology if it is not available **/
+ /* Can be used for loading the ontology if it is not available
// JE: Onto: check that the structure is properly filled (see build...)
public Ontology loadOntology( URI ref, OntologyCache ontologies ) throws SAXException, AlignmentException {
Ontology onto = null;
@@ -146,7 +133,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
}
return onto;
}
-
+ */
// JE: Onto: I am not sure of the meaning of this "get"
/*
private Ontology getOntology(OWLOntology ont) {
@@ -172,70 +159,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
}
*/
- private Set<Entity> getEntities(LoadedOntology<OWLOntology> ont, Class<? extends OWLEntity> c){
- OWLEntityCollector ec = new OWLEntityCollector();
- try {
- ont.getOntology().accept(ec);
- Set<Entity> entities = new HashSet<Entity>();
- for (Object obj : ec.entities()) {
- if (c.isInstance(obj) && (((OWLEntity) obj).getURI() != null) &&
- ((OWLEntity) obj).getURI().getSchemeSpecificPart().equals(ont.getURI().getSchemeSpecificPart())){
- //System.out.println(((OWLEntity) obj).getURI().getSchemeSpecificPart()+" - "+ont.getURI().getSchemeSpecificPart());
- //System.out.println(((OWLEntity) obj).getURI()+" : "+ont.getOntology().contains(obj));
- entities.add(new OWLAPIEntity((OWLEntity)obj, ont, ((OWLEntity)obj).getURI() ));
- }
- }
- return entities;
- } catch (OWLException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- private void addAnnotations(OWLAPIEntity ent) {
- for (String[] a : getAnnotations(ent.getObject(),(OWLOntology)ent.getOntology().getOntology())) {
- ent.getAnnotations().add(a[0]);
- if (a[1]!=null) {
- ent.getLangToAnnot(EntityAdapter.LANGUAGES.valueOf(a[1])).add(a[0]);
- }
- if (a[2].equals(RDFSVocabularyAdapter.INSTANCE.getComment())) {
- ent.getTypeToAnnot(EntityAdapter.TYPE.comment).add(a[0]);
- }
- else if (a[2].equals(RDFSVocabularyAdapter.INSTANCE.getLabel())) {
- ent.getTypeToAnnot(EntityAdapter.TYPE.comment).add(a[0]);
- }
- }
- }
-
-
- private Set<String[]> getAnnotations(OWLEntity e, OWLOntology o) {
- Set<String[]> res = new HashSet<String[]>();
- Set annots;
- try {
- annots = e.getAnnotations(o);
- for (Object annot : annots) {
- OWLAnnotationInstance annInst = ((OWLAnnotationInstance) annot);
- String val;
- String lang=null;
- String annotUri = annInst.getProperty().getURI().toString();
- if ( annInst.getContent() instanceof OWLDataValue ) {
- OWLDataValue odv = (OWLDataValue) annInst.getContent();
- val = odv.toString();
- lang = odv.getLang();
- }
- else
- val= (String) annInst.getContent();
- res.add(new String[]{val,lang,annotUri});
- }
- }
- catch (OWLException oe) {
- oe.printStackTrace();
- }
- return Collections.unmodifiableSet(res);
- }
-
-
+ /*
private class OWLAPIEntity extends EntityAdapter<OWLEntity> {
//private boolean toLoad=true;
@@ -253,5 +177,6 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
return super.getAnnotations(lang, type);
}
}
+ */
}
--
GitLab