diff --git a/lib/owlapi1/api.jar b/lib/owlapi1/api.jar
deleted file mode 100644
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diff --git a/lib/owlapi1/impl.jar b/lib/owlapi1/impl.jar
deleted file mode 100644
index cbdd34c82727d1ecd0088ce89af7a7ebf494dc23..0000000000000000000000000000000000000000
Binary files a/lib/owlapi1/impl.jar and /dev/null differ
diff --git a/lib/owlapi1/io.jar b/lib/owlapi1/io.jar
deleted file mode 100644
index 4d57e6c1da69761c2f052e3a745eea254d755bd1..0000000000000000000000000000000000000000
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diff --git a/lib/owlapi1/rdfapi.jar b/lib/owlapi1/rdfapi.jar
deleted file mode 100644
index 5499252ac2499e6c20ed89a6e32f294eecc6ef35..0000000000000000000000000000000000000000
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diff --git a/lib/owlapi1/rdfparser.jar b/lib/owlapi1/rdfparser.jar
deleted file mode 100644
index e967dd537c59dce44639026a8f4a10a2c9a4da83..0000000000000000000000000000000000000000
Binary files a/lib/owlapi1/rdfparser.jar and /dev/null differ
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIAnnotIt.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIAnnotIt.java
deleted file mode 100644
index ad0dc82502f126159a463ac7495efa586e04c3ce..0000000000000000000000000000000000000000
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIAnnotIt.java
+++ /dev/null
@@ -1,77 +0,0 @@
-package fr.inrialpes.exmo.align.onto.owlapi10;
-
-import java.util.Iterator;
-import java.util.NoSuchElementException;
-
-
-import org.semanticweb.owl.model.OWLAnnotationInstance;
-import org.semanticweb.owl.model.OWLDataValue;
-import org.semanticweb.owl.model.OWLEntity;
-import org.semanticweb.owl.model.OWLException;
-import org.semanticweb.owl.model.OWLOntology;
-
-
-/**
- * An iterator over annotations of an OWLEntity. This class permits to avoid the instantiation of HashSet for
- * each call of a getAnnotation method.
- * @author JD
- *
- */
-public class OWLAPIAnnotIt implements Iterator<String> {
-
- /*private OWLOntology o;
- private OWLEntity e;*/
- private String lang;
- private String typeAnnot;
-
- private Iterator it;
-
- private String currentElem=null;
-
- public OWLAPIAnnotIt(OWLOntology o, OWLEntity e , String lang , String typeAnnot) throws OWLException {
- /*this.o=o; this.e=e; */ this.lang=lang; this.typeAnnot=typeAnnot;
- it = e.getAnnotations(o).iterator();
- }
-
- public boolean hasNext() {
- try {
- setNext();
- return currentElem != null;
- }
- catch (NoSuchElementException e) {
- return false;
- }
- }
-
- public String next() {
- setNext();
- String returnVal = currentElem;
- currentElem=null;
- return returnVal;
- }
-
- private void setNext() throws NoSuchElementException {
- while (currentElem==null) {
- OWLAnnotationInstance annot = (OWLAnnotationInstance) it.next();
- try {
- String annotUri = annot.getProperty().getURI().toString();
- if (annotUri.equals(typeAnnot) || typeAnnot==null) {
- if ( annot.getContent() instanceof OWLDataValue &&
- ( lang==null || ((OWLDataValue) annot.getContent()).getLang().equals(lang)) ) {
- currentElem = ((OWLDataValue) annot.getContent()).getValue().toString();
- }
- }
- } catch (OWLException e) {
- e.printStackTrace();
- currentElem=null;
- }
- }
-
- }
-
- public void remove() {
- throw new UnsupportedOperationException();
- }
-
- }
-
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
deleted file mode 100644
index 8eee9c6ac81fcbf0ee1774be42c11bcaf2dc2f0d..0000000000000000000000000000000000000000
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntology.java
+++ /dev/null
@@ -1,578 +0,0 @@
-/*
- * $Id$
- *
- * Copyright (C) INRIA, 2007-2008
- *
- * This program is free software; you can redistribute it and/or modify
- * 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
- */
-
-/*
- * This should be turned into an HeavyLoadedOntology.
- * Some primitives are already avalible below
- *
- * The point is that these primitives may concern:
- * - Named entities / All entities
- * - Asserted information / Deduced information
- * - Inherited information... ()
- * In fact the OWL API does only provide asserted.
- *
- * This is not very well implemented: the OWL API mandates to implement this as visitors...
- */
-
-package fr.inrialpes.exmo.align.onto.owlapi10;
-
-import java.net.URI;
-import java.util.AbstractSet;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.HashSet;
-
-import org.semanticweb.owl.align.AlignmentException;
-
-import fr.inrialpes.exmo.align.onto.OntologyFactory;
-import fr.inrialpes.exmo.align.onto.HeavyLoadedOntology;
-import fr.inrialpes.exmo.align.onto.BasicOntology;
-
-import org.semanticweb.owl.io.vocabulary.RDFSVocabularyAdapter;
-import org.semanticweb.owl.model.OWLAnnotationInstance;
-import org.semanticweb.owl.model.OWLDataType;
-import org.semanticweb.owl.model.OWLDataValue;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLProperty;
-import org.semanticweb.owl.model.OWLClass;
-import org.semanticweb.owl.model.OWLObjectProperty;
-import org.semanticweb.owl.model.OWLDataProperty;
-import org.semanticweb.owl.model.OWLIndividual;
-import org.semanticweb.owl.model.OWLEntity;
-import org.semanticweb.owl.model.OWLRestriction;
-import org.semanticweb.owl.model.OWLDescription;
-import org.semanticweb.owl.model.OWLNaryBooleanDescription;
-import org.semanticweb.owl.model.OWLCardinalityRestriction;
-import org.semanticweb.owl.model.OWLDataAllRestriction;
-import org.semanticweb.owl.model.OWLObjectAllRestriction;
-import org.semanticweb.owl.model.OWLException;
-import org.semanticweb.owl.model.helper.OWLEntityCollector;
-
-/**
- * Store the information regarding ontologies in a specific structure
- * Acts as an interface with regard to an ontology APY
- */
-
-public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyLoadedOntology<OWLOntology> {
-
- /* For caching sizes */
- private int nbentities = -1;
- private int nbclasses = -1;
- private int nbproperties = -1;
- private int nbobjectproperties = -1;
- private int nbdataproperties = -1;
- private int nbindividuals = -1;
-
- public OWLAPIOntology() {
- setFormalism( "OWL1.0" );
- try {
- setFormURI( new URI("http://www.w3.org/2002/07/owl#") );
- } catch (Exception e) {}; // does not happen
- };
-
- // -----------------------------------------------------------------
- // Ontology interface [//DONE]
-
- public OWLOntology getOntology() { return onto; }
-
- public void setOntology( OWLOntology o ) { this.onto = o; }
-
- // -----------------------------------------------------------------
- // LoadedOntology interface [//DONE]
-
- public Object getEntity( URI uri ) throws AlignmentException {
- try {
- OWLEntity result = ((OWLOntology)onto).getClass( uri );
- if ( result == null ) result = ((OWLOntology)onto).getDataProperty( uri );
- if ( result == null ) result = ((OWLOntology)onto).getObjectProperty( uri );
- if ( result == null ) result = ((OWLOntology)onto).getIndividual( uri );
- return result;
- } catch (OWLException ex) {
- throw new AlignmentException( "Cannot dereference URI : "+uri );
- }
- }
-
- public URI getEntityURI( Object o ) throws AlignmentException {
- try {
- return ((OWLEntity)o).getURI();
- } catch (OWLException oex) {
- throw new AlignmentException( "Cannot get URI ", oex );
- }
- }
- public String getEntityName( Object o ) throws AlignmentException {
- 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 Set<String> getEntityNames( Object o , String lang ) throws AlignmentException {
- try {
- OWLEntity e = ((OWLEntity) o);
- return getAnnotations(e,lang,RDFSVocabularyAdapter.INSTANCE.getLabel());
- } catch (OWLException oex) {
- return null;
- }
- }
- public Set<String> getEntityNames( Object o ) throws AlignmentException {
- try {
- OWLEntity e = ((OWLEntity) o);
- return getAnnotations(e,null,RDFSVocabularyAdapter.INSTANCE.getLabel());
- } catch (OWLException oex) {
- return null;
- }
- };
-
-
- public Set<String> getEntityComments( Object o , String lang ) throws AlignmentException {
- try {
- OWLEntity e = ((OWLEntity) o);
- return getAnnotations(e,lang,RDFSVocabularyAdapter.INSTANCE.getComment());
- } catch (OWLException oex) {
- return null;
- }
- };
-
- public Set<String> getEntityComments( Object o ) throws AlignmentException {
- try {
- OWLEntity e = ((OWLEntity) o);
- return getAnnotations(e,null,RDFSVocabularyAdapter.INSTANCE.getComment());
- } catch (OWLException oex) {
- return null;
- }
- };
-
- protected Set<String> getAnnotations(final OWLEntity e , final String lang , final String typeAnnot ) throws OWLException {
- final OWLOntology o = this.onto;
- return new AbstractSet<String>() {
- int size=-1;
- public Iterator<String> iterator() {
- try {
- return new OWLAPIAnnotIt(o,e,lang,typeAnnot);
- } catch (OWLException e) {
- e.printStackTrace();
- return null;
- }
- }
- public int size() {
- if (size==-1) {
- for (String s : this) {
- size++;
- }
- size++;
- }
- return size;
- }
-
- };
- // OLD IMPLEMENTATION
- /*Set<String> annots = new HashSet<String>();
- 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 &&
- ( lang==null || ((OWLDataValue) annot.getContent()).getLang().equals(lang)) ) {
- annots.add(((OWLDataValue) annot.getContent()).getValue().toString());
- }
- }
- }
- return annots;*/
- }
-
- public Set<String> getEntityAnnotations( Object o ) throws AlignmentException {
- try {
- return getAnnotations(((OWLEntity) o),null,null);
- } catch (OWLException oex) {
- return null;
- }
- };
-
- public boolean isEntity( Object o ){
- return ( o instanceof OWLEntity );
- };
- public boolean isClass( Object o ){
- return ( o instanceof OWLClass );
- };
- public boolean isProperty( Object o ){
- return ( o instanceof OWLProperty );
- };
- public boolean isDataProperty( Object o ){
- return ( o instanceof OWLDataProperty );
- };
- public boolean isObjectProperty( Object o ){
- return ( o instanceof OWLObjectProperty );
- };
- public boolean isIndividual( Object o ){
- return ( o instanceof OWLIndividual );
- };
-
- // ***JE:
- // We should solve this issue, is it better to go this way or tu use the OWL API?
- // JD: allows to retrieve some specific entities by giving their class
- // This is not part of the interface...
- 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()) {
- // JD: OWLEntitytCollector seems to return anonymous entities :&& ((OWLEntity)obj).getURI()!=null
- if (c.isInstance(obj) && ((OWLEntity) obj).getURI()!=null) { // &&((OWLEntity) obj).getURI().toString().startsWith(onto.getURI().toString()) ){
- entities.add(obj);
- }
- }
- return entities;
- }
-
- // Here it shoud be better to report exception
- // JE: Onto this does not work at all, of course...!!!!
- public Set<?> getEntities() {
- try {
- return getEntities(OWLEntity.class);
- } catch (OWLException ex) {
- return null;
- }
- }
-
- public Set<?> getClasses() {
- try {
- return ((OWLOntology)onto).getClasses(); // [W:unchecked]
- //return getEntities(OWLClass.class);
- } catch (OWLException ex) {
- return null;
- }
- }
-
- public Set<?> getProperties() {
- try {
- //return ((OWLOntology)onto).getProperties(); // [W:unchecked]
- return getEntities(OWLProperty.class);
- } catch (OWLException ex) {
- return null;
- }
- }
-
- public Set<?> getDataProperties() {
- try {
- // This first method returns also Properties not defined in the Onto
- // i.e. properties having an namespace different from the ontology uri
- return ((OWLOntology)onto).getDataProperties(); // [W:unchecked]
- //return getEntities(OWLDataProperty.class);
- } catch (OWLException ex) {
- return null;
- }
- }
-
- public Set<?> getObjectProperties() {
- try {
- // [Warning:unchecked] due to OWL API not serving generic types
- // This first method returns also Properties not defined in the Onto
- // i.e. properties having an namespace different from the ontology uri
- return ((OWLOntology)onto).getObjectProperties(); // [W:unchecked]
- // This method works better (??)
- //return getEntities(OWLObjectProperty.class);
- } catch (OWLException ex) {
- return null;
- }
- }
-
- public Set<?> getIndividuals() {
- try {
- return ((OWLOntology)onto).getIndividuals(); // [W:unchecked]
- //return getEntities(OWLIndividual.class);
- } catch (OWLException ex) {
- return null;
- }
- }
-
- public int nbEntities() {
- if ( nbentities != -1 ) return nbentities;
- nbentities = nbClasses()+nbProperties()+nbIndividuals();
- return nbentities;
- }
-
- public int nbClasses() {
- if ( nbclasses != -1 ) return nbclasses;
- try {
- nbclasses = ((OWLOntology)onto).getClasses().size();
- return nbclasses;
- } catch (OWLException oex) {
- return 0;
- }
- }
-
- public int nbProperties() {
- if ( nbproperties != -1 ) return nbproperties;
- nbproperties = nbObjectProperties()+nbDataProperties();
- return nbproperties;
- }
-
- public int nbObjectProperties() {
- if ( nbobjectproperties != -1 ) return nbobjectproperties;
- try {
- nbobjectproperties = ((OWLOntology)onto).getObjectProperties().size();
- return nbobjectproperties;
- } catch (OWLException oex) {
- return 0;
- }
- }
-
- public int nbDataProperties() {
- if ( nbdataproperties != -1 ) return nbdataproperties;
- try {
- nbdataproperties = ((OWLOntology)onto).getDataProperties().size();
- return nbdataproperties;
- } catch (OWLException oex) {
- return 0;
- }
- }
-
- public int nbIndividuals() {
- if ( nbindividuals != -1 ) return nbindividuals;
- try {
- nbindividuals = ((OWLOntology)onto).getIndividuals().size();
- return nbindividuals;
- } catch (OWLException oex) {
- return 0;
- }
- }
-
- public void unload() {
- try {
- ((OWLOntology)onto).getOWLConnection().notifyOntologyDeleted( ((OWLOntology)onto) );
- } catch (OWLException ex) { System.err.println(ex); };
- }
-
- // -----------------------------------------------------------------
- // HeavyLoadedOntology interface [//TOCHECK]
-
- // [//TODO]
- public boolean getCapabilities( int Direct, int Asserted, int Named ){
- return true;
- }
-
- // Pretty inefficient but nothing seems to be stored
- public Set<Object> getSubClasses( Object cl, int local, int asserted, int named ){
- Set<Object> sbcl = new HashSet<Object>();
- for( Object c : getClasses() ) {
- if ( getSuperClasses( (OWLClass)c, local, asserted, named ).contains( cl ) ) sbcl.add( c );
- }
- return sbcl;
- }
- public Set<Object> getSuperClasses( Object cl, int local, int asserted, int named ){
- Set<Object> spcl = new HashSet<Object>();
- if ( asserted == OntologyFactory.ASSERTED ){
- try {
- for( Object rest : ((OWLClass)cl).getSuperClasses( getOntology() ) ){
- if (rest instanceof OWLClass) spcl.add( rest );
- }
- } catch (OWLException ex) {
- }
- } else {
- try {
- // JE: I do not feel that this is really correct
- Set<Object> sup = new HashSet<Object>();
- for( Object rest : ((OWLClass)cl).getSuperClasses( getOntology() ) ){
- if (rest instanceof OWLClass) {
- spcl.add( rest );
- sup.add( rest );
- }
- }
- } catch (OWLException ex) {
- };
- }
- return spcl;
- }
-
- /*
- * In the OWL API, there is no properties: there are SuperClasses which are restrictions
- */
- public Set<Object> getProperties( Object cl, int local, int asserted, int named ){
- Set<Object> prop = new HashSet<Object>();
- if ( asserted == OntologyFactory.ASSERTED && local == OntologyFactory.LOCAL ) {
- try {
- for ( Object ent : ((OWLClass)cl).getSuperClasses( getOntology() ) ){
- if ( ent instanceof OWLRestriction )
- prop.add( ((OWLRestriction)ent).getProperty() );
- }
- } catch (OWLException e) { e.printStackTrace(); }
- } else {
- prop = getInheritedProperties( (OWLClass)cl );
- }
- return prop;
- }
- // Not very efficient: 2n instead of n
- public Set<Object> getDataProperties( Object c, int local, int asserted, int named ){
- Set<Object> props = new HashSet<Object>();
- for ( Object p : getProperties( c, local, asserted, named ) ){
- if ( p instanceof OWLDataProperty ) props.add( p );
- }
- return props;
- }
- // Not very efficient: 2n instead of n
- public Set<Object> getObjectProperties( Object c, int local, int asserted, int named ){
- Set<Object> props = new HashSet<Object>();
- for ( Object p : getProperties( c, local, asserted, named ) ){
- if ( p instanceof OWLObjectProperty ) props.add( p );
- }
- return props;
- }
- // Pretty inefficient but nothing seems to be stored
- public Set<Object> getInstances( Object cl, int local, int asserted, int named ){
- Set<Object> sbcl = new HashSet<Object>();
- try {
- for( Object i : getIndividuals() ) {
- //if ( getClasses( (OWLIndividual)i, local, asserted, named ).contains( cl ) ) sbcl.add( i );
- if ( ((OWLIndividual)i).getTypes( getOntology() ).contains( cl ) ) sbcl.add( i );
- }
- } catch (OWLException ex) {};
- return sbcl;
- }
- // Pretty inefficient but nothing seems to be stored
- public Set<Object> getSubProperties( Object pr, int local, int asserted, int named ){
- Set<Object> sbpr = new HashSet<Object>();
- for( Object p : getProperties() ) {
- if ( getSuperProperties( (OWLProperty)p, local, asserted, named ).contains( pr ) ) sbpr.add( p );
- }
- return sbpr;
- }
- public Set<Object> getSuperProperties( Object pr, int local, int asserted, int named ){
- Set<Object> supers = new HashSet<Object>();
- if ( asserted == OntologyFactory.ASSERTED ){
- try {
- for( Object rest : ((OWLProperty)pr).getSuperProperties( getOntology() ) ){
- if (rest instanceof OWLProperty) supers.add( rest );
- }
- } catch (OWLException ex) {
- }
- } else {
- try {
- Set<Object> sup = new HashSet<Object>();
- for( Object rest : ((OWLProperty)pr).getSuperProperties( getOntology() ) ){
- if (rest instanceof OWLProperty) {
- sup.add( rest );
- supers.add( rest );
- }
- }
- } catch (OWLException ex) {
- };
- }
- return supers;
- }
- public Set<Object> getRange( Object p, int asserted ){
- Set resultSet = new HashSet();
- try {
- for ( Object ent : ((OWLProperty)p).getRanges( getOntology() ) ){
- // Not correct
- // Could be something else than class
- if ( ent instanceof OWLClass || ent instanceof OWLDataType ) {
- resultSet.add( ent );
- }
- }
- } catch (OWLException ex) {};
- return resultSet;
- }
- public Set<Object> getDomain( Object p, int asserted ){
- Set resultSet = new HashSet();
- try {
- for ( Object ent : ((OWLProperty)p).getDomains( getOntology() ) ){
- // Not correct
- // Could be something else than class
- if ( ent instanceof OWLClass ) {
- resultSet.add( ent );
- }
- }
- } catch (OWLException ex) {};
- return resultSet;
- }
- public Set<Object> getClasses( Object i, int local, int asserted, int named ){
- Set<Object> supers = null;
- try {
- supers = ((OWLIndividual)i).getTypes( getOntology() );
- } catch (OWLException ex) {};
- if ( local == OntologyFactory.LOCAL ) {
- return supers;
- } else {
- // inherits the superclasses (unless we have to reduce them...)
- return supers;
- }
- }
-
- // JE: note this may be wrong if p is a property
- public Set<Object> getCardinalityRestrictions( Object p ){//JFDK
- Set<Object> spcl = new HashSet<Object>();
- try {
- Set<Object> sup = ((OWLClass)p).getSuperClasses( getOntology() );
- for( Object rest : sup ){
- // This should be filtered
- if (rest instanceof OWLCardinalityRestriction) spcl.add( rest );
- }
- } catch (OWLException ex) {
- };
- return spcl;
- }
-
- /*
- * Inherits all properties of a class
- */
- private Set<Object> getInheritedProperties( OWLClass cl ) {
- Set resultSet = new HashSet();
- try { getProperties( cl, resultSet ); }
- catch (OWLException ex) {};
- return resultSet;
- }
-
- /* This traverse properties */
- public void getProperties( OWLDescription desc, Set<Object> list) throws OWLException {
- if ( desc instanceof OWLRestriction ){
- //getProperties( (OWLRestriction)desc, list );
- list.add( ((OWLRestriction)desc).getProperty() );
- } else if ( desc instanceof OWLClass ) {
- getProperties( (OWLClass)desc, list );
- } else if ( desc instanceof OWLNaryBooleanDescription ) {
- for ( Object d : ((OWLNaryBooleanDescription)desc).getOperands() ){
- getProperties( (OWLDescription)d, list );
- }
- //getProperties( (OWLNaryBooleanDescription)desc, list );
- }
- }
- public void getProperties( OWLRestriction rest, Set<Object> list) throws OWLException {
- list.add( (Object)rest.getProperty() );
- }
- public void getProperties( OWLNaryBooleanDescription d, Set<Object> list) throws OWLException {
- for ( Iterator it = d.getOperands().iterator(); it.hasNext() ;){
- getProperties( (OWLDescription)it.next(), list );
- }
- }
- public void getProperties( OWLClass cl, Set<Object> list) throws OWLException {
- for ( Object desc : cl.getSuperClasses( getOntology() ) ){
- getProperties( (OWLDescription)desc, list );
- }
- // JE: I suspect that this can be a cause for looping!!
- for ( Object desc : cl.getEquivalentClasses( getOntology() ) ){
- getProperties( (OWLDescription)desc, list );
- }
- }
-
-}
diff --git a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java b/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
deleted file mode 100644
index 0daf0cb067428875e3023b6ae01f098694e58598..0000000000000000000000000000000000000000
--- a/src/fr/inrialpes/exmo/align/onto/owlapi10/OWLAPIOntologyFactory.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * $Id$
- *
- * Copyright (C) INRIA, 2008
- *
- * This program is free software; you can redistribute it and/or modify
- * 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
- */
-
-package fr.inrialpes.exmo.align.onto.owlapi10;
-
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.Level;
-
-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.Ontology;
-import fr.inrialpes.exmo.align.onto.LoadedOntology;
-
-import org.semanticweb.owl.model.OWLException;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.util.OWLConnection;
-import org.semanticweb.owl.util.OWLManager;
-
-public class OWLAPIOntologyFactory extends OntologyFactory {
-
- private static URI formalismUri = null;
- private static String formalismId = "OWL1.0";
- private static OntologyCache<OWLAPIOntology> cache = null;
-
- public OWLAPIOntologyFactory() {
- cache = new OntologyCache<OWLAPIOntology>();
- try {
- formalismUri = new URI("http://www.w3.org/2002/07/owl#");
- } catch (URISyntaxException ex) { ex.printStackTrace(); } // should not happen
- };
-
- public void clearCache() {
- cache.clear();
- }
-
- public OWLAPIOntology newOntology( Object ontology ) throws AlignmentException {
- if ( ontology instanceof OWLOntology ) {
- OWLAPIOntology onto = new OWLAPIOntology();
- onto.setFormalism( formalismId );
- onto.setFormURI( formalismUri );
- onto.setOntology( (OWLOntology)ontology );
- //onto.setFile( uri );// unknown
- try {
- onto.setURI( ((OWLOntology)ontology).getLogicalURI() );
- } catch (OWLException e) {
- // Better put in the AlignmentException of loaded
- e.printStackTrace();
- }
- //cache.recordOntology( uri, onto );
- return onto;
- } else {
- throw new AlignmentException( "Argument is not an OWLOntology: "+ontology );
- }
- }
-
- public OWLAPIOntology loadOntology( URI uri ) throws AlignmentException {
- OWLAPIOntology onto = null;
- onto = cache.getOntologyFromURI( uri );
- if ( onto != null ) return onto;
- onto = cache.getOntology( uri );
- if ( onto != null ) return onto;
- OWLConnection connection = null;
- Map<Object,Object> parameters = new HashMap<Object, Object>();
- parameters.put(OWLManager.OWL_CONNECTION,
- "org.semanticweb.owl.impl.model.OWLConnectionImpl");
- try {
- connection = OWLManager.getOWLConnection(parameters);
- Level lev = Logger.getLogger("org.semanticweb.owl").getLevel();
- Logger.getLogger("org.semanticweb.owl").setLevel(Level.ERROR);
- OWLOntology ontology = connection.loadOntologyPhysical(uri);
- Logger.getLogger("org.semanticweb.owl").setLevel(lev);
- 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( uri );
- try {
- onto.setURI( ontology.getLogicalURI() );
- } catch (OWLException e) {
- // Better put in the AlignmentException of loaded
- e.printStackTrace();
- }
- cache.recordOntology( uri, onto );
- return onto;
- } catch (OWLException e) {
- throw new AlignmentException("Cannot load "+uri, e );
- }
- }
-}
-
diff --git a/test/src/OWLAPIAlignmentTest.java b/test/src/OWLAPIAlignmentTest.java
deleted file mode 100644
index 056986209e29f3cf5b1ac00d815a419e6b3b7ecc..0000000000000000000000000000000000000000
--- a/test/src/OWLAPIAlignmentTest.java
+++ /dev/null
@@ -1,162 +0,0 @@
-/*
- * $Id$
- *
- * Copyright (C) INRIA, 2008
- *
- * This program is free software; you can redistribute it and/or modify
- * 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
- */
-
-//package test.com.acme.dona.dep;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertTrue;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Configuration;
-import org.testng.annotations.Test;
-//import org.testng.annotations.*;
-
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLEntity;
-
-import org.semanticweb.owl.align.AlignmentVisitor;
-import org.semanticweb.owl.align.Cell;
-
-import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
-import fr.inrialpes.exmo.align.impl.OWLAPICell;
-import fr.inrialpes.exmo.align.impl.rel.EquivRelation;
-import fr.inrialpes.exmo.align.impl.URIAlignment;
-import fr.inrialpes.exmo.align.impl.Annotations;
-import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
-import fr.inrialpes.exmo.align.onto.LoadedOntology;
-import fr.inrialpes.exmo.align.onto.Ontology;
-import fr.inrialpes.exmo.align.parser.AlignmentParser;
-
-import java.io.ByteArrayOutputStream;
-import java.io.PrintWriter;
-import java.io.BufferedWriter;
-import java.io.OutputStreamWriter;
-import java.io.FileOutputStream;
-import java.net.URI;
-import java.util.Set;
-
-public class OWLAPIAlignmentTest {
-
- private String localURIPrefix = "file://" + System.getProperty("user.dir");
-
- private OWLAPIAlignment alignment = null;
- private Ontology onto1 = null;
- private Ontology onto2 = null;
-
- @BeforeClass(groups = { "full", "noling" })
- private void init(){
- alignment = new OWLAPIAlignment();
- }
-
- @Test(groups = { "full", "noling" })
- public void loadingAndConvertingTest() throws Exception {
- assertNotNull( alignment, "Alignment was null" );
- AlignmentParser aparser = new AlignmentParser( 0 );
- assertNotNull( aparser, "AlignmentParser was null" );
- URIAlignment result = (URIAlignment)aparser.parse( "file:examples/rdf/newsample.rdf" );
- assertNotNull( result, "URIAlignment(result) was null" );
- alignment = OWLAPIAlignment.toOWLAPIAlignment( result );
- assertNotNull( alignment, "toOWLAPIAlignment(result) was null" );
- result = alignment.toURIAlignment();
- assertNotNull( result, "toURIAlignment() was null" );
- assertTrue( result instanceof URIAlignment );
- }
-
- @Test(groups = { "full", "noling" }, dependsOnMethods = {"loadingAndConvertingTest"})
- public void basicAttributeTest() throws Exception {
- assertEquals( alignment.getLevel(), "0" );
- assertEquals( alignment.getType(), "**" );
- assertEquals( alignment.getExtension( Annotations.ALIGNNS, Annotations.METHOD), "fr.inrialpes.exmo.align.impl.method.StringDistAlignment" );
- assertEquals( alignment.getExtension( Annotations.ALIGNNS, Annotations.TIME), "7" );
- }
-
- @Test(groups = { "full", "noling" }, dependsOnMethods = {"loadingAndConvertingTest"})
- public void ontologyTest() throws Exception {
- onto1 = alignment.getOntologyObject1();
- onto2 = alignment.getOntologyObject2();
- assertTrue( onto1 instanceof LoadedOntology );
- assertTrue( onto2 instanceof LoadedOntology );
- assertTrue( alignment.getOntology1() instanceof OWLOntology );
- assertTrue( alignment.getOntology2() instanceof OWLOntology );
- assertEquals( alignment.getOntology1URI().toString(), "http://www.example.org/ontology1" );
- assertEquals( alignment.getOntology2URI().toString(), "http://www.example.org/ontology2" );
- assertEquals( onto1.getURI().toString(), "http://www.example.org/ontology1" );
- assertEquals( onto2.getURI().toString(), "http://www.example.org/ontology2" );
- assertEquals( onto1.getFile().toString(), "file:examples/rdf/onto1.owl" );
- assertEquals( onto2.getFile().toString(), "file:examples/rdf/onto2.owl" );
- assertEquals( onto1.getFormalism(), "OWL1.0" );
- assertEquals( onto2.getFormalism(), "OWL1.0" );
- assertEquals( onto1.getFormURI().toString(), "http://www.w3.org/2002/07/owl#" );
- assertEquals( onto2.getFormURI().toString(), "http://www.w3.org/2002/07/owl#" );
- }
-
- @Test(groups = { "full", "noling" }, dependsOnMethods = {"ontologyTest"})
- public void basicCellTest() throws Exception {
- assertEquals( alignment.nbCells(), 2 );
- Object ob2 = ((LoadedOntology)onto2).getEntity( new URI("http://www.example.org/ontology2#journalarticle") );
- assertTrue( ob2 instanceof OWLEntity );
- Set<Cell> s2 = alignment.getAlignCells2( ob2 );
- assertEquals( s2.size(), 2 );
- for( Cell c2 : s2 ){
- assertTrue( c2 instanceof OWLAPICell );
- assertTrue( c2.getRelation() instanceof EquivRelation );
- assertTrue( c2.getObject1() instanceof OWLEntity );
- }
- Object ob1 = ((LoadedOntology)onto1).getEntity( new URI("http://www.example.org/ontology1#journalarticle") );
- assertTrue( ob1 instanceof OWLEntity );
- Set<Cell> s1 = alignment.getAlignCells1( ob1 );
- assertEquals( s1.size(), 1 );
- for( Cell c1 : s1 ){
- assertTrue( c1 instanceof OWLAPICell );
- assertTrue( c1.getRelation() instanceof EquivRelation );
- assertEquals( c1.getStrength(), 1. );
- assertTrue( c1.getObject2() instanceof OWLEntity );
- assertEquals( ((LoadedOntology)onto2).getEntityURI( c1.getObject2() ).toString(), "http://www.example.org/ontology2#journalarticle" );
- }
- ob1 = ((LoadedOntology)onto1).getEntity( new URI("http://www.example.org/ontology1#reviewedarticle") );
- assertTrue( ob1 instanceof OWLEntity );
- s1 = alignment.getAlignCells1( ob1 );
- assertEquals( s1.size(), 1 );
- for( Cell c1 : s1 ){
- assertTrue( c1 instanceof OWLAPICell );
- assertTrue( c1.getRelation() instanceof EquivRelation );
- assertEquals( c1.getStrength(), .4666666666666667 );
- assertTrue( c1.getObject2() instanceof OWLEntity );
- assertEquals( ((LoadedOntology)onto2).getEntityURI( c1.getObject2() ).toString(), "http://www.example.org/ontology2#journalarticle" );
- }
- }
-
- @Test(groups = { "full", "noling" }, dependsOnMethods = {"loadingAndConvertingTest"})
- public void rendererTest() throws Exception {
- ByteArrayOutputStream stream = new ByteArrayOutputStream();
- //FileOutputStream stream = new FileOutputStream("result.rdf");
- PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( stream, "UTF-8" )), true);
-
- AlignmentVisitor renderer = new RDFRendererVisitor( writer );
- alignment.render( renderer );
- writer.flush();
- writer.close();
- assertEquals( stream.toString().length(), 1706, "Rendered differently" );
- }
-
-}