From 38514ba5eced6feabe90bd6b138bcdc8acaa7626 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Wed, 13 Jun 2007 19:41:27 +0000
Subject: [PATCH] - Added the new Ontology structure in the API implementation
and in the format
---
README.TXT | 2 +-
dtd/align.dtd | 27 +++-
.../exmo/align/impl/BasicAlignment.java | 69 ++++++---
.../exmo/align/impl/DistanceAlignment.java | 55 +++----
.../exmo/align/impl/OWLAPIAlignment.java | 48 +++---
.../inrialpes/exmo/align/impl/Ontology.java | 50 +++++++
.../exmo/align/impl/URIAlignment.java | 20 +--
.../exmo/align/parser/AlignmentParser.java | 140 +++++++++++++-----
8 files changed, 290 insertions(+), 121 deletions(-)
create mode 100644 src/fr/inrialpes/exmo/align/impl/Ontology.java
diff --git a/README.TXT b/README.TXT
index 8d73931a..1799ddce 100644
--- a/README.TXT
+++ b/README.TXT
@@ -57,7 +57,7 @@ $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/exa
$ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -t 0.4 -o examples/rdf/sample.rdf
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter examples/rdf/sample.rdf
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter examples/rdf/newsample.rdf
$ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -a examples/rdf/sample.rdf
diff --git a/dtd/align.dtd b/dtd/align.dtd
index 111c6971..95bf0c88 100644
--- a/dtd/align.dtd
+++ b/dtd/align.dtd
@@ -34,25 +34,38 @@
<!-- (11|1?|1+|1*|?1|??|?+|?*|+1|+?|++|+*|*1|*?|*+|**) -->
<!ELEMENT type (#PCDATA)>
<!ELEMENT level (#PCDATA)>
+<!-- uriX are only here for compatibility purposes -->
<!ELEMENT uri1 (#PCDATA)><!-- uri -->
<!ATTLIST uri1 rdf:resource %uri; #IMPLIED>
<!ELEMENT uri2 (#PCDATA)><!-- uri -->
<!ATTLIST uri2 rdf:resource %uri; #IMPLIED>
-<!ELEMENT onto1 (#PCDATA)><!-- uri -->
+<!ELEMENT onto1 (ANY)><!-- uri|Ontology -->
<!ATTLIST onto1 rdf:resource %uri; #IMPLIED>
-<!ELEMENT onto2 (#PCDATA)><!-- uri -->
+<!ELEMENT onto2 (ANY)><!-- uri|Ontology -->
<!ATTLIST onto2 rdf:resource %uri; #IMPLIED>
+
+<!ELEMENT Ontology (formalism)>
+<!ATTLIST Ontology rdf:about %uri; #IMPLIED>
+<!ELEMENT location (#PCDATA)>
+<!ELEMENT formalism (Formalism)>
+<!ELEMENT Formalism (EMPTY)>
+<!ATTLIST Formalism uri %uri; #IMPLIED
+ name CDATA #REQUIRED>
+
<!-- For compatibility reason it is authorized to put several Cells
- in a map element. However, the result is not RDF however -->
+ in a map element. However, the result is not RDF anymore -->
<!ELEMENT map (Cell*)>
<!ELEMENT Cell (entity1|entity2|measure|relation)*>
+<!ATTLIST Cell id %uri; #IMPLIED>
-<!ELEMENT entity1 EMPTY>
-<!ATTLIST entity1 rdf:resource %uri; #REQUIRED>
+<!-- either object or URI -->
+<!ELEMENT entity1 ANY>
+<!ATTLIST entity1 rdf:resource %uri; #IMPLIED>
-<!ELEMENT entity2 EMPTY>
-<!ATTLIST entity2 rdf:resource %uri; #REQUIRED>
+<!-- either object or URI -->
+<!ELEMENT entity2 ANY>
+<!ATTLIST entity2 rdf:resource %uri; #IMPLIED>
<!-- I should put the true value here -->
<!ATTLIST measure rdf:datatype %uri; #REQUIRED>
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index b9673537..395309ec 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -65,9 +65,11 @@ public class BasicAlignment implements Alignment {
//public static String TIME = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment:time";
public static String TIME = "time";
- protected Object onto1 = null;
-
- protected Object onto2 = null;
+ // JE: OMWG1
+ //protected Object onto1 = null;
+ //protected Object onto2 = null;
+ protected Ontology onto1 = null;
+ protected Ontology onto2 = null;
/* Set to true for rejecting the use of deprecated (non deterministic) primitives */
protected static boolean STRICT_IMPLEMENTATION = false;
@@ -93,9 +95,9 @@ public class BasicAlignment implements Alignment {
* This is NOT the Ontology URI which can be obtained by
* getOntology1URI()
*/
- protected URI uri1 = null;
-
- protected URI uri2 = null;
+ // JE: OMWG1
+ //protected URI uri1 = null;
+ //protected URI uri2 = null;
public BasicAlignment() {
hash1 = new Hashtable();
@@ -103,11 +105,23 @@ public class BasicAlignment implements Alignment {
extensions = new BasicParameters();
namespaces = new BasicParameters();
setExtension( METHOD, getClass().getName() );
+ // JE: OMWG1
+ onto1 = new Ontology();
+ onto2 = new Ontology();
}
public void init( Object onto1, Object onto2, Object cache ) throws AlignmentException {
- this.onto1 = onto1;
- this.onto2 = onto2;
+ System.err.println( "ONTO1[init()] = " +onto1 );
+ // JE: OMWG1
+ //this.onto1 = onto1;
+ //this.onto2 = onto2;
+ if ( onto1 instanceof Ontology ) {
+ this.onto1 = (Ontology)onto1;
+ this.onto2 = (Ontology)onto2;
+ } else {
+ this.onto1.setOntology( onto1 );
+ this.onto2.setOntology( onto2 );
+ }
}
public void init( Object onto1, Object onto2 ) throws AlignmentException {
@@ -128,24 +142,28 @@ public class BasicAlignment implements Alignment {
/** Alignment methods * */
public Object getOntology1() {
- return onto1;
+ return onto1.getOntology();
};
public Object getOntology2() {
- return onto2;
+ return onto2.getOntology();
};
public URI getOntology1URI() throws AlignmentException {
- if ( onto1 instanceof URI ) {
- return (URI)onto1;
+ // JE: OMWG1
+ Object ontology = onto1.getOntology();
+ if ( ontology != null && ontology instanceof URI ) {
+ return (URI)ontology;
} else {
throw new AlignmentException( "Cannot find URI for "+onto1 );
}
};
public URI getOntology2URI() throws AlignmentException {
- if ( onto2 instanceof URI ) {
- return (URI)onto2;
+ // JE: OMWG1
+ Object ontology = onto2.getOntology();
+ if ( ontology != null && ontology instanceof URI ) {
+ return (URI)ontology;
} else {
throw new AlignmentException( "Cannot find URI for "+onto2 );
}
@@ -153,12 +171,16 @@ public class BasicAlignment implements Alignment {
public void setOntology1(Object ontology) throws AlignmentException {
//*/onto1 = (OWLOntology)ontology;
- onto1 = ontology;
+ // JE: OMWG1
+ //onto1 = ontology;
+ onto1.setOntology( ontology );
};
public void setOntology2(Object ontology) throws AlignmentException {
//*/onto2 = (OWLOntology)ontology;
- onto2 = ontology;
+ // JE: OMWG1
+ //onto2 = ontology;
+ onto2.setOntology( ontology );
};
public void setType(String type) { this.type = type; };
@@ -169,13 +191,19 @@ public class BasicAlignment implements Alignment {
public String getLevel() { return level; };
- public URI getFile1() { return uri1; };
+ // JE: OMWG1
+ //public URI getFile1() { return uri1; };
+ //public void setFile1(URI u) { uri1 = u; };
+ //public URI getFile2() { return uri2; };
+ //public void setFile2(URI u) { uri2 = u; };
+
+ public URI getFile1() { return onto1.getFile(); };
- public void setFile1(URI u) { uri1 = u; };
+ public void setFile1(URI u) { onto1.setFile( u ); };
- public URI getFile2() { return uri2; };
+ public URI getFile2() { return onto2.getFile(); };
- public void setFile2(URI u) { uri2 = u; };
+ public void setFile2(URI u) { onto2.setFile( u ); };
public Parameters getExtensions(){ return extensions; }
@@ -614,6 +642,7 @@ public class BasicAlignment implements Alignment {
public void cleanUp() {}
}
+
class MEnumeration implements Enumeration {
private Enumeration set = null; // The enumeration of sets
private Iterator current = null; // The current set's enumeration
diff --git a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
index f70ee42e..5967b032 100644
--- a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
@@ -158,18 +158,21 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
boolean found = false;
double val = 0;
+ System.err.println( "ONTO1[extract()] = " +onto1 );
+ System.err.println( "ONTO1[extract().gO()] = " +onto1.getOntology() );
+
try {
// Extract for properties
ConcatenatedIterator pit1 = new
- ConcatenatedIterator(((OWLOntology)onto1).getObjectProperties().iterator(),
- ((OWLOntology)onto1).getDataProperties().iterator());
+ ConcatenatedIterator(((OWLOntology)(onto1.getOntology())).getObjectProperties().iterator(),
+ ((OWLOntology)(onto1.getOntology())).getDataProperties().iterator());
for ( ; pit1.hasNext(); ) {
OWLProperty prop1 = (OWLProperty)pit1.next();
found = false; max = threshold; val = 0;
OWLProperty prop2 = null;
ConcatenatedIterator pit2 = new
- ConcatenatedIterator(((OWLOntology)onto2).getObjectProperties().iterator(),
- ((OWLOntology)onto2).getDataProperties().iterator());
+ ConcatenatedIterator(((OWLOntology)(onto2.getOntology())).getObjectProperties().iterator(),
+ ((OWLOntology)(onto2.getOntology())).getDataProperties().iterator());
for ( ; pit2.hasNext(); ) {
OWLProperty current = (OWLProperty)pit2.next();
val = 1 - sim.getPropertySimilarity(prop1,current);
@@ -180,11 +183,11 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
if ( found ) addAlignCell(prop1,prop2, "=", max);
}
// Extract for classes
- for (Iterator it1 = ((OWLOntology)onto1).getClasses().iterator(); it1.hasNext(); ) {
+ for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getClasses().iterator(); it1.hasNext(); ) {
OWLClass class1 = (OWLClass)it1.next();
found = false; max = threshold; val = 0;
OWLClass class2 = null;
- for (Iterator it2 = ((OWLOntology)onto2).getClasses().iterator(); it2.hasNext(); ) {
+ for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getClasses().iterator(); it2.hasNext(); ) {
OWLClass current = (OWLClass)it2.next();
val = 1 - sim.getClassSimilarity(class1,current);
if (val > max) {
@@ -196,12 +199,12 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
// Extract for individuals
// This does not work, at least for the OAEI 2005 tests
if ( params.getParameter("noinst") == null ){
- for (Iterator it1 = ((OWLOntology)onto1).getIndividuals().iterator(); it1.hasNext();) {
+ for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getIndividuals().iterator(); it1.hasNext();) {
OWLIndividual ind1 = (OWLIndividual)it1.next();
if ( ind1.getURI() != null ) {
found = false; max = threshold; val = 0;
OWLIndividual ind2 = null;
- for (Iterator it2 = ((OWLOntology)onto2).getIndividuals().iterator(); it2.hasNext(); ) {
+ for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getIndividuals().iterator(); it2.hasNext(); ) {
OWLIndividual current = (OWLIndividual)it2.next();
if ( current.getURI() != null ) {
val = 1 - sim.getIndividualSimilarity(ind1,current);
@@ -230,17 +233,17 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
// (redoing the matrix instead of getting it)
// For each kind of stuff (cl, pr, ind)
// Create a matrix
- int nbclasses1 = ((OWLOntology)onto1).getClasses().size();
- int nbclasses2 = ((OWLOntology)onto2).getClasses().size();
+ int nbclasses1 = ((OWLOntology)(onto1.getOntology())).getClasses().size();
+ int nbclasses2 = ((OWLOntology)(onto2.getOntology())).getClasses().size();
double[][] matrix = new double[nbclasses1][nbclasses2];
OWLClass[] class1 = new OWLClass[nbclasses1];
OWLClass[] class2 = new OWLClass[nbclasses2];
int i = 0;
- for (Iterator it1 = ((OWLOntology)onto1).getClasses().iterator(); it1.hasNext(); i++) {
+ for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getClasses().iterator(); it1.hasNext(); i++) {
class1[i] = (OWLClass)it1.next();
}
int j = 0;
- for (Iterator it2 = ((OWLOntology)onto2).getClasses().iterator(); it2.hasNext(); j++) {
+ for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getClasses().iterator(); it2.hasNext(); j++) {
class2[j] = (OWLClass)it2.next();
}
for( i = 0; i < nbclasses1; i++ ){
@@ -265,22 +268,22 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
catch (AlignmentException alex) { alex.printStackTrace(); }
// For properties
try{
- int nbprop1 = ((OWLOntology)onto1).getDataProperties().size() + ((OWLOntology)onto1).getObjectProperties().size();
- int nbprop2 = ((OWLOntology)onto2).getDataProperties().size() + ((OWLOntology)onto2).getObjectProperties().size();
+ int nbprop1 = ((OWLOntology)(onto1.getOntology())).getDataProperties().size() + ((OWLOntology)(onto1.getOntology())).getObjectProperties().size();
+ int nbprop2 = ((OWLOntology)(onto2.getOntology())).getDataProperties().size() + ((OWLOntology)(onto2.getOntology())).getObjectProperties().size();
double[][] matrix = new double[nbprop1][nbprop2];
OWLProperty[] prop1 = new OWLProperty[nbprop1];
OWLProperty[] prop2 = new OWLProperty[nbprop2];
int i = 0;
ConcatenatedIterator pit1 = new
- ConcatenatedIterator(((OWLOntology)onto1).getObjectProperties().iterator(),
- ((OWLOntology)onto1).getDataProperties().iterator());
+ ConcatenatedIterator(((OWLOntology)(onto1.getOntology())).getObjectProperties().iterator(),
+ ((OWLOntology)(onto1.getOntology())).getDataProperties().iterator());
for (; pit1.hasNext(); i++) {
prop1[i] = (OWLProperty)pit1.next();
}
int j = 0;
ConcatenatedIterator pit2 = new
- ConcatenatedIterator(((OWLOntology)onto2).getObjectProperties().iterator(),
- ((OWLOntology)onto2).getDataProperties().iterator());
+ ConcatenatedIterator(((OWLOntology)(onto2.getOntology())).getObjectProperties().iterator(),
+ ((OWLOntology)(onto2.getOntology())).getDataProperties().iterator());
for (; pit2.hasNext(); j++) {
prop2[j] = (OWLProperty)pit2.next();
}
@@ -378,13 +381,13 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
// Plus a map from the objects to the cells
// O(n^2.log n)
ConcatenatedIterator pit1 = new
- ConcatenatedIterator(((OWLOntology)onto1).getObjectProperties().iterator(),
- ((OWLOntology)onto1).getDataProperties().iterator());
+ ConcatenatedIterator(((OWLOntology)(onto1.getOntology())).getObjectProperties().iterator(),
+ ((OWLOntology)(onto1.getOntology())).getDataProperties().iterator());
for (; pit1.hasNext(); ) {
ent1 = (OWLProperty)pit1.next();
ConcatenatedIterator pit2 = new
- ConcatenatedIterator(((OWLOntology)onto2).getObjectProperties().iterator(),
- ((OWLOntology)onto2).getDataProperties().iterator());
+ ConcatenatedIterator(((OWLOntology)(onto2.getOntology())).getObjectProperties().iterator(),
+ ((OWLOntology)(onto2.getOntology())).getDataProperties().iterator());
for (; pit2.hasNext(); ) {
ent2 = (OWLProperty)pit2.next();
val = 1 - sim.getPropertySimilarity((OWLProperty)ent1,(OWLProperty)ent2);
@@ -394,9 +397,9 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
}
}
}
- for (Iterator it1 = ((OWLOntology)onto1).getClasses().iterator(); it1.hasNext(); ) {
+ for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getClasses().iterator(); it1.hasNext(); ) {
ent1 = (OWLClass)it1.next();
- for (Iterator it2 = ((OWLOntology)onto2).getClasses().iterator(); it2.hasNext(); ) {
+ for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getClasses().iterator(); it2.hasNext(); ) {
ent2 = (OWLClass)it2.next();
val = 1 - sim.getClassSimilarity((OWLClass)ent1,(OWLClass)ent2);
//val = ((SimilarityMeasure)getSimilarity()).getSimilarity(ent1.getURI(),ent2.getURI());
@@ -407,11 +410,11 @@ public class DistanceAlignment extends OWLAPIAlignment implements AlignmentProce
}
// OLA with or without instances
if ( params.getParameter("noinst") == null ){
- for (Iterator it1 = ((OWLOntology)onto1).getIndividuals().iterator(); it1.hasNext();) {
+ for (Iterator it1 = ((OWLOntology)(onto1.getOntology())).getIndividuals().iterator(); it1.hasNext();) {
ent1 = (OWLIndividual)it1.next();
if ( ent1.getURI() != null ) {
- for (Iterator it2 = ((OWLOntology)onto2).getIndividuals().iterator(); it2.hasNext(); ) {
+ for (Iterator it2 = ((OWLOntology)(onto2.getOntology())).getIndividuals().iterator(); it2.hasNext(); ) {
ent2 = (OWLIndividual)it2.next();
if ( ent2.getURI() != null ) {
val = 1 - sim.getIndividualSimilarity((OWLIndividual)ent1,(OWLIndividual)ent2);
diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
index f2c88dfc..d36a5a85 100644
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
@@ -56,32 +56,32 @@ import org.semanticweb.owl.align.Parameters;
public class OWLAPIAlignment extends BasicAlignment {
- //protected OWLOntology onto1 = null;
-
- //protected OWLOntology onto2 = null;
-
protected OWLAPIAlignment init = null;
- public OWLAPIAlignment() {
- }
+ public OWLAPIAlignment() {}
public void init(Object onto1, Object onto2) throws AlignmentException {
init( onto1, onto2, (OntologyCache)null );
}
- public void init(Object onto1, Object onto2, Object ontologies) throws AlignmentException {
+ public void init(Object o1, Object o2, Object ontologies) throws AlignmentException {
OntologyCache cache = null;
if ( ontologies instanceof OntologyCache ) cache = (OntologyCache)ontologies;
else cache = (OntologyCache)null;
- if ( onto1 instanceof OWLOntology && onto2 instanceof OWLOntology ){
- super.init( onto1, onto2, ontologies );
- } else if ( onto1 instanceof URI && onto2 instanceof URI ) {
+ if ( (o1 instanceof OWLOntology && o2 instanceof OWLOntology)
+ || (o1 instanceof Ontology && o2 instanceof Ontology) ){
+ super.init( o1, o2, ontologies );
+ } else if ( o1 instanceof URI && o2 instanceof URI ) {
// JE: This contains the File and not the URI!
- setFile1( (URI)onto1 );
- setFile2( (URI)onto2 );
+ setFile1( (URI)o1 );
+ setFile2( (URI)o2 );
+ ((Ontology)onto1).setFormalism( "OWL1.0" );
+ ((Ontology)onto2).setFormalism( "OWL1.0" );
+ //onto1.setFormalismURI();
+ //onto2.setFormalismURI();
try {
- super.init( loadOntology( getFile1(), cache ),
- loadOntology( getFile2(), cache ) );
+ super.init( loadOntology( (URI)o1, cache ),
+ loadOntology( (URI)o2, cache ) );
} catch (OWLException e) {
throw new AlignmentException( "Cannot load ontologies", e );
} catch (SAXException e) {
@@ -109,7 +109,8 @@ public class OWLAPIAlignment extends BasicAlignment {
public URI getOntology1URI() throws AlignmentException {
try {
- return ((OWLOntology)onto1).getLogicalURI();
+ // JE: OWMG1
+ return ((OWLOntology)(onto1.getOntology())).getLogicalURI();
} catch ( OWLException e ) {
throw new AlignmentException( "URI conversion error for "+onto1, e );
}
@@ -117,7 +118,8 @@ public class OWLAPIAlignment extends BasicAlignment {
public URI getOntology2URI() throws AlignmentException {
try {
- return ((OWLOntology)onto2).getLogicalURI();
+ // JE: OWMG1
+ return ((OWLOntology)(onto2.getOntology())).getLogicalURI();
} catch ( OWLException e ) {
throw new AlignmentException( "URI conversion error for "+onto2, e );
}
@@ -216,7 +218,7 @@ public class OWLAPIAlignment extends BasicAlignment {
public Object clone() {
OWLAPIAlignment align = new OWLAPIAlignment();
try {
- align.init( (OWLOntology)getOntology1(), (OWLOntology)getOntology2() );
+ align.init( onto1, onto2 );
} catch ( AlignmentException e ) {};
align.setType( getType() );
align.setLevel( getLevel() );
@@ -264,6 +266,7 @@ public class OWLAPIAlignment extends BasicAlignment {
OWLAPIAlignment alignment = new OWLAPIAlignment();
//alignment.setFile1( al.getFile1() );
//alignment.setFile2( al.getFile2() );
+ System.err.println( "TOA: " + al.getFile1()+ " -- " + al.getFile2());
alignment.init( al.getFile1(), al.getFile2(), ontologies );
alignment.setType( al.getType() );
alignment.setLevel( al.getLevel() );
@@ -271,13 +274,16 @@ public class OWLAPIAlignment extends BasicAlignment {
String label = (String)e.nextElement();
alignment.setExtension( label, al.getExtension( label ) );
}
- OWLOntology onto1 = (OWLOntology)alignment.getOntology1();
- OWLOntology onto2 = (OWLOntology)alignment.getOntology2();
+ OWLOntology o1 = (OWLOntology)alignment.getOntology1();
+ OWLOntology o2 = (OWLOntology)alignment.getOntology2();
+ System.err.println( o1 );
for (Enumeration e = al.getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
+ System.err.println( c.getObject1AsURI() );
+ System.err.println( c.getObject2AsURI() );
alignment.addAlignCell( c.getId(),
- getEntity( onto1, c.getObject1AsURI() ),
- getEntity( onto2, c.getObject2AsURI() ),
+ getEntity( o1, c.getObject1AsURI() ),
+ getEntity( o2, c.getObject2AsURI() ),
c.getRelation(),
c.getStrength(),
c.getExtensions() );
diff --git a/src/fr/inrialpes/exmo/align/impl/Ontology.java b/src/fr/inrialpes/exmo/align/impl/Ontology.java
new file mode 100644
index 00000000..db126829
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/impl/Ontology.java
@@ -0,0 +1,50 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2007
+ * Copyright (C) CNR Pisa, 2005
+ *
+ * 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.impl;
+
+import java.net.URI;
+
+/**
+ * Store the information regarding ontologies in a specific structure
+ */
+
+public class Ontology {
+ protected URI uri = null;
+ protected URI file = null;
+ protected Object onto = null;
+ protected URI formalismURI = null;
+ protected String formalism = null;
+
+ public Ontology() {};
+
+ public URI getUri() { return uri; }
+ public URI getFile() { return file; }
+ public Object getOntology() { return onto; }
+ public URI getFormURI() { return formalismURI; }
+ public String getFormalism() { return formalism; }
+
+ public void setUri( URI uri ) { this.uri = uri; }
+ public void setFile( URI file ) { this.file = file; }
+ public void setOntology( Object o ) { this.onto = o; }
+ public void setFormURI( URI u ) { formalismURI = u; }
+ public void setFormalism( String name ) { formalism = name; }
+}
diff --git a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
index 871ba9a4..f6031c92 100644
--- a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
@@ -53,23 +53,23 @@ import org.semanticweb.owl.align.Parameters;
public class URIAlignment extends BasicAlignment {
- //protected URI onto1 = null;
+ public URIAlignment() {}
- //protected URI onto2 = null;
-
- public URIAlignment() {
- }
-
- public void init(URI onto1, URI onto2) throws AlignmentException {
- if ( onto1 instanceof URI && onto2 instanceof URI ){
+ // JE: OMWG1, not sure it works...
+ public void init(Object o1, Object o2) throws AlignmentException {
+ if ( o1 instanceof Ontology && o2 instanceof Ontology ){
+ super.init( o1, o2 );
+ } else if ( o1 instanceof URI && o2 instanceof URI ) {
super.init( onto1, onto2 );
+ this.onto1.setUri( (URI)o1 );
+ this.onto2.setUri( (URI)o2 );
} else {
throw new AlignmentException("arguments must be URIs");
};
}
public void setOntology1(Object ontology) throws AlignmentException {
- if ( ontology instanceof URI ){
+ if ( ontology instanceof URI || ontology instanceof Ontology ){
super.setOntology1( ontology );
} else {
throw new AlignmentException("arguments must be URIs");
@@ -77,7 +77,7 @@ public class URIAlignment extends BasicAlignment {
};
public void setOntology2(Object ontology) throws AlignmentException {
- if ( ontology instanceof URI ){
+ if ( ontology instanceof URI || ontology instanceof Ontology ){
super.setOntology2( ontology );
} else {
throw new AlignmentException("arguments must be URIs");
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index c3feeff0..faec0a30 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -20,6 +20,9 @@
package fr.inrialpes.exmo.align.parser;
+// Imported OMWG classes
+import org.omwg.mediation.parser.alignment.XpathParser;
+
//Imported SAX classes
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
@@ -30,10 +33,12 @@ import org.xml.sax.helpers.DefaultHandler;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.xpath.XPathExpressionException;
//Imported JAVA classes
import java.io.IOException;
import java.io.StringReader;
+import java.io.File;
import java.net.URI;
import java.net.URISyntaxException;
import java.lang.Integer;
@@ -45,6 +50,7 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Parameters;
+import fr.inrialpes.exmo.align.impl.Ontology;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.BasicParameters;
@@ -58,7 +64,8 @@ import fr.inrialpes.exmo.align.impl.BasicParameters;
*/
public class AlignmentParser extends DefaultHandler {
-
+
+ protected static String ALIGNNS = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment";
/**
* level of debug/warning information
*/
@@ -72,12 +79,13 @@ public class AlignmentParser extends DefaultHandler {
/**
* the first Ontology
*/
- Object onto1 = null;
+ Ontology onto1 = null;
+ Ontology curronto = null;
/**
* the second Ontology
*/
- Object onto2 = null;
+ Ontology onto2 = null;
/**
* The currently loaded ontologies
@@ -90,7 +98,9 @@ public class AlignmentParser extends DefaultHandler {
* This is a pitty but the idea of creating a particular alignment
* is not in accordance with using an interface.
*/
- protected URIAlignment alignment = null;
+ protected Alignment alignment = null;
+ // Used by the OMWGAlignments
+ //protected URIAlignment alignment = null;
/**
* the content found as text...
@@ -173,7 +183,10 @@ public class AlignmentParser extends DefaultHandler {
* @param loaded should be replaced by OntologyCache (by useless)
* @deprecated use parse( URI ) instead
*/
- public Alignment parse( String uri, Hashtable loaded ) throws SAXException, IOException {
+ public Alignment parse( String uri, Hashtable loaded ) throws SAXException, IOException, XPathExpressionException {
+ // Determine which parser to use through the use of Xpath?
+ //private static final XPath XPATH = XPathFactory.newInstance().newXPath();
+
//ontologies = loaded;
return parse( uri );
}
@@ -184,13 +197,25 @@ public class AlignmentParser extends DefaultHandler {
* parsed.
* @param uri URI of the document to parse
*/
- public Alignment parse( String uri ) throws SAXException, IOException {
+ public Alignment parse( String uri ) throws SAXException, IOException, XPathExpressionException {
this.uri = uri;
- parser.parse(uri,this);
+ try { parser.parse(uri,this); }
+ catch (SAXException e) {
+ if ( e.getMessage().equals("2OMWGAlignment") ) {
+ //alignment = new XpathParser().parse(((InputStream)new URL( uri ).openStream()));
+ alignment = new XpathParser().parse( new File( uri ) );
+ } else {
+ throw e; // unfortunatelly
+ }
+ }
return alignment;
}
- public Alignment parseString( String s ) throws SAXException, IOException {
+ /**
+ * Parses a string instead of a URI
+ * @param s String the string to parse
+ */
+ public Alignment parseString( String s ) throws SAXException, IOException, XPathExpressionException {
parser.parse( new InputSource( new StringReader( s ) ),
this );
return alignment;
@@ -209,7 +234,7 @@ public class AlignmentParser extends DefaultHandler {
if(debugMode > 2)
System.err.println("startElement AlignmentParser : " + pName);
parselevel++;
- if(namespaceURI.equals("http://knowledgeweb.semanticweb.org/heterogeneity/alignment")) {
+ if(namespaceURI.equals(ALIGNNS)) {
if (pName.equals("relation")) {
} else if (pName.equals("semantics")) {
} else if (pName.equals("measure")) {
@@ -245,13 +270,32 @@ public class AlignmentParser extends DefaultHandler {
cl2 = null;
} else if (pName.equals("map")) {
try {
- alignment.setOntology2( onto2 );
- alignment.setOntology1( onto1 );
+ // JE: OMWG1 //NOT SURE
+ alignment.init( onto1, onto2 );
} catch ( AlignmentException e ) {
throw new SAXException("Catched alignment exception", e );
}
+ } else if (pName.equals("Formalism")) {
+ // JE: OMWG1 leave it alone for the moment
+ //if ( atts.getValue("uri") != null )
+ // curronto.setFormalismURI( new URI(atts.getValue("uri")) );
+ if ( atts.getValue("name") != null )
+ curronto.setFormalism( atts.getValue("name") );
+ } else if (pName.equals("formalism")) {
+ } else if (pName.equals("location")) {
+ } else if (pName.equals("Ontology")) {
+ if ( atts.getValue("rdf:about") != null && !atts.getValue("rdf:about").equals("") ) {
+ try {
+ curronto.setOntology( new URI( atts.getValue("rdf:about") ) );
+ curronto.setUri( new URI( atts.getValue("rdf:about") ) );
+ } catch (URISyntaxException e) {
+ throw new SAXException("onto2: malformed URI");
+ }
+ }
} else if (pName.equals("onto2")) {
+ curronto = onto2;
} else if (pName.equals("onto1")) {
+ curronto = onto1;
} else if (pName.equals("uri2")) {
} else if (pName.equals("uri1")) {
} else if (pName.equals("type")) {
@@ -259,6 +303,8 @@ public class AlignmentParser extends DefaultHandler {
} else if (pName.equals("xml")) {
} else if (pName.equals("Alignment")) {
alignment = new URIAlignment();
+ onto1 = new Ontology();
+ onto2 = new Ontology();
} else {
if ( debugMode > 0 ) System.err.println("[AlignmentParser] Unknown element name : "+pName);
};
@@ -266,7 +312,7 @@ public class AlignmentParser extends DefaultHandler {
if ( !pName.equals("RDF") ) {
throw new SAXException("[AlignmentParser] unknown element name: "+pName); };
} else {
- if ( parselevel != 2 ) throw new SAXException("[AlignmentParser] Unknown namespace : "+namespaceURI);
+ if ( parselevel != 3 && parselevel != 5 ) throw new SAXException("[AlignmentParser("+parselevel+")] Unknown namespace : "+namespaceURI);
}
}
@@ -318,10 +364,10 @@ public class AlignmentParser extends DefaultHandler {
* @param pName The local name of the current element
* @param qname The name of the current element
*/
- public void endElement(String namespaceURI,String pName, String qName ) throws SAXException {
+ public void endElement(String namespaceURI, String pName, String qName ) throws SAXException {
if(debugMode > 2)
System.err.println("endElement AlignmentParser : " + pName);
- if(namespaceURI.equals("http://knowledgeweb.semanticweb.org/heterogeneity/alignment")) {
+ if(namespaceURI.equals(ALIGNNS)) {
try {
if (pName.equals("relation")) {
relation = content;
@@ -352,31 +398,54 @@ public class AlignmentParser extends DefaultHandler {
if ( extensions != null ) cell.setExtensions( extensions );
} else if (pName.equals("map")) {
} else if (pName.equals("uri1")) {
- try {
- onto1 = new URI( content );
- } catch (URISyntaxException e) {
- throw new SAXException("uri1: malformed URI");
+ if ( onto1.getOntology() != null ){
+ try {
+ // JE: OMWG1
+ URI u = new URI( content );
+ onto1.setOntology( u );
+ onto1.setUri( u );
+ } catch (URISyntaxException e) {
+ throw new SAXException("uri1: malformed URI");
+ }
}
} else if (pName.equals("uri2")) {
- try {
- onto2 = new URI( content );
- } catch (URISyntaxException e) {
- throw new SAXException("uri2: malformed URI");
+ if ( onto2.getOntology() != null ){
+ try {
+ // JE: OMWG1
+ URI u = new URI( content );
+ onto2.setOntology( u );
+ onto2.setUri( u );
+ } catch (URISyntaxException e) {
+ throw new SAXException("uri2: malformed URI");
+ }
}
- } else if (pName.equals("onto2")) {
- try { alignment.setFile2( new URI( content ) );
+ // JE: OMWG1
+ } else if (pName.equals("Ontology")) {
+ } else if (pName.equals("location")) {
+ try { curronto.setFile( new URI( content ) );
} catch (URISyntaxException e) {
throw new SAXException("onto2: malformed URI");
}
- } else if (pName.equals("onto1")) {
- try { alignment.setFile1( new URI( content ) );
- } catch (URISyntaxException e) {
- throw new SAXException("onto1: malformed URI");
- }
+ } else if (pName.equals("Formalism")) {
+ } else if (pName.equals("formalism")) {
+ } else if (pName.equals("onto1") || pName.equals("onto2")) {
+ if ( curronto.getFile() == null &&
+ content != null && !content.equals("") ) {
+ try { curronto.setFile( new URI( content ) );
+ } catch (URISyntaxException e) {
+ throw new SAXException(pName+": malformed URI");
+ }
+ };
+ curronto = null;
} else if (pName.equals("type")) {
alignment.setType( content );
} else if (pName.equals("level")) {
- alignment.setLevel( content );
+ if ( content.equals("2OMWG") ) {
+ //throw new AlignmentException("2OMWGAlignment");
+ throw new SAXException("2OMWGAlignment");
+ } else {
+ alignment.setLevel( content );
+ }
} else if (pName.equals("xml")) {
//if ( content.equals("no") )
// { throw new SAXException("Non parseable alignment"); }
@@ -385,9 +454,7 @@ public class AlignmentParser extends DefaultHandler {
if ( parselevel == 3 ){
alignment.setExtension( pName, content );
} else if ( parselevel == 5 ) {
- if ( extensions == null ) extensions = new BasicParameters();
- //cell.setExtension( pName, content );
- extensions.setParameter( pName, content );
+ extensions.setParameter( pName, content );
} else //if ( debugMode > 0 )
System.err.println("[AlignmentParser] Unknown element name : "+pName);
//throw new SAXException("[AlignmentParser] Unknown element name : "+pName);
@@ -398,11 +465,12 @@ public class AlignmentParser extends DefaultHandler {
throw new SAXException("[AlignmentParser] unknown element name: "+pName); };
} else {
if ( parselevel == 3 ){
- alignment.setExtension( pName, content );
+ alignment.setExtension( qName, content );
+ //alignment.addNamespace( namespaceURI, );
} else if ( parselevel == 5 ) {
if ( extensions == null ) extensions = new BasicParameters();
- //cell.setExtension( pName, content );
- extensions.setParameter( pName, content );
+ extensions.setParameter( qName, content );
+ //alignment.addNamespace( namespaceURI, );
} else throw new SAXException("[AlignmentParser] Unknown namespace : "+namespaceURI);
}
parselevel--;
--
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