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Commit 3f93aa09 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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- reimplemented SemPrecEvaluator 

- updated iddl to a version above 1.4
- implemented toObjectAlignment in relevant evaluators
parent d2f98752
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lib/iddl/iddl.jar
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lib/iddl/iddl.pom
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<project>
<modelVersion>4.0.0</modelVersion>
<groupId>fr.inrialpes.exmo</groupId>
<groupId>fr.paris8.iut.info.iddl</groupId>
<artifactId>iddl</artifactId>
<version>1.3-20100331</version>
<version>1.4d</version>
<!-- Unreleased version of 2013-03-01 -->
<name>Integrated Distributed Description Logic</name>
<description>A Resonner for Integrated Distributed Description Logic - special revision of 31/03/2010 (revision 49+)</description>
<description>A Resonner for Integrated Distributed Description Logic</description>
<licenses>
<license>
<name>GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999</name>
......@@ -14,17 +15,14 @@
</licenses>
<url>http://iddl.gforge.inria.fr/</url>
<!--distributionManagement>
<downloadUrl></downloadUrl>
</distributionManagement-->
<!-- align api? Pellet? OWLAPI? -->
<dependencies>
<!-- alignapi owlapi, clairement -->
<!--dependencies>
<dependency>
<groupId></groupId>
<artifactId></artifactId>
<version></version>
</dependency>
</dependencies>
</dependencies-->
</project>
src/fr/inrialpes/exmo/align/impl/BasicEvaluator.java
+ 19
− 14
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/*
* $Id$
*
* Copyright (C) INRIA, 2004, 2007-2008, 2010
* Copyright (C) INRIA, 2004, 2007-2008, 2010, 2013
*
* 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
......@@ -24,6 +24,9 @@ import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Evaluator;
import fr.inrialpes.exmo.align.impl.ObjectAlignment;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import java.io.PrintWriter;
/**
......@@ -40,23 +43,25 @@ public abstract class BasicEvaluator implements Evaluator {
/** Creation **/
public BasicEvaluator( Alignment align1, Alignment align2 ) throws AlignmentException {
/*
* JE: This is obviously a killer test.
* Most of the matcher do not fill this correctly
* This should be made smoother
if ( !align1.getOntology1URI().equals( align2.getOntology1URI() )
|| !align1.getOntology2URI().equals( align2.getOntology2URI() ) ) {
System.err.println( " r1: "+align1.getOntology1URI() +" -- "+align1.getFile1() );
System.err.println( " r2: "+align1.getOntology2URI() +" -- "+align1.getFile2() );
System.err.println( " u1: "+align2.getOntology1URI() +" -- "+align2.getFile1() );
System.err.println( " u2: "+align2.getOntology2URI() +" -- "+align2.getFile2() );
throw new AlignmentException( "The alignments must align the same ontologies\n" );
}
*/
this.align1 = align1;
this.align2 = align2;
}
public void convertToObjectAlignments( Alignment al1, Alignment al2 ) throws AlignmentException {
align1 = convertToObjectAlignment( al1 );
align2 = convertToObjectAlignment( al2 );
}
public ObjectAlignment convertToObjectAlignment( Alignment al ) throws AlignmentException {
if ( al instanceof ObjectAlignment ) {
return (ObjectAlignment)al;
} else if ( al instanceof URIAlignment ) {
return ObjectAlignment.toObjectAlignment( (URIAlignment)al );
} else {
throw new AlignmentException( "Cannot convert to ObjectAlignment : "+al );
}
}
public void write( PrintWriter writer ) throws java.io.IOException {
writer.print("<rdf:RDF>\n <Evaluation class=\"BasicEvaluator\">\n <result>");
writer.print(result);
......
src/fr/inrialpes/exmo/align/impl/IDDLOntologyNetwork.java
+ 12
− 10
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/*
* $Id: IDDLOntologyNetwork.java 987 2009-05-27 13:48:33Z euzenat $
*
* Copyright (C) INRIA, 2009-2010
* Copyright (C) INRIA, 2009-2010, 2013
*
* 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
......@@ -35,8 +35,9 @@ import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.LogicOntologyNetwork;
import fr.inrialpes.exmo.iddl.IDDLReasoner;
import fr.inrialpes.exmo.iddl.conf.Semantics;
import fr.paris8.iut.info.iddl.IDDLReasoner;
import fr.paris8.iut.info.iddl.IDDLException;
import fr.paris8.iut.info.iddl.conf.Semantics;
/**
* Represents a distributed system of aligned ontologies or network of ontologies.
......@@ -69,11 +70,7 @@ public class IDDLOntologyNetwork extends BasicOntologyNetwork implements LogicOn
public void setSemantics( String s ){
semantics = s;
if ( reasoner != null ) {
if ( semantics.equals( "DL" ) ) {
reasoner.setSemantics( Semantics.DL );
} else {
reasoner.setSemantics( Semantics.IDDL );
}
reasoner.setSemantics( Semantics.valueOf( s ) );
}
};
public String getSemantics(){
......@@ -83,9 +80,14 @@ public class IDDLOntologyNetwork extends BasicOntologyNetwork implements LogicOn
init();
return reasoner.isConsistent();
};
public boolean isEntailed( Alignment al ){
public boolean isEntailed( Alignment al ) {
init();
return reasoner.isEntailed( al );
try {
return reasoner.isEntailed( al );
} catch ( IDDLException idex ) {
idex.printStackTrace();
return false;
}
};
}
......
src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
+ 1
− 3
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......@@ -107,6 +107,7 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
/** Creation **/
public ExtPREvaluator(Alignment align1, Alignment align2) throws AlignmentException {
super(align1, align2);
convertToObjectAlignments( align1, align2 );
}
public void setConfidence( boolean b ) { withConfidence = b; }
......@@ -141,9 +142,6 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
public double eval( Properties params, Object cache ) throws AlignmentException {
if ( params.getProperty( "noconfidence" ) != null ) withConfidence = false;
if ( params.getProperty( "relations" ) != null ) relsensitive = true;
// Better to transform them instead...
if ( !( align1 instanceof ObjectAlignment ) || !( align2 instanceof ObjectAlignment ) )
throw new AlignmentException( "ExtPREvaluation: requires ObjectAlignments" );
LoadedOntology<Object> o1 = (LoadedOntology<Object>)((ObjectAlignment)align1).getOntologyObject1();
LoadedOntology<Object> o2 = (LoadedOntology<Object>)((ObjectAlignment)align1).getOntologyObject2();
if ( !( o1 instanceof HeavyLoadedOntology ) || !( o2 instanceof HeavyLoadedOntology ) )
......
src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java
+ 112
− 106
View file @ 3f93aa09
......@@ -40,10 +40,12 @@ import fr.inrialpes.exmo.ontowrap.Ontology;
import fr.inrialpes.exmo.ontowrap.LoadedOntology;
import fr.inrialpes.exmo.ontowrap.OntowrapException;
//import fr.paris8.iut.info.iddl.IDDLReasoner;
//import fr.paris8.iut.info.iddl.conf.Semantics;
// ---- IDDL
import fr.paris8.iut.info.iddl.IDDLReasoner;
import fr.paris8.iut.info.iddl.IDDLException;
import fr.paris8.iut.info.iddl.conf.Semantics;
// HermiT implementation
// ---- HermiT Implementation
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntology;
......@@ -64,6 +66,9 @@ import org.semanticweb.owlapi.reasoner.BufferingMode;
import org.semanticweb.HermiT.Reasoner;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
import java.io.FileWriter;
......@@ -75,6 +80,7 @@ import java.io.OutputStreamWriter;
import java.io.UnsupportedEncodingException;
import java.lang.Thread;
import java.lang.Runnable;
import java.lang.IllegalArgumentException;
import java.util.Properties;
import java.util.Enumeration;
......@@ -94,10 +100,12 @@ import java.net.URI;
public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
final Logger logger = LoggerFactory.getLogger( SemPRecEvaluator.class );
private int nbfoundentailed = 0; // nb of returned cells entailed by the reference alignment
private int nbexpectedentailed = 0; // nb of reference cells entailed by returned alignment
//private Semantics semantics = Semantics.DL; // the semantics used for interpreting alignments
private Semantics semantics = null; // the semantics used for interpreting alignments
// null means that we use the reduced semantics with HermiT, otherwise, this is an IDDL semantics
/** Creation
* Initiate Evaluator for precision and recall
......@@ -105,31 +113,20 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
* @param align2 : the alignment to evaluate
**/
public SemPRecEvaluator( Alignment al1, Alignment al2) throws AlignmentException {
super(((BasicAlignment)al1).toURIAlignment(), ((BasicAlignment)al2).toURIAlignment());
try {
if ( al1 instanceof ObjectAlignment ) {
align1 = al1;
} else {
align1 = ObjectAlignment.toObjectAlignment((URIAlignment)align1);
}
if ( al2 instanceof ObjectAlignment ) {
align2 = al2;
} else {
align2 = ObjectAlignment.toObjectAlignment((URIAlignment)align2);
}
} catch ( AlignmentException aex ) {
throw new AlignmentException( "SemPRecEvaluator can only work on ObjectAlignments", aex );
}
super( al1, al2 );
logger.info( "Created one SemPREvaluator" );
convertToObjectAlignments( al1, al2 );
}
public void init( Object sem ){
public void init( Properties params ){
super.init(); // ??
nbexpectedentailed = 0;
nbfoundentailed = 0;
// Better use Properties
//if ( sem instanceof Semantics ) {
// semantics = (Semantics)sem;
//}
// Set the semantics to be used
String sem = params.getProperty( "semantics" );
if ( sem != null ) {
semantics = Semantics.valueOf( sem );
}
}
/**
......@@ -146,10 +143,10 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
*
* In the implementation |B|=nbfound, |A|=nbexpected and |A inter B|=nbcorrect.
*
* This takes semantivs as a parameter which should be a litteral of fr.paris8.iut.info.iddl.conf.Semantics
* This takes semantics as a parameter which should be a litteral of fr.paris8.iut.info.iddl.conf.Semantics
*/
public double eval( Properties params ) throws AlignmentException {
init( params.getProperty( "semantics" ) );
init( params );
nbfound = align2.nbCells();
nbexpected = align1.nbCells();
......@@ -172,37 +169,47 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
}
public int nbEntailedCorrespondences( ObjectAlignment al1, ObjectAlignment al2 ) throws AlignmentException {
//System.err.println( "Computing correctness" );
//IDDLReasoner reasoner = new IDDLReasoner( semantics );
//loadOntology( reasoner, ((BasicAlignment)al1).getOntologyObject1() );
//loadOntology( reasoner, ((BasicAlignment)al1).getOntologyObject2() );
//reasoner.addAlignment( al1 );
loadPipedAlignedOntologies( al1 );
logger.debug( "Computing entailment (semantics: {})", semantics );
if ( semantics != null ) { // IDDL
IDDLReasoner iddlreasoner = new IDDLReasoner( semantics );
loadOntology( iddlreasoner, ((BasicAlignment)al1).getOntologyObject1() );
loadOntology( iddlreasoner, ((BasicAlignment)al1).getOntologyObject2() );
iddlreasoner.addAlignment( al1 );
reasoner = iddlreasoner;
} else { // Hermit
loadPipedAlignedOntologies( al1 );
}
if ( !reasoner.isConsistent() ) return al2.nbCells(); // everything is entailed
//System.err.println( al1+" is consistent" );
logger.debug( "{} is consistent", al1 );
int entailed = 0;
for ( Cell c2 : al2 ) {
// create alignment
//Alignment al = new ObjectAlignment();
//al.init( align2.getOntology1URI(), align2.getOntology2URI() );
// add the cell
//al.addAlignCell( c2.getObject1(), c2.getObject2(), c2.getRelation().getRelation(), 1. );
//System.err.println( c2.getObject1()+" "+c2.getRelation().getRelation()+" "+c2.getObject2() );
//if ( reasoner.isEntailed( al ) ) {
try {
if ( reasoner.isEntailed( correspToAxiom( al2, (ObjectCell)c2 ) ) ) {
//System.err.println( " --> entailed" );
entailed++;
logger.trace( c2.getObject1()+" {} {}", c2.getRelation().getRelation(), c2.getObject2() );
if ( semantics != null ) { // IDDL
try {
if ( ((IDDLReasoner)reasoner).isEntailed( al2, c2 ) ) {
logger.trace( " --> entailed" );
entailed++;
}
} catch (IDDLException idex) { // counted as non entailed
logger.warn( "Cannot be translated." );
}
} else { // Hermit
try {
if ( reasoner.isEntailed( correspToAxiom( al2, (ObjectCell)c2 ) ) ) {
logger.trace( " --> entailed" );
entailed++;
}
} catch ( AlignmentException aex ) { // type mismatch -> 0
logger.warn( "Cannot be translated." );
}
} catch ( AlignmentException aex ) { // type mismatch -> 0
//System.err.println( "Cannot be translated." );
}
}
return entailed;
}
/**
* It would be useful to do better since we have the two ontologies here
* It would be useful to directly use the Ontologies since they are already loaded
* Two implementation of Alignment loading: one with intermediate file and one without.
*/
protected OWLOntologyManager manager = null;
protected OWLReasoner reasoner = null;
......@@ -213,37 +220,42 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
public void loadPipedAlignedOntologies( final ObjectAlignment align ) throws AlignmentException {
PipedInputStream in = new PipedInputStream();
try {
final PipedOutputStream out = new PipedOutputStream(in);
new Thread(
new Runnable(){
public void run() {
PrintWriter writer;
try {
writer = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter( out, "UTF-8" )), true);
} catch ( Exception ex ) {
return; //throw new AlignmentException( "Cannot load alignments because of I/O errors" );
}
OWLAxiomsRendererVisitor renderer = new OWLAxiomsRendererVisitor( writer );
renderer.init( new Properties() );
// Generate the ontology as OWL Axioms
try {
align.render( renderer );
} catch ( AlignmentException aex ) {
return;
} finally {
writer.flush();
writer.close();
}
final PipedOutputStream out = new PipedOutputStream(in);
Thread myThread = new Thread(
new Runnable(){
public void run() {
PrintWriter writer = null;
try {
writer = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter( out, "UTF-8" )), true);
OWLAxiomsRendererVisitor renderer = new OWLAxiomsRendererVisitor( writer );
renderer.init( new Properties() );
// Generate the ontology as OWL Axioms
align.render( renderer );
} catch ( Exception ex ) {
// No way to handle this exception???
// At worse, the other end will raise an exception
logger.error( "Cannot render alignment to OWL", ex );
} finally {
if ( writer != null ) {
writer.flush();
writer.close();
}
}
).start();
} catch ( Exception ex ) {};//java.io.UnsupportedEncodingException
}
}
}
);
myThread.start();
} catch ( UnsupportedEncodingException ueex ) {
throw new AlignmentException( "Cannot render alignment to OWL", ueex );
} catch ( IOException ioex ) {
throw new AlignmentException( "Cannot render alignment to OWL", ioex );
}
manager = OWLManager.createOWLOntologyManager();
//System.err.println( al.getOntology1URI()+" ----> "+al.getFile1() );
//System.err.println( al.getOntology2URI()+" ----> "+al.getFile2() );
logger.debug( "{} ----> {}", align.getOntology1URI(), align.getFile1() );
logger.debug( "{} ----> {}", align.getOntology2URI(), align.getFile2() );
manager.addIRIMapper(new SimpleIRIMapper( IRI.create( align.getOntology1URI() ),
IRI.create( align.getFile1() ) ) );
manager.addIRIMapper(new SimpleIRIMapper( IRI.create( align.getOntology2URI() ),
......@@ -255,7 +267,9 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
OWLOntology ontology = manager.loadOntologyFromOntologyDocument( in );
reasoner = new Reasoner( ontology );
} catch ( OWLOntologyCreationException ooce ) {
ooce.printStackTrace();
throw new AlignmentException( "Hermit : Cannot load alignment", ooce );
} catch ( IllegalArgumentException ilex ) {
throw new AlignmentException( "Hermit : Cannot load alignment", ilex );
}
}
......@@ -271,14 +285,12 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
merged.deleteOnExit();
writer = new PrintWriter ( new FileWriter( merged, false ), true );
OWLAxiomsRendererVisitor renderer = new OWLAxiomsRendererVisitor(writer);
//renderer.init( new Properties() );
align.render(renderer);
} catch (UnsupportedEncodingException uee) {
uee.printStackTrace();
} catch (AlignmentException ae) {
ae.printStackTrace();
} catch (IOException ioe) {
ioe.printStackTrace();
renderer.init( new Properties() );
align.render( renderer );
} catch (UnsupportedEncodingException ueex) {
throw new AlignmentException( "Cannot render alignment to OWL", ueex );
} catch (IOException ioex) {
throw new AlignmentException( "Cannot render alignment to OWL", ioex );
} finally {
if ( writer != null ) {
writer.flush();
......@@ -288,17 +300,21 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
// Load the ontology
manager = OWLManager.createOWLOntologyManager();
logger.debug( "{} ----> {}", align.getOntology1URI(), align.getFile1() );
logger.debug( "{} ----> {}", align.getOntology2URI(), align.getFile2() );
manager.addIRIMapper(new SimpleIRIMapper( IRI.create( align.getOntology1URI() ),
IRI.create( align.getFile1() ) ) );
manager.addIRIMapper(new SimpleIRIMapper( IRI.create( align.getOntology2URI() ),
IRI.create( align.getFile2() ) ) );
try {
manager.addIRIMapper(new SimpleIRIMapper( IRI.create( align.getOntology1URI() ),
IRI.create( align.getFile1() ) ) );
manager.addIRIMapper(new SimpleIRIMapper( IRI.create( align.getOntology2URI() ),
IRI.create( align.getFile2() ) ) );
manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile1() ) );
manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile2() ) );
OWLOntology ontology = manager.loadOntologyFromOntologyDocument( merged );
reasoner = new Reasoner( ontology );
} catch (OWLOntologyCreationException ooce) {
ooce.printStackTrace();
} catch ( OWLOntologyCreationException ooce ) {
throw new AlignmentException( "Hermit : Cannot load alignment", ooce );
} catch ( IllegalArgumentException ilex ) {
throw new AlignmentException( "Hermit : Cannot load alignment", ilex );
}
}
......@@ -375,23 +391,13 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
throw new AlignmentException( "Cannot convert correspondence "+corresp );
}
// This method can be suppressed
public boolean isConsistent( OWLReasoner reasoner ) {
return reasoner.isConsistent();
}
// This method can be suppressed
public boolean isEntailed( OWLAxiom axiom ) {
return reasoner.isEntailed( axiom );
// load ontology for the IDDLReasoner
public void loadOntology( IDDLReasoner reasoner, Object onto ) {
Ontology oo = (Ontology)onto;
URI f = oo.getFile();
if ( f == null ) f = oo.getURI();
reasoner.addOntology( f );
}
//public void loadOntology( IDDLReasoner reasoner, Object onto ) {
// System.err.println( reasoner +" -- "+onto );
// Ontology oo = (Ontology)onto;
// URI f = oo.getFile();
// if ( f == null ) f = oo.getURI();
// reasoner.addOntology( f );
//}
}
src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java
+ 2
− 3
View file @ 3f93aa09
......@@ -62,9 +62,7 @@ public class SymMeanEvaluator extends BasicEvaluator implements Evaluator {
/** Creation **/
public SymMeanEvaluator( Alignment align1, Alignment align2 ) throws AlignmentException {
super(align1,align2);
if ( !( align1 instanceof ObjectAlignment ) ||
!( align2 instanceof ObjectAlignment ) )
throw new AlignmentException( "Alignments should be ObjectAlignments, try to " );
convertToObjectAlignments( align1, align2 );
}
public double eval( Properties params ) throws AlignmentException {
......@@ -78,6 +76,7 @@ public class SymMeanEvaluator extends BasicEvaluator implements Evaluator {
classScore = 0.;
propScore = 0.;
indScore = 0.;
// This seems to be correct
LoadedOntology onto1 = (LoadedOntology)((ObjectAlignment)align1).getOntologyObject1();
LoadedOntology onto2 = (LoadedOntology)((ObjectAlignment)align2).getOntologyObject1();
......
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