From 0eb7131484a66922fbcddf11c7926999143f9b97 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Fri, 25 Nov 2011 11:40:58 +0000
Subject: [PATCH] - gen reengineering: simplified TestGenerator
---
.../exmo/align/gen/ArbitraryTest.java | 161 ----------
.../exmo/align/gen/GenerateBenchmark.java | 274 +++++-------------
.../exmo/align/gen/OntologyModifier.java | 57 ++--
src/fr/inrialpes/exmo/align/gen/TestGen.java | 53 ++--
.../exmo/align/gen/TestGenerator.java | 245 ++++++++++------
.../gen/inter/AlignedOntologyGenerator.java | 8 +-
6 files changed, 280 insertions(+), 518 deletions(-)
delete mode 100644 src/fr/inrialpes/exmo/align/gen/ArbitraryTest.java
diff --git a/src/fr/inrialpes/exmo/align/gen/ArbitraryTest.java b/src/fr/inrialpes/exmo/align/gen/ArbitraryTest.java
deleted file mode 100644
index bcb870d0..00000000
--- a/src/fr/inrialpes/exmo/align/gen/ArbitraryTest.java
+++ /dev/null
@@ -1,161 +0,0 @@
-/*
- * $Id$
- *
- * Copyright (C) 2011, INRIA
- *
- * 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.
- */
-
-/*
- * Generates an arbitrary test.
- * The days of this class are counted: it is highly redundant with the first part of
- * GenerateBenchmark and should be merged with TestGenerator.
- */
-
-package fr.inrialpes.exmo.align.gen;
-
-//Java classes
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.io.File;
-import java.io.OutputStreamWriter;
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintWriter;
-import java.nio.charset.Charset;
-import java.util.Properties;
-
-//Jena API classes
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntModelSpec;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.RDFWriter;
-import com.hp.hpl.jena.util.FileManager;
-
-// Alignment API implementation classes
-import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
-import fr.inrialpes.exmo.ontowrap.jena25.JENAOntology;
-
-import org.semanticweb.owl.align.Alignment;
-import org.semanticweb.owl.align.AlignmentVisitor;
-
-public class ArbitraryTest {
- //private String fileName; //the initial file
- //private String testNumber; //the test number
- //private Properties parameters; //the parameters
- public final String namespace = "http://oaei.ontologymatching.org/2011/gen/";
-
- //constructor
- public ArbitraryTest() {
- //this.fileName = fileName;
- //this.testNumber = testNumber;
- //parameters = params;
- }
-
- //get the prefix to build the namespace
- public String getPrefix( String fileName ) {
- return fileName.substring(0, fileName.lastIndexOf("."));
- }
-
- //get the uri
- public String getURI( String fileName, String testNumber ) {
- return this.namespace + getPrefix(fileName) + "/" + testNumber + "/" + fileName + "#";
- }
-
- //load ontology
- public OntModel loadOntology ( String fileName ) {
- InputStream in = FileManager.get().open( fileName );
- OntModel model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );
- model.read( in, null );
- return model;
- }
-
- //write ontology
- public static void writeOntology( OntModel model, String destFile, String ns ) {
- try {
- File f = new File(destFile);
- FileOutputStream fout = new FileOutputStream(f);
- Charset defaultCharset = Charset.forName("UTF8");
- RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
- writer.setProperty("showXmlDeclaration","true");
- model.setNsPrefix("", ns);
-
- model.createOntology(ns);
-
- writer.setProperty( "xmlbase", ns );
- writer.write(model.getBaseModel(), new OutputStreamWriter(fout, defaultCharset), "");
- fout.close();
- } catch (Exception ex) {
- System.err.println("Exception " + ex.getMessage());
- }
- }
-
- // JE: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> THE REAL STUFF
-
- // JE: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> WE SHOULD HAVE INCREMENTAL HERE IN THE SAME WAY!
-
- //modify ontology
- public void modifyOntology( String fileName, String testNumber, Properties params ) {
- //modify the model
- try {
- OntModel model = loadOntology(fileName); //load the initial ontology
- JENAOntology onto = new JENAOntology(); //cast the model into Ontology
- onto.setOntology( (OntModel)model );
- //set the TestGenerator ontology
- TestGenerator t = new TestGenerator(); //build an instance of TestGenerator
- t.setOntology(onto);
- //set the namespace
- t.setNamespace( getURI( fileName, testNumber) );
- //t.setNamespace( "http://oaei.ontologymatching.org/2011/gen/onto/101/onto.rdf#" );
-
- Alignment align = t.generate( onto, params ); //generate the alignment
-
- JENAOntology modified = (JENAOntology)t.getModifiedOntology(); //get the modified ontology
-
-
- //build the directory to save the file
- boolean create;
- create = new File(testNumber).mkdir();
- if ( create ) System.err.println(" Succesufully created the directory ");
- else System.err.println(" Error creating the directory ");
-
- //new File(testNumber).mkdir();
- //write the ontology into the directory
- if ( modified.getOntology() instanceof OntModel )
- writeOntology(modified.getOntology(), testNumber + "/" + fileName, getURI( fileName, testNumber )); //write the ontology
- //write the alignment into the directory
- OutputStream stream = new FileOutputStream( testNumber + "/" + "refalign.rdf" );
- // Outputing
- PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( stream, "UTF-8" )), true);
- AlignmentVisitor renderer = new RDFRendererVisitor( writer );
- align.render(renderer);
- writer.flush();
- writer.close();
- }
- catch ( Exception ex ) {
- System.err.println( "Error " + ex.getMessage() );
- }
-
- System.err.println( "***" );
- System.err.println( "END" );
- System.err.println( "***" );
- }
-
-
-}
diff --git a/src/fr/inrialpes/exmo/align/gen/GenerateBenchmark.java b/src/fr/inrialpes/exmo/align/gen/GenerateBenchmark.java
index e6d9f0f7..8fc03710 100644
--- a/src/fr/inrialpes/exmo/align/gen/GenerateBenchmark.java
+++ b/src/fr/inrialpes/exmo/align/gen/GenerateBenchmark.java
@@ -29,182 +29,50 @@
package fr.inrialpes.exmo.align.gen;
-//Java classes
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.io.File;
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintWriter;
-import java.io.OutputStreamWriter;
-import java.nio.charset.Charset;
import java.util.Properties;
-//Jena API classes
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntModelSpec;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.RDFWriter;
-import com.hp.hpl.jena.util.FileManager;
-
-// Alignment API implementation classes
-import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
-import fr.inrialpes.exmo.ontowrap.jena25.JENAOntology;
-
-import org.semanticweb.owl.align.Alignment;
-import org.semanticweb.owl.align.AlignmentVisitor;
-
public class GenerateBenchmark {
- private String urlprefix = "http://example.com/"; // Prefix (before testnumber) of test URL
- private String dirprefix = ""; // Prefix (idem) of directory
- private String filename = "onto.rdf"; // name of ontology to generate
- private String alignname = "refalign.rdf"; // name of alignment to generate
-
- private String fileName; //the initial file
- //private String testNumber; //the test number
- private Properties parameters; //the parameters
- public final String namespace = "http://oaei.ontologymatching.org/2011/gen/";
- private TestGenerator generator; //build an instance of TestGenerator
+
+ private String initOntoFile; //the initial file
+ private Properties align; //the alignment parameter
+ private TestGenerator generator; // a TestGenerator
private boolean debug = false;
static String FULL = "1.0f";
//constructor
public GenerateBenchmark( String fileName ) {
- this.fileName = fileName;
+ initOntoFile = fileName;
generator = new TestGenerator();
}
- //gets the URI
- public String getURI( String testNumber ) {
- return urlprefix + "/" + testNumber + "/" + filename + "#"; // Do not like this #...
- //return urlprefix + getPrefix(fileName) + "/" + testNumber + "/" + fileName + "#";
- }
-
- private String directoryName( String dir, String suffix ) {
- if ( suffix == null ) return dir;
- else return dir+"-"+suffix;
- }
-
- //loads ontology
- public OntModel loadOntology ( String file ) {
- InputStream in = FileManager.get().open( file );
- OntModel model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );
- model.read( in, null );
- return model;
- }
-
- //writes ontology
- public static void writeOntology( OntModel model, String destFile, String ns ) {
- try {
- File f = new File( destFile );
- FileOutputStream fout = new FileOutputStream( f );
- Charset defaultCharset = Charset.forName("UTF8");
- RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
- writer.setProperty( "showXmlDeclaration","true" );
- model.setNsPrefix( "", ns );
- model.createOntology(ns);
-
- writer.setProperty( "xmlbase", ns );
- writer.write(model.getBaseModel(), new OutputStreamWriter(fout, defaultCharset), "");
- fout.close();
- } catch (Exception ex) {
- ex.printStackTrace();
- }
- }
-
- private void outputTestDirectory( JENAOntology onto, Alignment align, String testnumber, Properties params ) {
- // build the directory to save the file
- boolean create = new File( dirprefix+"/"+testnumber ).mkdir();
- /* if ( create ) System.err.println(" Succesufully created the directory ");
- else System.err.println(" Error creating the directory "); */
-
- // write the ontology into the directory
- if ( onto.getOntology() instanceof OntModel )
- writeOntology( onto.getOntology(), dirprefix+"/"+testnumber+"/"+filename, getURI( testnumber ));
-
- try {
- //write the alignment into the directory
- OutputStream stream = new FileOutputStream( dirprefix+"/"+testnumber+"/"+alignname );
- // Outputing
- PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( stream, "UTF-8" )), true);
- AlignmentVisitor renderer = new RDFRendererVisitor( writer );
- align.render( renderer );
- writer.flush();
- writer.close();
- } catch ( Exception ex ) {
- ex.printStackTrace();
- }
- }
-
- //modifies an ontology
- public Properties modifyOntology( String file, String testNumber, Properties params) {
- System.err.println( "Source: "+file+" generate "+testNumber );
- //modify the model
- if ( debug ) System.err.println( "From test " + file );
- if ( debug ) System.err.println( "Test " + testNumber );
- OntModel model = loadOntology( file ); //load the initial ontology
- JENAOntology onto = new JENAOntology(); //cast the model into Ontology
- onto.setOntology( (OntModel)model );
- //set the TestGenerator ontology
- generator.setOntology( onto );
- //set the namespace
- generator.setNamespace( getURI( testNumber ) );
- Alignment align = null;
- if ( file.equals(this.fileName) ) // JE: In my opinion this test is tricky... (and all should be in params)
- align = generator.generate( onto, params ); //generate the alignment
- else
- align = generator.generate( onto, params, parameters ); //generate the alignment
-
- JENAOntology modified = (JENAOntology)generator.getModifiedOntology(); //get the modified ontology
-
- outputTestDirectory( modified, align, testNumber, params );
- //retrieve the parameters
- //parameters = generator.getParameters();
- return generator.getParameters();
- }
-
- //modifies an ontology from an existing test
- public Properties incrementModifyOntology( String pKey, String pVal, String suffix, String prevTest, String testNb ) {
- Properties p = new Properties();
- p.setProperty( pKey, pVal );
- String prevDirName = directoryName( prevTest, suffix );
- String crtDirName = directoryName( testNb, suffix );
- return modifyOntology( dirprefix+"/"+prevDirName+"/"+this.fileName, crtDirName, p );
- }
-
-
//generates the Benchmark
public void generate( Properties params ) {
// Process params
- if ( params.getProperty( "urlprefix" ) != null ) urlprefix = params.getProperty( "urlprefix" );
- if ( params.getProperty( "outdir" )!= null ) dirprefix = params.getProperty( "outdir" );
- if ( params.getProperty( "filename" ) != null ) filename = params.getProperty( "filename" );
- if ( params.getProperty( "alignname" ) != null ) alignname = params.getProperty( "alignname" );
+ if ( params.getProperty( "urlprefix" ) != null ) generator.setURLPrefix( params.getProperty( "urlprefix" ) );
+ if ( params.getProperty( "outdir" )!= null ) generator.setDirPrefix( params.getProperty( "outdir" ) );
+ String ontoname = params.getProperty( "ontoname" );
+ if ( ontoname != null ) {
+ generator.setOntoFilename( params.getProperty( "ontoname" ) );
+ } else {
+ ontoname = "onto.rdf"; // could be better
+ }
+ if ( params.getProperty( "alignname" ) != null ) generator.setAlignFilename( params.getProperty( "alignname" ) );
- System.err.println( urlprefix+" / "+dirprefix+" / "+filename+" / "+alignname );
+ debug = ( params.getProperty( "debug" ) != null );
+ generator.setDebug( debug );
//private String testnumber = ""; // will not work if no number...
//testnumber = params.getProperty( "testNumber" );
//if ( testnumber == null )
- // JE: All this should have been solved before
-
-
//keep track of the alignment
- Properties paramsRenameResources; Properties paramsNoComments;
- Properties paramsNoInstance; Properties paramsNoProperty;
- Properties paramsFlatten; Properties paramsExpand;
- Properties paramsInitial;
+ Properties alignRenameResources;
+ Properties alignInitial;
Properties p = new Properties(); //modify the ontology according to this parameters
- this.parameters = new Properties();
String prevDirName;
- String crtDirName;
String mod = params.getProperty( "modality" ); // "mult"
String hard = params.getProperty( "increment" );
@@ -213,28 +81,21 @@ public class GenerateBenchmark {
String SUFFIX = null;
- // JE : >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SO FAR SO GOOD
/*
* Test 101
- * Here it would be good to change the :
+ * Generate the initial situation
*/
- parameters = modifyOntology( fileName, "101", p ); // JE ~~> The strange thing: it will generate the init
- // Because it calls with the "p", this is the second case,
- // Where the initial alignment is generated
- paramsInitial = (Properties)parameters.clone();
- paramsRenameResources = (Properties)parameters.clone();
+ align = generator.modifyOntology( initOntoFile, (Properties)null, "101", p );
+ alignInitial = (Properties)align.clone();
+ alignRenameResources = (Properties)align.clone();
prevDirName = "101"+"/";
/*
* Tests 201, 202, 248, 249, 253, 258, 259, 250, 254,
* 262, 257, 260, 265, 261, 266, 251, 252
*/
- // Increment from 20 to 20
- //for ( float i1=0.20f; i1<=1.00f; i1+=0.20f ) {
- // Increment from x to remaining
// JE: look at the (Float).toString() below...
boolean multModality = (mod != null && mod.startsWith( "mult" ));
- //float i1 = 0.20f;
float i1 = 0.0f;
int maximum = Integer.parseInt( "5" );
float incr = Float.parseFloat( "0.2" );
@@ -244,9 +105,9 @@ public class GenerateBenchmark {
ex.printStackTrace(); // continue with the default
}
for ( int i = 0; i1 < 1.00f ; i++ ) { // && i < maximum
- //System.err.println( " **************************** "+i+": i1 = "+i1 );
if ( !multModality ) i1 += incr; // traditional
else i1 += (1. - i1) * incr; // hardened
+ if ( debug ) System.err.println( " ******************************************************** "+i+": i1 = "+i1 );
if ( i1 < 1.0f ) {
SUFFIX = ((Float)i1).toString().substring(2, 3);
@@ -259,136 +120,139 @@ public class GenerateBenchmark {
p = new Properties();
p.setProperty( ParametersIds.RENAME_CLASSES, ((Float)i1).toString() );
p.setProperty( ParametersIds.RENAME_PROPERTIES, ((Float)i1).toString() );
- parameters = modifyOntology( dirprefix+"/"+prevDirName+this.fileName, directoryName( "201", SUFFIX ), p);
+ // This dirprefix business could have been solved before...
+ String dirprefix = params.getProperty( "outdir" );
+ if (dirprefix != null ) { dirprefix = dirprefix+"/"; } else { dirprefix = ""; }
+ align = generator.modifyOntology( dirprefix+prevDirName+ontoname, align, generator.directoryName( "201", SUFFIX ), p);
/* 202-x *** no names + no comments */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_COMMENTS, FULL, SUFFIX, "201", "202" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_COMMENTS, FULL, SUFFIX, "201", align, "202" );
/* 248-x *** no names + no comments + no hierarchy */
- parameters = incrementModifyOntology( ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY, SUFFIX, "202", "248" );
+ align = generator.incrementModifyOntology( ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY, SUFFIX, "202", align, "248" );
/* 253-x *** no names + no comments + no hierarchy + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "248", "253" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "248", align, "253" );
/* 249-x *** no names + no comments + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "202", "249" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "202", align, "249" );
////get the parameters
- paramsRenameResources = (Properties)this.parameters.clone();
+ alignRenameResources = (Properties)align.clone();
/* 250-x *** no names + no comments + no property */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_PROPERTIES, FULL, SUFFIX, "202", "250" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_PROPERTIES, FULL, SUFFIX, "202", align, "250" );
/* 254-x *** no names + no comments + no property + no hierarchy */
- parameters = incrementModifyOntology( ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY, SUFFIX, "250", "254" );
+ align = generator.incrementModifyOntology( ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY, SUFFIX, "250", align, "254" );
/* 262-x *** no names + no comments + no property + no hierarchy + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "254", "262" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "254", align, "262" );
/* 257-x *** no names + no comments + no property + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "250", "257" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "250", align, "257" );
/* 261-x *** no names + no comments + no property + expand */
- parameters = incrementModifyOntology( ParametersIds.ADD_CLASSES, FULL, SUFFIX, "250", "261" );
+ align = generator.incrementModifyOntology( ParametersIds.ADD_CLASSES, FULL, SUFFIX, "250", align, "261" );
/* 266-x *** no names + no comments + no property + expand + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "261", "266" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "261", align, "266" );
/* 260-x *** no names + no comments + no property + flatten */
- parameters = incrementModifyOntology( ParametersIds.LEVEL_FLATTENED, "2", SUFFIX, "250", "260" );
+ align = generator.incrementModifyOntology( ParametersIds.LEVEL_FLATTENED, "2", SUFFIX, "250", align, "260" );
/* 265-x *** no names + no comments + no property + flatten + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "260", "265" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "260", align, "265" );
//re-establish the parameters
- parameters = (Properties)paramsRenameResources.clone();
+ align = (Properties)alignRenameResources.clone();
/* 251-x *** no names + no comments + flatten */
- parameters = incrementModifyOntology( ParametersIds.LEVEL_FLATTENED, "2", SUFFIX, "202", "251" );
+ align = generator.incrementModifyOntology( ParametersIds.LEVEL_FLATTENED, "2", SUFFIX, "202", align, "251" );
/* 258-x *** no names + no comments + flatten + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "251", "258" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "251", align, "258" );
//re-establish the parameters
- parameters = (Properties)paramsRenameResources.clone();
+ align = (Properties)alignRenameResources.clone();
/* 252-x *** no names + no comments + expand */
- parameters = incrementModifyOntology( ParametersIds.ADD_CLASSES, FULL, SUFFIX, "202", "252" );
+ align = generator.incrementModifyOntology( ParametersIds.ADD_CLASSES, FULL, SUFFIX, "202", align, "252" );
/* 259-x *** no names + no comments + expand + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "252", "259" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "252", align, "259" );
-// paramsNoProperty = modifier.getProperties(); //get the modifed properties
+// alignNoProperty = modifier.getProperties(); //get the modifed properties
- parameters = (Properties)paramsRenameResources.clone();
- prevDirName = directoryName( "201", SUFFIX ) + "/";
+ align = (Properties)alignRenameResources.clone();
+ prevDirName = generator.directoryName( "201", SUFFIX ) + "/";
}
//re-establish the parameters
SUFFIX = null;
- parameters = (Properties)paramsInitial.clone();
+ align = (Properties)alignInitial.clone();
/* Tests 221, 232, 233, 241 */
/* 221 *** no hierarchy */
- parameters = incrementModifyOntology( ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY, SUFFIX, "101", "221" );
+ align = generator.incrementModifyOntology( ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY, SUFFIX, "101", align, "221" );
/* 232 *** no hierarchy + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "221", "232" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "221", align, "232" );
/* 233 *** no hierarchy + no property */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_PROPERTIES, FULL, SUFFIX, "221", "233" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_PROPERTIES, FULL, SUFFIX, "221", align, "233" );
/* 241 *** no hierarchy + no property + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "233", "241" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "233", align, "241" );
- //re-establish the parameters
- parameters = (Properties)paramsInitial.clone();
+ //re-establish the align
+ align = (Properties)alignInitial.clone();
/* Tests 222, 237 */
/* 222 *** flatten */
- parameters = incrementModifyOntology( ParametersIds.LEVEL_FLATTENED, "2", SUFFIX, "101", "222" );
+ align = generator.incrementModifyOntology( ParametersIds.LEVEL_FLATTENED, "2", SUFFIX, "101", align, "222" );
/* 237 *** flatten + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "222", "237" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "222", align, "237" );
//re-establish the parameters
- parameters = (Properties)paramsInitial.clone();
+ align = (Properties)alignInitial.clone();
/* Tests 223, 238 */
/* 223 *** expand */
- parameters = incrementModifyOntology( ParametersIds.ADD_CLASSES, FULL, SUFFIX, "101", "223" );
+ align = generator.incrementModifyOntology( ParametersIds.ADD_CLASSES, FULL, SUFFIX, "101", align, "223" );
/* 238 *** expand + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "223", "238" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "223", align, "238" );
/* 224 *** no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "101", "224" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "101", align, "224" );
/* 225 *** no restrictions */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_RESTRICTIONS, FULL, SUFFIX, "101", "225" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_RESTRICTIONS, FULL, SUFFIX, "101", align, "225" );
/* Tests 228, 239, 246, 236, 240, 247 */
/* 228 *** no property */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_PROPERTIES, FULL, SUFFIX, "101", "228" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_PROPERTIES, FULL, SUFFIX, "101", align, "228" );
/* 236 *** no property + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "228", "236" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "228", align, "236" );
/* 240 *** no property + expand */
- parameters = incrementModifyOntology( ParametersIds.ADD_CLASSES, FULL, SUFFIX, "228", "240" );
+ align = generator.incrementModifyOntology( ParametersIds.ADD_CLASSES, FULL, SUFFIX, "228", align, "240" );
/* 247 *** no property + expand + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "240", "247" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "240", align, "247" );
/* 239 *** no property + flatten */
- parameters = incrementModifyOntology( ParametersIds.LEVEL_FLATTENED, FULL, SUFFIX, "228", "239" );
+ align = generator.incrementModifyOntology( ParametersIds.LEVEL_FLATTENED, FULL, SUFFIX, "228", align, "239" );
/* 246 *** no property + flatten + no instance */
- parameters = incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "239", "246" );
+ align = generator.incrementModifyOntology( ParametersIds.REMOVE_INDIVIDUALS, FULL, SUFFIX, "239", align, "246" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
index 87bbbbed..324223c9 100644
--- a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
+++ b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
@@ -88,6 +88,7 @@ import edu.smu.tspell.wordnet.WordNetDatabase;
public class OntologyModifier {
private ClassHierarchy classHierarchy; //the class hierarchy
+ // JE: In all this class, model is useless!
private OntModel model; //the model - the original Ontology
private OntModel modifiedModel; //the modified Ontology
private String namespace; //the Namespace
@@ -95,15 +96,15 @@ public class OntologyModifier {
private Alignment alignment; //the alignment of the two Ontologies
private Properties params; //the alignment
private boolean isBuild; //keep track if the class hierarchy is build
- private boolean isAlign; //keep track it the initial alignment has already been computed
+ private boolean isAlign; //keep track if the initial alignment has already been computed
private boolean isChanged; //keep track if the namespace of the new ontology is changed
- public static String fileName = "refalign.rdf"; //the reference alignment
private String base; //
//Ontology init, Ontology modified, Alignment align
- public OntologyModifier ( OntModel model, OntModel modifiedModel, Alignment alignment ) {
+ // JE: Here the alignment is useless... it is used only if nothing is computed!
+ public OntologyModifier ( OntModel model, Alignment alignment ) {
this.model = model;
- this.modifiedModel = modifiedModel;
+ this.modifiedModel = model;
this.alignment = alignment;
this.isBuild = false;
this.isAlign = false;
@@ -1315,7 +1316,22 @@ public class OntologyModifier {
res.remove();
}
+ // isAlign is a not so good way to test initialisation
+ // (initialisation with an empty Properties is done in the initialiser)
+ // but the "params" is used everywhere...
+
//the initial reference alignment
+ // JE: !!!: no order guarantee in properties !!!
+ public void initializeAlignment( Properties params ) {
+ this.params = params;
+
+ Enumeration e = this.params.propertyNames();
+ String aux = (String)e.nextElement();
+ base = aux.substring(0, aux.lastIndexOf("#")+1);
+
+ this.isAlign = true;
+ }
+
public void initializeAlignment() {
List<OntClass> classes = this.modifiedModel.listNamedClasses().toList();//all classes
List<OntProperty> properties = this.modifiedModel.listAllOntProperties().toList();//all properties
@@ -1360,29 +1376,6 @@ public class OntologyModifier {
//System.out.println( "[" + key + "][" + value + "]" );
this.alignment.addAlignCell( uri1, uri2, "=", 1 );
}
-
- /*
- OutputStream stream ;//= new FileOutputStream(filename);
- if ( fileName == null ) {
- stream = System.out;
- } else {
- stream = new FileOutputStream( fileName );
- }
-
- // Outputing
- PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( stream, "UTF-8" )), true);
- AlignmentVisitor renderer = new RDFRendererVisitor( writer );
- this.alignment.render(renderer);
-
- //RDFRendererVisitor renderer = new RDFRendererVisitor(writer);
- //renderer.visit(this.alignment);
-
- writer.flush();
- writer.close();
- *
- */
} catch (AlignmentException aex) { System.out.println( "Exception " + aex.getMessage() );
} catch (Exception ex) { System.err.println("Exception " + ex.getMessage());
}
@@ -1499,16 +1492,6 @@ public class OntologyModifier {
return this.params;
}
- public void setProperties( Properties params ) {
- this.params = params;
-
- Enumeration e = this.params.propertyNames();
- String aux = (String)e.nextElement();
- base = aux.substring(0, aux.lastIndexOf("#")+1);
-
- this.isAlign = true;
- }
-
//returns the alignment
public Alignment getAlignment() {
return this.alignment;
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGen.java b/src/fr/inrialpes/exmo/align/gen/TestGen.java
index ce4894be..18ad49cc 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGen.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGen.java
@@ -67,20 +67,22 @@ public class TestGen {
}
public void run(String[] args) throws Exception {
- LongOpt[] longopts = new LongOpt[8];
+ LongOpt[] longopts = new LongOpt[10];
params = new Properties();
longopts[0] = new LongOpt("method", LongOpt.REQUIRED_ARGUMENT, null, 'm');
- longopts[1] = new LongOpt("fileName", LongOpt.REQUIRED_ARGUMENT, null, 'n');
+ longopts[1] = new LongOpt("init", LongOpt.REQUIRED_ARGUMENT, null, 'i');
longopts[2] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
longopts[3] = new LongOpt("testNumber", LongOpt.REQUIRED_ARGUMENT, null, 't');
longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
longopts[5] = new LongOpt("outdir", LongOpt.REQUIRED_ARGUMENT, null, 'o');
longopts[6] = new LongOpt("urlprefix", LongOpt.REQUIRED_ARGUMENT, null, 'u');
- longopts[7] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
+ longopts[7] = new LongOpt("ontoname", LongOpt.REQUIRED_ARGUMENT, null, 'n');
+ longopts[8] = new LongOpt("alignname", LongOpt.REQUIRED_ARGUMENT, null, 'a');
+ longopts[9] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
- Getopt g = new Getopt("", args, "d::o:u:h:m:n:D:t", longopts);
+ Getopt g = new Getopt("", args, "d::o:u:h:m:n:i:a:D:t", longopts);
int c;
String arg;
@@ -93,31 +95,33 @@ public class TestGen {
methodName = g.getOptarg();
System.err.println("method " + "[" + methodName + "]");
break;
- case 'n':
+ case 'i':
fileName = g.getOptarg();
params.setProperty( "filename", fileName );
System.err.println("fileName " + "[" + fileName + "]");
break;
+ case 'n':
+ params.setProperty( "ontoname", g.getOptarg() );
+ break;
+ case 'a':
+ params.setProperty( "alignname", g.getOptarg() );
+ break;
case 't':
testNumber = g.getOptarg();
System.err.println("testNumber " + "[" + testNumber + "]");
break;
- case 'o' :
- /* Use output directory */
+ case 'o' : /* Use output directory */
params.setProperty( "outdir", g.getOptarg() );
break;
- case 'u' :
- /* URLPrefix */
+ case 'u' : /* URLPrefix */
params.setProperty( "urlprefix", g.getOptarg() );
break;
- case 'd' :
- /* Debug level */
+ case 'd' : /* Debug level */
arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
+ if ( arg != null ) params.setProperty( "debug", arg.trim() );
+ else params.setProperty( "debug", "4" );
break;
- case 'D' :
- /* Parameter definition: could be used for all parameters */
+ case 'D' : /* Parameter definition: could be used for all parameters */
arg = g.getOptarg();
int index = arg.indexOf('=');
if ( index != -1 ) {
@@ -132,13 +136,10 @@ public class TestGen {
}
}
- //generate an arbitrary test
- if ( methodName.equals( ARBITRARY_TEST ) ) {
- //build an ArbitraryTest object and modify the ontology according to it
- ArbitraryTest at = new ArbitraryTest();
- at.modifyOntology( fileName, testNumber, params );
- } else if ( methodName.equals( GENERATE_BENCHMARK ) ) {
- //generate the benchmark
+ if ( methodName.equals( ARBITRARY_TEST ) ) { //generate an arbitrary test
+ TestGenerator tg = new TestGenerator();
+ tg.modifyOntology( fileName, (Properties)null, testNumber, params );
+ } else if ( methodName.equals( GENERATE_BENCHMARK ) ) { //generate the benchmark
GenerateBenchmark gb = new GenerateBenchmark( fileName );
gb.generate( params );
}
@@ -149,8 +150,14 @@ public class TestGen {
System.out.println("TestGen [options]");
System.out.println("options are");
System.out.println("--method=methodName, where methodName can be \""+ARBITRARY_TEST+"\" or \""+GENERATE_BENCHMARK+"\"");
- System.out.println("--fileName=file [default: onto.rdf]");
+ System.out.println("--initonto=filename (initial ontology)");
+ System.out.println("--alignname=filename [default: refalign.rdf]");
+ System.out.println("--ontoname=filename [default: onto.rdf]");
+ System.out.println("--urlprefix=url");
+ System.out.println("--outdir=directory [default: .]");
System.out.println("--testNumber=number, if the arbitraryTest is chosen");
+ System.out.println("--help");
+ System.out.println("--debug=number [default: 0]");
System.out.println("-Dparameter=value");
System.out.println("where the parameters are");
System.out.println( "[--------------------------------------------------------------------------]" );
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
index 844502fd..fb6cfbb6 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
@@ -30,127 +30,196 @@
package fr.inrialpes.exmo.align.gen;
-import com.hp.hpl.jena.ontology.OntModel;
+// Alignment API implementation classes
import fr.inrialpes.exmo.align.gen.inter.AlignedOntologyGenerator;
import fr.inrialpes.exmo.align.impl.URIAlignment;
-import fr.inrialpes.exmo.ontowrap.Ontology;
-import fr.inrialpes.exmo.ontowrap.jena25.JENAOntology;
-import java.util.Properties;
+import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
+
import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentVisitor;
+
+//Java classes
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.io.File;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.io.OutputStreamWriter;
+import java.nio.charset.Charset;
+import java.util.Properties;
+
+//Jena API classes
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.RDFWriter;
+import com.hp.hpl.jena.util.FileManager;
+
+import java.util.Properties;
public class TestGenerator implements AlignedOntologyGenerator {
- private Properties parameters; //the set of parameters
+ private String urlprefix = "http://example.com/"; // Prefix (before testnumber) of test URL
+ private String dirprefix = ""; // Prefix (idem) of directory
+ private String ontoname = "onto.rdf"; // name of ontology to generate
+ private String alignname = "refalign.rdf"; // name of alignment to generate
+
private Properties params; //the modifications
- private OntModel model; //initial ontology
- private OntModel modifiedModel; //modified ontology
- private Alignment alignment; //the reference alignment
- private String namespace = ""; //the namespace
+ private OntModel modifiedOntology; //modified ontology
+ private Alignment resultAlignment; //the reference alignment
+ private String namespace = ""; //the namespace
private OntologyModifier modifier = null; //the modifier
+ private boolean debug = false;
public TestGenerator() {}
+ // ******************************************************* SETTERS
+ public void setURLPrefix( String u ) { urlprefix = u; }
+
+ public void setDirPrefix( String d ) { dirprefix = d; }
+
+ public void setOntoFilename( String o ) { ontoname = o; }
+
+ public void setAlignFilename( String a ) { alignname = a; }
+
+ public void setDebug( boolean d ) { debug = d; }
+
//returns the modified ontology
- public Ontology getModifiedOntology() {
- JENAOntology onto = new JENAOntology(); //cast the model into Ontology
- onto.setOntology( this.modifiedModel );
- return onto; //return the ontology
+ public OntModel getModifiedOntology() { return modifiedOntology ; }
+
+ public void setNamespace( String ns ) { namespace = ns; }
+ //return the newNamespace
+ public String getNamespace() { return namespace; }
+
+ // ******************************************************* GB STUFF
+
+ //gets the URI
+ public String getURI( String testNumber ) {
+ return urlprefix + "/" + testNumber + "/" + ontoname + "#"; // Do not like this #...
+ //return urlprefix + getPrefix(ontoname) + "/" + testNumber + "/" + ontoname + "#";
}
- //set the initial ontology
- public void setOntology( Ontology o ) {
- if ( o instanceof JENAOntology ) {
- this.model = ((JENAOntology)o).getOntology();
- this.modifiedModel = ((JENAOntology)o).getOntology();
- } else {
- System.err.println("Error : The object given is not an OntModel");
- System.exit(-1);
- }
+ public static String directoryName( String dir, String suffix ) {
+ if ( suffix == null ) return dir;
+ else return dir+"-"+suffix;
}
- public void setNamespace(String namespace) {
- this.namespace = namespace;
+ // ******************************************************* FACILITIES
+
+ public OntModel loadOntology ( String file ) {
+ InputStream in = FileManager.get().open( file );
+ OntModel model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );
+ model.read( in, null );
+ return model;
}
- //return the newNamespace
- public String getNamespace() {
- return this.namespace;
+ //writes ontology
+ public static void writeOntology( OntModel model, String destFile, String ns ) {
+ try {
+ File f = new File( destFile );
+ FileOutputStream fout = new FileOutputStream( f );
+ Charset defaultCharset = Charset.forName("UTF8");
+ RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
+ writer.setProperty( "showXmlDeclaration","true" );
+ model.setNsPrefix( "", ns ); // JE: what about it?
+ writer.setProperty( "xmlbase", ns );
+ model.createOntology( ns );
+ writer.write( model.getBaseModel(), new OutputStreamWriter(fout, defaultCharset), "");
+ fout.close();
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ }
}
- //set the parameters
- // JE: modifier may not have been initialised
- public void setParameters(Properties p) {
- parameters = p;
- modifier.setProperties(parameters);
+ private void outputTestDirectory( OntModel onto, Alignment align, String testnumber ) {
+ // build the directory to save the file
+ boolean create = new File( dirprefix+"/"+testnumber ).mkdir();
+ /* if ( create ) System.err.println(" Succesufully created the directory ");
+ else System.err.println(" Error creating the directory "); */
+
+ // write the ontology into the directory
+ writeOntology( onto, dirprefix+"/"+testnumber+"/"+ontoname, getURI( testnumber ));
+
+ try {
+ //write the alignment into the directory
+ OutputStream stream = new FileOutputStream( dirprefix+"/"+testnumber+"/"+alignname );
+ // Outputing
+ PrintWriter writer = new PrintWriter (
+ new BufferedWriter(
+ new OutputStreamWriter( stream, "UTF-8" )), true);
+ AlignmentVisitor renderer = new RDFRendererVisitor( writer );
+ align.render( renderer );
+ writer.flush();
+ writer.close();
+ } catch ( Exception ex ) {
+ ex.printStackTrace();
+ }
}
- //get the parameters
- public Properties getParameters() {
- parameters = modifier.getProperties(); //get the properties
- return parameters;
+ //modifies an ontology from an existing test
+ /**
+ * Generate a test by altering an existing test
+ */
+ public Properties incrementModifyOntology( String pKey, String pVal, String suffix, String prevTest, Properties al, String testNb ) {
+ Properties p = new Properties();
+ p.setProperty( pKey, pVal );
+ String prevDirName = directoryName( prevTest, suffix );
+ String crtDirName = directoryName( testNb, suffix );
+ return modifyOntology( dirprefix+"/"+prevDirName+"/"+ontoname, al, crtDirName, p );
}
- //generate the alingnment
+ //modifies an ontology
/**
- * This in fact is dependent on:
- * - p
- * - model
- * - modifiedModel
- * - alignment
+ * Generate a test from an ontology
*/
- public Alignment generate( Ontology o, Properties p ) {
- this.params = p;
- this.alignment = new URIAlignment();
+ public Properties modifyOntology( String file, Properties al, String testNumber, Properties params) {
+ if ( debug ) System.err.println( "Source: "+file+" generate "+testNumber );
+ //set the TestGenerator ontology
+ OntModel onto = loadOntology( file ); // who needs model?
+ //set the namespace
+ setNamespace( getURI( testNumber ) );
+ Alignment align = null;
+ if ( al == null )
+ align = generate( onto, params );
+ else
+ align = generate( onto, params, al );
+
+ outputTestDirectory( getModifiedOntology(), align, testNumber );
+ return modifier.getProperties();
+ }
+
+ // ******************************************************* GENERATOR
+ //generate the alingnment
+ public Alignment generate( OntModel onto, Properties p, Properties initalign ) {
+ if ( debug ) System.err.println( urlprefix+" / "+dirprefix+" / "+ontoname+" / "+alignname );
+ params = p;
// Initialise the modifier class
- modifier = new OntologyModifier( this.model, this.modifiedModel, this.alignment); //build the ontology modifier for the first time
- modifier.setNewNamespace( this.namespace );
- // JE: This should be put OUT of the modifier (this generate Properties... instead of alignments...)
- modifier.initializeAlignment(); // initialize the reference alignment
+ modifier = new OntologyModifier( onto, new URIAlignment()); //build the ontology modifier for the first time
+ modifier.setNewNamespace( namespace );
+ // Initialize the reference alignment
+ if ( initalign == null ) {
+ modifier.initializeAlignment();
+ } else {
+ modifier.initializeAlignment( initalign );
+ }
// Apply all modifications
- //System.out.println( "[-------------------------------------------------]" );
- for( String key : this.params.stringPropertyNames() ) {
- String value = this.params.getProperty(key);
- //System.out.println( "[" +key + "] => [" + value + "]");
+ if ( debug ) System.out.println( "[-------------------------------------------------]" );
+ for( String key : params.stringPropertyNames() ) {
+ String value = params.getProperty(key);
+ if ( debug ) System.out.println( "[" +key + "] => [" + value + "]");
modifier.modifyOntology( key, value ); //modify the ontology according to it
}
- //System.out.println( "[-------------------------------------------------]" );
- // JE: this refalign should be variabilised
//saves the alignment into the file "refalign.rdf", null->System.out
- modifier.computeAlignment( "refalign.rdf" ); //at the end, compute the reference alignment
- this.alignment = modifier.getAlignment(); //get the reference alignment
- this.modifiedModel = modifier.getModifiedOntology(); //get the modified ontology
- return this.alignment;
+ modifier.computeAlignment( alignname ); //at the end, compute the reference alignment
+ resultAlignment = modifier.getAlignment(); //get the reference alignment
+ modifiedOntology = modifier.getModifiedOntology(); //get the modified ontology
+ return resultAlignment;
}
- //generate the alingnment
- //newParams => keeps track of the previous modifications
- public Alignment generate(Ontology o, Properties p, Properties newParams) {
- this.params = p;
- this.alignment = new URIAlignment();
- modifier = new OntologyModifier( this.model, this.modifiedModel, this.alignment); //build the ontology modifier for the first time
- // JE: These two lines (one commented and the next one) are the only difference with the other
- // The first one is a different between incremental (an alignment has been initialised)
- //modifier.initializeAlignment(); //initialize the reference alignment
-
- modifier.setProperties(newParams);
- //set the new namespace
- modifier.setNewNamespace( this.namespace );
-
- //System.out.println( "[-------------------------------------------------]" );
- for( String key : this.params.stringPropertyNames() ) {
- String value = this.params.getProperty(key);
- //System.out.println( "[" +key + "] => [" + value + "]");
- modifier.modifyOntology( key, value ); //modify the ontology according to it
- }
- //System.out.println( "[-------------------------------------------------]" );
-
- //saves the alignment into the file "referenceAlignment.rdf", null->System.out
- modifier.computeAlignment( "refalign.rdf" ); //at the end, compute the reference alignment
- this.alignment = modifier.getAlignment(); //get the reference alignment
- this.modifiedModel = modifier.getModifiedOntology(); //get the modified ontology
- return this.alignment;
+ public Alignment generate( OntModel onto, Properties p ) {
+ return generate( onto, p, (Properties)null );
}
-
-
}
diff --git a/src/fr/inrialpes/exmo/align/gen/inter/AlignedOntologyGenerator.java b/src/fr/inrialpes/exmo/align/gen/inter/AlignedOntologyGenerator.java
index 065e59c0..881679d2 100644
--- a/src/fr/inrialpes/exmo/align/gen/inter/AlignedOntologyGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/inter/AlignedOntologyGenerator.java
@@ -22,13 +22,13 @@
package fr.inrialpes.exmo.align.gen.inter;
-import fr.inrialpes.exmo.ontowrap.Ontology;
-import java.util.Properties;
+import com.hp.hpl.jena.ontology.OntModel;
import org.semanticweb.owl.align.Alignment;
+import java.util.Properties;
public interface AlignedOntologyGenerator {
- //generate an Alignment refering to the generated Ontology as onto2 (to be saved)
- public Alignment generate(Ontology o, Properties p);;
+ //generate an Alignment refering to the generated Ontology as onto2 (to be saved)
+ public Alignment generate( OntModel o, Properties p );
}
--
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