From abf101db728404455c2fbc7b94f3685f9444d0c5 Mon Sep 17 00:00:00 2001
From: Maria-Elena Rosoiu <rosoiu.maria@gmail.com>
Date: Fri, 22 Jul 2011 14:13:57 +0000
Subject: [PATCH] 'modular architecture'
---
.../exmo/align/gen/ArbitraryTest.java | 200 +++++++
.../exmo/align/gen/ClassHierarchy.java | 11 +-
.../exmo/align/gen/GenerateBenchmark.java | 545 ++++++++++++++++++
.../exmo/align/gen/OntologyModifier.java | 476 ++++++++-------
.../exmo/align/gen/ParametersIds.java | 35 +-
.../exmo/align/gen/TestGenerator.java | 97 +++-
src/fr/inrialpes/exmo/align/gen/URITree.java | 61 +-
7 files changed, 1144 insertions(+), 281 deletions(-)
create mode 100644 src/fr/inrialpes/exmo/align/gen/ArbitraryTest.java
create mode 100644 src/fr/inrialpes/exmo/align/gen/GenerateBenchmark.java
diff --git a/src/fr/inrialpes/exmo/align/gen/ArbitraryTest.java b/src/fr/inrialpes/exmo/align/gen/ArbitraryTest.java
new file mode 100644
index 00000000..fcf234f1
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/ArbitraryTest.java
@@ -0,0 +1,200 @@
+/*
+ * $Id: ArbitraryTest.java
+ *
+ * Copyright (C) 2003-2010, 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.
+ */
+
+package fr.inrialpes.exmo.align.gen;
+
+//Java classes
+import java.io.FileOutputStream;
+import java.io.InputStream;
+
+//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 java.io.File;
+import java.io.OutputStreamWriter;
+import java.nio.charset.Charset;
+import java.util.Properties;
+import fr.inrialpes.exmo.ontowrap.jena25.JENAOntology;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+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 String [] params; //vector to build the parameters
+ private Properties parameters; //the parameters
+ public final String namespace = "http://oaei.ontologymatching.org/2011/gen/";
+
+ //constructor
+ public ArbitraryTest(String fileName, String testNumber, String [] params) {
+ this.fileName = fileName;
+ this.testNumber = testNumber;
+ this.params = params;
+ }
+
+ //build the parameters
+ public void buildParameters() {
+ parameters = new Properties(); //initialize the parameters
+
+ for ( int i=0; i<params.length; i+=2 ) {
+ if ( params[i].equals("addClasses") ) /* add percentage classes */
+ parameters.setProperty(ParametersIds.ADD_CLASSES, params[i+1]);
+
+ if ( params[i].equals("addProperties") ) /* add percentage properties */
+ parameters.setProperty(ParametersIds.ADD_PROPERTIES, params[i+1]);
+
+ //add c classes beginning from level l -> the value of this parameters should be:
+ //beginning_level.number_of_classes_to_add
+ if ( params[i].equals("addClassesLevel") ) /* add c classes beginning from level l */
+ parameters.setProperty(ParametersIds.ADD_CLASSES, params[i+1]);
+
+ if ( params[i].equals("removeClasses") ) /* remove percentage classes */
+ parameters.setProperty(ParametersIds.REMOVE_CLASSES, params[i+1]);
+
+ if ( params[i].equals("removeProperties") ) /* remove percentage properties */
+ parameters.setProperty(ParametersIds.REMOVE_PROPERTIES, params[i+1]);
+
+ if ( params[i].equals("removeComments") ) /* remove percentage comments */
+ parameters.setProperty(ParametersIds.REMOVE_COMMENTS, params[i+1]);
+
+ if ( params[i].equals("removeRestrictions") ) /* remove percentage restrictions */
+ parameters.setProperty(ParametersIds.REMOVE_RESTRICTIONS, params[i+1]);
+
+ if ( params[i].equals("removeIndividuals") ) /* remove percentage individuals */
+ parameters.setProperty(ParametersIds.REMOVE_INDIVIDUALS, params[i+1]);
+
+ if ( params[i].equals("renameClasses") ) /* rename percentage classes */
+ parameters.setProperty(ParametersIds.RENAME_CLASSES, params[i+1]);
+
+ if ( params[i].equals("renameProperties") ) /* rename percentage properties */
+ parameters.setProperty(ParametersIds.RENAME_PROPERTIES, params[i+1]);
+
+ if ( params[i].equals("levelFlattened") ) /* flattened level */
+ parameters.setProperty(ParametersIds.LEVEL_FLATTENED, params[i+1]);
+
+ if ( params[i].equals( ("noHierarchy")) ) /* no hierarchy */
+ parameters.setProperty( ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY);
+ }
+ }
+
+ //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 + this.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);
+ writer.setProperty( "xmlbase", ns );
+ writer.write(model.getBaseModel(), new OutputStreamWriter(fout, defaultCharset), "");
+ fout.close();
+ } catch (Exception ex) {
+ System.out.println("Exception " + ex.getMessage());
+ }
+ }
+
+
+ //modify ontology
+ public void modifyOntology(){
+ //build the list of parameters
+ this.buildParameters();
+ //modify the model
+ try {
+ OntModel model = loadOntology(fileName); //load the initial ontology
+ TestGenerator t = new TestGenerator(); //build an instance of TestGenerator
+ JENAOntology onto = new JENAOntology(); //cast the model into Ontology
+ onto.setOntology( (OntModel)model );
+ //set the TestGenerator ontology
+ t.setOntology(onto);
+ //set the namespace
+ t.setNamespace( this.getURI(this.fileName, this.testNumber) );
+ //t.setNamespace( "http://oaei.ontologymatching.org/2011/gen/onto/101/onto.rdf#" );
+
+ Alignment align = t.generate(onto, parameters); //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.out.println(" Succesufully created the directory ");
+ else System.out.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, this.getURI(this.fileName, this.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.out.println( "***" );
+ System.out.println( "END" );
+ System.out.println( "***" );
+ }
+
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java b/src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java
index bc99d2de..253444ea 100644
--- a/src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java
+++ b/src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java
@@ -1,7 +1,7 @@
/*
- * $Id$
+ * $Id: ClassHierarchy.java
*
- * Copyright (C) 2010-2011, INRIA
+ * Copyright (C) 2003-2010, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -23,7 +23,6 @@
Iterates through all the classes in the hierarchy and builds the class hierarchy
*/
-
package fr.inrialpes.exmo.align.gen;
//Jena
@@ -66,9 +65,7 @@ public class ClassHierarchy {
public void addClass (String childURI, String parentURI) {
URITree node = null;
- //node = this.root.searchURITree( this.root, parentURI ); //the node from the hierarchy with the identifier parentURI
this.getRootClassHierarchy().add(this.root, parentURI, childURI); //we add the new childURI to the hierarchy
- //node._addChildToNode(this.root, parentURI, childURI);
}
//updates the class hierarchy
@@ -97,7 +94,7 @@ public class ClassHierarchy {
//remove the URI of the class from the hierarchy
//returns the parent of the class if it exists or 0 other way -> not owl:Thing
- public OntClass removeClass ( OntModel model, OntClass cls ) {
+ public OntClass removeClass (OntModel model, OntClass cls) {
URITree node = this.root.searchURITree( this.root, cls.getURI() ); //search for the class URI in the class hierarchy
URITree parentNode = null;
@@ -284,5 +281,3 @@ public class ClassHierarchy {
}
-
-
diff --git a/src/fr/inrialpes/exmo/align/gen/GenerateBenchmark.java b/src/fr/inrialpes/exmo/align/gen/GenerateBenchmark.java
new file mode 100644
index 00000000..8dc4a7c8
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/GenerateBenchmark.java
@@ -0,0 +1,545 @@
+/*
+ * $Id: GenerateBenchmark.java
+ *
+ * Copyright (C) 2003-2010, 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 the Benchmark dataset.
+ */
+
+package fr.inrialpes.exmo.align.gen;
+
+//Java classes
+import java.io.FileOutputStream;
+import java.io.InputStream;
+
+//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 java.io.File;
+import java.io.OutputStreamWriter;
+import java.nio.charset.Charset;
+import java.util.Properties;
+import fr.inrialpes.exmo.ontowrap.jena25.JENAOntology;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentVisitor;
+
+public class GenerateBenchmark {
+ 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 GenerateBenchmark(String fileName) {
+ this.fileName = fileName;
+ }
+
+ //gets the prefix to build the namespace
+ public String getPrefix(String fileName) {
+ return fileName.substring(0, fileName.lastIndexOf("."));
+ }
+
+ //gets the uri
+ public String getURI(String fileName, String testNumber) {
+ return this.namespace + this.getPrefix(fileName) + "/" + testNumber + "/" + fileName + "#";
+ }
+
+ //loads 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;
+ }
+
+ //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);
+ writer.setProperty( "xmlbase", ns );
+ writer.write(model.getBaseModel(), new OutputStreamWriter(fout, defaultCharset), "");
+ fout.close();
+ } catch (Exception ex) {
+ System.out.println("Exception " + ex.getMessage());
+ }
+ }
+
+
+ //modifies an ontology
+ public void modifyOntology(TestGenerator t, String fileName, String testNumber, Properties params) {
+ //modify the model
+ try {
+
+ System.out.println("From test " + fileName);
+ System.out.println("Test " + testNumber);
+ 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
+ t.setOntology(onto);
+ //set the namespace
+ t.setNamespace( this.getURI(this.fileName, testNumber) );
+ //t.setNamespace( "http://oaei.ontologymatching.org/2011/gen/onto/101/onto.rdf#" );
+
+ Alignment align = null;
+ if ( fileName.equals(this.fileName) )
+ align = t.generate(onto, params); //generate the alignment
+ else
+ align = t.generate(onto, params, this.parameters); //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.out.println(" Succesufully created the directory ");
+ else System.out.println(" Error creating the directory "); */
+
+ //write the ontology into the directory
+ if ( modified.getOntology() instanceof OntModel )
+ writeOntology(modified.getOntology(), testNumber + "/" + this.fileName, this.getURI( this.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();
+
+ //retrieve the parameters
+ this.parameters = t.getParameters();
+
+
+ //System.out.println("Alignmnent");
+
+
+
+ }
+ catch ( Exception ex ) {
+ System.err.println( "Error " + ex.getMessage() );
+ }
+
+ }
+
+ public String directoryName(float i1, String dir) {
+ String dirName = "";
+ if ( ((Float)i1).toString().substring(0, 1).equals("0") ) {
+ dirName = dir + "-" + ((Float)i1).toString().substring(2, 3);
+ }
+ else {
+ dirName = dir;
+ }
+
+ return dirName;
+ }
+
+ //generates the Benchmark
+ public void generate() {
+ //keep track of the alignment
+ Properties paramsRenameResources; Properties paramsNoComments;
+ Properties paramsNoInstance; Properties paramsNoProperty;
+ Properties paramsFlatten; Properties paramsExpand;
+ Properties paramsInitial;
+ Properties p = new Properties(); //modify the ontology according to this parameters
+
+ String prevDirName;
+ String crtDirName;
+
+ this.parameters = new Properties();
+ crtDirName = this.fileName;
+
+ TestGenerator t = new TestGenerator(); //build an instance of TestGenerator
+
+ /*
+ * Test 101
+ */
+ this.modifyOntology(t, this.fileName, "101", p);
+ paramsInitial = (Properties)parameters.clone();
+ paramsRenameResources = (Properties)parameters.clone();
+ prevDirName = "101" + "/";
+
+
+ /*
+ * Tests 201, 202, 248, 249, 253, 258, 259, 250, 254,
+ * 262, 257, 260, 265, 261, 266, 251, 252
+ */
+
+ for ( float i1=0.20f; i1<=1.00f; i1+=0.20f ) {
+
+ /*
+ * 201-x *** no names
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.RENAME_CLASSES, ((Float)i1).toString());
+ p.setProperty(ParametersIds.RENAME_PROPERTIES, ((Float)i1).toString());
+ crtDirName = directoryName(i1, "201");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 202-x *** no names + no comments
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_COMMENTS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "201") + "/";
+ crtDirName = directoryName(i1, "202");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 248-x *** no names + no comments + no hierarchy
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY);
+ prevDirName = directoryName(i1, "202") + "/";
+ crtDirName = directoryName(i1, "248");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 253-x *** no names + no comments + no hierarchy + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "248") + "/";
+ crtDirName = directoryName(i1, "253");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 249-x *** no names + no comments + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "202") + "/";
+ crtDirName = directoryName(i1, "249");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ ////get the parameters
+ paramsRenameResources = (Properties)this.parameters.clone();
+
+ /*
+ * 250-x *** no names + no comments + no property
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_PROPERTIES, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "202") + "/";
+ crtDirName = directoryName(i1, "250");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 254-x *** no names + no comments + no property + no hierarchy
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY);
+ prevDirName = directoryName(i1, "250") + "/";
+ crtDirName = directoryName(i1, "254");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 262-x *** no names + no comments + no property + no hierarchy + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "254") + "/";
+ crtDirName = directoryName(i1, "262");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 257-x *** no names + no comments + no property + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "250") + "/";
+ crtDirName = directoryName(i1, "257");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 261-x *** no names + no comments + no property + expand
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.ADD_CLASSES, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "250") + "/";
+ crtDirName = directoryName(i1, "261");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 266-x *** no names + no comments + no property + expand + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "261") + "/";
+ crtDirName = directoryName(i1, "266");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 260-x *** no names + no comments + no property + flatten
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.LEVEL_FLATTENED, "2");
+ prevDirName = directoryName(i1, "250") + "/";
+ crtDirName = directoryName(i1, "260");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 265-x *** no names + no comments + no property + flatten + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "260") + "/";
+ crtDirName = directoryName(i1, "265");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ //re-establish the parameters
+ this.parameters = (Properties)paramsRenameResources.clone();
+
+ /*
+ * 251-x *** no names + no comments + flatten
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.LEVEL_FLATTENED, "2");
+ prevDirName = directoryName(i1, "202") + "/";
+ crtDirName = directoryName(i1, "251");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 258-x *** no names + no comments + flatten + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "251") + "/";
+ crtDirName = directoryName(i1, "258");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ //re-establish the parameters
+ this.parameters = (Properties)paramsRenameResources.clone();
+
+ /*
+ * 252-x *** no names + no comments + expand
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.ADD_CLASSES, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "202") + "/";
+ crtDirName = directoryName(i1, "252");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 259-x *** no names + no comments + expand + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(i1, "252") + "/";
+ crtDirName = directoryName(i1, "259");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+// paramsNoProperty = modifier.getProperties(); //get the modifed properties
+
+ this.parameters = (Properties)paramsRenameResources.clone();
+ prevDirName = directoryName(i1, "201") + "/";
+ }
+
+ //re-establish the parameters
+ this.parameters = (Properties)paramsInitial.clone();
+
+ /*
+ * Tests 221, 232, 233, 241
+ */
+
+ /*
+ * 221 *** no hierarchy
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY);
+ prevDirName = directoryName(1.00f, "101") + "/";
+ crtDirName = directoryName(1.00f, "221");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 232 *** no hierarchy + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "221") + "/";
+ crtDirName = directoryName(1.00f, "232");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 233 *** no hierarchy + no property
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_PROPERTIES, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "221") + "/";
+ crtDirName = directoryName(1.00f, "233");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 241 *** no hierarchy + no property + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "233") + "/";
+ crtDirName = directoryName(1.00f, "241");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ //re-establish the parameters
+ this.parameters = (Properties)paramsInitial.clone();
+
+ /*
+ * Tests 222, 237
+ */
+
+ /*
+ * 222 *** flatten
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.LEVEL_FLATTENED, "2");
+ prevDirName = directoryName(1.00f, "101") + "/";
+ crtDirName = directoryName(1.00f, "222");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 237 *** flatten + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "222") + "/";
+ crtDirName = directoryName(1.00f, "237");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+
+ //re-establish the parameters
+ this.parameters = (Properties)paramsInitial.clone();
+
+ /*
+ * Tests 223, 238
+ */
+
+ /*
+ * 223 *** expand
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.ADD_CLASSES, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "101") + "/";
+ crtDirName = directoryName(1.00f, "223");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 238 *** expand + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "223") + "/";
+ crtDirName = directoryName(1.00f, "238");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 224 *** no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "101") + "/";
+ crtDirName = directoryName(1.00f, "224");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 225 *** no restrictions
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_RESTRICTIONS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "101") + "/";
+ crtDirName = directoryName(1.00f, "225");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * Tests 228, 239, 246, 236, 240, 247
+ */
+
+ /*
+ * 228 *** no property
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_PROPERTIES, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "101") + "/";
+ crtDirName = directoryName(1.00f, "228");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 236 *** no property + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "228") + "/";
+ crtDirName = directoryName(1.00f, "236");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 240 *** no property + expand
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.ADD_CLASSES, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "228") + "/";
+ crtDirName = directoryName(1.00f, "240");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 247 *** no property + expand + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "240") + "/";
+ crtDirName = directoryName(1.00f, "247");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 239 *** no property + flatten
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.LEVEL_FLATTENED, "2");
+ prevDirName = directoryName(1.00f, "228") + "/";
+ crtDirName = directoryName(1.00f, "239");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ /*
+ * 246 *** no property + flatten + no instance
+ */
+ p = new Properties();
+ p.setProperty(ParametersIds.REMOVE_INDIVIDUALS, ((Float)1.00f).toString());
+ prevDirName = directoryName(1.00f, "239") + "/";
+ crtDirName = directoryName(1.00f, "246");
+ this.modifyOntology(t, prevDirName + this.fileName, crtDirName, p);
+
+ }
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
index db99f2f0..96fe8275 100644
--- a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
+++ b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
@@ -1,7 +1,7 @@
/*
- * $Id$
+ * $Id: OntologyModifier.java
*
- * Copyright (C) 2010-2011, INRIA
+ * Copyright (C) 2003-2010, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -25,15 +25,9 @@
The file in which we store the alignment is "referenceAlignment.rdf"
*/
-
package fr.inrialpes.exmo.align.gen;
//Java classes
-import java.io.BufferedWriter;
-import java.io.FileOutputStream;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
import java.net.URI;
import java.util.HashMap;
import java.util.Iterator;
@@ -41,16 +35,11 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
import java.util.Random;
-import java.util.Set;
//Alignment API classes
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
-import org.semanticweb.owl.align.AlignmentVisitor;
-import fr.inrialpes.exmo.align.impl.Annotations;
-import fr.inrialpes.exmo.align.impl.Namespace;
-import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
import fr.inrialpes.exmo.align.service.jade.messageontology.Parameter;
//Google API classes
@@ -76,7 +65,6 @@ import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.RDFReader;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.util.ResourceUtils;
@@ -84,6 +72,7 @@ import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import fr.inrialpes.exmo.align.impl.URIAlignment;
+import java.util.Enumeration;
/*
//WordNet API classes
import edu.smu.tspell.wordnet.Synset;
@@ -105,7 +94,8 @@ public class OntologyModifier {
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 isChanged; //keep track if the namespace of the new ontology is changed
- public static String fileName = "referenceAlignment.rdf"; //the reference alignment
+ 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 ) {
@@ -116,14 +106,7 @@ public class OntologyModifier {
this.isBuild = false;
this.isAlign = false;
this.isChanged = false;
- this.namespace = model.getNsPrefixURI("");
- //if has no namespace, choose a default one
- if ( this.namespace == null ) {
- //RDFReader reader = this.model.getReader();
- this.model.setNsPrefix("", "http://oaei.ontologymatching.org/2010/benchmarks/101/onto.rdf#");
- this.namespace = model.getNsPrefixURI("");
- System.out.println( "Set default namespace [" + this.namespace + "]" );
- }
+ this.namespace = model.getNsPrefixURI("");
this.namespaceNew = "";
this.params = new Properties();
}
@@ -138,7 +121,7 @@ public class OntologyModifier {
//this.classHierarchy.printClassHierarchy();
}
- //generate random string with the length "length"
+ //generates a random string with the length "length"
public String getRandomString() {
Random generator = new Random();
String characters = "abcdefghijklmnopqrstuvwxyz";
@@ -150,7 +133,7 @@ public class OntologyModifier {
return new String(text).toUpperCase();
}
- //remove spaces from a string
+ //removes spaces from a string
public String removeSpaces ( String str ) {
//return str.replaceAll("\\s+", "");
if ( !str.contains( " " ) )
@@ -173,7 +156,7 @@ public class OntologyModifier {
return str;
}
- //translate the string from English to French
+ //translates the string from English to French
public String translateString( String source ) {
String translatedText = "";
GoogleAPI.setHttpReferrer("http://code.google.com/p/google-api-translate-java/");
@@ -249,11 +232,10 @@ public class OntologyModifier {
newString = newString.concat( getSynonym(str.substring(0)) );
return newString;
}
-
-
+
//count - the number of elements from the vector
//the random numElems that must be selected
- //use the Fisher and Yates method to shuffle integers from an array
+ //uses the Fisher and Yates method to shuffle integers from an array
public int [] randNumbers (int count, int numElems) {
int [] vect = new int[count];
int [] n = new int[numElems];
@@ -272,7 +254,7 @@ public class OntologyModifier {
return n;
}
- //replace the label of the property
+ //replaces the label of the property
public void replacePropertyLabel( String uri, String newLabel, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation ) {
OntProperty prop = this.modifiedModel.getOntProperty( uri );
if ( prop.getLabel( "en" ) != null ) {
@@ -287,35 +269,37 @@ public class OntologyModifier {
//gets the URIs of the properties and their translation
public HashMap<String, String> getPropertiesIdentifiers ( float percentage, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation) {
HashMap<String, String> propertiesIdentifiers = new HashMap<String, String>(); //the HashMap of the properties identifiers
- List<OntProperty> properties = getOntologyProperties(); //the list of all the properties
List<String> propertiesName = new ArrayList<String>(); //the properties identifiers
- List<OntProperty> propertiesTo = new ArrayList<OntProperty>();
- int nbProperties, toBeRenamed;
- List<OntProperty> notRenamedProperties = new ArrayList<OntProperty>();
- List<OntProperty> modelProperties = this.getOntologyProperties();
+ List<OntProperty> propertiesTo = new ArrayList<OntProperty>(); //the list of properties to be renamed
+ List<OntProperty> notRenamedProperties = new ArrayList<OntProperty>(); //the list of not renamed properties
+ List<OntProperty> properties = getOntologyProperties(); //the list of all the properties
+
+ int nbProperties, toBeRenamed, renamedProperties;
+
//builds the list of all unrenamed properties from the model
- for ( OntProperty p : modelProperties ) {
- String key = p.getURI();
- if ( this.params.containsKey( key ) ) {
+ for ( OntProperty p : properties ) {
+ String uri = base + p.getLocalName();
+ if ( this.params.containsKey( uri ) ) {
+ String key = uri;
String value = this.params.getProperty( key );
- if ( key.equals( value ) ) {
- notRenamedProperties.add( p ); //add the property to not renamed properties
- }
+ if ( key.equals( value ) )
+ notRenamedProperties.add( p ); //add the property to not renamed properties
}
}
+
+
nbProperties = properties.size(); //the number of renamed properties
- toBeRenamed = (int)( percentage*nbProperties );
+ renamedProperties = nbProperties - notRenamedProperties.size();
+ toBeRenamed = (int)(percentage*nbProperties) - renamedProperties; // -renamedProperties -> for Benchmark
- if ( notRenamedProperties.size() < 2*toBeRenamed )
- toBeRenamed = notRenamedProperties.size();
//builds the list of properties to be renamed
int [] n = this.randNumbers(notRenamedProperties.size(), toBeRenamed);
for ( int i=0; i<toBeRenamed; i++ ) {
OntProperty p = notRenamedProperties.get(n[i]);
propertiesTo.add(p);
- if ( p.getNameSpace().equals( this.namespace ) )
+ if ( p.getNameSpace().equals( this.namespace ) )
propertiesName.add( p.getLocalName() );
}
@@ -330,16 +314,16 @@ public class OntologyModifier {
propertiesIdentifiers.put( localName , translateStrg );
replacePropertyLabel( prop.getURI(), translateStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( prop.getURI() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( prop.getURI() , this.namespace + translateStrg );//the reference alignment
+ if ( params.containsKey( this.base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
+ this.params.put( this.base + prop.getLocalName() , this.base + translateStrg );//the reference alignment
}
}
else if ( activeRandomString ) { //replace the URI with a random string
String newStrg = getRandomString();
propertiesIdentifiers.put( localName , newStrg );
replacePropertyLabel( prop.getURI(), newStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( prop.getURI() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( prop.getURI() , this.namespace + newStrg);//the reference alignment
+ if ( params.containsKey( this.base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
+ this.params.put( this.base + prop.getLocalName() , this.base + newStrg);//the reference alignment
}
}
else if ( activeSynonym ) {
@@ -349,30 +333,30 @@ public class OntologyModifier {
else {
propertiesIdentifiers.put( localName, synonym );
replacePropertyLabel( prop.getURI(), synonym, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( prop.getURI() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( prop.getURI(), this.namespace + synonym ); //the reference alignment
+ if ( params.containsKey( this.base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
+ this.params.put( this.base + prop.getLocalName() , this.base + synonym ); //the reference alignment
}
}
}
else if ( activeStringOperation == 1 ) { //replace the URI with the UpperCase URI
propertiesIdentifiers.put( localName , toUpperCase( localName ) );
replacePropertyLabel( prop.getURI(), toUpperCase( localName ), activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( prop.getURI() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( prop.getURI(), this.namespace + toUpperCase( localName ) ); //the reference alignment
+ if ( params.containsKey( this.base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
+ this.params.put( this.base + prop.getLocalName() , this.base + toUpperCase( localName ) ); //the reference alignment
}
}
else if ( activeStringOperation == 2 ) {
propertiesIdentifiers.put( localName , toLowerCase( localName ) );
replacePropertyLabel( prop.getURI(), toLowerCase( localName ), activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( prop.getURI() ) ) { // this.params.remove( prop.getURI() );
- this.params.put( prop.getURI(), this.namespace + toLowerCase( localName ) ); //the reference alignment
+ if ( params.containsKey( this.base + prop.getLocalName() ) ) { // this.params.remove( prop.getURI() );
+ this.params.put( this.base + prop.getLocalName() , this.base + toLowerCase( localName ) ); //the reference alignment
}
}
else {
propertiesIdentifiers.put( localName, localName + "PROPERTY" );
replacePropertyLabel( prop.getURI(), localName + "PROPERTY", activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( prop.getURI() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( prop.getURI(), this.namespace + localName + "PROPERTY" );
+ if ( params.containsKey( this.base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
+ this.params.put( this.base + prop.getLocalName() , this.base + localName + "PROPERTY" );
}
}
}
@@ -380,8 +364,8 @@ public class OntologyModifier {
}
return propertiesIdentifiers;
}
-
- //replace the label of the class
+
+ //replaces the label of the class
public void replaceClassLabel( String uri, String newLabel, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation ) {
OntClass c = this.modifiedModel.getOntClass( uri );
@@ -396,30 +380,30 @@ public class OntologyModifier {
//gets the URIs of the classes and their translation
public HashMap<String, String> getClassesIdentifiers ( float percentage, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation ) {
HashMap<String, String> classesIdentifiers = new HashMap<String, String>(); //the HashMap of classes identifiers
- List<OntClass> classes = this.getOntologyClasses();
- List<OntClass> classesTo = new ArrayList<OntClass>();
- int nbClasses, toBeRenamed ;
- List<OntClass> notRenamedClasses = new ArrayList<OntClass>();
- List<OntClass> modelClasses = this.getOntologyClasses();
+ int nbClasses, toBeRenamed, renamedClasses;
+
+ List<OntClass> notRenamedClasses = new ArrayList<OntClass>(); //the list of not renamed classes
+ List<OntClass> classes = this.getOntologyClasses(); //the list of ontology classes
+ List<OntClass> classesTo = new ArrayList<OntClass>(); //the list of classes to be renamed
//builds the list of all unrenamed classes from the model
- for ( OntClass c : modelClasses ) {
- String uri = c.getURI();
+ for ( OntClass c : classes ) {
+ String uri = base + c.getLocalName();
//gets the pair <key, value>
if ( this.params.containsKey( uri ) ) {
String key = uri;
String value = this.params.getProperty( uri );
//they didnt change
- if ( key.equals( value ) )
+ if ( key.equals( value ) )
notRenamedClasses.add( c ); //add the class to not renamed classes
}
}
+
+ nbClasses = classes.size(); //the number of renamed classes
+ renamedClasses = nbClasses - notRenamedClasses.size();
+ toBeRenamed = (int)(percentage*nbClasses) - renamedClasses; // -renamedClasses -> for Benchmark
- nbClasses = classes.size(); //the number of renamed classes
- toBeRenamed = (int)( percentage*nbClasses ); //the number of classes to be renamed
- if ( notRenamedClasses.size() < 2 * toBeRenamed )
- toBeRenamed = notRenamedClasses.size();
//build the list of classes to be renamed
int [] n = this.randNumbers(notRenamedClasses.size(), toBeRenamed);
@@ -441,45 +425,45 @@ public class OntologyModifier {
String translateStrg = parseString (localName, true, false);
classesIdentifiers.put( localName , translateStrg );
replaceClassLabel( cls.getURI(), translateStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( cls.getURI() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( cls.getURI() , this.namespace + translateStrg); //the reference alignment
+ if ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
+ this.params.put( this.base + cls.getLocalName() , this.base + translateStrg); //the reference alignment
}
}
else if ( activeRandomString ) { //replace the URI with a random string
String newStrg = getRandomString();
classesIdentifiers.put( localName , newStrg );
replaceClassLabel( cls.getURI(), newStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( cls.getURI() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( cls.getURI(), this.namespace + newStrg ); //the reference alignment
+ if ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
+ this.params.put( this.base + cls.getLocalName() , this.base + newStrg ); //the reference alignment
}
}
else if ( activeSynonym ) { //replace the URI with a synonym
String synonym = parseString (localName, false, true);
classesIdentifiers.put( localName, synonym );
replaceClassLabel( cls.getURI(), synonym, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( cls.getURI() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( cls.getURI(), this.namespace + synonym );//the reference alignment
+ if ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
+ this.params.put( this.base + cls.getLocalName() , this.base + synonym );//the reference alignment
}
}
else if ( activeStringOperation == 1 ){ //replace the URI with the UpperCase URI
classesIdentifiers.put( localName , toUpperCase( localName ) );
replaceClassLabel( cls.getURI(), toUpperCase(localName), activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( cls.getURI() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( cls.getURI(), this.namespace + toUpperCase( localName ) ); //the reference alignment
+ if ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
+ this.params.put( this.base + cls.getLocalName() , this.base + toUpperCase( localName ) ); //the reference alignment
}
}
else if ( activeStringOperation == 2 ){ //replace the URI with the LowerCase URI
classesIdentifiers.put( localName , toLowerCase( localName ) );
replaceClassLabel( cls.getURI(), toLowerCase(localName), activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( cls.getURI() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( cls.getURI(), this.namespace + toLowerCase( localName ) ); //the reference alignment
+ if ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
+ this.params.put( this.base + cls.getLocalName() , this.base + toLowerCase( localName ) ); //the reference alignment
}
}
else {
classesIdentifiers.put( localName, localName + "CLASS" );
replaceClassLabel( cls.getURI(), localName + "CLASS", activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( cls.getURI() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( cls.getURI(), this.namespace + localName + "CLASS" );
+ if ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
+ this.params.put( this.base + cls.getLocalName() , this.base + localName + "CLASS" );
}
}
}
@@ -497,11 +481,14 @@ public class OntologyModifier {
List<Statement> statements = null; //the list of all statements
HashMap<String, String> propertiesIdentifiers = null; //the HashMap of the properties identifiers
HashMap<String, String> classesIdentifiers = null; //the HashMap of the classes identifiers
+
String subjectLocalName, subjectNameSpace;
String predicateLocalName, predicateNameSpace;
String objectLocalName, objectNameSpace;
+
boolean isPred, isSubj, isObj;
isPred = isSubj = isObj = false;
+
OntModel newModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);//create new Model
//get properties and classes identifiers
if ( activeProperties )
@@ -509,16 +496,19 @@ public class OntologyModifier {
if ( activeClasses )
classesIdentifiers = getClassesIdentifiers ( percentage, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation);
statements = this.modifiedModel.listStatements().toList(); //get all the statements of the model
-
+
//iterate and modify the identifiers
for ( Statement stm : statements ) {
+
Resource subject = stm.getSubject(); //the subject
Property predicate = stm.getPredicate(); //the predicate
RDFNode object = stm.getObject(); //the object
+
Resource subj = null;
Property pred = null;
Resource obj = null;
isPred = isSubj = isObj = false;
+
//if it is the subject of the statement
if ( subject.getLocalName() != null ) {
if ( activeProperties ) {
@@ -546,6 +536,7 @@ public class OntologyModifier {
}
}
}
+
//if it is the predicate of the statement
if ( activeProperties ) {
if ( propertiesIdentifiers.containsKey( predicate.getLocalName() ) ) {
@@ -572,6 +563,7 @@ public class OntologyModifier {
}
}
}
+
//if it is the object of the statement
if ( object.canAs( Resource.class ) )
if ( object.isURIResource() ) {
@@ -603,21 +595,29 @@ public class OntologyModifier {
if ( isSubj ) {
if ( isPred ) {
- if ( isObj ) newModel.add( subj, pred, obj );
- else newModel.add( subj, pred, object );
+ if ( isObj )
+ newModel.add( subj, pred, obj );
+ else
+ newModel.add( subj, pred, object );
}
else {
- if ( isObj ) newModel.add( subj, predicate, obj );
- else newModel.add( subj, predicate, object );
+ if ( isObj )
+ newModel.add( subj, predicate, obj );
+ else
+ newModel.add( subj, predicate, object );
}
} else {
if ( isPred ) {
- if ( isObj ) newModel.add( subject, pred, obj );
- else newModel.add( subject, pred, object );
+ if ( isObj )
+ newModel.add( subject, pred, obj );
+ else
+ newModel.add( subject, pred, object );
}
else {
- if ( isObj ) newModel.add( subject, predicate, obj );
- else newModel.add( subject, predicate, object );
+ if ( isObj )
+ newModel.add( subject, predicate, obj );
+ else
+ newModel.add( subject, predicate, object );
}
}
}
@@ -629,7 +629,7 @@ public class OntologyModifier {
return newModel;
}
- //checks if the class hierarchy is build
+ //check if the class hierarchy is build
public void checkClassHierarchy() {
if ( !this.isBuild ) {
buildClassHierarchy();
@@ -677,7 +677,7 @@ public class OntologyModifier {
List<OntClass> classes = getOntologyClasses(); //get the list of classes from the Ontology
int nbClasses = classes.size(); //number of classes from the Ontology
int toAdd = (int) ( percentage * nbClasses );
-
+
checkClassHierarchy(); //check if the classHierarchy is built
//build the list of properties to be renamed
int [] n = this.randNumbers(nbClasses, toAdd);
@@ -735,7 +735,7 @@ public class OntologyModifier {
String subjectNameSpace, subjectLocalName;
String objectNameSpace, objectLocalName;
String predicateNameSpace, predicateLocalName;
-
+
//iterate and modify the identifiers
for ( Statement stm : statements ) {
Resource subject = stm.getSubject(); //the subject
@@ -747,12 +747,12 @@ public class OntologyModifier {
isSubj = isObj = isPred = false;
//if the class appears as the subject of a proposition
- if ( subject.getURI() != null )
+ if ( subject.getURI() != null )
if ( uris.containsKey( subject.getURI() ) ) {
isSubj = true;
subj = newModel.createResource( uris.get( subject.getURI() ) );
}
-
+
//if appears as the predicate - never
if ( predicate.getURI() != null )
if ( uris.containsKey( predicate.getURI() ) ) {
@@ -789,11 +789,11 @@ public class OntologyModifier {
else newModel.add( subject, predicate, object );
}
}
- }
+ }
return newModel;
}
- //checks if the removed class appears as AllValueFrom or SomeValueFrom in a restriction
+ //check if the removed class appears as AllValueFrom or SomeValueFrom in a restriction
@SuppressWarnings("unchecked")
public void checkClassesRestrictions ( OntClass childClass, OntClass parentClass ) {
Restriction restr = null;
@@ -837,12 +837,12 @@ public class OntologyModifier {
for (OntClass clss : subClasses) //new superclass =>
clss.setSuperClass( parentClass ); //=>the superclass of the node
- checkClassesRestrictions( cls, parentClass );
+ checkClassesRestrictions( cls, parentClass );
cls.remove(); //remove the class from the Ontology
return parentClass.getURI();
}
- //removes the subClasses from the list
+ //remove the subClasses from the list
public void removeSubClasses ( float percentage ) {
List<OntClass> classes = this.getOntologyClasses(); //the list of classes from Ontologu
List<OntClass> removedClasses = new ArrayList<OntClass>();
@@ -868,18 +868,17 @@ public class OntologyModifier {
//checks if the class appears like unionOf.. and replaces its appearence with the superclass
this.modifiedModel = changeDomainRange( uris );
-
+
//remove the URI of the class from the reference alignment
for ( String key : this.params.stringPropertyNames() ) {
String value = this.params.getProperty( key );
- if ( cl.contains( key ) )
+ if ( cl.contains( this.namespace + key.substring(key.indexOf(this.base) + this.base.length() )) )
this.params.remove( key );
- if ( cl.contains( value ) ) //we iterate to check if the class appears only like value
+ if ( cl.contains( this.namespace + value.substring(value.indexOf(this.base) + this.base.length() )) ) //we iterate to check if the class appears only like value
this.params.remove( key );
}
}
-
//remove all the classes from a specific level
public void removeClassesFromLevel ( int level ) {
HashMap<String, String> uris = new HashMap<String, String>();
@@ -890,25 +889,12 @@ public class OntologyModifier {
List<OntClass> classes = new ArrayList<OntClass>();
checkClassHierarchy(); //check if the class hierarchy is built
classes = this.classHierarchy.getClassesFromLevel(this.modifiedModel, level);
-
- for ( OntClass cls : classes ) {
- parentURI = removeClass ( cls );
- OntClass parentClass = this.modifiedModel.getOntClass( parentURI );
- checkClassesRestrictions( cls, parentClass );
- uris.put( cls.getURI(), parentURI);
+ for ( int i=0; i<classes.size(); i++ ) { //remove the classes from the hierarchy
+ parentURI = removeClass ( classes.get(i) );
+ uris.put(classes.get(i).getURI(), parentURI);
}
-
//checks if the class appears like unionOf .. and replaces its appearence with the superclass
this.modifiedModel = changeDomainRange( uris );
- //remove the URI of the class from the reference alignment
- for ( String key : this.params.stringPropertyNames() ) {
- String value = this.params.getProperty( key );
- if ( uris.containsKey( key ) )
- this.params.remove( key );
- if ( uris.containsValue( value ) ) //we iterate to check if the class appears only like value
- this.params.remove( key );
- }
-
}
//remove percentage individuals from Ontology
@@ -919,7 +905,7 @@ public class OntologyModifier {
List<Statement> statements = this.modifiedModel.listStatements().toList();
int nbIndividuals = individuals.size(); //the number of individuals
int toBeRemoved = (int)( percentage*nbIndividuals ); //the number of individuals to be removed
-
+
int [] n = this.randNumbers(nbIndividuals, toBeRemoved); //build the list of individuals to be removed
for ( int i=0; i<toBeRemoved; i++ ) {
Individual indiv = individuals.get(n[i]); //remove the individual from the reference alignment
@@ -965,6 +951,7 @@ public class OntologyModifier {
propertiesToBeRemoved.add( p );
pr.add( p.getURI() );
+
//this.params.remove( p.getURI() );
for ( Iterator it = p.listReferringRestrictions(); it.hasNext(); ) {//get the restrictions of that property
restrictions.add( (Restriction)it.next() );
@@ -1001,10 +988,10 @@ public class OntologyModifier {
//since we don't respect any order the value can appear as a value, thus we must iterate among all params to delete it
for ( String key : this.params.stringPropertyNames() ) {
String value = this.params.getProperty(key);
- if ( pr.contains( key ) ) { //System.out.println( "Elimin " + key );
+ if ( pr.contains( this.namespace + key.substring(key.indexOf(this.base) + this.base.length()) ) ) { //System.out.println( "Elimin " + key );
this.params.remove( key );
}
- if ( pr.contains( value ) ) { //System.out.println( "Elimin " + key );
+ if ( pr.contains( this.namespace + value.substring(key.indexOf(this.base) + this.base.length()) ) ) { //System.out.println( "Elimin " + key );
this.params.remove( key );
}
}
@@ -1033,7 +1020,6 @@ public class OntologyModifier {
}
}
-
//add object properties to the Ontology
public void addProperties ( float percentage ) {
List<OntProperty> properties = this.getOntologyProperties();
@@ -1195,14 +1181,22 @@ public class OntologyModifier {
for ( OntClass cls : supCls ) {
if ( cls.isRestriction() ) {
Restriction r = cls.asRestriction();
- if ( r.isAllValuesFromRestriction() ) restr.add(r);
- if ( r.isCardinalityRestriction() ) restr.add(r);
- if ( r.isHasValueRestriction() ) restr.add(r);
- if ( r.isMaxCardinalityRestriction() ) restr.add(r);
- if ( r.isMinCardinalityRestriction() ) restr.add(r);
- if ( r.isSomeValuesFromRestriction() ) restr.add(r);
+ if ( r.isAllValuesFromRestriction() )
+ restr.add(r);
+ if ( r.isCardinalityRestriction() )
+ restr.add(r);
+ if ( r.isHasValueRestriction() )
+ restr.add(r);
+ if ( r.isMaxCardinalityRestriction() )
+ restr.add(r);
+ if ( r.isMinCardinalityRestriction() )
+ restr.add(r);
+ if ( r.isSomeValuesFromRestriction() )
+ restr.add(r);
+ //System.out.println( cls.getURI() + cls.getLocalName() );
}
}
+ //System.out.println( restr.size() );
if ( !restrictions.containsKey( parentClass.getURI() ) ) {
restrictions.put( parentClass.getURI(), restr );
@@ -1213,6 +1207,10 @@ public class OntologyModifier {
if ( active ) { //if ( !parentClass.getURI().equals( "Thing" ) ) {
OntClass superClass = superLevelClasses.get( i ); //parent class of the child class parents
+ //System.out.println("SuperClass class [" + superClass.getURI() + "]");
+ //System.out.println("Parent class [" + parentClass.getURI() + "]");
+ //System.out.println("Child class [" + childClass.getURI() + "]");
+
if ( this.modifiedModel.containsResource(parentClass) ) {
//to check if the class appears as unionOf, someValuesFrom, allValuesFrom ..
unionOf.put(parentClass.getURI(), superClass.getURI());
@@ -1223,15 +1221,18 @@ public class OntologyModifier {
parentClass.removeSubClass( childClass );
} else {
OntClass superClass = this.modifiedModel.createClass( OWL.Thing.getURI() ); //Thing class
+
if ( this.modifiedModel.containsResource(parentClass) ) {
//to check if the class appears as unionOf..
unionOf.put(parentClass.getURI(), superClass.getURI());
checkClassesRestrictions ( parentClass, superClass );
parentClass.remove();
}
+
parentClass.removeSubClass( childClass );
- }
+ }
}
+
int i = 0;
for ( String uri : parentURI ) {
OntClass childClass = levelClasses.get( i );
@@ -1241,18 +1242,21 @@ public class OntologyModifier {
}
i++;
}
+
//checks if the class appears like unionOf, someValuesFrom, allValuesFrom .. and replaces its appearence with the superclass
this.modifiedModel = changeDomainRange(unionOf);
+
//remove the parentClass from the alignment
for ( String key : this.params.stringPropertyNames() ) {
String value = this.params.getProperty(key);
- if ( parentURI.contains(key) ) { //this.classHierarchy.removeUri("Thing", key);
+ if ( parentURI.contains( this.namespace + key.substring(key.indexOf(this.base) + this.base.length()) ) ) { //this.classHierarchy.removeUri("Thing", key);
this.params.remove(key);
}
- if ( parentURI.contains( value ) ) { //this.classHierarchy.removeUri("Thing", value);
+ if ( parentURI.contains( this.namespace + value.substring(key.indexOf(this.base) + this.base.length() ))) { //this.classHierarchy.removeUri("Thing", value);
this.params.remove(key);
}
}
+
}
//flatten level - for noHierarchy
@@ -1288,6 +1292,7 @@ public class OntologyModifier {
//this.classHierarchy.printClassHierarchy();
_noHierarchy ( level );
level--;
+
}
}
@@ -1304,6 +1309,7 @@ public class OntologyModifier {
Restriction res = restrictions.get(n[i]);
restrictionsTo.add( res );
}
+
for ( Restriction res : restrictionsTo )
res.remove();
}
@@ -1314,8 +1320,12 @@ public class OntologyModifier {
List<OntProperty> properties = this.modifiedModel.listAllOntProperties().toList();//all properties
List<Individual> individuals = this.modifiedModel.listIndividuals().toList();//all individuals
List<Ontology> ontologies = this.modifiedModel.listOntologies().toList();//all Ontologies
- this.isAlign = true; //the alignment has been computed for the first time
+ this.params = new Properties();
+
+ this.isAlign = true; //the alignment has been computed for the first time
+ this.base = this.namespace;
+
for ( OntClass cls : classes ) //list all classes
if ( cls.getNameSpace().equals( this.namespace ) )
this.params.put( cls.getURI() , cls.getURI() ); //add them to the initial alignment
@@ -1331,68 +1341,63 @@ public class OntologyModifier {
URI onto1 = null;
URI onto2 = null;
- if ( !this.isChanged ) { //if the namespace of the ontology is not changed
- int index = this.namespace.indexOf("#");
- this.namespaceNew = this.namespace.substring(0, index) + "new#";
- //this.namespaceNew = "http://oaei.ontologymatching.org/2010/benchmarks/101/onto1.rdf#";
- }
-
this.alignment = new URIAlignment();
+
try {
- onto1 = new URI ( this.namespace );
- onto2 = new URI ( this.namespaceNew );
- this.alignment.init(onto1, onto2);
- long time = System.currentTimeMillis();
+ onto1 = new URI ( this.base.substring(0, this.base.lastIndexOf("#")) );
+ onto2 = new URI( this.namespaceNew.substring(0, this.namespaceNew.lastIndexOf("#")) );
+ this.alignment.init(onto1, onto2);
+ this.alignment.setFile1(onto1);
+ this.alignment.setFile2(onto2);
+
//Cell addAlignCell(Object ob1, Object ob2, String relation, double measure) throws AlignmentException {
for ( String key : this.params.stringPropertyNames() ) {
String value = this.params.getProperty(key);
- URI uri1 = URI.create( key );
- String newValue = null;
- URI uri2 = URI.create( value );
- if ( value.contains( this.namespace ) ) {
- newValue = value.substring( this.namespace.length() );
- uri2 = URI.create( this.namespaceNew + newValue );
- }
- else {
- newValue = value;
- uri2 = URI.create( newValue );
- }
+ URI uri1 = URI.create(key);
+ URI uri2 = URI.create(this.namespaceNew + value.substring(value.indexOf(this.base) + this.base.length()));
+ //System.out.println( "[" + key + "][" + value + "]" );
this.alignment.addAlignCell( uri1, uri2, "=", 1 );
}
- long newTime = System.currentTimeMillis();
- this.alignment.setExtension( Namespace.ALIGNMENT.uri, Annotations.TIME, Long.toString(newTime - time) );
-
+ /*
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());
}
}
+ public void setNewNamespace(String newNamespace) {
+ this.namespaceNew = newNamespace;
+ //System.out.println("New namespace [" + this.namespaceNew + "]");
+ }
+
//change the namespace of the modified ontology
public OntModel changeNamespace () {
List<Statement> statements = this.modifiedModel.listStatements().toList(); //the statements of the model
- String newNamespace;
-
- int index = this.namespace.indexOf("#");
- newNamespace = this.namespace.substring(0, index) + "new#";
- this.namespaceNew = newNamespace;
+
this.isChanged = true;
- boolean isSubj, isPred, isObj;
+ boolean isSubj, isPred, isObj;;
OntModel newModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );//create new Model
@@ -1401,7 +1406,7 @@ public class OntologyModifier {
Resource subject = stm.getSubject(); //the subject
Property predicate = stm.getPredicate(); //the predicate
RDFNode object = stm.getObject(); //the object
-
+
Resource subj = null;
Property pred = null;
Resource obj = null;
@@ -1411,7 +1416,7 @@ public class OntologyModifier {
if ( subject.getLocalName() != null )
if ( !subject.isLiteral() )
if ( subject.getNameSpace().equals( this.namespace ) ) {
- subj = newModel.createResource( newNamespace + subject.getLocalName() );
+ subj = newModel.createResource( this.namespaceNew + subject.getLocalName() );
isSubj = true;
}
@@ -1419,54 +1424,91 @@ public class OntologyModifier {
if ( object.canAs( Resource.class ) )
if ( object.isURIResource() )
if ( object.asResource().getNameSpace().equals( this.namespace ) ) {
- obj = newModel.createResource( newNamespace + object.asResource().getLocalName() );
+ obj = newModel.createResource( this.namespaceNew + object.asResource().getLocalName() );
isObj = true;
}
if ( !predicate.isLiteral() )
if ( predicate.getNameSpace().equals( this.namespace ) ) {
- pred = newModel.createProperty( newNamespace + predicate.getLocalName() );
+ pred = newModel.createProperty( this.namespaceNew + predicate.getLocalName() );
isPred = true;
}
if ( isSubj ) {
if ( isPred ) {
- if ( isObj ) newModel.add( subj, pred, obj );
- else newModel.add(subj, pred, object);
+ if ( isObj )
+ newModel.add( subj, pred, obj );
+ else
+ newModel.add(subj, pred, object);
}
else {
- if ( isObj ) newModel.add( subj, predicate, obj );
- else newModel.add( subj, predicate, object );
+ if ( isObj )
+ newModel.add( subj, predicate, obj );
+ else
+ newModel.add( subj, predicate, object );
}
} else {
if ( isPred ) {
- if ( isObj ) newModel.add( subject, pred, obj );
- else newModel.add( subject, pred, object );
+ if ( isObj )
+ newModel.add( subject, pred, obj );
+ else
+ newModel.add( subject, pred, object );
}
else {
- if ( isObj ) newModel.add( subject, predicate, obj );
- else newModel.add( subject, predicate, object );
+ if ( isObj )
+ newModel.add( subject, predicate, obj );
+ else
+ newModel.add( subject, predicate, object );
}
}
}
+
//rename the namespace of owl:Ontology
List<Ontology> ontos = newModel.listOntologies().toList();
for ( Ontology o : ontos ) {
- ResourceUtils.renameResource( o, newNamespace );
+ ResourceUtils.renameResource( o, this.namespaceNew );
}
- //this.namespace = newNamespace; //change the namespace
+
return newModel;
}
//returns the modified ontology after changing the namespace
public OntModel getModifiedOntology () {
//System.out.println( "->change namespace" );
- if ( !this.isChanged )
- this.modifiedModel = changeNamespace(); //change the namespace of the modified ontology
+ this.modifiedModel = changeNamespace(); //change the namespace of the modified ontology
//System.out.println( "->namespace changed" );
return this.modifiedModel;
}
+ //set the model
+ public void setModel( OntModel model ) {
+ this.model = model;
+ }
+
+ public void setModifiedModel(OntModel model) {
+ this.modifiedModel = model;
+ }
+
+ //ca ii schimbi namespace-ul, de-asta trebuie sa il intorci pe asta separat
+ public OntModel getModifiedModel() {
+ return this.modifiedModel;
+ }
+
+ //get properties
+ public Properties getProperties() {
+ 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;
@@ -1495,33 +1537,44 @@ public class OntologyModifier {
value = Float.valueOf( this.parameter.getValue() ).floatValue();
else
aux = this.parameter.getValue();
+
if ( !this.isAlign ) {
initializeAlignment(); //determine the elements from the initial reference alignment
}
//add percentage classes
- if ( name.equals( ParametersIds.ADD_SUBCLASS ) ) {
+ if ( name.equals( ParametersIds.ADD_CLASSES ) ) {
System.out.println( "Add Class" + "[" + value + "]");
addSubClasses( value );
- } //remove percentage classes
- if ( name.equals( ParametersIds.REMOVE_SUBCLASS ) ) {
+ }
+
+ //remove percentage classes
+ if ( name.equals( ParametersIds.REMOVE_CLASSES ) ) {
System.out.println( "Remove Class" + "[" + value + "]");
removeSubClasses( value );
- } //remove percentage comments
- if ( name.equals( ParametersIds.REMOVE_COMMENT ) ) {
+ }
+
+ //remove percentage comments
+ if ( name.equals( ParametersIds.REMOVE_COMMENTS ) ) {
System.out.println( "Remove Comments" + "[" + value + "]");
removeComments ( value );
- } //remove percentage properties
- if ( name.equals( ParametersIds.REMOVE_PROPERTY ) ) {
+ }
+
+ //remove percentage properties
+ if ( name.equals( ParametersIds.REMOVE_PROPERTIES ) ) {
System.out.println( "Remove Property" + "[" + value + "]");
removeProperties ( value );
- } //add percentage properties
- if ( name.equals( ParametersIds.ADD_PROPERTY ) ) {
+ }
+
+ //add percentage properties
+ if ( name.equals( ParametersIds.ADD_PROPERTIES ) ) {
System.out.println( "Add Property" + "[" + value + "]");
addProperties ( value );
- } //recursive add nbClasses starting from level level
- if ( name.equals( ParametersIds.ADD_CLASSES ) ) {
+ }
+
+ //recursive add nbClasses starting from level level
+ if ( name.equals( ParametersIds.ADD_CLASSESLEVEL ) ) {
aux = ((Float)value).toString();
int index = aux.indexOf(".");
int level = Integer.valueOf( aux.substring(0, index) );
@@ -1530,40 +1583,59 @@ public class OntologyModifier {
System.out.println( "nbClasses " + nbClasses );
float percentage = 1.00f;
addClasses ( level, nbClasses, percentage );
- } //remove all the classes from the level level
- if ( name.equals( ParametersIds.REMOVE_CLASSES ) ) {
+ }
+
+ //remove all the classes from the level level
+ if ( name.equals( ParametersIds.REMOVE_CLASSESLEVEL ) ) {
System.out.println("Remove all classes from level" + (int)value );
removeClassesFromLevel ( (int)value );
- } //flatten a level
+ }
+
+ //flatten a level
if ( name.equals( ParametersIds.LEVEL_FLATTENED ) ) {
//levelFlattened ( level );
levelFlattened ( (int)value );
System.out.println( "New class hierarchy level " + getMaxLevel() ) ;
- } //rename classes
+ }
+
+ //rename classes
if ( name.equals( ParametersIds.RENAME_CLASSES ) ) {
System.out.println("Rename classes" + "[" + value + "]" );
//System.out.println("\nValue = " + value + "\n"); //activeProperties, activeClasses, ..
this.modifiedModel = renameResource ( false, true, value, true, false, false, 0);
- } //rename properties
+ }
+
+ //rename properties
if ( name.equals( ParametersIds.RENAME_PROPERTIES ) ) {
System.out.println("Rename properties " + "[" + value + "]" );
//System.out.println("\nValue = " + value + "\n"); //activeProperties, activeClasses, ..
this.modifiedModel = renameResource ( true, false, value, true, false, false, 0);
- } //remove percentage restrictions
- if ( name.equals( ParametersIds.REMOVE_RESTRICTION ) ) {
+ }
+
+ //remove percentage restrictions
+ if ( name.equals( ParametersIds.REMOVE_RESTRICTIONS ) ) {
System.out.println("Remove restrictions" + "[" + value + "]");
removeRestrictions( value );
- } //remove percentage individuals
+ }
+
+ //remove percentage individuals
if ( name.equals( ParametersIds.REMOVE_INDIVIDUALS ) ) {
System.out.println("Remove individuals" + "[" + value + "]");
removeIndividuals( value );
- } //no hierarchy
+ }
+
+ //no hierarchy
if ( name.equals( ParametersIds.NO_HIERARCHY ) ) {
System.out.println( "NoHierarchy" );
noHierarchy();
}
+
+ //rebuild the class hierarchy every time
+ this.isBuild = false;
+ this.isChanged = false;
+
}
}
-}
+}
\ No newline at end of file
diff --git a/src/fr/inrialpes/exmo/align/gen/ParametersIds.java b/src/fr/inrialpes/exmo/align/gen/ParametersIds.java
index 77dc8c42..64e94049 100644
--- a/src/fr/inrialpes/exmo/align/gen/ParametersIds.java
+++ b/src/fr/inrialpes/exmo/align/gen/ParametersIds.java
@@ -1,7 +1,7 @@
/*
- * $Id$
+ * $Id: ParametersIds.java
*
- * Copyright (C) 2010, INRIA
+ * Copyright (C) 2003-2010, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -26,19 +26,20 @@
package fr.inrialpes.exmo.align.gen;
public class ParametersIds {
- public static String ADD_SUBCLASS = "addSubClass"; //adds random classes
- public static String REMOVE_SUBCLASS = "removeSubClass"; //removes random classes
- public static String REMOVE_PROPERTY = "removeProperty"; //removes random properties
- public static String REMOVE_COMMENT = "removeComment"; //removes random comments
- public static String LEVEL_FLATTENED = "levelFlattened"; //flattens a level
- public static String ADD_PROPERTY = "addProperty"; //adds random propeties
- public static String REMOVE_CLASSES = "removeClasses"; //remove classes from level
- public static String ADD_CLASSES = "addClasses"; //add c classes beginning from level l -> the value of this parameters should be:
- //beginning_level.number_of_classes_to_add
- public static String RENAME_PROPERTIES="renameProperties"; //renames properties
- public static String RENAME_CLASSES ="renameClasses"; //renames classes
- public static String RENAME_RESOURCES = "renameResources"; //renames properties + classes
- public static String REMOVE_RESTRICTION= "removeRestriction"; //removes restrictions
- public static String REMOVE_INDIVIDUALS= "removeIndividuals"; //removes individuals
- public static String NO_HIERARCHY = "noHierarchy"; //no hierarchy
+ public static String ADD_CLASSES = "addClasses"; //adds random classes
+ public static String REMOVE_CLASSES = "removeClasses"; //removes random classes
+ public static String REMOVE_PROPERTIES = "removeProperties"; //removes random properties
+ public static String REMOVE_COMMENTS = "removeComments"; //removes random comments
+ public static String LEVEL_FLATTENED = "levelFlattened"; //flattens a level
+ public static String ADD_PROPERTIES = "addProperties"; //adds random propeties
+ public static String REMOVE_CLASSESLEVEL= "removeClasses"; //remove classes from level
+ public static String ADD_CLASSESLEVEL = "addClassesLevel"; //add c classes beginning from level l -> the value of this parameters should be:
+ //beginning_level.number_of_classes_to_add
+ public static String RENAME_PROPERTIES = "renameProperties"; //renames properties
+ public static String RENAME_CLASSES = "renameClasses"; //renames classes
+ public static String RENAME_RESOURCES = "renameResources"; //renames properties + classes
+ public static String REMOVE_RESTRICTIONS= "removeRestrictions"; //removes restrictions
+ public static String REMOVE_INDIVIDUALS = "removeIndividuals"; //removes individuals
+ public static String NO_HIERARCHY = "noHierarchy"; //no hierarchy
}
+
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
index 9acbd901..3e88a003 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
@@ -1,7 +1,7 @@
/*
- * $Id$
+ * $Id: TestGenerator.java
*
- * Copyright (C) 2010-2011, INRIA
+ * Copyright (C) 2003-2010, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -38,12 +38,16 @@ import org.semanticweb.owl.align.Alignment;
public class TestGenerator implements AlignedOntologyGenerator {
private Properties parameters; //the set of parameters
+ 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 OntologyModifier modifier = null; //the modifier
+
public TestGenerator() {}
-
+
//returns the modified ontology
public Ontology getModifiedOntology() {
JENAOntology onto = new JENAOntology(); //cast the model into Ontology
@@ -53,17 +57,6 @@ public class TestGenerator implements AlignedOntologyGenerator {
//set the initial ontology
public void setOntology( Ontology o ) {
- try {
- this.model = ((JENAOntology)o).getOntology();
- this.modifiedModel = ((JENAOntology)o).getOntology();
- } catch ( Exception ex ) {
- System.err.println( "Exception " + ex.getMessage() );
- }
- }
-
-
- public Alignment generate(Ontology o, Properties p) {
- //cast the model into a Jena OntModel
if ( o instanceof JENAOntology ) {
this.model = ((JENAOntology)o).getOntology();
this.modifiedModel = ((JENAOntology)o).getOntology();
@@ -72,16 +65,41 @@ public class TestGenerator implements AlignedOntologyGenerator {
System.err.println("Error : The object given is not an OntModel");
System.exit(-1);
}
+ }
+ public void setNamespace(String namespace) {
+ this.namespace = namespace;
+ }
+
+ //return the newNamespace
+ public String getNamespace() {
+ return this.namespace;
+ }
+
+ //set the parameters
+ public void setParameters(Properties p) {
this.parameters = p;
- this.alignment = new URIAlignment();
- OntologyModifier modifier = new OntologyModifier( this.model, this.modifiedModel, this.alignment); //build the ontology modifier for the first time
+ modifier.setProperties(this.parameters);
+ }
+
+ //get the parameters
+ public Properties getParameters() {
+ this.parameters = modifier.getProperties(); //get the properties
+ return this.parameters;
+ }
+
+ //generate the alingnment
+ public Alignment generate(Ontology o, Properties p) {
+ this.params = p;
+ this.alignment = new URIAlignment();
+ modifier = new OntologyModifier( this.model, this.modifiedModel, this.alignment); //build the ontology modifier for the first time
modifier.initializeAlignment(); //initialize the reference alignment
- int level = modifier.getMaxLevel(); //get the max level of the class hierarchy of the ontology
+ //set the new namespace
+ modifier.setNewNamespace( this.namespace );
System.out.println( "[-------------------------------------------------]" );
- for(String key : this.parameters.stringPropertyNames()) {
- String value = this.parameters.getProperty(key); //System.out.println( "[" +key + "] => [" + value + "]");
+ for(String key : this.params.stringPropertyNames()) {
+ String value = this.params.getProperty(key); //System.out.println( "[" +key + "] => [" + value + "]");
//iterate through all the parameters
Parameter param = new Parameter(); //build a parameter
param.setName( key );
@@ -91,10 +109,43 @@ public class TestGenerator implements AlignedOntologyGenerator {
System.out.println( "[-------------------------------------------------]" );
//saves the alignment into the file "referenceAlignment.rdf", null->System.out
- modifier.computeAlignment( "referenceAlignment.rdf" ); //at the end, compute the reference alignment
- this.alignment = modifier.getAlignment(); //get the reference alignment
- this.modifiedModel = modifier.getModifiedOntology(); //get the modified ontology
+ 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;
}
-}
+
+
+ //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
+ //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 + "]");
+ //iterate through all the parameters
+ Parameter param = new Parameter(); //build a parameter
+ param.setName( key );
+ param.setValue( value );
+ modifier.modifyOntology( param ); //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;
+ }
+
+
+}
\ No newline at end of file
diff --git a/src/fr/inrialpes/exmo/align/gen/URITree.java b/src/fr/inrialpes/exmo/align/gen/URITree.java
index d69a9f49..9f055441 100644
--- a/src/fr/inrialpes/exmo/align/gen/URITree.java
+++ b/src/fr/inrialpes/exmo/align/gen/URITree.java
@@ -1,7 +1,7 @@
/*
- * $Id$
+ * $Id: URITree.java
*
- * Copyright (C) 2011, INRIA
+ * Copyright (C) 2003-2010, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -35,7 +35,7 @@ public class URITree {
private URITree parent; //the parent of the node
int depth; //the depth of the node
int maxDepth; //the max depth of the node
-
+
public URITree(String URI) {
this.URI = URI;
this.children = new ArrayList<URITree>();
@@ -48,47 +48,47 @@ public class URITree {
public String getURI () {
return this.URI;
}
-
+
//set the URI of the node
public void setURI(String URI) {
this.URI = URI;
}
-
+
//set the depth of the node
public void setDepth (int depth) {
this.depth = depth;
}
-
+
//get the depth of the node
public int getDepth() {
return this.depth;
}
-
+
//return the max depth
public int getMaxDepth() {
return this.maxDepth;
}
-
+
//set the parent of the node
public void setParent ( URITree parent ) {
this.parent = parent;
}
-
+
//get the parent of the node
public URITree getParent () {
return this.parent;
}
-
+
//returns a child from a specific position
public URITree getChildAt ( int index ) {
return this.children.get( index );
}
-
+
//return the list of children nodes
public ArrayList<URITree> getChildrenList() {
return this.children;
}
-
+
//returns the size of the children
public int getChildrenSize() {
return this.children.size();
@@ -96,7 +96,7 @@ public class URITree {
//add the node with the childURI to the parent with the URI parentURI
public void add(URITree root, String childURI, String parentURI) {
- //adds the node to the class hierarchy -> a class might have more than one
+ //adds the node to the class hierarchy -> a class might have more than one
//superclass we have to add it to each superclass in part, not only to one
_addChildToNode( root, parentURI, childURI );
}
@@ -105,7 +105,7 @@ public class URITree {
public void addChild (URITree root, URITree node, String URI) {
int index = 0;
URITree n = null;
-
+
while ( index < node.getChildrenSize() ) { //if the child is already in the list
if ( node.getChildAt( index ).getURI().equals( URI ) )
return;
@@ -123,15 +123,15 @@ public class URITree {
}
addChildToNode( node, URI );
}
-
+
//add child to a specific node
public void addChildToNode(URITree node, String URI) {
URITree child = new URITree( URI ); //creates a new node
child.setDepth( node.getDepth() + 1 ); //set the depth of the node
-
+
if ( this.maxDepth < node.getDepth()+1 ) //keeps track of the max depth of the hierarchy
this.maxDepth = node.getDepth() + 1;
-
+
child.setParent( node ); //sets the parent of the node
node.getChildrenList().add( child ); //adds the node to the parent children list
}
@@ -223,10 +223,10 @@ public class URITree {
int index = 0;
URITree node = root;
URITree ans = null;
-
+
if ( root.getURI().equals( URI ) ) //if the root has the URI as the URI searched
return root;
-
+
while ( index < root.getChildrenSize() ) { //we start to search recursively
if ( root.getChildAt( index ).getURI().equals( URI ) )
return root.getChildAt( index ); //we found the node with the given URI
@@ -271,12 +271,12 @@ public class URITree {
root.getChildrenList().remove( index ); //found the node to delete
//return;
}
-
+
remove(root.getChildAt( index ), new ArrayList(), 0, URI);
index++;
}
}
-
+
@SuppressWarnings("unchecked")
public void remove(URITree node, List occurs, int depth, String URI) {
int index = 0;
@@ -292,10 +292,10 @@ public class URITree {
child.setParent( parent ); //modify the parent
parent.getChildrenList().add( child ); //add the child to the parent of node
cnt++;
- }
+ }
parent.getChildrenList().remove( node ); //remove the node from the children list
}
-
+
while( index < node.getChildrenSize()) {
URITree n = node.getChildAt( index );
occurs.add( node );
@@ -334,7 +334,7 @@ public class URITree {
index++;
}
}
-
+
//change the depth if the nodes lower the level to node.getDepth()-1
@SuppressWarnings("unchecked")
public void changeDepth (URITree root, int level) {
@@ -349,12 +349,12 @@ public class URITree {
@SuppressWarnings("unchecked")
public void change (URITree node, List occurs, int depth, int level) {
int index = 0;
-
+
if ( node.getDepth() > level ) { //if it's on the level that we want, we add it to the hierarchy
int dept = node.getDepth();
node.setDepth( dept-1 );
}
-
+
while( index < node.getChildrenList().size() ) {
URITree n = node.getChildrenList().get(index);
occurs.add( node );
@@ -363,13 +363,13 @@ public class URITree {
index++;
}
}
-
+
//print the tree
@SuppressWarnings("unchecked")
public void printURITree( URITree root ) {
int index = 0;
//System.out.println( "[" + root.getURI() + "]" + "->" + root.getDepth() );
-
+
while ( index < root.getChildrenList().size() ) {
//recursively print all the children URITrees
print(root.getChildAt(index), new ArrayList(), 0);
@@ -382,7 +382,7 @@ public class URITree {
int index = 0;
indent( node.getDepth() );
System.out.println( "[" + node.getURI() + "]" + "->" + node.getDepth() );
-
+
while( index < node.getChildrenList().size() ) {
URITree n = node.getChildrenList().get( index );
occurs.add( node );
@@ -397,8 +397,7 @@ public class URITree {
System.out.print( " " );
}
}
-
+
}
-
--
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