diff --git a/src/fr/inrialpes/exmo/align/gen/Alterator.java b/src/fr/inrialpes/exmo/align/gen/Alterator.java
new file mode 100644
index 0000000000000000000000000000000000000000..b9b3d9762ddf04ec0fbbcf720041e693a48efccd
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/Alterator.java
@@ -0,0 +1,85 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen;
+
+import java.util.Properties;
+
+import org.semanticweb.owl.align.Alignment;
+
+import com.hp.hpl.jena.ontology.OntModel;
+
+/**
+ * An abstract test generator which takes as input an ontology and an
+ * alignment between this ontology and another one and transform the
+ * ontology and the alignment accordingly to a type of alteration.
+ *
+ * It follows a particular lifecycle
+ */
+public interface Alterator {
+
+ /**
+ * It is created either:
+ * - from a seed ontology and generate the alignment between this
+ * ontology itself
+ * - from a previous alterator from which it will take the output
+ * ontology and alignment as input.
+ */
+ //public Alterator( Alterator om );
+
+ /**
+ * the namespace of the input ontology
+ */
+ public String getNamespace();
+ /**
+ * the namespace of the source ontology in the input alignment
+ */
+ public String getBase();
+
+ /**
+ * modify applies the alteration to the input (the results are kept in
+ * internal structures.
+ */
+ public Alterator modify( Properties params );
+
+ // Temporary
+ /**
+ * getProtoAlignment, getProtoOntology, getHierarchy
+ * are used for accessing these internal structure at creation time.
+ */
+ public Properties getProtoAlignment();
+ public OntModel getProtoOntology();
+ public ClassHierarchy getHierarchy();
+
+ /**
+ * Modifies the namespaces of source and target ontologies
+ * (for the main purpose of outputing them)
+ */
+ public void relocateTest( String namespace1, String namespace2 );
+ public void relocateTest( String namespace2 );
+
+ /**
+ * Returns the altered Alignment and Ontology in output form
+ */
+ public Alignment getAlignment();
+ public OntModel getModifiedOntology();
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java b/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..1ee58eae25f7486c5d86a087ae229e69939131ba
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java
@@ -0,0 +1,159 @@
+/**
+ * $Id$
+ *
+ * Copyright (C) INRIA, 2011
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 2.1 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+package fr.inrialpes.exmo.align.gen;
+
+import java.util.Map;
+import java.util.HashMap;
+import java.util.Properties;
+
+import java.lang.reflect.InvocationTargetException;
+
+public class AlteratorFactory {
+
+ // The parameter Ids should be here
+ //public static final int ANY = 0;
+
+ // This should be largely improved with precedence
+ private static Map<String,String> alterators = null;
+
+ public static Alterator newInstance( String id, Alterator om ) {
+ if ( alterators == null ) init();
+ String classname = alterators.get( id );
+ Alterator alt = null;
+ if ( classname != null ) {
+ try {
+ // This should also be a static getInstance!
+ Class<?> altClass = Class.forName(classname);
+ Class[] cparams = {Class.forName("fr.inrialpes.exmo.align.gen.Alterator")};
+ java.lang.reflect.Constructor altConstructor = altClass.getConstructor(cparams);
+ Object[] mparams = { om };
+ alt = (Alterator)altConstructor.newInstance(mparams);
+ } catch (ClassNotFoundException cnfex ) {
+ cnfex.printStackTrace(); // better raise errors
+ } catch (NoSuchMethodException nsmex) {
+ nsmex.printStackTrace();
+ } catch (InstantiationException ieex) {
+ ieex.printStackTrace();
+ } catch (IllegalAccessException iaex) {
+ iaex.printStackTrace();
+ } catch (InvocationTargetException itex) {
+ itex.printStackTrace();
+ }
+ }
+ return alt;
+ }
+
+ public static void init() {
+ alterators = new HashMap<String, String>();
+ alterators.put( ParametersIds.REMOVE_CLASSES, "fr.inrialpes.exmo.align.gen.alt.RemoveClasses" );
+ alterators.put( ParametersIds.REMOVE_PROPERTIES, "fr.inrialpes.exmo.align.gen.alt.RemoveProperties" );
+ alterators.put( ParametersIds.REMOVE_RESTRICTIONS, "fr.inrialpes.exmo.align.gen.alt.RemoveRestrictions" );
+ alterators.put( ParametersIds.REMOVE_COMMENTS, "fr.inrialpes.exmo.align.gen.alt.RemoveComments" );
+ alterators.put( ParametersIds.RENAME_CLASSES, "fr.inrialpes.exmo.align.gen.alt.RenameClasses" );
+ alterators.put( ParametersIds.RENAME_PROPERTIES, "fr.inrialpes.exmo.align.gen.alt.RenameProperties" );
+ alterators.put( ParametersIds.REMOVE_INDIVIDUALS, "fr.inrialpes.exmo.align.gen.alt.RemoveIndividuals" );
+ alterators.put( ParametersIds.REMOVE_CLASSESLEVEL, "fr.inrialpes.exmo.align.gen.alt.RemoveClassLevel" );
+ alterators.put( ParametersIds.LEVEL_FLATTENED, "fr.inrialpes.exmo.align.gen.alt.FlattenLevel" );
+ alterators.put( ParametersIds.ADD_CLASSES, "fr.inrialpes.exmo.align.gen.alt.AddClasses" );
+ alterators.put( ParametersIds.ADD_PROPERTIES, "fr.inrialpes.exmo.align.gen.alt.AddProperties" );
+ alterators.put( ParametersIds.ADD_CLASSESLEVEL, "fr.inrialpes.exmo.align.gen.alt.AddClassLevel" );
+ alterators.put( ParametersIds.NO_HIERARCHY, "fr.inrialpes.exmo.align.gen.alt.SuppressHierarchy" );
+ //alterators.put( , "fr.inrialpes.exmo.align.gen.alt." );
+ //alterators.put( , "fr.inrialpes.exmo.align.gen.alt." );
+ //alterators.put( , "fr.inrialpes.exmo.align.gen.alt." );
+ }
+
+ public static void declareAlterator( String id, String classname ) {
+ if ( alterators == null ) init();
+ alterators.put( id, classname );
+ }
+
+ // I should add a run primitive
+ // which executes all the parameters in the given order
+ public static Alterator cascadeAlterators( Alterator init, Properties params ) {
+ Alterator modifier = init;
+ // JE: Of course, this could be improved (at least be rendered generic)
+ if ( params.getProperty( ParametersIds.REMOVE_CLASSES ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.REMOVE_CLASSES, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.REMOVE_PROPERTIES ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.REMOVE_PROPERTIES, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.REMOVE_RESTRICTIONS ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.REMOVE_RESTRICTIONS, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.REMOVE_COMMENTS ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.REMOVE_COMMENTS, modifier );
+ modifier.modify( params );
+ }
+
+ if ( params.getProperty( ParametersIds.RENAME_CLASSES ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.RENAME_CLASSES, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.RENAME_PROPERTIES ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.RENAME_PROPERTIES, modifier );
+ modifier.modify( params );
+ }
+ // UNTIL HERE, WE USE THE DOCUMENTED ORDER
+
+ if ( params.getProperty( ParametersIds.REMOVE_INDIVIDUALS ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.REMOVE_INDIVIDUALS, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.REMOVE_CLASSESLEVEL ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.REMOVE_CLASSESLEVEL, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.LEVEL_FLATTENED ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.LEVEL_FLATTENED, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.ADD_CLASSES ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.ADD_CLASSES, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.ADD_PROPERTIES ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.ADD_PROPERTIES, modifier );
+ modifier.modify( params );
+ }
+
+ if ( params.getProperty( ParametersIds.ADD_CLASSESLEVEL ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.ADD_CLASSESLEVEL, modifier );
+ modifier.modify( params );
+ }
+ if ( params.getProperty( ParametersIds.NO_HIERARCHY ) != null ) {
+ modifier = AlteratorFactory.newInstance( ParametersIds.NO_HIERARCHY, modifier );
+ modifier.modify( params );
+ }
+ /*
+ 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
+ }
+ */
+ return modifier;
+ }
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java b/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
index 264bcdf77d95006f54a29429d924e5fa07545406..f35d59358870b9cda20361b9f72123cd00b04751 100644
--- a/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
@@ -105,14 +105,16 @@ public class BenchmarkGenerator extends TestSet {
addTestChild( "250"+SUFFIX, "261"+SUFFIX,
newProperties( ParametersIds.ADD_CLASSES, FULL ) );
/* 266-x *** no names + no comments + no property + expand + no instance */
- addTestChild( "261"+SUFFIX, "266"+SUFFIX,
- newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
+ // This would generate graded 266 (which is nice, but not in bench)
+ //addTestChild( "261"+SUFFIX, "266"+SUFFIX,
+ // newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
/* 260-x *** no names + no comments + no property + flatten */
addTestChild( "250"+SUFFIX, "260"+SUFFIX,
newProperties( ParametersIds.LEVEL_FLATTENED, "2" ) );
/* 265-x *** no names + no comments + no property + flatten + no instance */
- addTestChild( "260"+SUFFIX, "265"+SUFFIX,
- newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
+ // This would generate graded 266 (which is nice, but not in bench)
+ //addTestChild( "260"+SUFFIX, "265"+SUFFIX,
+ // newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
/* 251-x *** no names + no comments + flatten */
addTestChild( "202"+SUFFIX, "251"+SUFFIX,
newProperties( ParametersIds.LEVEL_FLATTENED, "2" ) );
@@ -126,9 +128,22 @@ public class BenchmarkGenerator extends TestSet {
addTestChild( "252"+SUFFIX, "259"+SUFFIX,
newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
}
+ /* 203 *** no comments */
+ //Too easy
+ //addTestChild( "101", "203",
+ // newProperties( ParametersIds.REMOVE_COMMENTS, FULL ) );
+ /* 204 *** naming convention */
+ /* 205 *** synonyms */
+ /* 207 *** translation (classes) */
+ /* 206 *** translation (classes and properties) */
+ /* 208 *** naming convention + no comments */
+ /* 209 *** synonyms + no comments */
+ /* 210 *** translation + no comments */
/* 221 *** no hierarchy */
addTestChild( "101", "221",
newProperties( ParametersIds.NO_HIERARCHY, ParametersIds.NO_HIERARCHY ) );
+ /* 230 *** flattened classes */
+ /* 231 *** expanded classes */
/* 232 *** no hierarchy + no instance */
addTestChild( "221", "232",
newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
@@ -174,6 +189,13 @@ public class BenchmarkGenerator extends TestSet {
/* 246 *** no property + flatten + no instance */
addTestChild( "239", "246",
newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
+ /* 265-x *** no names + no comments + no property + flatten + no instance */
+ // Warning: For this to work, the suffix should be the more difficult test
+ addTestChild( "260"+SUFFIX, "265",
+ newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
+ /* 266-x *** no names + no comments + no property + expand + no instance */
+ addTestChild( "261"+SUFFIX, "266",
+ newProperties( ParametersIds.REMOVE_INDIVIDUALS, FULL ) );
}
/*
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
deleted file mode 100644
index e74514dcefd3cdfa7281d3262d130e99a2b94d07..0000000000000000000000000000000000000000
--- a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
+++ /dev/null
@@ -1,1615 +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.
- */
-
-/* This program receives as input two ontologies (the original ontology, the ontology that must be modified),
- an alignment and a parameter with the modification that must be applied to the input ontology.
- After the modification of the initial ontology the alignment must be computed
- The file in which we store the alignment is "referenceAlignment.rdf"
-*/
-
-/* This program receives as input two ontologies (the original ontology, the ontology that must be modified),
- an alignment and a parameter with the modification that must be applied to the input ontology.
- After the modification of the initial ontology the alignment must be computed
- The file in which we store the alignment is "referenceAlignment.rdf"
-*/
-
-package fr.inrialpes.exmo.align.gen;
-
-//Java classes
-import java.net.URI;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-import java.util.Random;
-
-//Alignment API classes
-import org.semanticweb.owl.align.Alignment;
-import org.semanticweb.owl.align.AlignmentException;
-
-//Google API classes
-import com.google.api.GoogleAPI;
-import com.google.api.translate.Language;
-import com.google.api.translate.Translate;
-
-//JENA classes
-import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
-import com.hp.hpl.jena.ontology.DatatypeProperty;
-import com.hp.hpl.jena.ontology.Individual;
-import com.hp.hpl.jena.ontology.ObjectProperty;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntClass;
-import com.hp.hpl.jena.ontology.OntModelSpec;
-import com.hp.hpl.jena.ontology.OntProperty;
-import com.hp.hpl.jena.ontology.OntResource;
-import com.hp.hpl.jena.ontology.Ontology;
-import com.hp.hpl.jena.ontology.Restriction;
-import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
-import com.hp.hpl.jena.ontology.UnionClass;
-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.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.util.ResourceUtils;
-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;
-import edu.smu.tspell.wordnet.WordNetDatabase;
-*/
-
-//activeRandomString is true -> we replace the label with a random string
-//activeTranslateString is true -> we translate the label
-
-public class OntologyModifier {
- private boolean debug = false;
-
- private ClassHierarchy classHierarchy; //the class hierarchy
- private OntModel modifiedModel; //the modified Ontology
- private Properties alignment; //the alignment
-
- private String namespace; //the Namespace
- private String namespaceNew;
-
- private boolean isBuild = false; //keep track if the class hierarchy is build
- private boolean isAlign = false; //keep track if the initial alignment has already been computed
- private boolean isChanged = false; //keep track if the namespace of the new ontology is changed
- private String base; //
-
- // -------------------------
- // Constructors
- //Ontology init, Ontology modified, Alignment align
- // JE: Here the alignment is useless... it is used only if nothing is computed!
- public OntologyModifier ( OntModel model, Alignment al ) {
- modifiedModel = model;
- // get the default namespace of the model
- namespace = model.getNsPrefixURI("");
- alignment = new Properties();
- }
-
- // -------------------------
- // Accessors
-
- public void setDebug( boolean d ) {
- debug = d;
- }
-
- public void setNewNamespace( String newNamespace ) {
- namespaceNew = newNamespace;
- //if ( debug ) System.err.println("New namespace [" + this.namespaceNew + "]");
- }
-
- //returns the modified ontology after changing the namespace
- public OntModel getModifiedOntology () {
- //if ( debug ) System.err.println( "->change namespace" );
- modifiedModel = changeNamespace(); //change the namespace of the modified ontology
- //if ( debug ) System.err.println( "->namespace changed" );
- return modifiedModel;
- }
-
- public void setModifiedModel(OntModel model) {
- modifiedModel = model;
- }
-
- public OntModel getModifiedModel() {
- return modifiedModel;
- }
-
- //get properties
- public Properties getProperties() {
- return alignment;
- }
-
- // -------------------------
- // Utility (string) functions
-
- //generates a random string with the length "length"
- public String getRandomString() {
- Random generator = new Random();
- String characters = "abcdefghijklmnopqrstuvwxyz";
- int length = characters.length();
- char[] text = new char[length];
- for (int i = 0; i < length; i++) {
- text[i] = characters.charAt( generator.nextInt(length) );
- }
- return new String(text); // JE suppressed toUpperCase()
- }
-
- //removes spaces from a string
- public String removeSpaces ( String str ) {
- //return str.replaceAll("\\s+", "");
- if ( !str.contains( " " ) )
- return str;
- else {
- String aux = "", aux1="";
- int index;
-
- if ( str.contains( " " ) ) {
- while ( str.indexOf( " " ) != -1 ) {
- index = str.indexOf( " " );
- aux += str.substring( 0, index );
- aux1 = str.substring(index+2);
- str = str.substring(index+1, index+2).toUpperCase().concat( aux1 );
- }
- aux += str;
- return aux;
- }
- }
- return str;
- }
-
- //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/");
- //Translate.setHttpReferrer("http://code.google.com/p/google-api-translate-java/");
- try {
- translatedText = Translate.execute(source, Language.ENGLISH, Language.FRENCH);
- } catch (Exception e) {
- System.err.println( "Exception " + e.getMessage() );
- }
- return removeSpaces ( translatedText );
- }
-
- //string to upperCase
- public String toUpperCase ( String source ) {
- return source.toUpperCase();
- }
-
- //string to lowerCase
- public String toLowerCase ( String source ) {
- return source.toLowerCase();
- }
-
- public String getSynonym( String source ) {
- return source;
- }
- /*
- //synonym of the word
- public String getSynonym ( String source ) {
- String synonym = "";
- //set this variable according to your WordNet installation folder
- //see : http://lyle.smu.edu/~tspell/jaws/index.html
- System.setProperty("wordnet.database.dir", "/usr/Wordnet/WordNet-3.0/dict");
- WordNetDatabase database = WordNetDatabase.getFileInstance();
- Synset[] synsets = database.getSynsets( source );
- if (synsets.length > 0) {
- for (int i = 0; i < synsets.length; i++) {
- String[] wordForms = synsets[i].getWordForms();
- for (int j = 0; j < wordForms.length; j++) {
- if ( !wordForms[j].equals( source ) ) {
- synonym = removeSpaces ( wordForms[j] );
- return synonym;
- }
- }
- }
- }
- else
- return source;
- return source;
- }
- */
-
- public String parseString (String str, boolean activeTranslateString, boolean activeSynonym) {
- // if ( debug ) System.err.println ( "str = [" + str + "]" );
- char [] parsed = str.toCharArray();
- String newString = "";
-
- for ( int i=1; i<parsed.length; i++ ) {
- if( Character.isUpperCase( parsed[i] ) ) {
- String aux = str.substring(0, i);
-
- if ( activeTranslateString )
- newString = newString.concat( translateString( str.substring(0, i) ) );
- if ( activeSynonym )
- newString = newString.concat( getSynonym( str.substring(0, i) ) );
-
- str = str.substring(i);
- }
- }
-
- if ( activeTranslateString )
- newString = newString.concat( translateString(str.substring(0)) );
- if ( activeSynonym )
- newString = newString.concat( getSynonym(str.substring(0)) );
- return newString;
- }
-
- // -------------------------
- // Utility (randomizing) functions
-
- //count - the number of elements from the vector
- //the random numElems that must be selected
- //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];
- int aux, rand;
- Random generator = new Random();
-
- for ( int i=0; i<count; i++ ) //fill the array with sorted elements
- vect[i] = i;
- for ( int j=0; j<numElems; j++ ) {
- rand = generator.nextInt( count-j ); //choose a random number from the interval
- n[j] = vect[rand]; //build the new vector
- aux = vect[rand]; //swap
- vect[rand] = vect[count-j-1];
- vect[count-j-1] = aux;
- }
- return n;
- }
-
- // -------------------------
- // Label replacement
-
- //replaces the label of the property
- public void replacePropertyLabel( String uri, String newLabel, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation ) {
- OntProperty prop = modifiedModel.getOntProperty( uri );
- if ( prop.getLabel( "en" ) != null ) {
- if ( activeTranslateString ) {
- prop.setLabel( newLabel, "fr" );
- } else {
- prop.setLabel( newLabel, "en" );
- }
- }
- }
-
- //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<String> propertiesName = new ArrayList<String>(); //the properties identifiers
-
- 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 : properties ) {
- String uri = base + p.getLocalName();
- // JE: I am affraid that alignment is a terible thing here
- if ( alignment.containsKey( uri ) ) {
- String key = uri;
- String value = alignment.getProperty( key );
- if ( key.equals( value ) )
- notRenamedProperties.add( p ); //add the property to not renamed properties
- }
- }
-
-
- nbProperties = properties.size(); //the number of renamed properties
- renamedProperties = nbProperties - notRenamedProperties.size();
- toBeRenamed = (int)(percentage*nbProperties) - renamedProperties; // -renamedProperties -> for Benchmark
-
- // JE: same thing as for classes... but strange
- // JE: should be the symptom of a bug
- if ( toBeRenamed < 0 ) toBeRenamed = 0;
- //builds the list of properties to be renamed
- int [] n = randNumbers(notRenamedProperties.size(), toBeRenamed);
- for ( int i=0; i<toBeRenamed; i++ ) {
- OntProperty p = notRenamedProperties.get(n[i]);
- propertiesTo.add(p);
- if ( p.getNameSpace().equals( namespace ) )
- propertiesName.add( p.getLocalName() );
- }
-
- for ( OntProperty prop : propertiesTo ) {
- String nameSpace = prop.getNameSpace();
- String localName = prop.getLocalName();
- //has the same Namespace as the Ontology Namespace
- if ( nameSpace.equals( namespace ) ) {
- if ( !propertiesIdentifiers.containsKey( localName ) ) {
- if ( activeTranslateString ) { //replace the URI with the translated one
- String translateStrg = parseString ( localName, true, false);
- propertiesIdentifiers.put( localName , translateStrg );
- replacePropertyLabel( prop.getURI(), translateStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
-
- if ( alignment.containsKey( base + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
- alignment.put( base + prop.getLocalName() , 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 ( alignment.containsKey( base + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
- alignment.put( base + prop.getLocalName() , base + newStrg);//the reference alignment
- }
- }
- else if ( activeSynonym ) {
- String synonym = parseString (localName, false, true);
- if ( propertiesName.contains( synonym ) )
- propertiesIdentifiers.put( localName, localName );
- else {
- propertiesIdentifiers.put( localName, synonym );
- replacePropertyLabel( prop.getURI(), synonym, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( alignment.containsKey( this.base + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
- alignment.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 ( alignment.containsKey( this.base + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
- alignment.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 ( alignment.containsKey( this.base + prop.getLocalName() ) ) { // alignment.remove( prop.getURI() );
- alignment.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 ( alignment.containsKey( this.base + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
- alignment.put( this.base + prop.getLocalName() , this.base + localName + "PROPERTY" );
- }
- }
- }
- }
- }
- return propertiesIdentifiers;
- }
-
- //replaces the label of the class
- public void replaceClassLabel( String uri, String newLabel, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation ) {
- OntClass c = modifiedModel.getOntClass( uri );
-
- if ( c.getLabel( "en" ) != null ) {
- if ( activeTranslateString ) {
- c.setLabel( newLabel, "fr" );
- } else
- c.setLabel( newLabel, "en" );
- }
- }
-
- //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
-
- int nbClasses, toBeRenamed, renamedClasses;
-
- List<OntClass> notRenamedClasses = new ArrayList<OntClass>(); //the list of not renamed classes
- List<OntClass> classes = getOntologyClasses(); //the list of ontology classes
- List<OntClass> classesTo = new ArrayList<OntClass>(); //the list of classes to be renamed
-
- // alignment contains those classes which have already been renamed
- //builds the list of all unrenamed classes from the model
- for ( OntClass c : classes ) {
- String uri = base + c.getLocalName();
- //gets the pair <key, value>
- if ( alignment.containsKey( uri ) ) {
- String key = uri;
- String value = alignment.getProperty( uri );
- //they didnt change
- if ( key.equals( value ) )
- notRenamedClasses.add( c ); //add the class to not renamed classes
- }
- }
-
- nbClasses = classes.size();
- renamedClasses = nbClasses - notRenamedClasses.size(); //the number of renamed classes
- toBeRenamed = (int)(percentage*nbClasses) - renamedClasses; // -renamedClasses -> for Benchmark
- // JE: toBeRenamed is negative when classes have been added to the model!
- // JE TOCHECK IF THIS IS STILL CORRECT
- if ( toBeRenamed < 0 ) toBeRenamed = 0;
- //build the list of classes to be renamed
- int[] n = randNumbers( notRenamedClasses.size(), toBeRenamed );
- for ( int i=0; i<toBeRenamed; i++ ) {
- OntClass cls = notRenamedClasses.get(n[i]);
- classesTo.add(cls);
- }
-
- for ( OntClass cls : classesTo ) {
- if ( !cls.isRestriction() ) {
- if ( !cls.isAnon() ) {
- String nameSpace = cls.getNameSpace();
- String localName = cls.getLocalName();
-
- //has the same Namespace as the Ontology Namespace
- if ( nameSpace.equals( namespace ) ) {
- if ( !classesIdentifiers.containsKey( localName ) ) {
- if ( activeTranslateString ) { //replace the URI with the translated one
- String translateStrg = parseString (localName, true, false);
- classesIdentifiers.put( localName , translateStrg );
- replaceClassLabel( cls.getURI(), translateStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( alignment.containsKey( this.base + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
- alignment.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 ( alignment.containsKey( this.base + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
- alignment.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 ( alignment.containsKey( this.base + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
- alignment.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 ( alignment.containsKey( this.base + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
- alignment.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 ( alignment.containsKey( this.base + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
- alignment.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 ( alignment.containsKey( this.base + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
- alignment.put( this.base + cls.getLocalName() , this.base + localName + "CLASS" );
- }
- }
- }
- }
- }
- }
- }
- return classesIdentifiers;
- }
-
- //renames percentage properties and classes
- //activeProperties -> if true, then rename properties
- //activeClasses -> if true, then rename classes
- public OntModel renameResource ( boolean activeProperties, boolean activeClasses, float percentage, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation) {
- 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
-
- OntModel newModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );//create new Model
- //get properties and classes identifiers
- if ( activeProperties )
- propertiesIdentifiers = getPropertiesIdentifiers( percentage, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation);
- if ( activeClasses )
- classesIdentifiers = getClassesIdentifiers( percentage, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
-
- //iterate and modify the identifiers
- for ( Statement stm : modifiedModel.listStatements().toList() ) {
-
- Resource subject = stm.getSubject(); //the subject
- Property predicate = stm.getPredicate(); //the predicate
- RDFNode object = stm.getObject(); //the object
-
- String subjectLocalName, subjectNameSpace;
- String predicateLocalName, predicateNameSpace;
- String objectLocalName, objectNameSpace;
-
- boolean isPred, isSubj, isObj;
-
- 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 ) {
- if ( propertiesIdentifiers.containsKey( subject.getLocalName() ) ) {
- //if the namespace of the subject is the same as the namespace of the property identifier
- if ( subject.getNameSpace().equals( namespace ) ) {//that we want to remove
- isSubj = true;
- subjectNameSpace = subject.getNameSpace();
- subjectLocalName = subject.getLocalName();
- subj = newModel.createResource( subjectNameSpace + propertiesIdentifiers.get( subjectLocalName ) );
- }
- }
- }
-
- if ( activeClasses ) {
- if ( classesIdentifiers.containsKey( subject.getLocalName() ) ) {
- //if the namespace of the subject is the same as the namespace of the property identifier
- //that we want to remove
- if (subject.getNameSpace().equals( namespace ) ) {
- isSubj = true;
- subjectNameSpace = subject.getNameSpace();
- subjectLocalName = subject.getLocalName();
- subj = newModel.createResource( subjectNameSpace + classesIdentifiers.get( subjectLocalName ) );
- }
- }
- }
- }
-
- //if it is the predicate of the statement
- if ( activeProperties ) {
- if ( propertiesIdentifiers.containsKey( predicate.getLocalName() ) ) {
- //if the namespace of the predicate is the same as the namespace of the property identifier
- //that we want to remove
- if ( predicate.getNameSpace().equals( this.namespace ) ) {
- isPred = true;
- predicateNameSpace = predicate.getNameSpace();
- predicateLocalName = predicate.getLocalName();
- pred = newModel.createProperty(predicateNameSpace, propertiesIdentifiers.get( predicateLocalName ) );
- }
- }
- }
-
- if ( activeClasses ) {
- if ( classesIdentifiers.containsKey( predicate.getLocalName() ) ) {
- //if the namespace of the predicate is the same as the namespace of the property identifier
- //that we want to remove
- if ( predicate.getNameSpace().equals( this.namespace ) ) {
- isPred = true;
- predicateNameSpace = predicate.getNameSpace();
- predicateLocalName = predicate.getLocalName();
- pred = newModel.createProperty(predicateNameSpace, classesIdentifiers.get( predicateLocalName ) );
- }
- }
- }
-
- //if it is the object of the statement
- if ( object.canAs( Resource.class ) )
- if ( object.isURIResource() ) {
- if ( activeProperties ) {
- if ( propertiesIdentifiers.containsKey( object.asResource().getLocalName() ) ) {
- //if the namespace of the object is the same as the namespace of the property identifier
- //that we want to remove
- if ( object.asResource().getNameSpace().equals( this.namespace ) ) {
- isObj = true;
- objectNameSpace = object.asResource().getNameSpace();
- objectLocalName = object.asResource().getLocalName();
- obj = newModel.createResource(objectNameSpace + propertiesIdentifiers.get( objectLocalName ) );
- }
- }
- }
-
- if ( activeClasses ) {
- if ( classesIdentifiers.containsKey( object.asResource().getLocalName() ) ) {
- //if the namespace of the object is the same as the namespace of the property identifier that we want to remove
- if ( object.asResource().getNameSpace().equals( this.namespace ) ) {
- isObj = true;
- objectNameSpace = object.asResource().getNameSpace();
- objectLocalName = object.asResource().getLocalName();
- obj = newModel.createResource(objectNameSpace + classesIdentifiers.get( objectLocalName ) );
- }
- }
- }
- }
-
- if ( isSubj ) {
- if ( isPred ) {
- 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 );
- }
- } else {
- if ( isPred ) {
- 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 ( activeClasses ) {
- checkClassHierarchy();
- //we update the class hierarchy according to the new modifications
- this.classHierarchy.updateClassHierarchy( alignment ); //this.classHierarchy.printClassHierarchy();
- }
- return newModel;
- }
-
- // -------------------------
- // Class hierarchy utilities
-
- //must have the max level of the class hierarchy
- public int getMaxLevel() {
- checkClassHierarchy(); //check if the class hierarchy is built
- return this.classHierarchy.getMaxLevel();
- }
-
- //if we add / remove a class we need to keep track of the class hierarchy
- public void buildClassHierarchy () {
- classHierarchy = new ClassHierarchy();
- classHierarchy.buildClassHierarchy( modifiedModel );
- //classHierarchy.printClassHierarchy();
- }
-
- //check if the class hierarchy is build
- public void checkClassHierarchy() {
- if ( !this.isBuild ) {
- buildClassHierarchy();
- this.isBuild = true;
- }
- }
-
- //gets the Ontology classes
- @SuppressWarnings("unchecked")
- public List<OntClass> getOntologyClasses () {
- List<OntClass> classes = new ArrayList<OntClass>();
- for ( Iterator it = modifiedModel.listNamedClasses(); it.hasNext(); ) {
- OntClass aux = (OntClass)it.next();
- if ( ( aux ).getNameSpace().equals( this.namespace ) ) {
- classes.add( aux );
- }
- }
- return classes;
- }
-
- //gets the Ontology properties
- @SuppressWarnings("unchecked")
- public List<OntProperty> getOntologyProperties () {
- List<OntProperty> properties = new ArrayList<OntProperty>();
- for ( Iterator it = modifiedModel.listAllOntProperties(); it.hasNext(); ) {
- OntProperty prop = (OntProperty)it.next();
- if ( prop.getNameSpace().equals( this.namespace ) )
- properties.add( prop );
- }
- return properties;
- }
-
- //adds a class with a random URI to the parent class parentURI
- public OntClass addClass ( OntClass parentClass, String name ) {
- String childURI = namespace+name;
- OntClass childClass = modifiedModel.createClass( childURI );//create a new class to the model
-
- classHierarchy.addClass( childURI, parentClass.getURI() );//add the node in the hierarchy of classes
- parentClass.addSubClass( childClass ); //add the childClass as subclass of parentClass
- modifiedModel.add( childClass, RDFS.subClassOf, parentClass ); //add the class to the model
- return childClass;
- }
-
- //add the percentage of the specified subclasses
- public void addSubClasses ( float percentage ) {
- 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 );
- for ( int i=0; i<toAdd; i++ ) {
- addClass( classes.get(n[i]), getRandomString() ); //give a random URI to the new class
- }
- }
-
- //add nbClasses beginning from level
- public void addClasses ( int level, int nbClasses, float percentage ) {
- String classURI;
- //the parent class -> if level is 1 then we create a new class
- //else we get a random class from the level : level-1 to be the parent of the class
- OntClass parentClass;
- OntClass childClass;
- List<OntClass> parentClasses = new ArrayList<OntClass>();
- List<OntClass> childClasses = new ArrayList<OntClass>();
-
- checkClassHierarchy(); //check if the class hierarchy is built
- if ( level == 1 ) { //the parent of the class is Thing, we add the class and then the rest of the classes
- classURI = this.getRandomString();
- parentClass = modifiedModel.createClass( this.namespace + classURI );//create a new class to the model
- this.classHierarchy.addClass( this.namespace + classURI, "Thing" ); //add the node in the hierarchy of classes
- childClasses.add(parentClass);
- }
- else {
- parentClasses = this.classHierarchy.getClassesFromLevel(modifiedModel, level);
- int nbParentClasses = parentClasses.size(); //number of classes from the Ontology
- int toAdd = (int) ( percentage * nbClasses ); // 1 can be replaced by percentage
-
- for ( OntClass pClass : parentClasses ) {
- classURI = this.getRandomString();
- childClass = addClass (pClass, classURI );
- pClass = childClass;
- childClasses.add( childClass );
- }
- }
-
- for ( OntClass pClass : childClasses ) {
- classURI = pClass.getLocalName();
- for ( int i=level+1; i<level + nbClasses; i++ ) {
- classURI = "IS_" + classURI;
- childClass = addClass (pClass, classURI);
- pClass = childClass;
- } //this.classHierarchy.printClassHierarchy();
- }
- }
-
- //changes the unionOf, intersectionOf
- public OntModel changeDomainRange ( HashMap<String, String> uris ) {
- OntModel newModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);//create new Model
- boolean isSubj, isObj, isPred;
- String subjectNameSpace, subjectLocalName;
- String objectNameSpace, objectLocalName;
- String predicateNameSpace, predicateLocalName;
-
- //iterate and modify the identifiers
- for ( Statement stm : modifiedModel.listStatements().toList() ) {
- 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;
- isSubj = isObj = isPred = false;
-
- //if the class appears as the subject of a proposition
- 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() ) ) {
- isPred = true;
- pred = newModel.createProperty( uris.get( predicate.getURI() ) );
- }
-
- //if appears as the object of the statement
- if ( object.canAs( Resource.class ) )
- if ( object.isURIResource() ) {
- if ( object.asResource().getURI() != null )
- if ( uris.containsKey( object.asResource().getURI() ) ) {
- isObj = true;
- obj = newModel.createResource( uris.get( object.asResource().getURI() ) );
- }
- }
-
- if ( isSubj ) {
- if ( isPred ) {
- 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 );
- }
- } else {
- if ( isPred ) {
- 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 );
- }
- }
- }
- return newModel;
- }
-
- //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;
- for ( Iterator it = modifiedModel.listRestrictions(); it.hasNext(); ) {
- restr = (Restriction)it.next(); //get the restriction
- /* isAllValuesFromRestriction */
- if ( restr.isAllValuesFromRestriction() ) {
- AllValuesFromRestriction av = restr.asAllValuesFromRestriction();
- if ( av.getAllValuesFrom().getURI() != null ) //if points to the childClass
- //if ( av.getNameSpace().equals( this.namespace ) )
- if ( av.getAllValuesFrom().getURI().equals( childClass.getURI() ) )
- av.setAllValuesFrom( parentClass ); //change to point to the parentClass
- }
- /* isHasValueRestriction */
- if ( restr.isSomeValuesFromRestriction() ) {
- SomeValuesFromRestriction sv = restr.asSomeValuesFromRestriction();
- if ( sv.getSomeValuesFrom().getURI() != null ) //if points to the childClass
- //if ( sv.getNameSpace().equals( this.namespace ) )
- if ( sv.getSomeValuesFrom().getURI().equals( childClass.getURI() ) )
- sv.setSomeValuesFrom( parentClass ); //change to point to the parentClass
- }
-
- }
- }
-
- //removes a class, returns the uri of his parent
- @SuppressWarnings("unchecked")
- public String removeClass ( OntClass cls ) {
- OntClass parentClass;
- ArrayList<OntClass> subClasses = new ArrayList<OntClass>(); //the list of all the subclasses of the class
- OntClass thing = modifiedModel.createClass( OWL.Thing.getURI() ); //Thing class
- checkClassHierarchy(); //check if the class hierarchy is built
- parentClass = this.classHierarchy.removeClass( modifiedModel, cls );//get the parent of the class
-
- for (Iterator it1 = cls.listSubClasses(); it1.hasNext(); ) { //build the list of subclasses
- OntClass subCls = (OntClass)it1.next(); //because we can't change the
- subClasses.add( subCls ); //model while we are iterating
- }
-
- if ( parentClass != thing ) //now we change the superclass of classes
- for (OntClass clss : subClasses) //new superclass =>
- clss.setSuperClass( parentClass ); //=>the superclass of the node
-
- checkClassesRestrictions( cls, parentClass );
- cls.remove(); //remove the class from the Ontology
- return parentClass.getURI();
- }
-
- //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>();
- List<String> cl = new ArrayList<String>();
- HashMap<String, String> uris = new HashMap<String, String>(); //the HashMap of strings
- String parentURI = "";
- int nbClasses = classes.size(); //number of classes
- checkClassHierarchy(); //check if the class hierarchy is built
- int toBeRemoved = (int) (percentage*nbClasses); //the number of classes to be removed
-
- //build the list of classes to be removed
- int [] n = this.randNumbers(nbClasses, toBeRemoved);
- for ( int i=0; i<toBeRemoved; i++ ) {
- OntClass cls = classes.get(n[i]);
- removedClasses.add( cls );
- cl.add( cls.getURI() ); //builds the list of labels of classes to be removed
- }
-
- for ( OntClass cls : removedClasses ) { //remove the classes from the list
- parentURI = removeClass (cls);
- uris.put(cls.getURI(), parentURI);
- }
-
- //checks if the class appears like unionOf.. and replaces its appearence with the superclass
- modifiedModel = changeDomainRange( uris );
-
- //remove the URI of the class from the reference alignment
- for ( String key : alignment.stringPropertyNames() ) {
- String value = alignment.getProperty( key );
- if ( cl.contains( this.namespace + key.substring(key.indexOf(this.base) + this.base.length() )) )
- alignment.remove( key );
- 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
- alignment.remove( key );
- }
- }
-
- //remove all the classes from a specific level
- public void removeClassesFromLevel ( int level ) {
- HashMap<String, String> uris = new HashMap<String, String>();
- String parentURI = "";
- //if ( debug ) System.err.println( "Level " + level );
- /* if ( level == 1 ) //except classes from level 1
- return; */
- List<OntClass> classes = new ArrayList<OntClass>();
- checkClassHierarchy(); //check if the class hierarchy is built
- classes = this.classHierarchy.getClassesFromLevel(modifiedModel, level);
- 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
- modifiedModel = changeDomainRange( uris );
- }
-
- //remove percentage individuals from Ontology
- public void removeIndividuals( float percentage ) {
- boolean isSubj, isObj; //the individual can appear as subject or object
- List<Individual> individuals = modifiedModel.listIndividuals().toList();
- List<Individual> individualsTo = new ArrayList<Individual>(); //the list of individuals to be removed
- 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
- individualsTo.add( indiv );
- //alignment.remove( indiv.getURI() );
- }
-
- for ( Statement st : modifiedModel.listStatements().toList() ) {
- Resource subject = st.getSubject();
- RDFNode object = st.getObject();
- isSubj = isObj = false;
-
- if ( individualsTo.contains( subject ) )
- isSubj = true;
- if ( object.canAs( Resource.class ) )
- if ( individualsTo.contains( object.asResource() ) )
- isObj = true;
- if ( isSubj ) //the individual appears as subject in the statement
- modifiedModel.remove( st );
- if ( isObj ) //the individual appears as object in the statement
- modifiedModel.remove( st );
- }
- }
-
- //remove properties from the model
- @SuppressWarnings("unchecked")
- public void removeProperties ( float percentage ) {
- List <OntProperty> properties = this.getOntologyProperties(); //the list of all properties from the model
- ArrayList <OntProperty> propertiesToBeRemoved = new ArrayList<OntProperty>();
- ArrayList<Restriction> restrictions = new ArrayList<Restriction>();
- ArrayList<OntClass> resources = new ArrayList<OntClass>();
- List<String> pr = new ArrayList<String>();
- boolean isObj, isSubj, isPred;
-
- int nbProperties = properties.size(); //the number of properties
- int toBeRemoved = (int)( percentage*nbProperties ); //the number of properties to be removed
-
- //build the list of classes to be removed
- int [] n = this.randNumbers(nbProperties, toBeRemoved);
- for ( int i=0; i<toBeRemoved; i++ ) { //build the list of properties to be removed
- OntProperty p = properties.get(n[i]);
- propertiesToBeRemoved.add( p );
- pr.add( p.getURI() );
-
-
- //alignment.remove( p.getURI() );
- for ( Iterator it = p.listReferringRestrictions(); it.hasNext(); ) {//get the restrictions of that property
- restrictions.add( (Restriction)it.next() );
- }
- for ( Restriction r : restrictions ) //delete all the restrictions
- r.remove();
-
- //the domain of the property is a unionOf class
- if ( p.hasDomain(null) ) {
- if ( p.getDomain().canAs( OntResource.class ) ) {
- OntResource res = p.getDomain();
- if ( res.canAs( UnionClass.class ) ) {
- OntClass cls = res.asClass();
- resources.add(cls);
- }
- }
- }
- //the range of the property is a unionOf class
- if ( p.hasRange(null) ) {
- if ( p.getRange().canAs( OntResource.class ) ) {
- OntResource res = p.getRange();
- if ( res.canAs( UnionClass.class ) ) {
- OntClass cls = res.asClass();
- resources.add(cls);
- }
- }
- }
- }
-
- for ( OntClass c : resources ) c.remove();
-
- //remove that property from alignment
- //since we don't respect any order the value can appear as a value, thus we must iterate among all alignment to delete it
- int baselength = base.length();
- for ( String key : alignment.stringPropertyNames() ) {
- String value = alignment.getProperty(key);
- if ( pr.contains( this.namespace + key.substring(key.indexOf(this.base) + baselength ) ) ) { //if ( debug ) System.err.println( "Elimin " + key );
- alignment.remove( key );
- }
- if ( pr.contains( this.namespace + value.substring(key.indexOf(this.base) + baselength) ) ) { //if ( debug ) System.err.println( "Elimin " + key );
- alignment.remove( key );
- }
- }
-
- for ( Statement st : modifiedModel.listStatements().toList() ) { //remove the declaration of properties from the model
- Resource subject = st.getSubject();
- Property predicate = st.getPredicate();
- RDFNode object = st.getObject();
- isSubj = isPred = isObj = false;
-
- if ( propertiesToBeRemoved.contains( subject ) ) //if appears as subject
- if ( subject.getNameSpace().equals( this.namespace ) )
- isSubj = true;
-
- if ( propertiesToBeRemoved.contains( predicate ) ) //if appears as predicate
- if ( predicate.getNameSpace().equals( this.namespace ) )
- isPred = true;
-
- if ( object.canAs( Resource.class ) ) //if appears as object
- if ( propertiesToBeRemoved.contains( object ) )
- if ( object.asResource().getNameSpace().equals( this.namespace ) )
- isObj = true;
-
- if ( isSubj || isPred || isObj ) //remove the statement in which the prop
- modifiedModel.remove( st ); //appears as subject, predicate or object
- }
- }
-
- //add object properties to the Ontology
- public void addProperties ( float percentage ) {
- List<OntProperty> properties = this.getOntologyProperties();
- List<OntClass> classes = this.getOntologyClasses();
- ObjectProperty p = null;
- DatatypeProperty d = null;
- Random classRand = new Random();
- int index;
- int nbClasses = classes.size(); //the number of classes
- int nbProperties = properties.size(); //the number of properties
- int toBeAdd = (int)( percentage*nbProperties ); //the number of properties to be add
-
- for ( int i=0; i<toBeAdd/2; i++ ) { //add object properties
- //p = modifiedModel.createObjectProperty( this.namespace + "OBJECT_PROPERTY_" + getRandomString() );
- p = modifiedModel.createObjectProperty( this.namespace + getRandomString() );
- index = classRand.nextInt( nbClasses ); //pick random domain
- p.addDomain( classes.get( index ) );
- index = classRand.nextInt( nbClasses ); //pick random range
- p.addRange( classes.get( index ) );
- }
-
- for ( int i=toBeAdd/2; i<toBeAdd; i++ ) { //add datatype properties
- //d = modifiedModel.createDatatypeProperty( this.namespace + "DATATYPE_PROPERTY_" + getRandomString() );
- d = modifiedModel.createDatatypeProperty( this.namespace + getRandomString() );
- index = classRand.nextInt( nbClasses ); //add domain
- d.addDomain( classes.get( index ) );
- d.addRange( XSD.xstring ); //add range -> string
- }
- }
-
- //remove classes comments
- @SuppressWarnings("unchecked")
- public void removeClassesComments ( float percentage ) {
- ArrayList<Literal> comments = new ArrayList<Literal>();
- List<OntClass> classes = modifiedModel.listNamedClasses().toList();
- ArrayList<OntClass> classesTo = new ArrayList<OntClass>();
- int nbClasses = classes.size();
- int toBeRemoved = (int)( percentage * nbClasses ); //number of classes comments to be removed
-
- int [] n = this.randNumbers(nbClasses, toBeRemoved);
- for ( int i=0; i<toBeRemoved; i++ ) {
- OntClass cls = classes.get(n[i]);
- classesTo.add( cls );
- }
-
- for ( OntClass c : classesTo ) {
- for (Iterator it2 = c.listComments(null); it2.hasNext();)
- comments.add(((Literal) it2.next()));
- for (Literal lit : comments) // remove comments
- c.removeComment( lit );
- comments.clear();
- }
- }
-
- //remove properties comments
- @SuppressWarnings("unchecked")
- public void removePropertiesComments ( float percentage ) {
- ArrayList<Literal> comments = new ArrayList<Literal>(); // an array list to hold all the comments
- List<OntProperty> properties = modifiedModel.listAllOntProperties().toList();
- ArrayList<OntProperty> propertiesTo = new ArrayList<OntProperty>();
- int nbProperties = properties.size();
- int toBeRemoved = (int)( percentage * nbProperties ); //the number of properties comments to be removed
-
- int [] n = this.randNumbers(nbProperties, toBeRemoved);
- for ( int i=0; i<toBeRemoved; i++ ) {
- OntProperty p = properties.get(n[i]);
- propertiesTo.add( p );
- }
-
- for ( OntProperty prop : propertiesTo ) {
- for (Iterator it2 = prop.listComments(null); it2.hasNext();) // get all comments
- comments.add(((Literal) it2.next()));
- for (Literal lit : comments) //remove comments
- prop.removeComment( lit );
- comments.clear();
- }
- }
-
- //remove individuals comments
- @SuppressWarnings("unchecked")
- public void removeIndividualsComments ( float percentage ) {
- ArrayList<Literal> comments = new ArrayList<Literal>(); // an array list to hold all the comments
- List<Individual> individuals = modifiedModel.listIndividuals().toList();
- ArrayList<Individual> individualsTo = new ArrayList<Individual>();
- int nbIndividuals = individuals.size();
- int toBeRemoved = (int)( percentage * nbIndividuals ); //number of classes to be removed
-
- int [] n = this.randNumbers(nbIndividuals, toBeRemoved);
- for ( int i=0; i<toBeRemoved; i++ ) {
- Individual indiv = individuals.get(n[i]);
- individualsTo.add( indiv );
- }
- for ( Individual indiv : individuals ) {
- for (Iterator it2 = indiv.listComments(null); it2.hasNext(); ) //get all comments
- comments.add( ((Literal) it2.next()) );
- for (Literal lit : comments ) //remove comments
- indiv.removeComment( lit );
- comments.clear();
- }
- }
-
- //remove Ontologies comments
- @SuppressWarnings("unchecked")
- public void removeOntologiesComments ( float percentage ) {
- ArrayList<Literal> comments = new ArrayList<Literal>(); // an array list to hold all the comments
- List<Ontology> ontologies = modifiedModel.listOntologies().toList();
- ArrayList<Ontology> ontologiesTo = new ArrayList<Ontology>();
- int nbOntologies = ontologies.size();
- int toBeRemoved = (int)( percentage * nbOntologies ); //the number of Ontologies comments to be removed
-
- int [] n = this.randNumbers(nbOntologies, toBeRemoved);
- for ( int i=0; i<toBeRemoved; i++ ) {
- Ontology onto = ontologies.get(n[i]);
- ontologiesTo.add( onto );
- }
-
- for ( Ontology onto : ontologies ) {
- for (Iterator it2 = onto.listComments(null); it2.hasNext(); ) // get all comments
- comments.add(((Literal) it2.next()));
- for ( Literal lit : comments ) //remove all comments
- onto.removeComment( lit );
- comments.clear();
- }
- }
-
- //remove percentage comments
- public void removeComments ( float percentage ) {
- removeClassesComments ( percentage );
- removeIndividualsComments ( percentage );
- removePropertiesComments ( percentage );
- removeOntologiesComments ( percentage );
- }
-
- //flatten level
- public void levelFlattened ( int level ) {
- int size;
- boolean active = false;
- ArrayList<OntClass> levelClasses = new ArrayList<OntClass>(); //the list of classes from that level
- ArrayList<OntClass> parentLevelClasses = new ArrayList<OntClass>(); //the list of parent of the child classes from that level
- ArrayList<OntClass> superLevelClasses = new ArrayList<OntClass>(); //the list of parent of the parent classes from that level
- if ( level == 1 ) //no change
- return;
- checkClassHierarchy(); //check if the class hierarchy is built
- active = this.classHierarchy.flattenClassHierarchy( modifiedModel, level, levelClasses, parentLevelClasses, superLevelClasses);
- size = levelClasses.size();
-
- /* remove duplicates from list */
- HashMap<String, ArrayList<Restriction>> restrictions = new HashMap<String, ArrayList<Restriction>>();
- List<String> parentURI = new ArrayList<String>();
- HashMap<String, String> unionOf = new HashMap<String, String>();
-
- for ( int i=0; i<size; i++ ) {
- OntClass childClass = levelClasses.get( i ); //child class
- OntClass parentClass = parentLevelClasses.get( i ); //parent class
-
- //build the list of restrictions of the parent class
- ArrayList<Restriction> restr = new ArrayList<Restriction>();
- List<OntClass> supCls = parentClass.listSuperClasses().toList();
- 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 ( debug ) System.err.println( cls.getURI() + cls.getLocalName() );
- }
- }
- //if ( debug ) System.err.println( restr.size() );
-
- if ( !restrictions.containsKey( parentClass.getURI() ) ) {
- restrictions.put( parentClass.getURI(), restr );
- }
- parentURI.add( parentClass.getURI() );
-
- //all the classes are subclasses of owl: Thing
- if ( active ) { //if ( !parentClass.getURI().equals( "Thing" ) ) {
- OntClass superClass = superLevelClasses.get( i ); //parent class of the child class parents
-
- //if ( debug ) System.err.println("SuperClass class [" + superClass.getURI() + "]");
- //if ( debug ) System.err.println("Parent class [" + parentClass.getURI() + "]");
- //if ( debug ) System.err.println("Child class [" + childClass.getURI() + "]");
-
- if ( modifiedModel.containsResource(parentClass) ) {
- //to check if the class appears as unionOf, someValuesFrom, allValuesFrom ..
- unionOf.put(parentClass.getURI(), superClass.getURI());
- checkClassesRestrictions ( parentClass, superClass );
- parentClass.remove();
- }
- childClass.addSuperClass( superClass );
- parentClass.removeSubClass( childClass );
- } else {
- OntClass superClass = modifiedModel.createClass( OWL.Thing.getURI() ); //Thing class
-
- if ( 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 );
- List<Restriction> restr = restrictions.get( uri );
- for ( Restriction r : restr ) {
- childClass.addSuperClass(r);
- }
- i++;
- }
-
- //checks if the class appears like unionOf, someValuesFrom, allValuesFrom .. and replaces its appearence with the superclass
- modifiedModel = changeDomainRange(unionOf);
-
- //remove the parentClass from the alignment
- int baselength = base.length();
- for ( String key : alignment.stringPropertyNames() ) {
- String value = alignment.getProperty(key);
- if ( parentURI.contains( this.namespace + key.substring(key.indexOf(this.base) + baselength) ) ) { //this.classHierarchy.removeUri("Thing", key);
- alignment.remove(key);
- }
- if ( parentURI.contains( this.namespace + value.substring(key.indexOf(this.base) + baselength ))) { //this.classHierarchy.removeUri("Thing", value);
- alignment.remove(key);
- }
- }
-
- }
-
- //flatten level - for noHierarchy
- public void _noHierarchy ( int level ) {
- if ( level == 1 ) return;
- int size;
- boolean active = false;
- ArrayList<OntClass> levelClasses = new ArrayList<OntClass>(); //the list of classes from that level
- ArrayList<OntClass> parentLevelClasses = new ArrayList<OntClass>(); //the list of parent of the child classes from that level
- ArrayList<OntClass> superLevelClasses = new ArrayList<OntClass>(); //the list of parent of the parent classes from that level
- checkClassHierarchy(); //check if the class hierarchy is built
- active = this.classHierarchy.flattenClassHierarchy( modifiedModel, level, levelClasses, parentLevelClasses, superLevelClasses);
- size = levelClasses.size();
-
- for ( int i=0; i<size; i++ ) {
- OntClass childClass = levelClasses.get( i ); //child class
- OntClass parentClass = parentLevelClasses.get( i ); //parent class
- //all the classes are subclasses of owl: Thing
- if ( active ) { //if ( !parentClass.getURI().equals( "Thing" ) ) {
- OntClass superClass = superLevelClasses.get( i ); //parent class of the child class parents
- childClass.addSuperClass( superClass );
- parentClass.removeSubClass( childClass );
- } else {
- parentClass.removeSubClass( childClass );
- }
- }
- }
-
- public void noHierarchy () {
- int level = this.getMaxLevel(); //this.classHierarchy.printClassHierarchy();
- while ( this.getMaxLevel() != 1 ) {
- //this.classHierarchy.printClassHierarchy();
- _noHierarchy ( level );
- level--;
-
- }
- }
-
- //remove percentage restrictions from the model
- public void removeRestrictions( float percentage ) {
- List<Restriction> restrictions = new ArrayList<Restriction>();
- List<Restriction> restrictionsTo = new ArrayList<Restriction>(); //the array list of restrictions to be removed
- restrictions = modifiedModel.listRestrictions().toList();
- int nbRestrictions = restrictions.size(); //the number of restrictions
- int toBeRemoved = (int)( percentage*nbRestrictions ); //the number of restrictions to be removed
-
- int [] n = this.randNumbers(nbRestrictions, toBeRemoved); //build the list of restrictions to be removed
- for ( int i=0; i<toBeRemoved; i++ ) {
- Restriction res = restrictions.get(n[i]);
- restrictionsTo.add( res );
- }
-
- for ( Restriction res : restrictionsTo )
- res.remove();
- }
-
- // -------------------------
- // Alignment management
-
- // isAlign is a not so good way to test initialisation
- // (initialisation with an empty Properties is done in the initialiser)
- // but the "alignment" is used everywhere...
-
- //the initial reference alignment
- // JE: !!!: no order guarantee in properties !!!
- public void initializeAlignment( Properties al ) {
- alignment = al;
-
- Enumeration e = alignment.propertyNames();
- String aux = (String)e.nextElement();
- base = aux.substring(0, aux.lastIndexOf("#")+1);
-
- isAlign = true;
- }
-
- /**
- * copy101 indicates if the ontology is copied in the directory and aligned with itself
- * or if it is not copied...
- */
- public void initializeAlignment( boolean copy101 ) {
- //if ( namespaceNew == null ) new AlignmentException( "New namespace should have been initialised" );
- List<OntClass> classes = modifiedModel.listNamedClasses().toList();//all classes
- List<OntProperty> properties = modifiedModel.listAllOntProperties().toList();//all properties
- List<Individual> individuals = modifiedModel.listIndividuals().toList();//all individuals
- List<Ontology> ontologies = modifiedModel.listOntologies().toList();//all Ontologies
-
- alignment = new Properties();
-
- if ( copy101 ) {
- base = namespaceNew;
- } else {
- base = namespace;
- }
-
- // JE: the namespace change is only correct for '#' namespaces...
- for ( OntClass cls : classes ) //list all classes
- if ( cls.getNameSpace().equals( namespace ) ) {
- // Change URI
- String u = cls.getURI();
- String frag = u.substring( namespace.length(), u.length() );
- String uri = base+frag;
- alignment.put( uri, uri ); //add them to the initial alignment
- }
-
- for ( OntProperty prop : properties ) //list all properties
- if ( prop.getNameSpace().equals( namespace ) ) {
- // Change URI
- String u = prop.getURI();
- String frag = u.substring( namespace.length(), u.length() );
- String uri = base+frag;
- alignment.put( uri, uri ); //add them to the initial alignment
- }
- isAlign = true; //the alignment has been computed for the first time
- }
-
- //compute the alignment after the modifications
- // JE: I'd rather have an alignment
- @SuppressWarnings("unchecked")
- public Alignment getAlignment() {
- Alignment extractedAlignment = new URIAlignment();
-
- try {
- URI onto1 = new URI( base.substring(0, base.lastIndexOf("#")) );
- URI onto2 = new URI( namespaceNew.substring(0, namespaceNew.lastIndexOf("#")) );
-
- extractedAlignment.init(onto1, onto2);
- extractedAlignment.setFile1(onto1);
- extractedAlignment.setFile2(onto2);
-
- //Cell addAlignCell(Object ob1, Object ob2, String relation, double measure) throws AlignmentException {
- for ( String key : alignment.stringPropertyNames() ) {
- String value = alignment.getProperty(key);
- URI uri1 = URI.create(key);
- URI uri2 = URI.create(this.namespaceNew + value.substring(value.indexOf(this.base) + this.base.length()));
- //if ( debug ) System.err.println( "[" + key + "][" + value + "]" );
- extractedAlignment.addAlignCell( uri1, uri2, "=", 1 );
- }
- } catch ( Exception ex ) {
- ex.printStackTrace();
- }
- return extractedAlignment;
- }
-
- // -------------------------
- // Namespace management and change
-
- //change the namespace of the modified ontology
- // JE: ??
- public OntModel changeNamespace () {
- this.isChanged = true;
- boolean isSubj, isPred, isObj;;
-
- OntModel newModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );//create new Model
-
- //iterate through all the statements and change the namespace
- for ( Statement stm : modifiedModel.listStatements().toList() ) {
- 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 ( subject.getLocalName() != null )
- if ( !subject.isLiteral() )
- if ( subject.getNameSpace().equals( this.namespace ) ) {
- subj = newModel.createResource( this.namespaceNew + subject.getLocalName() );
- isSubj = true;
- }
-
- if ( !object.isLiteral() )
- if ( object.canAs( Resource.class ) )
- if ( object.isURIResource() )
- if ( object.asResource().getNameSpace().equals( this.namespace ) ) {
- obj = newModel.createResource( this.namespaceNew + object.asResource().getLocalName() );
- isObj = true;
- }
-
- if ( !predicate.isLiteral() )
- if ( predicate.getNameSpace().equals( this.namespace ) ) {
- 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);
- }
- else {
- 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 );
- }
- else {
- 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, this.namespaceNew );
- }
-
- return newModel;
- }
-
- // -------------------------
- // Main entry point
-
- //OntModel model, OntModel modifiedModel, Alignment alignment
- public void modifyOntology( String name, String param ) {
- if ( param == null ) return;
- if ( name == null || name.equals("") ) {
- System.err.println( "No parameter" ); //no parameter as input
- return;
- };
- float value = 0.0f;
- String aux = "";
-
- if ( param.equals( ParametersIds.NO_HIERARCHY ) )
- ;
- else if( param != null) //the value of the parameter
- value = Float.valueOf( param ).floatValue(); // ??
- else
- aux = param;
-
- if ( !isAlign ) {
- initializeAlignment( false ); //determine the elements from the initial reference alignment
- }
-
- if ( name.equals( ParametersIds.ADD_CLASSES ) ) { //add percentage classes
- if ( debug ) System.err.println( "Add Class" + "[" + value + "]");
- addSubClasses( value );
- } else if ( name.equals( ParametersIds.REMOVE_CLASSES ) ) { //remove percentage classes
- if ( debug ) System.err.println( "Remove Class" + "[" + value + "]");
- removeSubClasses( value );
- } else if ( name.equals( ParametersIds.REMOVE_COMMENTS ) ) { //remove percentage comments
- if ( debug ) System.err.println( "Remove Comments" + "[" + value + "]");
- removeComments ( value );
- } else if ( name.equals( ParametersIds.REMOVE_PROPERTIES ) ) { //remove percentage properties
- if ( debug ) System.err.println( "Remove Property" + "[" + value + "]");
- removeProperties ( value );
- } else if ( name.equals( ParametersIds.ADD_PROPERTIES ) ) { //add percentage properties
- if ( debug ) System.err.println( "Add Property" + "[" + value + "]");
- addProperties ( value );
- } else if ( name.equals( ParametersIds.ADD_CLASSESLEVEL ) ) { //recursive add nbClasses starting from level level
- aux = ((Float)value).toString();
- int index = aux.indexOf(".");
- int level = Integer.valueOf( aux.substring(0, index) );
- int nbClasses = Integer.valueOf( aux.substring(index+1, aux.length()) );
- if ( debug ) System.err.println( "level " + level );
- if ( debug ) System.err.println( "nbClasses " + nbClasses );
- float percentage = 1.00f;
- addClasses ( level, nbClasses, percentage );
- } else if ( name.equals( ParametersIds.REMOVE_CLASSESLEVEL ) ) { //remove all the classes from the level level
- if ( debug ) System.err.println("Remove all classes from level" + (int)value );
- removeClassesFromLevel ( (int)value );
- } else if ( name.equals( ParametersIds.LEVEL_FLATTENED ) ) { //flatten a level
- //levelFlattened ( level );
- levelFlattened ( (int)value );
- if ( debug ) System.err.println( "New class hierarchy level " + getMaxLevel() ) ;
- } else if ( name.equals( ParametersIds.RENAME_CLASSES ) ) { //rename classes
- if ( debug ) System.err.println("Rename classes" + "[" + value + "]" );
- //if ( debug ) System.err.println("\nValue = " + value + "\n"); //activeProperties, activeClasses, ..
- modifiedModel = renameResource ( false, true, value, true, false, false, 0);
- } else if ( name.equals( ParametersIds.RENAME_PROPERTIES ) ) { //rename properties
- if ( debug ) System.err.println("Rename properties " + "[" + value + "]" );
- //if ( debug ) System.err.println("\nValue = " + value + "\n"); //activeProperties, activeClasses, ..
- modifiedModel = renameResource ( true, false, value, true, false, false, 0);
- } else if ( name.equals( ParametersIds.REMOVE_RESTRICTIONS ) ) { //remove percentage restrictions
- if ( debug ) System.err.println("Remove restrictions" + "[" + value + "]");
- removeRestrictions( value );
- } else if ( name.equals( ParametersIds.REMOVE_INDIVIDUALS ) ) { //remove percentage individuals
- if ( debug ) System.err.println("Remove individuals" + "[" + value + "]");
- removeIndividuals( value );
- } else if ( name.equals( ParametersIds.NO_HIERARCHY ) ) { //no hierarchy
- if ( debug ) System.err.println( "NoHierarchy" );
- noHierarchy();
- }
-
- //rebuild the class hierarchy every time
- this.isBuild = false;
- this.isChanged = false;
- }
-
-
-}
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
index 019f9e018f2886cb4b0c7cc887d14384aa0448f0..4ad44a4a0ecd9d9beae91cdba0cf75dae3e7fad3 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
@@ -31,7 +31,6 @@
package fr.inrialpes.exmo.align.gen;
// Alignment API implementation classes
-import fr.inrialpes.exmo.align.gen.inter.AlignedOntologyGenerator;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
@@ -57,20 +56,19 @@ import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFWriter;
import com.hp.hpl.jena.util.FileManager;
+import fr.inrialpes.exmo.align.gen.alt.EmptyModification;
+
import java.util.Properties;
-// implements AlignedOntologyGenerator
public class TestGenerator {
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 String initOntoURI = null; // URI of initial ontology
- private Properties params; //the modifications
private OntModel modifiedOntology; //modified ontology
private Alignment resultAlignment; //the reference alignment
- private String namespace = ""; //the namespace
- private OntologyModifier modifier = null; //the modifier
+ private Alterator modifier = null; //the modifier
private boolean debug = false;
public TestGenerator() {}
@@ -92,10 +90,6 @@ public class TestGenerator {
//returns the modified ontology
public void setInitOntoURI( String uri ) { initOntoURI = uri; }
- public void setNamespace( String ns ) { namespace = ns; }
- //return the newNamespace
- public String getNamespace() { return namespace; }
-
// ******************************************************* GB STUFF
//gets the URI
@@ -119,6 +113,7 @@ public class TestGenerator {
}
public static void writeOntology( OntModel model, String destFile, String ns ) {
+ //System.err.println( " ==> Writing: "+ns );
try {
File f = new File( destFile );
FileOutputStream fout = new FileOutputStream( f );
@@ -175,7 +170,6 @@ public class TestGenerator {
* Generate a test by altering an existing test
*/
public Properties incrementModifyOntology( String prevTestDir, Properties al, String testDir, Properties params ) {
- // JE: maybe ERROR crtDirName
return modifyOntology( dirprefix+"/"+prevTestDir+"/"+ontoname, al, testDir, params );
}
@@ -187,78 +181,35 @@ public class TestGenerator {
if ( debug ) System.err.println( "Source: "+file+" Target "+testNumber );
//set the TestGenerator ontology
OntModel onto = loadOntology( file );
- //set the namespace
- setNamespace( getURI( testNumber ) );
- Alignment align = generate( onto, params, al );
-
- outputTestDirectory( getModifiedOntology(), align, testNumber );
- return modifier.getProperties();
+ Alterator modifier = generate( onto, params, al );
+ // Prepare to generate
+ modifier.relocateTest( getURI( testNumber ) );
+ Alignment align = modifier.getAlignment(); // process, not just get
+ modifiedOntology = modifier.getModifiedOntology();
+ //saves the alignment into the file "refalign.rdf", null->System.out
+ //at the end, compute the reference alignment
+ outputTestDirectory( modifiedOntology, align, testNumber );
+ return modifier.getProtoAlignment();
}
// ******************************************************* GENERATOR
//generate the alingnment
- public Alignment generate( OntModel onto, Properties params, Properties initalign ) {
+ public Alterator generate( OntModel onto, Properties params, Properties initalign ) {
if ( debug ) {
System.err.println( "[-------------------------------------------------]" );
System.err.println( urlprefix+" / "+dirprefix+" / "+ontoname+" / "+alignname );
- System.err.println( namespace );
}
- // Initialise the modifier class
- modifier = new OntologyModifier( onto, new URIAlignment() );
- modifier.setDebug( debug );
- modifier.setNewNamespace( namespace );
+ // Load the ontology
+ Alterator modifier = new EmptyModification( onto );
+ ((EmptyModification)modifier).setDebug( debug );
// Initialize the reference alignment
- if ( initalign == null ) {
- if ( params.getProperty( "copy101" ) != null ) {
- modifier.initializeAlignment( true );
- } else {
- modifier.initializeAlignment( false );
- }
- } else {
- modifier.initializeAlignment( initalign );
- }
-
+ if ( initalign != null ) ((EmptyModification)modifier).initializeAlignment( initalign );
+ modifier.modify( params );
// Apply all modifications
- // JE: Here there is an obvious problems that the modifications are NOT applied in the specified order!
- // Hence we should have a mega reordering of these parameter (for all of these, if they are here, do something)
- // That would be better as a list in this case than parameters
- // But parameters are more flexible...
- applyModification( modifier, params, ParametersIds.REMOVE_CLASSES );
- applyModification( modifier, params, ParametersIds.REMOVE_PROPERTIES );
- applyModification( modifier, params, ParametersIds.REMOVE_RESTRICTIONS );
- applyModification( modifier, params, ParametersIds.REMOVE_COMMENTS );
-
- applyModification( modifier, params, ParametersIds.ADD_CLASSES );
- applyModification( modifier, params, ParametersIds.ADD_PROPERTIES );
-
- applyModification( modifier, params, ParametersIds.RENAME_CLASSES );
- applyModification( modifier, params, ParametersIds.RENAME_PROPERTIES );
- // UNTIL HERE, WE USE THE DOCUMENTED ORDER
-
- applyModification( modifier, params, ParametersIds.REMOVE_INDIVIDUALS );
- applyModification( modifier, params, ParametersIds.REMOVE_CLASSESLEVEL );
- applyModification( modifier, params, ParametersIds.LEVEL_FLATTENED );
- applyModification( modifier, params, ParametersIds.ADD_CLASSESLEVEL );
- applyModification( modifier, params, ParametersIds.NO_HIERARCHY );
-
- /*
- 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
- }
- */
-
- //saves the alignment into the file "refalign.rdf", null->System.out
- //at the end, compute the reference alignment
- resultAlignment = modifier.getAlignment(); //get the reference alignment
- modifiedOntology = modifier.getModifiedOntology(); //get the modified ontology
- return resultAlignment;
+ modifier = AlteratorFactory.cascadeAlterators( modifier, params );
+ return modifier;
}
- public void applyModification( OntologyModifier modifier, Properties p, String m ) {
- modifier.modifyOntology( m, p.getProperty( m ) );
- }
}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/AddClassLevel.java b/src/fr/inrialpes/exmo/align/gen/alt/AddClassLevel.java
new file mode 100755
index 0000000000000000000000000000000000000000..308a5d4082f3899872fa408a0df2bf689c7e7da7
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/AddClassLevel.java
@@ -0,0 +1,89 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+
+public class AddClassLevel extends BasicAlterator {
+
+ public AddClassLevel( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.ADD_CLASSESLEVEL );
+ if ( p == null ) return null;
+ // JE: FIND A BETTER ENCODING (or several parameters)
+ int index = p.indexOf(".");
+ int level = Integer.valueOf( p.substring(0, index) );
+ int nbClasses = Integer.valueOf( p.substring(index+1, p.length()) );
+ if ( debug ) System.err.println( "level " + level );
+ if ( debug ) System.err.println( "nbClasses " + nbClasses );
+ float percentage = 1.00f;
+ String classURI;
+ //the parent class -> if level is 1 then we create a new class
+ //else we get a random class from the level : level-1 to be the parent of the class
+ OntClass parentClass;
+ OntClass childClass;
+ List<OntClass> parentClasses = new ArrayList<OntClass>();
+ List<OntClass> childClasses = new ArrayList<OntClass>();
+
+ buildClassHierarchy(); //check if the class hierarchy is built
+ if ( level == 1 ) { //the parent of the class is Thing, we add the class and then the rest of the classes
+ classURI = this.getRandomString();
+ parentClass = modifiedModel.createClass( modifiedOntologyNS + classURI );//create a new class to the model
+ classHierarchy.addClass( modifiedOntologyNS + classURI, "Thing" ); //add the node in the hierarchy of classes
+ childClasses.add(parentClass);
+ }
+ else {
+ parentClasses = classHierarchy.getClassesFromLevel(modifiedModel, level);
+ int nbParentClasses = parentClasses.size(); //number of classes from the Ontology
+ int toAdd = Math.round( percentage*nbClasses ); // 1 can be replaced by percentage
+
+ for ( OntClass pClass : parentClasses ) {
+ classURI = this.getRandomString();
+ childClass = addClass (pClass, classURI );
+ pClass = childClass;
+ childClasses.add( childClass );
+ }
+ }
+
+ for ( OntClass pClass : childClasses ) {
+ classURI = pClass.getLocalName();
+ for ( int i=level+1; i<level + nbClasses; i++ ) {
+ classURI = "IS_" + classURI;
+ childClass = addClass (pClass, classURI);
+ pClass = childClass;
+ } //this.classHierarchy.printClassHierarchy();
+ }
+ return this; // useless
+ };
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/AddClasses.java b/src/fr/inrialpes/exmo/align/gen/alt/AddClasses.java
new file mode 100755
index 0000000000000000000000000000000000000000..db69d90d89ddf557727e0734363d3a63862eb0de
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/AddClasses.java
@@ -0,0 +1,57 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+
+import java.util.Properties;
+import java.util.List;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+
+public class AddClasses extends BasicAlterator {
+
+ public AddClasses( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.ADD_CLASSES );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ List<OntClass> classes = getOntologyClasses(); //get the list of classes from the Ontology
+ int nbClasses = classes.size(); //number of classes from the Ontology
+ int toAdd = Math.round( percentage*nbClasses );
+
+ buildClassHierarchy(); //check if the classHierarchy is built
+
+ //build the list of properties to be renamed
+ int[] n = this.randNumbers( nbClasses, toAdd );
+ for ( int i=0; i<toAdd; i++ ) {
+ addClass( classes.get(n[i]), getRandomString() ); //give a random URI to the new class
+ }
+ return this; // useless
+ };
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/AddProperties.java b/src/fr/inrialpes/exmo/align/gen/alt/AddProperties.java
new file mode 100755
index 0000000000000000000000000000000000000000..33731affb95eb058ef69c586a8f69f24b7dbeaa9
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/AddProperties.java
@@ -0,0 +1,78 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.ontology.ObjectProperty;
+import com.hp.hpl.jena.ontology.DatatypeProperty;
+import com.hp.hpl.jena.vocabulary.XSD;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Random;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+
+public class AddProperties extends BasicAlterator {
+
+ public AddProperties( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.ADD_PROPERTIES );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ List<OntProperty> properties = this.getOntologyProperties();
+ List<OntClass> classes = this.getOntologyClasses();
+ ObjectProperty property = null;
+ DatatypeProperty d = null;
+ Random classRand = new Random();
+ int index;
+ int nbClasses = classes.size(); //the number of classes
+ int nbProperties = properties.size(); //the number of properties
+ int toBeAdd = Math.round( percentage*nbProperties ); //the number of properties to be add
+
+ for ( int i=0; i<toBeAdd/2; i++ ) { //add object properties
+ //p = modifiedModel.createObjectProperty( modifiedOntologyNS + "OBJECT_PROPERTY_" + getRandomString() );
+ property = modifiedModel.createObjectProperty( modifiedOntologyNS + getRandomString() );
+ index = classRand.nextInt( nbClasses ); //pick random domain
+ property.addDomain( classes.get( index ) );
+ index = classRand.nextInt( nbClasses ); //pick random range
+ property.addRange( classes.get( index ) );
+ }
+
+ for ( int i=toBeAdd/2; i<toBeAdd; i++ ) { //add datatype properties
+ //d = modifiedModel.createDatatypeProperty( modifiedOntologyNS + "DATATYPE_PROPERTY_" + getRandomString() );
+ d = modifiedModel.createDatatypeProperty( modifiedOntologyNS + getRandomString() );
+ index = classRand.nextInt( nbClasses ); //add domain
+ d.addDomain( classes.get( index ) );
+ d.addRange( XSD.xstring ); //add range -> string
+ }
+ return this; // useless
+ };
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java b/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
new file mode 100644
index 0000000000000000000000000000000000000000..4b2180d7c067b23f4547661dccf1a2979a1506f6
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
@@ -0,0 +1,508 @@
+/**
+ * $Id$
+ *
+ * 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.
+ */
+
+/* This program receives as input two ontologies (the original ontology, the ontology that must be modified),
+ an alignment and a parameter with the modification that must be applied to the input ontology.
+ After the modification of the initial ontology the alignment must be computed
+ The file in which we store the alignment is "referenceAlignment.rdf"
+*/
+
+/* This program receives as input two ontologies (the original ontology, the ontology that must be modified),
+ an alignment and a parameter with the modification that must be applied to the input ontology.
+ After the modification of the initial ontology the alignment must be computed
+ The file in which we store the alignment is "referenceAlignment.rdf"
+*/
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+//Java classes
+import java.net.URI;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+import java.util.Random;
+import java.util.Enumeration;
+
+//Alignment API classes
+import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentException;
+
+import fr.inrialpes.exmo.align.impl.URIAlignment;
+
+//JENA classes
+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.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDFS;
+import com.hp.hpl.jena.util.ResourceUtils;
+import com.hp.hpl.jena.ontology.Individual;
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.ontology.Ontology;
+import com.hp.hpl.jena.ontology.Restriction;
+import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
+import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
+
+
+//gen
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ClassHierarchy;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+public abstract class BasicAlterator implements Alterator {
+ protected boolean debug = false;
+
+ protected ClassHierarchy classHierarchy; // the class hierarchy
+ protected OntModel modifiedModel; // the modified Ontology
+ protected Properties alignment; // the alignment
+ protected Alignment extractedAlignment; // the alignment corresponding to alignment
+
+ // Policy with respect to namespacess.
+ // See the doc in html... it explains well what an alterator should be...
+ // All this should go in the Parameters...
+
+ // Currently (as loaded in empty):
+ //
+ // modifiedOntologyNS -> the one from the loaded ontology (e.g, 201-2)
+ // modifiedOntologyNS is to be used in the loaded ontology
+ // initOntologyNS -> the one from the loaded alignment (e.g., 101) [it is 101->201-2]
+ // initOntologyNS is to be used in the alignment
+
+ // There are two possible path to improvements which would improve legibility and speed
+ // (1) do not put URIs in parameters!
+ // (2) replace alignment by real Alignments
+
+ protected String modifiedOntologyNS; // the namespace of the loaded OntModel
+ protected String initOntologyNS; // the namespace of the source ontology
+ // (the OntModel may already be a modified ontology wrt the source)
+
+ // -------------------------
+ // Constructors
+ // Ontology init, Ontology modified, Alignment align
+ // This could be a legitimate constructor in which the
+ // Alignment is transformed in properties
+ // At the moment it is useless and unused
+ //public BasicAlterator ( OntModel model, Alignment al ) {
+ // modifiedModel = model;
+ // // get the default namespace of the model
+ // modifiedOntologyNS = model.getNsPrefixURI("");
+ // alignment = new Properties();
+ //}
+
+ public BasicAlterator() {}
+
+ public BasicAlterator( Alterator om ) {
+ initModel( om );
+ }
+
+ protected void initModel( Alterator om ) {
+ // cloning
+ modifiedModel = om.getProtoOntology();
+ alignment = om.getProtoAlignment();
+ classHierarchy = om.getHierarchy();
+ modifiedOntologyNS = om.getNamespace();
+ initOntologyNS = om.getBase();
+ }
+
+ // abstract
+ public abstract Alterator modify( Properties params );
+
+ // -------------------------
+ // Accessors
+
+ public void setDebug( boolean d ) {
+ debug = d;
+ }
+
+ //returns the modified ontology after changing the namespace
+ public OntModel getModifiedOntology () {
+ return modifiedModel;
+ }
+
+ public void setModifiedModel(OntModel model) {
+ modifiedModel = model;
+ }
+
+ public OntModel getModifiedModel() {
+ return modifiedModel;
+ }
+
+ public ClassHierarchy getHierarchy() {
+ return classHierarchy;
+ }
+
+ //get properties
+ public Properties getProtoAlignment() {
+ return alignment;
+ }
+
+ public OntModel getProtoOntology() {
+ return modifiedModel;
+ }
+
+ public String getNamespace() {
+ return modifiedOntologyNS;
+ }
+
+ public String getBase() {
+ return initOntologyNS;
+ }
+
+ // -------------------------
+ // Utility (string) functions
+
+ //generates a random string with the length "length"
+ // JE: the name if these strings may be unusually too long...
+ // Think about some variation (based on average length and standard variation?)
+ // Length and upper casing may be an argument
+ public String getRandomString() {
+ Random generator = new Random();
+ String characters = "abcdefghijklmnopqrstuvwxyz";
+ int length = characters.length();
+ char[] text = new char[length];
+ for (int i = 0; i < length; i++) {
+ text[i] = characters.charAt( generator.nextInt(length) );
+ }
+ return new String(text); // JE suppressed toUpperCase()
+ }
+
+ // -------------------------
+ // Utility (randomizing) functions
+
+ //count - the number of elements from the vector
+ //the random numElems that must be selected
+ //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];
+ int aux, rand;
+ Random generator = new Random();
+
+ for ( int i=0; i<count; i++ ) vect[i] = i; //fill the array with sorted elements
+ for ( int j=0; j<numElems; j++ ) {
+ rand = generator.nextInt( count-j ); //choose a random number from the interval
+ n[j] = vect[rand]; //build the new vector
+ aux = vect[rand]; //swap
+ vect[rand] = vect[count-j-1];
+ vect[count-j-1] = aux;
+ }
+ return n;
+ }
+
+ // -------------------------
+ // Class hierarchy utilities
+
+ //if we add / remove a class we need to keep track of the class hierarchy
+ public void buildClassHierarchy () {
+ if ( classHierarchy == null ) {
+ classHierarchy = new ClassHierarchy();
+ classHierarchy.buildClassHierarchy( modifiedModel );
+ }
+ //classHierarchy.printClassHierarchy();
+ }
+
+ //gets the Ontology classes
+ @SuppressWarnings("unchecked")
+ public List<OntClass> getOntologyClasses () {
+ List<OntClass> classes = new ArrayList<OntClass>();
+ for ( Iterator it = modifiedModel.listNamedClasses(); it.hasNext(); ) {
+ OntClass aux = (OntClass)it.next();
+ if ( aux.getNameSpace().equals( modifiedOntologyNS ) ) {
+ classes.add( aux );
+ }
+ }
+ return classes;
+ }
+
+ //gets the Ontology properties
+ @SuppressWarnings("unchecked")
+ public List<OntProperty> getOntologyProperties () {
+ List<OntProperty> properties = new ArrayList<OntProperty>();
+ for ( Iterator it = modifiedModel.listAllOntProperties(); it.hasNext(); ) {
+ OntProperty prop = (OntProperty)it.next();
+ if ( prop.getNameSpace().equals( modifiedOntologyNS ) )
+ properties.add( prop );
+ }
+ return properties;
+ }
+
+ //adds a class with a random URI to the parent class parentURI
+ public OntClass addClass ( OntClass parentClass, String name ) {
+ String childURI = modifiedOntologyNS+name;
+ OntClass childClass = modifiedModel.createClass( childURI );//create a new class to the model
+
+ classHierarchy.addClass( childURI, parentClass.getURI() );//add the node in the hierarchy of classes
+ parentClass.addSubClass( childClass ); //add the childClass as subclass of parentClass
+ modifiedModel.add( childClass, RDFS.subClassOf, parentClass ); //add the class to the model
+ return childClass;
+ }
+
+ //changes the unionOf, intersectionOf
+ public OntModel changeDomainRange ( HashMap<String, String> uris ) {
+ OntModel newModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);//create new Model
+ boolean isSubj, isObj, isPred;
+ String subjectNameSpace, subjectLocalName;
+ String objectNameSpace, objectLocalName;
+ String predicateNameSpace, predicateLocalName;
+
+ //iterate and modify the identifiers
+ for ( Statement stm : modifiedModel.listStatements().toList() ) {
+ 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;
+ isSubj = isObj = isPred = false;
+
+ //if the class appears as the subject of a proposition
+ 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() ) ) {
+ isPred = true;
+ pred = newModel.createProperty( uris.get( predicate.getURI() ) );
+ }
+
+ //if appears as the object of the statement
+ if ( object.canAs( Resource.class ) )
+ if ( object.isURIResource() ) {
+ if ( object.asResource().getURI() != null )
+ if ( uris.containsKey( object.asResource().getURI() ) ) {
+ isObj = true;
+ obj = newModel.createResource( uris.get( object.asResource().getURI() ) );
+ }
+ }
+
+ if ( isSubj ) {
+ if ( isPred ) {
+ 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 );
+ }
+ } else {
+ if ( isPred ) {
+ 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 );
+ }
+ }
+ }
+ return newModel;
+ }
+
+ //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;
+ for ( Iterator it = modifiedModel.listRestrictions(); it.hasNext(); ) {
+ restr = (Restriction)it.next(); //get the restriction
+ /* isAllValuesFromRestriction */
+ if ( restr.isAllValuesFromRestriction() ) {
+ AllValuesFromRestriction av = restr.asAllValuesFromRestriction();
+ if ( av.getAllValuesFrom().getURI() != null ) //if points to the childClass
+ //if ( av.getNameSpace().equals( this.modifiedOntologyNS ) )
+ if ( av.getAllValuesFrom().getURI().equals( childClass.getURI() ) )
+ av.setAllValuesFrom( parentClass ); //change to point to the parentClass
+ }
+ /* isHasValueRestriction */
+ if ( restr.isSomeValuesFromRestriction() ) {
+ SomeValuesFromRestriction sv = restr.asSomeValuesFromRestriction();
+ if ( sv.getSomeValuesFrom().getURI() != null ) //if points to the childClass
+ //if ( sv.getNameSpace().equals( this.modifiedOntologyNS ) )
+ if ( sv.getSomeValuesFrom().getURI().equals( childClass.getURI() ) )
+ sv.setSomeValuesFrom( parentClass ); //change to point to the parentClass
+ }
+
+ }
+ }
+
+ //removes a class, returns the uri of his parent
+ @SuppressWarnings("unchecked")
+ public String removeClass ( OntClass cls ) {
+ OntClass parentClass;
+ ArrayList<OntClass> subClasses = new ArrayList<OntClass>(); //the list of all the subclasses of the class
+ OntClass thing = modifiedModel.createClass( OWL.Thing.getURI() ); //Thing class
+ buildClassHierarchy(); //check if the class hierarchy is built
+ parentClass = this.classHierarchy.removeClass( modifiedModel, cls );//get the parent of the class
+
+ for (Iterator it1 = cls.listSubClasses(); it1.hasNext(); ) { //build the list of subclasses
+ OntClass subCls = (OntClass)it1.next(); //because we can't change the
+ subClasses.add( subCls ); //model while we are iterating
+ }
+
+ if ( parentClass != thing ) //now we change the superclass of classes
+ for (OntClass clss : subClasses) //new superclass =>
+ clss.setSuperClass( parentClass ); //=>the superclass of the node
+
+ checkClassesRestrictions( cls, parentClass );
+ cls.remove(); //remove the class from the Ontology
+ return parentClass.getURI();
+ }
+
+ //compute the alignment after the modifications
+ public Alignment getAlignment() {
+ if ( extractedAlignment == null ) extractAlignment( initOntologyNS, modifiedOntologyNS );
+ return extractedAlignment;
+ }
+
+ /**
+ * Generates an Alignment from the property list hosting the alignment.
+ * On the fly rename the matched entities from the base1 (source) and
+ * base2 (target) namespaces.
+ *
+ * The property list is also modified for reflecting the renaming of entities.
+ * This is useful when the property list is reused when generating TestSets.
+ */
+ public void relocateTest( String namespaceNew ) {
+ relocateTest( initOntologyNS, namespaceNew );
+ }
+
+ public void relocateTest( String base1, String base2 ) {
+ extractedAlignment = extractAlignment( base1, base2 );
+ modifiedModel = changeNamespace( base2 );
+ }
+
+ @SuppressWarnings("unchecked")
+ public Alignment extractAlignment( String base1, String base2 ) {
+ Alignment extractedAlignment = new URIAlignment();
+
+ //System.err.println( "\n-----> "+initOntologyNS );
+ //System.err.println( "-----> "+base1 );
+ //System.err.println( "-----> "+base2 );
+ try {
+ URI onto1 = new URI( base1.substring(0, base1.lastIndexOf("#")) );
+ URI onto2 = new URI( base2.substring(0, base2.lastIndexOf("#")) );
+
+ extractedAlignment.init( onto1, onto2 );
+ // JE: not likely correct
+ extractedAlignment.setFile1( onto1 );
+ extractedAlignment.setFile2( onto2 );
+
+ int endBase = initOntologyNS.lastIndexOf("#")+1;
+ int endBase2 = base2.lastIndexOf("#")+1;
+ Properties newProp = new Properties();
+ for ( String key : alignment.stringPropertyNames() ) {
+ String value = alignment.getProperty(key);
+ String source = key;
+ // JE: This is useless in principle...
+ if ( !key.startsWith( base1 ) ) {
+ String fragment = key.substring( endBase );
+ source = base1+fragment;
+ }
+ // JE: not efficient certainly
+ String target = base2+value.substring( value.lastIndexOf("#")+1 );
+ //if ( debug ) System.err.println( "[" + source + "][" + target + "]" );
+ extractedAlignment.addAlignCell( URI.create( source ), URI.create( target ) );
+ newProp.put( source, target );
+ }
+ alignment = newProp;
+ } catch ( Exception ex ) {
+ ex.printStackTrace();
+ }
+ return extractedAlignment;
+ }
+
+ // -------------------------
+ // Namespace management and change
+
+ /**
+ * Modifies the namespace of the generated ontology
+ */
+ // It may be in fact faster to output in a String and to modify namespaces on the fly
+ // To be tested.
+ public OntModel changeNamespace ( String ns ) {
+ boolean isSubj, isPred, isObj;
+
+ OntModel newModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );//create new Model
+
+ //iterate through all the statements and change the namespace
+ for ( Statement stm : modifiedModel.listStatements().toList() ) {
+ 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 ( ( subject.getLocalName() != null ) && ( !subject.isLiteral() )
+ && ( subject.getNameSpace().equals( modifiedOntologyNS ) ) ) {
+ subj = newModel.createResource( ns + subject.getLocalName() );
+ isSubj = true;
+ }
+ if ( !object.isLiteral() && ( object.canAs( Resource.class ) ) && ( object.isURIResource() )
+ && ( object.asResource().getNameSpace().equals( modifiedOntologyNS ) ) ) {
+ obj = newModel.createResource( ns + object.asResource().getLocalName() );
+ isObj = true;
+ }
+ if ( !predicate.isLiteral() && ( predicate.getNameSpace().equals( modifiedOntologyNS ) ) ) {
+ pred = newModel.createProperty( ns + predicate.getLocalName() );
+ isPred = true;
+ }
+ if ( isSubj ) {
+ if ( isPred ) {
+ 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 );
+ } else if ( isPred ) {
+ 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 );
+ }
+
+ //rename the namespace of owl:Ontology
+ List<Ontology> ontos = newModel.listOntologies().toList();
+ for ( Ontology o : ontos ) {
+ ResourceUtils.renameResource( o, ns );
+ }
+
+ return newModel;
+ }
+
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/EmptyModification.java b/src/fr/inrialpes/exmo/align/gen/alt/EmptyModification.java
new file mode 100755
index 0000000000000000000000000000000000000000..af02be9802ca1f42284fad7dd9c4c634dcddf82d
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/EmptyModification.java
@@ -0,0 +1,91 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.ontology.Individual;
+import com.hp.hpl.jena.ontology.Ontology;
+
+import java.util.Properties;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+import org.semanticweb.owl.align.Alignment;
+
+public class EmptyModification extends BasicAlterator {
+
+ protected boolean relocateSource = false;
+
+ public EmptyModification( OntModel o ) {
+ modifiedModel = o;
+ // get the default namespace of the model
+ modifiedOntologyNS = modifiedModel.getNsPrefixURI("");
+ };
+
+ // Clearly here setDebug, setNamespace are important
+
+ public Alterator modify( Properties params ) {
+ relocateSource = ( params.getProperty( "copy101" ) != null );
+
+ if ( alignment == null ) {
+ initOntologyNS = modifiedOntologyNS;
+
+ alignment = new Properties();
+
+ for ( OntClass cls : modifiedModel.listNamedClasses().toList() ) {
+ if ( cls.getNameSpace().equals( modifiedOntologyNS ) ) {
+ String uri = cls.getURI();
+ alignment.put( uri, uri ); //add them to the initial alignment
+ }
+ }
+ for ( OntProperty prop : modifiedModel.listAllOntProperties().toList() ) {
+ if ( prop.getNameSpace().equals( modifiedOntologyNS ) ) {
+ String uri = prop.getURI();
+ alignment.put( uri, uri ); //add them to the initial alignment
+ }
+ }
+ }
+ return this;
+ }
+
+ // In case of 101, I want to have the empty test
+ public void relocateTest( String base1, String base2 ) {
+ super.relocateTest( relocateSource?base2:base1, base2 );
+ }
+
+ //the initial reference alignment
+ public void initializeAlignment( Properties al ) {
+ alignment = al;
+
+ Enumeration e = alignment.propertyNames();
+ String aux = (String)e.nextElement();
+ initOntologyNS = aux.substring(0, aux.lastIndexOf("#")+1);
+ }
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/FlattenLevel.java b/src/fr/inrialpes/exmo/align/gen/alt/FlattenLevel.java
new file mode 100755
index 0000000000000000000000000000000000000000..38d0b5a0aedefb7953d1f73ec5cd792c73d17cdf
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/FlattenLevel.java
@@ -0,0 +1,151 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.Restriction;
+import com.hp.hpl.jena.vocabulary.OWL;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+public class FlattenLevel extends BasicAlterator {
+
+ public FlattenLevel( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.LEVEL_FLATTENED );
+ if ( p == null ) return null;
+ // Should be an float casted in int!!!
+ int level = (int)Float.parseFloat( p );
+ int size;
+ boolean active = false;
+ ArrayList<OntClass> levelClasses = new ArrayList<OntClass>(); //the list of classes from that level
+ ArrayList<OntClass> parentLevelClasses = new ArrayList<OntClass>(); //the list of parent of the child classes from that level
+ ArrayList<OntClass> superLevelClasses = new ArrayList<OntClass>(); //the list of parent of the parent classes from that level
+ if ( level == 1 ) return this; //no change
+ buildClassHierarchy(); //check if the class hierarchy is built
+ active = classHierarchy.flattenClassHierarchy( modifiedModel, level, levelClasses, parentLevelClasses, superLevelClasses);
+ size = levelClasses.size();
+
+ /* remove duplicates from list */
+ HashMap<String, ArrayList<Restriction>> restrictions = new HashMap<String, ArrayList<Restriction>>();
+ List<String> parentURI = new ArrayList<String>();
+ HashMap<String, String> unionOf = new HashMap<String, String>();
+
+ for ( int i=0; i<size; i++ ) {
+ OntClass childClass = levelClasses.get( i ); //child class
+ OntClass parentClass = parentLevelClasses.get( i ); //parent class
+
+ //build the list of restrictions of the parent class
+ ArrayList<Restriction> restr = new ArrayList<Restriction>();
+ List<OntClass> supCls = parentClass.listSuperClasses().toList();
+ 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 ( debug ) System.err.println( cls.getURI() + cls.getLocalName() );
+ }
+ }
+ //if ( debug ) System.err.println( restr.size() );
+
+ if ( !restrictions.containsKey( parentClass.getURI() ) ) {
+ restrictions.put( parentClass.getURI(), restr );
+ }
+ parentURI.add( parentClass.getURI() );
+
+ //all the classes are subclasses of owl: Thing
+ if ( active ) { //if ( !parentClass.getURI().equals( "Thing" ) ) {
+ OntClass superClass = superLevelClasses.get( i ); //parent class of the child class parents
+
+ //if ( debug ) System.err.println("SuperClass class [" + superClass.getURI() + "]");
+ //if ( debug ) System.err.println("Parent class [" + parentClass.getURI() + "]");
+ //if ( debug ) System.err.println("Child class [" + childClass.getURI() + "]");
+
+ if ( modifiedModel.containsResource(parentClass) ) {
+ //to check if the class appears as unionOf, someValuesFrom, allValuesFrom ..
+ unionOf.put(parentClass.getURI(), superClass.getURI());
+ checkClassesRestrictions ( parentClass, superClass );
+ parentClass.remove();
+ }
+ childClass.addSuperClass( superClass );
+ parentClass.removeSubClass( childClass );
+ } else {
+ OntClass superClass = modifiedModel.createClass( OWL.Thing.getURI() ); //Thing class
+
+ if ( 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 );
+ List<Restriction> restr = restrictions.get( uri );
+ for ( Restriction r : restr ) {
+ childClass.addSuperClass(r);
+ }
+ i++;
+ }
+
+ //checks if the class appears like unionOf, someValuesFrom, allValuesFrom .. and replaces its appearence with the superclass
+ modifiedModel = changeDomainRange(unionOf);
+
+ //remove the parentClass from the alignment
+ int baselength = initOntologyNS.length(); // key.indexOf+baselenght == baselenght...
+ for ( String key : alignment.stringPropertyNames() ) {
+ String value = alignment.getProperty( key );
+ if ( parentURI.contains( modifiedOntologyNS + key.substring( key.indexOf( initOntologyNS ) + baselength) ) ) { //this.classHierarchy.removeUri("Thing", key);
+ alignment.remove( key );
+ }
+ if ( parentURI.contains( modifiedOntologyNS + value.substring( key.indexOf( initOntologyNS ) + baselength ))) { //this.classHierarchy.removeUri("Thing", value);
+ alignment.remove( key );
+ }
+ }
+ return this; // useless
+ };
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RemoveClassLevel.java b/src/fr/inrialpes/exmo/align/gen/alt/RemoveClassLevel.java
new file mode 100755
index 0000000000000000000000000000000000000000..a0f1c08d66b6210c50adbb473d520824079a776e
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RemoveClassLevel.java
@@ -0,0 +1,61 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+public class RemoveClassLevel extends BasicAlterator {
+
+ public RemoveClassLevel( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.REMOVE_CLASSESLEVEL );
+ if ( p == null ) return null;
+ int level = Integer.parseInt( p );
+ HashMap<String, String> uris = new HashMap<String, String>();
+ String parentURI = "";
+ //if ( debug ) System.err.println( "Level " + level );
+ /* if ( level == 1 ) //except classes from level 1
+ return; */
+ List<OntClass> classes = new ArrayList<OntClass>();
+ buildClassHierarchy(); //check if the class hierarchy is built
+ classes = this.classHierarchy.getClassesFromLevel(modifiedModel, level);
+ 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
+ modifiedModel = changeDomainRange( uris );
+ return this; // useless
+ };
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RemoveClasses.java b/src/fr/inrialpes/exmo/align/gen/alt/RemoveClasses.java
new file mode 100755
index 0000000000000000000000000000000000000000..ffc83d066498ff1ccae722cb8f93d9f107d7e47b
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RemoveClasses.java
@@ -0,0 +1,78 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+public class RemoveClasses extends BasicAlterator {
+
+ public RemoveClasses( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.REMOVE_CLASSES );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ List<OntClass> classes = this.getOntologyClasses(); //the list of classes from Ontologu
+ List<OntClass> removedClasses = new ArrayList<OntClass>();
+ List<String> cl = new ArrayList<String>();
+ HashMap<String, String> uris = new HashMap<String, String>(); //the HashMap of strings
+ String parentURI = "";
+ int nbClasses = classes.size(); //number of classes
+ buildClassHierarchy(); //check if the class hierarchy is built
+ int toBeRemoved = Math.round(percentage*nbClasses); //the number of classes to be removed
+
+ //build the list of classes to be removed
+ int [] n = this.randNumbers(nbClasses, toBeRemoved);
+ for ( int i=0; i<toBeRemoved; i++ ) {
+ OntClass cls = classes.get(n[i]);
+ removedClasses.add( cls );
+ cl.add( cls.getURI() ); //builds the list of labels of classes to be removed
+ }
+
+ for ( OntClass cls : removedClasses ) { //remove the classes from the list
+ parentURI = removeClass (cls);
+ uris.put(cls.getURI(), parentURI);
+ }
+
+ //checks if the class appears like unionOf.. and replaces its appearence with the superclass
+ modifiedModel = changeDomainRange( uris );
+
+ //remove the URI of the class from the reference alignment
+ for ( String key : alignment.stringPropertyNames() ) {
+ if ( cl.contains( alignment.getProperty( key ) ) )
+ alignment.remove( key );
+ }
+ return this; // useless
+ };
+
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RemoveComments.java b/src/fr/inrialpes/exmo/align/gen/alt/RemoveComments.java
new file mode 100755
index 0000000000000000000000000000000000000000..66c6887a2206b1cd1701b25099a9a261f8d01f78
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RemoveComments.java
@@ -0,0 +1,154 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.ontology.Ontology;
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.ontology.Individual;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Iterator;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+
+public class RemoveComments extends BasicAlterator {
+
+ public RemoveComments( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.REMOVE_COMMENTS );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ removeClassesComments ( percentage );
+ removeIndividualsComments ( percentage );
+ removePropertiesComments ( percentage );
+ removeOntologiesComments ( percentage );
+ return this; // useless
+ };
+
+ //remove classes comments
+ @SuppressWarnings("unchecked")
+ public void removeClassesComments ( float percentage ) {
+ ArrayList<Literal> comments = new ArrayList<Literal>();
+ List<OntClass> classes = modifiedModel.listNamedClasses().toList();
+ ArrayList<OntClass> classesTo = new ArrayList<OntClass>();
+ int nbClasses = classes.size();
+ int toBeRemoved = Math.round( percentage*nbClasses ); //number of classes comments to be removed
+
+ int [] n = this.randNumbers(nbClasses, toBeRemoved);
+ for ( int i=0; i<toBeRemoved; i++ ) {
+ OntClass cls = classes.get(n[i]);
+ classesTo.add( cls );
+ }
+
+ for ( OntClass c : classesTo ) {
+ for (Iterator it2 = c.listComments(null); it2.hasNext();)
+ comments.add(((Literal) it2.next()));
+ for (Literal lit : comments) // remove comments
+ c.removeComment( lit );
+ comments.clear();
+ }
+ }
+
+ //remove properties comments
+ @SuppressWarnings("unchecked")
+ public void removePropertiesComments ( float percentage ) {
+ ArrayList<Literal> comments = new ArrayList<Literal>(); // an array list to hold all the comments
+ List<OntProperty> properties = modifiedModel.listAllOntProperties().toList();
+ ArrayList<OntProperty> propertiesTo = new ArrayList<OntProperty>();
+ int nbProperties = properties.size();
+ int toBeRemoved = Math.round( percentage*nbProperties ); //the number of properties comments to be removed
+
+ int [] n = this.randNumbers(nbProperties, toBeRemoved);
+ for ( int i=0; i<toBeRemoved; i++ ) {
+ OntProperty p = properties.get(n[i]);
+ propertiesTo.add( p );
+ }
+
+ for ( OntProperty prop : propertiesTo ) {
+ for (Iterator it2 = prop.listComments(null); it2.hasNext();) // get all comments
+ comments.add(((Literal) it2.next()));
+ for (Literal lit : comments) //remove comments
+ prop.removeComment( lit );
+ comments.clear();
+ }
+ }
+
+ //remove individuals comments
+ @SuppressWarnings("unchecked")
+ public void removeIndividualsComments ( float percentage ) {
+ ArrayList<Literal> comments = new ArrayList<Literal>(); // an array list to hold all the comments
+ List<Individual> individuals = modifiedModel.listIndividuals().toList();
+ ArrayList<Individual> individualsTo = new ArrayList<Individual>();
+ int nbIndividuals = individuals.size();
+ int toBeRemoved = Math.round( percentage*nbIndividuals ); //number of classes to be removed
+
+ int [] n = this.randNumbers(nbIndividuals, toBeRemoved);
+ for ( int i=0; i<toBeRemoved; i++ ) {
+ Individual indiv = individuals.get(n[i]);
+ individualsTo.add( indiv );
+ }
+ for ( Individual indiv : individuals ) {
+ for (Iterator it2 = indiv.listComments(null); it2.hasNext(); ) //get all comments
+ comments.add( ((Literal) it2.next()) );
+ for (Literal lit : comments ) //remove comments
+ indiv.removeComment( lit );
+ comments.clear();
+ }
+ }
+
+ //remove Ontologies comments
+ @SuppressWarnings("unchecked")
+ public void removeOntologiesComments ( float percentage ) {
+ ArrayList<Literal> comments = new ArrayList<Literal>(); // an array list to hold all the comments
+ List<Ontology> ontologies = modifiedModel.listOntologies().toList();
+ ArrayList<Ontology> ontologiesTo = new ArrayList<Ontology>();
+ int nbOntologies = ontologies.size();
+ int toBeRemoved = Math.round( percentage*nbOntologies ); //the number of Ontologies comments to be removed
+
+ int [] n = this.randNumbers(nbOntologies, toBeRemoved);
+ for ( int i=0; i<toBeRemoved; i++ ) {
+ Ontology onto = ontologies.get(n[i]);
+ ontologiesTo.add( onto );
+ }
+
+ for ( Ontology onto : ontologies ) {
+ for (Iterator it2 = onto.listComments(null); it2.hasNext(); ) // get all comments
+ comments.add(((Literal) it2.next()));
+ for ( Literal lit : comments ) //remove all comments
+ onto.removeComment( lit );
+ comments.clear();
+ }
+ }
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RemoveIndividuals.java b/src/fr/inrialpes/exmo/align/gen/alt/RemoveIndividuals.java
new file mode 100755
index 0000000000000000000000000000000000000000..c564ac57f74a4aaa88ae260c1b63950e265daf0c
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RemoveIndividuals.java
@@ -0,0 +1,79 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.ontology.Individual;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+
+public class RemoveIndividuals extends BasicAlterator {
+
+ public RemoveIndividuals( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.REMOVE_INDIVIDUALS );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ boolean isSubj, isObj; //the individual can appear as subject or object
+ List<Individual> individuals = modifiedModel.listIndividuals().toList();
+ List<Individual> individualsTo = new ArrayList<Individual>(); //the list of individuals to be removed
+ int nbIndividuals = individuals.size(); //the number of individuals
+ int toBeRemoved = Math.round( 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
+ individualsTo.add( indiv );
+ //alignment.remove( indiv.getURI() );
+ }
+
+ for ( Statement st : modifiedModel.listStatements().toList() ) {
+ Resource subject = st.getSubject();
+ RDFNode object = st.getObject();
+ isSubj = isObj = false;
+
+ if ( individualsTo.contains( subject ) )
+ isSubj = true;
+ if ( object.canAs( Resource.class ) )
+ if ( individualsTo.contains( object.asResource() ) )
+ isObj = true;
+ if ( isSubj ) //the individual appears as subject in the statement
+ modifiedModel.remove( st );
+ if ( isObj ) //the individual appears as object in the statement
+ modifiedModel.remove( st );
+ }
+ return this; // useless
+ };
+
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RemoveProperties.java b/src/fr/inrialpes/exmo/align/gen/alt/RemoveProperties.java
new file mode 100755
index 0000000000000000000000000000000000000000..a8b00bdac66887ccf446956cb31baa1ec3536c6b
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RemoveProperties.java
@@ -0,0 +1,137 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.ontology.OntResource;
+import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.UnionClass;
+import com.hp.hpl.jena.ontology.Restriction;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Iterator;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+
+public class RemoveProperties extends BasicAlterator {
+
+ public RemoveProperties( Alterator om ) {
+ initModel( om );
+ };
+
+ //@SuppressWarnings("unchecked")
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.REMOVE_PROPERTIES );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ List <OntProperty> properties = getOntologyProperties(); //the list of all properties from the model
+ ArrayList <OntProperty> propertiesToBeRemoved = new ArrayList<OntProperty>();
+ ArrayList<Restriction> restrictions = new ArrayList<Restriction>();
+ ArrayList<OntClass> resources = new ArrayList<OntClass>();
+ List<String> pr = new ArrayList<String>();
+ boolean isObj, isSubj, isPred;
+
+ int nbProperties = properties.size(); //the number of properties
+
+ int toBeRemoved = Math.round( percentage*nbProperties ); //the number of properties to be removed
+
+ //build the list of classes to be removed
+ int[] n = randNumbers( nbProperties, toBeRemoved );
+ for ( int i=0; i<toBeRemoved; i++ ) { //build the list of properties to be removed
+ OntProperty property = properties.get( n[i] );
+ propertiesToBeRemoved.add( property );
+ pr.add( property.getURI() );
+
+ //alignment.remove( p.getURI() );
+ //get the restrictions of that property
+ for ( Iterator it = property.listReferringRestrictions(); it.hasNext(); ) {
+ restrictions.add( (Restriction)it.next() );
+ }
+ //delete all the restrictions
+ for ( Restriction r : restrictions ) r.remove();
+
+ //the domain of the property is a unionOf class
+ if ( property.hasDomain(null) ) {
+ if ( property.getDomain().canAs( OntResource.class ) ) {
+ OntResource res = property.getDomain();
+ if ( res.canAs( UnionClass.class ) ) {
+ OntClass cls = res.asClass();
+ resources.add(cls);
+ }
+ }
+ }
+ //the range of the property is a unionOf class
+ if ( property.hasRange(null) ) {
+ if ( property.getRange().canAs( OntResource.class ) ) {
+ OntResource res = property.getRange();
+ if ( res.canAs( UnionClass.class ) ) {
+ OntClass cls = res.asClass();
+ resources.add(cls);
+ }
+ }
+ }
+ }
+
+ for ( OntClass c : resources ) c.remove(); // Remove the class descriptions
+
+ //remove that property from alignment
+ for ( String key : alignment.stringPropertyNames() ) {
+ if ( pr.contains( alignment.getProperty( key ) ) ) {
+ alignment.remove( key );
+ }
+ }
+
+ for ( Statement st : modifiedModel.listStatements().toList() ) { //remove the declaration of properties from the model
+ Resource subject = st.getSubject();
+ Property predicate = st.getPredicate();
+ RDFNode object = st.getObject();
+ isSubj = isPred = isObj = false;
+
+ if ( propertiesToBeRemoved.contains( subject ) ) //if appears as subject
+ if ( subject.getNameSpace().equals( modifiedOntologyNS ) )
+ isSubj = true;
+
+ if ( propertiesToBeRemoved.contains( predicate ) ) //if appears as predicate
+ if ( predicate.getNameSpace().equals( modifiedOntologyNS ) )
+ isPred = true;
+
+ if ( object.canAs( Resource.class ) ) //if appears as object
+ if ( propertiesToBeRemoved.contains( object ) )
+ if ( object.asResource().getNameSpace().equals( modifiedOntologyNS ) )
+ isObj = true;
+
+ if ( isSubj || isPred || isObj ) //remove the statement in which the prop
+ modifiedModel.remove( st ); //appears as subject, predicate or object
+ }
+ return this; // useless
+ };
+
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RemoveRestrictions.java b/src/fr/inrialpes/exmo/align/gen/alt/RemoveRestrictions.java
new file mode 100755
index 0000000000000000000000000000000000000000..6e15105ec5580a5b1549e0ebdf3159da86473b42
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RemoveRestrictions.java
@@ -0,0 +1,59 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.Restriction;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+public class RemoveRestrictions extends BasicAlterator {
+
+ public RemoveRestrictions( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.REMOVE_RESTRICTIONS );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ List<Restriction> restrictions = new ArrayList<Restriction>();
+ List<Restriction> restrictionsTo = new ArrayList<Restriction>(); //the array list of restrictions to be removed
+ restrictions = modifiedModel.listRestrictions().toList();
+ int nbRestrictions = restrictions.size(); //the number of restrictions
+ int toBeRemoved = Math.round( percentage*nbRestrictions ); //the number of restrictions to be removed
+
+ int [] n = this.randNumbers(nbRestrictions, toBeRemoved); //build the list of restrictions to be removed
+ for ( int i=0; i<toBeRemoved; i++ ) {
+ Restriction res = restrictions.get(n[i]);
+ restrictionsTo.add( res );
+ }
+ for ( Restriction res : restrictionsTo ) res.remove();
+ return this; // useless
+ };
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RenameClasses.java b/src/fr/inrialpes/exmo/align/gen/alt/RenameClasses.java
new file mode 100755
index 0000000000000000000000000000000000000000..f52bd1ce1d16f6777ea6e8922cbaf789769cf6f9
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RenameClasses.java
@@ -0,0 +1,47 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.Restriction;
+import com.hp.hpl.jena.vocabulary.OWL;
+
+import java.util.Properties;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+public class RenameClasses extends RenameThings {
+
+ public RenameClasses( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.RENAME_CLASSES );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ modifiedModel = renameResource ( false, true, percentage, true, false, false, 0);
+ return this; // useless
+ };
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/inter/AlignedOntologyGenerator.java b/src/fr/inrialpes/exmo/align/gen/alt/RenameProperties.java
old mode 100644
new mode 100755
similarity index 59%
rename from src/fr/inrialpes/exmo/align/gen/inter/AlignedOntologyGenerator.java
rename to src/fr/inrialpes/exmo/align/gen/alt/RenameProperties.java
index 881679d26134026e4c5dcee2fdc6a213c4f16d8a..2d0da7b76b1dae5d56e82182be4d297240fd45ca
--- a/src/fr/inrialpes/exmo/align/gen/inter/AlignedOntologyGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RenameProperties.java
@@ -19,16 +19,25 @@
* USA.
*/
+package fr.inrialpes.exmo.align.gen.alt;
-package fr.inrialpes.exmo.align.gen.inter;
-
-import com.hp.hpl.jena.ontology.OntModel;
-import org.semanticweb.owl.align.Alignment;
import java.util.Properties;
-public interface AlignedOntologyGenerator {
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+public class RenameProperties extends RenameThings {
+
+ public RenameProperties( Alterator om ) {
+ initModel( om );
+ };
- //generate an Alignment refering to the generated Ontology as onto2 (to be saved)
- public Alignment generate( OntModel o, Properties p );
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.RENAME_PROPERTIES );
+ if ( p == null ) return null;
+ float percentage = Float.parseFloat( p );
+ modifiedModel = renameResource ( true, false, percentage, true, false, false, 0);
+ return this; // useless
+ };
}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RenameThings.java b/src/fr/inrialpes/exmo/align/gen/alt/RenameThings.java
new file mode 100755
index 0000000000000000000000000000000000000000..044b409b3fbbc76d47910ba98533a549e4b5fc76
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RenameThings.java
@@ -0,0 +1,524 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntProperty;
+import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.ontology.OntClass;
+
+//Google API classes
+import com.google.api.GoogleAPI;
+import com.google.api.translate.Language;
+import com.google.api.translate.Translate;
+
+/*
+//WordNet API classes
+import edu.smu.tspell.wordnet.Synset;
+import edu.smu.tspell.wordnet.WordNetDatabase;
+*/
+
+// JE: reengineer this class... (what have we to rename)
+
+//activeRandomString is true -> we replace the label with a random string
+//activeTranslateString is true -> we translate the label
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+/**
+ * This is only an abstract class gathering the renaming routines
+ */
+public abstract class RenameThings extends BasicAlterator {
+
+ // -------------------------
+ // Label replacement
+
+ //replaces the label of the property
+ public void replacePropertyLabel( String uri, String newLabel, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation ) {
+ OntProperty prop = modifiedModel.getOntProperty( uri );
+ if ( prop.getLabel( "en" ) != null ) {
+ if ( activeTranslateString ) {
+ prop.setLabel( newLabel, "fr" );
+ } else {
+ prop.setLabel( newLabel, "en" );
+ }
+ }
+ }
+
+ // get 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<String> propertiesName = new ArrayList<String>(); //the properties identifiers
+
+ 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;
+
+ // build the list of all unrenamed properties from the model
+ for ( OntProperty p : properties ) {
+ String local = p.getLocalName();
+ String uri = initOntologyNS+local;
+ if ( alignment.containsKey( uri ) ) {
+ if ( alignment.getProperty( uri ).equals( modifiedOntologyNS+local ) )
+ notRenamedProperties.add( p ); //add the property to not renamed properties
+ }
+ }
+
+ nbProperties = properties.size(); //the number of renamed properties
+ renamedProperties = nbProperties - notRenamedProperties.size();
+ toBeRenamed = Math.round(percentage*nbProperties) - renamedProperties; // -renamedProperties -> for Benchmark
+
+ // toBeRenamed is negative when properties have been added to the model
+ if ( toBeRenamed < 0 ) toBeRenamed = 0;
+ //builds the list of properties to be renamed
+ int [] n = randNumbers(notRenamedProperties.size(), toBeRenamed);
+ for ( int i=0; i<toBeRenamed; i++ ) {
+ OntProperty p = notRenamedProperties.get(n[i]);
+ propertiesTo.add(p);
+ if ( p.getNameSpace().equals( modifiedOntologyNS ) )
+ propertiesName.add( p.getLocalName() );
+ }
+
+ for ( OntProperty prop : propertiesTo ) {
+ String prefix = prop.getNameSpace();
+ String localName = prop.getLocalName();
+ //has the same Namespace as the Ontology Namespace
+ if ( prefix.equals( modifiedOntologyNS ) ) {
+ if ( !propertiesIdentifiers.containsKey( localName ) ) {
+ if ( activeTranslateString ) { //replace the URI with the translated one
+ String translateStrg = parseString ( localName, true, false);
+ propertiesIdentifiers.put( localName , translateStrg );
+ replacePropertyLabel( prop.getURI(), translateStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+
+ if ( alignment.containsKey( initOntologyNS + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
+ alignment.put( initOntologyNS + prop.getLocalName() , initOntologyNS + 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 ( alignment.containsKey( initOntologyNS + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
+ alignment.put( initOntologyNS + prop.getLocalName() , initOntologyNS + newStrg);//the reference alignment
+ }
+ } else if ( activeSynonym ) {
+ String synonym = parseString (localName, false, true);
+ if ( propertiesName.contains( synonym ) )
+ propertiesIdentifiers.put( localName, localName );
+ else {
+ propertiesIdentifiers.put( localName, synonym );
+ replacePropertyLabel( prop.getURI(), synonym, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+ if ( alignment.containsKey( initOntologyNS + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
+ alignment.put( initOntologyNS + prop.getLocalName() , initOntologyNS + synonym ); //the reference alignment
+ }
+ }
+ } else if ( activeStringOperation == 1 ) { //replace the URI with the UpperCase URI
+ propertiesIdentifiers.put( localName , localName.toUpperCase() );
+ replacePropertyLabel( prop.getURI(), localName.toUpperCase(), activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+ if ( alignment.containsKey( initOntologyNS + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
+ alignment.put( initOntologyNS + prop.getLocalName() , initOntologyNS + localName.toUpperCase() ); //the reference alignment
+ }
+ } else if ( activeStringOperation == 2 ) {
+ propertiesIdentifiers.put( localName , localName.toLowerCase() );
+ replacePropertyLabel( prop.getURI(), localName.toLowerCase(), activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+ if ( alignment.containsKey( initOntologyNS + prop.getLocalName() ) ) { // alignment.remove( prop.getURI() );
+ alignment.put( initOntologyNS + prop.getLocalName() , initOntologyNS + localName.toLowerCase() ); //the reference alignment
+ }
+ } else {
+ propertiesIdentifiers.put( localName, localName + "PROPERTY" );
+ replacePropertyLabel( prop.getURI(), localName + "PROPERTY", activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+ if ( alignment.containsKey( initOntologyNS + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
+ alignment.put( initOntologyNS + prop.getLocalName() , initOntologyNS + localName + "PROPERTY" );
+ }
+ }
+ }
+ }
+ }
+ return propertiesIdentifiers;
+ }
+
+ //replaces the label of the class
+ public void replaceClassLabel( String uri, String newLabel, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation ) {
+ OntClass c = modifiedModel.getOntClass( uri );
+
+ if ( c.getLabel( "en" ) != null ) {
+ if ( activeTranslateString ) {
+ c.setLabel( newLabel, "fr" );
+ } else
+ c.setLabel( newLabel, "en" );
+ }
+ }
+
+ //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
+
+ int nbClasses, toBeRenamed, renamedClasses;
+
+ List<OntClass> notRenamedClasses = new ArrayList<OntClass>(); //the list of not renamed classes
+ List<OntClass> classes = getOntologyClasses(); //the list of ontology classes
+ List<OntClass> classesTo = new ArrayList<OntClass>(); //the list of classes to be renamed
+
+ // alignment contains those classes which have already been renamed
+ //builds the list of all unrenamed classes from the model
+ // JE: All these operations are very expensive (be better with either no namespace or alignment)
+ for ( OntClass c : classes ) {
+ String local = c.getLocalName();
+ String uri = initOntologyNS + local;
+ if ( alignment.containsKey( uri ) ) {
+ if ( alignment.getProperty( uri ).equals( modifiedOntologyNS+local ) )
+ notRenamedClasses.add( c ); //add the class to not renamed classes
+ }
+ }
+
+ nbClasses = classes.size();
+ renamedClasses = nbClasses - notRenamedClasses.size(); //the number of renamed classes
+ toBeRenamed = Math.round(percentage*nbClasses) - renamedClasses; // -renamedClasses -> for Benchmark
+
+ //System.err.println( "NbClasses = "+nbClasses+ " YetToRename = "+notRenamedClasses.size()+" I will rename = "+toBeRenamed );
+
+ // toBeRenamed is negative when classes have been added to the model
+ if ( toBeRenamed < 0 ) toBeRenamed = 0;
+ //build the list of classes to be renamed
+ int[] n = randNumbers( notRenamedClasses.size(), toBeRenamed );
+ for ( int i=0; i<toBeRenamed; i++ ) {
+ OntClass cls = notRenamedClasses.get(n[i]);
+ classesTo.add(cls);
+ }
+
+ for ( OntClass cls : classesTo ) {
+ if ( !cls.isRestriction() ) {
+ if ( !cls.isAnon() ) {
+ String prefix = cls.getNameSpace();
+ String localName = cls.getLocalName();
+
+ //has the same Namespace as the Ontology Namespace
+ if ( prefix.equals( modifiedOntologyNS ) ) {
+ if ( !classesIdentifiers.containsKey( localName ) ) {
+ if ( activeTranslateString ) { //replace the URI with the translated one
+ String translateStrg = parseString (localName, true, false);
+ classesIdentifiers.put( localName , translateStrg );
+ replaceClassLabel( cls.getURI(), translateStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+ if ( alignment.containsKey( initOntologyNS + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
+ alignment.put( initOntologyNS + cls.getLocalName() , initOntologyNS + 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 ( alignment.containsKey( initOntologyNS + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
+ alignment.put( initOntologyNS + cls.getLocalName() , initOntologyNS + 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 ( alignment.containsKey( initOntologyNS + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
+ alignment.put( initOntologyNS + cls.getLocalName() , initOntologyNS + synonym );//the reference alignment
+ }
+ } else if ( activeStringOperation == 1 ){ //replace the URI with the UpperCase URI
+ classesIdentifiers.put( localName , localName.toUpperCase() );
+ replaceClassLabel( cls.getURI(), localName.toUpperCase(), activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+ if ( alignment.containsKey( initOntologyNS + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
+ alignment.put( initOntologyNS + cls.getLocalName() , initOntologyNS + localName.toUpperCase() ); //the reference alignment
+ }
+ } else if ( activeStringOperation == 2 ){ //replace the URI with the LowerCase URI
+ classesIdentifiers.put( localName , localName.toLowerCase() );
+ replaceClassLabel( cls.getURI(), localName.toLowerCase(), activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+ if ( alignment.containsKey( initOntologyNS + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
+ alignment.put( initOntologyNS + cls.getLocalName() , initOntologyNS + localName.toLowerCase() ); //the reference alignment
+ }
+ } else {
+ classesIdentifiers.put( localName, localName + "CLASS" );
+ replaceClassLabel( cls.getURI(), localName + "CLASS", activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+ if ( alignment.containsKey( initOntologyNS + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
+ alignment.put( initOntologyNS + cls.getLocalName() , initOntologyNS + localName + "CLASS" );
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return classesIdentifiers;
+ }
+
+ //renames percentage properties and classes
+ //activeProperties -> if true, then rename properties
+ //activeClasses -> if true, then rename classes
+ public OntModel renameResource ( boolean activeProperties, boolean activeClasses, float percentage, boolean activeRandomString, boolean activeTranslateString, boolean activeSynonym, int activeStringOperation) {
+ 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
+
+ OntModel newModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );//create new Model
+ //get properties and classes identifiers
+ if ( activeProperties )
+ propertiesIdentifiers = getPropertiesIdentifiers( percentage, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation);
+ if ( activeClasses )
+ classesIdentifiers = getClassesIdentifiers( percentage, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
+
+ //iterate and modify the identifiers
+ for ( Statement stm : modifiedModel.listStatements().toList() ) {
+
+ Resource subject = stm.getSubject(); //the subject
+ Property predicate = stm.getPredicate(); //the predicate
+ RDFNode object = stm.getObject(); //the object
+
+ String subjectLocalName, subjectNameSpace;
+ String predicateLocalName, predicateNameSpace;
+ String objectLocalName, objectNameSpace;
+
+ boolean isPred, isSubj, isObj;
+
+ 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 ) {
+ if ( propertiesIdentifiers.containsKey( subject.getLocalName() ) ) {
+ //if the namespace of the subject is the same as the namespace of the property identifier
+ if ( subject.getNameSpace().equals( modifiedOntologyNS ) ) {//that we want to remove
+ isSubj = true;
+ subjectNameSpace = subject.getNameSpace();
+ subjectLocalName = subject.getLocalName();
+ subj = newModel.createResource( subjectNameSpace + propertiesIdentifiers.get( subjectLocalName ) );
+ }
+ }
+ }
+
+ if ( activeClasses ) {
+ if ( classesIdentifiers.containsKey( subject.getLocalName() ) ) {
+ //if the namespace of the subject is the same as the namespace of the property identifier
+ //that we want to remove
+ if (subject.getNameSpace().equals( modifiedOntologyNS ) ) {
+ isSubj = true;
+ subjectNameSpace = subject.getNameSpace();
+ subjectLocalName = subject.getLocalName();
+ subj = newModel.createResource( subjectNameSpace + classesIdentifiers.get( subjectLocalName ) );
+ }
+ }
+ }
+ }
+
+ //if it is the predicate of the statement
+ if ( activeProperties ) {
+ if ( propertiesIdentifiers.containsKey( predicate.getLocalName() ) ) {
+ //if the namespace of the predicate is the same as the namespace of the property identifier
+ //that we want to remove
+ if ( predicate.getNameSpace().equals( modifiedOntologyNS ) ) {
+ isPred = true;
+ predicateNameSpace = predicate.getNameSpace();
+ predicateLocalName = predicate.getLocalName();
+ pred = newModel.createProperty(predicateNameSpace, propertiesIdentifiers.get( predicateLocalName ) );
+ }
+ }
+ }
+
+ if ( activeClasses ) {
+ if ( classesIdentifiers.containsKey( predicate.getLocalName() ) ) {
+ //if the namespace of the predicate is the same as the namespace of the property identifier
+ //that we want to remove
+ if ( predicate.getNameSpace().equals( modifiedOntologyNS ) ) {
+ isPred = true;
+ predicateNameSpace = predicate.getNameSpace();
+ predicateLocalName = predicate.getLocalName();
+ pred = newModel.createProperty(predicateNameSpace, classesIdentifiers.get( predicateLocalName ) );
+ }
+ }
+ }
+
+ //if it is the object of the statement
+ if ( object.canAs( Resource.class ) )
+ if ( object.isURIResource() ) {
+ if ( activeProperties ) {
+ if ( propertiesIdentifiers.containsKey( object.asResource().getLocalName() ) ) {
+ //if the namespace of the object is the same as the namespace of the property identifier
+ //that we want to remove
+ if ( object.asResource().getNameSpace().equals( modifiedOntologyNS ) ) {
+ isObj = true;
+ objectNameSpace = object.asResource().getNameSpace();
+ objectLocalName = object.asResource().getLocalName();
+ obj = newModel.createResource(objectNameSpace + propertiesIdentifiers.get( objectLocalName ) );
+ }
+ }
+ }
+
+ if ( activeClasses ) {
+ if ( classesIdentifiers.containsKey( object.asResource().getLocalName() ) ) {
+ //if the namespace of the object is the same as the namespace of the property identifier that we want to remove
+ if ( object.asResource().getNameSpace().equals( modifiedOntologyNS ) ) {
+ isObj = true;
+ objectNameSpace = object.asResource().getNameSpace();
+ objectLocalName = object.asResource().getLocalName();
+ obj = newModel.createResource(objectNameSpace + classesIdentifiers.get( objectLocalName ) );
+ }
+ }
+ }
+ }
+
+ if ( isSubj ) {
+ if ( isPred ) {
+ 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 );
+ }
+ } else {
+ if ( isPred ) {
+ 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 ( activeClasses ) {
+ buildClassHierarchy();
+ //we update the class hierarchy according to the new modifications
+ classHierarchy.updateClassHierarchy( alignment );
+ //classHierarchy.printClassHierarchy();
+ }
+ return newModel;
+ }
+
+ // -------------------------
+ // Utility (string) functions
+
+ //removes spaces from a string
+ public String removeSpaces ( String str ) {
+ //return str.replaceAll("\\s+", "");
+ if ( !str.contains( " " ) )
+ return str;
+ else {
+ String aux = "", aux1="";
+ int index;
+
+ if ( str.contains( " " ) ) {
+ while ( str.indexOf( " " ) != -1 ) {
+ index = str.indexOf( " " );
+ aux += str.substring( 0, index );
+ aux1 = str.substring(index+2);
+ str = str.substring(index+1, index+2).toUpperCase().concat( aux1 );
+ }
+ aux += str;
+ return aux;
+ }
+ }
+ return str;
+ }
+
+ //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/");
+ //Translate.setHttpReferrer("http://code.google.com/p/google-api-translate-java/");
+ try {
+ translatedText = Translate.execute(source, Language.ENGLISH, Language.FRENCH);
+ } catch (Exception e) {
+ System.err.println( "Exception " + e.getMessage() );
+ }
+ return removeSpaces ( translatedText );
+ }
+
+ public String getSynonym( String source ) {
+ return source;
+ }
+ /*
+ //synonym of the word
+ public String getSynonym ( String source ) {
+ String synonym = "";
+ //set this variable according to your WordNet installation folder
+ //see : http://lyle.smu.edu/~tspell/jaws/index.html
+ System.setProperty("wordnet.database.dir", "/usr/Wordnet/WordNet-3.0/dict");
+ WordNetDatabase database = WordNetDatabase.getFileInstance();
+ Synset[] synsets = database.getSynsets( source );
+ if (synsets.length > 0) {
+ for (int i = 0; i < synsets.length; i++) {
+ String[] wordForms = synsets[i].getWordForms();
+ for (int j = 0; j < wordForms.length; j++) {
+ if ( !wordForms[j].equals( source ) ) {
+ synonym = removeSpaces ( wordForms[j] );
+ return synonym;
+ }
+ }
+ }
+ }
+ else
+ return source;
+ return source;
+ }
+ */
+
+ public String parseString (String str, boolean activeTranslateString, boolean activeSynonym) {
+ // if ( debug ) System.err.println ( "str = [" + str + "]" );
+ char [] parsed = str.toCharArray();
+ String newString = "";
+
+ for ( int i=1; i<parsed.length; i++ ) {
+ if( Character.isUpperCase( parsed[i] ) ) {
+ String aux = str.substring(0, i);
+
+ if ( activeTranslateString )
+ newString = newString.concat( translateString( str.substring(0, i) ) );
+ if ( activeSynonym )
+ newString = newString.concat( getSynonym( str.substring(0, i) ) );
+
+ str = str.substring(i);
+ }
+ }
+
+ if ( activeTranslateString )
+ newString = newString.concat( translateString(str.substring(0)) );
+ if ( activeSynonym )
+ newString = newString.concat( getSynonym(str.substring(0)) );
+ return newString;
+ }
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/SuppressHierarchy.java b/src/fr/inrialpes/exmo/align/gen/alt/SuppressHierarchy.java
new file mode 100755
index 0000000000000000000000000000000000000000..de9971dac00686c4a3d31512cb3b19aa4f159ce7
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/alt/SuppressHierarchy.java
@@ -0,0 +1,83 @@
+/*
+ * $Id$
+ *
+ * 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.
+ */
+
+package fr.inrialpes.exmo.align.gen.alt;
+
+import com.hp.hpl.jena.ontology.OntClass;
+
+import java.util.Properties;
+import java.util.List;
+import java.util.ArrayList;
+
+import fr.inrialpes.exmo.align.gen.Alterator;
+import fr.inrialpes.exmo.align.gen.ParametersIds;
+
+public class SuppressHierarchy extends BasicAlterator {
+
+ public SuppressHierarchy( Alterator om ) {
+ initModel( om );
+ };
+
+ public Alterator modify( Properties params ) {
+ String p = params.getProperty( ParametersIds.NO_HIERARCHY );
+ if ( p == null ) return null;
+ int level = getMaxLevel();
+ while ( getMaxLevel() != 1 ) { // JE: dangerous to not use level
+ //this.classHierarchy.printClassHierarchy();
+ noHierarchy ( level );
+ level--;
+ }
+ return this; // useless
+ };
+
+ // flatten level
+ public void noHierarchy ( int level ) {
+ if ( level == 1 ) return;
+ int size;
+ boolean active = false;
+ ArrayList<OntClass> levelClasses = new ArrayList<OntClass>(); //the list of classes from that level
+ ArrayList<OntClass> parentLevelClasses = new ArrayList<OntClass>(); //the list of parent of the child classes from that level
+ ArrayList<OntClass> superLevelClasses = new ArrayList<OntClass>(); //the list of parent of the parent classes from that level
+ buildClassHierarchy(); //check if the class hierarchy is built
+ active = this.classHierarchy.flattenClassHierarchy( modifiedModel, level, levelClasses, parentLevelClasses, superLevelClasses);
+ size = levelClasses.size();
+
+ for ( int i=0; i<size; i++ ) {
+ OntClass childClass = levelClasses.get( i ); //child class
+ OntClass parentClass = parentLevelClasses.get( i ); //parent class
+ //all the classes are subclasses of owl: Thing
+ if ( active ) { //if ( !parentClass.getURI().equals( "Thing" ) ) {
+ OntClass superClass = superLevelClasses.get( i ); //parent class of the child class parents
+ childClass.addSuperClass( superClass );
+ parentClass.removeSubClass( childClass );
+ } else {
+ parentClass.removeSubClass( childClass );
+ }
+ }
+ }
+
+ //must have the max level of the class hierarchy
+ public int getMaxLevel() {
+ buildClassHierarchy(); //check if the class hierarchy is built
+ return classHierarchy.getMaxLevel();
+ }
+
+}