diff --git a/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java b/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
index b7bcd474338a0a06c4725ccfaa38b950a296de86..264bcdf77d95006f54a29429d924e5fa07545406 100644
--- a/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
@@ -35,6 +35,9 @@ public class BenchmarkGenerator extends TestSet {
// Process params
debug = ( params.getProperty( "debug" ) != null );
+ // JE: ugly
+ secondOntoFile = params.getProperty( "outdir" )+"/101/onto.rdf";
+
// Test configuration parameters
int maximum = 5;
float incr = 0.2f;
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
index 7fb23b119116d9482546cefd60a46e2991eda445..e74514dcefd3cdfa7281d3262d130e99a2b94d07 100644
--- a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
+++ b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
@@ -88,29 +88,28 @@ import edu.smu.tspell.wordnet.WordNetDatabase;
public class OntologyModifier {
private boolean debug = false;
- private ClassHierarchy classHierarchy; //the class hierarchy
- // JE: In all this class, model is useless!
- private OntModel model; //the model - the original Ontology
- private OntModel modifiedModel; //the modified Ontology
- private String namespace; //the Namespace
+
+ 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 Alignment alignment; //the alignment of the two Ontologies
- private Properties params; //the alignment
- 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; //
+
+ 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 alignment ) {
+ public OntologyModifier ( OntModel model, Alignment al ) {
modifiedModel = model;
- this.alignment = alignment;
- namespace = model.getNsPrefixURI(""); // JE: ???
- namespaceNew = "";
- params = new Properties();
+ // get the default namespace of the model
+ namespace = model.getNsPrefixURI("");
+ alignment = new Properties();
}
// -------------------------
@@ -120,8 +119,8 @@ public class OntologyModifier {
debug = d;
}
- public void setNewNamespace(String newNamespace) {
- this.namespaceNew = newNamespace;
+ public void setNewNamespace( String newNamespace ) {
+ namespaceNew = newNamespace;
//if ( debug ) System.err.println("New namespace [" + this.namespaceNew + "]");
}
@@ -143,12 +142,7 @@ public class OntologyModifier {
//get properties
public Properties getProperties() {
- return this.params;
- }
-
- //returns the alignment
- public Alignment getAlignment() {
- return this.alignment;
+ return alignment;
}
// -------------------------
@@ -319,10 +313,10 @@ public class OntologyModifier {
//builds the list of all unrenamed properties from the model
for ( OntProperty p : properties ) {
String uri = base + p.getLocalName();
- // JE: I am affraid that this.params is a terible thing here
- if ( this.params.containsKey( uri ) ) {
+ // JE: I am affraid that alignment is a terible thing here
+ if ( alignment.containsKey( uri ) ) {
String key = uri;
- String value = this.params.getProperty( key );
+ String value = alignment.getProperty( key );
if ( key.equals( value ) )
notRenamedProperties.add( p ); //add the property to not renamed properties
}
@@ -356,16 +350,16 @@ public class OntologyModifier {
propertiesIdentifiers.put( localName , translateStrg );
replacePropertyLabel( prop.getURI(), translateStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( base + prop.getLocalName() , base + translateStrg );//the reference alignment
+ 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 ( params.containsKey( base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( base + prop.getLocalName() , base + newStrg);//the reference alignment
+ if ( alignment.containsKey( base + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
+ alignment.put( base + prop.getLocalName() , base + newStrg);//the reference alignment
}
}
else if ( activeSynonym ) {
@@ -375,30 +369,30 @@ public class OntologyModifier {
else {
propertiesIdentifiers.put( localName, synonym );
replacePropertyLabel( prop.getURI(), synonym, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( this.base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( this.base + prop.getLocalName() , this.base + synonym ); //the reference alignment
+ 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 ( params.containsKey( this.base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( this.base + prop.getLocalName() , this.base + toUpperCase( localName ) ); //the reference alignment
+ 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 ( params.containsKey( this.base + prop.getLocalName() ) ) { // this.params.remove( prop.getURI() );
- this.params.put( this.base + prop.getLocalName() , this.base + toLowerCase( localName ) ); //the reference alignment
+ 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 ( params.containsKey( this.base + prop.getLocalName() ) ) { //this.params.remove( prop.getURI() );
- this.params.put( this.base + prop.getLocalName() , this.base + localName + "PROPERTY" );
+ if ( alignment.containsKey( this.base + prop.getLocalName() ) ) { //alignment.remove( prop.getURI() );
+ alignment.put( this.base + prop.getLocalName() , this.base + localName + "PROPERTY" );
}
}
}
@@ -429,14 +423,14 @@ public class OntologyModifier {
List<OntClass> classes = getOntologyClasses(); //the list of ontology classes
List<OntClass> classesTo = new ArrayList<OntClass>(); //the list of classes to be renamed
- // params contains those classes which have already been 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 ( this.params.containsKey( uri ) ) {
+ if ( alignment.containsKey( uri ) ) {
String key = uri;
- String value = this.params.getProperty( uri );
+ String value = alignment.getProperty( uri );
//they didnt change
if ( key.equals( value ) )
notRenamedClasses.add( c ); //add the class to not renamed classes
@@ -469,45 +463,45 @@ public class OntologyModifier {
String translateStrg = parseString (localName, true, false);
classesIdentifiers.put( localName , translateStrg );
replaceClassLabel( cls.getURI(), translateStrg, activeRandomString, activeTranslateString, activeSynonym, activeStringOperation );
- if ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( this.base + cls.getLocalName() , this.base + translateStrg); //the reference alignment
+ 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 ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( this.base + cls.getLocalName() , this.base + newStrg ); //the reference alignment
+ 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 ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( this.base + cls.getLocalName() , this.base + synonym );//the reference alignment
+ 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 ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( this.base + cls.getLocalName() , this.base + toUpperCase( localName ) ); //the reference alignment
+ 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 ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( this.base + cls.getLocalName() , this.base + toLowerCase( localName ) ); //the reference alignment
+ 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 ( params.containsKey( this.base + cls.getLocalName() ) ) { //this.params.remove( cls.getURI() );
- this.params.put( this.base + cls.getLocalName() , this.base + localName + "CLASS" );
+ if ( alignment.containsKey( this.base + cls.getLocalName() ) ) { //alignment.remove( cls.getURI() );
+ alignment.put( this.base + cls.getLocalName() , this.base + localName + "CLASS" );
}
}
}
@@ -666,7 +660,7 @@ public class OntologyModifier {
if ( activeClasses ) {
checkClassHierarchy();
//we update the class hierarchy according to the new modifications
- this.classHierarchy.updateClassHierarchy( params ); //this.classHierarchy.printClassHierarchy();
+ this.classHierarchy.updateClassHierarchy( alignment ); //this.classHierarchy.printClassHierarchy();
}
return newModel;
}
@@ -927,12 +921,12 @@ public class OntologyModifier {
modifiedModel = changeDomainRange( uris );
//remove the URI of the class from the reference alignment
- for ( String key : this.params.stringPropertyNames() ) {
- String value = this.params.getProperty( key );
+ for ( String key : alignment.stringPropertyNames() ) {
+ String value = alignment.getProperty( key );
if ( cl.contains( this.namespace + key.substring(key.indexOf(this.base) + this.base.length() )) )
- this.params.remove( key );
+ 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
- this.params.remove( key );
+ alignment.remove( key );
}
}
@@ -966,7 +960,7 @@ public class OntologyModifier {
for ( int i=0; i<toBeRemoved; i++ ) {
Individual indiv = individuals.get(n[i]); //remove the individual from the reference alignment
individualsTo.add( indiv );
- //this.params.remove( indiv.getURI() );
+ //alignment.remove( indiv.getURI() );
}
for ( Statement st : modifiedModel.listStatements().toList() ) {
@@ -1007,7 +1001,7 @@ public class OntologyModifier {
pr.add( p.getURI() );
- //this.params.remove( p.getURI() );
+ //alignment.remove( p.getURI() );
for ( Iterator it = p.listReferringRestrictions(); it.hasNext(); ) {//get the restrictions of that property
restrictions.add( (Restriction)it.next() );
}
@@ -1036,18 +1030,18 @@ public class OntologyModifier {
}
}
- for ( OntClass c : resources )
- c.remove();
+ for ( OntClass c : resources ) c.remove();
- //remove that property from params
- //since we don't respect any order the value can appear as a value, thus we must iterate among all params to delete it
- for ( String key : this.params.stringPropertyNames() ) {
- String value = this.params.getProperty(key);
- if ( pr.contains( this.namespace + key.substring(key.indexOf(this.base) + this.base.length()) ) ) { //if ( debug ) System.err.println( "Elimin " + key );
- this.params.remove( key );
+ //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) + this.base.length()) ) ) { //if ( debug ) System.err.println( "Elimin " + key );
- this.params.remove( key );
+ if ( pr.contains( this.namespace + value.substring(key.indexOf(this.base) + baselength) ) ) { //if ( debug ) System.err.println( "Elimin " + key );
+ alignment.remove( key );
}
}
@@ -1302,13 +1296,14 @@ public class OntologyModifier {
modifiedModel = changeDomainRange(unionOf);
//remove the parentClass from the alignment
- for ( String key : this.params.stringPropertyNames() ) {
- String value = this.params.getProperty(key);
- if ( parentURI.contains( this.namespace + key.substring(key.indexOf(this.base) + this.base.length()) ) ) { //this.classHierarchy.removeUri("Thing", key);
- this.params.remove(key);
+ 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) + this.base.length() ))) { //this.classHierarchy.removeUri("Thing", value);
- this.params.remove(key);
+ if ( parentURI.contains( this.namespace + value.substring(key.indexOf(this.base) + baselength ))) { //this.classHierarchy.removeUri("Thing", value);
+ alignment.remove(key);
}
}
@@ -1373,67 +1368,86 @@ public class OntologyModifier {
// isAlign is a not so good way to test initialisation
// (initialisation with an empty Properties is done in the initialiser)
- // but the "params" is used everywhere...
+ // but the "alignment" is used everywhere...
//the initial reference alignment
// JE: !!!: no order guarantee in properties !!!
- public void initializeAlignment( Properties params ) {
- this.params = params;
+ public void initializeAlignment( Properties al ) {
+ alignment = al;
- Enumeration e = this.params.propertyNames();
+ Enumeration e = alignment.propertyNames();
String aux = (String)e.nextElement();
base = aux.substring(0, aux.lastIndexOf("#")+1);
- this.isAlign = true;
+ isAlign = true;
}
- public void initializeAlignment() {
+ /**
+ * 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
- this.params = new Properties();
+ alignment = new Properties();
- this.isAlign = true; //the alignment has been computed for the first time
- this.base = this.namespace;
-
+ 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( this.namespace ) )
- this.params.put( cls.getURI() , cls.getURI() ); //add them to the initial alignment
+ 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( this.namespace ) )
- this.params.put( prop.getURI() , prop.getURI() ); //add them to the initial alignment
+ 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 void computeAlignment( String fileName ) {
- URI onto1 = null;
- URI onto2 = null;
-
- this.alignment = new URIAlignment();
+ public Alignment getAlignment() {
+ Alignment extractedAlignment = new URIAlignment();
try {
- onto1 = new URI ( this.base.substring(0, this.base.lastIndexOf("#")) );
- onto2 = new URI( this.namespaceNew.substring(0, this.namespaceNew.lastIndexOf("#")) );
+ URI onto1 = new URI( base.substring(0, base.lastIndexOf("#")) );
+ URI onto2 = new URI( namespaceNew.substring(0, namespaceNew.lastIndexOf("#")) );
- this.alignment.init(onto1, onto2);
- this.alignment.setFile1(onto1);
- this.alignment.setFile2(onto2);
+ 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 : this.params.stringPropertyNames() ) {
- String value = this.params.getProperty(key);
+ 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 + "]" );
- this.alignment.addAlignCell( uri1, uri2, "=", 1 );
+ extractedAlignment.addAlignCell( uri1, uri2, "=", 1 );
}
- } catch (AlignmentException aex) { System.err.println( "Exception " + aex.getMessage() );
- } catch (Exception ex) { System.err.println("Exception " + ex.getMessage());
+ } catch ( Exception ex ) {
+ ex.printStackTrace();
}
+ return extractedAlignment;
}
// -------------------------
@@ -1538,8 +1552,8 @@ public class OntologyModifier {
else
aux = param;
- if ( !this.isAlign ) {
- initializeAlignment(); //determine the elements from the initial reference alignment
+ if ( !isAlign ) {
+ initializeAlignment( false ); //determine the elements from the initial reference alignment
}
if ( name.equals( ParametersIds.ADD_CLASSES ) ) { //add percentage classes
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
index ad2f31375ec553e94f46529e5301913b2e30d194..e67cc5d8721ee16a88cf23eb062b62d5272fa513 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
@@ -59,12 +59,13 @@ import com.hp.hpl.jena.util.FileManager;
import java.util.Properties;
-public class TestGenerator implements AlignedOntologyGenerator {
+// 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
@@ -86,7 +87,10 @@ public class TestGenerator implements AlignedOntologyGenerator {
public void setDebug( boolean d ) { debug = d; }
//returns the modified ontology
- public OntModel getModifiedOntology() { return modifiedOntology ; }
+ public OntModel getModifiedOntology() { return modifiedOntology; }
+
+ //returns the modified ontology
+ public void setInitOntoURI( String uri ) { initOntoURI = uri; }
public void setNamespace( String ns ) { namespace = ns; }
//return the newNamespace
@@ -189,11 +193,7 @@ public class TestGenerator implements AlignedOntologyGenerator {
OntModel onto = loadOntology( file );
//set the namespace
setNamespace( getURI( testNumber ) );
- Alignment align = null;
- if ( al == null )
- align = generate( onto, params );
- else
- align = generate( onto, params, al );
+ Alignment align = generate( onto, params, al );
outputTestDirectory( getModifiedOntology(), align, testNumber );
return modifier.getProperties();
@@ -206,6 +206,7 @@ public class TestGenerator implements AlignedOntologyGenerator {
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() );
@@ -213,7 +214,11 @@ public class TestGenerator implements AlignedOntologyGenerator {
modifier.setNewNamespace( namespace );
// Initialize the reference alignment
if ( initalign == null ) {
- modifier.initializeAlignment();
+ if ( params.getProperty( "copy101" ) != null ) {
+ modifier.initializeAlignment( true );
+ } else {
+ modifier.initializeAlignment( false );
+ }
} else {
modifier.initializeAlignment( initalign );
}
@@ -231,17 +236,15 @@ public class TestGenerator implements AlignedOntologyGenerator {
applyModification( modifier, params, ParametersIds.ADD_CLASSES );
applyModification( modifier, params, ParametersIds.ADD_PROPERTIES );
- // SUPPRESSED FOR TESTING THAT THIS IS THE CULPRIT
- //if ( params.getProperty( ParametersIds.ADD_CLASSES ) == null ) applyModification( modifier, params, ParametersIds.RENAME_CLASSES );
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.NO_HIERARCHY );
applyModification( modifier, params, ParametersIds.ADD_CLASSESLEVEL );
- applyModification( modifier, params, ParametersIds.REMOVE_INDIVIDUALS );
+ applyModification( modifier, params, ParametersIds.NO_HIERARCHY );
/*
for( String key : params.stringPropertyNames() ) {
@@ -252,16 +255,12 @@ public class TestGenerator implements AlignedOntologyGenerator {
*/
//saves the alignment into the file "refalign.rdf", null->System.out
- modifier.computeAlignment( alignname ); //at the end, compute the reference alignment
- resultAlignment = modifier.getAlignment(); //get the reference alignment
+ //at the end, compute the reference alignment
+ resultAlignment = modifier.getAlignment(); //get the reference alignment
modifiedOntology = modifier.getModifiedOntology(); //get the modified ontology
return resultAlignment;
}
- public Alignment generate( OntModel onto, Properties p ) {
- return generate( onto, p, (Properties)null );
- }
-
public void applyModification( OntologyModifier modifier, Properties p, String m ) {
modifier.modifyOntology( m, p.getProperty( m ) );
}
diff --git a/src/fr/inrialpes/exmo/align/gen/TestSet.java b/src/fr/inrialpes/exmo/align/gen/TestSet.java
index e6ab04610a5991231b56cd72fb0771d39a7c05f4..a70e471b990565c369be88ab400014c58d73363b 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestSet.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestSet.java
@@ -40,6 +40,7 @@ import java.util.HashSet;
public abstract class TestSet {
private String initOntoFile; //the initial ontology file
+ protected String secondOntoFile; //the secondary ontology file
protected boolean continuous = false;
protected boolean debug = false;
@@ -86,10 +87,6 @@ public abstract class TestSet {
// ----------------------------------------------------------
// Generates the test set
public void generate( Properties params ) {
- // Initialises test cases tree
- initTestCases( params );
- // Print it
- if ( debug ) printTestHierarchy( root, 0 );
// Generator parameters... are these OK?
generator.setDebug( debug );
initOntoFile = params.getProperty( "filename" ); // If no filename error
@@ -102,15 +99,23 @@ public abstract class TestSet {
} else {
ontoname = "onto.rdf"; // could be better
}
+ secondOntoFile = initOntoFile; // default value
+
+ // Initialises test cases tree
+ initTestCases( params );
+ // Print it
+ if ( debug ) printTestHierarchy( root, 0 );
if ( params.getProperty( "alignname" ) != null ) generator.setAlignFilename( params.getProperty( "alignname" ) );
// Generate all tests
startTestGeneration();
}
// Recursively generate tests
+ // All this is really tied to
public void startTestGeneration() {
- Properties newalign;
- newalign = generator.modifyOntology( initOntoFile, (Properties)null, root.name, new Properties() );
+ Properties parameters = new Properties();
+ parameters.setProperty( "copy101", "" );
+ Properties newalign = generator.modifyOntology( initOntoFile, (Properties)null, root.name, parameters );
for ( TestCase sub : root.subTests ) {
generateTest( sub, newalign );
}
@@ -121,7 +126,8 @@ public abstract class TestSet {
if ( continuous ) {
newalign = generator.incrementModifyOntology( c.father.name, (Properties)align.clone(), c.name, c.parameters );
} else {
- newalign = generator.modifyOntology( initOntoFile, (Properties)null, c.name, c.cumulated );
+ // Here we should start from the initOntoFile 101
+ newalign = generator.modifyOntology( secondOntoFile, (Properties)null, c.name, c.cumulated );
}
for ( TestCase sub : c.subTests ) {
generateTest( sub, newalign );