diff --git a/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java b/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
index 23357d1972096a2f36f8dc8bb388ad1e865a7ca3..b7bcd474338a0a06c4725ccfaa38b950a296de86 100644
--- a/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
@@ -36,37 +36,36 @@ public class BenchmarkGenerator extends TestSet {
debug = ( params.getProperty( "debug" ) != null );
// Test configuration parameters
+ int maximum = 5;
+ float incr = 0.2f;
String mod = params.getProperty( "modality" ); // "mult"
- String hard = params.getProperty( "increment" );
- String max = params.getProperty( "maximum" );
- if ( debug ) System.err.println( " Mod: "+mod+" / Incr: "+hard );
- String SUFFIX = null;
-
- /* Test 101 Generate the initial situation */
- root = initTests( "101" );
-
- /*
- * Tests 201, 202, 248, 249, 253, 258, 259, 250, 254,
- * 262, 257, 260, 265, 261, 266, 251, 252
- */
boolean multModality = (mod != null && mod.startsWith( "mult" ));
- float i1 = 0.0f;
- int maximum = Integer.parseInt( "5" );
- float incr = Float.parseFloat( "0.2" );
+ String hard = params.getProperty( "increment" );
try {
if ( hard != null && !hard.equals("") ) incr = Float.parseFloat( hard );
} catch ( Exception ex ) {
ex.printStackTrace(); // continue with the default
}
+ String max = params.getProperty( "maximum" );
+ if ( max != null ) maximum = Integer.parseInt( max );
+ if ( debug ) System.err.println( " Mod: "+mod+" / Incr: "+incr+" / Max: "+maximum );
+
+ /* Test 101 Generate the initial situation */
+ root = initTests( "101" );
String PREVTEST = "101";
- for ( int i = 0; i1 < 1.00f ; i++ ) { // && i < maximum
+
+ String SUFFIX = null;
+ float i1 = 0.0f;
+
+ /* Iterator for gradual change */
+ for ( int i = 0; i1 < 1.00f && i < maximum ; i++ ) { //
if ( i > 0 ) PREVTEST = "201"+SUFFIX; // The previous suffix
if ( !multModality ) i1 += incr; // traditional
else i1 += (1. - i1) * incr; // hardened
//if ( debug ) System.err.println( " ******************************************************** "+i+": i1 = "+i1 );
if ( i1 < 1.0f ) {
- SUFFIX = "-"+((Float)i1).toString().substring(2, 3); // 2 4 6 8
+ SUFFIX = "-"+(i+1)*2; //((Float)i1).toString().substring(2, 3); // 2 4 6 8
} else {
SUFFIX = "";
}
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
index 01c637350cd0701bf5b72b148aac72bd2ecc8dc9..7fb23b119116d9482546cefd60a46e2991eda445 100644
--- a/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
+++ b/src/fr/inrialpes/exmo/align/gen/OntologyModifier.java
@@ -87,6 +87,7 @@ import edu.smu.tspell.wordnet.WordNetDatabase;
//activeTranslateString is true -> we translate the label
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
@@ -95,34 +96,64 @@ public class OntologyModifier {
private String namespaceNew;
private Alignment alignment; //the alignment of the two Ontologies
private Properties params; //the alignment
- private boolean isBuild; //keep track if the class hierarchy is build
- private boolean isAlign; //keep track if the initial alignment has already been computed
- private boolean isChanged; //keep track if the namespace of the new ontology is changed
+ 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 ) {
modifiedModel = model;
- namespace = model.getNsPrefixURI(""); // JE: ???
this.alignment = alignment;
- isBuild = false;
- isAlign = false;
- isChanged = false;
+ namespace = model.getNsPrefixURI(""); // JE: ???
namespaceNew = "";
params = new Properties();
}
- //no-args constructor
- public OntologyModifier () { }
+ // -------------------------
+ // Accessors
- //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();
+ public void setDebug( boolean d ) {
+ debug = d;
+ }
+
+ public void setNewNamespace(String newNamespace) {
+ this.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 this.params;
+ }
+
+ //returns the alignment
+ public Alignment getAlignment() {
+ return this.alignment;
+ }
+
+ // -------------------------
+ // Utility (string) functions
+
//generates a random string with the length "length"
public String getRandomString() {
Random generator = new Random();
@@ -211,7 +242,7 @@ public class OntologyModifier {
*/
public String parseString (String str, boolean activeTranslateString, boolean activeSynonym) {
- // System.err.println ( "str = [" + str + "]" );
+ // if ( debug ) System.err.println ( "str = [" + str + "]" );
char [] parsed = str.toCharArray();
String newString = "";
@@ -235,6 +266,9 @@ public class OntologyModifier {
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
@@ -256,6 +290,9 @@ public class OntologyModifier {
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 );
@@ -634,6 +671,22 @@ public class OntologyModifier {
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 ) {
@@ -887,7 +940,7 @@ public class OntologyModifier {
public void removeClassesFromLevel ( int level ) {
HashMap<String, String> uris = new HashMap<String, String>();
String parentURI = "";
- //System.err.println( "Level " + level );
+ //if ( debug ) System.err.println( "Level " + level );
/* if ( level == 1 ) //except classes from level 1
return; */
List<OntClass> classes = new ArrayList<OntClass>();
@@ -990,10 +1043,10 @@ public class OntologyModifier {
//since we don't respect any order the value can appear as a value, thus we must iterate among all params to delete it
for ( String key : this.params.stringPropertyNames() ) {
String value = this.params.getProperty(key);
- if ( pr.contains( this.namespace + key.substring(key.indexOf(this.base) + this.base.length()) ) ) { //System.err.println( "Elimin " + 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 );
}
- if ( pr.contains( this.namespace + value.substring(key.indexOf(this.base) + this.base.length()) ) ) { //System.err.println( "Elimin " + 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 );
}
}
@@ -1195,10 +1248,10 @@ public class OntologyModifier {
restr.add(r);
if ( r.isSomeValuesFromRestriction() )
restr.add(r);
- //System.err.println( cls.getURI() + cls.getLocalName() );
+ //if ( debug ) System.err.println( cls.getURI() + cls.getLocalName() );
}
}
- //System.err.println( restr.size() );
+ //if ( debug ) System.err.println( restr.size() );
if ( !restrictions.containsKey( parentClass.getURI() ) ) {
restrictions.put( parentClass.getURI(), restr );
@@ -1209,9 +1262,9 @@ public class OntologyModifier {
if ( active ) { //if ( !parentClass.getURI().equals( "Thing" ) ) {
OntClass superClass = superLevelClasses.get( i ); //parent class of the child class parents
- //System.err.println("SuperClass class [" + superClass.getURI() + "]");
- //System.err.println("Parent class [" + parentClass.getURI() + "]");
- //System.err.println("Child class [" + childClass.getURI() + "]");
+ //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 ..
@@ -1315,6 +1368,9 @@ public class OntologyModifier {
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 "params" is used everywhere...
@@ -1372,7 +1428,7 @@ public class OntologyModifier {
String value = this.params.getProperty(key);
URI uri1 = URI.create(key);
URI uri2 = URI.create(this.namespaceNew + value.substring(value.indexOf(this.base) + this.base.length()));
- //System.err.println( "[" + key + "][" + value + "]" );
+ //if ( debug ) System.err.println( "[" + key + "][" + value + "]" );
this.alignment.addAlignCell( uri1, uri2, "=", 1 );
}
} catch (AlignmentException aex) { System.err.println( "Exception " + aex.getMessage() );
@@ -1380,10 +1436,8 @@ public class OntologyModifier {
}
}
- public void setNewNamespace(String newNamespace) {
- this.namespaceNew = newNamespace;
- //System.err.println("New namespace [" + this.namespaceNew + "]");
- }
+ // -------------------------
+ // Namespace management and change
//change the namespace of the modified ontology
// JE: ??
@@ -1464,37 +1518,8 @@ public class OntologyModifier {
return newModel;
}
- //returns the modified ontology after changing the namespace
- public OntModel getModifiedOntology () {
- //System.err.println( "->change namespace" );
- modifiedModel = changeNamespace(); //change the namespace of the modified ontology
- //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 this.params;
- }
-
- //returns the alignment
- public Alignment getAlignment() {
- return this.alignment;
- }
-
- //must have the max level of the class hierarchy
- public int getMaxLevel() {
- checkClassHierarchy(); //check if the class hierarchy is built
- return this.classHierarchy.getMaxLevel();
- }
+ // -------------------------
+ // Main entry point
//OntModel model, OntModel modifiedModel, Alignment alignment
public void modifyOntology( String name, String param ) {
@@ -1518,52 +1543,52 @@ public class OntologyModifier {
}
if ( name.equals( ParametersIds.ADD_CLASSES ) ) { //add percentage classes
- System.err.println( "Add Class" + "[" + value + "]");
+ if ( debug ) System.err.println( "Add Class" + "[" + value + "]");
addSubClasses( value );
} else if ( name.equals( ParametersIds.REMOVE_CLASSES ) ) { //remove percentage classes
- System.err.println( "Remove Class" + "[" + value + "]");
+ if ( debug ) System.err.println( "Remove Class" + "[" + value + "]");
removeSubClasses( value );
} else if ( name.equals( ParametersIds.REMOVE_COMMENTS ) ) { //remove percentage comments
- System.err.println( "Remove Comments" + "[" + value + "]");
+ if ( debug ) System.err.println( "Remove Comments" + "[" + value + "]");
removeComments ( value );
} else if ( name.equals( ParametersIds.REMOVE_PROPERTIES ) ) { //remove percentage properties
- System.err.println( "Remove Property" + "[" + value + "]");
+ if ( debug ) System.err.println( "Remove Property" + "[" + value + "]");
removeProperties ( value );
} else if ( name.equals( ParametersIds.ADD_PROPERTIES ) ) { //add percentage properties
- System.err.println( "Add Property" + "[" + value + "]");
+ 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()) );
- System.err.println( "level " + level );
- System.err.println( "nbClasses " + nbClasses );
+ 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
- System.err.println("Remove all classes from level" + (int)value );
+ 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 );
- System.err.println( "New class hierarchy level " + getMaxLevel() ) ;
+ if ( debug ) System.err.println( "New class hierarchy level " + getMaxLevel() ) ;
} else if ( name.equals( ParametersIds.RENAME_CLASSES ) ) { //rename classes
- System.err.println("Rename classes" + "[" + value + "]" );
- //System.err.println("\nValue = " + value + "\n"); //activeProperties, activeClasses, ..
+ 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
- System.err.println("Rename properties " + "[" + value + "]" );
- //System.err.println("\nValue = " + value + "\n"); //activeProperties, activeClasses, ..
+ 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
- System.err.println("Remove restrictions" + "[" + value + "]");
+ if ( debug ) System.err.println("Remove restrictions" + "[" + value + "]");
removeRestrictions( value );
} else if ( name.equals( ParametersIds.REMOVE_INDIVIDUALS ) ) { //remove percentage individuals
- System.err.println("Remove individuals" + "[" + value + "]");
+ if ( debug ) System.err.println("Remove individuals" + "[" + value + "]");
removeIndividuals( value );
} else if ( name.equals( ParametersIds.NO_HIERARCHY ) ) { //no hierarchy
- System.err.println( "NoHierarchy" );
+ if ( debug ) System.err.println( "NoHierarchy" );
noHierarchy();
}
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGen.java b/src/fr/inrialpes/exmo/align/gen/TestGen.java
index e7ca9c7b6f85c613d0e54210e0f880739830dbe9..593a44df0a5e2068451506a2fe5d926f7b7bced5 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGen.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGen.java
@@ -88,28 +88,26 @@ public class TestGen {
while ((c = g.getopt()) != -1) {
switch (c) {
- case 'h':
- printUsage();
- return;
- case 'm':
- methodName = g.getOptarg();
- System.err.println("method " + "[" + methodName + "]");
- break;
- case 'i':
- fileName = g.getOptarg();
- params.setProperty( "filename", fileName );
- System.err.println("fileName " + "[" + fileName + "]");
- break;
- case 'n':
- params.setProperty( "ontoname", g.getOptarg() );
- break;
- case 'a':
- params.setProperty( "alignname", g.getOptarg() );
- break;
- case 't':
- testNumber = g.getOptarg();
- System.err.println("testNumber " + "[" + testNumber + "]");
- break;
+ case 'h':
+ printUsage();
+ return;
+ case 'm':
+ methodName = g.getOptarg();
+ break;
+ case 'i':
+ fileName = g.getOptarg();
+ params.setProperty( "filename", fileName );
+ break;
+ case 'n':
+ params.setProperty( "ontoname", g.getOptarg() );
+ break;
+ case 'a':
+ params.setProperty( "alignname", g.getOptarg() );
+ break;
+ case 't':
+ testNumber = g.getOptarg();
+ System.err.println("testNumber " + "[" + testNumber + "]");
+ break;
case 'o' : /* Use output directory */
params.setProperty( "outdir", g.getOptarg() );
break;
@@ -136,6 +134,8 @@ public class TestGen {
}
}
+ if ( debug > 0 ) System.err.println( " >>>> "+methodName+" from "+fileName );
+
if ( methodName.equals( ARBITRARY_TEST ) ) { //generate an arbitrary test
TestGenerator tg = new TestGenerator();
tg.modifyOntology( fileName, (Properties)null, testNumber, params );
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
index c5bb6fb5ff44a665a401464367100eb75c10ec70..ad2f31375ec553e94f46529e5301913b2e30d194 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
@@ -209,6 +209,7 @@ public class TestGenerator implements AlignedOntologyGenerator {
}
// Initialise the modifier class
modifier = new OntologyModifier( onto, new URIAlignment() );
+ modifier.setDebug( debug );
modifier.setNewNamespace( namespace );
// Initialize the reference alignment
if ( initalign == null ) {
@@ -218,15 +219,14 @@ public class TestGenerator implements AlignedOntologyGenerator {
}
// 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_COMMENTS );
applyModification( modifier, params, ParametersIds.REMOVE_RESTRICTIONS );
+ applyModification( modifier, params, ParametersIds.REMOVE_COMMENTS );
applyModification( modifier, params, ParametersIds.ADD_CLASSES );
applyModification( modifier, params, ParametersIds.ADD_PROPERTIES );
@@ -242,12 +242,14 @@ public class TestGenerator implements AlignedOntologyGenerator {
applyModification( modifier, params, ParametersIds.NO_HIERARCHY );
applyModification( modifier, params, ParametersIds.ADD_CLASSESLEVEL );
applyModification( modifier, params, ParametersIds.REMOVE_INDIVIDUALS );
- */
+
+ /*
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
modifier.computeAlignment( alignname ); //at the end, compute the reference alignment