From bc952b77ce6999c4f90138a12fa4883959fdad9d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Sat, 21 May 2011 16:54:24 +0000
Subject: [PATCH] - reengineered OntologyNetworkWeakener as an interface -
added OntologyNetworkGenerator - added new weakeners
---
html/credits.html | 1 +
html/relnotes.html | 9 +-
.../align/gen/NetworkAlignmentDropper.java | 76 +++++
.../align/gen/NetworkAlignmentWeakener.java | 92 ++++++
.../gen/NetworkCorrespondenceDropper.java | 114 ++++++++
.../exmo/align/gen/NetworkDeconnector.java | 57 ++++
.../align/gen/OntologyNetworkGenerator.java | 54 ++++
.../align/gen/OntologyNetworkWeakener.java | 104 +------
test/src/OntologyNetworkTest.java | 275 ++++++++++++++++--
9 files changed, 665 insertions(+), 117 deletions(-)
create mode 100644 src/fr/inrialpes/exmo/align/gen/NetworkAlignmentDropper.java
create mode 100644 src/fr/inrialpes/exmo/align/gen/NetworkAlignmentWeakener.java
create mode 100644 src/fr/inrialpes/exmo/align/gen/NetworkCorrespondenceDropper.java
create mode 100644 src/fr/inrialpes/exmo/align/gen/NetworkDeconnector.java
create mode 100644 src/fr/inrialpes/exmo/align/gen/OntologyNetworkGenerator.java
diff --git a/html/credits.html b/html/credits.html
index dc7214cc..bd3cb332 100644
--- a/html/credits.html
+++ b/html/credits.html
@@ -38,6 +38,7 @@ IDDN.FR. 001.050019 .000.S.P.2 011.000.2090 0
storage layer and the web service profile for the Alignment Server</dd>
<dt><a href="http://www.eurecom.fr/~troncy/">Raphaël Troncy</a></dt><dd>fixed the basic
implementation of BasicAlignment for n:m alignments.</dd>
+<dt>Maria Rosoiu</dt><dd>developed the generator interface (gen).</dd>
<dt>Arun Sharma</dt><dd>Developed the query interface</dd>
<dt><a href="http://www.scharffe.fr/">François Scharffe</a></dt><dd>developed the initial version of EDOAL</dd>
<dt><a href="http://web.comlab.ox.ac.uk/isg/people/giorgos.stoilos/">Giorgos
diff --git a/html/relnotes.html b/html/relnotes.html
index df285fe7..2f4d925f 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -52,26 +52,33 @@ The development of 4 versions continues.
<li>Render alignments as module descriptions (impl)</li>
<li>Implement extensive evaluation framework (impl)</li>
<li>Implement debug options with log4j</li>
+<li>Matcher plugin for OpenII? (util)</li>
<li>Add more tests</li>
</ul></p>
<h2>Current SVN trunk version</h2>
<!--h2>Version 4.3 (): xx/xx/xxxx - Zimt</h2-->
-<!--h2>Version 4.2 (): xx/05/2011 - Tring</h2-->
+<!--h2>Version 4.2 (16xx): 29/05/2011 - Tring</h2-->
<p><ul compact="1">
+<li>Added minimal API implementation for embedded devices (android)</li>
<li>Added type checking to EDOAL parser (parser)</li>
<li>Added <tt>WeightedPRecEvaluator</tt> weighting confidences (eval)</li>
<li>Added <tt>toURIAlignment</tt> and <tt>toEDOALAlignment</tt> for <tt>EDOALAlignment</tt> (edoal)</li>
<li>Added matching test generator facility (gen)</li>
<li>Added autoselecting <tt>BasicOntology.load()</tt> (ontowrap)</li>
+<li>Reengineered <tt>OntologyNetworkWeakener</tt> and added further weakening methods (gen)</li>
+<!--li>Added <tt>SEALSAlignment</tt> for SEALS evaluation (impl)</li-->
+<li>Added a few statistical primitives to BasicAlignment (impl)</li>
<li>Suppressed <tt>EDOALRelation</tt>: EDOAL uses <tt>BasicRelation</tt> (edoal)</li>
<li>EDOAL default printout now uses pretty relations, i.e., <, >, =, % (edoal)</li>
+<li>Modified server answers so that namespaces are well placed in REST (server)</li>
<li>Changed order of display to precision/F-measure/recall (util)</li>
<li><span style="color: red;">Suppressed</span> incorrect computation of fallout (eval)</li>
<li>Upgraded to <span style="color: green">OntoSim 2.1??</span> (lib)</li>
<li>Minor display changes in HTML display (server)</li>
+<li>Suppressed <tt>PreAlignment</tt> (impl)</li>
</ul></p>
<h2>Version 4.1 (1534): 13/10/2010 - Napjakmandu</h2>
diff --git a/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentDropper.java b/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentDropper.java
new file mode 100644
index 00000000..98437ff3
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentDropper.java
@@ -0,0 +1,76 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA, 2009-2011
+ *
+ * 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 org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.Cell;
+import org.semanticweb.owl.align.OntologyNetwork;
+
+import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
+
+import java.net.URI;
+import java.util.Properties;
+import java.util.Set;
+import java.util.Collections;
+import java.util.ArrayList;
+
+/**
+ * NetworkAlignmentDropper
+ *
+ * randomly drops n% of all alignments
+ * n is a number between 0. and 1.
+ * Returns a brand new BasicOntologyNetwork (with the initial alignments)
+ */
+public class NetworkAlignmentDropper implements OntologyNetworkWeakener {
+
+ public OntologyNetwork weaken( OntologyNetwork on, double n, Properties p ) throws AlignmentException {
+ //System.err.println( " >>>> "+n );
+ if ( on == null ) throw new AlignmentException( "cannot weaken null ontology network" );
+ if ( n < 0. || n > 1. )
+ throw new AlignmentException( "Argument must be between 0 and 1.: "+n );
+ return weaken( on, (int)(n*(double)on.getAlignments().size()), p );
+ }
+
+ public OntologyNetwork weaken( OntologyNetwork on, int n, Properties p ) throws AlignmentException {
+ //System.err.println( " >>>> "+n );
+ if ( on == null ) throw new AlignmentException( "cannot weaken null ontology network" );
+ if ( n < 0 )
+ throw new AlignmentException( "Argument must be a positive integer: "+n );
+ OntologyNetwork newon = new BasicOntologyNetwork();
+ for ( URI ontouri : on.getOntologies() ){
+ newon.addOntology( ontouri );
+ }
+ Set<Alignment> alignments = on.getAlignments();
+ int size = alignments.size();
+ if ( n > size ) return newon;
+ ArrayList<Alignment> array = new ArrayList<Alignment>( size );
+ for ( Alignment al : alignments ){
+ array.add( al );
+ }
+ Collections.shuffle( array );
+ for ( int i = size - n -1; i >= 0; i-- ) {
+ newon.addAlignment( array.get( i ) );
+ }
+ return newon;
+ }
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentWeakener.java b/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentWeakener.java
new file mode 100644
index 00000000..b02ecade
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentWeakener.java
@@ -0,0 +1,92 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA, 2009-2011
+ *
+ * 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 org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.Cell;
+import org.semanticweb.owl.align.OntologyNetwork;
+
+import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Properties;
+import java.net.URI;
+
+/**
+ * AlignmentWeakener
+ *
+ * suppress n% of the correspondences at random in each alignments
+ * n is a number between 0. and 1.
+ * Returns a brand new BasicOntologyNetwork (with new alignments and cells)
+ * the @threshold parameter tells if the corrrespondences are suppressed at random (false) of by suppressing the n% of lower confidence (true)
+ */
+
+public class NetworkAlignmentWeakener implements OntologyNetworkWeakener {
+
+ public OntologyNetwork weaken( OntologyNetwork on, int n, Properties p ) throws AlignmentException {
+ throw new AlignmentException( "Cannot weaken alignments by fixed number of correspondences" );
+ }
+
+ public OntologyNetwork weaken( OntologyNetwork on, double n, Properties p ) throws AlignmentException {
+ if ( on == null ) throw new AlignmentException( "cannot weaken null ontology network" );
+ if ( n < 0. || n > 1. )
+ throw new AlignmentException( "Argument must be between 0 and 1.: "+n );
+ boolean threshold = (p != null && p.getProperty("threshold") != null);
+ OntologyNetwork newon = new BasicOntologyNetwork();
+ for ( URI ontouri : on.getOntologies() ){
+ newon.addOntology( ontouri );
+ }
+ for ( Alignment al : on.getAlignments() ){
+ Alignment newal = (Alignment)al.clone();
+ if ( threshold ) {
+ newal.cut( "perc", 1.-n );
+ } else {
+ int size = newal.nbCells();
+ // --------------------------------------------------------------------
+ // JE: Here is a tricky one.
+ // Using collection schuffle randomly reorganises a list
+ // Then choosing the fist n% and destroying them in the Set is performed
+ // The complexity is O(copy=N)+O(shuffle=N)+n%*O(delete=N)
+ // That's not bad... (and also avoid checking if the same nb is drawn)
+ // But in practice other solutions may be better, like:
+ // Generating randomly n%*N numbers between 0 and N (util.Random)
+ // Ordering them
+ // Traversing the initial structure and deleting the choosen ones...
+ // This one (deleting when traversing) is tricky in Java.
+ // --------------------------------------------------------------------
+ ArrayList<Cell> array = new ArrayList<Cell>( size );
+ for ( Cell c : newal ) {
+ array.add( c );
+ }
+ Collections.shuffle( array );
+ for ( int i = (int)(n*size)-1; i >= 0; i-- ){
+ newal.remCell( array.get( i ) );
+ }
+ }
+ newon.addAlignment( newal );
+ }
+ return newon;
+ }
+
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/NetworkCorrespondenceDropper.java b/src/fr/inrialpes/exmo/align/gen/NetworkCorrespondenceDropper.java
new file mode 100644
index 00000000..2efb03f8
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/NetworkCorrespondenceDropper.java
@@ -0,0 +1,114 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA, 2009-2011
+ *
+ * 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 org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.Cell;
+import org.semanticweb.owl.align.OntologyNetwork;
+
+import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
+
+import java.net.URI;
+import java.util.Collections;
+import java.util.Collection;
+import java.util.TreeSet;
+import java.util.ArrayList;
+import java.util.Properties;
+
+/**
+ * NetworkCorrespondenceDropper
+ *
+ * suppress n% of the correspondences at random in all alignments (globally)
+ * n is a number between 0. and 1.
+ * Returns a brand new BasicOntologyNetwork (with new alignments and cells)
+ * the @threshold parameter tells if the corrrespondences are suppressed at random (false) of by suppressing the n% of lower confidence (true)
+ */
+
+public class NetworkCorrespondenceDropper implements OntologyNetworkWeakener {
+
+ public OntologyNetwork weaken( OntologyNetwork on, int n, Properties p ) throws AlignmentException {
+ throw new AlignmentException( "Cannot weaken alignments by fixed number of correspondences" );
+ }
+
+ public OntologyNetwork weaken( OntologyNetwork on, double n, Properties p ) throws AlignmentException {
+ if ( on == null ) throw new AlignmentException( "cannot weaken null ontology network" );
+ if ( n < 0. || n > 1. )
+ throw new AlignmentException( "Argument must be between 0 and 1.: "+n );
+ boolean threshold = (p != null && p.getProperty("threshold") != null);
+ OntologyNetwork newon = new BasicOntologyNetwork();
+ for ( URI ontouri : on.getOntologies() ){
+ newon.addOntology( ontouri );
+ }
+ // Put all the cell/alignment in a array
+ Collection<LCell> corresp = null;
+ if ( threshold ) {
+ corresp = new TreeSet<LCell>();
+ } else {
+ corresp = new ArrayList<LCell>();
+ }
+ for ( Alignment al : on.getAlignments() ) {
+ Alignment newal = (Alignment)al.clone();
+ for ( Cell c : newal ) {
+ corresp.add( new LCell( c, newal ) );
+ }
+ newon.addAlignment( newal );
+ }
+ // Select these correspondences to delete: either shuffle or order
+ //System.err.println( n+" * "+corresp.size()+" = "+n*(double)(corresp.size()) );
+ int q = (int)(n*(double)(corresp.size()));
+ if ( !threshold ) Collections.shuffle( (ArrayList)corresp );
+ // Suppress the n*size() last ones or those which are under threshold
+ for ( LCell c : corresp ) {
+ if ( q == 0 ) break;
+ q--;
+ //System.err.println( "Cell ["+c.getCell().getStrength()+"] : "+c );
+ c.getAlignment().remCell( c.getCell() );
+ }
+ // Cut
+ return newon;
+ }
+}
+
+class LCell implements Comparable<LCell> {
+ Alignment alignment = null;
+ Cell cell = null;
+
+ LCell( Cell c, Alignment al ) {
+ alignment = al;
+ cell = c;
+ }
+
+ /**
+ * This is not the standard required definition of compareTo
+ * But this is the one which works exactly here (we want the structure ordered,
+ * we do not want that two cells be equated (in case of 0)
+ */
+ public int compareTo( LCell c ) {
+ if ( cell.getStrength() > c.getCell().getStrength() ) return 1;
+ else return -1;/*if ( cell.getStrength() < c.getCell().getStrength() ) return -1;
+ else return 0;*/
+ }
+
+ Alignment getAlignment() { return alignment; }
+ Cell getCell() { return cell; }
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/NetworkDeconnector.java b/src/fr/inrialpes/exmo/align/gen/NetworkDeconnector.java
new file mode 100644
index 00000000..b3f567f9
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/NetworkDeconnector.java
@@ -0,0 +1,57 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA, 2009-2011
+ *
+ * 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 org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.Cell;
+import org.semanticweb.owl.align.OntologyNetwork;
+
+import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
+
+import java.util.Properties;
+
+/**
+ * NetworkDeconnector
+ *
+ * suppress alignments in the ontology network so that it retain n-connectivity,
+ * i.e., any pairs of ontologies connected by less than n alignments
+ * are still connected through at most n alignments.
+ * JE: this is an interesting graph theoretic problem and I do not know where
+ * to find it.
+ *
+ * NOT IMPLEMENTED
+ */
+
+public class NetworkDeconnector implements OntologyNetworkWeakener {
+
+ public OntologyNetwork weaken( OntologyNetwork on, int n, Properties p ) throws AlignmentException {
+ if ( on == null ) throw new AlignmentException( "cannot weaken null ontology network" );
+ return on;
+ }
+ public OntologyNetwork weaken( OntologyNetwork on, double n, Properties p ) throws AlignmentException {
+ if ( on == null ) throw new AlignmentException( "cannot weaken null ontology network" );
+ if ( n < 0. || n > 1. )
+ throw new AlignmentException( "Argument must be between 0 and 1.: "+n );
+ return on;
+ }
+}
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyNetworkGenerator.java b/src/fr/inrialpes/exmo/align/gen/OntologyNetworkGenerator.java
new file mode 100644
index 00000000..65afafb8
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/gen/OntologyNetworkGenerator.java
@@ -0,0 +1,54 @@
+/*
+ * $Id$
+ *
+ * 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 org.semanticweb.owl.align.OntologyNetwork;
+
+import fr.inrialpes.exmo.ontowrap.Ontology;
+
+import java.util.Properties;
+
+/**
+ * OntologyNetworkGenerator
+ *
+ * An interface for generating an ontology network from an ontology or an ontology generator.
+ *
+ */
+
+public interface OntologyNetworkGenerator {
+
+ /**
+ * Returns an ontology network of size n (the number of ontologies)
+ * starting from an ontology o.
+ * Parameters may further specify the requirements.
+ */
+ public OntologyNetwork generate( int n, Ontology o, Properties params );
+
+ /**
+ * Returns an ontology network of size n (the number of ontologies)
+ * with ontologies generated by the generator g.
+ * Parameters may further specify the requirements.
+ */
+ //public OntologyNetwork generate( int n, OntologyGenerator o, Properties params );
+
+}
+
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java b/src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java
index ca21f7d0..d044fac1 100644
--- a/src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java
+++ b/src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java
@@ -21,113 +21,29 @@
package fr.inrialpes.exmo.align.gen;
-import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
-import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.OntologyNetwork;
-import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
-
-import java.net.URI;
-import java.util.Set;
-import java.util.Collections;
-import java.util.ArrayList;
+import java.util.Properties;
/**
* OntologyNetworkWeakener
*
- * A class which alters ontology networks, usually by altering alignments
+ * A interface which alters ontology networks.
+ * NOTE: These two primitives would benefit from the hability to declare static in ineterfaces...
+ * Now we have to create instances of the implementing classes.
+ *
*/
-public class OntologyNetworkWeakener {
+public interface OntologyNetworkWeakener {
/**
- * suppress alignments in the ontology network so that it retain n-connectivity,
- * i.e., any pairs of ontologies connected by less than n alignments
- * are still connected through at most n alignments.
- * JE: this is an interesting graph theoretic problem and I do not know where
- * to find it.
+ * Weakens the ontology network of n units
*/
- public static OntologyNetwork unconnect( OntologyNetwork on, int n ){
- return on;
- }
+ public OntologyNetwork weaken( OntologyNetwork on, int n, Properties p ) throws AlignmentException;
/**
- * suppress n% of the correspondences at random in all alignments
- * n is a number between 0. and 1.
- * Returns a brand new BasicOntologyNetwork (with new alignments and cells)
- * the @threshold parameter tells if the corrrespondences are suppressed at random (false) of by suppressing the n% of lower confidence (true)
+ * Weakens the ontology network of n%
*/
- public static OntologyNetwork weakenAlignments( OntologyNetwork on, double n, boolean threshold ) throws AlignmentException {
- if ( n < 0. || n > 1. )
- throw new AlignmentException( "Argument must be between 0 and 1.: "+n );
- OntologyNetwork newon = new BasicOntologyNetwork();
- for ( URI ontouri : on.getOntologies() ){
- newon.addOntology( ontouri );
- }
- for ( Alignment al : on.getAlignments() ){
- Alignment newal = (Alignment)al.clone();
- if ( threshold ) {
- newal.cut( "perc", 1.-n );
- } else {
- int size = newal.nbCells();
- // --------------------------------------------------------------------
- // JE: Here is a tricky one.
- // Using collection schuffle randomly reorganises a list
- // Then choosing the fist n% and destroying them in the Set is performed
- // The complexity is O(copy=N)+O(shuffle=N)+n%*O(delete=N)
- // That's not bad... (and also avoid checking if the same nb is drawn)
- // But in practice other solutions may be better, like:
- // Generating randomly n%*N numbers between 0 and N (util.Random)
- // Ordering them
- // Traversing the initial structure and deleting the choosen ones...
- // This one (deleting when traversing) is tricky in Java.
- // --------------------------------------------------------------------
- ArrayList<Cell> array = new ArrayList<Cell>( size );
- for ( Cell c : newal ) {
- array.add( c );
- }
- Collections.shuffle( array );
- for ( int i = (int)(n*size)-1; i >= 0; i-- ){
- newal.remCell( array.get( i ) );
- }
- }
- newon.addAlignment( newal );
- }
- return newon;
- }
-
- /**
- * randomly drops n% of all alignments
- * n is a number between 0. and 1.
- * Returns a brand new BasicOntologyNetwork (with the initial alignments)
- */
- public static OntologyNetwork dropAlignments( OntologyNetwork on, double n ) throws AlignmentException {
- //System.err.println( " >>>> "+n );
- if ( n < 0. || n > 1. )
- throw new AlignmentException( "Argument must be between 0 and 1.: "+n );
- return dropAlignments( on, (int)(n*on.getAlignments().size()) );
- }
-
- public static OntologyNetwork dropAlignments( OntologyNetwork on, int n ) throws AlignmentException {
- //System.err.println( " >>>> "+n );
- if ( n < 0 || n > on.getAlignments().size() )
- throw new AlignmentException( "Argument must be a positive integer: "+n );
- OntologyNetwork newon = new BasicOntologyNetwork();
- for ( URI ontouri : on.getOntologies() ){
- newon.addOntology( ontouri );
- }
- Set<Alignment> alignments = on.getAlignments();
- int size = alignments.size();
- ArrayList<Alignment> array = new ArrayList<Alignment>( size );
- for ( Alignment al : alignments ){
- array.add( al );
- }
- Collections.shuffle( array );
- for ( int i = size - (int)(n*size); i > 0; i-- ) {
- newon.addAlignment( array.get( i ) );
- }
- return newon;
- }
-
+ public OntologyNetwork weaken( OntologyNetwork on, double n, Properties p ) throws AlignmentException;
}
diff --git a/test/src/OntologyNetworkTest.java b/test/src/OntologyNetworkTest.java
index ee414d7e..fda54b39 100644
--- a/test/src/OntologyNetworkTest.java
+++ b/test/src/OntologyNetworkTest.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2008-2010
+ * Copyright (C) INRIA, 2008-2011
*
* 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
@@ -18,11 +18,10 @@
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
-//package test.com.acme.dona.dep;
-
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Configuration;
import org.testng.annotations.Test;
@@ -31,13 +30,11 @@ import org.testng.annotations.Test;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.Set;
+import java.util.Properties;
import java.io.IOException;
import javax.xml.parsers.ParserConfigurationException;
import org.xml.sax.SAXException;
-// JE: this one is too much
-//import org.omwg.mediation.parser.rdf.RDFParserException;
-
import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
@@ -47,7 +44,11 @@ import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.OntologyNetwork;
import fr.inrialpes.exmo.ontowrap.Ontology;
import fr.inrialpes.exmo.ontowrap.OntologyFactory;
-import fr.inrialpes.exmo.align.util.OntologyNetworkWeakener;
+import fr.inrialpes.exmo.align.gen.OntologyNetworkWeakener;
+import fr.inrialpes.exmo.align.gen.NetworkAlignmentDropper;
+import fr.inrialpes.exmo.align.gen.NetworkCorrespondenceDropper;
+import fr.inrialpes.exmo.align.gen.NetworkAlignmentWeakener;
+import fr.inrialpes.exmo.align.gen.NetworkDeconnector;
public class OntologyNetworkTest {
private OntologyNetwork noo = null;
@@ -127,33 +128,263 @@ public class OntologyNetworkTest {
}
@Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"})
- public void weakenTest() throws URISyntaxException, AlignmentException {
+ public void expandTest() throws URISyntaxException, AlignmentException {
+
+ assertEquals( noo.getOntologies().size(), 4);
+ assertEquals( noo.getAlignments().size(), 2);
+
+ Alignment al2 = new URIAlignment();
+ al2.init( new URI("http://www.example.org/ontology1"), new URI("file:examples/rdf/edu.mit.visus.bibtex.owl") );
+ al2.addAlignCell( new URI("http://www.example.org/ontology1#reviewedarticle"), new URI("http://purl.org/net/nknouf/ns/bibtex#Article"), "<", 1.0 );
+ al2.addAlignCell( new URI("http://www.example.org/ontology1#journalarticle"), new URI("http://purl.org/net/nknouf/ns/bibtex#Article"), "<", 1.0 );
+ al2.addAlignCell( new URI("http://www.example.org/ontology1#journalarticle"), new URI("http://purl.org/net/nknouf/ns/bibtex#Article"), "=", .5 );
+ assertEquals( al2.nbCells(), 3);
+ noo.addAlignment( al2 );
+
+ al2 = new URIAlignment();
+ al2.init( new URI("http://www.example.org/ontology2"), new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl") );
+ al2.addAlignCell( new URI("http://www.example.org/ontology2#journalarticle"), new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Article"), "<", .78 );
+ al2.addAlignCell( new URI("http://www.example.org/ontology2#article"), new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Article"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://www.example.org/ontology2#reference"), new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Publication"), "=", .6 );
+ assertEquals( al2.nbCells(), 3);
+ noo.addAlignment( al2 );
+
+ al2 = new URIAlignment();
+ al2.init( new URI("file:examples/rdf/edu.mit.visus.bibtex.owl"), new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl") );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasPublisher"), new URI("http://www.example.org/ontology1#publisher"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasURL"), new URI("http://www.example.org/ontology1#softCopyURI"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Inproceedings"), new URI("http://www.example.org/ontology1#InProceedings"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasEditor"), new URI("http://www.example.org/ontology1#editor"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasNumber"), new URI("http://www.example.org/ontology1#number"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasNote"), new URI("http://www.example.org/ontology1#note"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasType"), new URI("http://www.example.org/ontology1#type"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasBooktitle"), new URI("http://www.example.org/ontology1#booktitle"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasJournal"), new URI("http://www.example.org/ontology1#journal"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasKeywords"), new URI("http://www.example.org/ontology1#keyword"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Article"), new URI("http://www.example.org/ontology1#Article"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasChapter"), new URI("http://www.example.org/ontology1#chapter"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Techreport"), new URI("http://www.example.org/ontology1#TechReport"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasSchool"), new URI("http://www.example.org/ontology1#school"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Misc"), new URI("http://www.example.org/ontology1#Misc"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasPages"), new URI("http://www.example.org/ontology1#pages"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Phdthesis"), new URI("http://www.example.org/ontology1#PhdThesis"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Mastersthesis"), new URI("http://www.example.org/ontology1#MastersThesis"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Incollection"), new URI("http://www.example.org/ontology1#InCollection"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasAbstract"), new URI("http://www.example.org/ontology1#abstract"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasAddress"), new URI("http://www.example.org/ontology1#address"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Book"), new URI("http://www.example.org/ontology1#Book"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasSeries"), new URI("http://www.example.org/ontology1#series"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasTitle"), new URI("http://www.example.org/ontology1#title"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Inbook"), new URI("http://www.example.org/ontology1#InBook"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasInstitution"), new URI("http://www.example.org/ontology1#institution"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasEdition"), new URI("http://www.example.org/ontology1#edition"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasVolume"), new URI("http://www.example.org/ontology1#volume"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#Proceedings"), new URI("http://www.example.org/ontology1#Proceedings"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasSize"), new URI("http://www.example.org/ontology1#softCopySize"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasAuthor"), new URI("http://www.example.org/ontology1#author"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://purl.org/net/nknouf/ns/bibtex#hasOrganization"), new URI("http://www.example.org/ontology1#organization"), "=", 1.0 );
+ assertEquals( al2.nbCells(), 32);
+ noo.addAlignment( al2 );
+
+ al2 = new URIAlignment();
+ al2.init( new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl"), new URI("file:examples/rdf/edu.mit.visus.bibtex.owl") );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Article"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Article"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#volume"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasVolume"), "=", 0.8 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#note"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasNote"), "=", 0.73 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#type"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasType"), "=", 0.73 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#address"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasAddress"), "=", 0.82 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#TechReport"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Techreport"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#SoftCopy"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Conference"), "=", 0.22 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#InBook"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Inbook"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#chapter"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasChapter"), "=", 0.82 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#series"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasSeries"), "=", 0.8 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#author"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasAuthor"), "=", 0.8 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Misc"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Misc"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Book"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Book"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#publishedOn"), new URI( "http://purl.org/net/nknouf/ns/bibtex#howPublished"), "=", 0.78 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#firstAuthor"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasAuthor"), "=", 0.6 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#InCollection"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Incollection"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Resource"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Phdthesis"), "=", 0.23 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#publisher"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasPublisher"), "=", 0.86 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#school"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasSchool"), "=", 0.8 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#softCopy"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasCopyright"), "=", 0.4 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#version"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasEdition"), "=", 0.35 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#softCopyURI"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasCopyright"), "=", 0.35 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#description"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasEdition"), "=", 0.38 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#MastersThesis"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Mastersthesis"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Proceedings"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Proceedings"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#PhdThesis"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Phdthesis"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#institution"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasInstitution"), "=", 0.88 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#number"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasNumber"), "=", 0.8 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#keyword"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasKeywords"), "=", 0.78 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#softCopyFormat"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasCopyright"), "=", 0.31 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#title"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasTitle"), "=", 0.77 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#journal"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasJournal"), "=", 0.82 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/person.owl#Person"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Mastersthesis"), "=", 0.32 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#InProceedings"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Inproceedings"), "=", 1.0 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#edition"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasEdition"), "=", 0.82 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#abstract"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasAbstract"), "=", 0.84 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#editor"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasEditor"), "=", 0.8 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#counter"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasChapter"), "=", 0.35 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#softCopySize"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasSize"), "=", 0.42 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#organization"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasOrganization"), "=", 0.89 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#pages"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasPages"), "=", 0.77 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#booktitle"), new URI( "http://purl.org/net/nknouf/ns/bibtex#hasBooktitle"), "=", 0.86 );
+ al2.addAlignCell( new URI("http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Publication"), new URI( "http://purl.org/net/nknouf/ns/bibtex#Unpublished"), "=", 0.45 );
+ assertEquals( al2.nbCells(), 43);
+ noo.addAlignment( al2 );
+
+ assertEquals( noo.getOntologies().size(), 4);
+ assertEquals( noo.getAlignments().size(), 6);
+
+ URI u = new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl");
+ assertEquals( noo.getTargetingAlignments(u).size(), 2 );
+ assertEquals( noo.getSourceAlignments(u).size(), 1 );
+ u = new URI("file:examples/rdf/edu.mit.visus.bibtex.owl");
+ assertEquals( noo.getTargetingAlignments(u).size(), 2 );
+ assertEquals( noo.getSourceAlignments(u).size(), 1 );
+ u = new URI("http://www.example.org/ontology1");
+ assertEquals( noo.getTargetingAlignments(u).size(), 0 );
+ assertEquals( noo.getSourceAlignments(u).size(), 3 );
+ u = new URI("http://www.example.org/ontology2");
+ assertEquals( noo.getTargetingAlignments(u).size(), 2 );
+ assertEquals( noo.getSourceAlignments(u).size(), 1 );
+ }
+
+ // Then I would apply the weakening
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"expandTest"})
+ public void weakenAlignmentDropper() throws URISyntaxException, AlignmentException {
OntologyNetwork noon = null;
- noon = OntologyNetworkWeakener.weakenAlignments( noo, 1., true );
+ OntologyNetworkWeakener weakener = new NetworkAlignmentDropper();
+ Properties propThres = new Properties();
+ noon = weakener.weaken( noo, 1., propThres );
Set<Alignment> s = noon.getTargetingAlignments(new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl"));
+ assertEquals( noon.getAlignments().size(), 0);
+ noon = weakener.weaken( noo, .5, propThres );
+ assertEquals( noon.getAlignments().size(), 3);
+ noon = weakener.weaken( noo, 0., propThres );
+ assertEquals( noon.getAlignments().size(), 6);
+ noon = weakener.weaken( noo, 1., (Properties)null );
+ assertEquals( noon.getAlignments().size(), 0);
+ noon = weakener.weaken( noo, .5, (Properties)null );
+ assertEquals( noon.getAlignments().size(), 3);
+ noon = weakener.weaken( noo, 0., (Properties)null );
+ assertEquals( noon.getAlignments().size(), 6);
+ }
+ //@Test(groups = { "full", "raw" }, dependsOnMethods = {"expandTest"})
+ // public void weakenNetworkDeconnector() throws URISyntaxException, AlignmentException {
+ //}
- noon = OntologyNetworkWeakener.weakenAlignments( noo, .5, true );
- noon = OntologyNetworkWeakener.weakenAlignments( noo, 0., true );
- noon = OntologyNetworkWeakener.weakenAlignments( noo, 0., false );
- noon = OntologyNetworkWeakener.weakenAlignments( noo, .5, false );
- noon = OntologyNetworkWeakener.weakenAlignments( noo, 1., false );
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"expandTest"})
+ public void weakenCorrespondenceDropper() throws URISyntaxException, AlignmentException {
+ OntologyNetwork noon = null;
+ OntologyNetworkWeakener weakener = new NetworkCorrespondenceDropper();
+ Properties propThres = new Properties();
+ propThres.setProperty( "threshold", "true" );
+
+ int init = 0;
+ for ( Alignment al : noo.getAlignments() ) { init += al.nbCells(); }
+
+ int size = 0;
+ noon = weakener.weaken( noo, 1., propThres );
+ for ( Alignment al : noon.getAlignments() ) { size += al.nbCells(); }
+ assertEquals( size, 0);
+ noon = weakener.weaken( noo, .5, propThres );
+ size = 0;
+ for ( Alignment al : noon.getAlignments() ) { size += al.nbCells(); }
+ assertTrue( init/2 <= size && size <= init/2 + 1, "Expected "+init/2+" but got "+size );
+ noon = weakener.weaken( noo, 0., propThres );
+ size = 0;
+ for ( Alignment al : noon.getAlignments() ) { size += al.nbCells(); }
+ assertEquals( size, init);
+ noon = weakener.weaken( noo, 1., (Properties)null );
+ size = 0;
+ for ( Alignment al : noon.getAlignments() ) { size += al.nbCells(); }
+ assertEquals( size, 0);
+ noon = weakener.weaken( noo, .5, (Properties)null );
+ size = 0;
+ for ( Alignment al : noon.getAlignments() ) { size += al.nbCells(); }
+ assertTrue( init/2 <= size && size <= init/2 + 1, "Expected "+init/2+" but got "+size );
+ noon = weakener.weaken( noo, 0., (Properties)null );
+ size = 0;
+ for ( Alignment al : noon.getAlignments() ) { size += al.nbCells(); }
+ assertEquals( size, init);
+ }
+
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"expandTest"})
+ public void weakenAlignmentWeakener() throws URISyntaxException, AlignmentException {
+ OntologyNetwork noon = null;
+ OntologyNetworkWeakener weakener = new NetworkAlignmentWeakener();
+ Properties propThres = new Properties();
+ int init = noo.getSourceAlignments(new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl")).iterator().next().nbCells();
+
+ propThres.setProperty( "threshold", "true" );
+ noon = weakener.weaken( noo, 1., propThres );
+ assertEquals( noon.getSourceAlignments(new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl")).iterator().next().nbCells(), 0);
+ noon = weakener.weaken( noo, .5, propThres );
+ int val = noon.getSourceAlignments(new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl")).iterator().next().nbCells();
+ assertTrue( init/2 <= val && val <= init/2+1, "Expected "+init/2+" but got "+val );
+ noon = weakener.weaken( noo, 0., propThres );
+ assertEquals( noon.getSourceAlignments(new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl")).iterator().next().nbCells(), init);
+ noon = weakener.weaken( noo, 1., (Properties)null );
+ assertEquals( noon.getSourceAlignments(new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl")).iterator().next().nbCells(), 0);
+ noon = weakener.weaken( noo, .5, (Properties)null );
+ val = noon.getSourceAlignments(new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl")).iterator().next().nbCells();
+ assertTrue( init/2 <= val && val <= init/2+1, "Expected "+init/2+" but got "+val );
+ noon = weakener.weaken( noo, 0., (Properties)null );
+ assertEquals( noon.getSourceAlignments(new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl")).iterator().next().nbCells(), init);
+ }
+
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
+ public void weakenNADExceptionTest10() throws URISyntaxException, AlignmentException {
+ new NetworkAlignmentDropper().weaken( (OntologyNetwork)null, .5, (Properties)null );
+ }
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
+ public void weakenNADExceptionTest11() throws URISyntaxException, AlignmentException {
+ new NetworkAlignmentDropper().weaken( noo, 1.2, (Properties)null );
+ }
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
+ public void weakenNADExceptionTest12() throws URISyntaxException, AlignmentException {
+ new NetworkAlignmentDropper().weaken( noo, -.2, (Properties)null );
}
@Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
- public void weakenExceptionTest1() throws URISyntaxException, AlignmentException {
- OntologyNetworkWeakener.weakenAlignments( noo, 1.2, true );
+ public void weakenNCDExceptionTest10() throws URISyntaxException, AlignmentException {
+ new NetworkCorrespondenceDropper().weaken( (OntologyNetwork)null, .5, (Properties)null );
+ }
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
+ public void weakenNCDExceptionTest11() throws URISyntaxException, AlignmentException {
+ new NetworkCorrespondenceDropper().weaken( noo, 1.2, (Properties)null );
}
@Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
- public void weakenExceptionTest2() throws URISyntaxException, AlignmentException {
- OntologyNetworkWeakener.weakenAlignments( noo, -.2, true );
+ public void weakenNCDExceptionTest12() throws URISyntaxException, AlignmentException {
+ new NetworkCorrespondenceDropper().weaken( noo, -.2, (Properties)null );
+ }
+
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
+ public void weakenNAWExceptionTest10() throws URISyntaxException, AlignmentException {
+ new NetworkAlignmentWeakener().weaken( (OntologyNetwork)null, .5, (Properties)null );
+ }
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
+ public void weakenNAWExceptionTest11() throws URISyntaxException, AlignmentException {
+ new NetworkAlignmentWeakener().weaken( noo, 1.2, (Properties)null );
+ }
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
+ public void weakenNAWExceptionTest12() throws URISyntaxException, AlignmentException {
+ new NetworkAlignmentWeakener().weaken( noo, -.2, (Properties)null );
+ }
+
+ @Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
+ public void weakenNDExceptionTest10() throws URISyntaxException, AlignmentException {
+ new NetworkDeconnector().weaken( (OntologyNetwork)null, .5, (Properties)null );
}
@Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
- public void weakenExceptionTest3() throws URISyntaxException, AlignmentException {
- OntologyNetworkWeakener.weakenAlignments( noo, 1.2, false );
+ public void weakenNDExceptionTest11() throws URISyntaxException, AlignmentException {
+ new NetworkDeconnector().weaken( noo, 1.2, (Properties)null );
}
@Test(groups = { "full", "raw" }, dependsOnMethods = {"lambdaTest"},expectedExceptions = AlignmentException.class)
- public void weakenExceptionTest4() throws URISyntaxException, AlignmentException {
- OntologyNetworkWeakener.weakenAlignments( noo, -.2, false );
+ public void weakenNDExceptionTest12() throws URISyntaxException, AlignmentException {
+ new NetworkDeconnector().weaken( noo, -.2, (Properties)null );
}
}
--
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