From f7f2dc0352a12beb45f427da749556958beac96f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Sat, 23 Feb 2008 11:16:09 +0000
Subject: [PATCH] - introduced Annotation class for defining namespaces and
annotation tags
---
.../exmo/align/impl/Annotations.java | 33 +++++++++++++++++++
.../inrialpes/exmo/align/impl/BasicCell.java | 2 +-
.../inrialpes/exmo/align/impl/Ontology.java | 3 +-
.../exmo/align/impl/URIAlignment.java | 6 ++--
.../exmo/align/impl/eval/PRecEvaluator.java | 3 +-
.../renderer/COWLMappingRendererVisitor.java | 4 +--
.../impl/renderer/HTMLRendererVisitor.java | 4 +--
.../impl/renderer/RDFRendererVisitor.java | 9 +++--
.../impl/renderer/XSLTRendererVisitor.java | 17 ++--------
.../exmo/align/parser/AlignmentParser.java | 4 +--
.../exmo/align/service/WSAServProfile.java | 4 +--
.../inrialpes/exmo/align/util/GroupAlign.java | 4 +--
.../inrialpes/exmo/align/util/Procalign.java | 4 +--
13 files changed, 57 insertions(+), 40 deletions(-)
create mode 100644 src/fr/inrialpes/exmo/align/impl/Annotations.java
diff --git a/src/fr/inrialpes/exmo/align/impl/Annotations.java b/src/fr/inrialpes/exmo/align/impl/Annotations.java
new file mode 100644
index 00000000..08f33b04
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/impl/Annotations.java
@@ -0,0 +1,33 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA Rhône-Alpes, 2008
+ *
+ * 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.impl;
+
+public class Annotations {
+
+ public static String ALIGNNS = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment#";
+ public static String METHOD = "method";
+ public static String TIME = "time";
+ public static String ID = "id";
+
+ /* Set to true for rejecting the use of deprecated (non deterministic) primitives */
+ protected static boolean STRICT_IMPLEMENTATION = false;
+
+}
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicCell.java b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
index 4ee69ad3..5e988621 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicCell.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
@@ -144,7 +144,7 @@ public class BasicCell implements Cell, Comparable {
result.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
}
- result.getExtensions().unsetParameter( BasicAlignment.ALIGNNS+BasicAlignment.ID );
+ result.getExtensions().unsetParameter( Annotations.ALIGNNS+Annotations.ID );
// The sae should be done for the measure
return result;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/Ontology.java b/src/fr/inrialpes/exmo/align/impl/Ontology.java
index 72ad8a44..f2420716 100644
--- a/src/fr/inrialpes/exmo/align/impl/Ontology.java
+++ b/src/fr/inrialpes/exmo/align/impl/Ontology.java
@@ -1,8 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2007
- * Copyright (C) CNR Pisa, 2005
+ * Copyright (C) INRIA Rhône-Alpes, 2007
*
* 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
diff --git a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
index 3deaba55..59085d10 100644
--- a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
@@ -129,7 +129,7 @@ public class URIAlignment extends BasicAlignment {
// Deprecated: implement as the one retrieving the highest strength correspondence (
public Cell getAlignCell1(Object ob) throws AlignmentException {
- if ( BasicAlignment.STRICT_IMPLEMENTATION == true ){
+ if ( Annotations.STRICT_IMPLEMENTATION == true ){
throw new AlignmentException("getAlignCell1: deprecated (use getAlignCells1 instead)");
} else {
if ( ob instanceof URI ){
@@ -141,7 +141,7 @@ public class URIAlignment extends BasicAlignment {
}
public Cell getAlignCell2(Object ob) throws AlignmentException {
- if ( BasicAlignment.STRICT_IMPLEMENTATION == true ){
+ if ( Annotations.STRICT_IMPLEMENTATION == true ){
throw new AlignmentException("getAlignCell2: deprecated (use getAlignCells2 instead)");
} else {
if ( ob instanceof URI ){
@@ -175,7 +175,7 @@ public class URIAlignment extends BasicAlignment {
for ( Object ext : ((BasicParameters)extensions).getValues() ){
align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
- align.getExtensions().unsetParameter( ALIGNNS+"id" );
+ align.getExtensions().unsetParameter( Annotations.ALIGNNS+"id" );
try {
align.ingest( this );
} catch (AlignmentException ex) { ex.printStackTrace(); }
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
index 3f022da0..dd236a66 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
@@ -27,6 +27,7 @@ import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.BasicEvaluator;
import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.Annotations;
import java.util.Enumeration;
import java.util.Iterator;
@@ -133,7 +134,7 @@ public class PRecEvaluator extends BasicEvaluator {
fmeasure = 2 * precision * recall / (precision + recall);
overall = recall * (2 - (1 / precision));
result = recall / precision;
- String timeExt = align2.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.TIME );
+ String timeExt = align2.getExtension( Annotations.ALIGNNS, Annotations.TIME );
if ( timeExt != null ) time = Long.parseLong(timeExt);
//System.err.println(">>>> " + nbcorrect + " : " + nbfound + " : " + nbexpected);
return (result);
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
index 47376d27..a2008b23 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2007-2008
*
* 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
@@ -84,7 +84,6 @@ public class COWLMappingRendererVisitor implements AlignmentVisitor
}
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
- //OWLOntology onto1 = (OWLOntology)alignment.getOntology1();
writer.print(" <cowl:bridgeRule>\n");
cell.getRelation().accept( this );
writer.print(" </cowl:bridgeRule>\n");
@@ -166,7 +165,6 @@ public class COWLMappingRendererVisitor implements AlignmentVisitor
} catch (InvocationTargetException e) {
e.printStackTrace();
}
- // } catch (OWLException e) { throw new AlignmentException("Dispatching problem ", e); };
}
public void printObject( URI uri, OWLOntology onto ) throws OWLException {
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
index d74b4327..dba5a84b 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
@@ -29,7 +29,7 @@ import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
-import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicParameters;
/**
@@ -93,7 +93,7 @@ public class HTMLRendererVisitor implements AlignmentVisitor
if ( cell.getId() != null ) {
String id = cell.getId();
// Would be useful to test for the Alignment URI
- if ( id.startsWith( (String)alignment.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID ) ) ){
+ if ( id.startsWith( (String)alignment.getExtension( Annotations.ALIGNNS, Annotations.ID ) ) ){
writer.print("<td>"+id.substring( id.indexOf( '#' ) )+"</td>");
} else {
writer.print("<td>"+id+"</td>");
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
index a59677e3..5cfd8c4e 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
@@ -30,8 +30,7 @@ import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
-// JE: this has been introduced here for the sole purpose of
-// using the namespace facility of BasicAlignment
+import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicAlignment;
import fr.inrialpes.exmo.align.impl.BasicParameters;
@@ -64,7 +63,7 @@ public class RDFRendererVisitor implements AlignmentVisitor
String extensionString = "";
alignment = align;
nslist = new Hashtable();
- nslist.put(BasicAlignment.ALIGNNS,"align");
+ nslist.put(Annotations.ALIGNNS,"align");
nslist.put("http://www.w3.org/1999/02/22-rdf-syntax-ns#","rdf");
nslist.put("http://www.w3.org/2001/XMLSchema#","xsd");
//nslist.put("http://www.omwg.org/TR/d7/ontology/alignment","omwg");
@@ -84,7 +83,7 @@ public class RDFRendererVisitor implements AlignmentVisitor
}
writer.print("<?xml version='1.0' encoding='utf-8");
writer.print("' standalone='no'?>\n");
- writer.print("<rdf:RDF xmlns='"+BasicAlignment.ALIGNNS+"'");
+ writer.print("<rdf:RDF xmlns='"+Annotations.ALIGNNS+"'");
for ( Enumeration e = nslist.keys() ; e.hasMoreElements(); ) {
String k = (String)e.nextElement();
writer.print("\n xmlns:"+nslist.get(k)+"='"+k+"'");
@@ -99,7 +98,7 @@ public class RDFRendererVisitor implements AlignmentVisitor
}
writer.print(">\n");
writer.print("<Alignment");
- String idext = align.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID );
+ String idext = align.getExtension( Annotations.ALIGNNS, Annotations.ID );
if ( idext != null ) {
writer.print(" rdf:about=\""+idext+"\"");
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
index 967105a2..a4955b86 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2006-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2004, 2006-2008
*
* 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
@@ -72,10 +72,6 @@ public class XSLTRendererVisitor implements AlignmentVisitor
writer.println(" xmlns:"+namespaces.get(ns)+"=\""+ns+"\"");
}
writer.println(" >\n");
- // writer.println(" xmlns:owl=\"http://www.w3.org/2002/07/owl#\"");
- //writer.println(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"");
- //writer.println(" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\" ");
- //writer.println(" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\">\n");
for ( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
Cell c = (Cell)e.nextElement();
@@ -99,16 +95,7 @@ public class XSLTRendererVisitor implements AlignmentVisitor
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
- // This was here for avoiding to treat individuals...
- //OWLOntology onto1 = (OWLOntology)alignment.getOntology1();
- //try {
- // URI entity1URI = ((OWLEntity)cell.getObject1()).getURI();
- // if ( ((OWLEntity)onto1.getClass( entity1URI ) != null )
- // || ((OWLEntity)onto1.getDataProperty( entity1URI ) != null)
- // || ((OWLEntity)onto1.getObjectProperty( entity1URI ) != null )) {
- cell.getRelation().accept( this );
- // }
- //} catch (OWLException e) { throw new AlignmentException("getURI problem", e); };
+ cell.getRelation().accept( this );
}
private void collectURIs ( Cell cell ) throws AlignmentException {
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index 8a6fe127..6b3f7979 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -55,7 +55,7 @@ import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.Ontology;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.Annotations;
/**
* This class allows the creation of a parser for an Alignment file.
@@ -312,7 +312,7 @@ public class AlignmentParser extends DefaultHandler {
onto1 = new Ontology();
onto2 = new Ontology();
if ( atts.getValue("rdf:about") != null && !atts.getValue("rdf:about").equals("") ) {
- alignment.setExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID, atts.getValue("rdf:about") );
+ alignment.setExtension( Annotations.ALIGNNS, Annotations.ID, atts.getValue("rdf:about") );
};
} else {
if ( debugMode > 0 ) System.err.println("[AlignmentParser] Unknown element name : "+pName);
diff --git a/src/fr/inrialpes/exmo/align/service/WSAServProfile.java b/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
index 51897994..12ec5dd6 100644
--- a/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
@@ -21,7 +21,7 @@
package fr.inrialpes.exmo.align.service;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.Annotations;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Parameters;
@@ -219,7 +219,7 @@ public class WSAServProfile implements AlignmentServiceProfile {
} else if ( method.equals("listalignmentsRequest") ) {
msg += "<listalignmentsResponse><alignmentList>";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension(BasicAlignment.ALIGNNS, BasicAlignment.ID);
+ String id = ((Alignment)e.nextElement()).getExtension(Annotations.ALIGNNS, Annotations.ID);
msg += "<alid>"+id+"</alid>";
}
msg += "</alignmentList></listalignmentsResponse>";
diff --git a/src/fr/inrialpes/exmo/align/util/GroupAlign.java b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
index 372c326d..55c77571 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupAlign.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
@@ -36,7 +36,7 @@ import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Parameters;
-import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicParameters;
import fr.inrialpes.exmo.align.impl.OntologyCache;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
@@ -304,7 +304,7 @@ public class GroupAlign {
long time = System.currentTimeMillis();
result.align(init, params); // add opts
long newTime = System.currentTimeMillis();
- result.setExtension( BasicAlignment.ALIGNNS, BasicAlignment.TIME, Long.toString(newTime - time) );
+ result.setExtension( Annotations.ALIGNNS, Annotations.TIME, Long.toString(newTime - time) );
if (debug > 1) System.err.println(" Alignment performed");
diff --git a/src/fr/inrialpes/exmo/align/util/Procalign.java b/src/fr/inrialpes/exmo/align/util/Procalign.java
index 3b425b4d..0a0fd689 100644
--- a/src/fr/inrialpes/exmo/align/util/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/util/Procalign.java
@@ -32,7 +32,7 @@ import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Parameters;
-import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicParameters;
import fr.inrialpes.exmo.align.impl.OntologyCache;
@@ -247,7 +247,7 @@ public class Procalign {
long time = System.currentTimeMillis();
result.align( init, params ); // add opts
long newTime = System.currentTimeMillis();
- result.setExtension( BasicAlignment.ALIGNNS, BasicAlignment.TIME, Long.toString(newTime - time) );
+ result.setExtension( Annotations.ALIGNNS, Annotations.TIME, Long.toString(newTime - time) );
// Thresholding
if (threshold != 0) result.cut( cutMethod, threshold );
--
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