From e84a08a0455b5e377c6b98a3c3d31fa3fdf113fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Sat, 26 Jan 2008 16:32:12 +0000
Subject: [PATCH] - modifed extension interface for better dealing with
namespaces
---
.../exmo/align/impl/BasicAlignment.java | 56 +++--------
.../inrialpes/exmo/align/impl/BasicCell.java | 18 ++--
.../exmo/align/impl/OWLAPIAlignment.java | 19 ++--
.../exmo/align/impl/URIAlignment.java | 11 +--
.../align/impl/eval/PRGraphEvaluator.java | 8 +-
.../exmo/align/impl/eval/PRecEvaluator.java | 4 +-
.../impl/renderer/HTMLRendererVisitor.java | 12 ++-
.../impl/renderer/RDFRendererVisitor.java | 82 ++++++++-------
.../exmo/align/parser/AlignmentParser.java | 19 ++--
.../align/service/AServProtocolManager.java | 22 ++---
.../exmo/align/service/CacheImpl.java | 99 ++++++++++---------
.../exmo/align/service/HTMLAServProfile.java | 21 ++--
.../inrialpes/exmo/align/util/GroupAlign.java | 4 +-
.../inrialpes/exmo/align/util/Procalign.java | 4 +-
src/org/semanticweb/owl/align/Alignment.java | 6 +-
15 files changed, 189 insertions(+), 196 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index b985535c..5c4b57ed 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2008
* Copyright (C) CNR Pisa, 2005
*
* This program is free software; you can redistribute it and/or modify
@@ -61,14 +61,11 @@ public class BasicAlignment implements Alignment {
visitor.visit(this);
}
- //public static String METHOD = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment:method";
+ public static String ALIGNNS = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment#";
public static String METHOD = "method";
- //public static String TIME = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment:time";
public static String TIME = "time";
+ public static String ID = "id";
- // JE: OMWG1
- //protected Object onto1 = null;
- //protected Object onto2 = null;
protected Ontology onto1 = null;
protected Ontology onto2 = null;
@@ -96,25 +93,18 @@ public class BasicAlignment implements Alignment {
* This is NOT the Ontology URI which can be obtained by
* getOntology1URI()
*/
- // JE: OMWG1
- //protected URI uri1 = null;
- //protected URI uri2 = null;
public BasicAlignment() {
hash1 = new Hashtable();
hash2 = new Hashtable();
extensions = new BasicParameters();
namespaces = new BasicParameters();
- if ( this instanceof AlignmentProcess ) setExtension( METHOD, getClass().getName() );
- // JE: OMWG1
+ if ( this instanceof AlignmentProcess ) setExtension( ALIGNNS, METHOD, getClass().getName() );
onto1 = new Ontology();
onto2 = new Ontology();
}
public void init( Object onto1, Object onto2, Object cache ) throws AlignmentException {
- // JE: OMWG1
- //this.onto1 = onto1;
- //this.onto2 = onto2;
if ( onto1 instanceof Ontology ) {
this.onto1 = (Ontology)onto1;
this.onto2 = (Ontology)onto2;
@@ -158,7 +148,6 @@ public class BasicAlignment implements Alignment {
};
public URI getOntology1URI() throws AlignmentException {
- // JE: OMWG1
Object ontology = onto1.getOntology();
if ( ontology != null && ontology instanceof URI ) {
return (URI)ontology;
@@ -168,7 +157,6 @@ public class BasicAlignment implements Alignment {
};
public URI getOntology2URI() throws AlignmentException {
- // JE: OMWG1
Object ontology = onto2.getOntology();
if ( ontology != null && ontology instanceof URI ) {
return (URI)ontology;
@@ -178,16 +166,10 @@ public class BasicAlignment implements Alignment {
};
public void setOntology1(Object ontology) throws AlignmentException {
- //*/onto1 = (OWLOntology)ontology;
- // JE: OMWG1
- //onto1 = ontology;
onto1.setOntology( ontology );
};
public void setOntology2(Object ontology) throws AlignmentException {
- //*/onto2 = (OWLOntology)ontology;
- // JE: OMWG1
- //onto2 = ontology;
onto2.setOntology( ontology );
};
@@ -199,12 +181,6 @@ public class BasicAlignment implements Alignment {
public String getLevel() { return level; };
- // JE: OMWG1
- //public URI getFile1() { return uri1; };
- //public void setFile1(URI u) { uri1 = u; };
- //public URI getFile2() { return uri2; };
- //public void setFile2(URI u) { uri2 = u; };
-
public URI getFile1() { return onto1.getFile(); };
public void setFile1(URI u) { onto1.setFile( u ); };
@@ -215,12 +191,14 @@ public class BasicAlignment implements Alignment {
public Parameters getExtensions(){ return extensions; }
- public void setExtension( String label, String value ) {
- extensions.setParameter( label, value );
+ public void setExtension( String uri, String label, String value ) {
+ final String[] ext = { uri, label, value };
+ extensions.setParameter( uri+label, ext);
};
- public String getExtension( String label ) {
- return (String)extensions.getParameter( label );
+ public String getExtension( String uri, String label ) {
+ String [] ext = (String [])extensions.getParameter( uri+label );
+ return (ext==null)?(String)null:ext[2];
};
public Parameters getXNamespaces(){ return namespaces; }
@@ -574,11 +552,10 @@ public class BasicAlignment implements Alignment {
result.setType( getType() );
result.setLevel( getLevel() );
// Must add an inverse to the method extension
- for ( Enumeration e = extensions.getNames() ; e.hasMoreElements(); ){
- String label = (String)e.nextElement();
- result.setExtension( label, getExtension( label ) );
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ result.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
- result.getExtensions().unsetParameter( "id" );
+ result.getExtensions().unsetParameter( ALIGNNS+"id" );
for ( Enumeration e = namespaces.getNames() ; e.hasMoreElements(); ){
String label = (String)e.nextElement();
result.setXNamespace( label, getXNamespace( label ) );
@@ -620,11 +597,10 @@ public class BasicAlignment implements Alignment {
align.setLevel( getLevel() );
align.setFile1( getFile1() );
align.setFile2( getFile2() );
- for ( Enumeration e = extensions.getNames() ; e.hasMoreElements(); ){
- String label = (String)e.nextElement();
- align.setExtension( label, getExtension( label ) );
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
- align.getExtensions().unsetParameter( "id" );
+ align.getExtensions().unsetParameter( ALIGNNS+"id" );
for ( Enumeration e = namespaces.getNames() ; e.hasMoreElements(); ){
String label = (String)e.nextElement();
align.setXNamespace( label, getXNamespace( label ) );
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicCell.java b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
index 165192d2..c97f3e19 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicCell.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 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
@@ -122,15 +122,16 @@ public class BasicCell implements Cell, Comparable {
extensions = p;
}
- public void setExtension( String label, String value ) {
+ public void setExtension( String uri, String label, String value ) {
if ( extensions == null )
extensions = new BasicParameters();
- extensions.setParameter( label, value );
+ String [] ext = { uri, label, value };
+ extensions.setParameter( uri+label, ext );
};
- public String getExtension( String label ) {
+ public String getExtension( String uri, String label ) {
if ( extensions != null ) {
- return (String)extensions.getParameter( label );
+ return ((String [])extensions.getParameter( uri+label ))[2];
} else {
return (String)null;
}
@@ -139,12 +140,11 @@ public class BasicCell implements Cell, Comparable {
public Cell inverse() throws AlignmentException {
Cell result = (Cell)new BasicCell( (String)null, object2, object1, relation.inverse(), strength );
if ( extensions != null ) {
- for ( Enumeration e = extensions.getNames() ; e.hasMoreElements(); ){
- String label = (String)e.nextElement();
- result.setExtension( label, getExtension( label ) );
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ result.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
}
- result.getExtensions().unsetParameter( "id" );
+ result.getExtensions().unsetParameter( BasicAlignment.ALIGNNS+BasicAlignment.ID );
// The sae should be done for the measure
return result;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
index d91365cb..bd656fa4 100644
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2008
*
* 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
@@ -224,11 +224,10 @@ public class OWLAPIAlignment extends BasicAlignment {
align.setLevel( getLevel() );
align.setFile1( getFile1() );
align.setFile2( getFile2() );
- for ( Enumeration e = extensions.getNames() ; e.hasMoreElements(); ){
- String label = (String)e.nextElement();
- align.setExtension( label, getExtension( label ) );
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
- align.getExtensions().unsetParameter( "id" );
+ align.getExtensions().unsetParameter( ALIGNNS+"id" );
try {
align.ingest( this );
} catch (AlignmentException ex) { ex.printStackTrace(); }
@@ -246,9 +245,8 @@ public class OWLAPIAlignment extends BasicAlignment {
align.setLevel( getLevel() );
align.setFile1( getFile1() );
align.setFile2( getFile2() );
- for ( Enumeration e = extensions.getNames() ; e.hasMoreElements(); ){
- String label = (String)e.nextElement();
- align.setExtension( label, getExtension( label ) );
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
for (Enumeration e = getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
@@ -270,9 +268,8 @@ public class OWLAPIAlignment extends BasicAlignment {
alignment.init( al.getFile1(), al.getFile2(), ontologies );
alignment.setType( al.getType() );
alignment.setLevel( al.getLevel() );
- for ( Enumeration e = al.getExtensions().getNames() ; e.hasMoreElements(); ){
- String label = (String)e.nextElement();
- alignment.setExtension( label, al.getExtension( label ) );
+ for ( Object ext : ((BasicParameters)al.getExtensions()).getValues() ){
+ alignment.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
OWLOntology o1 = (OWLOntology)alignment.getOntology1();
OWLOntology o2 = (OWLOntology)alignment.getOntology2();
diff --git a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
index f286ef37..3deaba55 100644
--- a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2008
*
* 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
@@ -172,11 +172,10 @@ public class URIAlignment extends BasicAlignment {
align.setLevel( getLevel() );
align.setFile1( getFile1() );
align.setFile2( getFile2() );
- for ( Enumeration e = extensions.getNames() ; e.hasMoreElements(); ){
- String label = (String)e.nextElement();
- align.setExtension( label, getExtension( label ) );
- }
- align.getExtensions().unsetParameter( "id" );
+ for ( Object ext : ((BasicParameters)extensions).getValues() ){
+ align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
+ }
+ align.getExtensions().unsetParameter( ALIGNNS+"id" );
try {
align.ingest( this );
} catch (AlignmentException ex) { ex.printStackTrace(); }
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
index ebddc604..40af58c3 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
@@ -68,9 +68,15 @@ public class PRGraphEvaluator extends BasicEvaluator {
private Vector points;
- /** Creation **/
+ /** Creation:
+ * A priori, evaluators can deal with any kind of alignments.
+ * However, it will not work if these are not of the same type.
+ **/
public PRGraphEvaluator(Alignment align1, Alignment align2) {
super(align1, align2);
+ if ( align1.getClass() != align2.getClass() ) {
+ // This should throw an exception...
+ }
points = new Vector();
}
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
index 2e38ce44..3f022da0 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2004-2007
+ * Copyright (C) INRIA Rhône-Alpes, 2004-2008
*
* 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
@@ -133,7 +133,7 @@ public class PRecEvaluator extends BasicEvaluator {
fmeasure = 2 * precision * recall / (precision + recall);
overall = recall * (2 - (1 / precision));
result = recall / precision;
- String timeExt = align2.getExtension("time");
+ String timeExt = align2.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.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/HTMLRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
index 255ba11e..d74b4327 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2006-2007
+ * Copyright (C) INRIA Rhône-Alpes, 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
@@ -29,6 +29,9 @@ 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.BasicParameters;
+
/**
* Renders an alignment in HTML
*
@@ -66,9 +69,8 @@ public class HTMLRendererVisitor implements AlignmentVisitor
writer.print("<tr><td>level</td><td>"+align.getLevel()+"</td></tr>\n" );
writer.print("<tr><td>type</td><td>"+align.getType()+"</td></tr>\n" );
// Get the keys of the parameter
- for( Enumeration e = align.getExtensions().getNames() ; e.hasMoreElements() ; ){
- String tag = (String)e.nextElement();
- writer.print("<tr><td>"+tag+"</td><td>"+align.getExtension(tag)+"</td></tr>\n");
+ for ( Object ext : ((BasicParameters)align.getExtensions()).getValues() ){
+ writer.print("<tr><td>"+((String[])ext)[0]+" : "+((String[])ext)[1]+"</td><td>"+((String[])ext)[2]+"</td></tr>\n");
}
writer.print("</table>\n");
writer.print("<h2>Correspondences</h2>\n");
@@ -91,7 +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( "id" ) ) ){
+ if ( id.startsWith( (String)alignment.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.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 68dc88eb..a59677e3 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
@@ -22,7 +22,7 @@ package fr.inrialpes.exmo.align.impl.renderer;
import java.util.Enumeration;
import java.io.PrintWriter;
-//import java.util.Set;
+import java.util.Hashtable;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
@@ -33,16 +33,12 @@ 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.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.BasicParameters;
import org.omwg.mediation.language.export.omwg.OmwgSyntaxFormat;
-//import org.omwg.mediation.language.export.rdf.RdfSyntaxFormat;
import org.omwg.mediation.parser.alignment.NamespaceDefs;
import org.omwg.mediation.language.objectmodel.api.Expression;
-// JE: we need jena... only for this renderer!
-//import com.hp.hpl.jena.rdf.model.Model;
-//import com.hp.hpl.jena.rdf.model.ModelFactory;
-
/**
* Renders an alignment in its RDF format
@@ -58,39 +54,60 @@ public class RDFRendererVisitor implements AlignmentVisitor
Alignment alignment = null;
Cell cell = null;
OmwgSyntaxFormat oMWGformatter = null;
- //RdfSyntaxFormat oMWGformatter = null;
- //Model model = null;
+ Hashtable nslist = null;
public RDFRendererVisitor( PrintWriter writer ){
this.writer = writer;
- //Model model = ModelFactory.createDefaultModel();
}
public void visit( Alignment align ) throws AlignmentException {
+ String extensionString = "";
alignment = align;
+ nslist = new Hashtable();
+ nslist.put(BasicAlignment.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");
+ // Get the keys of the parameter
+ int gen = 0;
+ for ( Object ext : ((BasicParameters)align.getExtensions()).getValues() ){
+ String prefix = ((String[])ext)[0];
+ String name = ((String[])ext)[1];
+ String tag = (String)nslist.get(prefix);
+ if ( tag == null ) {
+ tag = "ns"+gen++;
+ nslist.put( prefix, tag );
+ }
+ if ( tag.equals("align") ) { tag = name; }
+ else { tag += ":"+name; }
+ extensionString += " <"+tag+">"+((String[])ext)[2]+"</"+tag+">\n";
+ }
writer.print("<?xml version='1.0' encoding='utf-8");
writer.print("' standalone='no'?>\n");
- writer.print("<rdf:RDF xmlns='http://knowledgeweb.semanticweb.org/heterogeneity/alignment'\n xmlns:align='http://knowledgeweb.semanticweb.org/heterogeneity/alignment'\n xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'\n xmlns:xsd='http://www.w3.org/2001/XMLSchema#'\n");
+ writer.print("<rdf:RDF xmlns='"+BasicAlignment.ALIGNNS+"'");
+ for ( Enumeration e = nslist.keys() ; e.hasMoreElements(); ) {
+ String k = (String)e.nextElement();
+ writer.print("\n xmlns:"+nslist.get(k)+"='"+k+"'");
+ }
if ( align instanceof BasicAlignment ) {
for ( Enumeration e = ((BasicAlignment)align).getXNamespaces().getNames() ; e.hasMoreElements(); ){
String label = (String)e.nextElement();
if ( !label.equals("rdf") && !label.equals("xsd")
&& !label.equals("<default>") )
- writer.print(" xmlns:"+label+"='"+((BasicAlignment)align).getXNamespace( label )+"'\n");
+ writer.print("\n xmlns:"+label+"='"+((BasicAlignment)align).getXNamespace( label )+"'");
}
}
writer.print(">\n");
writer.print("<Alignment");
- if ( align.getExtension("id") != null ) {
- writer.print(" rdf:about=\""+align.getExtension("id")+"\"");
+ String idext = align.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID );
+ if ( idext != null ) {
+ writer.print(" rdf:about=\""+idext+"\"");
}
writer.print(">\n <xml>yes</xml>\n");
writer.print(" <level>");
writer.print( align.getLevel() );
if ( align.getLevel().equals("2OMWG") ) {
oMWGformatter = new OmwgSyntaxFormat( true, " " );
- //oMWGformatter = new RdfSyntaxFormat();
- // Provide the list of declared namespaces (should be related to above)
oMWGformatter.setDefaultNamespace( NamespaceDefs.ALIGNMENT );
// Set the offset at which element starts (fortunately always the same)
oMWGformatter.setPrefixCount(4);
@@ -98,25 +115,7 @@ public class RDFRendererVisitor implements AlignmentVisitor
writer.print("</level>\n <type>");
writer.print( align.getType() );
writer.print("</type>\n");
- // Get the keys of the parameter
- for( Enumeration e = align.getExtensions().getNames() ; e.hasMoreElements() ; ){
- String tag = (String)e.nextElement();
- // Here I should reverse namespace
- writer.print(" <"+tag+">"+align.getExtension(tag)+"</"+tag+">\n");
- }
- // JE: real new version of the format...
- /*
- if ( align.getFile1() != null )
- writer.print(" <onto1>"+align.getFile1().toString()+"</onto1>\n");
- if ( align.getFile2() != null )
- writer.print(" <onto2>"+align.getFile2().toString()+"</onto2>\n");
- writer.print(" <uri1>");
- writer.print( align.getOntology1URI().toString() );
- writer.print("</uri1>\n");
- writer.print(" <uri2>");
- writer.print( align.getOntology2URI().toString() );
- writer.print("</uri2>\n");
- */
+ writer.print(extensionString);
writer.print(" <onto1>\n <Ontology");
if ( align.getOntology1URI() != null ) {
writer.print(" rdf:about=\""+align.getOntology1URI()+"\">");
@@ -133,7 +132,7 @@ public class RDFRendererVisitor implements AlignmentVisitor
}
writer.print("\n <location>"+align.getFile2()+"</location>");
if ( align instanceof BasicAlignment && ((BasicAlignment)align).getOntologyObject2().getFormalism() != null ) {
- writer.print("\n <formalism>\n <Formalism name=\""+((BasicAlignment)align).getOntologyObject2().getFormalism()+"\" uri=\""+((BasicAlignment)align).getOntologyObject2().getFormURI()+"\"/>\n </formalism>");
+ writer.print("\n <formalism>\n <Formalism align:name=\""+((BasicAlignment)align).getOntologyObject2().getFormalism()+"\" align:uri=\""+((BasicAlignment)align).getOntologyObject2().getFormURI()+"\"/>\n </formalism>");
}
writer.print("\n </Ontology>\n </onto2>\n");
@@ -185,10 +184,17 @@ public class RDFRendererVisitor implements AlignmentVisitor
writer.print(" <semantics>"+cell.getSemantics()+"</semantics>\n");
if ( cell.getExtensions() != null ) {
// could certainly be done better
- for ( Enumeration e = cell.getExtensions().getNames() ; e.hasMoreElements(); ){
- String label = (String)e.nextElement();
+ for ( Object ext : ((BasicParameters)cell.getExtensions()).getValues() ){
+ String uri = ((String[])ext)[0];
+ String tag = (String)nslist.get( uri );
+ if ( tag == null ){
+ tag = ((String[])ext)[1];
+ } else {
+ tag += ":"+((String[])ext)[1];
+ }
+ // JE: Bug: namespace may not have been declared!
// Here I should reverse namespace
- writer.print(" <"+label+">"+cell.getExtension(label)+"</"+label+">\n");
+ writer.print(" <"+tag+">"+((String[])ext)[2]+"</"+tag+">\n");
}
}
writer.print(" </Cell>\n </map>\n");
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index 752551d3..fd7440d0 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -55,6 +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;
/**
* This class allows the creation of a parser for an Alignment file.
@@ -67,7 +68,7 @@ import fr.inrialpes.exmo.align.impl.BasicParameters;
public class AlignmentParser extends DefaultHandler {
- protected static String ALIGNNS = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment";
+ private static String ALIGNNS = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment#";
/**
* level of debug/warning information
*/
@@ -160,7 +161,7 @@ public class AlignmentParser extends DefaultHandler {
* and can find metadata
*/
protected int parselevel = 0;
-
+
/**
* Creates an XML Parser.
* @param debugMode The value of the debug mode
@@ -309,7 +310,7 @@ public class AlignmentParser extends DefaultHandler {
onto1 = new Ontology();
onto2 = new Ontology();
if ( atts.getValue("rdf:about") != null && !atts.getValue("rdf:about").equals("") ) {
- alignment.setExtension( "id", atts.getValue("rdf:about") );
+ alignment.setExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID, atts.getValue("rdf:about") );
};
} else {
if ( debugMode > 0 ) System.err.println("[AlignmentParser] Unknown element name : "+pName);
@@ -458,9 +459,10 @@ public class AlignmentParser extends DefaultHandler {
} else if (pName.equals("Alignment")) {
} else {
if ( parselevel == 3 ){
- alignment.setExtension( pName, content );
+ alignment.setExtension( namespaceURI, pName, content );
} else if ( parselevel == 5 ) {
- extensions.setParameter( pName, content );
+ String[] ext = {namespaceURI, pName, content};
+ extensions.setParameter( namespaceURI+pName, ext );
} else //if ( debugMode > 0 )
System.err.println("[AlignmentParser] Unknown element name : "+pName);
//throw new SAXException("[AlignmentParser] Unknown element name : "+pName);
@@ -471,12 +473,11 @@ public class AlignmentParser extends DefaultHandler {
throw new SAXException("[AlignmentParser] unknown element name: "+pName); };
} else {
if ( parselevel == 3 ){
- alignment.setExtension( qName, content );
- //alignment.addNamespace( namespaceURI, );
+ alignment.setExtension( namespaceURI, pName, content );
} else if ( parselevel == 5 ) {
if ( extensions == null ) extensions = new BasicParameters();
- extensions.setParameter( qName, content );
- //alignment.addNamespace( namespaceURI, );
+ String[] ext = {namespaceURI, pName, content};
+ extensions.setParameter( namespaceURI+pName, ext );
} else throw new SAXException("[AlignmentParser] Unknown namespace : "+namespaceURI);
}
parselevel--;
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 35877d96..607b6a9b 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2006-2007
+ * Copyright (C) INRIA Rhône-Alpes, 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
@@ -232,7 +232,7 @@ public class AServProtocolManager {
Set alignments = alignmentCache.getAlignments( uri1, uri2 );
String msg = "";
for( Iterator it = alignments.iterator(); it.hasNext(); ){
- msg += ((Alignment)it.next()).getExtension( "id" );
+ msg += ((Alignment)it.next()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID );
msg += " ";
}
return new AlignmentIds(newId(),mess,myId,mess.getSender(),msg,(Parameters)null);
@@ -355,12 +355,10 @@ public class AServProtocolManager {
Parameters params = new BasicParameters();
params.setParameter( "file1", al.getFile1() );
params.setParameter( "file2", al.getFile2() );
- params.setParameter( "level", al.getLevel() );
- params.setParameter( "type", al.getType() );
- Parameters extensions = al.getExtensions();
- for ( Enumeration e = extensions.getNames(); e.hasMoreElements(); ){
- String name = (String)e.nextElement();
- params.setParameter( name, extensions.getParameter( name ) );
+ params.setParameter( BasicAlignment.ALIGNNS+"level", al.getLevel() );
+ params.setParameter( BasicAlignment.ALIGNNS+"type", al.getType() );
+ for ( Object ext : ((BasicParameters)al.getExtensions()).getValues() ){
+ params.setParameter( ((String[])ext)[0]+((String[])ext)[1], ((String[])ext)[2] );
}
return new AlignmentMetadata(newId(),mess,myId,mess.getSender(),id,params);
}
@@ -441,7 +439,7 @@ public class AServProtocolManager {
} catch (Exception e) {
return false;
}
- if ( al.getExtension(CacheImpl.STORED) != null && al.getExtension(CacheImpl.STORED) != "" ) {
+ if ( al.getExtension(CacheImpl.SVCNS, CacheImpl.STORED) != null && al.getExtension(CacheImpl.SVCNS, CacheImpl.STORED) != "" ) {
return true;
} else {
return false;
@@ -725,8 +723,8 @@ public class AServProtocolManager {
if ( alignments != null && params.getParameter("force") == null ) {
for ( Iterator it = alignments.iterator(); it.hasNext() && (id == null); ){
Alignment al = ((Alignment)it.next());
- if ( al.getExtension( "method" ).equals(method) )
- id = al.getExtension( "id" );
+ if ( al.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.METHOD ).equals(method) )
+ id = al.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID );
}
}
// Otherwise compute
@@ -755,7 +753,7 @@ public class AServProtocolManager {
}
long newTime = System.currentTimeMillis();
- aresult.setExtension( "time", Long.toString(newTime - time) );
+ aresult.setExtension( BasicAlignment.ALIGNNS, BasicAlignment.TIME, Long.toString(newTime - time) );
// ask to store A'
id = alignmentCache.recordNewAlignment( aresult, true );
} catch (ClassNotFoundException e) {
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 5903fe77..4580fc02 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -2,7 +2,7 @@
* $Id$
*
* Copyright (C) Seungkeun Lee, 2006
- * Copyright (C) INRIA Rhône-Alpes, 2006-2007
+ * Copyright (C) INRIA Rhône-Alpes, 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
@@ -39,6 +39,7 @@ import java.sql.SQLException;
import fr.inrialpes.exmo.align.impl.BasicRelation;
import fr.inrialpes.exmo.align.impl.BasicAlignment;
+import fr.inrialpes.exmo.align.impl.BasicParameters;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.URICell;
@@ -62,10 +63,11 @@ public class CacheImpl implements Cache {
String port = null;
int rights = 1; // writing rights in the database (default is 1)
- final int VERSION = 302; // Version of the API to be stored in the database
+ final int VERSION = 310; // Version of the API to be stored in the database
/* 300: initial database format
301: added alignment id as primary key
302: changed cached/stored/ouri tag forms
+ 310: changed extension table with added URIs and method -> val
*/
Statement st = null; // JE: not sure that this should persist
@@ -75,10 +77,11 @@ public class CacheImpl implements Cache {
final int SUCCESS = 2;
final int INIT_ERROR = 3;
- static public final String CACHED = "http://exmo.inrialpes.fr/align/service:cached";
- static public final String STORED = "http://exmo.inrialpes.fr/align/service:stored";
- static public final String OURI1 = "http://exmo.inrialpes.fr/align/service:ouri1";
- static public final String OURI2 = "http://exmo.inrialpes.fr/align/service:ouri2";
+ static public final String SVCNS = "http://exmo.inrialpes.fr/align/service";
+ static public final String CACHED = "cached";
+ static public final String STORED = "stored";
+ static public final String OURI1 = "ouri1";
+ static public final String OURI2 = "ouri2";
//**********************************************************************
public CacheImpl( DBService service ) {
@@ -166,7 +169,7 @@ public class CacheImpl implements Cache {
String query;
ResultSet rs;
String tag;
- String method;
+ String value;
Alignment result = new URIAlignment();
@@ -178,8 +181,8 @@ public class CacheImpl implements Cache {
// Either uri1 or file1
result.setFile1( new URI( rs.getString("file1") ) );
result.setFile2( new URI( rs.getString("file2") ) );
- result.setExtension( OURI1, rs.getString("owlontology1") );
- result.setExtension( OURI2, rs.getString("owlontology2") );
+ result.setExtension( SVCNS, OURI1, rs.getString("owlontology1") );
+ result.setExtension( SVCNS, OURI2, rs.getString("owlontology2") );
result.setLevel(rs.getString("level"));
result.setType(rs.getString("type"));
}
@@ -189,8 +192,8 @@ public class CacheImpl implements Cache {
rs = (ResultSet) st.executeQuery(query);
while(rs.next()) {
tag = rs.getString("tag");
- method = rs.getString("method");
- result.setExtension(tag, method);
+ value = rs.getString("val");
+ result.setExtension( rs.getString("ns"), tag, value);
}
} catch (Exception e) { // URI exception that should not occur
System.err.println("Unlikely URI exception!");
@@ -198,9 +201,9 @@ public class CacheImpl implements Cache {
return null;
}
// should be there
- //result.setExtension(STORED, "DATE");
+ //result.setExtension( SVCNS, STORED, "DATE");
// not yet cached
- result.setExtension(CACHED, "");
+ result.setExtension(SVCNS, CACHED, "");
return result;
}
@@ -218,8 +221,8 @@ public class CacheImpl implements Cache {
URI ent1 = null, ent2 = null;
Cell cell = null;
- alignment.setOntology1( new URI( alignment.getExtension( OURI1 ) ) );
- alignment.setOntology2( new URI( alignment.getExtension( OURI2 ) ) );
+ alignment.setOntology1( new URI( alignment.getExtension( SVCNS, OURI1 ) ) );
+ alignment.setOntology2( new URI( alignment.getExtension( SVCNS, OURI2 ) ) );
// Get cells
query = "SELECT * FROM cell WHERE id = '" + id + "'";
@@ -242,8 +245,9 @@ public class CacheImpl implements Cache {
query = "SELECT * FROM extension WHERE id = '" + cid + "'";
ResultSet rse = (ResultSet) st.executeQuery(query);
while ( rse.next() ){
- cell.setExtension( rse.getString("tag"),
- rse.getString("method") );
+ cell.setExtension( rse.getString("ns"),
+ rse.getString("tag"),
+ rse.getString("val") );
}
}
}
@@ -297,8 +301,8 @@ public class CacheImpl implements Cache {
throw new Exception("getAlignment: Cannot find alignment");
// If not cached, retrieve it now
- if ( result.getExtension(CACHED) == ""
- && result.getExtension(STORED) != "") {
+ if ( result.getExtension( SVCNS, CACHED) == ""
+ && result.getExtension(SVCNS, STORED) != "") {
retrieveAlignment( id, result );
}
@@ -317,7 +321,7 @@ public class CacheImpl implements Cache {
for( Iterator it = potentials.iterator(); it.hasNext(); ) {
Alignment al = (Alignment)it.next();
// This is not the best because URI are not resolved here...
- if ( al.getExtension(OURI2).equals( uri2.toString() ) ) result.add( al );
+ if ( al.getExtension(SVCNS, OURI2).equals( uri2.toString() ) ) result.add( al );
}
}
return result;
@@ -338,12 +342,12 @@ public class CacheImpl implements Cache {
*/
public String recordNewAlignment( String id, Alignment al, boolean force ) throws AlignmentException {
Alignment alignment = al;
- alignment.setExtension(OURI1, alignment.getOntology1URI().toString());
- alignment.setExtension(OURI2, alignment.getOntology2URI().toString());
+ alignment.setExtension(SVCNS, OURI1, alignment.getOntology1URI().toString());
+ alignment.setExtension(SVCNS, OURI2, alignment.getOntology2URI().toString());
// Index
recordAlignment( id, alignment, force );
// Not yet stored
- alignment.setExtension(STORED, "");
+ alignment.setExtension(SVCNS, STORED, "");
// Cached now
resetCacheStamp(alignment);
return id;
@@ -354,12 +358,12 @@ public class CacheImpl implements Cache {
*/
public String recordAlignment( String id, Alignment alignment, boolean force ){
// record the Id!
- if ( alignment.getExtension("id") == null )
- alignment.setExtension( "id", id );
+ if ( alignment.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID ) == null )
+ alignment.setExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID, id );
// Store it
try {
- URI ouri1 = new URI( alignment.getExtension(OURI1) );
- URI ouri2 = new URI( alignment.getExtension(OURI2) );
+ URI ouri1 = new URI( alignment.getExtension( SVCNS, OURI1) );
+ URI ouri2 = new URI( alignment.getExtension( SVCNS, OURI2) );
if ( force || alignmentTable.get( id ) == null ) {
Set s1 = (Set)ontologyTable.get( ouri1 );
if ( s1 == null ) {
@@ -421,13 +425,13 @@ public class CacheImpl implements Cache {
alignment = getAlignment( id );
// We store stored date
- alignment.setExtension(STORED, new Date().toString());
+ alignment.setExtension( SVCNS, STORED, new Date().toString());
// We empty cached date
- alignment.setExtension(CACHED, "");
+ alignment.setExtension( SVCNS, CACHED, "");
try {
- String s_O1 = alignment.getExtension(OURI1);
- String s_O2 = alignment.getExtension(OURI2);
+ String s_O1 = alignment.getExtension(SVCNS, OURI1);
+ String s_O2 = alignment.getExtension(SVCNS, OURI2);
// file attribute
String s_File1 = null;
@@ -448,12 +452,13 @@ public class CacheImpl implements Cache {
"(id, owlontology1, owlontology2, type, level, file1, file2, uri1, uri2) " +
"VALUES ('" + quote(id) + "','" + quote(s_O1) + "','" + quote(s_O2) + "','" + quote(type) + "','" + quote(level) + "','" + quote(s_File1) + "','" + quote(s_File2) + "','" + quote(s_uri1) + "','" + quote(s_uri2) + "')";
st.executeUpdate(query);
- for( Enumeration e = alignment.getExtensions().getNames() ; e.hasMoreElements() ; ){
- String tag = (String)e.nextElement();
- String s_method = alignment.getExtension(tag);
+ for ( Object ext : ((BasicParameters)alignment.getExtensions()).getValues() ){
+ String uri = ((String[])ext)[0];
+ String tag = ((String[])ext)[1];
+ String val = ((String[])ext)[2];
query = "INSERT INTO extension " +
- "(id, tag, method) " +
- "VALUES ('" + quote(id) + "','" + quote(tag) + "','" + quote(s_method) + "')";
+ "(id, uri, tag, val) " +
+ "VALUES ('" + quote(id) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
st.executeUpdate(query);
}
@@ -464,7 +469,7 @@ public class CacheImpl implements Cache {
cellid = c.getId();
if ( cellid != null ){
if ( cellid.startsWith("#") ) {
- cellid = alignment.getExtension("id") + cellid;
+ cellid = alignment.getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID ) + cellid;
}
} else if ( c.getExtensions() != null ) {
// JE: In case of extensions create an ID
@@ -487,12 +492,14 @@ public class CacheImpl implements Cache {
}
if ( cellid != null && !cellid.equals("") && c.getExtensions() != null ) {
// JE: I must now store all the extensions
- for( Enumeration e2 = c.getExtensions().getNames() ; e2.hasMoreElements() ; ){
- String tag = (String)e2.nextElement();
- String s_method = c.getExtension(tag);
+ // JE:EXT
+ for ( Object ext : ((BasicParameters)c.getExtensions()).getValues() ){
+ String uri = ((String[])ext)[0];
+ String tag = ((String[])ext)[1];
+ String val = ((String[])ext)[2];
query = "INSERT INTO extension " +
- "(id, tag, method) " +
- "VALUES ('" + quote(cellid) + "','" + quote(tag) + "','" + quote(s_method) + "')";
+ "(id, uri, tag, val) " +
+ "VALUES ('" + quote(cellid) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
st.executeUpdate(query);
}
}
@@ -505,13 +512,13 @@ public class CacheImpl implements Cache {
//**********************************************************************
// CACHE MANAGEMENT (Not implemented yet)
public void resetCacheStamp( Alignment result ){
- result.setExtension(CACHED, new Date().toString() );
+ result.setExtension(SVCNS, CACHED, new Date().toString() );
}
public void cleanUpCache() {
// for each alignment in the table
// set currentDate = Date();
- // if ( DateFormat.parse( result.getExtension(CACHED) ).before( ) ) {
+ // if ( DateFormat.parse( result.getExtension(SVCNS, CACHED) ).before( ) ) {
// - for each ontology if no other alignment => unload
// - clean up cells
// }
@@ -559,7 +566,7 @@ public class CacheImpl implements Cache {
create table extension(
id varchar(100),
tag varchar(100),
- method varchar(500));
+ val varchar(500));
*/
@@ -567,7 +574,7 @@ public class CacheImpl implements Cache {
// Create tables
st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), owlontology1 VARCHAR(250), owlontology2 VARCHAR(250), type VARCHAR(5), level VARCHAR(1), file1 VARCHAR(250), file2 VARCHAR(250), uri1 VARCHAR(250), uri2 VARCHAR(250), primary key (id))");
st.executeUpdate("CREATE TABLE cell(id VARCHAR(100), cell_id VARCHAR(250), uri1 VARCHAR(250), uri2 VARCHAR(250), semantics VARCHAR(30), measure VARCHAR(20), relation VARCHAR(5))");
- st.executeUpdate("CREATE TABLE extension(id VARCHAR(100), tag VARCHAR(100), method VARCHAR(500))");
+ st.executeUpdate("CREATE TABLE extension(id VARCHAR(100), uri VARCHAR(200), tag VARCHAR(50), val VARCHAR(500))");
st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), edit BOOLEAN, version VARCHAR(5))");
st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('dbms', 'port', 0, '"+VERSION+"')");
}
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index 7e4a56ae..a83687db 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2006-2007.
+ * Copyright (C) INRIA Rhône-Alpes, 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
@@ -21,6 +21,7 @@
package fr.inrialpes.exmo.align.service;
import fr.inrialpes.exmo.align.impl.BasicParameters;
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Parameters;
@@ -352,7 +353,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
if ( perf.equals("listalignments") ){
msg = "<h1>Available alignments</h1><ul compact=\"1\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID );
msg += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id+"\">"+id+"</a></li>";
}
msg += "</ul>";
@@ -436,7 +437,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "Alignment id: <select name=\"id\">";
// JE: only those non stored please (retrieve metadata + stored)
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID);
params.setParameter("id", id);
if ( !manager.storedAlignment( new Message(newId(),(Message)null,myId,serverId,"", params ) ) ){
msg += "<option value=\""+id+"\">"+id+"</option>";
@@ -469,7 +470,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg ="<h1>Trim alignments</h1><form action=\"cut\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID);
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br />";
@@ -490,7 +491,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg ="<h1>Inverse alignment</h1><form action=\"inv\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID);
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br />";
@@ -514,7 +515,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
}
msg += "</select><br />Initial alignment id: <select name=\"id\"><option value=\"\" selected=\"1\"></option>";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID);
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br />";
@@ -542,7 +543,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Retrieve alignment</h1><form action=\"retrieve\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID);
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br />";
@@ -566,7 +567,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Retrieve alignment metadata</h1><form action=\"metadata\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID);
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br /><input type=\"submit\" value=\"Get metadata\"/></form>";
@@ -604,7 +605,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Translate query</h1><form action=\"translate\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID);
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br />";
@@ -624,7 +625,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Retrieve alignment metadata</h1><form action=\"metadata\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension("id");
+ String id = ((Alignment)e.nextElement()).getExtension( BasicAlignment.ALIGNNS, BasicAlignment.ID);
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br /><input type=\"submit\" value=\"Get metadata\"/></form>";
diff --git a/src/fr/inrialpes/exmo/align/util/GroupAlign.java b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
index c5ad41ce..3145617e 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupAlign.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2007, INRIA Rhône-Alpes
+ * Copyright (C) 2003-2008, INRIA Rhône-Alpes
* Copyright (C) 2004, Université de Montréal
*
* Modifications to the initial code base are copyright of their
@@ -331,7 +331,7 @@ public class GroupAlign {
long time = System.currentTimeMillis();
result.align(init, params); // add opts
long newTime = System.currentTimeMillis();
- result.setExtension( BasicAlignment.TIME, Long.toString(newTime - time) );
+ result.setExtension( BasicAlignment.ALIGNNS, BasicAlignment.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 ab809681..3b425b4d 100644
--- a/src/fr/inrialpes/exmo/align/util/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/util/Procalign.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2007, INRIA Rhône-Alpes
+ * Copyright (C) 2003-2008, INRIA Rhône-Alpes
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -247,7 +247,7 @@ public class Procalign {
long time = System.currentTimeMillis();
result.align( init, params ); // add opts
long newTime = System.currentTimeMillis();
- result.setExtension( BasicAlignment.TIME, Long.toString(newTime - time) );
+ result.setExtension( BasicAlignment.ALIGNNS, BasicAlignment.TIME, Long.toString(newTime - time) );
// Thresholding
if (threshold != 0) result.cut( cutMethod, threshold );
diff --git a/src/org/semanticweb/owl/align/Alignment.java b/src/org/semanticweb/owl/align/Alignment.java
index 4cbf7ff7..90154ac0 100644
--- a/src/org/semanticweb/owl/align/Alignment.java
+++ b/src/org/semanticweb/owl/align/Alignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 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
@@ -146,8 +146,8 @@ public interface Alignment extends Cloneable
* to the alignment structure itself.
*/
public Parameters getExtensions();
- public String getExtension( String label );
- public void setExtension( String label, String value );
+ public String getExtension( String uri, String label );
+ public void setExtension( String uri, String label, String value );
public Enumeration getElements();
public int nbCells();
--
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