From 8abaa507a50e6576c69e370012ac3514ee1cd4bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Wed, 9 May 2012 23:22:05 +0000
Subject: [PATCH] - fixed buf with confidence parsing
---
examples/omwg/total.xml | 6 +-
examples/omwg/wine.xml | 6 +-
examples/rdf/bibref.owl | 62 +++++++++++++++++++
examples/rdf/newsample.rdf | 2 +-
.../exmo/align/parser/XMLParser.java | 61 +++++++++---------
test/src/IOTest.java | 10 +++
test/src/RendererTest.java | 2 +-
7 files changed, 107 insertions(+), 42 deletions(-)
diff --git a/examples/omwg/total.xml b/examples/omwg/total.xml
index 46029d50..eeb79e09 100644
--- a/examples/omwg/total.xml
+++ b/examples/omwg/total.xml
@@ -33,10 +33,8 @@
<onto1>
<Ontology rdf:about="&wine;">
<formalism>
- <Formalism>
- <uri>http://www.w3.org/TR/owl-guide/</uri>
- <name>owl</name>
- </Formalism>
+ <Formalism align:uri="http://www.w3.org/TR/owl-guide/"
+ align:name="owl" />
</formalism>
</Ontology>
</onto1>
diff --git a/examples/omwg/wine.xml b/examples/omwg/wine.xml
index d5213261..3233f1ed 100644
--- a/examples/omwg/wine.xml
+++ b/examples/omwg/wine.xml
@@ -32,10 +32,8 @@
<onto1>
<Ontology rdf:about="&wine;">
<formalism>
- <Formalism>
- <uri>http://www.w3.org/TR/owl-guide/</uri>
- <name>owl</name>
- </Formalism>
+ <Formalism align:uri="http://www.w3.org/TR/owl-guide/"
+ align:name="owl" />
</formalism>
</Ontology>
</onto1>
diff --git a/examples/rdf/bibref.owl b/examples/rdf/bibref.owl
index 44ce6aec..da89351b 100644
--- a/examples/rdf/bibref.owl
+++ b/examples/rdf/bibref.owl
@@ -19,218 +19,280 @@
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#TechReport'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Techreport'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#InBook'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Inbook'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Misc'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Misc'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Book'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Book'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#InCollection'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Incollection'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#MastersThesis'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Mastersthesis'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#PhdThesis'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Phdthesis'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#InProceedings'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Inproceedings'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Proceedings'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#Proceedings'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
<!-- HERE ARE THE PROPERTIES -->
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#title'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasTitle'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#editor'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasEditor'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#edition'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasEdition'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#series'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasSeries'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#volume'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasVolume'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#note'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasNote'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#organization'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasOrganization'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#booktitle'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasBooktitle'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#type'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasType'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#keyword'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasKeywords'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#softCopyURI'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasURL'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#softCopySize'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasSize'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#author'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasAuthor'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#publisher'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasPublisher'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#chapter'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasChapter'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#pages'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasPages'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#number'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasNumber'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#address'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasAddress'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#journal'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasJournal'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#school'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasSchool'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#institution'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasInstitution'/>
<measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>1.0</measure>
<relation>=</relation>
</Cell>
+ </map>
+ <map>
<Cell>
<entity1 rdf:resource='http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#abstract'/>
<entity2 rdf:resource='file://localhost/Volumes/Phata/JAVA/ontoalign/samples/rdf/edu.mit.visus.bibtex.owl#hasAbstract'/>
diff --git a/examples/rdf/newsample.rdf b/examples/rdf/newsample.rdf
index f00dce61..4e9cb354 100644
--- a/examples/rdf/newsample.rdf
+++ b/examples/rdf/newsample.rdf
@@ -35,7 +35,7 @@
<entity2 rdf:resource='http://www.example.org/ontology2#journalarticle'/>
<relation>=</relation>
<kha:myCorrespondenceTag>Testing tags in correspondences</kha:myCorrespondenceTag>
- <measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>0.4666666666666667</measure>
+ <measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>46.66666666666667E-2</measure>
<!--invalidTag>This tag would be ignored</invalidTag-->
</Cell>
</map>
diff --git a/src/fr/inrialpes/exmo/align/parser/XMLParser.java b/src/fr/inrialpes/exmo/align/parser/XMLParser.java
index 459f0bb1..2c26e142 100644
--- a/src/fr/inrialpes/exmo/align/parser/XMLParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/XMLParser.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2005, 2007-2011
+ * Copyright (C) INRIA, 2003-2005, 2007-2012
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -310,11 +310,11 @@ public class XMLParser extends DefaultHandler {
} else if (pName.equals( SyntaxElement.FORMALISM.name )) {
if ( atts.getValue( SyntaxElement.URI.name ) != null )
try {
- curronto.setFormURI( new URI(atts.getValue("uri")) );
+ curronto.setFormURI( new URI(atts.getValue( SyntaxElement.URI.name )) );
} catch ( URISyntaxException e ) {
- throw new SAXException("Malformed URI"+atts.getValue("uri"), e );
+ throw new SAXException("Malformed URI"+atts.getValue( SyntaxElement.URI.name ), e );
};
- if ( atts.getValue("name") != null )
+ if ( atts.getValue( SyntaxElement.NAME.name ) != null )
curronto.setFormalism( atts.getValue( SyntaxElement.NAME.name ) );
} else if (pName.equals( SyntaxElement.FORMATT.name )) {
} else if (pName.equals( SyntaxElement.LOCATION.name )) {
@@ -371,39 +371,31 @@ public class XMLParser extends DefaultHandler {
/**
* Put the content in a variable
- */
public void characters(char ch[], int start, int length) {
content = new String( ch, start, length );
if(debugMode > 2)
System.err.println("content XMLParser : " + content);
}
-
- /*
- // Patch proposed by Sabine Massmann
- // If to be integrated, then put it in the proper place
- // There is no reasons to test for Double in characters
- public void characters(char ch[], int start, int length) {
- String oldContent = "" + content;
- content = new String( ch, start, length );
- if ( content != null && !content.equals("\n")
- && !content.startsWith("\n ")
- // && oldContent.contains(".")
- && oldContent.indexOf('.',0) != -1
- ){
- oldContent = oldContent.concat(content);
- try {
- double test = Double.parseDouble(oldContent);
- content = oldContent;
- } catch (NumberFormatException e) {
- // TODO Auto-generated catch block
- // e.printStackTrace();
- }
- }
- if(debugMode > 2)
- System.err.println("content XMLParser : " + content);
- }
*/
+ /* From a patch proposed by Sabine Massmann
+ * Get around some nasty double parsing bug. Sometimes it parses
+ * 6.925955630686735E-4 as
+ * content XMLParser : 6.925955630686735
+ * content XMLParser : E-4
+ */
+ public void characters( char ch[], int start, int length ) {
+ String newContent = new String( ch, start, length );
+ if ( content != null && content.indexOf('.',0) != -1 // a float
+ && newContent != null && !newContent.startsWith("\n ")
+ ) {
+ content += newContent;
+ } else {
+ content = newContent;
+ }
+ if ( debugMode > 2 ) System.err.println("content XMLParser : " + content);
+ }
+
/**
* Called by the XML parser at the end of an element.
*
@@ -440,7 +432,11 @@ public class XMLParser extends DefaultHandler {
} else if ( measure == null || relation == null ){
cell = alignment.addAlignCell( cl1, cl2);
} else {
- cell = alignment.addAlignCell( cl1, cl2, relation, Double.parseDouble(measure) );}
+ // This test must be revised for more generic confidence (which should then be strings)
+ double conf = Double.parseDouble( measure );
+ if ( conf > 1. || conf < 0. )
+ throw new SAXException( "Bad confidence value : "+conf+" (should belong to [0. 1.])" );
+ cell = alignment.addAlignCell( cl1, cl2, relation, conf );}
if ( id != null ) cell.setId( id );
if ( sem != null ) cell.setSemantics( sem );
if ( extensions != null ) ((BasicCell)cell).setExtensions( extensions );
@@ -493,7 +489,7 @@ public class XMLParser extends DefaultHandler {
//if ( content.equals("no") )
// { throw new SAXException("Cannot parse non XML alignments"); }
} else if (pName.equals( SyntaxElement.ALIGNMENT.name )) {
- parseLevel = alignLevel; // restore level²<
+ parseLevel = alignLevel; // restore level<
alignLevel = -1;
} else {
if ( namespaceURI.equals( Namespace.ALIGNMENT.uri+"#" ) ) namespaceURI = Namespace.ALIGNMENT.uri;
@@ -523,6 +519,7 @@ public class XMLParser extends DefaultHandler {
extensions.setExtension( namespaceURI, pName, content );
} else if ( !embedded ) throw new SAXException("[XMLParser] Unknown namespace : "+namespaceURI);
}
+ content = null; // JE2012: set it for the character patch
parseLevel--;
} //end endElement
diff --git a/test/src/IOTest.java b/test/src/IOTest.java
index b557a4fd..1a249d41 100644
--- a/test/src/IOTest.java
+++ b/test/src/IOTest.java
@@ -28,6 +28,7 @@ import org.testng.annotations.Test;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.Cell;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
import fr.inrialpes.exmo.align.impl.URIAlignment;
@@ -108,6 +109,15 @@ public class IOTest {
assertNotNull( alignment );
assertTrue( alignment instanceof URIAlignment );
assertEquals( alignment.nbCells(), 2 );
+ double min = 1.;
+ double max = 0.;
+ for ( Cell c : alignment ) {
+ double v = c.getStrength();
+ if ( v < min ) min = v;
+ if ( v > max ) max = v;
+ }
+ assertEquals( min, 0.4666666666666667 );
+ assertEquals( max, 1. );
}
@Test(groups = { "full", "io", "raw" }, dependsOnMethods = {"loadSOAPStringErrorTest"})
diff --git a/test/src/RendererTest.java b/test/src/RendererTest.java
index 44e1388f..50589ef5 100644
--- a/test/src/RendererTest.java
+++ b/test/src/RendererTest.java
@@ -69,7 +69,7 @@ public class RendererTest {
AlignmentParser aparser = new AlignmentParser( 0 );
assertNotNull( aparser );
aparser.initAlignment( null );
- alignment = aparser.parse( "test/output/bibref2.rdf" );
+ alignment = aparser.parse( "file:test/output/bibref2.rdf" );
assertNotNull( alignment );
assertEquals( alignment.nbCells(), 32);
oalignment = ObjectAlignment.toObjectAlignment( (URIAlignment)alignment );
--
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