From 801c35985205f382a73ea4a5c097b5c804aeef96 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Wed, 25 Jun 2008 14:23:27 +0000
Subject: [PATCH] - Modified Cell interface so that object URIs can be found in
a generic way -> solves a database storage bug
---
.../exmo/align/impl/OWLAPIAlignment.java | 10 +++---
.../exmo/align/impl/ObjectAlignment.java | 6 ++--
.../align/impl/eval/PRGraphEvaluator.java | 18 +++++-----
.../exmo/align/impl/eval/PRecEvaluator.java | 25 +++++++++++++
.../impl/renderer/HTMLRendererVisitor.java | 16 ++++-----
.../impl/renderer/SKOSRendererVisitor.java | 4 +--
.../impl/renderer/XSLTRendererVisitor.java | 9 ++---
.../align/service/AServProtocolManager.java | 35 ++++++++++++++++++
.../exmo/align/service/CacheImpl.java | 36 +++++++++++++++----
.../exmo/align/service/QueryMediator.java | 5 +--
src/org/semanticweb/owl/align/Cell.java | 10 ++++++
11 files changed, 134 insertions(+), 40 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
index 928df006..cb92ed2a 100644
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
@@ -223,7 +223,7 @@ public class OWLAPIAlignment extends ObjectAlignment {
for (Enumeration e = getElements(); e.hasMoreElements();) {
OWLAPICell c = (OWLAPICell)e.nextElement(); //[W:Deprecated]
try {
- align.addAlignCell( c.getId(), c.getObject1AsURI(), c.getObject2AsURI(), c.getRelation(), c.getStrength() );
+ align.addAlignCell( c.getId(), c.getObject1AsURI(this), c.getObject2AsURI(this), c.getRelation(), c.getStrength() );
} catch (AlignmentException aex) {
// Sometimes URIs are null, this is ignored
}
@@ -245,11 +245,11 @@ public class OWLAPIAlignment extends ObjectAlignment {
//System.err.println( o1 );
for (Enumeration e = al.getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
- //System.err.println( c.getObject1AsURI() );
- //System.err.println( c.getObject2AsURI() );
+ //System.err.println( c.getObject1AsURI(this) );
+ //System.err.println( c.getObject2AsURI(this) );
alignment.addAlignCell( c.getId(),
- getEntity( o1, c.getObject1AsURI() ),
- getEntity( o2, c.getObject2AsURI() ),
+ getEntity( o1, c.getObject1AsURI(al) ),
+ getEntity( o2, c.getObject2AsURI(al) ),
c.getRelation(),
c.getStrength(),
c.getExtensions() );
diff --git a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
index cd0ef1d3..1af66e28 100644
--- a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
@@ -150,7 +150,7 @@ public class ObjectAlignment extends BasicAlignment {
for (Enumeration e = getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
try {
- align.addAlignCell( c.getId(), c.getObject1AsURI(), c.getObject2AsURI(), c.getRelation(), c.getStrength() );
+ align.addAlignCell( c.getId(), c.getObject1AsURI(this), c.getObject2AsURI(this), c.getRelation(), c.getStrength() );
} catch (AlignmentException aex) {
// Sometimes URIs are null, this is ignore
}
@@ -171,8 +171,8 @@ public class ObjectAlignment extends BasicAlignment {
for (Enumeration e = al.getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
alignment.addAlignCell( c.getId(),
- o1.getEntity( c.getObject1AsURI() ),
- o2.getEntity( c.getObject2AsURI() ),
+ o1.getEntity( c.getObject1AsURI(alignment) ),
+ o2.getEntity( c.getObject2AsURI(alignment) ),
c.getRelation(),
c.getStrength(),
c.getExtensions() );
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
index 1e7fc6e9..7ff3e81f 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
@@ -116,17 +116,17 @@ public class PRGraphEvaluator extends BasicEvaluator {
} else if ( ((Cell)o1).getStrength() < ((Cell)o2).getStrength() ){
return 1;
//The comparator must always tell that things are different!
- } else if ( (((Cell)o1).getObject1AsURI().getFragment() == null)
- || (((Cell)o2).getObject1AsURI().getFragment() == null) ) {
+ } else if ( (((Cell)o1).getObject1AsURI(align1).getFragment() == null)
+ || (((Cell)o2).getObject1AsURI(align2).getFragment() == null) ) {
return -1;
- } else if ( ((Cell)o1).getObject1AsURI().getFragment().compareTo(((Cell)o2).getObject1AsURI().getFragment()) > 0) {
+ } else if ( ((Cell)o1).getObject1AsURI(align1).getFragment().compareTo(((Cell)o2).getObject1AsURI(align2).getFragment()) > 0) {
return -1;
- } else if ( ((Cell)o1).getObject1AsURI().getFragment().compareTo(((Cell)o2).getObject1AsURI().getFragment()) < 0 ) {
+ } else if ( ((Cell)o1).getObject1AsURI(align1).getFragment().compareTo(((Cell)o2).getObject1AsURI(align2).getFragment()) < 0 ) {
return 1;
- } else if ( (((Cell)o1).getObject2AsURI().getFragment() == null)
- || (((Cell)o2).getObject2AsURI().getFragment() == null) ) {
+ } else if ( (((Cell)o1).getObject2AsURI(align1).getFragment() == null)
+ || (((Cell)o2).getObject2AsURI(align2).getFragment() == null) ) {
return -1;
- } else if ( ((Cell)o1).getObject2AsURI().getFragment().compareTo(((Cell)o2).getObject2AsURI().getFragment()) > 0) {
+ } else if ( ((Cell)o1).getObject2AsURI(align1).getFragment().compareTo(((Cell)o2).getObject2AsURI(align2).getFragment()) > 0) {
return -1;
// We assume that they have different names
} else { return 1; }
@@ -151,8 +151,8 @@ public class PRGraphEvaluator extends BasicEvaluator {
if( s1 != null ){ // for all cells matching our first entity
for( Iterator it1 = s1.iterator(); it1.hasNext() && c2 != null; ){
Cell c1 = (Cell)it1.next();
- URI uri1 = c1.getObject2AsURI();
- URI uri2 = c2.getObject2AsURI();
+ URI uri1 = c1.getObject2AsURI(align1);
+ URI uri2 = c2.getObject2AsURI(align2);
if (uri1.toString().equals(uri2.toString())) { //This cell matches a correct one
nbcorrect++;
double recall = (double)nbcorrect / (double)nbexpected;
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
index dd236a66..706b07b2 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
@@ -140,6 +140,31 @@ public class PRecEvaluator extends BasicEvaluator {
return (result);
}
+ public String HTMLString (){
+ String result = "";
+ result += " <div xmlns:map='http://www.atl.external.lmco.com/projects/ontology/ResultsOntology.n3#' typeof=\"map:output\" href=''>";
+ result += " <dl>";
+ //if ( ) {
+ // result += " <dt>algorithm</dt><dd property=\"map:algorithm\">"+align1.get+"</dd>";
+ //}
+ try {
+ result += " <dt>input1</dt><dd rel=\"map:input1\" href=\""+align1.getOntology1URI()+"\">"+align1.getOntology1URI()+"</dd>";
+ result += " <dt>input2</dt><dd rel=\"map:input2\" href=\""+align1.getOntology2URI()+"\">"+align1.getOntology2URI()+"</dd>";
+ } catch (AlignmentException e) { e.printStackTrace(); };
+ // Other missing items (easy to get)
+ // result += " <map:falseNegative>");
+ // result += " <map:falsePositive>");
+ result += " <dt>precision</dt><dd property=\"map:precision\">"+precision+"</dd>\n";
+ result += " <dt>recall</dt><dd property=\"map:recall\">"+recall+"</dd>\n";
+ result += " <dt>fallout</dt><dd property=\"map:fallout\">"+fallout+"</dd>\n";
+ result += " <dt>F-measure</dt><dd property=\"map:fMeasure\">"+fmeasure+"</dd>\n";
+ result += " <dt>O-measure</dt><dd property=\"map:oMeasure\">"+overall+"</dd>\n";
+ if ( time != 0 ) result += " <dt>time</dt><dd property=\"map:time\">"+time+"</dd>\n";
+ result += " <dt>result</dt><dd property=\"map:result\">"+result+"</dd>\n";
+ result += " </dl>\n </div>\n";
+return result;
+ }
+
/**
* This now output the results in Lockheed format.
*/
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
index 7e50be42..4c8d2bf5 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
@@ -130,14 +130,14 @@ public class HTMLRendererVisitor implements AlignmentVisitor
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
URI u1, u2;
- if ( cell instanceof ObjectCell ) {
- u1 = ((LoadedOntology)((BasicAlignment)alignment).getOntologyObject1()).getEntityURI( cell.getObject1() );
- u2 = ((LoadedOntology)((BasicAlignment)alignment).getOntologyObject2()).getEntityURI( cell.getObject2() );
- } else {
- System.err.println( cell );
- u1 = cell.getObject1AsURI();
- u2 = cell.getObject2AsURI();
- }
+ // JE: I think that now these two clauses should be unified (3.4)
+ //if ( cell instanceof ObjectCell ) {
+ // u1 = ((LoadedOntology)((BasicAlignment)alignment).getOntologyObject1()).getEntityURI( cell.getObject1() );
+ // u2 = ((LoadedOntology)((BasicAlignment)alignment).getOntologyObject2()).getEntityURI( cell.getObject2() );
+ //} else {
+ u1 = cell.getObject1AsURI( alignment );
+ u2 = cell.getObject2AsURI( alignment );
+ //}
writer.print(" <tr typeof=\"align:Cell\">");
writer.print("<td rel=\"align:entity1\" href=\""+u1+"\">"+u1+"</td><td property=\"align:relation\">");
cell.getRelation().accept( this );
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SKOSRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SKOSRendererVisitor.java
index 691ba69c..0079d490 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SKOSRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SKOSRendererVisitor.java
@@ -76,7 +76,7 @@ public class SKOSRendererVisitor implements AlignmentVisitor {
if ( onto2 != null ) {
return onto2.getEntityURI( cell.getObject2() );
} else {
- return cell.getObject2AsURI();
+ return cell.getObject2AsURI( alignment );
}
}
@@ -85,7 +85,7 @@ public class SKOSRendererVisitor implements AlignmentVisitor {
if ( onto1 != null ) {
writer.print(" <skos:Concept rdf:about=\""+onto1.getEntityURI( cell.getObject1() )+"\">\n");
} else {
- writer.print(" <skos:Concept rdf:about=\""+cell.getObject1AsURI()+"\">\n");
+ writer.print(" <skos:Concept rdf:about=\""+cell.getObject1AsURI( alignment )+"\">\n");
}
cell.getRelation().accept( this );
writer.print(" </skos:Concept>\n\n");
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
index 56b500bc..49c00b26 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
@@ -107,12 +107,13 @@ public class XSLTRendererVisitor implements AlignmentVisitor {
private void collectURIs ( Cell cell ) throws AlignmentException {
URI entity1URI, entity2URI;
+ // JE: I think that now these two clauses should be unified (3.4)
if ( onto1 != null ){
entity1URI = onto1.getEntityURI( cell.getObject1() );
entity2URI = onto2.getEntityURI( cell.getObject2() );
} else {
- entity1URI = cell.getObject1AsURI();
- entity2URI = cell.getObject2AsURI();
+ entity1URI = cell.getObject1AsURI(alignment);
+ entity2URI = cell.getObject2AsURI(alignment);
}
if ( entity1URI != null ) {
String ns1 = entity1URI.getScheme()+":"+entity1URI.getSchemeSpecificPart()+"#";
@@ -134,8 +135,8 @@ public class XSLTRendererVisitor implements AlignmentVisitor {
writer.println(" <xsl:template match=\""+namespacify(onto1.getEntityURI( cell.getObject1() ))+"\">");
writer.println(" <xsl:element name=\""+namespacify(onto2.getEntityURI( cell.getObject2() ))+"\">");
} else {
- writer.println(" <xsl:template match=\""+namespacify(cell.getObject1AsURI())+"\">");
- writer.println(" <xsl:element name=\""+namespacify(cell.getObject2AsURI())+"\">");
+ writer.println(" <xsl:template match=\""+namespacify(cell.getObject1AsURI(alignment))+"\">");
+ writer.println(" <xsl:element name=\""+namespacify(cell.getObject2AsURI(alignment))+"\">");
}
writer.println(" <xsl:apply-templates select=\"*|@*|text()\"/>");
writer.println(" </xsl:element>");
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 7036a887..c0b24288 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -450,6 +450,7 @@ public class AServProtocolManager {
} catch (Exception e) {
return new UnknownAlignment(newId(),mess,myId,mess.getSender(),"unknown/Alignment/"+id,(Parameters)null);
}
+System.err.println( id +" -- "+al);
// Invert it
try { al = al.inverse(); }
catch (AlignmentException e) {
@@ -474,6 +475,40 @@ public class AServProtocolManager {
return new AlignmentId(newId(),mess,myId,mess.getSender(),"dummy//",(Parameters)null);
}
+ // It is also possible to try a groupeval ~> with a zipfile containing results
+ // ~~> But it is more difficut to know where is the reference (non public)
+ // There should also be options for selecting the result display
+ // ~~> PRGraph (but this may be a Evaluator)
+ // ~~> Triangle
+ // ~~> Cross
+ public Message eval( Message mess ){
+ Parameters params = mess.getParameters();
+ // Retrieve the alignment
+ String id = (String)params.getParameter("id");
+ Alignment al = null;
+ try {
+ al = alignmentCache.getAlignment( id );
+ } catch (Exception e) {
+ return new UnknownAlignment(newId(),mess,myId,mess.getSender(),"unknown/Alignment/"+id,(Parameters)null);
+ }
+ // Retrieve the reference alignment
+ String rid = (String)params.getParameter("ref");
+ Alignment ref = null;
+ try {
+ ref = alignmentCache.getAlignment( rid );
+ } catch (Exception e) {
+ return new UnknownAlignment(newId(),mess,myId,mess.getSender(),"unknown/Alignment/"+rid,(Parameters)null);
+ }
+ // Set the comparison method
+ // Compare it
+ try { al = al.inverse(); }
+ catch (AlignmentException e) {
+ return new ErrorMsg(newId(),mess,myId,mess.getSender(),"dummy//",(Parameters)null);
+ }
+ // Return it, not easy
+ return new AlignmentId(newId(),mess,myId,mess.getSender(),"dummy//",(Parameters)null);
+ }
+
public boolean storedAlignment( Message mess ) {
// Retrieve the alignment
String id = (String)mess.getParameters().getParameter("id");
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 1fad9412..ce3af168 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -37,6 +37,7 @@ import java.sql.ResultSet;
import java.sql.Statement;
import java.sql.SQLException;
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
import fr.inrialpes.exmo.align.impl.BasicRelation;
import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicParameters;
@@ -439,8 +440,25 @@ public class CacheImpl {
public boolean isAlignmentStored( Alignment alignment ) {
if ( alignment.getExtension( SVCNS, STORED ) != null &&
!alignment.getExtension( SVCNS, STORED ).equals("") )
- return false;
- else return true;
+ return true;
+ else return false;
+ }
+
+ /**
+ * Non publicised class
+ */
+ public void unStoreAlignment( String id ) throws Exception {
+ Alignment alignment = getAlignment( id );
+ if ( alignment != null ) {
+ Statement st = (Statement) conn.createStatement();
+ String query = "DELETE FROM extension WHERE id=''";
+ st.executeUpdate(query);
+ query = "DELETE FROM alignment WHERE id=''";
+ st.executeUpdate(query);
+ query = "DELETE FROM cell WHERE id=''";
+ st.executeUpdate(query);
+ alignment.setExtension( SVCNS, STORED, "");
+ }
}
public void storeAlignment( String id ) throws Exception {
@@ -501,8 +519,8 @@ public class CacheImpl {
cellid = c.getId();
}
else cellid = "";
- String uri1 = c.getObject1AsURI().toString();
- String uri2 = c.getObject2AsURI().toString();
+ String uri1 = c.getObject1AsURI(alignment).toString();
+ String uri2 = c.getObject2AsURI(alignment).toString();
String strength = c.getStrength() + ""; // crazy Java
String sem;
if ( !c.getSemantics().equals("first-order") )
@@ -528,7 +546,11 @@ public class CacheImpl {
}
}
}
- } catch (Exception e) { e.printStackTrace(); };
+ } catch (Exception e) {
+ // We should cancel this... IF NOT STORED!
+ alignment.setExtension( SVCNS, STORED, "");
+ e.printStackTrace();
+ };
// We reset cached date
resetCacheStamp(alignment);
}
@@ -644,7 +666,7 @@ public class CacheImpl {
Statement st2 = (Statement) conn.createStatement();
while ( rse.next() ){
String tag = rse.getString("tag");
- System.err.println(" Treating tag "+tag+" of "+rse.getString("id"));
+ //System.err.println(" Treating tag "+tag+" of "+rse.getString("id"));
if ( !tag.equals("") ){
int pos;
String ns;
@@ -662,7 +684,7 @@ public class CacheImpl {
ns = Annotations.ALIGNNS;
name = tag;
}
- System.err.println(" >> "+ns+" : "+name);
+ //System.err.println(" >> "+ns+" : "+name);
st2.executeUpdate("UPDATE extension SET tag='"+name+"', uri='"+ns+"' WHERE id='"+rse.getString("id")+"' AND tag='"+tag+"'");
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/QueryMediator.java b/src/fr/inrialpes/exmo/align/service/QueryMediator.java
index 946bb810..572dbc35 100644
--- a/src/fr/inrialpes/exmo/align/service/QueryMediator.java
+++ b/src/fr/inrialpes/exmo/align/service/QueryMediator.java
@@ -30,6 +30,7 @@ package fr.inrialpes.exmo.align.service;
import fr.inrialpes.exmo.queryprocessor.QueryProcessor;
import fr.inrialpes.exmo.queryprocessor.Result;
import fr.inrialpes.exmo.queryprocessor.Type;
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
@@ -188,8 +189,8 @@ public class QueryMediator implements QueryProcessor {
for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
Cell cell = (Cell)e.nextElement();
mainQuery = mainQuery.replaceAll(
- cell.getObject1AsURI().toString(),
- cell.getObject2AsURI().toString() );
+ cell.getObject1AsURI(align).toString(),
+ cell.getObject2AsURI(align).toString() );
}
return mainQuery;
}
diff --git a/src/org/semanticweb/owl/align/Cell.java b/src/org/semanticweb/owl/align/Cell.java
index 5a8b2efb..0e5d247e 100644
--- a/src/org/semanticweb/owl/align/Cell.java
+++ b/src/org/semanticweb/owl/align/Cell.java
@@ -51,8 +51,18 @@ public interface Cell extends Comparable<Cell> {
public void setSemantics( String s );
public Object getObject1();
public Object getObject2();
+ /**
+ * //@deprecated use getObject1AsURI( null ) instead
+ */
+ //@Deprecated
public URI getObject1AsURI() throws AlignmentException;
+ /**
+ * //@deprecated use getObject2AsURI( null ) instead
+ */
+ //@Deprecated
public URI getObject2AsURI() throws AlignmentException;
+ public URI getObject1AsURI( Alignment al ) throws AlignmentException;
+ public URI getObject2AsURI( Alignment al ) throws AlignmentException;
public void setObject1( Object ob ) throws AlignmentException;
public void setObject2( Object ob ) throws AlignmentException;
public Relation getRelation();
--
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