diff --git a/build.xml b/build.xml
index 2f81fc3932deee3ab0a36cf1acca84b35377b20f..85761bb79c3ac9ea3c5bed13d5ded4e57e8df5ec 100644
--- a/build.xml
+++ b/build.xml
@@ -10,7 +10,8 @@
<include name="**/*.jar"/>
<!-- several useless (and may be harmful) things at the moment -->
<exclude name="seals/seals-omt-client.jar" />
- <exclude name="log4j/slf4j-log4j.jar" />
+ <!--exclude name="log4j/logback-core-1.0.9.jar" />
+ <exclude name="log4j/logback-classic-1.0.9.jar" /-->
</fileset>
</path>
@@ -50,7 +51,7 @@
<!-- tested -->
<target name="init" depends="bind">
- <property name="jarclasspath" value="skosapi/skosapi.jar owlapi30/owlapi-bin.jar ontosim/ontosim.jar getopt/getopt.jar log4j/commons-logging.jar log4j/log4j.jar log4j/slf4j-api.jar jwnl/jwnl.jar lucene/lucene-core.jar jena/jena.jar jena/iri.jar jena/icu4j.jar iddl/iddl.jar xerces/xercesImpl.jar xerces/resolver.jar xerces/xml-apis.jar hermit/HermiT.jar align.jar ontowrap.jar procalign.jar"/>
+ <property name="jarclasspath" value="skosapi/skosapi.jar owlapi30/owlapi-bin.jar ontosim/ontosim.jar getopt/getopt.jar log4j/jcl-over-slf4j.jar log4j/log4j-over-slf4j.jar log4j/slf4j-api.jar jwnl/jwnl.jar lucene/lucene-core.jar jena/jena.jar jena/iri.jar jena/icu4j.jar iddl/iddl.jar xerces/xercesImpl.jar xerces/resolver.jar xerces/xml-apis.jar hermit/HermiT.jar align.jar ontowrap.jar procalign.jar"/>
</target>
<target name="versionnumber" depends="init" description="Establishes the version number">
@@ -520,9 +521,9 @@
<onepom file="jetty/jetty-util" />
<onepom file="jetty/jetty" />
<onepom file="jwnl/jwnl" />
- <onepom file="log4j/log4j" />
<onepom file="log4j/slf4j-api" />
<onepom file="log4j/jcl-over-slf4j" />
+ <onepom file="log4j/log4j-over-slf4j" />
<onepom file="lucene/lucene-core" />
<onepom file="ontosim/ontosim" />
<onepom file="owlapi10/api" />
diff --git a/html/relnotes.html b/html/relnotes.html
index 73121f12d9ba40f13104cc09e474e619e2c78ab1..542c1d5ef78ebc0925061fec097f81b81a9c435d 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -39,9 +39,6 @@ The development of 4 versions continues.
<p><ul compact="1">
<li>Adding <tt>ontowrap</tt> support in database store (server)</li>
-<li>Adding Silk renderer (impl)</li>
-<li>Modifying evaluators needing <tt>ObjectAlignment</tt> to convert them (impl)</li>
-<li>All evaluators work in server (server)</li>
<li>Make URIs dependent on a urlprefix (server [4.6])</li>
<li>Provide several URIs for the same alignment (server [4.6])</li>
<li>Adopt, overall, slf4j (impl/server [4.6])</li>
@@ -84,22 +81,25 @@ with a warning:
<!--h2>Version 4.6 (1xxx): ??/??/201X - Da lec'h all</h2-->
<!--h2>Version 4.5 (18xx): ??/03/2013 - Building 16</h2-->
<p><ul compact="1">
-<li>Upgraded to <span style="color: green">IDDL</span> to 1.4 (lib)</li>
-<li>Upgraded to <span style="color: green">OWL API</span> to 3.4.2 (lib)</li>
-<li>Replaced Pellet by <span style="color: green">HermiT</span> as default reasonner (lib)</li>
<li>Added several EDOAL-SPARQL renderers (impl)</li>
<li>Added alignment selection per ontologies in list alignment interface (server)</li>
<li>Added relation sensitiveness to evaluators (impl)</li>
-<li>Implemented transactions in database store (server)</li>
<li>Added generation of local <a href="maven.html">maven repository</a> in build.xml</li>
-<li>Bug in weighted (can be more than 1.) (impl)</li>
+<li>Implemented transactions in database store (server)</li>
+<li>Modified evaluators needing <tt>ObjectAlignment</tt> to convert them on the fly (impl)</li>
+<li>Evaluators report better errors on the server (server)</li>
+<li>Fixed a bug in <tt>WeightedPREvaluator</tt> (can be more than 1.) (impl)</li>
<li>Fixed strong bug in the implementation of relaxed precision and recall (impl)</li>
<li>Fixed a (non manifested) bug in cache management (server)</li>
<li>Fixed a bug in displaying evaluation tables (cli)</li>
<li>Fixed a bug with subsumption statements in <tt>OWLAxiomsRendererVisitor</tt> (impl)</li>
<li>Simplified and rewritten <tt>SemPRecEvaluator</tt> (impl)</li>
-<li>Fixed all issues but IDDL in tutorial4 (impl)</li>
-<li>Suppressed inclusion of slf4j-log4j (impl)</li>
+<li>Fixed all issues but IDDL in <a href="tutorial/tutorial4/index.html">tutorial4</a> (impl)</li>
+<li>Upgraded to <span style="color: green">IDDL</span> to 1.4 (lib)</li>
+<li>Upgraded to <span style="color: green">OWL API</span> to 3.4.2 (lib)</li>
+<li>Upgraded to <span style="color: green">SLF4J</span> to 1.7.2; suppressed slf4j-log4j (lib)</li>
+<li>Replaced Pellet by <span style="color: green">HermiT</span> as default reasonner (lib)</li>
+<li>Replaced Commons-Logging and Log4j by jcl-over-slf4j and log4j-over-slf4j (lib)</li>
</ul></p>
<a name="4.4"></a><h2>Version 4.4 (1754): 17/07/2012 - Casa Cirilo</h2>
diff --git a/lib/log4j/jcl-over-slf4j.pom b/lib/log4j/jcl-over-slf4j.pom
index 1e3e208fb780a28c5bb69f600b5db432edbbbdbc..e0dc88161d9ac46e18ea325b66af62d0b79168eb 100644
--- a/lib/log4j/jcl-over-slf4j.pom
+++ b/lib/log4j/jcl-over-slf4j.pom
@@ -9,6 +9,11 @@
<artifactId>jcl-over-slf4j</artifactId>
<packaging>jar</packaging>
<name>Java Commons Logging over SLF4J Module</name>
+ <organization>
+ <name>QOS.ch</name>
+ <url>http://www.qos.ch</url>
+ </organization>
+ <inceptionYear>2005</inceptionYear>
<!-- Copyright (c) 2004-2011 QOS.ch -->
<licenses>
<license>
diff --git a/lib/log4j/slf4j-api.pom b/lib/log4j/slf4j-api.pom
index 6d4c9456430e2a88d217e574a1f723e9c846d7c1..6e069f09a69a5d02e202eaed856c14d6c69ba69d 100644
--- a/lib/log4j/slf4j-api.pom
+++ b/lib/log4j/slf4j-api.pom
@@ -9,6 +9,11 @@
<artifactId>slf4j-api</artifactId>
<packaging>jar</packaging>
<name>SLF4J API Module</name>
+ <organization>
+ <name>QOS.ch</name>
+ <url>http://www.qos.ch</url>
+ </organization>
+ <inceptionYear>2005</inceptionYear>
<!-- Copyright (c) 2004-2011 QOS.ch -->
<licenses>
<license>
diff --git a/lib/ontosim/ontosim.jar b/lib/ontosim/ontosim.jar
index a773be186c9b2479b0b460a32fa22470291ca872..2c04c9e020142250fb1561c3fc33d5c73a25a1f6 100644
Binary files a/lib/ontosim/ontosim.jar and b/lib/ontosim/ontosim.jar differ
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupAlign.java b/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
index cfbe2f7cff1fe7918f2af76279398cbc40c016fb..f9480feda3acb13b2adb1c28d1cbe695952ebba9 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
@@ -54,8 +54,6 @@ import org.xml.sax.SAXException;
import gnu.getopt.LongOpt;
import gnu.getopt.Getopt;
-import org.apache.log4j.BasicConfigurator;
-
/** A batch class for an OWL ontology alignment processing.
It aligns all the ontology pairs denoted
under subdirectory of the current directory.
@@ -255,7 +253,6 @@ public class GroupAlign {
//System.err.println("Here it is "+prefix+" (end by /?)");
try {
- BasicConfigurator.configure();
if ( !source.equalsIgnoreCase("onto1.rdf")
&& !target.equalsIgnoreCase("onto1.rdf") ) {
uri1 = new URI(prefix+source);
diff --git a/src/fr/inrialpes/exmo/align/cli/Procalign.java b/src/fr/inrialpes/exmo/align/cli/Procalign.java
index 2dfec619227471c04d49547ecb09c686f51abfd5..7a3103d1811664a7396f983f2e40d9b939b7a6c7 100644
--- a/src/fr/inrialpes/exmo/align/cli/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/cli/Procalign.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2008, 2010-2012 INRIA
+ * Copyright (C) 2003-2008, 2010-2013 INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -49,8 +49,6 @@ import java.lang.Long;
import org.xml.sax.SAXException;
-import org.apache.log4j.BasicConfigurator;
-
import gnu.getopt.LongOpt;
import gnu.getopt.Getopt;
@@ -199,8 +197,6 @@ public class Procalign {
}
try {
- BasicConfigurator.configure();
-
URI uri1 = null;
URI uri2 = null;
diff --git a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
index 9bdbe41807740de7244bc657978949c968ee745e..37a43cc5d585d20f9593126fa24662097a1b33b5 100644
--- a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2011
+ * Copyright (C) INRIA, 2003-2011, 2013
*
* 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
@@ -28,9 +28,6 @@ import java.util.Set;
import java.util.Collection;
import java.net.URI;
-import org.apache.log4j.Logger;
-import org.apache.log4j.Level;
-
import org.xml.sax.SAXException;
import org.semanticweb.owl.align.Alignment;
@@ -164,6 +161,9 @@ public class ObjectAlignment extends BasicAlignment {
} catch ( NullPointerException npe ) {
throw new AlignmentException( "Cannot dereference entity "+c.getObject2AsURI( alignment ), npe );
}
+ //System.err.println( obj1+" "+obj2+" "+c.getRelation()+" "+c.getStrength() );
+ if ( obj1 == null ) throw new AlignmentException( "Cannot dereference entity "+c.getObject1AsURI( alignment ) );
+ if ( obj2 == null ) throw new AlignmentException( "Cannot dereference entity "+c.getObject2AsURI( alignment ) );
Cell newc = alignment.addAlignCell( c.getId(), obj1, obj2,
c.getRelation(), c.getStrength() );
Collection<String[]> exts = c.getExtensions();
diff --git a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java
index 7cabf2caaed87f438b84a0d6bedde886f0e3967f..fc7ee6ea690d7ea36bcd7e80f9796a9248e1bb98 100644
--- a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java
@@ -1,7 +1,7 @@
/*
* $Id: OWLAPIOntologyFactory.java 842 2008-09-19 20:41:29Z euzenat $
*
- * Copyright (C) INRIA, 2008, 2010
+ * Copyright (C) INRIA, 2008, 2010, 2013
*
* 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
@@ -28,9 +28,6 @@ import java.util.HashSet;
import java.util.Map;
import java.util.Set;
-import org.apache.log4j.Logger;
-import org.apache.log4j.Level;
-
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.util.OWLConnection;
@@ -91,10 +88,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
"org.semanticweb.owl.impl.model.OWLConnectionImpl");
try {
connection = OWLManager.getOWLConnection(parameters);
- Level lev = Logger.getLogger("org.semanticweb.owl").getLevel();
- Logger.getLogger("org.semanticweb.owl").setLevel(Level.ERROR);
OWLOntology ontology = connection.loadOntologyPhysical(uri);
- Logger.getLogger("org.semanticweb.owl").setLevel(lev);
onto = new OWLAPIOntology();
// It may be possible to fill this as final in OWLAPIOntology...
onto.setFormalism( formalismId );