- moved from log4j to slf4j

- suppressed any trace of log4j

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" />

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>

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>

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>

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);

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, Universit de Montral
  *
  * 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;
 

src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java

 /*
  * $Id$
  *
- * 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();

src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java

 /*
  * $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 );