diff --git a/html/impl.html b/html/impl.html
index 70338f619250b9f785d6fa16b8352902d8f70684..0aa1e7fd89a1c88437189b3e4159d2c8f355b3b3 100644
--- a/html/impl.html
+++ b/html/impl.html
@@ -172,7 +172,17 @@ Approaches</a>, Proc. International Conference on Complex, Intelligent and
Software Intensive Systems (CISIS), pp.879-885, 2008</small>
</dd>
-
+<dt>[<a href="https://sites.google.com/site/charbelweb/ontologies">ATOPAI</a>]</dt>
+<dd>
+ATOPAI (Alignment and annotation Tool framewOrk for Plug and plAy
+Interoperability) is a graphical interface on top of the Alignment API for
+matching ontologies, manipulating alignments and extracting patterns
+from the Alignments.
+<br />
+<small>Charbel El Kaed, Yves Denneulin, François Ottogalli, <a href="http://www.computer.org/portal/web/csdl/doi/10.1109/MDM.2011.47">On the Fly Proxy Generation for Home Devices
+ Interoperability</a>, Proc. 12th IEEE International Conference on
+ Mobile Data Management (Industrial Track), Lulea (SW), pp299-302, 2011</small>
+</dd>
</dl></p>
@@ -543,6 +553,16 @@ Atlanta (GA US) paper 41, 2006
</small>
</dd>
+<dt>[noname]</dt>
+<dd>
+The Alignment API has been used matching classes in Java code to be migrated.
+<br /><small>
+Davide Ancona, Viviana Mascardi, Ombretta Pavarino. <a href="">Ontology-based
+ documentation extraction for semi-automatic migration of Java
+ code</a>, Proc. ACM Symposium on Applied Computing (SAC), 2012
+</small>
+</dd>
+
</dl>
diff --git a/html/relnotes.html b/html/relnotes.html
index daf714c9b80f0cda51f919ea04657e2b1166a416..2b275568260f602c64d7dcba676633343d117020 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -63,7 +63,8 @@ with a warning:
<h2>Current SVN trunk version</h2>
-<!--h2>Version 4.3 (): xx/xx/2011 - Zimt</h2-->
+<!--h2>Version 4.3 (): xx/02/2012 - Zimt</h2-->
+
<p><span style="color: red;">BEWARE:</span> All command-line utilities
are now found in the <span style="color: red;">cli</span> package
instead of <b>util</b>.</p>
@@ -85,6 +86,7 @@ with a warning:
<li>Added better error checking in <tt>toObjectAlignment</tt> (impl)</li>
<li>Fixed a bug on <tt>DistanceAlignment</tt> 1:1 extraction when the
second ontology is larger than the first one (impl)</li>
+<li>Used more systematically <tt>finally</tt></li>
</ul></p>
<h2>Version 4.2 (1618): 31/05/2011 - Tring</h2>
diff --git a/src/fr/inrialpes/exmo/align/cli/EvalAlign.java b/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
index 257835bacf42fed9ba46e78b2795283be05f2da3..3436829645e5e52003dace678abc73a572b45e7c 100644
--- a/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
+++ b/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2008, 2010-2011
+ * Copyright (C) INRIA, 2003-2008, 2010-2012
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -197,10 +197,11 @@ public class EvalAlign {
new BufferedWriter(
new OutputStreamWriter( stream, "UTF-8" )), true);
eval.write( writer );
- writer.flush();
- writer.close();
} catch ( IOException ex ) {
ex.printStackTrace();
+ } finally {
+ writer.flush();
+ writer.close();
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java b/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
index 17bb9c289697de1dc0e3e25ee8f1ec20e9836c96..d69dc4438305b9ea16d361d0daec1d97a79797e8 100644
--- a/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2005, 2007-2011 INRIA
+ * Copyright (C) 2003-2005, 2007-2012 INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -439,8 +439,12 @@ public class ExtGroupEval {
writer.println("<p><small>n/a: result alignment not provided or not readable<br />");
writer.println("NaN: division per zero, likely due to empty alignent.</small></p>");
writer.println("</body></html>");
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ } finally {
+ writer.flush();
writer.close();
- } catch (Exception ex) { ex.printStackTrace(); }
+ }
}
public void usage() {
diff --git a/src/fr/inrialpes/exmo/align/cli/GenPlot.java b/src/fr/inrialpes/exmo/align/cli/GenPlot.java
index eca997441ee7a4df834c0fe7ce63267327c2cde2..dff2c9615a48726b5546cf9bc620d1e677a833e3 100644
--- a/src/fr/inrialpes/exmo/align/cli/GenPlot.java
+++ b/src/fr/inrialpes/exmo/align/cli/GenPlot.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003-2011, INRIA
+ * Copyright (C) 2003-2012, INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -424,7 +424,7 @@ public class GenPlot {
for( Vector<Pair> table : result ) {
String algo = listAlgo.get(i);
// Open one file
- PrintWriter writer;
+ PrintWriter writer = null;
try {
writer = new PrintWriter (
new BufferedWriter(
@@ -446,8 +446,11 @@ public class GenPlot {
if ( debug > 1 ) System.err.println( " >> "+p.getX()+" - "+p.getY() );
writer.println( p.getX()*10+" "+ p.getY()*10 );
}
- writer.close();
- } catch (Exception ex) { ex.printStackTrace(); }
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ } finally {
+ if ( writer != null ) writer.close();
+ }
// UnsupportedEncodingException + FileNotFoundException
i++;
}
diff --git a/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java b/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
index 9b2e60542e1b591bcd8facd64d5da0ad15304904..54ab358f0d70f0744ac6194a53f22069775cb3a1 100644
--- a/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
+++ b/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2004, 2007-2008, 2011
+ * Copyright (C) INRIA, 2003-2004, 2007-2008, 2011-2012
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -234,9 +234,10 @@ public class ParserPrinter {
// Throw the initial one
throw aex;
}
+ } finally {
+ writer.flush();
+ writer.close();
}
- writer.flush();
- writer.close();
} catch (Exception ex) {
ex.printStackTrace();
diff --git a/src/fr/inrialpes/exmo/align/cli/Procalign.java b/src/fr/inrialpes/exmo/align/cli/Procalign.java
index be94bf2210e180294f9f0521ce860a6de50891d1..8736bd45a2a22bd69b97c588f35f1cccd95172f4 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, 2010-2011 INRIA
+ * Copyright (C) 2003-2008, 2010-2012 INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -272,14 +272,16 @@ public class Procalign {
usage();
throw ex;
}
-
+
// Output
result.render(renderer);
- writer.flush();
- writer.close();
-
} catch (Exception ex) {
throw ex;
+ } finally {
+ if ( writer != null ) {
+ writer.flush();
+ writer.close();
+ }
}
return result;
}
diff --git a/src/fr/inrialpes/exmo/align/cli/WGroupEval.java b/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
index 42a6819f3698a1fc4a81f858868a4630bb97a3c0..97c8bba4fd8f9e5db75540d2eddc4c5e6b10e5be 100644
--- a/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2003 The University of Manchester
* Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2011, INRIA
+ * Copyright (C) 2003-2012, INRIA
* Copyright (C) 2004, Université de Montréal
*
* This program is free software; you can redistribute it and/or
@@ -559,9 +559,10 @@ which the program does...
writer.println("<p><small>n/a: result alignment not provided or not readable<br />");
writer.println("NaN: division per zero, likely due to empty alignment.</small></p>");
if ( embedded != true ) writer.println("</body></html>");
- writer.close();
} catch (Exception ex) {
ex.printStackTrace();
+ } finally {
+ writer.close();
}
}
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
index 4ad44a4a0ecd9d9beae91cdba0cf75dae3e7fad3..154a88c71fa6a6a0371f6e49558e524d875b8dc9 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011, INRIA
+ * Copyright (C) 2011-2012, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -114,12 +114,14 @@ public class TestGenerator {
public static void writeOntology( OntModel model, String destFile, String ns ) {
//System.err.println( " ==> Writing: "+ns );
+ FileOutputStream fout = null;
try {
File f = new File( destFile );
- FileOutputStream fout = new FileOutputStream( f );
+ fout = new FileOutputStream( f );
Charset defaultCharset = Charset.forName("UTF8");
RDFWriter writer = model.getWriter("RDF/XML-ABBREV");
writer.setProperty( "showXmlDeclaration","true" );
+ writer.setProperty("relativeURIs","");//faster
// Instructions below are Jena specific
// They ensure that the default prefix (that of the ontology) is ns
// This also warrants that the owl:Ontology element is generated
@@ -128,31 +130,36 @@ public class TestGenerator {
writer.setProperty( "xmlbase", ns );
model.createOntology( ns );
writer.write( model.getBaseModel(), new OutputStreamWriter(fout, defaultCharset), "");
- fout.close();
} catch (Exception ex) {
ex.printStackTrace();
- }
+ } finally {
+ try { fout.close(); } catch (Exception ex) {};
+ }
}
private void outputTestDirectory( OntModel onto, Alignment align, String testnumber ) {
// build the directory to save the file
boolean create = new File( dirprefix+"/"+testnumber ).mkdir();
+ PrintWriter writer = null;
// write the ontology into the directory
writeOntology( onto, dirprefix+"/"+testnumber+"/"+ontoname, getURI( testnumber ));
try {
//write the alignment into the directory
OutputStream stream = new FileOutputStream( dirprefix+"/"+testnumber+"/"+alignname );
// Outputing
- PrintWriter writer = new PrintWriter (
- new BufferedWriter(
- new OutputStreamWriter( stream, "UTF-8" )), true);
+ writer = new PrintWriter (
+ new BufferedWriter(
+ new OutputStreamWriter( stream, "UTF-8" )), true);
AlignmentVisitor renderer = new RDFRendererVisitor( writer );
align.render( renderer );
- writer.flush();
- writer.close();
} catch ( Exception ex ) {
ex.printStackTrace();
- }
+ } finally {
+ if ( writer != null ) {
+ writer.flush();
+ writer.close();
+ }
+ }
}
/**
diff --git a/src/fr/inrialpes/exmo/align/parser/RDFParser.java b/src/fr/inrialpes/exmo/align/parser/RDFParser.java
index d34b783e7a7aadb9337484f9b7161f9e32add32b..008e6bc4620d39faef7bbf2c243884a2b8a43b0b 100644
--- a/src/fr/inrialpes/exmo/align/parser/RDFParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/RDFParser.java
@@ -3,7 +3,7 @@
*
* Copyright (C) 2006 Digital Enterprise Research Insitute (DERI) Innsbruck
* Sourceforge version 1.7 - 2008
- * Copyright (C) INRIA, 2008-2011
+ * Copyright (C) INRIA, 2008-2010
*
* 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
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index b143db3e7ea20cf37d0663a983fac426dbf41801..acf4aaf140f90050faa4c0ccbef68f207df8d642 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, 2006-2011
+ * Copyright (C) INRIA, 2006-2012
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -411,17 +411,15 @@ public class AServProtocolManager {
al = ObjectAlignment.toObjectAlignment( (URIAlignment)al );
al.render( renderer );
}
- writer.flush();
- writer.close();
} catch (AlignmentException e) {
- writer.flush();
- writer.close();
return new UnknownMethod(newId(),mess,myId,mess.getSender(),method,(Properties)null);
} catch (Exception e) { // These are exceptions related to I/O
writer.flush();
- writer.close();
- System.err.println(result.toString());
+ System.err.println( result.toString() );
e.printStackTrace();
+ } finally {
+ writer.flush();
+ writer.close();
}
return new RenderedAlignment(newId(),mess,myId,mess.getSender(),result.toString(),(Properties)null);
@@ -874,21 +872,27 @@ public class AServProtocolManager {
if ( debug ) System.err.println("JAR "+entryName);
visited.add( entryName );
//System.err.println( "jarEntry is a jarfile="+je.getName() );
+ InputStream jarSt = null;
+ OutputStream out = null;
+ File f = null;
try {
- InputStream jarSt = jar.getInputStream( (ZipEntry)entry );
- File f = File.createTempFile( "aservTmpFile"+visited.size(), "jar" );
- OutputStream out = new FileOutputStream( f );
+ jarSt = jar.getInputStream( (ZipEntry)entry );
+ f = File.createTempFile( "aservTmpFile"+visited.size(), "jar" );
+ out = new FileOutputStream( f );
byte buf[]=new byte[1024];
int len1 ;
while( (len1 = jarSt.read(buf))>0 )
out.write(buf,0,len1);
- out.close();
- jarSt.close();
JarFile inJar = new JarFile( f );
exploreJar( list, visited, tosubclass, inJar, debug );
- f.delete();
} catch (IOException ioex) {
System.err.println( "Cannot read embedded jar: "+ioex );
+ } finally {
+ try {
+ jarSt.close();
+ out.close();
+ f.delete();
+ } catch (Exception ex) {};
}
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 2d4183b6478fb311af5bf8edf394c1bde77b439b..0c39e850aaf20dccb3a8107fd6dbc032e1aded25 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, 2006-2011
+ * Copyright (C) INRIA, 2006-2012
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -220,9 +220,9 @@ public class CacheImpl {
String value;
URIAlignment result = new URIAlignment();
-
+ Statement st = null;
try {
- Statement st = createStatement();
+ st = createStatement();
// Get basic ontology metadata
query = "SELECT * FROM alignment WHERE id = '" + id +"'";
rs = st.executeQuery(query);
@@ -246,11 +246,12 @@ public class CacheImpl {
value = rs.getString("val");
result.setExtension( rs.getString("uri"), tag, value);
}
- st.close();
} catch (Exception e) { // URI exception that should not occur
System.err.println("Unlikely URI exception!");
e.printStackTrace();
return null;
+ } finally {
+ try { st.close(); } catch (Exception ex) {};
}
// has been extracted from the database
//result.setExtension( SVCNS, STORED, "DATE");
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index 0bac60f043b897ef76baa5a66339cff6d38dbac3..e73a68ae53e4752add7b884e72e45e3ea7539ec6 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, 2006-2011
+ * Copyright (C) INRIA, 2006-2012
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -232,9 +232,10 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
if (bytes < 0) break;
fos.write(buffer, 0, bytes);
}
+ } catch (Exception e) {
+ } finally {
fos.flush();
fos.close();
- } catch (Exception e) {
}
is.close();
params.setProperty( "content", "" );