From 8ea779342bac146740ef93577e97ef0be73d34f8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Tue, 14 Jan 2014 14:34:59 +0000
Subject: [PATCH] - upgraded to slf4j 1.7.5 - all logging through slf4j - all
command-line parameters through commons cli, duly tested
---
README.AServ | 2 +-
README.TXT | 14 +-
build.xml | 11 +-
examples/omwg/total.xml | 3 +-
html/cli.html | 61 +-
html/eval.html | 48 +-
html/img/aserv-network.png | Bin 0 -> 21206 bytes
html/labels.html | 2 +-
html/lib.html | 15 +-
html/relnotes.html | 19 +-
html/testgen.html | 21 +
lib/cli/commons-cli.jar | Bin 0 -> 41123 bytes
lib/cli/commons-cli.pom | 21 +
lib/slf4j/jcl-over-slf4j.jar | Bin 16457 -> 16517 bytes
lib/slf4j/jcl-over-slf4j.pom | 4 +-
lib/slf4j/log4j-over-slf4j.jar | Bin 20886 -> 21762 bytes
lib/slf4j/log4j-over-slf4j.pom | 4 +-
lib/slf4j/slf4j-api.jar | Bin 26083 -> 26084 bytes
lib/slf4j/slf4j-api.pom | 4 +-
plugins/android/build.xml | 1 +
.../inrialpes/exmo/align/cli/CommonCLI.java | 147 +++
.../inrialpes/exmo/align/cli/EvalAlign.java | 152 +--
.../exmo/align/cli/ExtGroupEval.java | 235 ++--
src/fr/inrialpes/exmo/align/cli/GenPlot.java | 355 +++--
.../inrialpes/exmo/align/cli/GroupAlign.java | 238 ++--
.../inrialpes/exmo/align/cli/GroupEval.java | 235 ++--
.../inrialpes/exmo/align/cli/GroupOutput.java | 224 ++--
.../exmo/align/cli/ParserPrinter.java | 188 +--
.../inrialpes/exmo/align/cli/Procalign.java | 231 ++--
src/fr/inrialpes/exmo/align/cli/TestGen.java | 190 ++-
.../inrialpes/exmo/align/cli/WGroupEval.java | 576 ++++-----
.../exmo/align/gen/AlteratorFactory.java | 19 +-
.../exmo/align/gen/BenchmarkGenerator.java | 13 +-
.../exmo/align/gen/ClassHierarchy.java | 23 +-
.../exmo/align/gen/DiscriminantGenerator.java | 11 +-
.../align/gen/NetworkAlignmentDropper.java | 10 +-
.../gen/NetworkCorrespondenceDropper.java | 10 +-
.../exmo/align/gen/TestGenerator.java | 19 +-
src/fr/inrialpes/exmo/align/gen/TestSet.java | 16 +-
src/fr/inrialpes/exmo/align/gen/URITree.java | 9 +-
.../exmo/align/gen/alt/AddClassLevel.java | 11 +-
.../exmo/align/gen/alt/BasicAlterator.java | 24 +-
.../exmo/align/gen/alt/EmptyModification.java | 8 +-
.../exmo/align/gen/alt/FlattenLevel.java | 16 +-
.../exmo/align/gen/alt/RemoveClassLevel.java | 8 +-
.../exmo/align/gen/alt/RemoveProperties.java | 8 +-
.../exmo/align/gen/alt/RenameThings.java | 12 +-
.../exmo/align/impl/BasicAlignment.java | 23 +-
.../exmo/align/impl/BasicParameters.java | 22 +-
.../exmo/align/impl/BasicRelation.java | 10 +-
.../exmo/align/impl/DistanceAlignment.java | 55 +-
.../impl/InstanceBasedMatrixMeasure.java | 12 +-
.../exmo/align/impl/MatrixMeasure.java | 26 +-
.../exmo/align/impl/ObjectAlignment.java | 10 +-
.../align/impl/aggr/ConsensusAggregator.java | 8 +-
.../exmo/align/impl/edoal/EDOALAlignment.java | 98 +-
.../impl/eval/AveragePRGraphEvaluator.java | 14 +-
.../exmo/align/impl/eval/DiffEvaluator.java | 17 +-
.../exmo/align/impl/eval/ExtPREvaluator.java | 16 +-
.../exmo/align/impl/eval/GraphEvaluator.java | 8 +-
.../align/impl/eval/PRGraphEvaluator.java | 14 +-
.../exmo/align/impl/eval/PRecEvaluator.java | 9 +-
.../align/impl/eval/SemPRecEvaluator.java | 10 +-
.../impl/eval/ThresholdGraphEvaluator.java | 8 +-
.../align/impl/eval/WeightedPREvaluator.java | 49 +-
.../impl/method/ClassStructAlignment.java | 12 +-
.../impl/method/NameAndPropertyAlignment.java | 21 +-
.../impl/method/StringDistAlignment.java | 15 +-
.../impl/method/StrucSubsDistAlignment.java | 22 +-
.../renderer/COWLMappingRendererVisitor.java | 2 +-
.../renderer/GenericReflectiveVisitor.java | 12 +-
.../renderer/GraphPatternRendererVisitor.java | 6 +-
.../renderer/OWLAxiomsRendererVisitor.java | 12 +-
.../impl/renderer/RDFRendererVisitor.java | 12 +-
.../renderer/SEKTMappingRendererVisitor.java | 2 +-
.../SPARQLConstructRendererVisitor.java | 2 +-
.../renderer/SPARQLSelectRendererVisitor.java | 2 +-
.../impl/renderer/SWRLRendererVisitor.java | 89 +-
.../impl/renderer/XSLTRendererVisitor.java | 14 +-
.../exmo/align/ling/JWNLAlignment.java | 9 +-
.../exmo/align/parser/AlignmentParser.java | 33 +-
.../exmo/align/parser/RDFParser.java | 55 +-
.../align/parser/TypeCheckingVisitor.java | 8 +-
.../exmo/align/parser/XMLParser.java | 67 +-
.../align/service/AServProtocolManager.java | 2 +-
.../exmo/align/service/AlignmentService.java | 350 ++---
.../exmo/align/service/DBServiceImpl.java | 7 +-
.../exmo/align/service/QueryMediator.java | 4 +-
.../exmo/align/service/WSAlignment.java | 2 +-
.../service/jade/JadeFIPAAServProfile.java | 21 +-
.../service/jade/JadeFIPAAServiceAgent.java | 77 +-
.../JADEFIPAAlignmentServerOntology.java | 30 +-
.../exmo/align/service/msg/AlignmentIds.java | 10 +-
.../exmo/ontowrap/OntologyCache.java | 19 +-
.../exmo/ontowrap/OntologyFactory.java | 8 +-
.../exmo/ontowrap/jena25/JENAOntology.java | 4 +-
.../ontowrap/jena25/JENAOntologyFactory.java | 10 +-
.../exmo/ontowrap/owlapi10/OWLAPIAnnotIt.java | 8 +-
.../ontowrap/owlapi10/OWLAPIOntology.java | 20 +-
.../owlapi10/OWLAPIOntologyFactory.java | 12 +-
.../ontowrap/owlapi30/OWLAPI3Ontology.java | 3 -
.../owlapi30/OWLAPI3OntologyFactory.java | 34 +-
.../ontowrap/skosapi/SKOSOntologyFactory.java | 10 +-
.../exmo/ontowrap/skosapi/SKOSThesaurus.java | 8 +-
.../skoslite/SKOSLiteOntologyFactory.java | 9 +-
.../ontowrap/skoslite/SKOSLiteThesaurus.java | 15 +-
.../exmo/ontowrap/util/EntityFilter.java | 10 +-
.../owl/align/AlignmentException.java | 11 +-
test/clitest.sh | 1143 +++++++++++++++++
test/src/EDOALTest.java | 7 +-
test/src/RendererTest.java | 2 +-
111 files changed, 3492 insertions(+), 2366 deletions(-)
create mode 100644 html/img/aserv-network.png
create mode 100644 lib/cli/commons-cli.jar
create mode 100644 lib/cli/commons-cli.pom
create mode 100644 src/fr/inrialpes/exmo/align/cli/CommonCLI.java
create mode 100644 test/clitest.sh
diff --git a/README.AServ b/README.AServ
index 6fc9c4ab..1d1fbcc0 100644
--- a/README.AServ
+++ b/README.AServ
@@ -1,6 +1,6 @@
#######################################################################
# Alignment Server launch instructions #
-# 30/03/2013, version 4.5 #
+# 11/01/2014, version 4.5 #
#######################################################################
Using the alignment server requires an SQL database server.
diff --git a/README.TXT b/README.TXT
index dfea4a95..445a22e4 100644
--- a/README.TXT
+++ b/README.TXT
@@ -1,10 +1,10 @@
#######################################################################
# Ontology alignment API and implementation #
-# 01/01/2013, version 4.4 #
+# 11/01/2014, version 4.5 #
# http://alignapi.gforge.inria.fr #
#######################################################################
-Copyright (C) 2003-2013 INRIA.
+Copyright (C) 2003-2014 INRIA.
Copyright (C) 2004-2005 Universit� de Montr�al.
Copyright (C) 2005 CNR Pisa.
Copyright (C) 2005 Konstantinos A. Nedas.
@@ -91,16 +91,16 @@ LAST RELEASE
The last release is available from: http://gforge.inria.fr/frs/?group_id=117
+DOCUMENTATION
+-------------
+
+The documentation can be found online at http://alignapi.gforge.inria.fr
+
SOURCE REPOSITORY
-----------------
See http://gforge.inria.fr/scm/?group_id=117 for SVN Access.
-DOCUMENTATION
--------------
-
-The documentation can be found on http://gforge.inria.fr/docman/?group_id=117
-
FILES
-----
diff --git a/build.xml b/build.xml
index c0136749..6d9bc8f0 100644
--- a/build.xml
+++ b/build.xml
@@ -55,7 +55,7 @@
<tstamp><format locale="fr,fr" pattern="dd/MM/yyyy" property="date"/></tstamp>
<property name="version.major" value="4"/>
<property name="version.minor" value="5"/>
- <property name="copyyear" value="2003-2013"/>
+ <property name="copyyear" value="2003-2014"/>
<!-- first attempt -->
<exec executable="svnversion" outputproperty="svn.rev" failifexecutionfails="false"/>
<condition property="svn.revision" value="${svn.rev}" else="nosvn">
@@ -224,7 +224,7 @@
group="fr.inrialpes.exmo.align"
desc="Alignment API implementation"
main="fr.inrialpes.exmo.align.cli.Procalign"
- path="skosapi/skosapi.jar owlapi30/owlapi-bin.jar ontosim/ontosim.jar getopt/getopt.jar slf4j/jcl-over-slf4j.jar slf4j/log4j-over-slf4j.jar slf4j/slf4j-api.jar jwnl/jwnl.jar lucene/lucene-core.jar jena/jena.jar jena/iri.jar jena/icu4j.jar iddl/iddl.jar xerces/xercesImpl.jar xerces/resolver.jar xerces/xml-apis.jar hermit/hermit.jar align.jar ontowrap.jar procalign.jar">
+ path="skosapi/skosapi.jar owlapi30/owlapi-bin.jar ontosim/ontosim.jar cli/commons-cli.jar slf4j/jcl-over-slf4j.jar slf4j/log4j-over-slf4j.jar slf4j/slf4j-api.jar jwnl/jwnl.jar lucene/lucene-core.jar jena/jena.jar jena/iri.jar jena/icu4j.jar iddl/iddl.jar xerces/xercesImpl.jar xerces/resolver.jar xerces/xml-apis.jar hermit/hermit.jar align.jar ontowrap.jar procalign.jar">
<files>
<fileset dir="classes">
<include name="fr/inrialpes/exmo/align/impl/**/*.class"/>
@@ -285,7 +285,7 @@
<attribute name="Built-Date" value="${date}"/>
<attribute name="Main-Class" value="fr.inrialpes.exmo.align.service.AlignmentService"/>
<!-- usually each MANIFEST knows what it needs, add here -->
- <!-- semanticmapper-0.2.jar jwnl.jar sboa.jar TaxoMap.jar AROMA_aserv.jaroyster2.jar, semanticmapper-0.2.jar, sboalgorithms.jar -->
+ <!-- semanticmapper-0.2.jar jwnl.jar sboa.jar TaxoMap.jar AROMA_aserv.jar oyster2.jar, semanticmapper-0.2.jar, sboalgorithms.jar -->
<!-- others should be there naturally -->
<attribute name="Class-Path" value="alignsvc.jar"/>
<attribute name="Implementation-Title" value="Alignment server custom launcher"/>
@@ -313,6 +313,7 @@
<!-- tested -->
<target name="test" depends="bind" description="Unit test code">
<echo message="Testing..."/>
+ <echo message="You may also want to try sh test/clitest.sh"/>
<taskdef name="testng" classpath="${tooldir}/testng/testng.jar" classname="org.testng.TestNGAntTask" />
<javac srcdir="test/src" includeantruntime="false" destdir="test/classes" debug="on"
classpath="tools/testng/testng.jar" encoding="iso8859-15">
@@ -344,7 +345,7 @@
<delete>
<fileset dir="test/classes" includes="**/*.class"/>
<fileset dir="test/output" includes="**/*.*"/>
- <fileset dir="test/html" includes="**/*.html,**/*.xml,**/*.css"/>
+ <fileset dir="test/html" includes="**/*.*"/>
</delete>
<delete dir="test/html/Ant suite"/>
</target>
@@ -515,7 +516,7 @@
<echo message="@{file}" />
<onepom file="@{file}" />
</for-->
- <onepom file="getopt/getopt" />
+ <onepom file="cli/commons-cli" />
<onepom file="google-translate/google-api-translate-java" />
<onepom file="google-translate/json" />
<onepom file="hermit/hermit" />
diff --git a/examples/omwg/total.xml b/examples/omwg/total.xml
index 43540d4a..322b38a6 100644
--- a/examples/omwg/total.xml
+++ b/examples/omwg/total.xml
@@ -40,8 +40,7 @@
<Ontology rdf:about="&vin;">
<location>http://www.scharffe.fr/ontologies/OntologieDuVin.wsml</location>
<formalism>
- <Formalism align:uri="http://www.wsmo.org/wsml/wsml-syntax/wsml-dl"
- align:name="wsml" />
+ <Formalism align:uri="http://www.wsmo.org/wsml/wsml-syntax/wsml-dl" align:name="wsml" />
</formalism>
</Ontology>
</onto2>
diff --git a/html/cli.html b/html/cli.html
index bd8c1603..76568591 100644
--- a/html/cli.html
+++ b/html/cli.html
@@ -33,7 +33,7 @@ the <tt>fr.inrialpes.exmo.align.cli</tt> package:
These command line operations usually share switch conventions:
<ul>
<li>displaying help (-h);</li>
-<li>displaying debug information (-d);</li>
+<li>taking parameerst (-Dv=n) and parameter files (-P);</li>
<li>directing the output to a file (-o);</li>
</ul></p>
@@ -46,7 +46,7 @@ the <tt>align</tt> method.
<h2>Matching</h2>
<p>
-The implementation offers a stand-alone program (<tt>fr.inrialpes.exmo.align.util.Procalign</tt>) which:
+The implementation offers a stand-alone program (<tt>fr.inrialpes.exmo.align.cli.Procalign</tt>) which:
<ul>
<li>Reads two OWL/RDF ontologies;</li>
<li>Creates an alignment object;</li>
@@ -65,21 +65,23 @@ Additional options are available:
<p>Running the program is achieved through:
<div class="terminal">
$ java -jar lib/procalign.jar
-Two URIs required
-usage: Procalign [options] URI1 URI2
-options are:
- --impl=className -i classname Use the given alignment implementation.
- --renderer=className -r className Specifies the alignment renderer
- --output=filename -o filename Output the alignment in filename
- --params=filename -p filename Reads parameters from filename
- --alignment=filename -a filename Start from an XML alignment file
- --threshold=double -t double Filters the similarities under threshold
- --cutmethod=hard|perc|prop|best|span -T hard|perc|prop|best|span method for computing the threshold
- --debug[=n] -d [n] Report debug info at level n
- -Dparam=value Set parameter
- --help -h Print this message
+usage: java fr.inrialpes.exmo.align.cli.Procalign [options] ontoURI ontoURI
+ Matches the two ontologies identified by <ontoURI>
-$Id$
+Options:
+ -a,--alignment <FILE> Use initial alignment FILE
+ -D <NAME=VALUE> Use value for given property
+ -d,--debug <LEVEL> debug argument is deprecated, use logging instead
+ See http://alignapi.gforge.inria.fr/logging.html
+ -h,--help Print this page
+ -i,--impl <CLASS> Use the given CLASS for matcher
+ -o,--output <FILENAME> Send output to FILENAME
+ -P,--params <FILE> Read parameters from FILE
+ -r,--renderer <CLASS> Use the given CLASS for output
+ -T,--cutmethod <METHOD> Method to use for triming (hard|perc|prop|best|span)
+ -t,--threshold <DOUBLE> Trim the alignment with regard to threshold
+
+Alignment API implementation 4.5 (1864M)
</div>
</p>
<p>
@@ -89,10 +91,33 @@ Parameters can be passed to all the command line interfaces through the "-Dname=
<h2>Batch matching</h2>
<p>There is a small utility (<tt>GroupAlign</tt>) which allows to implement batch matching. It starts with a directory containing a set of subdirectories. Each subdirectory contains an ontology to align (usually called <tt>onto.rdf</tt>) and there exist an ontology to be aligned againts these (-n argument, e.g., named <tt>./onto.rdf</tt>).</p>
+<div class="terminal">
+$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.GroupAlign --help
+usage: java fr.inrialpes.exmo.align.cli.GroupAlign [options]
+ Matches pairs of ontologies in subdirectories
+
+Options:
+ -a,--alignment <FILE> Use an initial alignment FILE
+ -D <NAME=VALUE> Use value for given property
+ -d,--debug <LEVEL> debug argument is deprecated, use logging instead
+ See http://alignapi.gforge.inria.fr/logging.html
+ -h,--help Print this page
+ -i,--impl <CLASS> Use the given Alignment implementation
+ -n,--name <URI> Use the given URI as common source ontology
+ -o,--output <FILENAME> Send output to FILENAME
+ -P,--params <FILE> Read parameters from FILE
+ -r,--renderer <CLASS> Use the given CLASS for rendering
+ -s,--source <FILE> Source ontology FILEname (default onto1.rdf)
+ -t,--target <FILE> Target ontology FILEname (default onto.rdf)
+ -u,--uriprefix <URI> URI prefix of the target
+ -w,--directory <DIR> The DIRectory containing the data to match
+
+Alignment API implementation 4.5 (1864M)
+</div>
-<p>Invoking <tt>GroupAlign</tt> with some implementation (-i argument), some set of parameters (-p argument), the name of the output file (-o argument) and optionally a renderer (-r argument) will output the resulting alignment in each of these directories:
+<p>Invoking <tt>GroupAlign</tt> with some implementation (-i argument), some set of parameters (-P argument), the name of the output file (-o argument) and optionally a renderer (-r argument) will output the resulting alignment in each of these directories:
<div class="terminal">
-$ java -cp $CWD/../lib/procalign.jar fr.inrialpes.exmo.align.util.GroupAlign
+$ java -cp $CWD/../lib/procalign.jar fr.inrialpes.exmo.align.cli@.GroupAlign
-o edna -n file://$CWD/101/onto.rdf
-i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment
</div>
diff --git a/html/eval.html b/html/eval.html
index 26e2af02..424fe9eb 100644
--- a/html/eval.html
+++ b/html/eval.html
@@ -60,15 +60,20 @@ See below for more graphical formats.
<p>
The option of <tt>EvalAlign</tt> are:
<div class="terminal">
-$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.EvalAlign --help
-usage: EvalAlign [options] file1 file2
-options are:
- --debug[=n] -d [n] Report debug info at level n
- --impl=className -i classname Use the given Evaluator implementation.
- --output=filename -o filename Output the result in filename
- --help -h Print this message
+$ java -cp lib/procalign.jar fr.inrialpeS.exmo.align.cli.EvalAlign --help
+usage: java fr.inrialpes.exmo.align.cli.EvalAlign [options] alignURI alignURI
+ Evaluate two alignments identified by <alignURI>
-Alignment API implementation 4.3 (1698M) ($Id$)
+Options:
+ -D <NAME=VALUE> Use value for given property
+ -d,--debug <LEVEL> debug argument is deprecated, use logging instead
+ See http://alignapi.gforge.inria.fr/logging.html
+ -h,--help Print this page
+ -i,--impl <CLASS> Use the given CLASS for evaluator
+ -o,--output <FILENAME> Send output to FILENAME
+ -P,--params <FILE> Read parameters from FILE
+
+Alignment API implementation 4.5 (1864M)
</div>
The <tt>-i</tt> switch enables changing the evaluator to be used (by
default, <tt>PRecEvaluator</tt> is used).
@@ -289,14 +294,25 @@ $ java -cp ../lib/procalign.jar fr.inrialpes.exmo.align.cli.GenPlot -l "refalign
<tt>GenPlot</tt> accepts the following arguments:
<div class="terminal">
$ java -cp /Java/alignapi/lib/procalign.jar fr.inrialpes.exmo.align.cli.GenPlot --help
-usage: GenPlot [options]
-options are:
- --type=tsv|tex|html(|xml) -t tsv|tex|html(|xml) Specifies the output format
- --graph=class -g class Specifies the class of Evaluator to be used
- --evaluator=class -e class Specifies the class of GraphEvaluator (plotter) to be used
- --list=algo1,...,algon -l algo1,...,algon Sequence of the filenames to consider
- --debug[=n] -d [n] Report debug info at level n
- --help -h Print this message
+usage: java fr.inrialpes.exmo.align.cli.GenPlot [options]
+ Generate a graphic presentation of evaluation results
+
+Options:
+ -D <NAME=VALUE> Use value for given property
+ -d,--debug <LEVEL> debug argument is deprecated, use logging
+ instead
+ See
+ http://alignapi.gforge.inria.fr/logging.html
+ -e,--evaluator <CLASS> Use CLASS as evaluation plotter
+ -g,--grapher <CLASS> Use CLASS as graph generator
+ -h,--help Print this page
+ -l,--list <FILE> Consider this list of FILEs for inclusion in
+ the results
+ -o,--output <FILENAME> Send output to FILENAME
+ -P,--params <FILE> Read parameters from FILE
+ -t,--type <tsv|tex|html(|xml)> Output in the specified FORMAT (values
+
+Alignment API implementation 4.5 (1864M)
</div>
The <tt>-t</tt> switch specifies the type output.
The plots are provided for PGF LaTeX as gnuplot tables.
diff --git a/html/img/aserv-network.png b/html/img/aserv-network.png
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diff --git a/html/labels.html b/html/labels.html
index 0d2761d1..70935c17 100644
--- a/html/labels.html
+++ b/html/labels.html
@@ -64,7 +64,7 @@
<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment#certificate</dd>
<dd>STRING a certificate from an issuing source</dd>
<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment#time</dd>
-<dd>DURATION of the matching process.</dd>
+<dd>DURATION (default: INTEGER in milliseconds) of the matching process.</dd>
<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment#limitations</dd>
<dd>STRING the validity range of the correspondence</dd>
<dt>http://knowledgeweb.semanticweb.org/heterogeneity/alignment#properties</dd>
diff --git a/html/lib.html b/html/lib.html
index 176c3a25..536b7998 100644
--- a/html/lib.html
+++ b/html/lib.html
@@ -39,15 +39,14 @@ This is a simplified view: <a href="img/dependencies.png">click here
<h2>Required for the API implementation (procalign)</h2>
<dl>
-<dt><a href="http://www.urbanophile.com/arenn/hacking/download.html">Gnu
- getopt</a> 1.0.13: getopt.jar
- [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt>
-<dd>Gnu library for parsing command line arguments. Required
- everywhere (included by OWL-API).</dd>
-<dt><a href="http://www.slf4j.org/">SLF4J</a> 1.7.2:
+<dt><a href="http://commons.apache.org/proper/commons-cli/">Commons CLI</a> 1.2: commons-cli.jar
+ [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>]</dt>
+<dd>Library for parsing command line arguments. Required for the
+ command line use (cli package; included by OWL-API).</dd>
+<dt><a href="http://www.slf4j.org/">SLF4J</a> 1.7.5:
slf4j-api.jar log4j-over-slf4j.jar jcl-over-slf4j.jar [<a href="http://www.slf4j.org/license.html">MIT license</a>]
</dt>
-<dd>At last some clean-up in the Java logging realm.</dd>
+<dd>Java unified logging library!</dd>
</dl>
<h3>Required for using EDOAL</h3>
@@ -118,7 +117,7 @@ and this will compile again.
<h2>Required for the Alignment server (alignsvc)</h2>
<dl>
-<dt><a href="http://dev.mysql.com/downloads/connector/j/3.0.html">MySQL
+<dt><a href="http://dev.mysql.com/downloads/connector/j/">MySQL
JDBC Connectors</a> 5.1.12: mysql-connector-java-5.0.3-bin.jar
[<a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GPL</a>]
or <a href="http://jdbc.postgresql.org/">Postgres JDBC
diff --git a/html/relnotes.html b/html/relnotes.html
index eda8d866..eb504151 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -38,14 +38,13 @@ The development of 4 versions continues.
<p><ul compact="1">
<li>Provide several URIs for the same alignment (server)</li>
-<li>Adopt, overall, slf4j (impl/server)</li>
<li>Implement database store for EDOAL (server)</li>
<li>Add simple "harder" test generator (gen)</li>
<li>Add simple "hidden" test generator (gen)</li>
<li>Add a <tt>dependsOn</tt> alignment property (api)</li>
<li>Consolidate alignment based on <tt>dependsOn</tt> (loop checking, cell ingestion) (impl)</li>
-<li>Use the OWLReasoner interface and HermiT for adding inference to Ontowrap (ontowrap)</li>
<li>Add a JSON interface (server)</li>
+<li>Use the OWLReasoner interface and HermiT for adding inference to Ontowrap (ontowrap)</li>
<li>Integrate tests from generator (test)</li>
<li>Integrate some basic reasoning (impl).</li>
<li>Complete tutorial4 with distributed reasoning.</li>
@@ -74,9 +73,23 @@ with a warning:
<!--h2>Version 4.9 (1xxx): ??/??/201X - Al pesto</h2-->
<!--h2>Version 4.8 (1xxx): ??/??/201x - Ant�sine</h2-->
<!--h2>Version 4.7 (1xxx): ??/??/201x - Letraset</h2-->
-<!--h2>Version 4.6 (1xxx): ??/??/201X - Da lec'h all</h2-->
+<!--h2>Version 4.6 (1xxx): ??/01/2014 - Da lec'h all</h2-->
<p><ul compact="1">
+<li>Fixed a bug in <tt>EDOALAlignment.init()</tt> which would prohibit rendering (edoal)</li>
+<li>Fixed a bug in <tt>OWLAxiomsRendererVisitor</tt>, <tt>SWRLRendererVisitor</tt>, <tt>SEKTMappingRendererVisitor</tt>, <tt>COWLMappingRendererVisitor</tt> <tt>SPARQLConstructRendererVisitor</tt>, and <tt>SPARQLSelectRendererVisitor</tt> which sometimes rendered alignments empty (impl)</li>
+<li>All logging and signaling is now through slf4j (impl/server)</li>
+<li>Replaced getopt by <span style="color: green">commons cli</span> 1.2 as command line interpreter (lib/cli)</li>
+<li>Completed <tt>SWRLRendererVisitor</tt> to fill equivalence and subsumption statements (impl)</li>
<li>Declared Alignment server as an OSGi service (server)</li>
+<li>Made EDOAL vocabulary dereferenceable (edoal)</li>
+<li>Fixed the build.xml file for using slf4j in microalign (android)</li>
+<li>Fixed several bugs in <tt>WeightedPREvaluator</tt>, now two versions (impl)</li>
+<li>Fixed display bugs in <tt>GroupEval</tt> and <tt>WGroupEval</tt> (cli)</li>
+<li>Cancelled test <tt>EDOALTest.anotherRoundTripTest()</tt> because would try to load a WSMO ontology (test)</li>
+<li>Changed <tt>-o</tt> option in <tt>GroupAlign</tt> to be homogeneous (cli)</li>
+<li>Updated tutorial2 with deprecated <tt>BasicParameters</tt> (tutorial)</li>
+<li>Added complete command line option tests in <tt>tests/clitest.sh</tt> (cli)</li>
+<li>Upgraded to <span style="color: green">SLF4J</span> to 1.7.5 (lib)</li>
</ul></p>
<h2>Version 4.5 (1847): 25/03/2013 - Building 16</h2>
diff --git a/html/testgen.html b/html/testgen.html
index 600a6592..a78aa112 100644
--- a/html/testgen.html
+++ b/html/testgen.html
@@ -349,6 +349,27 @@ a test set altering regularly one or several dimensions (each one
represented by an alterator).
</p>
+<h4>Definitely harder benchmarks</h4>
+
+<p>
+Benchmark is a test set were a seed ontology is altered and any test
+has to match the seed ontology with the altered ontology. However, we can also ask
+to match two differently altered ontologies. Since altered ontologies
+come from the same seed ontology and the generateed alignments are
+equivalence alignment, the reference alignment can be generated
+automatically. Indeed, if benchmark test <i>X</i> generates
+alignment <i>A<sub>X</sub></i> and test <i>Y</i> generates
+alignment <i>A<sub>Y</sub></i>, then for the task of matching
+ontology <i>o<sub>X</sub></i> to ontology <i>o<sub>Y</sub></i>, the
+reference alignment will be:
+<center>
+<i>A<sub>X-Y</sub></i> = <i>A<sub>X</sub></i><sup>-1</sup> o <i>A<sub>Y</sub></i>
+</center>
+The two operations (<sup>-1</sup> and o) being part of the Alignment
+API, this is easy to generate.
+</p>
+<p>Not available yet.</p>
+
<h4>Hidden ontology generator</h4>
<p>Not available yet.</p>
diff --git a/lib/cli/commons-cli.jar b/lib/cli/commons-cli.jar
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diff --git a/lib/cli/commons-cli.pom b/lib/cli/commons-cli.pom
new file mode 100644
index 00000000..0be86694
--- /dev/null
+++ b/lib/cli/commons-cli.pom
@@ -0,0 +1,21 @@
+<project>
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-cli</artifactId>
+ <version>1.2</version>
+ <name>Apache Commons CLI</name>
+ <inceptionYear>2002</inceptionYear>
+ <description>
+ Commons CLI provides a simple API for presenting, processing and validating a command line interface.
+ </description>
+ <packaging>jar</packaging>
+ <licenses>
+ <license>
+ <name>Apache License Version 2.0, January 2004</name>
+ <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
+ </license>
+ </licenses>
+ <url>http://commons.apache.org/cli/</url>
+
+</project>
diff --git a/lib/slf4j/jcl-over-slf4j.jar b/lib/slf4j/jcl-over-slf4j.jar
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diff --git a/lib/slf4j/jcl-over-slf4j.pom b/lib/slf4j/jcl-over-slf4j.pom
index c5a6d2de..59979200 100644
--- a/lib/slf4j/jcl-over-slf4j.pom
+++ b/lib/slf4j/jcl-over-slf4j.pom
@@ -3,7 +3,7 @@
<parent>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-parent</artifactId>
- <version>1.7.2</version>
+ <version>1.7.5</version>
</parent>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
@@ -14,7 +14,7 @@
<url>http://www.qos.ch</url>
</organization>
<inceptionYear>2005</inceptionYear>
- <!-- Copyright (c) 2004-2011 QOS.ch -->
+ <!-- Copyright (c) 2004-2013 QOS.ch -->
<licenses>
<license>
<name>MIT License</name>
diff --git a/lib/slf4j/log4j-over-slf4j.jar b/lib/slf4j/log4j-over-slf4j.jar
index cd04c46a124f2c17e71125e5a7e452b5bb199b9e..7caf77291dda4ce28cc3afb54be8786dd053a269 100644
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diff --git a/lib/slf4j/log4j-over-slf4j.pom b/lib/slf4j/log4j-over-slf4j.pom
index 94553cca..5399331c 100644
--- a/lib/slf4j/log4j-over-slf4j.pom
+++ b/lib/slf4j/log4j-over-slf4j.pom
@@ -3,7 +3,7 @@
<parent>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-parent</artifactId>
- <version>1.7.2</version>
+ <version>1.7.5</version>
</parent>
<groupId>org.slf4j</groupId>
<artifactId>log4j-over-slf4j</artifactId>
@@ -14,7 +14,7 @@
<url>http://www.qos.ch</url>
</organization>
<inceptionYear>2005</inceptionYear>
- <!-- Copyright (c) 2004-2011 QOS.ch -->
+ <!-- Copyright (c) 2004-2013 QOS.ch -->
<licenses>
<license>
<name>MIT License</name>
diff --git a/lib/slf4j/slf4j-api.jar b/lib/slf4j/slf4j-api.jar
index 73f38db9ce6973b8247c2cf267a5fd4a1464c7b3..8766455d8756ebdac09d36eea2c08db90c18b124 100644
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diff --git a/lib/slf4j/slf4j-api.pom b/lib/slf4j/slf4j-api.pom
index 6e069f09..91928f15 100644
--- a/lib/slf4j/slf4j-api.pom
+++ b/lib/slf4j/slf4j-api.pom
@@ -3,7 +3,7 @@
<parent>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-parent</artifactId>
- <version>1.7.2</version>
+ <version>1.7.5</version>
</parent>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
@@ -14,7 +14,7 @@
<url>http://www.qos.ch</url>
</organization>
<inceptionYear>2005</inceptionYear>
- <!-- Copyright (c) 2004-2011 QOS.ch -->
+ <!-- Copyright (c) 2004-2013 QOS.ch -->
<licenses>
<license>
<name>MIT License</name>
diff --git a/plugins/android/build.xml b/plugins/android/build.xml
index 784da804..18d38987 100644
--- a/plugins/android/build.xml
+++ b/plugins/android/build.xml
@@ -70,6 +70,7 @@
<condition property="tempdir" value="${tempdir}" else="/tmp">
<isset property="tempdit"/>
</condition>
+ <!-- two first jars seem useless -->
<property name="jarclasspath" value="slf4j/jcl-over-slf4j.jar slf4j/log4j-over-slf4j.jar slf4j/slf4j-api.jar jena/jena.jar jena/iri.jar jena/icu4j.jar xerces/xercesImpl.jar xerces/resolver.jar align.jar microalign.jar"/>
<tstamp><format locale="fr,fr" pattern="dd/MM/yyyy" property="date"/></tstamp>
<exec executable="svnversion" outputproperty="svn.rev" failifexecutionfails="false"/>
diff --git a/src/fr/inrialpes/exmo/align/cli/CommonCLI.java b/src/fr/inrialpes/exmo/align/cli/CommonCLI.java
new file mode 100644
index 00000000..442b46bf
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/cli/CommonCLI.java
@@ -0,0 +1,147 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) 2013 INRIA
+ *
+ * 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 the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ * USA.
+ */
+
+/*
+ * Common command line parameter parsing based on Apache commons cli wrt
+ */
+
+package fr.inrialpes.exmo.align.cli;
+
+import java.util.Properties;
+import java.io.FileInputStream;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.PosixParser;
+//import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.HelpFormatter;
+
+/**
+ * For instanciating this class:
+ * - extends CommonCLI
+ * - call to super() in constructor
+ * - add options in constructor
+ * - CommandLine line = parseCommandLine( args ); in main
+ * - retrieve new options
+ * - retrieve remaining args
+ * - redefine usage() with specific first line
+ * - use parameters
+ */
+
+public abstract class CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( CommonCLI.class );
+
+ protected Options options = null;
+
+ protected String outputfilename = null;
+
+ protected Properties parameters = null;
+
+ public CommonCLI() {
+ parameters = new Properties();
+ options = new Options();
+ options.addOption( "h", "help", false, "Print this page" );
+ options.addOption( OptionBuilder.withLongOpt( "output" ).hasArg().withDescription( "Send output to FILE" ).withArgName("FILE").create( 'o' ) );
+ options.addOption( OptionBuilder.withLongOpt( "debug" ).hasOptionalArg().withDescription( "debug argument is deprecated, use logging instead\nSee http://alignapi.gforge.inria.fr/logging.html" ).withArgName("LEVEL").create( 'd' ) );
+ options.addOption( OptionBuilder.withLongOpt( "params" ).hasArg().withDescription( "Read parameters from FILE" ).withArgName("FILE").create( 'P' ) );
+ options.addOption( OptionBuilder.withArgName( "NAME=VALUE" ).hasArgs(2).withValueSeparator().withDescription( "Use value for given property" ).create( 'D' ) );
+ }
+
+ // This is an example of using the interface
+ private void run( String[] args ) {
+ parseSpecificCommandLine( args );
+ // Usually do process here
+ }
+
+ // This is an example of processing the arguments
+ // In principle, use super.
+ public void parseSpecificCommandLine( String[] args ) {
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return;
+ // Here deal with command specific arguments
+ for ( Object o : line.getArgList() ) {
+ logger.info( " Arg: {}", o );
+ }
+ for ( String k : parameters.stringPropertyNames() ) {
+ logger.info( " Param: {} = {}", k, parameters.getProperty( k ) );
+ }
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
+ usage();
+ }
+ }
+
+ // In spirit, this is final
+ public CommandLine parseCommandLine( String[] args ) throws ParseException {
+ CommandLineParser parser = new PosixParser();
+ CommandLine line = parser.parse( options, args );
+ parameters = line.getOptionProperties( "D" );
+ if ( line.hasOption( 'd' ) ) {
+ logger.warn( "debug command-line switch DEPRECATED, use logging" );
+ }
+ if ( line.hasOption( 'o' ) ) {
+ outputfilename = line.getOptionValue( 'o' );
+ }
+ if ( line.hasOption( 'P' ) ) {
+ try {
+ String paramfile = line.getOptionValue( 'P' );
+ parameters.loadFromXML( new FileInputStream( paramfile ) );
+ } catch ( Exception ex ) {
+ logger.warn( "Cannot parse parameter file", ex );
+ }
+ }
+ if ( line.hasOption( 'h' ) ) {
+ usage();
+ line = null;
+ }
+ return line;
+ }
+
+ public void exit( int returnCode ) {
+ System.exit( returnCode );
+ }
+
+ // This is an example of using the interface
+ public abstract void usage();
+
+ /*
+ * The subclasses may define usage() by calling this:
+ * usage( "java "+this.getClass().getName()+" [options] alignfile\nParse the given <alignfile> and prints it\nOptions:" );
+ * In spirit, this is final
+ */
+ public void usage( String firstlines ) {
+ usage( firstlines, "" );
+ }
+ public void usage( String firstlines, String footer ) {
+ Package pkg = this.getClass().getPackage();
+ String rfooter = footer;
+ if ( pkg != null )
+ rfooter += "\n"+pkg.getImplementationTitle()+" "+pkg.getImplementationVersion();
+ new HelpFormatter().printHelp( 80, firstlines, "\nOptions:", options, rfooter );
+ }
+}
diff --git a/src/fr/inrialpes/exmo/align/cli/EvalAlign.java b/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
index 6e56ca00..45a5c4c9 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, 2010-2013
+ * Copyright (C) INRIA, 2003-2008, 2010-2014
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -29,7 +29,6 @@ import fr.inrialpes.exmo.align.impl.eval.PRecEvaluator;
import fr.inrialpes.exmo.align.impl.ObjectAlignment;
import fr.inrialpes.exmo.align.impl.URIAlignment;
-//Imported JAVA classes
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
@@ -44,8 +43,13 @@ import java.io.BufferedWriter;
import java.io.OutputStreamWriter;
import java.lang.reflect.InvocationTargetException;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
/** A really simple utility that loads and alignment and prints it.
A basic class for an OWL ontology alignment processing. The processor
@@ -75,100 +79,62 @@ $Id$
@author J�r�me Euzenat
*/
-public class EvalAlign {
+public class EvalAlign extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( EvalAlign.class );
- public static void main(String[] args) {
- new EvalAlign().run( args );
+ public EvalAlign() {
+ super();
+ options.addOption( OptionBuilder.withLongOpt( "impl" ).hasArg().withDescription( "Use the given CLASS for evaluator" ).withArgName("CLASS").create( 'i' ) );
}
+ public static void main(String[] args) {
+ try { new EvalAlign().run( args ); }
+ catch ( Exception ex ) { ex.printStackTrace(); };
+ }
- public void run(String[] args) {
- Properties params = new Properties();
+ public void run(String[] args) throws Exception {
Evaluator eval = null;
String alignName1 = null;
String alignName2 = null;
- String filename = null;
String classname = null;
PrintWriter writer = null;
- LongOpt[] longopts = new LongOpt[7];
- int debug = 0;
-
- // abcdefghijklmnopqrstuvwxyz?
- // x x i x x x x x
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[3] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
- longopts[4] = new LongOpt("impl", LongOpt.REQUIRED_ARGUMENT, null, 'i');
-
- Getopt g = new Getopt("", args, "ho:d::i:D:", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch(c) {
- case 'h':
- usage();
- return;
- case 'o':
- /* Output */
- filename = g.getOptarg();
- break;
- case 'i':
- /* Evaluator class */
- classname = g.getOptarg();
- break;
- case 'd':
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
- case 'D' :
- /* Parameter definition */
- arg = g.getOptarg();
- int index = arg.indexOf('=');
- if ( index != -1 ) {
- params.setProperty( arg.substring( 0, index),
- arg.substring(index+1));
- } else {
- System.err.println("Bad parameter syntax: "+g);
- usage();
- System.exit(0);
- }
- break;
- }
- }
-
- int i = g.getOptind();
+ CommandLine line = null;
- params.setProperty( "debug", Integer.toString( debug ) );
- // debug = Integer.parseInt( params.getProperty("debug") );
-
- if (args.length > i+1 ) {
- alignName1 = args[i];
- alignName2 = args[i+1];
+ try {
+ line = parseCommandLine( args );
+ if ( line == null ) return; // --help
+ } catch( ParseException exp ) {
+ logger.error( "Cannot parse command line", exp );
+ usage();
+ System.exit(-1);
+ }
+ if ( line.hasOption( 'i' ) ) classname = line.getOptionValue( 'i' );
+ String[] argList = line.getArgs();
+ if ( argList.length > 1 ) {
+ alignName1 = argList[0];
+ alignName2 = argList[1];
} else {
- System.err.println("Require two alignement filenames");
+ logger.error( "Require the alignment URIs" );
usage();
- return;
+ System.exit(-1);
}
- if ( debug > 1 ) System.err.println(" Filename"+alignName1+"/"+alignName2);
+ logger.debug(" Filename: {}/{}", alignName1, alignName2);
- Alignment align1=null, align2 = null;
+ Alignment align1 = null, align2 = null;
try {
// Load alignments
- AlignmentParser aparser = new AlignmentParser( debug );
+ AlignmentParser aparser = new AlignmentParser();
align1 = aparser.parse( alignName1 );
- if ( debug > 0 ) System.err.println(" Alignment structure1 parsed");
+ //logger.trace(" Alignment structure1 parsed");
aparser.initAlignment( null );
align2 = aparser.parse( alignName2 );
- if ( debug > 0 ) System.err.println(" Alignment structure2 parsed");
- } catch ( Exception ex ) { ex.printStackTrace(); }
+ //logger.trace(" Alignment structure2 parsed");
+ } catch ( Exception ex ) {
+ ex.printStackTrace();
+ }
- boolean totry = true;
- try {
+ boolean totry = true; // 2013: This should not be necessary anymore
while ( totry ) {
totry = false;
if ( classname != null ) {
@@ -181,23 +147,23 @@ public class EvalAlign {
java.lang.reflect.Constructor evaluatorConstructor = evaluatorClass.getConstructor(cparams);
eval = (Evaluator)evaluatorConstructor.newInstance(mparams);
} catch (ClassNotFoundException ex) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
} catch (InstantiationException ex) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
} catch (InvocationTargetException ex) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
} catch (IllegalAccessException ex) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
} catch (NoSuchMethodException ex) {
- ex.printStackTrace();
+ logger.error( "No such method: {}", classname );
usage();
- return;
+ throw( ex );
}
} else { eval = new PRecEvaluator( align1, align2 ); };
// Compare
try {
- eval.eval(params) ;
+ eval.eval( parameters ) ;
} catch ( AlignmentException aex ) {
if ( align1 instanceof ObjectAlignment ) {
throw aex;
@@ -210,25 +176,24 @@ public class EvalAlign {
}
}
}
- } catch ( Exception ex ) { ex.printStackTrace(); }
// Set output file
try {
OutputStream stream;
- if (filename == null) {
+ if ( outputfilename == null ) {
//writer = (PrintStream) System.out;
stream = System.out;
} else {
//writer = new PrintStream(new FileOutputStream(filename));
- stream = new FileOutputStream(filename);
+ stream = new FileOutputStream( outputfilename );
}
writer = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter( stream, "UTF-8" )), true);
eval.write( writer );
} catch ( IOException ex ) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
} finally {
writer.flush();
writer.close();
@@ -236,15 +201,6 @@ public class EvalAlign {
}
public void usage() {
- System.err.println("usage: EvalAlign [options] file1 file2");
- System.err.println("options are:");
- System.err.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
- System.err.println("\t--impl=className -i classname\t\tUse the given evaluator implementation.");
- System.err.println("\t--output=filename -o filename\tOutput the result in filename");
- System.err.println("\t-Dparam=value\t\t\tSet parameter");
- System.err.println("\t--help -h\t\t\tPrint this message");
- System.err.print("\n"+EvalAlign.class.getPackage().getImplementationTitle()+" "+EvalAlign.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
-
+ usage( "java "+this.getClass().getName()+" [options] alignURI alignURI\nEvaluate two alignments identified by <alignURI>" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java b/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
index 200241ae..5547dfdf 100644
--- a/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
@@ -1,9 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003 The University of Manchester
- * Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2005, 2007-2012 INRIA
+ * Copyright (C) 2003-2005, 2007-2014 INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -52,8 +50,14 @@ import java.util.Properties;
import org.xml.sax.SAXException;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
/** A basic class for synthesizing the results of a set of alignments provided
by different algorithms. The output is a table showing various generalisations
@@ -68,7 +72,6 @@ import gnu.getopt.Getopt;
<pre>
-o filename --output=filename
-f format = sepr (symetric/effort-based/precision-oriented/recall-oriented) --format=sepr
- -d debug --debug=level
-r filename --reference=filename
-s algo/measure
-l list of compared algorithms
@@ -87,106 +90,64 @@ import gnu.getopt.Getopt;
$Id$
</pre>
-@author Sean K. Bechhofer
-@author J�r�me Euzenat
*/
-public class ExtGroupEval {
+public class ExtGroupEval extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( ExtGroupEval.class );
- Properties params = null;
- String filename = null;
String reference = "refalign.rdf";
String format = "s";
int fsize = 2;
String type = "html";
boolean embedded = false;
- String dominant = "s";
- Vector<String> listAlgo = null;
- int debug = 0;
+ //String dominant = "s";
+ String[] listAlgo = null;
+ int size = 0;
String color = null;
String ontoDir = null;
+ public ExtGroupEval() {
+ super();
+ options.addOption( OptionBuilder.withLongOpt( "list" ).hasArgs().withValueSeparator(',').withDescription( "List of FILEs to be included in the results (required)" ).withArgName("FILE").create( 'l' ) );
+ options.addOption( OptionBuilder.withLongOpt( "color" ).hasOptionalArg().withDescription( "Color even lines of the output in COLOR (default: lightblue)" ).withArgName("COLOR").create( 'c' ) );
+ options.addOption( OptionBuilder.withLongOpt( "format" ).hasArg().withDescription( "Extended MEASures and order (symetric/effort-based/precision-oriented/recall-oriented) (default: "+format+")" ).withArgName("MEAS (sepr)").create( 'f' ) );
+ //options.addOption( OptionBuilder.withLongOpt( "type" ).hasArg().withDescription( "Output TYPE (html|xml|tex|ascii|triangle; default: "+type+")" ).withArgName("TYPE").create( 't' ) );
+ options.addOption( OptionBuilder.withLongOpt( "type" ).hasArg().withDescription( "Output TYPE (only html available so far)" ).withArgName("TYPE").create( 't' ) );
+ //options.addOption( OptionBuilder.withLongOpt( "sup" ).hasArg().withDescription( "Are dominant columns algorithms or measure (default: s)" ).withArgName("algo").create( 's' ) );
+ options.addOption( OptionBuilder.withLongOpt( "reference" ).hasArg().withDescription( "Name of the reference alignment FILE (default: "+reference+")" ).withArgName("FILE").create( 'r' ) );
+ options.addOption( OptionBuilder.withLongOpt( "directory" ).hasOptionalArg().withDescription( "The DIRectory containing the data to evaluate" ).withArgName("DIR").create( 'w' ) );
+ // .setRequired( true )
+ Option opt = options.getOption( "list" );
+ if ( opt != null ) opt.setRequired( true );
+ }
+
public static void main(String[] args) {
try { new ExtGroupEval().run( args ); }
catch (Exception ex) { ex.printStackTrace(); };
}
public void run(String[] args) throws Exception {
- String listFile = "";
- LongOpt[] longopts = new LongOpt[10];
-
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("format", LongOpt.REQUIRED_ARGUMENT, null, 'f');
- longopts[3] = new LongOpt("type", LongOpt.REQUIRED_ARGUMENT, null, 't');
- longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[5] = new LongOpt("sup", LongOpt.REQUIRED_ARGUMENT, null, 's');
- longopts[6] = new LongOpt("list", LongOpt.REQUIRED_ARGUMENT, null, 'l');
- longopts[7] = new LongOpt("color", LongOpt.OPTIONAL_ARGUMENT, null, 'c');
- longopts[8] = new LongOpt("reference", LongOpt.REQUIRED_ARGUMENT, null, 'r');
- longopts[9] = new LongOpt("directory", LongOpt.REQUIRED_ARGUMENT, null, 'w');
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return; // --help
- Getopt g = new Getopt("", args, "ho:a:d::l:f:t:r:w:c::", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h' :
- usage();
- return;
- case 'o' :
- /* Write output here */
- filename = g.getOptarg();
- break;
- case 'r' :
- /* File name for the reference alignment */
- reference = g.getOptarg();
- break;
- case 'f' :
- /* Sequence of results to print */
- format = g.getOptarg();
- break;
- case 't' :
- /* Type of output (tex/html/xml/ascii) */
- type = g.getOptarg();
- break;
- case 's' :
- /* Print per type or per algo */
- dominant = g.getOptarg();
- break;
- case 'c' :
- /* Print colored lines */
- color = "lightblue";
- //dominant = g.getOptarg();
- break;
- case 'l' :
- /* List of filename */
- listFile = g.getOptarg();
- break;
- case 'd' :
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
- case 'w' :
- /* Use the given ontology directory */
- arg = g.getOptarg();
- if ( arg != null ) ontoDir = g.getOptarg();
- else ontoDir = null;
- break;
+ // Here deal with command specific arguments
+ if ( line.hasOption( 'f' ) ) format = line.getOptionValue( 'f' );
+ if ( line.hasOption( 'r' ) ) reference = line.getOptionValue( 'r' );
+ //if ( line.hasOption( 's' ) ) dominant = line.getOptionValue( 's' );
+ if ( line.hasOption( 't' ) ) type = line.getOptionValue( 't' );
+ if ( line.hasOption( 'c' ) ) color = line.getOptionValue( 'c', "lightblue" );
+ if ( line.hasOption( 'l' ) ) {
+ listAlgo = line.getOptionValues( 'l' );
+ size = listAlgo.length;
}
+ if ( line.hasOption( 'w' ) ) ontoDir = line.getOptionValue( 'w' );
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
+ usage();
+ System.exit( -1 );
}
- listAlgo = new Vector<String>();
- for ( String s : listFile.split(",") ) {
- listAlgo.add( s );
- }
-
- params = new Properties();
- if (debug > 0) params.setProperty( "debug", Integer.toString( debug-1 ) );
-
print( iterateDirectories() );
}
@@ -200,7 +161,7 @@ public class ExtGroupEval {
subdir = (new File(ontoDir)).listFiles();
}
} catch (Exception e) {
- System.err.println("Cannot stat dir "+ e.getMessage());
+ logger.error("Cannot stat dir", e);
usage();
}
int size = subdir.length;
@@ -209,7 +170,7 @@ public class ExtGroupEval {
int i = 0;
for ( int j=0 ; j < size; j++ ) {
if( subdir[j].isDirectory() ) {
- if ( debug > 0 ) System.err.println("\nEntering directory "+subdir[j]);
+ //logger.trace("Entering directory {}", subdir[j]);
// eval the alignments in a subdirectory
// store the result
Vector vect = (Vector)iterateAlignments( subdir[j] );
@@ -234,7 +195,7 @@ public class ExtGroupEval {
// call eval
// store the result in a record
// return the record.
- if ( debug > 1) System.err.println(" Considering result "+i);
+ //logger.trace(" Considering result {}", i);
Evaluator evaluator = eval( prefix+reference, prefix+m+".rdf");
if ( evaluator != null ) ok = true;
result.add( i, evaluator );
@@ -242,8 +203,8 @@ public class ExtGroupEval {
// Unload the ontologies.
try {
OntologyFactory.clear();
- } catch ( OntowrapException owex ) { // only report
- owex.printStackTrace();
+ } catch ( OntowrapException owex ) {
+ logger.debug( "INGORED Exception", owex );
}
if ( ok == true ) return result;
@@ -253,29 +214,20 @@ public class ExtGroupEval {
public Evaluator eval( String alignName1, String alignName2 ) {
Evaluator eval = null;
try {
- int nextdebug;
- if ( debug < 2 ) nextdebug = 0;
- else nextdebug = debug - 2;
// Load alignments
- AlignmentParser aparser = new AlignmentParser( nextdebug );
+ AlignmentParser aparser = new AlignmentParser();
Alignment align1 = aparser.parse( alignName1 );
- if ( debug > 1 ) System.err.println(" Alignment structure1 parsed");
+ //logger.trace(" Alignment structure1 parsed");
aparser.initAlignment( null );
Alignment align2 = aparser.parse( alignName2 );
- if ( debug > 1 ) System.err.println(" Alignment structure2 parsed");
+ //logger.trace(" Alignment structure2 parsed");
// Create evaluator object
eval = new ExtPREvaluator(ObjectAlignment.toObjectAlignment( (URIAlignment)align1 ),
ObjectAlignment.toObjectAlignment( (URIAlignment)align2 ) );
// Compare
- params.setProperty( "debug", Integer.toString( nextdebug ) );
- eval.eval( params ) ;
+ eval.eval( parameters ) ;
} catch (Exception ex) {
- if ( debug > 1 ) {
- ex.printStackTrace();
- } else {
- System.err.println("ExtGroupEval: "+ex);
- System.err.println(alignName1+ " - "+alignName2 );
- }
+ logger.debug( "IGNORED Extension", ex );
};
return eval;
}
@@ -284,6 +236,23 @@ public class ExtGroupEval {
* This does not only print the results but compute the average as well
*/
public void print( Vector<Vector> result ) {
+ PrintStream writer = null;
+ try {
+ if ( outputfilename == null ) {
+ writer = System.out;
+ } else {
+ writer = new PrintStream( new FileOutputStream( outputfilename ) );
+ }
+
+ printHTML( result, writer );
+ } catch (Exception ex) {
+ logger.debug( "IGNORED Exception", ex );
+ } finally {
+ writer.close();
+ }
+ }
+
+ public void printHTML( Vector<Vector> result, PrintStream writer ) {
// variables for computing iterative harmonic means
int expected = 0; // expected so far
int foundVect[]; // found so far
@@ -291,17 +260,10 @@ public class ExtGroupEval {
double effVect[]; // effort-based similarity
double precOrVect[]; // precision-oriented similarity
double recOrVect[]; // recall-oriented similarity
- PrintStream writer = null;
fsize = format.length();
try {
- // Print result
- if ( filename == null ) {
- writer = System.out;
- } else {
- writer = new PrintStream(new FileOutputStream( filename ));
- }
- Formatter formatter = new Formatter(writer);
+ Formatter formatter = new Formatter( writer );
// Print the header
writer.println("<html><head></head><body>");
writer.println("<table border='2' frame='sides' rules='groups'>");
@@ -333,12 +295,12 @@ public class ExtGroupEval {
//writer.println("<td>Prec.</td><td>Rec.</td>");
}
writer.println("</tr></tbody><tbody>");
- foundVect = new int[ listAlgo.size() ];
- symVect = new double[ listAlgo.size() ];
- effVect = new double[ listAlgo.size() ];
- precOrVect = new double[ listAlgo.size() ];
- recOrVect = new double[ listAlgo.size() ];
- for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect = new int[ size ];
+ symVect = new double[ size ];
+ effVect = new double[ size ];
+ precOrVect = new double[ size ];
+ recOrVect = new double[ size ];
+ for( int k = size-1; k >= 0; k-- ) {
foundVect[k] = 0;
symVect[k] = 0.;
effVect[k] = 0.;
@@ -376,29 +338,29 @@ public class ExtGroupEval {
writer.print("<td>");
if ( format.charAt(i) == 's' ) {
formatter.format("%1.2f", eval.getSymPrecision());
- System.out.print("</td><td>");
+ writer.print("</td><td>");
formatter.format("%1.2f", eval.getSymRecall());
symVect[k] += eval.getSymSimilarity();
} else if ( format.charAt(i) == 'e' ) {
formatter.format("%1.2f", eval.getEffPrecision());
- System.out.print("</td><td>");
+ writer.print("</td><td>");
formatter.format("%1.2f", eval.getEffRecall());
effVect[k] += eval.getEffSimilarity();
} else if ( format.charAt(i) == 'p' ) {
formatter.format("%1.2f", eval.getPrecisionOrientedPrecision());
- System.out.print("</td><td>");
+ writer.print("</td><td>");
formatter.format("%1.2f", eval.getPrecisionOrientedRecall());
precOrVect[k] += eval.getPrecisionOrientedSimilarity();
} else if ( format.charAt(i) == 'r' ) {
formatter.format("%1.2f", eval.getRecallOrientedPrecision());
- System.out.print("</td><td>");
+ writer.print("</td><td>");
formatter.format("%1.2f", eval.getRecallOrientedRecall());
recOrVect[k] += eval.getRecallOrientedSimilarity();
}
- writer.println("</td>");
+ writer.print("</td>");
}
} else {
- writer.println("<td>n/a</td><td>n/a</td>");
+ for ( int i = 0 ; i < fsize; i++) writer.print("<td>n/a</td>");
}
}
writer.println("</tr>");
@@ -411,19 +373,19 @@ public class ExtGroupEval {
writer.print("<td>");
if ( format.charAt(i) == 's' ) {
formatter.format("%1.2f", symVect[k]/foundVect[k]);
- System.out.print("</td><td>");
+ writer.print("</td><td>");
formatter.format("%1.2f", symVect[k]/expected);
} else if ( format.charAt(i) == 'e' ) {
formatter.format("%1.2f", effVect[k]/foundVect[k]);
- System.out.print("</td><td>");
+ writer.print("</td><td>");
formatter.format("%1.2f", effVect[k]/expected);
} else if ( format.charAt(i) == 'p' ) {
formatter.format("%1.2f", precOrVect[k]/foundVect[k]);
- System.out.print("</td><td>");
+ writer.print("</td><td>");
formatter.format("%1.2f", precOrVect[k]/expected);
} else if ( format.charAt(i) == 'r' ) {
formatter.format("%1.2f", recOrVect[k]/foundVect[k]);
- System.out.print("</td><td>");
+ writer.print("</td><td>");
formatter.format("%1.2f", recOrVect[k]/expected);
}
writer.println("</td>");
@@ -440,7 +402,7 @@ public class ExtGroupEval {
writer.println("NaN: division per zero, likely due to empty alignent.</small></p>");
writer.println("</body></html>");
} catch (Exception ex) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
} finally {
writer.flush();
writer.close();
@@ -448,19 +410,6 @@ public class ExtGroupEval {
}
public void usage() {
- System.out.println("usage: ExtGroupEval [options]");
- System.out.println("options are:");
- System.out.println("\t--format=sepr -f sepr\tSpecifies the extended measures used (symetric/effort-based/precision-oriented/recall-oriented)");
- System.out.println("\t--reference=filename -r filename\tSpecifies the name of the reference alignment file (default: refalign.rdf)");
- System.out.println("\t--output=filename -o filename\tSpecifies a file to which the output will go");
- // Apparently not implemented
- //System.out.println("\t--dominant=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
- System.out.println("\t--type=html|xml|tex|ascii -t html|xml|tex|ascii\tSpecifies the output format");
- System.out.println("\t--list=algo1,...,algon -l algo1,...,algon\tSequence of the filenames to consider");
- System.out.println("\t--color=color -c color\tSpecifies if the output must color even lines of the output");
- System.out.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
- System.out.println("\t--help -h\t\t\tPrint this message");
- System.err.print("\n"+ExtGroupEval.class.getPackage().getImplementationTitle()+" "+ExtGroupEval.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
+ usage( "java "+this.getClass().getName()+" [options]\nEvaluates (with extended evaluators) in parallel several matching results on several tests in subdirectories" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/GenPlot.java b/src/fr/inrialpes/exmo/align/cli/GenPlot.java
index 9d82165c..f2a92e13 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) 2003-2012, INRIA
+ * Copyright (C) 2003-2014, INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -51,8 +51,14 @@ import java.lang.InstantiationException;
import org.xml.sax.SAXException;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
@@ -71,7 +77,6 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
* where the options are:
* <pre>
* -o filename --output=filename
- * -d debug --debug=level
* -l list of compared algorithms
* -t output --type=output: xml/tex/html/ascii
* -e classname --evaluator=classname
@@ -93,22 +98,33 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
* @author J�r�me Euzenat
*/
-public class GenPlot {
+public class GenPlot extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( GenPlot.class );
int STEP = 10;
- Properties params = new Properties();
- Vector<String> listAlgo;
+ String[] listAlgo = null;
Vector<GraphEvaluator> listEvaluators;
String fileNames = "";
- String outFile = null;
Constructor evalConstructor = null;
Constructor graphConstructor = null;
String xlabel;
String ylabel;
- String type = "tsv";
- int debug = 0;
+ String type = "tex";
int size = 0; // the set of algo to compare
- PrintWriter output = null;
+ String ontoDir = null;
+
+ public GenPlot() {
+ super();
+ options.addOption( OptionBuilder.withLongOpt( "list" ).hasArgs().withValueSeparator(',').withDescription( "List of FILEs to be included in the results (required)" ).withArgName("FILE").create( 'l' ) );
+ options.addOption( OptionBuilder.withLongOpt( "type" ).hasArg().withDescription( "Output in the specified FORMAT (values" ).withArgName("tsv|tex|html(|xml)").create( 't' ) );
+ options.addOption( OptionBuilder.withLongOpt( "evaluator" ).hasArg().withDescription( "Use CLASS as evaluation plotter" ).withArgName("CLASS").create( 'e' ) );
+ options.addOption( OptionBuilder.withLongOpt( "grapher" ).hasArg().withDescription( "Use CLASS as graph generator" ).withArgName("CLASS").create( 'g' ) );
+ //options.addOption( OptionBuilder.withLongOpt( "step" ).hasArg().withDescription( "" ).withArgName("").create( 's' ) );
+ options.addOption( OptionBuilder.withLongOpt( "directory" ).hasOptionalArg().withDescription( "The DIRectory containing the data to match" ).withArgName("DIR").create( 'w' ) );
+ // .setRequired( true )
+ Option opt = options.getOption( "list" );
+ if ( opt != null ) opt.setRequired( true );
+ }
public static void main(String[] args) {
try { new GenPlot().run( args ); }
@@ -116,74 +132,26 @@ public class GenPlot {
}
public void run(String[] args) throws Exception {
- LongOpt[] longopts = new LongOpt[10];
-
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[3] = new LongOpt("type", LongOpt.REQUIRED_ARGUMENT, null, 't');
- longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[5] = new LongOpt("evaluator", LongOpt.REQUIRED_ARGUMENT, null, 'e');
- longopts[6] = new LongOpt("grapher", LongOpt.REQUIRED_ARGUMENT, null, 'g');
- longopts[7] = new LongOpt("list", LongOpt.REQUIRED_ARGUMENT, null, 'l');
- longopts[8] = new LongOpt("step", LongOpt.REQUIRED_ARGUMENT, null, 's');
- longopts[9] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
-
- Getopt g = new Getopt("", args, "ho:d::l:D:e:g:s:t:", longopts);
- int step = 10;
- int c;
- String arg;
String evalCN = "fr.inrialpes.exmo.align.impl.eval.PRecEvaluator";
String graphCN = "fr.inrialpes.exmo.align.impl.eval.PRGraphEvaluator";
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h' :
- usage();
- return;
- case 'o' :
- /* Write output here */
- outFile = g.getOptarg();
- break;
- case 'e' :
- /* Name of the evaluator to use */
- evalCN = g.getOptarg();
- break;
- case 'g' :
- /* Name of the graph display to use */
- graphCN = g.getOptarg();
- break;
- case 't' :
- /* Type of output (tex/tsv(/html/xml/ascii)) */
- type = g.getOptarg();
- break;
- case 'l' :
- /* List of filename */
- fileNames = g.getOptarg();
- break;
- //case 's' :
- /* Step */
- //fileNames = g.getOptarg();
- //break;
- case 'd' :
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
- case 'D' :
- /* Parameter definition */
- arg = g.getOptarg();
- int index = arg.indexOf('=');
- if ( index != -1 ) {
- params.setProperty( arg.substring( 0, index),
- arg.substring(index+1));
- } else {
- System.err.println("Bad parameter syntax: "+g);
- usage();
- System.exit(0);
- }
- break;
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return; // --help
+
+ // Here deal with command specific arguments
+ if ( line.hasOption( 'e' ) ) evalCN = line.getOptionValue( 'e' );
+ if ( line.hasOption( 'g' ) ) graphCN = line.getOptionValue( 'g' );
+ if ( line.hasOption( 't' ) ) type = line.getOptionValue( 't' );
+ if ( line.hasOption( 'l' ) ) {
+ listAlgo = line.getOptionValues( 'l' );
+ size = listAlgo.length;
}
+ if ( line.hasOption( 'w' ) ) ontoDir = line.getOptionValue( 'w' );
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
+ usage();
+ System.exit(-1);
}
Class<?> graphClass = Class.forName(graphCN);
@@ -193,14 +161,6 @@ public class GenPlot {
//Class<?> evalClass = Class.forName(evalCN);
//evalConstructor = evalClass.getConstructor( cparams );
- listAlgo = new Vector<String>();
- for ( String s : fileNames.split(",") ) {
- size++;
- listAlgo.add( s );
- }
-
- if (debug > 0) params.setProperty( "debug", Integer.toString( debug-1 ) );
-
// Collect correspondences from alignments in all directories
// . -> Vector<EvalCell>
listEvaluators = iterateDirectories();
@@ -211,7 +171,7 @@ public class GenPlot {
int n = e.nbCells();
if ( n > max ) max = n;
}
- params.setProperty( "scale", Integer.toString( max ) );
+ parameters.setProperty( "scale", Integer.toString( max ) );
xlabel = listEvaluators.get(0).xlabel();
ylabel = listEvaluators.get(0).ylabel();
@@ -223,18 +183,18 @@ public class GenPlot {
for( int i = 0; i < size ; i++ ) {
// Convert it with the adequate GraphPlotter
// Scale the point pairs to the current display (local)
- toplot.add( i, listEvaluators.get(i).eval( params ) );
+ toplot.add( i, listEvaluators.get(i).eval( parameters ) );
//scaleResults( STEP,
}
// Set output file
OutputStream stream;
- if (outFile == null) {
+ if ( outputfilename == null) {
stream = System.out;
} else {
- stream = new FileOutputStream(outFile);
+ stream = new FileOutputStream( outputfilename );
}
- output = new PrintWriter (
+ PrintWriter writer = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter( stream, "UTF-8" )), true);
@@ -242,12 +202,16 @@ public class GenPlot {
// Display the required type of output
// Vector<Pair> -> .
if ( type.equals("tsv") ){
- printTSV( toplot );
+ printTSV( toplot, writer );
} else if ( type.equals("html") ) {
- printHTMLGGraph( toplot );
+ printHTMLGGraph( toplot, writer );
} else if ( type.equals("tex") ) {
- printPGFTex( toplot );
- } else System.err.println("Flag -t "+type+" : not implemented yet");
+ printPGFTex( toplot, writer );
+ } else {
+ logger.error( "Flag -t {} : not implemented yet", type );
+ usage();
+ System.exit(-1);
+ }
}
/**
@@ -265,17 +229,22 @@ public class GenPlot {
ev.setStep( STEP );
evaluators.add( i, ev );
}
- } catch (Exception ex) { //InstantiationException, IllegalAccessException
- ex.printStackTrace();
+ } catch ( Exception ex ) { //InstantiationException, IllegalAccessException
+ logger.error( "FATAL Exception", ex );
System.exit(-1);
}
File [] subdir = null;
try {
- subdir = (new File(System.getProperty("user.dir"))).listFiles();
- } catch (Exception e) {
- System.err.println("Cannot stat dir "+ e.getMessage());
+ if (ontoDir == null) {
+ subdir = (new File(System.getProperty("user.dir"))).listFiles();
+ } else {
+ subdir = (new File(ontoDir)).listFiles();
+ }
+ } catch ( Exception e ) {
+ logger.error( "Cannot stat dir", e );
usage();
+ System.exit(-1);
}
// Evaluate the results in each directory
@@ -289,42 +258,31 @@ public class GenPlot {
}
public void iterateAlignments ( File dir, Vector<GraphEvaluator> evaluators ) {
- if ( debug > 0 ) System.err.println("Directory : "+dir);
+ //logger.trace( "Directory : {}", dir );
String prefix = dir.toURI().toString()+"/";
- int nextdebug;
- if ( debug < 2 ) nextdebug = 0;
- else nextdebug = debug - 2;
- AlignmentParser aparser = new AlignmentParser( nextdebug );
+ AlignmentParser aparser = new AlignmentParser();
Alignment refalign = null;
try { // Load the reference alignment...
refalign = aparser.parse( prefix+"refalign.rdf" );
- if ( debug > 1 ) System.err.println(" Reference alignment parsed");
+ //logger.trace(" Reference alignment parsed");
} catch ( Exception aex ) {
- if ( debug > 1 ) {
- aex.printStackTrace();
- } else {
- System.err.println("GenPlot cannot parse refalign : "+aex);
- };
- return;
+ logger.error( "GenPlot cannot parse refalign", aex );
+ System.exit(-1);
}
// for all alignments there,
for( int i = 0; i < size; i++ ) {
- String algo = listAlgo.get(i);
+ String algo = listAlgo[i];
Alignment al = null;
- if ( debug > 0 ) System.err.println(" Considering result "+algo+" ("+i+")");
+ //logger.trace(" Considering result {} ({})", algo, i );
try {
aparser.initAlignment( null );
al = aparser.parse( prefix+algo+".rdf" );
- if ( debug > 1 ) System.err.println(" Alignment "+algo+" parsed");
- } catch (Exception ex) {
- if ( debug > 1 ) {
- ex.printStackTrace();
- } else {
- System.err.println("GenPlot: "+ex);
- };
+ //logger.trace(" Alignment {} parsed", algo );
+ } catch ( Exception ex ) {
+ logger.error( "IGNORED Exception", ex );
}
// even if empty, declare refalign
evaluators.get(i).ingest( al, refalign );
@@ -333,7 +291,7 @@ public class GenPlot {
try {
OntologyFactory.clear();
} catch ( OntowrapException owex ) { // only report
- owex.printStackTrace();
+ logger.error( "IGNORED Exception", owex );
}
}
@@ -370,86 +328,86 @@ public class GenPlot {
* This does average plus plot
*
*/
- public void printPGFTex( Vector<Vector<Pair>> result ){
+ public void printPGFTex( Vector<Vector<Pair>> result, PrintWriter writer ){
int i = 0;
String marktable[] = { "+", "*", "x", "-", "|", "o", "asterisk", "star", "oplus", "oplus*", "otimes", "otimes*", "square", "square*", "triangle", "triangle*", "diamond", "diamond*", "pentagon", "pentagon*"};
String colortable[] = { "black", "red", "green!50!black", "blue", "cyan", "magenta" } ;
- output.println("\\documentclass[11pt]{book}");
- output.println();
- output.println("\\usepackage{pgf}");
- output.println("\\usepackage{tikz}");
- output.println("\\usetikzlibrary{plotmarks}");
- output.println();
- output.println("\\begin{document}");
- output.println("\\date{today}");
- output.println("");
- output.println("\n%% Plot generated by GenPlot of alignapi");
- output.println("\\begin{tikzpicture}[cap=round]");
- output.println("% Draw grid");
- output.println("\\draw[step="+(STEP/10)+"cm,very thin,color=gray] (-0.2,-0.2) grid ("+STEP+","+STEP+");");
- output.println("\\draw[->] (-0.2,0) -- (10.2,0);");
- output.println("\\draw (5,-0.3) node {$"+xlabel+"$}; ");
- output.println("\\draw (0,-0.3) node {0.}; ");
- output.println("\\draw (10,-0.3) node {1.}; ");
- output.println("\\draw[->] (0,-0.2) -- (0,10.2);");
- output.println("\\draw (-0.3,0) node {0.}; ");
- output.println("\\draw (-0.3,5) node[rotate=90] {$"+ylabel+"$}; ");
- output.println("\\draw (-0.3,10) node {1.}; ");
- output.println("% Plots");
+ writer.println("\\documentclass[11pt]{book}");
+ writer.println();
+ writer.println("\\usepackage{pgf}");
+ writer.println("\\usepackage{tikz}");
+ writer.println("\\usetikzlibrary{plotmarks}");
+ writer.println();
+ writer.println("\\begin{document}");
+ writer.println("\\date{today}");
+ writer.println("");
+ writer.println("\n%% Plot generated by GenPlot of alignapi");
+ writer.println("\\begin{tikzpicture}[cap=round]");
+ writer.println("% Draw grid");
+ writer.println("\\draw[step="+(STEP/10)+"cm,very thin,color=gray] (-0.2,-0.2) grid ("+STEP+","+STEP+");");
+ writer.println("\\draw[->] (-0.2,0) -- (10.2,0);");
+ writer.println("\\draw (5,-0.3) node {$"+xlabel+"$}; ");
+ writer.println("\\draw (0,-0.3) node {0.}; ");
+ writer.println("\\draw (10,-0.3) node {1.}; ");
+ writer.println("\\draw[->] (0,-0.2) -- (0,10.2);");
+ writer.println("\\draw (-0.3,0) node {0.}; ");
+ writer.println("\\draw (-0.3,5) node[rotate=90] {$"+ylabel+"$}; ");
+ writer.println("\\draw (-0.3,10) node {1.}; ");
+ writer.println("% Plots");
i = 0;
for ( String m : listAlgo ) {
- output.print("\\draw["+colortable[i%6] );
- if ( !listEvaluators.get(i).isValid() ) output.print(",dotted");
- output.println("] plot[mark="+marktable[i%19]+"] file {"+m+".table};");
+ writer.print("\\draw["+colortable[i%6] );
+ if ( !listEvaluators.get(i).isValid() ) writer.print(",dotted");
+ writer.println("] plot[mark="+marktable[i%19]+"] file {"+m+".table};");
//,smooth
i++;
}
// And a legend
- output.println("% Legend");
+ writer.println("% Legend");
i = 0;
for ( String m : listAlgo ) {
- output.print("\\draw["+colortable[i%6] );
- if ( !listEvaluators.get(i).isValid() ) output.print(",dotted");
- output.println("] plot[mark="+marktable[i%19]+"] coordinates {("+((i%3)*3+1)+","+(-(i/3)*.8-1)+") ("+((i%3)*3+3)+","+(-(i/3)*.8-1)+")};");
+ writer.print("\\draw["+colortable[i%6] );
+ if ( !listEvaluators.get(i).isValid() ) writer.print(",dotted");
+ writer.println("] plot[mark="+marktable[i%19]+"] coordinates {("+((i%3)*3+1)+","+(-(i/3)*.8-1)+") ("+((i%3)*3+3)+","+(-(i/3)*.8-1)+")};");
//,smooth
- output.println("\\draw["+colortable[i%6]+"] ("+((i%3)*3+2)+","+(-(i/3)*.8-.8)+") node {"+m+"};");
- output.printf("\\draw["+colortable[i%6]+"] ("+((i%3)*3+2)+","+(-(i/3)*.8-1.2)+") node {%1.2f};\n", listEvaluators.get(i).getGlobalResult() );
+ writer.println("\\draw["+colortable[i%6]+"] ("+((i%3)*3+2)+","+(-(i/3)*.8-.8)+") node {"+m+"};");
+ writer.printf("\\draw["+colortable[i%6]+"] ("+((i%3)*3+2)+","+(-(i/3)*.8-1.2)+") node {%1.2f};\n", listEvaluators.get(i).getGlobalResult() );
i++;
}
- output.println("\\end{tikzpicture}");
- output.println();
- output.println("\\end{document}");
+ writer.println("\\end{tikzpicture}");
+ writer.println();
+ writer.println("\\end{document}");
i = 0;
for( Vector<Pair> table : result ) {
- String algo = listAlgo.get(i);
+ String algo = listAlgo[i];
// Open one file
- PrintWriter writer = null;
+ PrintWriter auxwriter = null;
try {
- writer = new PrintWriter (
+ auxwriter = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter(
new FileOutputStream(algo+".table"), "UTF-8" )), true);
// Print header
- writer.println("#Curve 0, "+(STEP+1)+" points");
- writer.println("#x y type");
- writer.println("%% Plot generated by GenPlot of alignapi");
- writer.println("%% Include in PGF tex by:\n");
- writer.println("%% \\begin{tikzpicture}[cap=round]");
- writer.println("%% \\draw[step="+(STEP/10)+"cm,very thin,color=gray] (-0.2,-0.2) grid ("+STEP+","+STEP+");");
- writer.println("%% \\draw[->] (-0.2,0) -- (10.2,0) node[right] {$"+xlabel+"$}; ");
- writer.println("%% \\draw[->] (0,-0.2) -- (0,10.2) node[above] {$"+ylabel+"$}; ");
- writer.println("%% \\draw plot[mark=+,smooth] file {"+algo+".table};");
- writer.println("%% \\end{tikzpicture}");
- writer.println();
+ auxwriter.println("#Curve 0, "+(STEP+1)+" points");
+ auxwriter.println("#x y type");
+ auxwriter.println("%% Plot generated by GenPlot of alignapi");
+ auxwriter.println("%% Include in PGF tex by:\n");
+ auxwriter.println("%% \\begin{tikzpicture}[cap=round]");
+ auxwriter.println("%% \\draw[step="+(STEP/10)+"cm,very thin,color=gray] (-0.2,-0.2) grid ("+STEP+","+STEP+");");
+ auxwriter.println("%% \\draw[->] (-0.2,0) -- (10.2,0) node[right] {$"+xlabel+"$}; ");
+ auxwriter.println("%% \\draw[->] (0,-0.2) -- (0,10.2) node[above] {$"+ylabel+"$}; ");
+ auxwriter.println("%% \\draw plot[mark=+,smooth] file {"+algo+".table};");
+ auxwriter.println("%% \\end{tikzpicture}");
+ auxwriter.println();
for( Pair p : table ) {
- if ( debug > 1 ) System.err.println( " >> "+p.getX()+" - "+p.getY() );
- writer.println( p.getX()*10+" "+ p.getY()*10 );
+ //logger.trace( " >> {} - {}", p.getX(), p.getY() );
+ auxwriter.println( p.getX()*10+" "+ p.getY()*10 );
}
- } catch (Exception ex) {
- ex.printStackTrace();
+ } catch ( Exception ex ) {
+ logger.error( "IGNORED Exception", ex );
} finally {
- if ( writer != null ) writer.close();
+ if ( auxwriter != null ) auxwriter.close();
}
// UnsupportedEncodingException + FileNotFoundException
i++;
@@ -460,30 +418,30 @@ public class GenPlot {
* This does average plus generate the call for Google Chart API
*
*/
- public void printHTMLGGraph( Vector<Vector<Pair>> result ){
- output.print("<img src=\"http://chart.apis.google.com/chart?");
- output.print("chs=600x500&cht=lxy&chg=10,10&chof=png");
- output.print("&chxt=x,x,y,y&chxr=0,0.0,1.0,0.1|2,0.0,1.0,0.1&chxl=1:|"+xlabel+"|3:|"+ylabel+"&chma=b&chxp=1,50|3,50&chxs=0N*sz1*|2N*sz1*");
- output.print("&chd=t:"); // data
+ public void printHTMLGGraph( Vector<Vector<Pair>> result, PrintWriter writer ){
+ writer.print("<img src=\"http://chart.apis.google.com/chart?");
+ writer.print("chs=600x500&cht=lxy&chg=10,10&chof=png");
+ writer.print("&chxt=x,x,y,y&chxr=0,0.0,1.0,0.1|2,0.0,1.0,0.1&chxl=1:|"+xlabel+"|3:|"+ylabel+"&chma=b&chxp=1,50|3,50&chxs=0N*sz1*|2N*sz1*");
+ writer.print("&chd=t:"); // data
boolean firstalg = true;
for( Vector<Pair> table : result ) {
- if ( !firstalg ) output.print("|");
+ if ( !firstalg ) writer.print("|");
firstalg = false;
boolean firstpoint = true;
String Yval = "|";
for( Pair p : table ) {
if ( !firstpoint ) {
- output.print(",");
+ writer.print(",");
Yval += ",";
}
firstpoint = false;
Yval += String.format("%1.2f", p.getY()*10);
- if ( debug > 1 ) System.err.println( " >> "+p.getX()+" - "+p.getY() );
- output.printf( "%1.2f", p.getX()*10 );
+ //logger.trace( " >> {} - {}", p.getX(), p.getY() );
+ writer.printf( "%1.2f", p.getX()*10 );
}
- output.print( Yval );
+ writer.print( Yval );
}
- output.print("&chdl="); // labels
+ writer.print("&chdl="); // labels
int i = 0;
//String marktable[] = { "+", "*", "x", "-", "|", "o", "asterisk", "star", "oplus", "oplus*", "otimes", "otimes*", "square", "square*", "triangle", "triangle*", "diamond", "diamond*", "pentagon", "pentagon*"};
//String colortable[] = { "black", "red", "green!50!black", "blue", "cyan", "magenta" };
@@ -492,11 +450,11 @@ public class GenPlot {
String color = "";
for ( String m : listAlgo ) {
if ( i > 0 ) {
- output.print( "|" );
+ writer.print( "|" );
color += ",";
style += "|";
}
- output.print( m );
+ writer.print( m );
color += colortable[i%28];
if ( !listEvaluators.get(i).isValid() ) {
style += "2,6,3";
@@ -505,39 +463,32 @@ public class GenPlot {
}
i++;
}
- //output.print("&chdlp=b"); // legend position (but ugly)
- output.print("&chco="+color); // colors
- output.print("&chls="+style); // linestyle
- output.println("&chds=0,10\"/>");
+ //writer.print("&chdlp=b"); // legend position (but ugly)
+ writer.print("&chco="+color); // colors
+ writer.print("&chls="+style); // linestyle
+ writer.println("&chds=0,10\"/>");
}
// 2010: TSV output is not finished
// It is supposed to provide
// List of algo
// List of STEP + points
- public void printTSV( Vector<Vector<Pair>> points ) {
+ public void printTSV( Vector<Vector<Pair>> points, PrintWriter writer ) {
// Print first line
for ( String m : listAlgo ) {
- output.print("\t"+m );
+ writer.print("\t"+m );
}
// Print others
for ( int i= 0; i < 100 ; i += STEP ) {
for( int j = 0; j < size; j++ ){
Pair precrec = points.get(j).get(i);
- output.println( precrec.getX()+" "+precrec.getY() );
+ writer.println( precrec.getX()+" "+precrec.getY() );
}
}
- output.println();
+ writer.println();
}
public void usage() {
- System.out.println("usage: GenPlot [options]");
- System.out.println("options are:");
- System.out.println("\t--type=tsv|tex|html(|xml) -t tsv|tex|html(|xml)\tSpecifies the output format");
- System.out.println("\t--graph=class -g class\tSpecifies the class of Evaluator to be used");
- System.out.println("\t--evaluator=class -e class\tSpecifies the class of GraphEvaluator (plotter) to be used");
- System.out.println("\t--list=algo1,...,algon -l algo1,...,algon\tSequence of the filenames to consider");
- System.out.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
- System.out.println("\t--help -h\t\t\tPrint this message");
+ usage( "java "+this.getClass().getName()+" [options]\nGenerate a graphic presentation of evaluation results" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupAlign.java b/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
index f9480fed..01298e58 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
@@ -1,9 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003 The University of Manchester
- * Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2008, 2010-2013 INRIA
+ * Copyright (C) 2003-2008, 2010-2014 INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -22,8 +20,6 @@
* USA.
*/
-/* This program evaluates the results of several ontology aligners in a row.
-*/
package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
@@ -38,7 +34,6 @@ import fr.inrialpes.exmo.ontowrap.OntologyFactory;
import java.io.File;
import java.io.FileOutputStream;
-import java.io.FileInputStream;
import java.io.PrintWriter;
import java.io.BufferedWriter;
import java.io.OutputStreamWriter;
@@ -51,8 +46,14 @@ import java.util.Properties;
import org.xml.sax.SAXException;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
/** A batch class for an OWL ontology alignment processing.
It aligns all the ontology pairs denoted
@@ -69,32 +70,37 @@ import gnu.getopt.Getopt;
--name=filename -n filename output results in filename.rdf
--impl=className -i classname Use the given alignment implementation.
--renderer=className -r className Specifies the alignment renderer
- --debug=level -d level
</pre>
<pre>
$Id$
</pre>
+*/
-@author Sean K. Bechhofer
-@author J�r�me Euzenat
- */
-
-public class GroupAlign {
+public class GroupAlign extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( GroupAlign.class );
- Properties params = null;
- String filename = "align";
- String paramfile = null;
String urlprefix = null;
String source = "onto1.rdf";
String target = "onto.rdf";
URI uri1 = null;
String initName = null;
- int debug = 0;
String alignmentClassName = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
String rendererClass = "fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor";
String ontoDir = null;
+ public GroupAlign() {
+ super();
+ options.addOption( OptionBuilder.withLongOpt( "alignment" ).hasArg().withDescription( "Use an initial alignment FILE" ).withArgName("FILE").create( 'a' ) );
+ options.addOption( OptionBuilder.withLongOpt( "renderer" ).hasArg().withDescription( "Use the given CLASS for rendering" ).withArgName("CLASS").create( 'r' ) );
+ options.addOption( OptionBuilder.withLongOpt( "impl" ).hasArg().withDescription( "Use the given Alignment implementation" ).withArgName("CLASS").create( 'i' ) );
+ options.addOption( OptionBuilder.withLongOpt( "name" ).hasArg().withDescription( "Use the given URI as common source ontology" ).withArgName("URI").create( 'n' ) );
+ options.addOption( OptionBuilder.withLongOpt( "uriprefix" ).hasArg().withDescription( "URI prefix of the target" ).withArgName("URI").create( 'u' ) );
+ options.addOption( OptionBuilder.withLongOpt( "source" ).hasArg().withDescription( "Source ontology FILEname (default "+source+")" ).withArgName("FILE").create( 's' ) );
+ options.addOption( OptionBuilder.withLongOpt( "target" ).hasArg().withDescription( "Target ontology FILEname (default "+target+")" ).withArgName("FILE").create( 't' ) );
+ options.addOption( OptionBuilder.withLongOpt( "directory" ).hasOptionalArg().withDescription( "The DIRectory containing the data to match" ).withArgName("DIR").create( 'w' ) );
+ }
+
public static void main(String[] args) {
try { new GroupAlign().run( args ); }
catch (Exception ex) { ex.printStackTrace(); };
@@ -102,109 +108,32 @@ public class GroupAlign {
public void run(String[] args) throws Exception {
- LongOpt[] longopts = new LongOpt[13];
- params = new Properties();
-
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("alignment", LongOpt.REQUIRED_ARGUMENT, null, 'a');
- longopts[3] = new LongOpt("renderer", LongOpt.REQUIRED_ARGUMENT, null, 'r');
- longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[5] = new LongOpt("impl", LongOpt.REQUIRED_ARGUMENT, null, 'i');
- longopts[6] = new LongOpt("params", LongOpt.REQUIRED_ARGUMENT, null, 'p');
- longopts[7] = new LongOpt("name", LongOpt.REQUIRED_ARGUMENT, null, 'n');
- longopts[8] = new LongOpt("prefix", LongOpt.REQUIRED_ARGUMENT, null, 'u');
- longopts[9] = new LongOpt("source", LongOpt.REQUIRED_ARGUMENT, null, 's');
- longopts[10] = new LongOpt("target", LongOpt.REQUIRED_ARGUMENT, null, 't');
- // Is there a way for that in LongOpt ???
- longopts[11] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
- longopts[12] = new LongOpt("directory", LongOpt.REQUIRED_ARGUMENT, null, 'w');
-
- Getopt g = new Getopt("", args, "ho:a:d::n:u:r:i:s:t:p:D:w:", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h' :
- usage();
- return;
- case 'o' :
- /* Write output in given filename */
- filename = g.getOptarg();
- break;
- case 'n' :
- arg = g.getOptarg();
- /* Use common ontology to compare */
- if(arg!=null){
- try { uri1 = new URI(g.getOptarg());
- } catch (Exception e) { e.printStackTrace(); }
- }
- else{uri1 = null;}
- break;
- case 'p' :
- /* Read parameters from filename */
- paramfile = g.getOptarg();
- params.loadFromXML( new FileInputStream( paramfile ) );
- break;
- case 'r' :
- /* Use the given class for rendering */
- rendererClass = g.getOptarg();
- break;
- case 'i' :
- /* Use the given class for the alignment */
- alignmentClassName = g.getOptarg();
- break;
- case 'a' :
- /* Use the given file as a partial alignment */
- initName = g.getOptarg();
- break;
- case 'u' :
- /* Use the given url prefix for fetching the ontologies */
- urlprefix = g.getOptarg();
- break;
- case 's' :
- /* Use the given filename for source ontology */
- source = g.getOptarg();
- break;
- case 't' :
- /* Use the given filename for target ontology */
- target = g.getOptarg();
- break;
- case 'D' :
- /* Parameter definition */
- arg = g.getOptarg();
- int index = arg.indexOf('=');
- if ( index != -1 ) {
- params.setProperty( arg.substring( 0, index),
- arg.substring(index+1));
- } else {
- System.err.println("Bad parameter syntax: "+g);
- usage();
- System.exit(0);
- }
- break;
- case 'd' :
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
- case 'w' :
- /* Use the given ontology directory */
- arg = g.getOptarg();
- if ( arg != null ) ontoDir = g.getOptarg();
- else ontoDir = null;
- break;
- }
- }
+ try {
+ outputfilename = "align";
+
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return; // --help
- //int i = g.getOptind();
+ // Here deal with command specific arguments
- if (debug == 0 && params.getProperty("debug") != null) {
- debug = Integer.parseInt(params.getProperty("debug"));
+ if ( line.hasOption( 'n' ) ) {
+ try { uri1 = new URI( line.getOptionValue('n') );
+ } catch ( Exception e ) {
+ logger.debug( "IGNORED Exception (cannot create source URI)", e );
+ }
+ }
+ if ( line.hasOption( 'r' ) ) rendererClass = line.getOptionValue( 'r' );
+ if ( line.hasOption( 'i' ) ) alignmentClassName = line.getOptionValue( 'i' );
+ if ( line.hasOption( 'a' ) ) initName = line.getOptionValue( 'a' );
+ if ( line.hasOption( 'u' ) ) urlprefix = line.getOptionValue( 'u' );
+ if ( line.hasOption( 's' ) ) source = line.getOptionValue( 's' );
+ if ( line.hasOption( 't' ) ) target = line.getOptionValue( 't' );
+ if ( line.hasOption( 'w' ) ) ontoDir = line.getOptionValue( 'w' );
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
+ usage();
+ System.exit(-1);
}
- if (debug > 0) params.setProperty( "debug", Integer.toString( debug-1 ) );
iterateDirectories();
}
@@ -219,14 +148,14 @@ public class GroupAlign {
subdir = (new File(ontoDir)).listFiles();
}
} catch ( Exception e ) {
- System.err.println("Cannot stat dir "+ e.getMessage());
+ logger.error( "Cannot stat dir", e );
usage();
}
int size = subdir.length;
for ( int i=0 ; i < size; i++ ) {
if( subdir[i].isDirectory() ) {
// Align
- if ( debug > 0 ) System.err.println("Directory: "+subdir[i]);
+ //logger.trace("Directory: {}", subdir[i]);
align( subdir[i] );
}
}
@@ -250,56 +179,56 @@ public class GroupAlign {
// file://localhost/localpath
// Apparently should be file:///c:/localpath
}
- //System.err.println("Here it is "+prefix+" (end by /?)");
+ //logger.trace{}("Here it is {} (end by /?)", prefix );
try {
if ( !source.equalsIgnoreCase("onto1.rdf")
&& !target.equalsIgnoreCase("onto1.rdf") ) {
- uri1 = new URI(prefix+source);
- } else if ( uri1 == null ) uri1 = new URI(prefix+source);
- URI uri2 = new URI(prefix+target);
+ uri1 = new URI( prefix+source );
+ } else if ( uri1 == null ) uri1 = new URI( prefix+source );
+ URI uri2 = new URI( prefix+target );
- if (debug > 1) System.err.println(" Handler set");
- if (debug > 1) System.err.println(" URI1: "+uri1);
- if (debug > 1) System.err.println(" URI2: "+uri2);
+ //logger.trace(" Handler set");
+ //logger.trace(" URI1: {}", uri1);
+ //logger.trace(" URI2: {}", uri2);
try {
- if (initName != null) {
- AlignmentParser aparser = new AlignmentParser(debug-1);
- init = aparser.parse( initName );
+ if ( initName != null ) {
+ AlignmentParser aparser = new AlignmentParser();
+ init = aparser.parse( prefix+initName );
uri1 = init.getFile1();
uri2 = init.getFile2();
- if (debug > 1) System.err.println(" Init parsed");
+ logger.debug(" Init parsed");
}
// Create alignment object
Object[] mparams = {};
Class[] cparams = {};
- Class<?> alignmentClass = Class.forName(alignmentClassName);
+ Class<?> alignmentClass = Class.forName( alignmentClassName );
java.lang.reflect.Constructor alignmentConstructor =
alignmentClass.getConstructor(cparams);
- result = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
+ result = (AlignmentProcess)alignmentConstructor.newInstance( mparams );
result.init( uri1, uri2 );
} catch (Exception ex) {
- System.err.println("Cannot create alignment "+ alignmentClassName+ "\n"+ ex.getMessage());
+ logger.debug( "Cannot create alignment {}", alignmentClassName );
throw ex;
}
- if (debug > 1) System.err.println(" Alignment structure created");
+ logger.debug(" Alignment structure created");
// Compute alignment
long time = System.currentTimeMillis();
- result.align(init, params); // add opts
+ result.align( init, parameters );
long newTime = System.currentTimeMillis();
result.setExtension( Namespace.ALIGNMENT.uri, Annotations.TIME, Long.toString(newTime - time) );
- if (debug > 1) System.err.println(" Alignment performed");
+ logger.debug(" Alignment performed");
// Set output file
writer = new PrintWriter (
new BufferedWriter(
new OutputStreamWriter(
- new FileOutputStream(dir+File.separator+filename+".rdf"), "UTF-8" )), true);
+ new FileOutputStream(dir+File.separator+outputfilename), "UTF-8" )), true);
AlignmentVisitor renderer = null;
try {
@@ -309,41 +238,30 @@ public class GroupAlign {
Class.forName(rendererClass).getConstructor(cparams);
renderer = (AlignmentVisitor)rendererConstructor.newInstance(mparams);
} catch (Exception ex) {
- System.err.println("Cannot create renderer "+rendererClass+"\n"+ ex.getMessage());
+ logger.debug( "Cannot create renderer {}", rendererClass );
throw ex;
}
- if (debug > 1) System.err.println(" Outputing result to "+dir+File.separator+filename+".rdf");
+ logger.debug(" Outputing result to {}/{}", dir, outputfilename );
+
// Output
result.render( renderer);
- if (debug > 1) System.err.println(" Done..."+renderer+"\n");
- } catch (Exception ex) {
- if ( debug > 1 ) ex.printStackTrace();
+ logger.debug(" Done...{}", renderer );
+ } catch (Exception ex) {
+ logger.debug( "IGNORED Exception", ex );
} finally {
// JE: This instruction is very important
if ( writer != null ) writer.close();
// Unload the ontologies
- try { OntologyFactory.clear(); } catch (Exception e) {};
+ try { OntologyFactory.clear();
+ } catch (Exception e) {
+ logger.debug( "IGNORED Exception on close", e );
+ };
}
}
public void usage() {
- System.err.println("usage: GroupAlign [options]");
- System.err.println("options are:");
- System.err.println("\t--name=uri -n uri\t\tUse the given uri to compare with.");
- System.err.println("\t--source=filename -s filename Source filename (default onto1.rdf)");
- System.err.println("\t--target=filename -t filename Target filename (default onto.rdf)");
- System.err.println("\t--prefix=uriprefix -u uriprefix URI prefix of the target");
- System.err.println("\t--output=filename -o filename\tOutput the alignment in filename.rdf");
- System.err.println("\t--impl=className -i classname\t\tUse the given alignment implementation.");
- System.err.println("\t--renderer=className -r className\tSpecifies the alignment renderer");
- System.err.println("\t--alignment=filename -a filename Start from an XML alignment file");
- System.err.println("\t--params=filename -p filename\tReads parameters from filename");
- System.err.println("\t-Dparam=value\t\t\tSet parameter");
- System.err.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
- System.err.println("\t--help -h\t\t\tPrint this message");
- System.err.print("\n"+GroupAlign.class.getPackage().getImplementationTitle()+" "+GroupAlign.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
+ usage( "java "+this.getClass().getName()+" [options]\nMatches pairs of ontologies in subdirectories" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupEval.java b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
index 99448170..ec3acb6a 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
@@ -1,9 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003 The University of Manchester
- * Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2012, INRIA
+ * Copyright (C) 2003-2014, INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -48,8 +46,14 @@ import java.util.Properties;
import org.xml.sax.SAXException;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
@@ -65,7 +69,6 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
<pre>
-o filename --output=filename
-f format = prfot (precision/recall/f-measure/overall/time) --format=prfot
- -d debug --debug=level
-r filename --reference=filename
-s algo/measure
-l list of compared algorithms
@@ -83,108 +86,65 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
$Id$
</pre>
-@author Sean K. Bechhofer
-@author J�r�me Euzenat
*/
-public class GroupEval {
+public class GroupEval extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( GroupEval.class );
- Properties params = null;
- String filename = null;
String reference = "refalign.rdf";
String format = "pr";
int fsize = 2;
String type = "html";
boolean embedded = false;
String dominant = "s";
- Vector<String> listAlgo = null;
- int debug = 0;
+ String[] listAlgo = null;
+ int size = 0;
String color = null;
String ontoDir = null;
+ public GroupEval() {
+ super();
+ options.addOption( OptionBuilder.withLongOpt( "list" ).hasArgs().withValueSeparator(',').withDescription( "List of FILEs to be included in the results (required)" ).withArgName("FILE").create( 'l' ) );
+ options.addOption( OptionBuilder.withLongOpt( "color" ).hasOptionalArg().withDescription( "Color even lines of the output in COLOR (default: lightblue)" ).withArgName("COLOR").create( 'c' ) );
+ options.addOption( OptionBuilder.withLongOpt( "format" ).hasArg().withDescription( "Used MEASures and order (precision/recall/f-measure/overall/time) (default: "+format+")" ).withArgName("MEAS").create( 'f' ) );
+ options.addOption( OptionBuilder.withLongOpt( "type" ).hasArg().withDescription( "Output TYPE (html|xml|tex|ascii|triangle; default: "+type+")" ).withArgName("TYPE").create( 't' ) );
+ //options.addOption( OptionBuilder.withLongOpt( "sup" ).hasArg().withDescription( "Specifies if dominant columns are algorithms or measure" ).withArgName("algo").create( 's' ) );
+ options.addOption( OptionBuilder.withLongOpt( "reference" ).hasArg().withDescription( "Name of the reference alignment FILE (default: "+reference+")" ).withArgName("FILE").create( 'r' ) );
+ options.addOption( OptionBuilder.withLongOpt( "directory" ).hasOptionalArg().withDescription( "The DIRectory containing the data to evaluate" ).withArgName("DIR").create( 'w' ) );
+ // .setRequired( true )
+ Option opt = options.getOption( "list" );
+ if ( opt != null ) opt.setRequired( true );
+ }
+
+
public static void main(String[] args) {
try { new GroupEval().run( args ); }
catch (Exception ex) { ex.printStackTrace(); };
}
public void run(String[] args) throws Exception {
- String listFile = "";
- LongOpt[] longopts = new LongOpt[10];
-
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("format", LongOpt.REQUIRED_ARGUMENT, null, 'f');
- longopts[3] = new LongOpt("type", LongOpt.REQUIRED_ARGUMENT, null, 't');
- longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[5] = new LongOpt("sup", LongOpt.REQUIRED_ARGUMENT, null, 's');
- longopts[6] = new LongOpt("list", LongOpt.REQUIRED_ARGUMENT, null, 'l');
- longopts[7] = new LongOpt("color", LongOpt.OPTIONAL_ARGUMENT, null, 'c');
- longopts[8] = new LongOpt("reference", LongOpt.REQUIRED_ARGUMENT, null, 'r');
- longopts[9] = new LongOpt("directory", LongOpt.REQUIRED_ARGUMENT, null, 'w');
-
- Getopt g = new Getopt("", args, "ho:a:d::l:f:t:r:w:c::", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h' :
- usage();
- return;
- case 'o' :
- /* Write output here */
- filename = g.getOptarg();
- break;
- case 'r' :
- /* File name for the reference alignment */
- reference = g.getOptarg();
- break;
- case 'f' :
- /* Sequence of results to print */
- format = g.getOptarg();
- break;
- case 't' :
- /* Type of output (tex/html/xml/ascii) */
- type = g.getOptarg();
- break;
- case 's' :
- /* Print per type or per algo */
- dominant = g.getOptarg();
- break;
- case 'c' :
- /* Print colored lines */
- arg = g.getOptarg();
- if ( arg != null ) {
- color = arg.trim();
- } else color = "lightblue";
- break;
- case 'l' :
- /* List of filename */
- listFile = g.getOptarg();
- break;
- case 'd' :
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
- case 'w' :
- /* Use the given ontology directory */
- arg = g.getOptarg();
- if ( arg != null ) ontoDir = g.getOptarg();
- else ontoDir = null;
- break;
- }
- }
- listAlgo = new Vector<String>();
- for ( String s : listFile.split(",") ) {
- listAlgo.add( s );
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return; // --help
+
+ // Here deal with command specific arguments
+ if ( line.hasOption( 'f' ) ) format = line.getOptionValue( 'f' );
+ if ( line.hasOption( 'r' ) ) reference = line.getOptionValue( 'r' );
+ if ( line.hasOption( 's' ) ) dominant = line.getOptionValue( 's' );
+ if ( line.hasOption( 't' ) ) type = line.getOptionValue( 't' );
+ if ( line.hasOption( 'c' ) ) color = line.getOptionValue( 'c', "lightblue" );
+ if ( line.hasOption( 'l' ) ) {
+ listAlgo = line.getOptionValues( 'l' );
+ size = listAlgo.length;
+ }
+ if ( line.hasOption( 'w' ) ) ontoDir = line.getOptionValue( 'w' );
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
+ usage();
+ System.exit( -1 );
}
- params = new Properties();
- if (debug > 0) params.setProperty( "debug", Integer.toString( debug-1 ) );
-
print( iterateDirectories() );
}
@@ -192,13 +152,13 @@ public class GroupEval {
Vector<Vector> result = null;
File [] subdir = null;
try {
- if (ontoDir == null) {
- subdir = (new File(System.getProperty("user.dir"))).listFiles();
- } else {
- subdir = (new File(ontoDir)).listFiles();
- }
- } catch (Exception e) {
- System.err.println("Cannot stat dir "+ e.getMessage());
+ if (ontoDir == null) {
+ subdir = (new File(System.getProperty("user.dir"))).listFiles();
+ } else {
+ subdir = (new File(ontoDir)).listFiles();
+ }
+ } catch ( Exception e ) {
+ logger.error( "Cannot stat dir ", e );
usage();
}
int size = subdir.length;
@@ -207,7 +167,7 @@ public class GroupEval {
int i = 0;
for ( int j=0 ; j < size; j++ ) {
if( subdir[j].isDirectory() ) {
- if ( debug > 0 ) System.err.println("\nEntering directory "+subdir[j]);
+ //logger.trace( "Entering directory {}", subdir[j] );
// eval the alignments in a subdirectory
// store the result
Vector vect = iterateAlignments( subdir[j] );
@@ -232,7 +192,7 @@ public class GroupEval {
// call eval
// store the result in a record
// return the record.
- if ( debug > 2) System.err.println(" Considering result "+i);
+ //logger.trace( " Considering result {}", i );
Evaluator evaluator = eval( prefix+reference, prefix+m+".rdf");
if ( evaluator != null ) ok = true;
result.add( i, evaluator );
@@ -240,8 +200,8 @@ public class GroupEval {
// Unload the ontologies.
try {
OntologyFactory.clear();
- } catch ( OntowrapException owex ) { // only report
- owex.printStackTrace();
+ } catch ( OntowrapException owex ) {
+ logger.debug( "IGNORED Exception", owex );
}
if ( ok == true ) return result;
@@ -251,28 +211,19 @@ public class GroupEval {
public Evaluator eval( String alignName1, String alignName2 ) {
Evaluator eval = null;
try {
- int nextdebug;
- if ( debug < 2 ) nextdebug = 0;
- else nextdebug = debug - 2;
// Load alignments
- AlignmentParser aparser = new AlignmentParser( nextdebug );
+ AlignmentParser aparser = new AlignmentParser();
Alignment align1 = aparser.parse( alignName1 );
- if ( debug > 2 ) System.err.println(" Alignment structure1 parsed");
+ //logger.trace(" Alignment structure1 parsed");
aparser.initAlignment( null );
Alignment align2 = aparser.parse( alignName2 );
- if ( debug > 2 ) System.err.println(" Alignment structure2 parsed");
+ //logger.trace(" Alignment structure2 parsed");
// Create evaluator object
eval = new PRecEvaluator( align1, align2 );
// Compare
- params.setProperty( "debug", Integer.toString( nextdebug ) );
- eval.eval( params ) ;
+ eval.eval( parameters ) ;
} catch (Exception ex) {
- if ( debug > 1 ) {
- ex.printStackTrace();
- } else {
- System.err.println("GroupEval: "+ex);
- System.err.println(alignName1+ " - "+alignName2 );
- }
+ logger.debug( "IGNORED Exception", ex );
};
return eval;
}
@@ -283,16 +234,16 @@ public class GroupEval {
public void print( Vector<Vector> result ) {
PrintStream writer = null;
try {
- if ( filename == null ) {
+ if ( outputfilename == null ) {
writer = System.out;
} else {
- writer = new PrintStream(new FileOutputStream( filename ));
+ writer = new PrintStream( new FileOutputStream( outputfilename ) );
}
if ( type.equals("html") ) printHTML( result, writer );
else if ( type.equals("tex") ) printLATEX( result, writer );
else if ( type.equals("triangle") ) printTRIANGLE( result, writer );
} catch ( FileNotFoundException fnfex) {
- fnfex.printStackTrace();
+ logger.error( "Cannot open file", fnfex );
} finally {
writer.close();
}
@@ -309,10 +260,10 @@ public class GroupEval {
int foundVect[]; // found so far
int correctVect[]; // correct so far
long timeVect[]; // time so far
- foundVect = new int[ listAlgo.size() ];
- correctVect = new int[ listAlgo.size() ];
- timeVect = new long[ listAlgo.size() ];
- for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect = new int[ size ];
+ correctVect = new int[ size ];
+ timeVect = new long[ size ];
+ for( int k = size-1; k >= 0; k-- ) {
foundVect[k] = 0;
correctVect[k] = 0;
timeVect[k] = 0;
@@ -399,9 +350,11 @@ public class GroupEval {
double prec2 = precision*precision;
double a = ((prec2-(recall*recall)+1)/2);
double b = java.lang.Math.sqrt( prec2 - (a*a) );
- a = a*10; b = b*10; //for printing scale 10.
- writer.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
- writer.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+m+"};");
+ if ( b == b ) { // Test if b is not NaN! Otherwise, no square root: the point is out of the triangle
+ a = a*10; b = b*10; //for printing scale 10.
+ writer.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
+ writer.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+m+"};");
+ }
k++;
}
writer.println("\\end{tikzpicture}");
@@ -454,10 +407,10 @@ public class GroupEval {
//writer.println("<td>Prec.</td><td>Rec.</td>");
}
writer.println("</tr></tbody><tbody>");
- foundVect = new int[ listAlgo.size() ];
- correctVect = new int[ listAlgo.size() ];
- timeVect = new long[ listAlgo.size() ];
- for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect = new int[ size ];
+ correctVect = new int[ size ];
+ timeVect = new long[ size ];
+ for( int k = size-1; k >= 0; k-- ) {
foundVect[k] = 0;
correctVect[k] = 0;
timeVect[k] = 0;
@@ -508,10 +461,10 @@ public class GroupEval {
} else if ( format.charAt(i) == 'r' ) {
formatter.format("%1.2f", eval.getRecall());
}
- writer.println("</td>");
+ writer.print("</td>");
}
} else {
- for ( int i = 0 ; i < fsize; i++) writer.println("<td>n/a</td>");
+ for ( int i = 0 ; i < fsize; i++) writer.print("<td>n/a</td>");
}
}
writer.println("</tr>");
@@ -575,7 +528,7 @@ public class GroupEval {
writer.println("\\setlength{\\tabcolsep}{3pt} % May be changed");
writer.println("\\begin{table}");
writer.print("\\begin{tabular}{|l||");
- for ( int i = listAlgo.size(); i > 0; i-- ) {
+ for ( int i = size; i > 0; i-- ) {
for ( int j = fsize; j > 0; j-- ) writer.print("c");
writer.print("|");
}
@@ -607,10 +560,10 @@ public class GroupEval {
}
}
writer.println(" \\\\ \\hline");
- foundVect = new int[ listAlgo.size() ];
- correctVect = new int[ listAlgo.size() ];
- timeVect = new long[ listAlgo.size() ];
- for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect = new int[ size ];
+ correctVect = new int[ size ];
+ timeVect = new long[ size ];
+ for( int k = size-1; k >= 0; k-- ) {
foundVect[k] = 0;
correctVect[k] = 0;
timeVect[k] = 0;
@@ -697,21 +650,7 @@ public class GroupEval {
}
public void usage() {
- System.out.println("usage: GroupEval [options]");
- System.out.println("options are:");
- System.out.println("\t--format=prfot -r prfot\tSpecifies the output order (precision/recall/f-measure/overall/time)");
- // Apparently not implemented
- //System.out.println("\t--sup=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
- System.out.println("\t--output=filename -o filename\tSpecifies a file to which the output will go");
- System.out.println("\t--reference=filename -r filename\tSpecifies the name of the reference alignment file (default: refalign.rdf)");
-
- System.out.println("\t--type=html|xml|tex|ascii|triangle -t html|xml|tex|ascii\tSpecifies the output format");
- System.out.println("\t--list=algo1,...,algon -l algo1,...,algon\tSequence of the filenames to consider");
- System.out.println("\t--color=color -c color\tSpecifies if the output must color even lines of the output");
- System.out.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
- System.out.println("\t--help -h\t\t\tPrint this message");
- System.err.print("\n"+GroupEval.class.getPackage().getImplementationTitle()+" "+GroupEval.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
+ usage( "java "+this.getClass().getName()+" [options]\nEvaluates in parallel several matching results on several tests in subdirectories" );
}
/*
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupOutput.java b/src/fr/inrialpes/exmo/align/cli/GroupOutput.java
index 33342e94..56e84b54 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupOutput.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupOutput.java
@@ -1,9 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003 The University of Manchester
- * Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2012, INRIA
+ * Copyright (C) 2003-2014, INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -25,6 +23,7 @@
/* This program evaluates the results of several ontology aligners
and generates a LaTeX diagram for each of these
*/
+
package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
@@ -49,12 +48,18 @@ import java.util.Vector;
import java.util.Enumeration;
import java.util.Properties;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
-/** A basic class for synthesizing the alignment results of an algorithm with
+/**
+ * A basic class for synthesizing the alignment results of an algorithm with
* regard to the ontology characteristics as a colored module.
*
* These modules are however computed on averaging the precision recall/graphs
@@ -70,12 +75,11 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
* <pre>
* -o filename --output=filename
* -c --color
- * -v --value
+ * -v --values
* -e --labels
* -m --measure
- * -d debug --debug=level
* -l list of compared algorithms
- * -t output --type=output: xml/tex/html/ascii
+ * -t output --type=output: tex/html
* </pre>
*
* The input is taken in the current directory in a set of subdirectories (one per
@@ -123,7 +127,8 @@ But it is less informative than the above presentation.
\end{tikzpicture}
*/
-public class GroupOutput {
+public class GroupOutput extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( GroupOutput.class );
static int SIZE = 16;// Nb of cells = 2^ = 16
static int cellSpec[][] = { {101}, //liph=0
@@ -142,102 +147,78 @@ public class GroupOutput {
{257},//h=13
{254,260,261},//i=14
{262,265,266} };//emptyset=15
- Properties params = null;
- Vector<String> listAlgo;
- String fileNames = "";
- String outFile = null;
+ String[] listAlgo;
String type = "tex";
- String color = null;
+ String color = "blue";
boolean labels = false;
- boolean value = false;
- int debug = 0;
+ boolean values = false;
int measure = 0;
PrintWriter output = null;
-
+ String ontoDir = null;
+ String prefix = null;
+
+ public GroupOutput() {
+ super();
+ options.addOption( "v", "values", false, "Displays the values" );
+ options.addOption( "e", "labels", false, "Displays graph labels" );
+ options.addOption( OptionBuilder.withLongOpt( "color" ).hasOptionalArg().withDescription( "Use COLOR to fill cells (default: "+color+")" ).withArgName("COLOR").create( 'c' ) );
+ options.addOption( OptionBuilder.withLongOpt( "type" ).hasArg().withDescription( "Specifies the output TYPE (html|tex; default: "+type+")" ).withArgName("TYPE").create( 't' ) );
+ options.addOption( OptionBuilder.withLongOpt( "list" ).hasArgs().withValueSeparator(',').withDescription( "Consider this list of FILEs for inclusion in the results" ).withArgName("FILE").create( 'l' ) );
+ options.addOption( OptionBuilder.withLongOpt( "format" ).hasArg().withDescription( "Display MEASure (prof; default: f)" ).withArgName("MEAS").create( 'f' ) );
+ options.addOption( OptionBuilder.withLongOpt( "directory" ).hasOptionalArg().withDescription( "The DIRectory containing the data to match" ).withArgName("DIR").create( 'w' ) );
+ }
public static void main(String[] args) {
try { new GroupOutput().run( args ); }
catch (Exception ex) { ex.printStackTrace(); };
}
public void run(String[] args) throws Exception {
- LongOpt[] longopts = new LongOpt[10];
-
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("color", LongOpt.OPTIONAL_ARGUMENT, null, 'c');
- longopts[3] = new LongOpt("type", LongOpt.REQUIRED_ARGUMENT, null, 't');
- longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[6] = new LongOpt("list", LongOpt.REQUIRED_ARGUMENT, null, 'l');
- longopts[7] = new LongOpt("value", LongOpt.NO_ARGUMENT, null, 'v');
- longopts[8] = new LongOpt("labels", LongOpt.NO_ARGUMENT, null, 'e');
- longopts[9] = new LongOpt("measure", LongOpt.REQUIRED_ARGUMENT, null, 'm');
-
- Getopt g = new Getopt("", args, "hveo:c::d::l:t:m:", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h' :
- usage();
- return;
- case 'v' :
- value = true;
- break;
- case 'e' :
- labels = true;
- break;
- case 'o' :
- /* Write output here */
- outFile = g.getOptarg();
- break;
- case 'c' :
- /* Cell color */
- arg = g.getOptarg();
- if ( arg != null ) {
- color = arg.trim();
- } else color = "blue";
- break;
- case 't' :
- /* Type of output (tex/tsv(/html/xml/ascii)) */
- type = g.getOptarg();
- break;
- case 'l' :
- /* List of filename */
- fileNames = g.getOptarg();
- break;
- case 'm' :
- /* measure to be used */
- String s = g.getOptarg();
+
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return; // --help
+
+ // Here deal with command specific arguments
+ if ( line.hasOption( 'v' ) ) values = true;
+ if ( line.hasOption( 'e' ) ) labels = true;
+ if ( line.hasOption( 'c' ) ) color = line.getOptionValue( 'c', "blue" );
+ if ( line.hasOption( 't' ) ) type = line.getOptionValue( 't' );
+ if ( line.hasOption( 'l' ) ) listAlgo = line.getOptionValues( 'l' );
+ if ( line.hasOption( 'f' ) ) {
+ String s = line.getOptionValue( 'f' );
if ( s.equals("p") ) measure = 1;
else if ( s.equals("r") ) measure = 2;
else if ( s.equals("o") ) measure = 3;
- break;
- case 'd' :
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
}
+ if ( line.hasOption( 'w' ) ) ontoDir = line.getOptionValue( 'w' );
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
+ usage();
+ System.exit(-1);
}
- listAlgo = new Vector<String>();
- for ( String s : fileNames.split(",") ) {
- listAlgo.add( s );
- }
+ parameters.setProperty( "step", Integer.toString(SIZE) );
- params = new Properties();
- if (debug > 0) params.setProperty( "debug", Integer.toString(debug-1) );
-
- params.setProperty( "step", Integer.toString(SIZE) );
+ try {
+ File dir = null;
+ if ( ontoDir == null ) {
+ dir = new File( System.getProperty("user.dir") );
+ } else {
+ dir = new File( ontoDir );
+ }
+ prefix = dir.toURI().toString();
+ } catch ( Exception e ) {
+ logger.error( "Cannot stat dir ", e );
+ usage();
+ System.exit(-1);
+ }
// Set output file
OutputStream stream;
- if (outFile == null) {
+ if ( outputfilename == null) {
stream = System.out;
} else {
- stream = new FileOutputStream(outFile);
+ stream = new FileOutputStream( outputfilename );
}
output = new PrintWriter (
new BufferedWriter(
@@ -268,11 +249,13 @@ public class GroupOutput {
public void iterateAlgorithm(){
// for all alignments there,
for ( String algo : listAlgo ) {
- if ( debug > 0 ) System.err.println("Algorithm: "+algo);
+ //logger.trace("Algorithm: {}", algo);
// type
if ( type.equals("tex") ) {
printPGFTeX( algo, iterateCells( algo ) );
- } else System.err.println("Flag -t "+type+" : not implemented yet");
+ } else {
+ logger.warn( "Flag -t {} : not implemented yet", type );
+ }
}
}
@@ -285,53 +268,46 @@ public class GroupOutput {
}
public double iterateTests( String algo, int[] tests ){
- File dir = (new File(System.getProperty("user.dir")));
double result = 0.0;
int nbtests = 0;
for ( int i=0; i<tests.length; i++ ){//size() or length
- if ( debug > 1 ) System.err.println(" tests: "+tests[i]);
- String prefix = dir.toURI().toString()+"/"+tests[i]+"/";
+ //logger.trace(" tests: {}", tests[i]);
+ String testdir = prefix+"/"+tests[i]+"/";
try {
- PRecEvaluator evaluator = (PRecEvaluator)eval( prefix+"refalign.rdf", prefix+algo+".rdf");
+ PRecEvaluator evaluator = (PRecEvaluator)eval( testdir+"refalign.rdf", testdir+algo+".rdf");
result += getMeasure( evaluator );
nbtests++; // Only the tests that succeed
- } catch ( AlignmentException aex ) { // simple error message
- if ( aex.getCause() != null )
- System.err.println( aex.getCause().getMessage() );
- else System.err.println( aex );
+ } catch ( AlignmentException aex ) {
+ logger.debug( "IGNORED Exception", aex );
}
}
// Unload the ontologies.
try {
OntologyFactory.clear();
- } catch ( OntowrapException owex ) { // only report
- owex.printStackTrace();
+ } catch ( OntowrapException owex ) {
+ logger.debug( "IGNORED Exception", owex );
}
return result/(double)nbtests;
}
public Evaluator eval( String alignName1, String alignName2 ) throws AlignmentException {
Evaluator eval = null;
- int nextdebug;
- if ( debug < 3 ) nextdebug = 0;
- else nextdebug = debug - 3;
// Load alignments
Alignment align1=null, align2=null;
try {
- AlignmentParser aparser = new AlignmentParser( nextdebug );
+ AlignmentParser aparser = new AlignmentParser();
align1 = aparser.parse( alignName1 );
- if ( debug > 2 ) System.err.println(" Alignment structure1 parsed");
+ //logger.trace(" Alignment structure1 parsed");
aparser.initAlignment( null );
align2 = aparser.parse( alignName2 );
- if ( debug > 2 ) System.err.println(" Alignment structure2 parsed");
+ //logger.trace(" Alignment structure2 parsed");
} catch (Exception ex) {
throw new AlignmentException( "Cannot parse ", ex );
}
// Create evaluator object
eval = new PRecEvaluator( align1, align2 );
// Compare
- params.setProperty( "debug", Integer.toString( nextdebug ) );
- eval.eval( params ) ;
+ eval.eval( parameters ) ;
return eval;
}
@@ -350,35 +326,35 @@ public class GroupOutput {
}
output.println("\\draw (0,2.) node[diamond"+colorFormat(cells[11])+"] {}; % l");
- if (value) output.println("\\draw (0,2.) node {"+stringFormat(cells[11])+"}; % l");
+ if (values) output.println("\\draw (0,2.) node {"+stringFormat(cells[11])+"}; % l");
output.println("\\draw (0,1.) node[diamond"+colorFormat(cells[5])+"] {}; % lp");
- if (value) output.println("\\draw (0,1.) node {"+stringFormat(cells[5])+"}; % lp");
+ if (values) output.println("\\draw (0,1.) node {"+stringFormat(cells[5])+"}; % lp");
output.println("\\draw (0.5,1.5) node[diamond"+colorFormat(cells[2])+"] {}; % lip");
- if (value) output.println("\\draw (0.5,1.5) node {"+stringFormat(cells[2])+"}; % lip");
+ if (values) output.println("\\draw (0.5,1.5) node {"+stringFormat(cells[2])+"}; % lip");
output.println("\\draw (1.,2.) node[diamond"+colorFormat(cells[6])+"] {}; %li");
- if (value) output.println("\\draw (1.,2.) node {"+stringFormat(cells[6])+"}; %li");
+ if (values) output.println("\\draw (1.,2.) node {"+stringFormat(cells[6])+"}; %li");
output.println("\\draw (-0.5,-0.5) node[diamond"+colorFormat(cells[9])+"] {}; % ip");
- if (value) output.println("\\draw (-0.5,-0.5) node {"+stringFormat(cells[9])+"}; % ip");
+ if (values) output.println("\\draw (-0.5,-0.5) node {"+stringFormat(cells[9])+"}; % ip");
output.println("\\draw (0,0) node[diamond"+colorFormat(cells[12])+"] {}; %p");
- if (value) output.println("\\draw (0,0) node {"+stringFormat(cells[12])+"}; %p");
+ if (values) output.println("\\draw (0,0) node {"+stringFormat(cells[12])+"}; %p");
output.println("\\draw (.5,.5) node[diamond"+colorFormat(cells[3])+"] {}; % lph");
- if (value) output.println("\\draw (.5,.5) node {"+stringFormat(cells[3])+"}; % lph");
+ if (values) output.println("\\draw (.5,.5) node {"+stringFormat(cells[3])+"}; % lph");
output.println("\\draw (1.,1.) node[diamond"+colorFormat(cells[0])+"] {}; % liph");
- if (value) output.println("\\draw (1.,1.) node {"+stringFormat(cells[0])+"}; % liph");
+ if (values) output.println("\\draw (1.,1.) node {"+stringFormat(cells[0])+"}; % liph");
output.println("\\draw (1.5,1.5) node[diamond"+colorFormat(cells[4])+"] {}; %hil");
- if (value) output.println("\\draw (1.5,1.5) node {"+stringFormat(cells[4])+"}; %hil");
+ if (values) output.println("\\draw (1.5,1.5) node {"+stringFormat(cells[4])+"}; %hil");
output.println("\\draw (2.,2.) node[diamond"+colorFormat(cells[14])+"] {}; %i");
- if (value) output.println("\\draw (2.,2.) node {"+stringFormat(cells[14])+"}; %i");
+ if (values) output.println("\\draw (2.,2.) node {"+stringFormat(cells[14])+"}; %i");
output.println("\\draw (2.,1.) node[diamond"+colorFormat(cells[10])+"] {}; % hi");
- if (value) output.println("\\draw (2.,1.) node {"+stringFormat(cells[10])+"}; % hi");
+ if (values) output.println("\\draw (2.,1.) node {"+stringFormat(cells[10])+"}; % hi");
output.println("\\draw (1.5,0.5) node[diamond"+colorFormat(cells[1])+"] {}; % phi");
- if (value) output.println("\\draw (1.5,0.5) node {"+stringFormat(cells[1])+"}; % phi");
+ if (values) output.println("\\draw (1.5,0.5) node {"+stringFormat(cells[1])+"}; % phi");
output.println("\\draw (1.,0) node[diamond"+colorFormat(cells[8])+"] {}; % ph");
- if (value) output.println("\\draw (1.,0) node {"+stringFormat(cells[8])+"}; % ph");
+ if (values) output.println("\\draw (1.,0) node {"+stringFormat(cells[8])+"}; % ph");
output.println("\\draw (2.,0) node[diamond"+colorFormat(cells[13])+"] {}; % h");
- if (value) output.println("\\draw (2.,0) node {"+stringFormat(cells[13])+"}; % h");
+ if (values) output.println("\\draw (2.,0) node {"+stringFormat(cells[13])+"}; % h");
output.println("\\draw (2.5,-0.5) node[diamond"+colorFormat(cells[7])+"] {}; % hl");
- if (value) output.println("\\draw (2.5,-0.5) node {"+stringFormat(cells[7])+"}; % hl");
+ if (values) output.println("\\draw (2.5,-0.5) node {"+stringFormat(cells[7])+"}; % hl");
output.println("\\end{scope}");
@@ -422,14 +398,6 @@ public class GroupOutput {
}
public void usage() {
- System.out.println("usage: GenPlot [options]");
- System.out.println("options are:");
- System.out.println("\t--values -v\tSpecifies if the values should be displayed");
- System.out.println("\t--label -e\tSpecifies if the labels should be displayed");
- System.out.println("\t--measure=[prf] -c [prf]\tThe measure to display [F-measure]");
- System.out.println("\t--color=color -c color\tSpecifies the color to use [blue]");
- System.out.println("\t--list=algo1,...,algon -l algo1,...,algon\tSequence of the filenames to consider");
- System.out.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
- System.out.println("\t--help -h\t\t\tPrint this message");
+ usage( "java "+this.getClass().getName()+" [options]\nDisplays matcher results in a topological display" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java b/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
index ff336caa..33247689 100644
--- a/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
+++ b/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
@@ -18,14 +18,12 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-/*
-*/
package fr.inrialpes.exmo.align.cli;
-//Imported JAVA classes
import java.lang.Integer;
import java.lang.Double;
import java.util.Hashtable;
+import java.util.List;
import java.util.Properties;
import java.io.File;
@@ -37,8 +35,13 @@ import java.io.OutputStreamWriter;
import org.xml.sax.SAXException;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
@@ -64,7 +67,6 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
--inverse -i Inverse first and second ontology
--threshold=threshold -t threshold Trim the alugnment with regard to threshold
--cutmethod=hard|perc|prop|best|span -T hard|perc|prop|best|span Method to use for triming
- --debug[=n] -d [n] Report debug info at level n,
--output=filename -o filename Output the alignment in filename
--help -h Print this message
</pre>
@@ -79,7 +81,19 @@ $Id$
*/
-public class ParserPrinter {
+public class ParserPrinter extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( ParserPrinter.class );
+
+ public ParserPrinter() {
+ super();
+ options.addOption( "i", "inverse", false, "Inverse first and second ontology" );
+ options.addOption( "e", "embedded", false, "Read the alignment as embedded in a XML file" );
+ options.addOption( OptionBuilder.withLongOpt( "renderer" ).hasArg().withDescription( "Use the given CLASS for rendering" ).withArgName("CLASS").create( 'r' ) );
+ options.addOption( OptionBuilder.withLongOpt( "parser" ).hasArg().withDescription( "Use the given CLASS for parsing" ).withArgName("CLASS").create( 'p' ) );
+ options.addOption( OptionBuilder.withLongOpt( "threshold" ).hasArg().withDescription( "Trim the alignment with regard to threshold" ).withArgName("DOUBLE").create( 't' ) );
+ options.addOption( OptionBuilder.withLongOpt( "cutmethod" ).hasArg().withDescription( "Method to use for triming (hard|perc|prop|best|span)" ).withArgName("METHOD").create( 'T' ) );
+ options.addOption( OptionBuilder.withLongOpt( "outputDir" ).hasArg().withDescription( "Split the output in a DIRectory (SPARQL)" ).withArgName("DIR").create( 'w' ) );
+ }
public static void main(String[] args) {
try { new ParserPrinter().run( args ); }
@@ -89,118 +103,57 @@ public class ParserPrinter {
public void run(String[] args) throws Exception {
Alignment result = null;
String initName = null;
- String filename = null;
String dirName = null;
PrintWriter writer = null;
AlignmentVisitor renderer = null;
- LongOpt[] longopts = new LongOpt[11];
- int debug = 0;
String rendererClass = null;
String parserClass = null;
boolean inverse = false;
boolean embedded = false;
double threshold = 0;
String cutMethod = "hard";
- Properties params = new Properties();
-
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[3] = new LongOpt("renderer", LongOpt.REQUIRED_ARGUMENT, null, 'r');
- longopts[4] = new LongOpt("parser", LongOpt.REQUIRED_ARGUMENT, null, 'p');
- longopts[5] = new LongOpt("inverse", LongOpt.NO_ARGUMENT, null, 'i');
- longopts[6] = new LongOpt("threshold", LongOpt.REQUIRED_ARGUMENT, null, 't');
- longopts[7] = new LongOpt("cutmethod", LongOpt.REQUIRED_ARGUMENT, null, 'T');
- longopts[8] = new LongOpt("embedded", LongOpt.NO_ARGUMENT, null, 'e');
- longopts[9] = new LongOpt("dirName", LongOpt.REQUIRED_ARGUMENT, null, 'c');
- // Is there a way for that in LongOpt ???
- longopts[10] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
-
- Getopt g = new Getopt("", args, "ehio:t:T:d::r:p:c:D:", longopts);
- int c;
- String arg;
- while ((c = g.getopt()) != -1) {
- switch(c) {
- case 'h':
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return; // --help
+
+ // Here deal with command specific arguments
+ if ( line.hasOption( 'i' ) ) inverse = true;
+ if ( line.hasOption( 'e' ) ) embedded = true;
+ if ( line.hasOption( 'c' ) ) dirName = line.getOptionValue( 'c' );
+ if ( line.hasOption( 'r' ) ) rendererClass = line.getOptionValue( 'r' );
+ if ( line.hasOption( 'p' ) ) parserClass = line.getOptionValue( 'p' );
+ if ( line.hasOption( 't' ) ) threshold = Double.parseDouble(line.getOptionValue( 't' ));
+ if ( line.hasOption( 'T' ) ) cutMethod = line.getOptionValue( 'T' );
+ String[] argList = line.getArgs();
+ if ( argList.length > 0 ) {
+ initName = argList[0];
+ } else {
+ logger.error("Require the alignement filename");
usage();
- return;
- case 'i':
- inverse = true;
- break;
- case 'e':
- embedded = true;
- break;
- case 'o':
- /* Write warnings to stdout rather than stderr */
- filename = g.getOptarg();
- break;
- case 'c':
- dirName = g.getOptarg();
- break;
- case 'r':
- /* Use the given class for rendernig */
- rendererClass = g.getOptarg();
- break;
- case 'p':
- /* Use the given class for rendernig */
- parserClass = g.getOptarg();
- break;
- case 't' :
- /* Threshold */
- threshold = Double.parseDouble(g.getOptarg());
- break;
- case 'T' :
- /* Cut method */
- cutMethod = g.getOptarg();
- break;
- case 'd':
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
- case 'D' :
- /* Parameter definition */
- arg = g.getOptarg();
- int index = arg.indexOf('=');
- if ( index != -1 ) {
- params.setProperty( arg.substring( 0, index),
- arg.substring(index+1));
- } else {
- System.err.println("Bad parameter syntax: "+g);
- usage();
- System.exit(0);
- }
- break;
+ System.exit(-1);
}
- }
-
- int i = g.getOptind();
-
- if (args.length > i ) {
- initName = args[i];
- } else {
- System.out.println("Require the alignement filename");
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
usage();
- return;
+ System.exit(-1);
}
- if ( debug > 1 ) System.err.println(" Filename"+initName);
+ //logger.trace("Filename: {}", initName);
try {
// Create parser
AlignmentParser aparser = null;
- if ( parserClass == null ) aparser = new AlignmentParser( debug );
+ if ( parserClass == null ) aparser = new AlignmentParser();
else {
try {
- Object[] mparams = { (Object)debug };
- java.lang.reflect.Constructor[] parserConstructors =
- Class.forName(parserClass).getConstructors();
- aparser = (AlignmentParser) parserConstructors[0].newInstance(mparams);
+ Class[] cparams = {};
+ java.lang.reflect.Constructor parserConstructor =
+ Class.forName(parserClass).getConstructor(cparams);
+ Object[] mparams = {};
+ aparser = (AlignmentParser) parserConstructor.newInstance(mparams);
} catch (Exception ex) {
- System.err.println("Cannot create parser " +
- parserClass + "\n" + ex.getMessage() );
+ logger.error("Cannot create parser {}", parserClass );
usage();
return;
}
@@ -208,22 +161,21 @@ public class ParserPrinter {
aparser.setEmbedded( embedded );
result = aparser.parse( initName );
- if ( debug > 0 ) System.err.println(" Alignment structure parsed");
+ logger.debug(" Alignment structure parsed");
// Set output file
OutputStream stream;
- if (filename == null) {
+ if ( outputfilename == null ) {
//writer = (PrintStream) System.out;
stream = System.out;
- }
- else {
- //writer = new PrintStream(new FileOutputStream(filename));
- stream = new FileOutputStream(filename);
+ } else {
+ //writer = new PrintStream(new FileOutputStream(outputfilename));
+ stream = new FileOutputStream( outputfilename );
}
if ( dirName != null ) {
File f = new File(dirName);
f.mkdir();
- params.setProperty( "dir", dirName );
- params.setProperty( "split", "true" );
+ parameters.setProperty( "dir", dirName );
+ parameters.setProperty( "split", "true" );
}
writer = new PrintWriter (
new BufferedWriter(
@@ -239,19 +191,19 @@ public class ParserPrinter {
else {
try {
Object[] mparams = {(Object) writer };
+ // JE: Not terrible: use the right constructor
java.lang.reflect.Constructor[] rendererConstructors =
Class.forName(rendererClass).getConstructors();
renderer =
(AlignmentVisitor) rendererConstructors[0].newInstance(mparams);
} catch (Exception ex) {
- System.err.println("Cannot create renderer " +
- rendererClass + "\n" + ex.getMessage() );
+ logger.error( "Cannot create renderer {}", rendererClass );
usage();
return;
}
}
- renderer.init( params );
+ renderer.init( parameters );
// Render the alignment
try {
@@ -264,27 +216,11 @@ public class ParserPrinter {
}
} catch (Exception ex) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
}
}
public void usage() {
- System.out.println("usage: ParserPrinter [options] URI");
- System.out.println("options are:");
- //System.out.println("\t--alignment=filename -a filename Start from an XML alignment file");
- System.out.println("\t--debug[=n] -d [n]\t\tReport debug info at level ,");
- System.out.println("\t--renderer=className -r\t\tUse the given class for output.");
- System.out.println("\t--parser=className -p\t\tUse the given class for input.");
- System.out.println("\t--embedded -e\t\tRead the alignment as embedded in XML file");
- System.out.println("\t--inverse -i\t\tInverse first and second ontology");
- System.out.println("\t--threshold=threshold -t threshold\t\tTrim the alugnment with regard to threshold");
- System.out.println("\t--cutmethod=hard|perc|prop|best|span -T hard|perc|prop|best|span\t\tMethod to use for triming");
- System.out.println("\t--output=filename -o filename\tOutput the alignment in filename");
- System.out.println("\t--outputDir=dirName -c dirName\tSplit the output in a directory (SPARQL)");
- System.out.println("\t--help -h\t\t\tPrint this message");
- System.err.println("\t-Dparam=value\t\t\tSet parameter");
- System.err.print("\n"+ParserPrinter.class.getPackage().getImplementationTitle()+" "+ParserPrinter.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
-
+ usage( "java "+this.getClass().getName()+" [options] alignfile\nParse the given <alignfile> and prints it" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/Procalign.java b/src/fr/inrialpes/exmo/align/cli/Procalign.java
index 7a3103d1..7bac26a6 100644
--- a/src/fr/inrialpes/exmo/align/cli/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/cli/Procalign.java
@@ -1,8 +1,6 @@
/*
* $Id$
*
- * Copyright (C) 2003 The University of Manchester
- * Copyright (C) 2003 The University of Karlsruhe
* Copyright (C) 2003-2008, 2010-2013 INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
@@ -22,9 +20,6 @@
* USA.
*/
-/* This program is an adaptation of the Processor.java class of the
- initial release of the OWL-API
-*/
package fr.inrialpes.exmo.align.cli;
import org.semanticweb.owl.align.Alignment;
@@ -36,21 +31,27 @@ import fr.inrialpes.exmo.align.impl.Namespace;
import java.io.OutputStream;
import java.io.FileOutputStream;
-import java.io.FileInputStream;
import java.io.PrintWriter;
import java.io.BufferedWriter;
import java.io.OutputStreamWriter;
import java.net.URI;
+import java.net.URISyntaxException;
import java.util.Hashtable;
import java.util.Properties;
import java.lang.Double;
import java.lang.Integer;
import java.lang.Long;
+import java.lang.reflect.Constructor;
import org.xml.sax.SAXException;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
@@ -71,7 +72,6 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
<pre>
--alignment=filename -a filename Start from an XML alignment file
--params=filename -p filename Read the parameters in file
- --debug[=n] -d [n] Report debug info at level n,
--output=filename -o filename Output the alignment in filename
--impl=className -i classname Use the given alignment implementation.
--renderer=className -r className Specifies the alignment renderer
@@ -86,15 +86,27 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
$Id$
</pre>
-@author Sean K. Bechhofer
@author J�r�me Euzenat
- */
+*/
-public class Procalign {
+public class Procalign extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( Procalign.class );
- public static void main(String[] args) {
+ public Procalign() {
+ super();
+ options.addOption( OptionBuilder.withLongOpt( "renderer" ).hasArg().withDescription( "Use the given CLASS for output" ).withArgName("CLASS").create( 'r' ) );
+ options.addOption( OptionBuilder.withLongOpt( "impl" ).hasArg().withDescription( "Use the given CLASS for matcher" ).withArgName("CLASS").create( 'i' ) );
+ options.addOption( OptionBuilder.withLongOpt( "alignment" ).hasArg().withDescription( "Use initial alignment FILE" ).withArgName("FILE").create( 'a' ) );
+ options.addOption( OptionBuilder.withLongOpt( "threshold" ).hasArg().withDescription( "Trim the alignment with regard to threshold" ).withArgName("DOUBLE").create( 't' ) );
+ options.addOption( OptionBuilder.withLongOpt( "cutmethod" ).hasArg().withDescription( "Method to use for triming (hard|perc|prop|best|span)" ).withArgName("METHOD").create( 'T' ) );
+ }
+
+ public static void main( String[] args ) {
try { new Procalign().run( args ); }
- catch ( Exception ex ) { ex.printStackTrace(); };
+ catch ( Exception ex ) {
+ ex.printStackTrace();
+ System.exit(-1);
+ };
}
public Alignment run(String[] args) throws Exception {
@@ -105,152 +117,84 @@ public class Procalign {
String initName = null;
Alignment init = null;
String alignmentClassName = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
- String filename = null;
- String paramfile = null;
String rendererClass = "fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor";
PrintWriter writer = null;
AlignmentVisitor renderer = null;
- int debug = 0;
double threshold = 0;
- Properties params = new Properties();
-
- LongOpt[] longopts = new LongOpt[10];
-
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("alignment", LongOpt.REQUIRED_ARGUMENT, null, 'a');
- longopts[3] = new LongOpt("renderer", LongOpt.REQUIRED_ARGUMENT, null, 'r');
- longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[5] = new LongOpt("impl", LongOpt.REQUIRED_ARGUMENT, null, 'i');
- longopts[6] = new LongOpt("threshold", LongOpt.REQUIRED_ARGUMENT, null, 't');
- longopts[7] = new LongOpt("cutmethod", LongOpt.REQUIRED_ARGUMENT, null, 'T');
- longopts[8] = new LongOpt("params", LongOpt.REQUIRED_ARGUMENT, null, 'p');
- // Is there a way for that in LongOpt ???
- longopts[9] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
-
- Getopt g = new Getopt("", args, "ho:a:p:d::r:t:T:i:D:", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h' :
+ CommandLine line = null;
+
+ try {
+ line = parseCommandLine( args );
+ } catch( ParseException exp ) {
+ logger.error( "Cannot parse command line", exp );
+ usage();
+ exit( -1 );
+ }
+ if ( line == null ) exit(1); // --help
+ if ( line.hasOption( 'r' ) ) rendererClass = line.getOptionValue( 'r' );
+ if ( line.hasOption( 'i' ) ) alignmentClassName = line.getOptionValue( 'i' );
+ if ( line.hasOption( 'a' ) ) initName = line.getOptionValue( 'a' );
+ if ( line.hasOption( 't' ) ) threshold = Double.parseDouble(line.getOptionValue( 't' ));
+ if ( line.hasOption( 'T' ) ) cutMethod = line.getOptionValue( 'T' );
+ String[] argList = line.getArgs();
+ if ( argList.length > 1 ) {
+ try {
+ onto1 = new URI( argList[0] );
+ onto2 = new URI( argList[1] );
+ } catch( URISyntaxException usex ) {
+ logger.error( "Error in ontology URIs", usex );
usage();
- return null;
- case 'o' :
- /* Use filename instead of stdout */
- filename = g.getOptarg();
- break;
- case 'p' :
- /* Read parameters from filename */
- paramfile = g.getOptarg();
- params.loadFromXML( new FileInputStream( paramfile ) );
- break;
- case 'r' :
- /* Use the given class for rendering */
- rendererClass = g.getOptarg();
- break;
- case 'i' :
- /* Use the given class for the alignment */
- alignmentClassName = g.getOptarg();
- break;
- case 'a' :
- /* Use the given file as a partial alignment */
- initName = g.getOptarg();
- break;
- case 't' :
- /* Threshold */
- threshold = Double.parseDouble(g.getOptarg());
- break;
- case 'T' :
- /* Cut method */
- cutMethod = g.getOptarg();
- break;
- case 'd' :
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
- case 'D' :
- /* Parameter definition */
- arg = g.getOptarg();
- int index = arg.indexOf('=');
- if ( index != -1 ) {
- params.setProperty( arg.substring( 0, index),
- arg.substring(index+1));
- } else {
- System.err.println("Bad parameter syntax: "+g);
- usage();
- System.exit(0);
- }
- break;
+ exit( -1 );
}
+ } else {
+ logger.error( "Require the ontology URIs" );
+ usage();
+ exit(-1);
}
-
- int i = g.getOptind();
- if (debug > 0) {
- params.setProperty( "debug", Integer.toString(debug) );
- } else if ( params.getProperty("debug") != null ) {
- debug = Integer.parseInt( params.getProperty("debug") );
- }
+ logger.debug( "Ready to match {} and {}", onto1, onto2 );
try {
- URI uri1 = null;
- URI uri2 = null;
-
- if (args.length > i + 1) {
- uri1 = new URI(args[i++]);
- uri2 = new URI(args[i]);
- } else if (initName == null) {
- System.err.println("Two URIs required");
- usage();
- System.exit(0);
+ if (initName != null) {
+ AlignmentParser aparser = new AlignmentParser();
+ Alignment al = aparser.parse( initName );
+ init = al;
+ logger.debug("Init parsed");
}
- if (debug > 0) System.err.println(" Ready");
+ // Create alignment object
+ Class<?> alignmentClass = Class.forName( alignmentClassName );
+ Class[] cparams = {};
+ Constructor alignmentConstructor = alignmentClass.getConstructor(cparams);
+ Object[] mparams = {};
+ result = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
+ result.init( onto1, onto2 );
+ } catch ( Exception ex ) {
+ logger.error( "Cannot create alignment {}", alignmentClassName );
+ usage();
+ throw ex;
+ }
- try {
- if (initName != null) {
- AlignmentParser aparser = new AlignmentParser(debug);
- Alignment al = aparser.parse( initName );
- init = al;
- if (debug > 0) System.err.println(" Init parsed");
- }
+ logger.debug("Alignment structure created");
- // Create alignment object
- Object[] mparams = {};
- Class<?> alignmentClass = Class.forName(alignmentClassName);
- Class[] cparams = {};
- java.lang.reflect.Constructor alignmentConstructor = alignmentClass.getConstructor(cparams);
- result = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
- result.init( uri1, uri2 );
- } catch (Exception ex) {
- System.err.println("Cannot create alignment "+alignmentClassName+"\n"
- +ex.getMessage());
- usage();
- throw ex;
- }
-
- if (debug > 0) System.err.println(" Alignment structure created");
+ try {
// Compute alignment
long time = System.currentTimeMillis();
- result.align( init, params ); // add opts
+ result.align( init, parameters ); // add opts
long newTime = System.currentTimeMillis();
result.setExtension( Namespace.ALIGNMENT.uri, Annotations.TIME, Long.toString(newTime - time) );
// Thresholding
if (threshold != 0) result.cut( cutMethod, threshold );
- if (debug > 0) System.err.println(" Matching performed");
+ logger.debug( "Matching performed" );
// Set output file
OutputStream stream;
- if (filename == null) {
+ if ( outputfilename == null ) {
stream = System.out;
} else {
- stream = new FileOutputStream(filename);
+ stream = new FileOutputStream( outputfilename );
}
writer = new PrintWriter (
new BufferedWriter(
@@ -261,18 +205,19 @@ public class Procalign {
Object[] mparams = {(Object) writer };
java.lang.reflect.Constructor[] rendererConstructors =
Class.forName(rendererClass).getConstructors();
+ // JE: Not terrible: use the right constructor
renderer =
(AlignmentVisitor) rendererConstructors[0].newInstance(mparams);
} catch (Exception ex) {
- System.err.println("Cannot create renderer "+rendererClass+"\n"
- + ex.getMessage());
+ logger.error( "Cannot create renderer {}", rendererClass );
usage();
throw ex;
}
// Output
result.render(renderer);
- } catch (Exception ex) {
+ logger.debug( "Output printed" );
+ } catch ( Exception ex ) {
throw ex;
} finally {
if ( writer != null ) {
@@ -284,18 +229,6 @@ public class Procalign {
}
public void usage() {
- System.err.println(Procalign.class.getPackage().getImplementationTitle()+" "+Procalign.class.getPackage().getImplementationVersion());
- System.err.println("\nusage: Procalign [options] URI1 URI2");
- System.err.println("options are:");
- System.err.println("\t--impl=className -i classname\t\tUse the given alignment implementation.");
- System.err.println("\t--renderer=className -r className\tSpecifies the alignment renderer");
- System.err.println("\t--output=filename -o filename\tOutput the alignment in filename");
- System.err.println("\t--params=filename -p filename\tReads parameters from filename");
- System.err.println("\t--alignment=filename -a filename Start from an XML alignment file");
- System.err.println("\t--threshold=double -t double\tFilters the similarities under threshold");
- System.err.println("\t--cutmethod=hard|perc|prop|best|span -T hard|perc|prop|best|span\tmethod for computing the threshold");
- System.err.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
- System.err.println("\t-Dparam=value\t\t\tSet parameter");
- System.err.println("\t--help -h\t\t\tPrint this message");
+ usage( "java "+this.getClass().getName()+" [options] ontoURI ontoURI\nMatches the two ontologies identified by <ontoURI>" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/TestGen.java b/src/fr/inrialpes/exmo/align/cli/TestGen.java
index 33be1e29..b5077d29 100644
--- a/src/fr/inrialpes/exmo/align/cli/TestGen.java
+++ b/src/fr/inrialpes/exmo/align/cli/TestGen.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -21,11 +21,17 @@
package fr.inrialpes.exmo.align.cli;
-import gnu.getopt.Getopt;
-import gnu.getopt.LongOpt;
-
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
+
import fr.inrialpes.exmo.align.gen.TestGenerator;
import fr.inrialpes.exmo.align.gen.BenchmarkGenerator;
import fr.inrialpes.exmo.align.gen.TestSet;
@@ -40,23 +46,29 @@ import fr.inrialpes.exmo.align.gen.ParametersIds;
</pre>
where filename is the seed ontology,
- and the options are:
- <pre>
- --debug[=n] -d [n] --> Report debug info at level n,
- </pre>
*/
-public class TestGen {
- private Properties params = null;
- private String methodName = null; //the name of the method
- private String fileName = null; //the name of the input file
- private String dir = "."; //
- private String url; //
- private int debug = 0;
+public class TestGen extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( TestGen.class );
+
+ private String methodName = null; //the name of the method
+ private String fileName = "onto.rdf"; //the name of the input file
+ private String dir = "."; //
+ private String url; //
public TestGen() {
- fileName = "onto.rdf";
+ super();
+ options.addOption( OptionBuilder.withLongOpt( "testset" ).hasArg().withDescription( "Use CLASS for generating the test set" ).withArgName("CLASS").create( 't' ) );
+ options.addOption( OptionBuilder.withLongOpt( "outdir" ).hasArg().withDescription( "Output DIRectory (default: current)" ).withArgName("DIR").create( 'w' ) );
+ options.addOption( OptionBuilder.withLongOpt( "uriprefix" ).hasArg().withDescription( "URI prefix of the seed ontology (REQUIRED)" ).withArgName("URI").create( 'u' ) );
+ options.addOption( OptionBuilder.withLongOpt( "alignname" ).hasArg().withDescription( "FILEname of generated alignment (default: refalign.rdf)" ).withArgName("FILE").create( 'a' ) );
+ // .setRequired( true )
+ Option opt = options.getOption( "uriprefix" );
+ if ( opt != null ) opt.setRequired( true );
+ // We redefine the message for -o
+ opt = options.getOption( "output" );
+ if ( opt != null ) opt.setDescription( "FILEname of the generated ontology (default: "+fileName+")" );
}
public static void main(String[] args) {
@@ -65,83 +77,49 @@ public class TestGen {
}
public void run(String[] args) throws Exception {
- LongOpt[] longopts = new LongOpt[10];
- params = new Properties();
-
- longopts[0] = new LongOpt("testset", LongOpt.REQUIRED_ARGUMENT, null, 't');
- longopts[1] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[2] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[3] = new LongOpt("outdir", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[4] = new LongOpt("urlprefix", LongOpt.REQUIRED_ARGUMENT, null, 'u');
- longopts[5] = new LongOpt("ontoname", LongOpt.REQUIRED_ARGUMENT, null, 'n');
- longopts[6] = new LongOpt("alignname", LongOpt.REQUIRED_ARGUMENT, null, 'a');
- longopts[7] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
-
- Getopt g = new Getopt("", args, "d::o:u:m:n:a:D:t:h", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h':
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return; // --help
+
+ outputfilename = fileName; // likely useless
+
+ // Here deal with command specific arguments
+ if ( line.hasOption( 't' ) ) methodName = line.getOptionValue( 't' );
+ if ( line.hasOption( 'o' ) ) parameters.setProperty( "ontoname", line.getOptionValue( 'o' ) );
+ if ( line.hasOption( 'a' ) ) parameters.setProperty( "alignname", line.getOptionValue( 'a' ) );
+ if ( line.hasOption( 'w' ) ) {
+ dir = line.getOptionValue( 'w' );
+ parameters.setProperty( "outdir", dir );
+ }
+ if ( line.hasOption( 'u' ) ) {
+ url = line.getOptionValue( 'u' );
+ parameters.setProperty( "urlprefix", url ); // JE: Danger urlprefix/uriprefix
+ }
+ String[] argList = line.getArgs();
+ if ( argList.length > 0 ) {
+ fileName = argList[0];
+ parameters.setProperty( "filename", fileName );
+ } else {
+ logger.error("Require the seed ontology filename");
usage();
- return;
- case 't':
- methodName = g.getOptarg();
- break;
- case 'n':
- params.setProperty( "ontoname", g.getOptarg() );
- break;
- case 'a':
- params.setProperty( "alignname", g.getOptarg() );
- break;
- case 'o' : /* Use output directory */
- dir = g.getOptarg();
- params.setProperty( "outdir", dir );
- break;
- case 'u' : /* URLPrefix */
- url = g.getOptarg();
- params.setProperty( "urlprefix", url );
- break;
- case 'd' : /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) params.setProperty( "debug", arg.trim() );
- else params.setProperty( "debug", "4" );
- break;
- case 'D' : /* Parameter definition: could be used for all parameters */
- arg = g.getOptarg();
- int index = arg.indexOf('=');
- if ( index != -1 ) {
- params.setProperty( arg.substring( 0, index),
- arg.substring(index+1));
- } else {
- System.err.println("Bad parameter syntax: "+g);
- usage();
- System.exit(0);
- }
- break;
+ System.exit(-1);
}
- }
-
- // We need an ontology
- int i = g.getOptind();
-
- if ( args.length > i ) {
- fileName = args[i];
- params.setProperty( "filename", fileName );
- } else {
- System.out.println("Require the seed ontology filename");
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
usage();
- return;
+ System.exit(-1);
}
- if ( debug > 0 ) System.err.println( " >>>> "+methodName+" from "+fileName );
+ logger.debug( " >>>> {} from {}", methodName, fileName );
if ( methodName == null ) { // generate one test
TestGenerator tg = new TestGenerator();
+ // It would certainly be better to initialise the generator with parameters
tg.setDirPrefix( dir );
tg.setURLPrefix( url );
- tg.modifyOntology( fileName, (Properties)null, (String)null, params );
+ if ( parameters.getProperty( "ontoname" ) != null ) tg.setOntoFilename( parameters.getProperty( "ontoname" ) );
+ if ( parameters.getProperty( "alignname" ) != null ) tg.setAlignFilename( parameters.getProperty( "alignname" ) );
+ tg.modifyOntology( fileName, (Properties)null, (String)null, parameters );
} else { // generate a test set
TestSet tset = null;
try {
@@ -151,38 +129,30 @@ public class TestGen {
java.lang.reflect.Constructor testSetConstructor = testSetClass.getConstructor(cparams);
tset = (TestSet)testSetConstructor.newInstance(mparams);
} catch (Exception ex) {
- System.err.println("Cannot create TestSet "+methodName+"\n"+ex.getMessage());
+ logger.error("Cannot create TestSet {}", methodName );
+ logger.error("Caught error", ex );
usage();
- throw ex;
+ System.exit(-1);
}
- tset.generate( params );
+ tset.generate( parameters );
}
}
public void usage() {
- System.out.println("TestGen [options] filename");
- System.out.println("such that filename is the filename of the seed ontology\n");
- System.out.println("options are:");
- System.out.println("\t--urlprefix=url");
- System.out.println("\t--testset=classname, where classname is the name of an implementation of TestSet");
- System.out.println("\t--alignname=filename [default: refalign.rdf]");
- System.out.println("\t--ontoname=filename [default: onto.rdf]");
- System.out.println("\t--outdir=directory [default: .]");
- System.out.println("\t--help");
- System.out.println("\t--debug=number [default: 0]");
- System.out.println("\t-Dparameter=value");
- System.out.println("where the parameters are");
- System.out.println( "\tRemove percentage subclasses \""+ParametersIds.REMOVE_CLASSES+"\"" );
- System.out.println( "\tRemove percentage properties \""+ParametersIds.REMOVE_PROPERTIES+"\"" );
- System.out.println( "\tRemove percentage comments \""+ParametersIds.REMOVE_COMMENTS+"\"" );
- System.out.println( "\tRemove percentage restrictions \""+ParametersIds.REMOVE_RESTRICTIONS+"\"" );
- System.out.println( "\tRemove individuals \""+ParametersIds.REMOVE_INDIVIDUALS+"\"" );
- System.out.println( "\tAdd percentage subclasses \""+ParametersIds.ADD_CLASSES+"\"" );
- System.out.println( "\tAdd percentage properties \""+ParametersIds.ADD_PROPERTIES+"\"" );
- System.out.println( "\tRename percentage classes \""+ParametersIds.RENAME_CLASSES+"\"" );
- System.out.println( "\tRename percentage properties \""+ParametersIds.RENAME_PROPERTIES+"\"" );
- System.out.println( "\tnoHierarchy \""+ParametersIds.NO_HIERARCHY+"\"" );
- System.out.println( "\tLevel flattened \""+ParametersIds.LEVEL_FLATTENED+"\"" );
- System.out.println( "\tAdd nbClasses to a specific level \""+ParametersIds.ADD_CLASSESLEVEL+"\"" );
+ usage( "java "+this.getClass().getName()+" [options] -u uriprefix filename\nGenerate ontology matching tests from the seed ontology file",
+ "Such that parameters may be:"+
+ "\tRemove percentage subclasses \""+ParametersIds.REMOVE_CLASSES+"\""+
+ "\tRemove percentage properties \""+ParametersIds.REMOVE_PROPERTIES+"\""+
+ "\tRemove percentage comments \""+ParametersIds.REMOVE_COMMENTS+"\""+
+ "\tRemove percentage restrictions \""+ParametersIds.REMOVE_RESTRICTIONS+"\""+
+ "\tRemove individuals \""+ParametersIds.REMOVE_INDIVIDUALS+"\""+
+ "\tAdd percentage subclasses \""+ParametersIds.ADD_CLASSES+"\""+
+ "\tAdd percentage properties \""+ParametersIds.ADD_PROPERTIES+"\""+
+ "\tRename percentage classes \""+ParametersIds.RENAME_CLASSES+"\""+
+ "\tRename percentage properties \""+ParametersIds.RENAME_PROPERTIES+"\""+
+ "\tnoHierarchy \""+ParametersIds.NO_HIERARCHY+"\""+
+ "\tLevel flattened \""+ParametersIds.LEVEL_FLATTENED+"\""+
+ "\tAdd nbClasses to a specific level \""+ParametersIds.ADD_CLASSESLEVEL+"\""
+ );
}
}
diff --git a/src/fr/inrialpes/exmo/align/cli/WGroupEval.java b/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
index efc5656f..4dc2580f 100644
--- a/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
@@ -1,9 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003 The University of Manchester
- * Copyright (C) 2003 The University of Karlsruhe
- * Copyright (C) 2003-2012, INRIA
+ * Copyright (C) 2003-2014, INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -47,8 +45,14 @@ import java.util.Properties;
import org.xml.sax.SAXException;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
@@ -64,7 +68,6 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
<pre>
-o filename --output=filename
-f format = prfot (precision/recall/f-measure/overall/time) --format=prfot
- -d debug --debug=level
-r filename --reference=filename
-s algo/measure
-l list of compared algorithms
@@ -82,108 +85,65 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
$Id$
</pre>
-@author Sean K. Bechhofer
-@author J�r�me Euzenat
- */
+*/
-public class WGroupEval {
+public class WGroupEval extends CommonCLI {
+ final static Logger logger = LoggerFactory.getLogger( WGroupEval.class );
- Properties params = null;
- String filename = null;
String reference = "refalign.rdf";
String format = "pr";
int fsize = 2;
String type = "html";
boolean embedded = false;
String dominant = "s";
- Vector<String> listAlgo = null;
- int debug = 0;
+ String[] listAlgo = null;
+ int size = 0;
String color = null;
String ontoDir = null;
+ public WGroupEval() {
+ super();
+ options.addOption( OptionBuilder.withLongOpt( "list" ).hasArgs().withValueSeparator(',').withDescription( "List of FILEs to be included in the results (required)" ).withArgName("FILE").create( 'l' ) );
+ options.addOption( OptionBuilder.withLongOpt( "color" ).hasOptionalArg().withDescription( "Color even lines of the output in COLOR (default: lightblue)" ).withArgName("COLOR").create( 'c' ) );
+ options.addOption( OptionBuilder.withLongOpt( "format" ).hasArg().withDescription( "Used (weighted) MEASures and order (precision/recall/f-measure/overall/time) (default: "+format+")" ).withArgName("MEAS (prfot)").create( 'f' ) );
+ options.addOption( OptionBuilder.withLongOpt( "type" ).hasArg().withDescription( "Output TYPE (html|xml|tex|ascii|triangle; default: "+type+")" ).withArgName("TYPE").create( 't' ) );
+ //options.addOption( OptionBuilder.withLongOpt( "sup" ).hasArg().withDescription( "Specifies if dominant columns are algorithms or measure" ).withArgName("algo").create( 's' ) );
+ options.addOption( OptionBuilder.withLongOpt( "reference" ).hasArg().withDescription( "Name of the reference alignment FILE (default: "+reference+")" ).withArgName("FILE").create( 'r' ) );
+ options.addOption( OptionBuilder.withLongOpt( "directory" ).hasOptionalArg().withDescription( "The DIRectory containing the data to evaluate" ).withArgName("DIR").create( 'w' ) );
+ // .setRequired( true )
+ Option opt = options.getOption( "list" );
+ if ( opt != null ) opt.setRequired( true );
+ }
+
+
public static void main(String[] args) {
try { new WGroupEval().run( args ); }
catch (Exception ex) { ex.printStackTrace(); };
}
public void run(String[] args) throws Exception {
- String listFile = "";
- LongOpt[] longopts = new LongOpt[10];
-
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("format", LongOpt.REQUIRED_ARGUMENT, null, 'f');
- longopts[3] = new LongOpt("type", LongOpt.REQUIRED_ARGUMENT, null, 't');
- longopts[4] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[5] = new LongOpt("sup", LongOpt.REQUIRED_ARGUMENT, null, 's');
- longopts[6] = new LongOpt("list", LongOpt.REQUIRED_ARGUMENT, null, 'l');
- longopts[7] = new LongOpt("color", LongOpt.OPTIONAL_ARGUMENT, null, 'c');
- longopts[8] = new LongOpt("reference", LongOpt.REQUIRED_ARGUMENT, null, 'r');
- longopts[9] = new LongOpt("directory", LongOpt.REQUIRED_ARGUMENT, null, 'w');
-
- Getopt g = new Getopt("", args, "ho:a:d::l:f:t:r:w:c::", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h' :
- usage();
- return;
- case 'o' :
- /* Write output here */
- filename = g.getOptarg();
- break;
- case 'r' :
- /* File name for the reference alignment */
- reference = g.getOptarg();
- break;
- case 'f' :
- /* Sequence of results to print */
- format = g.getOptarg();
- break;
- case 't' :
- /* Type of output (tex/html/xml/ascii) */
- type = g.getOptarg();
- break;
- case 's' :
- /* Print per type or per algo */
- dominant = g.getOptarg();
- break;
- case 'c' :
- /* Print colored lines */
- arg = g.getOptarg();
- if ( arg != null ) {
- color = arg.trim();
- } else color = "lightblue";
- break;
- case 'l' :
- /* List of filename */
- listFile = g.getOptarg();
- break;
- case 'd' :
- /* Debug level */
- arg = g.getOptarg();
- if ( arg != null ) debug = Integer.parseInt(arg.trim());
- else debug = 4;
- break;
- case 'w' :
- /* Use the given ontology directory */
- arg = g.getOptarg();
- if ( arg != null ) ontoDir = g.getOptarg();
- else ontoDir = null;
- break;
- }
- }
- listAlgo = new Vector<String>();
- for ( String s : listFile.split(",") ) {
- listAlgo.add( s );
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) return; // --help
+
+ // Here deal with command specific arguments
+ if ( line.hasOption( 'f' ) ) format = line.getOptionValue( 'f' );
+ if ( line.hasOption( 'r' ) ) reference = line.getOptionValue( 'r' );
+ if ( line.hasOption( 's' ) ) dominant = line.getOptionValue( 's' );
+ if ( line.hasOption( 't' ) ) type = line.getOptionValue( 't' );
+ if ( line.hasOption( 'c' ) ) color = line.getOptionValue( 'c', "lightblue" );
+ if ( line.hasOption( 'l' ) ) {
+ listAlgo = line.getOptionValues( 'l' );
+ size = listAlgo.length;
+ }
+ if ( line.hasOption( 'w' ) ) ontoDir = line.getOptionValue( 'w' );
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
+ usage();
+ System.exit( -1 );
}
- params = new Properties();
- if (debug > 0) params.setProperty( "debug", Integer.toString( debug-1 ) );
-
print( iterateDirectories() );
}
@@ -197,8 +157,9 @@ public class WGroupEval {
subdir = (new File(ontoDir)).listFiles();
}
} catch (Exception e) {
- System.err.println("Cannot stat dir "+ e.getMessage());
+ logger.error("Cannot stat dir ", e);
usage();
+ System.exit(-1);
}
int size = subdir.length;
Arrays.sort(subdir);
@@ -206,7 +167,7 @@ public class WGroupEval {
int i = 0;
for ( int j=0 ; j < size; j++ ) {
if( subdir[j].isDirectory() ) {
- if ( debug > 0 ) System.err.println("\nEntering directory "+subdir[j]);
+ //logger.trace("Entering directory {}", subdir[j]);
// eval the alignments in a subdirectory
// store the result
Vector vect = iterateAlignments( subdir[j] );
@@ -231,7 +192,7 @@ public class WGroupEval {
// call eval
// store the result in a record
// return the record.
- if ( debug > 2) System.err.println(" Considering result "+i);
+ //logger.trace(" Considering result {}", i);
Evaluator evaluator = eval( prefix+reference, prefix+m+".rdf");
if ( evaluator != null ) ok = true;
result.add( i, evaluator );
@@ -239,8 +200,8 @@ public class WGroupEval {
// Unload the ontologies.
try {
OntologyFactory.clear();
- } catch ( OntowrapException owex ) { // only report
- owex.printStackTrace();
+ } catch ( OntowrapException owex ) {
+ logger.debug( "IGNORED Exception", owex );
}
if ( ok == true ) return result;
@@ -250,57 +211,69 @@ public class WGroupEval {
public Evaluator eval( String alignName1, String alignName2 ) {
Evaluator eval = null;
try {
- int nextdebug;
- if ( debug < 2 ) nextdebug = 0;
- else nextdebug = debug - 2;
// Load alignments
- AlignmentParser aparser = new AlignmentParser( nextdebug );
+ AlignmentParser aparser = new AlignmentParser();
Alignment align1 = aparser.parse( alignName1 );
- if ( debug > 2 ) System.err.println(" Alignment structure1 parsed");
+ //logger.trace(" Alignment structure1 parsed");
aparser.initAlignment( null );
Alignment align2 = aparser.parse( alignName2 );
- if ( debug > 2 ) System.err.println(" Alignment structure2 parsed");
+ //logger.trace(" Alignment structure2 parsed");
// Create evaluator object
eval = new WeightedPREvaluator( align1, align2 );
// Compare
- params.setProperty( "debug", Integer.toString( nextdebug ) );
- eval.eval( params ) ;
+ eval.eval( parameters ) ;
} catch (Exception ex) {
- if ( debug > 1 ) {
- ex.printStackTrace();
- } else {
- System.err.println("WGroupEval: "+ex);
- System.err.println(alignName1+ " - "+alignName2 );
- }
+ logger.debug( "IGNORED Exception", ex );
};
return eval;
}
+ /**
+ * The writer used to print the result
+ */
+ PrintStream writer = null;
+
/**
* This does not only print the results but compute the average as well
*/
public void print( Vector<Vector> result ) {
- if ( type.equals("html") ) printHTML( result );
- else if ( type.equals("tex") ) printLATEX( result );
- else if ( type.equals("triangle") ) printTRIANGLE( result );
+ PrintStream writer = null;
+ try {
+ if ( outputfilename == null ) {
+ writer = System.out;
+ } else {
+ writer = new PrintStream( new FileOutputStream( outputfilename ) );
+ }
+
+ if ( type.equals("html") ) printHTML( result, writer );
+ else if ( type.equals("tex") ) printLATEX( result, writer );
+ else if ( type.equals("triangle") ) printTRIANGLE( result, writer );
+ } catch (Exception ex) {
+ logger.debug( "IGNORED Exception", ex );
+ } finally {
+ writer.close();
+ }
}
- public void printTRIANGLE( Vector<Vector> result ) {
+ public void printTRIANGLE( Vector<Vector> result, PrintStream writer ) {
// variables for computing iterative harmonic means
double expected = 0.; // expected so far
double foundVect[]; // found so far
- double correctVect[]; // correct so far
+ double correctFoundVect[]; // correct so far
+ double correctExpVect[]; // correct so far
long timeVect[]; // time so far
- foundVect = new double[ listAlgo.size() ];
- correctVect = new double[ listAlgo.size() ];
- timeVect = new long[ listAlgo.size() ];
- for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect = new double[ size ];
+ correctFoundVect = new double[ size ];
+ correctExpVect = new double[ size ];
+ timeVect = new long[ size ];
+ for( int k = size-1; k >= 0; k-- ) {
foundVect[k] = 0.;
- correctVect[k] = 0.;
+ correctFoundVect[k] = 0.;
+ correctExpVect[k] = 0.;
timeVect[k] = 0;
}
for ( Vector test : result ) {
- int nexpected = -1;
+ double newexpected = -1.;
Enumeration f = test.elements();
// Too bad the first element must be skipped
f.nextElement();
@@ -308,56 +281,59 @@ public class WGroupEval {
WeightedPREvaluator eval = (WeightedPREvaluator)f.nextElement();
if ( eval != null ){
// iterative H-means computation
- if ( nexpected == -1 ){
- nexpected = 0;
- expected += eval.getExpected();
+ if ( newexpected == -1. ){
+ newexpected = eval.getExpected();
+ expected += newexpected;
}
foundVect[k] += eval.getFound();
- correctVect[k] += eval.getCorrect();
+ correctFoundVect[k] += eval.getCorrectFound();
+ correctExpVect[k] += eval.getCorrectExpected();
timeVect[k] += eval.getTime();
+ } else {
+ correctExpVect[k] += newexpected;
}
}
}
- System.out.println("\\documentclass[11pt]{book}");
- System.out.println();
- System.out.println("\\usepackage{pgf}");
- System.out.println("\\usepackage{tikz}");
- System.out.println();
- System.out.println("\\begin{document}");
- System.out.println("\\date{today}");
- System.out.println("");
- System.out.println("\n%% Plot generated by GenPlot of alignapi");
- System.out.println("\\begin{tikzpicture}[cap=round]");
- System.out.println("% Draw grid");
- System.out.println("\\draw[step=1cm,very thin,color=gray] (-0.2,-0.2) grid (10.0,9.0);");
- System.out.println("\\draw[|-|] (-0,0) -- (10,0);");
- System.out.println("%\\draw[dashed,very thin] (0,0) -- (5,8.66) -- (10,0);");
- System.out.println("\\draw[dashed,very thin] (10,0) arc (0:60:10cm);");
- System.out.println("\\draw[dashed,very thin] (0,0) arc (180:120:10cm);");
-
- System.out.println("\\draw (0,-0.3) node {$recall$}; ");
- System.out.println("\\draw (10,-0.3) node {$precision$}; ");
- //System.out.println("\\draw (0,-0.3) node {0.}; ");
- //System.out.println("\\draw (10,-0.3) node {1.}; ");
- System.out.println("% Plots");
+ writer.println("\\documentclass[11pt]{book}");
+ writer.println();
+ writer.println("\\usepackage{pgf}");
+ writer.println("\\usepackage{tikz}");
+ writer.println();
+ writer.println("\\begin{document}");
+ writer.println("\\date{today}");
+ writer.println("");
+ writer.println("\n%% Plot generated by GenPlot of alignapi");
+ writer.println("\\begin{tikzpicture}[cap=round]");
+ writer.println("% Draw grid");
+ writer.println("\\draw[step=1cm,very thin,color=gray] (-0.2,-0.2) grid (10.0,9.0);");
+ writer.println("\\draw[|-|] (-0,0) -- (10,0);");
+ writer.println("%\\draw[dashed,very thin] (0,0) -- (5,8.66) -- (10,0);");
+ writer.println("\\draw[dashed,very thin] (10,0) arc (0:60:10cm);");
+ writer.println("\\draw[dashed,very thin] (0,0) arc (180:120:10cm);");
+
+ writer.println("\\draw (0,-0.3) node {$recall$}; ");
+ writer.println("\\draw (10,-0.3) node {$precision$}; ");
+ //writer.println("\\draw (0,-0.3) node {0.}; ");
+ //writer.println("\\draw (10,-0.3) node {1.}; ");
+ writer.println("% Plots");
int k = 0;
for ( String m: listAlgo ) {
- double precision = correctVect[k]/foundVect[k];
- double recall = correctVect[k]/expected;
+ double precision = 1. - correctFoundVect[k]/foundVect[k];
+ double recall = 1. - correctExpVect[k]/expected;
double prec2 = precision*precision;
double a = ((prec2-(recall*recall)+1)/2);
double b = java.lang.Math.sqrt( prec2 - (a*a) );
a = a*10; b = b*10; //for printing scale 10.
- System.out.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
- System.out.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+m+"};");
+ writer.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
+ writer.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+m+"};");
k++;
}
- System.out.println("\\end{tikzpicture}");
- System.out.println();
- System.out.println("\\end{document}");
+ writer.println("\\end{tikzpicture}");
+ writer.println();
+ writer.println("\\end{document}");
}
- public void printLATEX( Vector result ) {
+ public void printLATEX( Vector result, PrintStream writer ) {
}
/* A few comments on how and why computing "weighted harmonic means"
@@ -406,182 +382,162 @@ and
which the program does...
*/
- public void printHTML( Vector<Vector> result ) {
+ public void printHTML( Vector<Vector> result, PrintStream writer ) {
// variables for computing iterative harmonic means
int expected = 0; // expected so far
int foundVect[]; // found so far
- int correctVect[]; // correct so far
+ int correctFoundVect[]; // correct so far
+ int correctExpVect[]; // correct so far
long timeVect[]; // time so far
- PrintStream writer = null;
fsize = format.length();
// JE: the writer should be put out
// JE: the h-means computation should be put out as well
- try {
- // Print result
- if ( filename == null ) {
- writer = System.out;
- } else {
- writer = new PrintStream(new FileOutputStream( filename ));
- }
- Formatter formatter = new Formatter(writer);
-
- // Print the header
- if ( embedded != true ) writer.println("<html><head></head><body>");
- writer.println("<table border='2' frame='sides' rules='groups'>");
- writer.println("<colgroup align='center' />");
- // for each algo <td spancol='2'>name</td>
- for ( String m : listAlgo ) {
- writer.println("<colgroup align='center' span='"+fsize+"' />");
- }
- // For each file do a
- writer.println("<thead valign='top'><tr><th>algo</th>");
- // for each algo <td spancol='2'>name</td>
- for ( String m : listAlgo ) {
- writer.println("<th colspan='"+fsize+"'>"+m+"</th>");
- }
- writer.println("</tr></thead><tbody><tr><td>test</td>");
- // for each algo <td>Prec.</td><td>Rec.</td>
- for ( String m : listAlgo ) {
- for ( int i = 0; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- writer.print("Prec.");
- } else if ( format.charAt(i) == 'f' ) {
- writer.print("FMeas.");
- } else if ( format.charAt(i) == 'o' ) {
- writer.print("Over.");
- } else if ( format.charAt(i) == 't' ) {
- writer.print("Time");
- } else if ( format.charAt(i) == 'r' ) {
- writer.print("Rec.");
- }
- writer.println("</td>");
+ Formatter formatter = new Formatter( writer );
+
+ // Print the header
+ if ( embedded != true ) writer.println("<html><head></head><body>");
+ writer.println("<table border='2' frame='sides' rules='groups'>");
+ writer.println("<colgroup align='center' />");
+ // for each algo <td spancol='2'>name</td>
+ for ( String m : listAlgo ) {
+ writer.println("<colgroup align='center' span='"+fsize+"' />");
+ }
+ // For each file do a
+ writer.println("<thead valign='top'><tr><th>algo</th>");
+ // for each algo <td spancol='2'>name</td>
+ for ( String m : listAlgo ) {
+ writer.println("<th colspan='"+fsize+"'>"+m+"</th>");
+ }
+ writer.println("</tr></thead><tbody><tr><td>test</td>");
+ // for each algo <td>Prec.</td><td>Rec.</td>
+ for ( String m : listAlgo ) {
+ for ( int i = 0; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ writer.print("Prec.");
+ } else if ( format.charAt(i) == 'f' ) {
+ writer.print("FMeas.");
+ } else if ( format.charAt(i) == 'o' ) {
+ writer.print("Over.");
+ } else if ( format.charAt(i) == 't' ) {
+ writer.print("Time");
+ } else if ( format.charAt(i) == 'r' ) {
+ writer.print("Rec.");
}
- //writer.println("<td>Prec.</td><td>Rec.</td>");
+ writer.println("</td>");
}
- writer.println("</tr></tbody><tbody>");
- foundVect = new int[ listAlgo.size() ];
- correctVect = new int[ listAlgo.size() ];
- timeVect = new long[ listAlgo.size() ];
- for( int k = listAlgo.size()-1; k >= 0; k-- ) {
- foundVect[k] = 0;
- correctVect[k] = 0;
- timeVect[k] = 0;
- }
- // </tr>
- // For each directory <tr>
- boolean colored = false;
- for ( Vector test : result ) {
- int nexpected = -1;
- if ( colored == true && color != null ){
- colored = false;
- writer.println("<tr bgcolor=\""+color+"\">");
- } else {
- colored = true;
- writer.println("<tr>");
- };
- // Print the directory <td>bla</td>
- writer.println("<td>"+(String)test.get(0)+"</td>");
- // For each record print the values <td>bla</td>
- Enumeration f = test.elements();
- f.nextElement();
- for( int k = 0 ; f.hasMoreElements() ; k++) {
- WeightedPREvaluator eval = (WeightedPREvaluator)f.nextElement();
- if ( eval != null ){
- // iterative H-means computation
- if ( nexpected == -1 ){
- expected += eval.getExpected();
- nexpected = 0;
- }
- foundVect[k] += eval.getFound();
- correctVect[k] += eval.getCorrect();
- timeVect[k] += eval.getTime();
-
- for ( int i = 0 ; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- formatter.format("%1.2f", eval.getPrecision());
- } else if ( format.charAt(i) == 'f' ) {
- formatter.format("%1.2f", eval.getFmeasure());
- } else if ( format.charAt(i) == 'o' ) {
- formatter.format("%1.2f", eval.getOverall());
- } else if ( format.charAt(i) == 't' ) {
- if ( eval.getTime() == 0 ){
- writer.print("-");
- } else {
- formatter.format("%1.2f", eval.getTime());
- }
- } else if ( format.charAt(i) == 'r' ) {
- formatter.format("%1.2f", eval.getRecall());
+ //writer.println("<td>Prec.</td><td>Rec.</td>");
+ }
+ writer.println("</tr></tbody><tbody>");
+ foundVect = new int[ size ];
+ correctFoundVect = new int[ size ];
+ correctExpVect = new int[ size ];
+ timeVect = new long[ size ];
+ for( int k = size-1; k >= 0; k-- ) {
+ foundVect[k] = 0;
+ correctFoundVect[k] = 0;
+ correctExpVect[k] = 0;
+ timeVect[k] = 0;
+ }
+ // </tr>
+ // For each directory <tr>
+ boolean colored = false;
+ for ( Vector test : result ) {
+ double newexpected = -1.;
+ if ( colored == true && color != null ){
+ colored = false;
+ writer.println("<tr bgcolor=\""+color+"\">");
+ } else {
+ colored = true;
+ writer.println("<tr>");
+ };
+ // Print the directory <td>bla</td>
+ writer.println("<td>"+(String)test.get(0)+"</td>");
+ // For each record print the values <td>bla</td>
+ Enumeration f = test.elements();
+ f.nextElement();
+ for( int k = 0 ; f.hasMoreElements() ; k++) {
+ WeightedPREvaluator eval = (WeightedPREvaluator)f.nextElement();
+ if ( eval != null ) {
+ // iterative H-means computation
+ if ( newexpected == -1. ){
+ newexpected = eval.getExpected();
+ expected += newexpected;
+ }
+ foundVect[k] += eval.getFound();
+ correctFoundVect[k] += eval.getCorrectFound();
+ correctExpVect[k] += eval.getCorrectExpected();
+ timeVect[k] += eval.getTime();
+
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", eval.getPrecision());
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", eval.getFmeasure());
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", eval.getOverall());
+ } else if ( format.charAt(i) == 't' ) {
+ if ( eval.getTime() == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", eval.getTime());
}
- writer.println("</td>");
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", eval.getRecall());
}
- } else {
- writer.println("<td>n/a</td><td>n/a</td>");
+ writer.println("</td>");
}
+ } else { // JE 2013: will break if the previous tests are all NULL
+ correctExpVect[k] += newexpected;
+ // Nothing needs to be incremented for precision
+ for ( int i = 0 ; i < fsize; i++) writer.print("<td>n/a</td>");
+ writer.println();
}
- writer.println("</tr>");
- }
- writer.print("<tr bgcolor=\"yellow\"><td>H-mean</td>");
- // Here we are computing a sheer average.
- // While in the column results we print NaN when the returned
- // alignment is empty,
- // here we use the real values, i.e., add 0 to both correctVect and
- // foundVect, so this is OK for computing the average.
- int k = 0;
- // ???
- for ( String m : listAlgo ) {
- double precision = (double)correctVect[k]/foundVect[k];
- double recall = (double)correctVect[k]/expected;
- for ( int i = 0 ; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- formatter.format("%1.2f", precision);
- } else if ( format.charAt(i) == 'f' ) {
- formatter.format("%1.2f", 2 * precision * recall / (precision + recall));
- } else if ( format.charAt(i) == 'o' ) {
- formatter.format("%1.2f", recall * (2 - (1 / precision)));
- } else if ( format.charAt(i) == 't' ) {
- if ( timeVect[k] == 0 ){
- writer.print("-");
- } else {
- formatter.format("%1.2f", timeVect[k]);
- }
- } else if ( format.charAt(i) == 'r' ) {
- formatter.format("%1.2f", recall);
- }
- writer.println("</td>");
- };
- k++;
}
writer.println("</tr>");
- writer.println("</tbody></table>");
- 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>");
- } catch (Exception ex) {
- ex.printStackTrace();
- } finally {
- writer.close();
}
- }
+ writer.print("<tr bgcolor=\"yellow\"><td>H-mean</td>");
+ // Here we are computing a sheer average.
+ // While in the column results we print NaN when the returned
+ // alignment is empty,
+ // here we use the real values, i.e., add 0 to both correctVect and
+ // foundVect, so this is OK for computing the average.
+ int k = 0;
+ // ???
+ for ( String m : listAlgo ) {
+ double precision = 1. - (double)correctFoundVect[k]/foundVect[k];
+ double recall = 1. - (double)correctExpVect[k]/expected;
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", precision);
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", 2 * precision * recall / (precision + recall));
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", recall * (2 - (1 / precision)));
+ } else if ( format.charAt(i) == 't' ) {
+ if ( timeVect[k] == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", timeVect[k]);
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", recall);
+ }
+ writer.println("</td>");
+ };
+ k++;
+ }
+ writer.println("</tr>");
+ writer.println("</tbody></table>");
+ 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>");
+ }
public void usage() {
- System.out.println("usage: WGroupEval [options]");
- System.out.println("options are:");
- System.out.println("\t--format=prfot -f prfot\tSpecifies the output order (precision/recall/f-measure/overall/time)");
- // Apparently not implemented
- //System.out.println("\t--sup=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
- System.out.println("\t--output=filename -o filename\tSpecifies a file to which the output will go");
- System.out.println("\t--reference=filename -r filename\tSpecifies the name of the reference alignment file (default: refalign.rdf)");
-
- System.out.println("\t--type=html|xml|tex|ascii|triangle -t html|xml|tex|ascii\tSpecifies the output format");
- System.out.println("\t--list=algo1,...,algon -l algo1,...,algon\tSequence of the filenames to consider");
- System.out.println("\t--color=color -c color\tSpecifies if the output must color even lines of the output");
- System.out.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");
- System.out.println("\t--help -h\t\t\tPrint this message");
- System.err.print("\n"+WGroupEval.class.getPackage().getImplementationTitle()+" "+WGroupEval.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
+ usage( "java "+this.getClass().getName()+" [options]\nEvaluates (with weighted measures) in parallel several matching results on several tests in subdirectories" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java b/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java
index d80cd615..a3277c3b 100644
--- a/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java
+++ b/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java
@@ -1,7 +1,7 @@
/**
* $Id$
*
- * Copyright (C) INRIA, 2011
+ * Copyright (C) INRIA, 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
@@ -23,10 +23,13 @@ package fr.inrialpes.exmo.align.gen;
import java.util.Map;
import java.util.HashMap;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.lang.reflect.InvocationTargetException;
public class AlteratorFactory {
+ final static Logger logger = LoggerFactory.getLogger( AlteratorFactory.class );
// The parameter Ids should be here
//public static final int ANY = 0;
@@ -35,7 +38,7 @@ public class AlteratorFactory {
private static Map<String,String> alterators = null;
public static Alterator newInstance( String id, Alterator om ) {
- //System.err.println( ">>>>>>>> "+id );
+ //logger.trace( ">>>>>>>> {}", id );
if ( alterators == null ) init();
String classname = alterators.get( id );
Alterator alt = null;
@@ -48,15 +51,15 @@ public class AlteratorFactory {
Object[] mparams = { om };
alt = (Alterator)altConstructor.newInstance(mparams);
} catch (ClassNotFoundException cnfex ) {
- cnfex.printStackTrace(); // better raise errors
+ logger.debug( "IGNORED Exception", cnfex ); // better raise errors
} catch (NoSuchMethodException nsmex) {
- nsmex.printStackTrace();
+ logger.debug( "IGNORED Exception", nsmex );
} catch (InstantiationException ieex) {
- ieex.printStackTrace();
+ logger.debug( "IGNORED Exception", ieex );
} catch (IllegalAccessException iaex) {
- iaex.printStackTrace();
+ logger.debug( "IGNORED Exception", iaex );
} catch (InvocationTargetException itex) {
- itex.printStackTrace();
+ logger.debug( "IGNORED Exception", itex );
}
}
return alt;
@@ -151,7 +154,7 @@ public class AlteratorFactory {
/*
for( String key : params.stringPropertyNames() ) {
String value = params.getProperty(key);
- //if ( debug ) System.out.println( "[" +key + "] => [" + value + "]");
+ //logger.trace( "[{}] = [{}]", key, value );
modifier.modifyOntology( key, value ); //modify the ontology according to it
}
*/
diff --git a/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java b/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
index 10a35ea5..5bcad129 100644
--- a/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/BenchmarkGenerator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011, INRIA
+ * Copyright (C) 2011, 2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -29,11 +29,14 @@ package fr.inrialpes.exmo.align.gen;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
public class BenchmarkGenerator extends TestSet {
+ final static Logger logger = LoggerFactory.getLogger( BenchmarkGenerator.class );
public void initTestCases( Properties params ) {
// Process params
- debug = ( params.getProperty( "debug" ) != null );
// JE: ugly
secondOntoFile = params.getProperty( "outdir" )+"/101/onto.rdf";
@@ -47,11 +50,11 @@ public class BenchmarkGenerator extends TestSet {
try {
if ( hard != null && !hard.equals("") ) incr = Float.parseFloat( hard );
} catch ( Exception ex ) {
- ex.printStackTrace(); // continue with the default
+ logger.debug( "IGNORED Exception (continue with default)", ex );
}
String max = params.getProperty( "maximum" );
if ( max != null ) maximum = Integer.parseInt( max );
- if ( debug ) System.err.println( " Mod: "+mod+" / Incr: "+incr+" / Max: "+maximum );
+ logger.trace( " Mod: {} / Incr: {} / Max: {}", mod, incr, maximum );
/* Test 101 Generate the initial situation */
initTests( "101" );
@@ -65,7 +68,7 @@ public class BenchmarkGenerator extends TestSet {
if ( i > 0 ) PREVTEST = "201"+SUFFIX; // The previous suffix
if ( !multModality ) i1 += incr; // traditional
else i1 += (1. - i1) * incr; // hardened
- //if ( debug ) System.err.println( " ******************************************************** "+i+": i1 = "+i1 );
+ //logger.trace( " ******************************************************** {}: i1 = {}", i, i1 );
if ( i1 < 1.0f ) {
SUFFIX = "-"+(i+1)*2; //((Float)i1).toString().substring(2, 3); // 2 4 6 8
diff --git a/src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java b/src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java
index 5a57f078..d5aeea90 100644
--- a/src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java
+++ b/src/fr/inrialpes/exmo/align/gen/ClassHierarchy.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -43,7 +43,12 @@ import java.util.ArrayList;
import java.util.Random;
import java.util.Iterator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
public class ClassHierarchy {
+ final static Logger logger = LoggerFactory.getLogger( ClassHierarchy.class );
+
private URITree root; //the root of the tree
private Map<AnonId,String> m_anonIDs = new HashMap<AnonId,String>();
private int m_anonCount = 0;
@@ -119,23 +124,23 @@ public class ClassHierarchy {
}
/*
if ( childClasses.get(childClasses.size()-1) != null ) {
- System.err.print( childClasses.get(childClasses.size()-1).getURI() );
+ logger.trace( childClasses.get(childClasses.size()-1).getURI() );
} else {
- System.err.print( "**NULL**" );
+ logger.trace( "**NULL**" );
}
System.err.print( " < ");
if ( parentClasses.get(childClasses.size()-1) != null ) {
- System.err.print( parentClasses.get(childClasses.size()-1).getURI() );
+ logger.trace( parentClasses.get(childClasses.size()-1).getURI() );
} else {
- System.err.print( "**NULL**" );
+ logger.trace( "**NULL**" );
}
- System.err.print( " < ");
+ logger.trace( " < ");
if ( superLevelClasses.get(childClasses.size()-1) != null ) {
- System.err.print( superLevelClasses.get(childClasses.size()-1).getURI() );
+ logger.trace( superLevelClasses.get(childClasses.size()-1).getURI() );
} else {
- System.err.print( "**NULL**" );
+ logger.trace( "**NULL**" );
}
- System.err.println();
+ logger.trace("------------------");
*/
childNode.setParent( superNode ); //change the parent of my superclass to the [parent of the "parent node"]
// JE : likely wrong in multiple inheritance
diff --git a/src/fr/inrialpes/exmo/align/gen/DiscriminantGenerator.java b/src/fr/inrialpes/exmo/align/gen/DiscriminantGenerator.java
index 54a9347a..412bfc27 100644
--- a/src/fr/inrialpes/exmo/align/gen/DiscriminantGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/DiscriminantGenerator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2012, INRIA
+ * Copyright (C) 2012-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -29,6 +29,9 @@ package fr.inrialpes.exmo.align.gen;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* This class serves as an example for systematically generating the
* alteration space at a particular resolution.
@@ -38,10 +41,10 @@ import java.util.Properties;
* All this could be achieved by using the parameters which could be Alterator/Step
*/
public class DiscriminantGenerator extends TestSet {
+ final static Logger logger = LoggerFactory.getLogger( DiscriminantGenerator.class );
public void initTestCases( Properties params ) {
// Process params
- debug = ( params.getProperty( "debug" ) != null );
// JE: ugly
secondOntoFile = params.getProperty( "outdir" )+"/000/onto.rdf";
@@ -52,10 +55,10 @@ public class DiscriminantGenerator extends TestSet {
try {
if ( stepval != null && !stepval.equals("") ) STEP = Integer.parseInt( stepval );
} catch ( Exception ex ) {
- ex.printStackTrace(); // continue with the default
+ logger.debug( "IGNORED Exception (continue with defaults)", ex );
}
final float INCR = 1.0f/(STEP-1);
- if ( debug ) System.err.println( " STEP: "+STEP+" / INCR: "+INCR );
+ //logger.trace( " STEP: {} / INCR: {}", STEP, INCR );
/* Test 000 Generate the initial situation */
initTests( "000" );
diff --git a/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentDropper.java b/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentDropper.java
index 98437ff3..fe068502 100644
--- a/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentDropper.java
+++ b/src/fr/inrialpes/exmo/align/gen/NetworkAlignmentDropper.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2009-2011
+ * Copyright (C) INRIA, 2009-2011, 2013
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -34,6 +34,9 @@ import java.util.Set;
import java.util.Collections;
import java.util.ArrayList;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* NetworkAlignmentDropper
*
@@ -42,9 +45,10 @@ import java.util.ArrayList;
* Returns a brand new BasicOntologyNetwork (with the initial alignments)
*/
public class NetworkAlignmentDropper implements OntologyNetworkWeakener {
+ final static Logger logger = LoggerFactory.getLogger( NetworkAlignmentDropper.class );
public OntologyNetwork weaken( OntologyNetwork on, double n, Properties p ) throws AlignmentException {
- //System.err.println( " >>>> "+n );
+ //logger.trace( " >>>> {}", n );
if ( on == null ) throw new AlignmentException( "cannot weaken null ontology network" );
if ( n < 0. || n > 1. )
throw new AlignmentException( "Argument must be between 0 and 1.: "+n );
@@ -52,7 +56,7 @@ public class NetworkAlignmentDropper implements OntologyNetworkWeakener {
}
public OntologyNetwork weaken( OntologyNetwork on, int n, Properties p ) throws AlignmentException {
- //System.err.println( " >>>> "+n );
+ //logger.trace( " >>>> {}", n );
if ( on == null ) throw new AlignmentException( "cannot weaken null ontology network" );
if ( n < 0 )
throw new AlignmentException( "Argument must be a positive integer: "+n );
diff --git a/src/fr/inrialpes/exmo/align/gen/NetworkCorrespondenceDropper.java b/src/fr/inrialpes/exmo/align/gen/NetworkCorrespondenceDropper.java
index 2efb03f8..54bc4f80 100644
--- a/src/fr/inrialpes/exmo/align/gen/NetworkCorrespondenceDropper.java
+++ b/src/fr/inrialpes/exmo/align/gen/NetworkCorrespondenceDropper.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2009-2011
+ * Copyright (C) INRIA, 2009-2011, 2013
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -35,6 +35,9 @@ import java.util.TreeSet;
import java.util.ArrayList;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* NetworkCorrespondenceDropper
*
@@ -45,6 +48,7 @@ import java.util.Properties;
*/
public class NetworkCorrespondenceDropper implements OntologyNetworkWeakener {
+ final static Logger logger = LoggerFactory.getLogger( NetworkCorrespondenceDropper.class );
public OntologyNetwork weaken( OntologyNetwork on, int n, Properties p ) throws AlignmentException {
throw new AlignmentException( "Cannot weaken alignments by fixed number of correspondences" );
@@ -74,14 +78,14 @@ public class NetworkCorrespondenceDropper implements OntologyNetworkWeakener {
newon.addAlignment( newal );
}
// Select these correspondences to delete: either shuffle or order
- //System.err.println( n+" * "+corresp.size()+" = "+n*(double)(corresp.size()) );
+ //logger.trace( "{} * {} = {}", n, corresp.size(), n*(double)(corresp.size()) );
int q = (int)(n*(double)(corresp.size()));
if ( !threshold ) Collections.shuffle( (ArrayList)corresp );
// Suppress the n*size() last ones or those which are under threshold
for ( LCell c : corresp ) {
if ( q == 0 ) break;
q--;
- //System.err.println( "Cell ["+c.getCell().getStrength()+"] : "+c );
+ //logger.trace( "Cell [{}]: {}", c.getCell().getStrength(), c );
c.getAlignment().remCell( c.getCell() );
}
// Cut
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
index 044a75ed..37242c79 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) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -49,6 +49,9 @@ import java.io.OutputStreamWriter;
import java.nio.charset.Charset;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
//Jena API classes
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
@@ -61,6 +64,8 @@ import fr.inrialpes.exmo.align.gen.alt.EmptyModification;
import java.util.Properties;
public class TestGenerator {
+ final static Logger logger = LoggerFactory.getLogger( TestGenerator.class );
+
private String urlprefix = "http://example.com/"; // Prefix (before testnumber) of test URL
private String dirprefix = ""; // Prefix (idem) of directory
private String ontoname = "onto.rdf"; // name of ontology to generate
@@ -69,7 +74,6 @@ public class TestGenerator {
private OntModel modifiedOntology; //modified ontology
private Alignment resultAlignment; //the reference alignment
private Alterator modifier = null; //the modifier
- private boolean debug = false;
public TestGenerator() {}
@@ -82,8 +86,6 @@ public class TestGenerator {
public void setAlignFilename( String a ) { alignname = a; }
- public void setDebug( boolean d ) { debug = d; }
-
//returns the modified ontology
public OntModel getModifiedOntology() { return modifiedOntology; }
@@ -191,7 +193,7 @@ public class TestGenerator {
* Generate a test from an ontology
*/
public Properties modifyOntology( String file, Properties al, String dirName, Properties params) {
- if ( debug ) System.err.println( "Source: "+file+" Target "+dirName );
+ logger.trace( "Source: {}; Target {}", file, dirName );
//set the TestGenerator ontology
OntModel onto = loadOntology( file );
Alterator modifier = generate( onto, params, al );
@@ -209,13 +211,10 @@ public class TestGenerator {
// ******************************************************* GENERATOR
//generate the alingnment
public Alterator generate( OntModel onto, Properties params, Properties initalign ) {
- if ( debug ) {
- System.err.println( "[-------------------------------------------------]" );
- System.err.println( urlprefix+" / "+dirprefix+" / "+ontoname+" / "+alignname );
- }
+ logger.debug( "[-------------------------------------------------]" );
+ logger.debug( "{} / {} / {} / {}", urlprefix, dirprefix, ontoname, alignname );
// Load the ontology
Alterator modifier = new EmptyModification( onto );
- ((EmptyModification)modifier).setDebug( debug );
// Initialize the reference alignment
if ( initalign != null ) ((EmptyModification)modifier).initializeAlignment( initalign );
modifier.modify( params );
diff --git a/src/fr/inrialpes/exmo/align/gen/TestSet.java b/src/fr/inrialpes/exmo/align/gen/TestSet.java
index de5b7e5d..d05f33a0 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestSet.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestSet.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -28,6 +28,10 @@
* or generate tests independently.
*
* Variations can also be obtained.
+ *
+ * The API is:
+ * initTestCases: creates the test structure (abstract) made of TestCases
+ * generate: generates the actual tests using a TestGenerator
*/
package fr.inrialpes.exmo.align.gen;
@@ -37,12 +41,15 @@ import java.util.HashMap;
import java.util.Set;
import java.util.HashSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
public abstract class TestSet {
+ final static Logger logger = LoggerFactory.getLogger( TestSet.class );
private String initOntoFile; //the initial ontology file
protected String secondOntoFile; //the secondary ontology file
protected boolean continuous = false;
- protected boolean debug = false;
private TestGenerator generator; // a TestGenerator
@@ -59,7 +66,7 @@ public abstract class TestSet {
addTestChild( tests.get( from ), name, params );
}
public void addTestChild( TestCase father, String name, Properties params ) {
- //System.err.println( name + " ["+father+"]" );
+ //logger.trace( "{} [{}]", name, father );
TestCase c = father.addSubTest( name, params );
tests.put( name, c );
}
@@ -89,7 +96,6 @@ public abstract class TestSet {
// Generates the test set
public void generate( Properties params ) {
// Generator parameters... are these OK?
- generator.setDebug( debug );
initOntoFile = params.getProperty( "filename" ); // If no filename error
if ( params.getProperty( "urlprefix" ) != null ) generator.setURLPrefix( params.getProperty( "urlprefix" ) );
if ( params.getProperty( "outdir" ) != null ) generator.setDirPrefix( params.getProperty( "outdir" ) );
@@ -105,7 +111,7 @@ public abstract class TestSet {
// Initialises test cases tree
initTestCases( params );
// Print it
- if ( debug ) printTestHierarchy( root, 0 );
+ // printTestHierarchy( root, 0 );
if ( params.getProperty( "alignname" ) != null ) generator.setAlignFilename( params.getProperty( "alignname" ) );
// Generate all tests
startTestGeneration();
diff --git a/src/fr/inrialpes/exmo/align/gen/URITree.java b/src/fr/inrialpes/exmo/align/gen/URITree.java
index fdb77700..15266226 100644
--- a/src/fr/inrialpes/exmo/align/gen/URITree.java
+++ b/src/fr/inrialpes/exmo/align/gen/URITree.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -29,9 +29,14 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.align.gen.alt.BasicAlterator;
public class URITree {
+ final static Logger logger = LoggerFactory.getLogger( URITree.class );
+
private String URI; //the URI of the node
private ArrayList<URITree> children;//the list of children
private URITree parent; //the parent of the node
@@ -208,7 +213,7 @@ public class URITree {
public void print( int depth ) {
indent( getDepth() );
- System.err.println( "[" + getURI() + "]" + "->" + getDepth() );
+ //logger.trace( "[{}] -> {}", getURI(), getDepth() );
for( URITree n : getChildrenList() ) {
n.print( depth+1 );
}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/AddClassLevel.java b/src/fr/inrialpes/exmo/align/gen/alt/AddClassLevel.java
index 6e9116a9..50e754f1 100755
--- a/src/fr/inrialpes/exmo/align/gen/alt/AddClassLevel.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/AddClassLevel.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -27,11 +27,14 @@ import java.util.Properties;
import java.util.List;
import java.util.ArrayList;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.align.gen.Alterator;
import fr.inrialpes.exmo.align.gen.ParametersIds;
-
public class AddClassLevel extends BasicAlterator {
+ final static Logger logger = LoggerFactory.getLogger( AddClassLevel.class );
public AddClassLevel( Alterator om ) {
initModel( om );
@@ -44,8 +47,8 @@ public class AddClassLevel extends BasicAlterator {
int index = p.indexOf(".");
int level = Integer.valueOf( p.substring(0, index) );
int nbClasses = Integer.valueOf( p.substring(index+1, p.length()) );
- if ( debug ) System.err.println( "level " + level );
- if ( debug ) System.err.println( "nbClasses " + nbClasses );
+ logger.trace( "level : {}", level );
+ logger.trace( "nbClasses : {}", nbClasses );
//float percentage = 1.00f;
//the parent class -> if level is 1 then we create a new class
//else we get a random class from the level : level-1 to be the parent of the class
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java b/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
index 2475e307..14d850a7 100644
--- a/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
@@ -1,7 +1,7 @@
/**
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -48,7 +48,9 @@ import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.OutputStream;
import java.io.StringWriter;
-import com.hp.hpl.jena.rdf.model.RDFWriter;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
//Alignment API classes
import org.semanticweb.owl.align.Alignment;
@@ -57,6 +59,7 @@ import org.semanticweb.owl.align.AlignmentException;
import fr.inrialpes.exmo.align.impl.URIAlignment;
//JENA classes
+import com.hp.hpl.jena.rdf.model.RDFWriter;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
@@ -75,14 +78,13 @@ import com.hp.hpl.jena.ontology.Restriction;
import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
-
//gen
import fr.inrialpes.exmo.align.gen.Alterator;
import fr.inrialpes.exmo.align.gen.ClassHierarchy;
import fr.inrialpes.exmo.align.gen.ParametersIds;
public abstract class BasicAlterator implements Alterator {
- protected boolean debug = false;
+ final static Logger logger = LoggerFactory.getLogger( BasicAlterator.class );
protected ClassHierarchy classHierarchy; // the class hierarchy
protected OntModel modifiedModel; // the modified Ontology
@@ -142,8 +144,6 @@ public abstract class BasicAlterator implements Alterator {
// -------------------------
// Accessors
- public void setDebug( boolean d ) { debug = d; }
-
//returns the modified ontology after changing the namespace
public OntModel getModifiedOntology () { return modifiedModel; }
@@ -383,9 +383,9 @@ public abstract class BasicAlterator implements Alterator {
public Alignment extractAlignment( String base1, String base2 ) {
Alignment extractedAlignment = new URIAlignment();
- //System.err.println( "\n-----> "+initOntologyNS );
- //System.err.println( "-----> "+base1 );
- //System.err.println( "-----> "+base2 );
+ //logger.trace( "-----> {}", initOntologyNS );
+ //logger.trace( "-----> {}", base1 );
+ //logger.trace( "-----> {}", base2 );
try {
URI onto1 = new URI( getNameSpace( base1 ) );
URI onto2 = new URI( getNameSpace( base2 ) );
@@ -398,13 +398,13 @@ public abstract class BasicAlterator implements Alterator {
for ( String key : alignment.stringPropertyNames() ) {
if ( !key.equals("##") ) {
String value = alignment.getProperty(key);
- //if ( debug ) System.err.println( "[" + source + "][" + target + "]" );
+ //logger.trace( "[{} --> {}]", source, target );
extractedAlignment.addAlignCell( URI.create( base1+key ), URI.create( base2+value ) );
}
}
alignment.setProperty( "##", base1 );
} catch ( Exception ex ) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
}
return extractedAlignment;
}
@@ -481,7 +481,7 @@ public abstract class BasicAlterator implements Alterator {
ByteArrayInputStream in = new ByteArrayInputStream( sout.getBytes("UTF8") );
model.read( in, null );
} catch ( Exception ex ) { //UnsupportedEncodingException;
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
}
return model;
}
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/EmptyModification.java b/src/fr/inrialpes/exmo/align/gen/alt/EmptyModification.java
index 6edcb002..dd7e2649 100755
--- a/src/fr/inrialpes/exmo/align/gen/alt/EmptyModification.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/EmptyModification.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -33,12 +33,16 @@ import java.util.List;
import java.util.ArrayList;
import java.util.HashMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.align.gen.Alterator;
import fr.inrialpes.exmo.align.gen.ParametersIds;
import org.semanticweb.owl.align.Alignment;
public class EmptyModification extends BasicAlterator {
+ final static Logger logger = LoggerFactory.getLogger( EmptyModification.class );
protected boolean relocateSource = false;
@@ -51,7 +55,7 @@ public class EmptyModification extends BasicAlterator {
// Clearly here setDebug, setNamespace are important
public Alterator modify( Properties params ) {
- //System.err.println( "********************************************************************************************" );
+ //logger.trace( "NEW MODIFICATION ------------------------------------" );
relocateSource = ( params.getProperty( "copy101" ) != null );
if ( alignment == null ) {
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/FlattenLevel.java b/src/fr/inrialpes/exmo/align/gen/alt/FlattenLevel.java
index 632065fd..8b221041 100755
--- a/src/fr/inrialpes/exmo/align/gen/alt/FlattenLevel.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/FlattenLevel.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -30,10 +30,14 @@ import java.util.List;
import java.util.ArrayList;
import java.util.HashMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.align.gen.Alterator;
import fr.inrialpes.exmo.align.gen.ParametersIds;
public class FlattenLevel extends BasicAlterator {
+ final static Logger logger = LoggerFactory.getLogger( FlattenLevel.class );
public FlattenLevel( Alterator om ) {
initModel( om );
@@ -81,10 +85,10 @@ public class FlattenLevel extends BasicAlterator {
restr.add(r);
if ( r.isSomeValuesFromRestriction() )
restr.add(r);
- //if ( debug ) System.err.println( cls.getURI() );
+ //logger.trace( "Class {}", cls.getURI() );
}
}
- //if ( debug ) System.err.println( restr.size() );
+ //logger.trace( "Size: {}", restr.size() );
if ( !restrictions.containsKey( parentClass.getURI() ) ) {
restrictions.put( parentClass.getURI(), restr );
@@ -93,9 +97,9 @@ public class FlattenLevel extends BasicAlterator {
OntClass superClass = superLevelClasses.get( i ); //parent class of the child class parents
if ( superClass == null ) superClass = modifiedModel.createClass( OWL.Thing.getURI() ); //Thing class
- //if ( debug ) System.err.println("SuperClass class [" + superClass.getURI() + "]");
- //if ( debug ) System.err.println("Parent class [" + parentClass.getURI() + "]");
- //if ( debug ) System.err.println("Child class [" + childClass.getURI() + "]");
+ //logger.trace("SuperClass class [{}]", superClass.getURI() );
+ //logger.trace("Parent class [{}]", parentClass.getURI() );
+ //logger.trace("Child class [{}]", childClass.getURI() );
if ( modifiedModel.containsResource( parentClass ) ) {
//to check if the class appears as unionOf, someValuesFrom, allValuesFrom ..
unionOf.put( parentClass.getURI(), superClass.getURI() );
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RemoveClassLevel.java b/src/fr/inrialpes/exmo/align/gen/alt/RemoveClassLevel.java
index c38b5d22..84dc6e7d 100755
--- a/src/fr/inrialpes/exmo/align/gen/alt/RemoveClassLevel.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RemoveClassLevel.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -28,10 +28,14 @@ import java.util.List;
import java.util.ArrayList;
import java.util.HashMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.align.gen.Alterator;
import fr.inrialpes.exmo.align.gen.ParametersIds;
public class RemoveClassLevel extends BasicAlterator {
+ final static Logger logger = LoggerFactory.getLogger( RemoveClassLevel.class );
public RemoveClassLevel( Alterator om ) {
initModel( om );
@@ -42,7 +46,7 @@ public class RemoveClassLevel extends BasicAlterator {
if ( p == null ) return null;
int level = Integer.parseInt( p );
HashMap<String, String> uris = new HashMap<String, String>();
- //if ( debug ) System.err.println( "Level " + level );
+ //logger.trace( "Level {}", level );
buildClassHierarchy(); //build the class hierarchy if necessary
for ( OntClass cl : classHierarchy.getClassesFromLevel( modifiedModel, level ) ) { //remove the classes from the hierarchy
String parentURI = removeClass( cl );
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RemoveProperties.java b/src/fr/inrialpes/exmo/align/gen/alt/RemoveProperties.java
index 2cda9180..ebb35822 100755
--- a/src/fr/inrialpes/exmo/align/gen/alt/RemoveProperties.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RemoveProperties.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -36,11 +36,15 @@ import java.util.List;
import java.util.ArrayList;
import java.util.Iterator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.align.gen.Alterator;
import fr.inrialpes.exmo.align.gen.ParametersIds;
public class RemoveProperties extends BasicAlterator {
+ final static Logger logger = LoggerFactory.getLogger( RemoveProperties.class );
public RemoveProperties( Alterator om ) {
initModel( om );
@@ -60,7 +64,7 @@ public class RemoveProperties extends BasicAlterator {
int nbProperties = properties.size(); //the number of properties
- //System.err.println( percentage );
+ //logger.trace( "Percentage {}", percentage );
int toBeRemoved = Math.round( percentage*nbProperties ); //the number of properties to be removed
//build the list of classes to be removed
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/RenameThings.java b/src/fr/inrialpes/exmo/align/gen/alt/RenameThings.java
index 72c83853..9c95208e 100755
--- a/src/fr/inrialpes/exmo/align/gen/alt/RenameThings.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/RenameThings.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2012, INRIA
+ * Copyright (C) 2011-2013, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -52,6 +52,9 @@ import java.util.List;
import java.util.ArrayList;
import java.util.HashMap;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.align.gen.Alterator;
import fr.inrialpes.exmo.align.gen.ParametersIds;
@@ -59,6 +62,7 @@ import fr.inrialpes.exmo.align.gen.ParametersIds;
* This is only an abstract class gathering the renaming routines
*/
public abstract class RenameThings extends BasicAlterator {
+ final static Logger logger = LoggerFactory.getLogger( RenameThings.class );
// -------------------------
// Label replacement
@@ -203,7 +207,7 @@ public abstract class RenameThings extends BasicAlterator {
renamedClasses = nbClasses - notRenamedClasses.size(); //the number of renamed classes
toBeRenamed = Math.round(percentage*nbClasses) - renamedClasses; // -renamedClasses -> for Benchmark
- //System.err.println( "NbClasses = "+nbClasses+ " YetToRename = "+notRenamedClasses.size()+" I will rename = "+toBeRenamed );
+ //logger.trace( "NbClasses = {}; YetToRename = {}; I will rename = {};", nbClasses, notRenamedClasses.size(), toBeRenamed );
// toBeRenamed is negative when classes have been added to the model
if ( toBeRenamed < 0 ) toBeRenamed = 0;
@@ -451,7 +455,7 @@ public abstract class RenameThings extends BasicAlterator {
try {
translatedText = Translate.execute(source, Language.ENGLISH, Language.FRENCH);
} catch (Exception e) {
- System.err.println( "Exception " + e.getMessage() );
+ logger.debug( "IGNORED Exception", e );
}
return removeSpaces ( translatedText );
}
@@ -486,7 +490,7 @@ public abstract class RenameThings extends BasicAlterator {
*/
public String parseString (String str, boolean activeTranslateString, boolean activeSynonym) {
- // if ( debug ) System.err.println ( "str = [" + str + "]" );
+ // logger.trace( "str = [{}]", str );
char [] parsed = str.toCharArray();
String newString = "";
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 31979f25..1a464575 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -34,6 +34,9 @@ import java.util.Set;
import java.util.ArrayList;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.xml.sax.ContentHandler;
import org.semanticweb.owl.align.Alignment;
@@ -54,11 +57,12 @@ import fr.inrialpes.exmo.ontowrap.OntowrapException;
* In version 3.0 this class is virtually abstract.
* But it cannot be declared abstract because it uses its own constructor.
*
- * @author J�r�me Euzenat, David Loup, Rapha�l Troncy
+ * @author J�r�me Euzenat, David Loup, Rapha�l Troncy
* @version $Id$
*/
public class BasicAlignment implements Alignment {
+ final static Logger logger = LoggerFactory.getLogger( BasicAlignment.class );
public void accept( AlignmentVisitor visitor ) throws AlignmentException {
visitor.visit( this );
@@ -67,8 +71,6 @@ public class BasicAlignment implements Alignment {
protected Ontology<Object> onto1 = null;
protected Ontology<Object> onto2 = null;
- protected int debug = 0;
-
protected String level = "0";
protected String type = "**";
@@ -676,8 +678,10 @@ public class BasicAlignment implements Alignment {
if ( pretty != null ){
newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty+"/"+label );
};
- newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE,
- extensions.getExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE )+"" );
+ if ( extensions.getExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE ) != null ) {
+ newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE,
+ extensions.getExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE ) );
+ }
newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.METHOD, method );
return newext;
}
@@ -731,7 +735,10 @@ public class BasicAlignment implements Alignment {
public Object clone() {
BasicAlignment align;
try { align = createNewAlignment( onto1, onto2 ); }
- catch (AlignmentException ae) { ae.printStackTrace(); return null; }
+ catch (AlignmentException ae) {
+ logger.debug( "IGNORED Exception: alignment not cloned", ae );
+ return null;
+ }
align.setType( getType() );
align.setLevel( getLevel() );
align.setFile1( getFile1() );
@@ -743,7 +750,9 @@ public class BasicAlignment implements Alignment {
align.setXNamespace( label, getXNamespace( label ) );
}
try { align.ingest( this ); }
- catch (AlignmentException ex) { ex.printStackTrace(); }
+ catch (AlignmentException ex) {
+ logger.debug( "IGNORED Exception: alignment not ingested", ex );
+ }
return align;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicParameters.java b/src/fr/inrialpes/exmo/align/impl/BasicParameters.java
index 837c7d3d..0cbaa053 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicParameters.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicParameters.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2004-2005, 2008-2010, 2012
+ * Copyright (C) INRIA, 2004-2005, 2008-2010, 2012-2014
* Copyright (C) University of Montr�al, 2004
*
* This program is free software; you can redistribute it and/or
@@ -30,6 +30,9 @@ import java.util.Properties;
import java.io.PrintStream;
import java.io.File;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.w3c.dom.Document;
import org.w3c.dom.NodeList;
import org.w3c.dom.Element;
@@ -63,8 +66,9 @@ import org.semanticweb.owl.align.Parameters;
* @version $Id$
*/
-//@Deprecated
+@Deprecated
public class BasicParameters extends Properties implements Parameters, Cloneable {
+ final static Logger logger = LoggerFactory.getLogger( BasicParameters.class );
static final long serialVersionUID = 400L;
@@ -153,13 +157,13 @@ public class BasicParameters extends Properties implements Parameters, Cloneable
String paramValue = paramContent.item(0).getNodeValue().trim();
p.setParameter(paramName, paramValue);
}
- } catch (SAXParseException err) {
- System.err.println("** Parsing error: ["+ err.getLineNumber()+"]: "+err.getSystemId());
- System.err.println(" " + err.getMessage());
- } catch (SAXException e) {
- Exception x = e.getException();
- ((x == null) ? e : x).printStackTrace();
- } catch (Throwable t) { t.printStackTrace(); }
+ } catch ( SAXParseException err ) {
+ logger.debug( "IGNORED SAX Parsing exception", err );
+ } catch ( SAXException e ) {
+ logger.debug( "IGNORED SAX exception", e );
+ } catch ( Throwable t ) {
+ logger.debug( "IGNORED Exception", t );
+ }
return p;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicRelation.java b/src/fr/inrialpes/exmo/align/impl/BasicRelation.java
index 1370d674..f1dc9691 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicRelation.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicRelation.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2005, 2007, 2009-2012
+ * Copyright (C) INRIA, 2003-2005, 2007, 2009-2013
*
* 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
@@ -35,6 +35,9 @@ import java.io.PrintWriter;
import java.util.HashMap;
import java.util.Map;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* Represents an ontology alignment relation.
*
@@ -43,6 +46,7 @@ import java.util.Map;
*/
public class BasicRelation implements Relation {
+ final static Logger logger = LoggerFactory.getLogger( BasicRelation.class );
private static Map<String, Class<?>> classIndex = null;
@@ -87,7 +91,7 @@ public class BasicRelation implements Relation {
classIndex.put( "~>", nti );
classIndex.put( "~>", nti );
} catch ( ClassNotFoundException cnfe ) {
- cnfe.printStackTrace(); // should never occur
+ logger.debug( "IGNORED Exception (should never occur)", cnfe );
}
}
return classIndex.get(label);
@@ -150,7 +154,7 @@ public class BasicRelation implements Relation {
Constructor relationConstructor = relationClass.getConstructor((Class[])null);
return (Relation)relationConstructor.newInstance((Object[])null);
} catch ( Exception ex ) {
- //ex.printStackTrace();
+ logger.debug( "IGNORED Exception: created Basic Relation)", ex );
//Otherwise, just create a Basic relation
return new BasicRelation( rel );
}
diff --git a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
index 76385ec7..fd124508 100644
--- a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.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
@@ -28,6 +28,9 @@ import java.util.SortedSet;
import java.util.Comparator;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentException;
@@ -51,6 +54,7 @@ import fr.inrialpes.exmo.ontosim.util.HungarianAlgorithm;
*/
public abstract class DistanceAlignment extends ObjectAlignment implements AlignmentProcess {
+ final static Logger logger = LoggerFactory.getLogger( DistanceAlignment.class );
Similarity sim;
/** Creation **/
@@ -134,7 +138,7 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
if ( params.getProperty("threshold") != null )
threshold = Double.parseDouble( params.getProperty("threshold") );
- //System.err.println("The type is "+type+" with length = "+type.length());
+ //logger.trace("The type is {} with length = {}", type, type.length() );
if ( type.equals("?*") || type.equals("1*") || type.equals("?+") || type.equals("1+") ) return extractqs( threshold, params );
else if ( type.equals("??") || type.equals("1?") || type.equals("?1") || type.equals("11") ) return extractqq( threshold, params );
else if ( type.equals("*?") || type.equals("+?") || type.equals("*1") || type.equals("+1") ) return extractqs( threshold, params );
@@ -209,8 +213,11 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
}
}
}
- } catch (OntowrapException owex) { owex.printStackTrace(); //}
- } catch (AlignmentException alex) { alex.printStackTrace(); }
+ } catch (OntowrapException owex) {
+ logger.debug( "IGNORED Exception", owex );
+ } catch (AlignmentException alex) {
+ logger.debug( "IGNORED Exception", alex );
+ }
return((Alignment)this);
}
@@ -259,8 +266,11 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
}
}
}
- } catch (OntowrapException owex) { owex.printStackTrace(); //}
- } catch (AlignmentException alex) { alex.printStackTrace(); }
+ } catch (OntowrapException owex) {
+ logger.debug( "IGNORED Exception", owex );
+ } catch (AlignmentException alex) {
+ logger.debug( "IGNORED Exception", alex );
+ }
return((Alignment)this);
}
@@ -316,8 +326,11 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
}
}
}
- } catch ( AlignmentException alex) { alex.printStackTrace(); }
- catch ( OntowrapException owex) { owex.printStackTrace(); }
+ } catch (OntowrapException owex) {
+ logger.debug( "IGNORED Exception", owex );
+ } catch (AlignmentException alex) {
+ logger.debug( "IGNORED Exception", alex );
+ }
// For properties
try{
int nbprop1 = ontology1().nbProperties();
@@ -358,8 +371,11 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
}
}
}
- } catch (AlignmentException alex) { alex.printStackTrace(); }
- catch (OntowrapException owex) { owex.printStackTrace(); }
+ } catch (OntowrapException owex) {
+ logger.debug( "IGNORED Exception", owex );
+ } catch (AlignmentException alex) {
+ logger.debug( "IGNORED Exception", alex );
+ }
// For individuals
if ( params.getProperty("noinst") == null ){
try {
@@ -405,8 +421,11 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
}
}
}
- } catch (AlignmentException alex) { alex.printStackTrace(); //}
- } catch (OntowrapException owex) { owex.printStackTrace(); }
+ } catch (OntowrapException owex) {
+ logger.debug( "IGNORED Exception", owex );
+ } catch (AlignmentException alex) {
+ logger.debug( "IGNORED Exception", alex );
+ }
}
return((Alignment)this);
}
@@ -451,7 +470,7 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
public int compare( Cell o1, Cell o2 )
throws ClassCastException{
try {
- //System.err.println(o1.getObject1()+" -- "+o1.getObject2()+" // "+o2.getObject1()+" -- "+o2.getObject2());
+ //logger.trace("{} -- {} // {}�-- {}", o1.getObject1(), o1.getObject2(), o2.getObject1(), o2.getObject2());
if ( o1.getStrength() > o2.getStrength() ){
return -1;
} else if ( o1.getStrength() < o2.getStrength() ){
@@ -533,11 +552,11 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
}
};
- } catch (AlignmentException alex) {
- alex.printStackTrace();
- } catch (OntowrapException owex) {
- owex.printStackTrace();
- };
+ } catch (OntowrapException owex) {
+ logger.debug( "IGNORED Exception", owex );
+ } catch (AlignmentException alex) {
+ logger.debug( "IGNORED Exception", alex );
+ }
return((Alignment)this);
}
diff --git a/src/fr/inrialpes/exmo/align/impl/InstanceBasedMatrixMeasure.java b/src/fr/inrialpes/exmo/align/impl/InstanceBasedMatrixMeasure.java
index 72fd167a..e1de26d8 100644
--- a/src/fr/inrialpes/exmo/align/impl/InstanceBasedMatrixMeasure.java
+++ b/src/fr/inrialpes/exmo/align/impl/InstanceBasedMatrixMeasure.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2010
+ * Copyright (C) INRIA, 2010, 2013
*
* Modifications to the initial code base are copyright of their
* respective authors, or their employers as appropriate. Authorship
@@ -43,6 +43,9 @@ import java.util.Set;
import java.util.Properties;
import java.util.Vector;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* InstanceBasedMatrixMeasure
*
@@ -59,6 +62,7 @@ import java.util.Vector;
*/
public abstract class InstanceBasedMatrixMeasure extends MatrixMeasure {
+ final static Logger logger = LoggerFactory.getLogger( InstanceBasedMatrixMeasure.class );
Set<Object>[] classinst1 = null;
Set<Object>[] classinst2 = null;
@@ -89,9 +93,9 @@ public abstract class InstanceBasedMatrixMeasure extends MatrixMeasure {
classinst2[ classlist2.get( cl2 ).intValue() ] = ontology2.getInstances( cl2, OntologyFactory.LOCAL, OntologyFactory.FULL, OntologyFactory.NAMED );
}
} catch (OntowrapException owex) {
- owex.printStackTrace();
+ logger.debug( "IGNORED Exception", owex );
} catch (AlignmentException alex) {
- alex.printStackTrace();
+ logger.debug( "IGNORED Exception", alex );
}
}
@@ -208,7 +212,7 @@ public abstract class InstanceBasedMatrixMeasure extends MatrixMeasure {
return 0.;
}
public double individualMeasure( Object id1, Object id2 ) throws Exception {
- //if ( debug > 4 ) System.err.println( "ID:"+id1+" -- "+id2);
+ //logger.trace( "ID: {} -- {}", id1, id2 );
// compute edit distance between both norms
//norm1[indlist1.get(ob1).intValue()], norm2[indlist2.get(ob2).intValue()]
return 0.;
diff --git a/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java b/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
index 04d3002c..5c844fdb 100644
--- a/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
+++ b/src/fr/inrialpes/exmo/align/impl/MatrixMeasure.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2010
+ * Copyright (C) INRIA, 2003-2010, 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
@@ -26,6 +26,9 @@ import java.util.Properties;
import java.util.Set;
import java.text.NumberFormat;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentException;
@@ -47,6 +50,7 @@ import fr.inrialpes.exmo.align.impl.ObjectAlignment;
public abstract class MatrixMeasure implements Similarity {
+ final static Logger logger = LoggerFactory.getLogger( MatrixMeasure.class );
public boolean similarity = true;
@@ -126,7 +130,7 @@ public abstract class MatrixMeasure implements Similarity {
proplist1 = new HashMap<Object,Integer>(); // onto1 properties
indlist2 = new HashMap<Object,Integer>(); // onto2 instances
indlist1 = new HashMap<Object,Integer>(); // onto1 instances
- //System.err.println(" >> "+onto1+"/"+onto2 );
+ //logger.trace(" >> {}/{}", onto1, onto2 );
try {
// Create class lists
@@ -136,7 +140,7 @@ public abstract class MatrixMeasure implements Similarity {
for( Object cl : onto1.getClasses() ){
classlist1.put( cl, new Integer(nbclass1++) );
}
- //System.err.println(" >> NbClasses: "+nbclass1+"/"+nbclass2 );
+ //logger.trace(" >> NbClasses: {}/{}", nbclass1, nbclass2 );
clmatrix = new double[nbclass1+1][nbclass2+1];
// Create property lists
@@ -152,7 +156,7 @@ public abstract class MatrixMeasure implements Similarity {
for( Object pr : onto1.getDataProperties() ){
proplist1.put( pr, new Integer(nbprop1++) );
}
- //System.err.println(" >> NbProp: "+nbprop1+"/"+nbprop2 );
+ //logger.trace(" >> NbProp: {}/{}", nbprop1, nbprop2 );
prmatrix = new double[nbprop1+1][nbprop2+1];
// Create individual lists
@@ -168,9 +172,11 @@ public abstract class MatrixMeasure implements Similarity {
indlist1.put( ind, new Integer(nbind1++) );
}
}
- //System.err.println(" >> NbInd: "+nbind1+"/"+nbind2 );
+ //logger.trace(" >> NbInd: {}/{}", nbind1, nbind2 );
indmatrix = new double[nbind1+1][nbind2+1];
- } catch (OntowrapException e) { e.printStackTrace(); };
+ } catch (OntowrapException e) {
+ logger.debug( "IGNORED Exception", e );
+ };
}
@SuppressWarnings("unchecked") //ConcatenatedIterator
@@ -206,7 +212,9 @@ public abstract class MatrixMeasure implements Similarity {
}
}
// What is caught is really Exceptions
- } catch (Exception e) { e.printStackTrace(); }
+ } catch (Exception e) {
+ logger.debug( "IGNORED Exception", e );
+ }
}
public double getIndividualSimilarity( Object i1, Object i2 ){
@@ -241,7 +249,9 @@ public abstract class MatrixMeasure implements Similarity {
}
System.out.println("\\\\");
}
- } catch (OntowrapException e) { e.printStackTrace(); };
+ } catch (OntowrapException e) {
+ logger.debug( "IGNORED Exception", e );
+ };
System.out.println("\n\\end{tabular}");
}
diff --git a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
index 37a43cc5..ab3334af 100644
--- a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
@@ -28,6 +28,9 @@ import java.util.Set;
import java.util.Collection;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.xml.sax.SAXException;
import org.semanticweb.owl.align.Alignment;
@@ -52,13 +55,14 @@ import fr.inrialpes.exmo.ontowrap.OntowrapException;
*/
public class ObjectAlignment extends BasicAlignment {
+ final static Logger logger = LoggerFactory.getLogger( ObjectAlignment.class );
protected ObjectAlignment init = null;
public ObjectAlignment() {}
- public void init(Object onto1, Object onto2) throws AlignmentException {
- if ( (onto1 instanceof LoadedOntology && onto2 instanceof LoadedOntology) ){
+ public void init( Object onto1, Object onto2 ) throws AlignmentException {
+ if ( (onto1 instanceof LoadedOntology) && (onto2 instanceof LoadedOntology) ){
super.init( onto1, onto2 );
} else if ( onto1 instanceof URI && onto2 instanceof URI ) {
super.init( loadOntology( (URI)onto1 ),
@@ -161,7 +165,7 @@ 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() );
+ //logger.trace( "{} {} {} {}", 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,
diff --git a/src/fr/inrialpes/exmo/align/impl/aggr/ConsensusAggregator.java b/src/fr/inrialpes/exmo/align/impl/aggr/ConsensusAggregator.java
index f29e7021..154cb29f 100644
--- a/src/fr/inrialpes/exmo/align/impl/aggr/ConsensusAggregator.java
+++ b/src/fr/inrialpes/exmo/align/impl/aggr/ConsensusAggregator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2010
+ * Copyright (C) INRIA, 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
@@ -24,6 +24,9 @@ import java.util.Hashtable;
import java.util.Set;
import java.util.HashSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
@@ -54,6 +57,7 @@ import fr.inrialpes.exmo.align.impl.BasicAlignment;
*/
public class ConsensusAggregator extends BasicAlignment {
+ final static Logger logger = LoggerFactory.getLogger( ConsensusAggregator.class );
int nbAlignments = 0;
Hashtable<Cell, CountCell> count;
@@ -144,7 +148,7 @@ public class ConsensusAggregator extends BasicAlignment {
}
}
} catch (Exception ex) {
- ex.printStackTrace();
+ logger.debug( "IGNORED Exception", ex );
}
return null;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java b/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
index 095151a1..108771a9 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
@@ -2,7 +2,7 @@
* $Id$
*
* Sourceforge version 1.6 - 2008 - was OMWGAlignment
- * Copyright (C) INRIA, 2007-2012
+ * Copyright (C) INRIA, 2007-2013
*
* 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
@@ -29,12 +29,16 @@ import java.util.Collection;
import java.util.Set;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
+import fr.inrialpes.exmo.ontowrap.OntologyFactory;
import fr.inrialpes.exmo.ontowrap.Ontology;
import fr.inrialpes.exmo.ontowrap.LoadedOntology;
import fr.inrialpes.exmo.ontowrap.OntologyFactory;
@@ -56,6 +60,7 @@ import fr.inrialpes.exmo.align.parser.TypeCheckingVisitor;
*
*/
public class EDOALAlignment extends BasicAlignment {
+ final static Logger logger = LoggerFactory.getLogger( EDOALAlignment.class );
/*
* An eventual initial alignment
@@ -82,20 +87,13 @@ public class EDOALAlignment extends BasicAlignment {
public void init( Object onto1, Object onto2 ) throws AlignmentException {
if ( (onto1 == null) || (onto2 == null) )
throw new AlignmentException("The source and target ontologies must not be null");
- if ( (onto1 instanceof Ontology && onto2 instanceof Ontology) ){
- super.init( onto1, onto2 );
- }
- else if ((onto1 instanceof URI && onto2 instanceof URI)) {
- OntologyFactory fact = OntologyFactory.getFactory();
- try {
- super.init(fact.loadOntology((URI) onto1), fact.loadOntology((URI) onto2));
- } catch (OntowrapException e) {
- throw new AlignmentException("Could not load ontologies",e);
- }
- }
- else {
- throw new AlignmentException("arguments must be LoadedOntology or deferencable URIs");
- };
+ Ontology o1 = null;
+ if ( onto1 instanceof Ontology ) o1 = (Ontology)onto1;
+ else o1 = loadOntology( (URI)onto1 );
+ Ontology o2 = null;
+ if ( onto2 instanceof Ontology ) o2 = (Ontology)onto2;
+ else o2 = loadOntology( (URI)onto2 );
+ super.init( o1, o2 );
}
public void loadInit( Alignment al ) throws AlignmentException {
@@ -259,30 +257,61 @@ public class EDOALAlignment extends BasicAlignment {
// It would be better to implement this for ObjectAlignment
// and to use return toEDOALAlignment( ObjectAlignment.toObjectAlignment( al ) );
// for URIAlignment
+ //
+ // Basic -> URI
+ // -> Object
+ // -> EDOAL
+ public static LoadedOntology loadOntology( URI onto ) throws AlignmentException {
+ if ( onto == null ) throw new AlignmentException("The source and target ontologies must not be null");
+ try {
+ OntologyFactory fact = OntologyFactory.getFactory();
+ return fact.loadOntology( onto );
+ } catch ( OntowrapException owex ) {
+ throw new AlignmentException( "Cannot load ontologies", owex );
+ }
+ }
+ public static LoadedOntology loadOntology( Ontology onto ) throws AlignmentException {
+ if ( onto == null ) throw new AlignmentException("The source and target ontologies must not be null");
+ if ( onto instanceof LoadedOntology ) return (LoadedOntology)onto;
+ try {
+ OntologyFactory fact = OntologyFactory.getFactory();
+ return fact.loadOntology( onto );
+ } catch ( OntowrapException owex ) {
+ throw new AlignmentException( "Cannot load ontologies", owex );
+ }
+ }
+
public static EDOALAlignment toEDOALAlignment( URIAlignment al ) throws AlignmentException {
return toEDOALAlignment( (BasicAlignment)al );
}
public static EDOALAlignment toEDOALAlignment( ObjectAlignment al ) throws AlignmentException {
- return toEDOALAlignment( (BasicAlignment)al );
+ logger.debug( "Converting ObjectAlignment to EDOALAlignment" );
+ EDOALAlignment alignment = new EDOALAlignment();
+ // They are obviously loaded
+ alignment.init( al.getOntologyObject1(), al.getOntologyObject2() );
+ alignment.convertToEDOAL( al );
+ return alignment;
}
public static EDOALAlignment toEDOALAlignment( BasicAlignment al ) throws AlignmentException {
+ logger.debug( "Converting BasicAlignment to EDOALAlignment" );
EDOALAlignment alignment = new EDOALAlignment();
- try {
- alignment.init( al.getFile1(), al.getFile2() );
- } catch ( AlignmentException aex ) {
- try { // Really a friendly fallback
- alignment.init( al.getOntology1URI(), al.getOntology2URI() );
- } catch ( AlignmentException xx ) {
- throw aex;
- }
- }
- alignment.setType( al.getType() );
- alignment.setExtensions( al.convertExtension( "EDOALConverted", "fr.inrialpes.exmo.align.edoal.EDOALAlignment#toEDOAL" ) );
- LoadedOntology<Object> o1 = (LoadedOntology<Object>)alignment.getOntologyObject1(); // [W:unchecked]
- LoadedOntology<Object> o2 = (LoadedOntology<Object>)alignment.getOntologyObject2(); // [W:unchecked]
+ LoadedOntology onto1 = loadOntology( al.getOntologyObject1() );
+ LoadedOntology onto2 = loadOntology( al.getOntologyObject2() );
+ alignment.init( onto1, onto2 );
+ alignment.convertToEDOAL( al );
+ return alignment;
+ }
+ /**
+ * The EDOALAlignment has LoadedOntologies as ontologies
+ */
+ public void convertToEDOAL( BasicAlignment al ) throws AlignmentException {
+ setType( al.getType() );
+ setExtensions( al.convertExtension( "toEDOAL", "fr.inrialpes.exmo.align.edoal.EDOALAlignment#toEDOAL" ) );
+ LoadedOntology<Object> o1 = (LoadedOntology<Object>)getOntologyObject1(); // [W:unchecked]
+ LoadedOntology<Object> o2 = (LoadedOntology<Object>)getOntologyObject2(); // [W:unchecked]
for ( Cell c : al ) {
try {
- Cell newc = alignment.addAlignCell( c.getId(),
+ Cell newc = addAlignCell( c.getId(),
createEDOALExpression( o1, c.getObject1AsURI( al ) ),
createEDOALExpression( o2, c.getObject2AsURI( al ) ),
c.getRelation(),
@@ -294,12 +323,11 @@ public class EDOALAlignment extends BasicAlignment {
}
}
} catch ( AlignmentException aex ) {
- aex.printStackTrace(); // continue to concert the rest
+ logger.debug( "IGNORED Exception (continue importing)", aex );
} catch ( OntowrapException owex ) {
throw new AlignmentException( "Cannot dereference entity", owex );
}
}
- return alignment;
}
private static Id createEDOALExpression( LoadedOntology<Object> o, URI u ) throws OntowrapException, AlignmentException {
@@ -312,7 +340,7 @@ public class EDOALAlignment extends BasicAlignment {
return new RelationId( u );
} else if ( o.isIndividual( e ) ) {
return new InstanceId( u );
- } else throw new AlignmentException( "Cannot interpret URI" );
+ } else throw new AlignmentException( "Cannot interpret URI "+u );
}
@@ -335,7 +363,9 @@ public class EDOALAlignment extends BasicAlignment {
align.setExtensions( convertExtension( "cloned", this.getClass().getName()+"#clone" ) );
try {
align.ingest( this );
- } catch (AlignmentException ex) { ex.printStackTrace(); }
+ } catch (AlignmentException ex) {
+ logger.debug( "IGNORED Exception", ex );
+ }
return align;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/AveragePRGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/AveragePRGraphEvaluator.java
index 2fce4974..afbb08a9 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/AveragePRGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/AveragePRGraphEvaluator.java
@@ -1,7 +1,7 @@
/*
* $Id: AveragePRGraphEvaluator.java 1196 2010-01-10 19:58:52Z euzenat $
*
- * Copyright (C) INRIA, 2004-2005, 2007-2010
+ * Copyright (C) INRIA, 2004-2005, 2007-2010, 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
@@ -36,6 +36,9 @@ import java.util.Vector;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* Compute the precision recall graph on 11 points
* The first alignment is thus the expected one.
@@ -72,6 +75,7 @@ import java.net.URI;
*/
public class AveragePRGraphEvaluator extends GraphEvaluator {
+ final static Logger logger = LoggerFactory.getLogger( AveragePRGraphEvaluator.class );
private int size = 0; // for averaging
@@ -93,10 +97,10 @@ public class AveragePRGraphEvaluator extends GraphEvaluator {
public Vector<Pair> eval(){
Vector<Pair> result = new Vector<Pair>(STEP+1);
// Compute the average and build the vector pair
- //System.err.println( " Size: "+size );
+ //logger.trace( " Size: {}", size );
for( int j = 0; j <= STEP; j++ ) {
// JE: better with j/10
- //System.err.println( " prec at "+j+" : "+precisions[j] );
+ //logger.trace( " prec at {} : {}�", j, precisions[j] );
result.add( new Pair( ((double)j)/10, precisions[j] / size ) );
}
map = rawmap / size; // average map
@@ -115,7 +119,7 @@ public class AveragePRGraphEvaluator extends GraphEvaluator {
try {
evalAlignment( reference, al );
} catch ( AlignmentException aex ) {
- aex.printStackTrace();
+ logger.debug( "IGNORED Exception", aex );
}
}
@@ -166,7 +170,7 @@ public class AveragePRGraphEvaluator extends GraphEvaluator {
// It works backward in the vector,
// (in the same spirit as before, the maximum value so far -best- is retained)
int j = inflexion.size()-1; // index in recall-ordered vector of points
- //System.err.println( "Inflexion: "+j);
+ //logger.trace( "Inflexion: {}", j);
int i = STEP; // index of the current recall interval
double level = (double)i/STEP; // max level of that interval
double best = 0.; // best value found for that interval
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/DiffEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/DiffEvaluator.java
index 5d35ff1d..a3c73934 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/DiffEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/DiffEvaluator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2010, 2012
+ * Copyright (C) INRIA, 2010, 2012-2013
*
* 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
@@ -39,16 +39,25 @@ import java.util.HashSet;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* Evaluate proximity between two alignments.
* This function implements Precision/Recall/Fallout. The first alignment
* is thus the expected one.
*
+ * @author: Cassia Trojahn dos Santos
* @version $Id$
+ *
+ * Possible improvements:
+ * (1) make it work with EDOAL
+ * (2) write a tool that is able to pair falsenegative and falsepositive (this has been returned instead of ...)
+ *
*/
public class DiffEvaluator extends BasicEvaluator implements Evaluator {
+ final static Logger logger = LoggerFactory.getLogger( DiffEvaluator.class );
Set<Cell> truepositive;
Set<Cell> falsenegative;
@@ -103,7 +112,7 @@ public class DiffEvaluator extends BasicEvaluator implements Evaluator {
}
}
} catch (Exception e) {
- e.printStackTrace();
+ logger.debug( "IGNORED Exception", e );
}
// False negative
@@ -133,7 +142,7 @@ public class DiffEvaluator extends BasicEvaluator implements Evaluator {
}
}
} catch (Exception e) {
- e.printStackTrace();
+ logger.debug( "IGNORED Exception", e );
}
}
@@ -167,7 +176,7 @@ public class DiffEvaluator extends BasicEvaluator implements Evaluator {
}
result += "</dd>\n";
} catch (AlignmentException e) {
- e.printStackTrace();
+ logger.debug( "IGNORED Exception", e );
}
return result;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
index f2a41482..34dd560d 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
@@ -43,6 +43,9 @@ import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* Implements extended precision and recall between alignments.
* These are the measures corresponding to [Ehrig&Euzenat2005].
@@ -75,6 +78,7 @@ import java.net.URI;
*/
public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
+ final static Logger logger = LoggerFactory.getLogger( ExtPREvaluator.class );
private HeavyLoadedOntology<Object> onto1;
private HeavyLoadedOntology<Object> onto2;
@@ -194,8 +198,9 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
if ( nbexpected != 0 ) precorientrec = orientPrecsimilarity / (double) nbexpected;
if ( nbfound != 0 ) recorientprec = orientRecsimilarity / (double) nbfound;
if ( nbexpected != 0 ) recorientrec = orientRecsimilarity / (double) nbexpected;
- //System.err.println(">>>> " + nbcorrect + " : " + nbfound + " : " + nbexpected);
- //System.err.println(">>>> " + symsimilarity + " : " + effsimilarity + " : " + orientRecsimilarity + " : " + orientPrecsimilarity);
+ //logger.trace(">>>> {}�: {}�: {}", nbcorrect, nbfound, nbexpected);
+ //logger.trace(">>>> {} : {}", symsimilarity, effsimilarity );
+ //logger.trace(">>>> {} : {}", orientRecsimilarity, orientPrecsimilarity);
return (result);
}
@@ -216,19 +221,20 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
val1 = 0;
} else {
val1 = Math.abs( relativePosition( c1.getObject1(), c2.getObject1(), onto1 ) );
- //System.err.println( c1.getObject1()+" -- "+c2.getObject1()+" = "+val1 );
+ //logger.trace( "{} -- {} = {}", c1.getObject1(), c2.getObject1(), val1 );
if ( val1 == 0 ) continue;
}
if ( onto2.getEntityURI( c1.getObject2() ).equals( onto2.getEntityURI(c2.getObject2()) ) ){
val2 = 0;
} else {
val2 = Math.abs( relativePosition( c1.getObject2(), c2.getObject2(), onto2 ) );
- //System.err.println( c1.getObject2()+" -- "+c2.getObject2()+" = "+val2 );
+ //logger.trace( "{} -- {} = {}", c1.getObject2(), c2.getObject2(), val2 );
if ( val2 == 0 ) continue;
}
double val = Math.pow( symALPHA, val1 + val2 );
if ( withConfidence ) val *= 1. - Math.abs( c1.getStrength() - c2.getStrength() );
- //System.err.println( " => "+symALPHA+"^"+val1+"+"+val2+" * "+(1. - Math.abs( c1.getStrength() - c2.getStrength() ))+" = "+val );
+ // Does not write 5 {}
+ //logger.trace( " => {}^{}+{}*{} = {}", symALPHA, val1, val2, (1. - Math.abs( c1.getStrength() - c2.getStrength() )), val );
if ( relsensitive && !c1.getRelation().equals( c2.getRelation() ) ) {
if ( ( c1.getRelation().getRelation().equals("=") &&
( c2.getRelation().getRelation().equals("<") || c2.getRelation().getRelation().equals(">") ))
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/GraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/GraphEvaluator.java
index e96157ca..821cc294 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/GraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/GraphEvaluator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2004-2005, 2007-2010
+ * Copyright (C) INRIA, 2004-2005, 2007-2010, 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
@@ -38,6 +38,9 @@ import java.util.Comparator;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* GraphEvaluator: an abstraction that is used for providing evaluation curves
* instead of values (or sets of values)
@@ -57,6 +60,7 @@ import java.net.URI;
*/
public abstract class GraphEvaluator {
+ final static Logger logger = LoggerFactory.getLogger( GraphEvaluator.class );
/**
* The resolution of the provided result: by STEP steps
@@ -181,7 +185,7 @@ public abstract class GraphEvaluator {
}
}
} catch ( AlignmentException aex ) {
- aex.printStackTrace();
+ logger.debug( "IGNORED Exception", aex );
}
return false;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
index 5fb62cbc..1b321b8e 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2004-2005, 2007-2010
+ * Copyright (C) INRIA, 2004-2005, 2007-2010, 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
@@ -39,6 +39,9 @@ import java.util.Vector;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* Compute the precision recall graph on 11 points
*
@@ -65,6 +68,7 @@ import java.net.URI;
*/
public class PRGraphEvaluator extends GraphEvaluator {
+ final static Logger logger = LoggerFactory.getLogger( PRGraphEvaluator.class );
private int STEP = 10;
@@ -105,7 +109,7 @@ public class PRGraphEvaluator extends GraphEvaluator {
int nbcorrect = 0;
int nbfound = 0;
int increment = (STEP*nbexpected)/100; // 2010 should be computed with the total expected (in negrapheval)
- //System.err.println(" INCREMENT SET "+increment );
+ //logger.trace(" INCREMENT SET {}", increment );
int next = 0;
points.add( new Pair( 0., 1. ) ); // [R=0%]
next += increment;
@@ -148,7 +152,7 @@ public class PRGraphEvaluator extends GraphEvaluator {
int nbfound = 0;
int increment = (STEP*nbexpected)/100; // 2010 should be computed with the total expected (in negrapheval)
Vector<Pair> inflexion = new Vector<Pair>();
- //System.err.println(" INCREMENT SET "+increment );
+ //logger.trace(" INCREMENT SET {}", increment );
int next = 0;
// Collect the points that change recall
// (the other provide lower precision from the same recall and are not considered)
@@ -181,7 +185,7 @@ public class PRGraphEvaluator extends GraphEvaluator {
// It works backward in the vector,
// (in the same spirit as before, the maximum value so far -best- is retained)
int j = inflexion.size()-1; // index in recall-ordered vector of points
- //System.err.println( "Inflexion: "+j);
+ //logger.trace( "Inflexion: {}", j);
int i = STEP; // index of the current recall interval
double level = (double)i/STEP; // max level of that interval
double best = 0.; // best value found for that interval
@@ -199,7 +203,7 @@ public class PRGraphEvaluator extends GraphEvaluator {
for( i = 0; i <= STEP; i++ ) {
// JE: better with j/10
- //System.err.println( " prec at "+j+" : "+precisions[j] );
+ //logger.trace( " prec at {} : {}", j, precisions[j] );
points.add( new Pair( ((double)i)/10, precisions[i] ) );
}
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
index c5faa40d..0817f36b 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
@@ -38,6 +38,8 @@ import java.util.Set;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* Evaluate proximity between two alignments.
@@ -51,6 +53,7 @@ import java.net.URI;
*/
public class PRecEvaluator extends BasicEvaluator implements Evaluator {
+ final static Logger logger = LoggerFactory.getLogger( PRecEvaluator.class );
protected double precision = 1.;
@@ -148,7 +151,7 @@ public class PRecEvaluator extends BasicEvaluator implements Evaluator {
} else { result = 0.; }
String timeExt = align2.getExtension( Namespace.ALIGNMENT.uri, Annotations.TIME );
if ( timeExt != null ) time = Long.parseLong(timeExt);
- //System.err.println(">>>> " + nbcorrect + " : " + nbfound + " : " + nbexpected);
+ //logger.trace(">>>> {}�: {} : {}", nbcorrect, nbfound, nbexpected);
return (result);
}
@@ -162,7 +165,9 @@ public class PRecEvaluator extends BasicEvaluator implements Evaluator {
try {
result += " <dt>input1</dt><dd rel=\""+Namespace.ATLMAP.shortCut+":input1\" href=\""+align1.getOntology1URI()+"\">"+align1.getOntology1URI()+"</dd>";
result += " <dt>input2</dt><dd rel=\""+Namespace.ATLMAP.shortCut+":input2\" href=\""+align1.getOntology2URI()+"\">"+align1.getOntology2URI()+"</dd>";
- } catch (AlignmentException e) { e.printStackTrace(); };
+ } catch (AlignmentException e) {
+ logger.debug( "IGNORED Exception", e );
+ };
// Other missing items (easy to get)
// result += " <"+Namespace.ATLMAP.shortCut+":falseNegative>");
// result += " <"+Namespace.ATLMAP.shortCut+":falsePositive>");
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java
index 58f9281a..7faad399 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java
@@ -264,8 +264,9 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
manager.addIRIMapper(new SimpleIRIMapper( IRI.create( align.getOntology2URI() ),
IRI.create( align.getFile2() ) ) );
try {
- manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile1() ) );
- manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile2() ) );
+ // JE: The two next lines should be useless
+ //manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile1() ) );
+ //manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile2() ) );
// Load the ontology stream
OWLOntology ontology = manager.loadOntologyFromOntologyDocument( in );
reasoner = new Reasoner( ontology );
@@ -310,8 +311,9 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
manager.addIRIMapper(new SimpleIRIMapper( IRI.create( align.getOntology2URI() ),
IRI.create( align.getFile2() ) ) );
try {
- manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile1() ) );
- manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile2() ) );
+ // JE: The two next lines should be useless
+ //manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile1() ) );
+ //manager.loadOntologyFromOntologyDocument( IRI.create( align.getFile2() ) );
OWLOntology ontology = manager.loadOntologyFromOntologyDocument( merged );
reasoner = new Reasoner( ontology );
} catch ( OWLOntologyCreationException ooce ) {
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/ThresholdGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/ThresholdGraphEvaluator.java
index 76e260f8..6b7c332a 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/ThresholdGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/ThresholdGraphEvaluator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2004-2005, 2007-2010
+ * Copyright (C) INRIA, 2004-2005, 2007-2010, 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
@@ -39,6 +39,9 @@ import java.util.Vector;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* Compute the F-measure/precision/recall at various thresholds
*
@@ -48,6 +51,7 @@ import java.net.URI;
*/
public class ThresholdGraphEvaluator extends GraphEvaluator {
+ final static Logger logger = LoggerFactory.getLogger( ThresholdGraphEvaluator.class );
private int STEP = 50;
@@ -106,7 +110,7 @@ public class ThresholdGraphEvaluator extends GraphEvaluator {
// This is the version with increment
// Determine what the increment is
double increment = 1./(double)STEP;
- //System.err.println(" INCREMENT SET "+increment );
+ //logger.trace(" INCREMENT SET {}", increment );
double next = 1.;
next -= increment;
for ( EvalCell c : cellSet ) {
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/WeightedPREvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/WeightedPREvaluator.java
index 6d22c9e0..e91fbed1 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/WeightedPREvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/WeightedPREvaluator.java
@@ -38,11 +38,13 @@ import java.util.Set;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* Evaluate proximity between two alignments.
- * This function implements Precision/Recall. The first alignment
- * is thus the expected one.
+ * This function implements weighted Precision/Recall.
+ * The first alignment is thus the expected one.
*
* Basic relation sensitivity has been implemented
*
@@ -51,10 +53,11 @@ import java.net.URI;
*/
public class WeightedPREvaluator extends BasicEvaluator implements Evaluator {
+ final static Logger logger = LoggerFactory.getLogger( WeightedPREvaluator.class );
protected double precision = 1.;
- protected double recall = 1.;
+ protected double recall = 0.;
protected double overall = 0.;
@@ -85,7 +88,7 @@ public class WeightedPREvaluator extends BasicEvaluator implements Evaluator {
public void init(){
precision = 1.;
- recall = 1.;
+ recall = 0.;
overall = 0.;
fmeasure = 0.;
time = 0;
@@ -117,39 +120,51 @@ public class WeightedPREvaluator extends BasicEvaluator implements Evaluator {
for ( Cell c1 : align1 ) {
URI uri1 = c1.getObject2AsURI();
- nbexpected += c1.getStrength();
+ // measure 1
+ nbexpected += 1.;
+ // measure 2
+ //nbexpected += c1.getStrength();
Set<Cell> s2 = align2.getAlignCells1( c1.getObject1() );
- double diff = -1.0;
+ double diff = -2.0;
if( s2 != null ){
for( Cell c2 : s2 ) {
URI uri2 = c2.getObject2AsURI();
if ( uri1.equals( uri2 )
&& ( !relsensitive || c1.getRelation().equals( c2.getRelation() ) ) ) {
diff = c1.getStrength() - c2.getStrength();
- nbcorrect1 += ((diff>0.)?diff:-diff); //1. -
+ // measure 1
+ nbcorrect1 += ((diff>0.)?diff:-diff);
+ // measure 2
+ //nbcorrect1 += Math.min( c1.getStrength(), ((diff>0.)?diff:-diff) );
break;
}
}
}
- if ( diff == -1.0 ) nbcorrect1 += c1.getStrength(); // the c1 not found
+ if ( diff == -2.0 ) nbcorrect1 += c1.getStrength(); // the c1 not found
}
for ( Cell c2 : align2 ) {
URI uri2 = c2.getObject2AsURI();
- nbfound += c2.getStrength();
+ // measure 1
+ nbfound += 1.;
+ // measure 2
+ //nbfound += c2.getStrength();
Set<Cell> s1 = align1.getAlignCells1( c2.getObject1() );
- double diff = -1.0;
+ double diff = -2.0;
if( s1 != null ){
for( Cell c1 : s1 ) {
URI uri1 = c1.getObject2AsURI();
if ( uri2.equals( uri1 )
&& ( !relsensitive || c1.getRelation().equals( c2.getRelation() ) ) ) {
diff = c1.getStrength() - c2.getStrength();
- nbcorrect2 += ((diff>0.)?diff:-diff); //1. -
+ // measure 1
+ nbcorrect2 += ((diff>0.)?diff:-diff);
+ // measure 2
+ //nbcorrect2 += Math.min( c2.getStrength(), ((diff>0.)?diff:-diff) );
break;
}
}
}
- if ( diff == -1.0 ) nbcorrect2 += c2.getStrength(); // the c2 not found
+ if ( diff == -2.0 ) nbcorrect2 += c2.getStrength(); // the c2 not found
}
// What is the definition if:
@@ -159,6 +174,7 @@ public class WeightedPREvaluator extends BasicEvaluator implements Evaluator {
// precision is 0 [= nbcorrect is 0]
if ( nbfound != 0. ) precision = 1. - (nbcorrect2 / nbfound);
if ( nbexpected != 0. ) recall = 1. - (nbcorrect1 / nbexpected);
+ else { recall = 1.; precision = 0.; }
return computeDerived();
}
public double eval( Properties params, Object cache ) throws AlignmentException {
@@ -173,7 +189,7 @@ public class WeightedPREvaluator extends BasicEvaluator implements Evaluator {
} else { result = 0.; }
String timeExt = align2.getExtension( Namespace.ALIGNMENT.uri, Annotations.TIME );
if ( timeExt != null ) time = Long.parseLong(timeExt);
- //System.err.println(">>>> " + nbcorrect + " : " + nbfound + " : " + nbexpected);
+ //logger.trace(">>>> {} : {} : {}", nbcorrect, nbfound, nbexpected);
return (result);
}
@@ -187,7 +203,8 @@ public class WeightedPREvaluator extends BasicEvaluator implements Evaluator {
try {
result += " <dt>input1</dt><dd rel=\""+Namespace.ATLMAP.shortCut+":input1\" href=\""+align1.getOntology1URI()+"\">"+align1.getOntology1URI()+"</dd>";
result += " <dt>input2</dt><dd rel=\""+Namespace.ATLMAP.shortCut+":input2\" href=\""+align1.getOntology2URI()+"\">"+align1.getOntology2URI()+"</dd>";
- } catch (AlignmentException e) { e.printStackTrace(); };
+ } catch (AlignmentException e) {
+ logger.debug( "IGNORED exception", e ); };
// Other missing items (easy to get)
// result += " <"+Namespace.ATLMAP.shortCut+":falseNegative>");
// result += " <"+Namespace.ATLMAP.shortCut+":falsePositive>");
@@ -256,8 +273,8 @@ return result;
public double getFound() { return nbfound; }
// JE 2013: does not fit in WGroupEval anymore
public double getCorrect() { return nbcorrect1; }
- public double getCorrect1() { return nbcorrect1; }
- public double getCorrect2() { return nbcorrect2; }
+ public double getCorrectExpected() { return nbcorrect1; }
+ public double getCorrectFound() { return nbcorrect2; }
public long getTime() { return time; }
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
index 294d042d..9c91fb02 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
@@ -1,7 +1,7 @@
/*
* $id: ClassStructAlignment.java 1189 2010-01-03 17:57:13Z euzenat $
*
- * Copyright (C) INRIA, 2003-2004, 2007-2010
+ * Copyright (C) INRIA, 2003-2004, 2007-2010, 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
@@ -24,6 +24,9 @@ import java.util.Vector;
import java.util.Set;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.Cell;
@@ -54,11 +57,12 @@ import fr.inrialpes.exmo.ontosim.string.StringDistances;
* - pia3 [ignored=0]: weigth for property domain
* - pia4 [ignored=0]: weigth for property range
*
- * @author J�r�me Euzenat
+ * @author J�r�me Euzenat
* @version $Id$
*/
public class ClassStructAlignment extends DistanceAlignment implements AlignmentProcess {
+ final static Logger logger = LoggerFactory.getLogger( ClassStructAlignment.class );
private HeavyLoadedOntology<Object> honto1 = null;
private HeavyLoadedOntology<Object> honto2 = null;
@@ -109,7 +113,7 @@ public class ClassStructAlignment extends DistanceAlignment implements Alignment
}
classmatrix = new double[nbclass1+1][nbclass2+1];
- if (debug > 0) System.err.println("Initializing class distances");
+ logger.debug("Initializing class distances");
// Initialize class distances
// JE: Here AlignmentException is raised if cl or classlist2.get(j)
@@ -126,7 +130,7 @@ public class ClassStructAlignment extends DistanceAlignment implements Alignment
throw new AlignmentException( "Cannot find entity URI", owex );
}
- if (debug > 0) System.err.print("Computing class distances\n");
+ logger.debug("Computing class distances");
// Compute classes distances
// -- for all of its attribute, find the best match if possible... easy
// -- simply replace in the matrix the value by the value plus the
diff --git a/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
index d5092eab..c7abb0bc 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
@@ -1,7 +1,7 @@
/*
* $id: NameAndPropertyAlignment.java 1189 2010-01-03 17:57:13Z euzenat $
*
- * Copyright (C) INRIA, 2003-2004, 2007-2010
+ * Copyright (C) INRIA, 2003-2004, 2007-2010, 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
@@ -26,6 +26,9 @@ import java.util.Vector;
import java.util.Set;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentException;
@@ -50,11 +53,12 @@ import fr.inrialpes.exmo.ontosim.string.StringDistances;
* - pia3 [ignored=0]: weigth for property domain
* - pia4 [ignored=0]: weigth for property range
*
- * @author J�r�me Euzenat / Jerome Pierson
+ * @author J�r�me Euzenat / J�r�me Pierson
* @version $Id$
*/
public class NameAndPropertyAlignment extends DistanceAlignment implements AlignmentProcess {
+ final static Logger logger = LoggerFactory.getLogger( NameAndPropertyAlignment.class );
private HeavyLoadedOntology<Object> honto1 = null;
private HeavyLoadedOntology<Object> honto2 = null;
@@ -97,9 +101,6 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
double pia1 = 1.; // relation weight for name
double epsillon = 0.05; // stoping condition
- if ( params.getProperty("debug") != null )
- debug = Integer.parseInt( params.getProperty("debug") );
-
try {
// Create property lists and matrix
for ( Object prop : honto1.getObjectProperties() ){
@@ -131,7 +132,7 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
}
classmatrix = new double[nbclass1+1][nbclass2+1];
- if (debug > 0) System.err.println("Initializing property distances");
+ logger.debug("Initializing property distances");
for ( i=0; i<nbprop1; i++ ){
Object cl1 = proplist1.get(i);
String st1 = honto1.getEntityName( cl1 );
@@ -149,7 +150,7 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
}
// Initialize class distances
- if (debug > 0) System.err.println("Initializing class distances");
+ logger.debug("Initializing class distances");
for ( i=0; i<nbclass1; i++ ){
Object cl1 = classlist1.get(i);
for ( j=0; j<nbclass2; j++ ){
@@ -168,7 +169,7 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
// Here create the best matches for property distance already
// -- FirstExp: goes directly in the alignment structure
// since it will never be refined anymore...
- if (debug > 0) System.err.print("Storing property alignment\n");
+ logger.debug("Storing property alignment");
for ( i=0; i<nbprop1; i++ ){
boolean found = false;
int best = 0;
@@ -182,7 +183,7 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
}
if ( found && max < 0.5) { addAlignCell( proplist1.get(i), proplist2.get(best), "=", 1.-max ); }
}
- if (debug > 0) System.err.print("Computing class distances\n");
+ logger.debug("Computing class distances");
// Compute classes distances
// -- for all of its attribute, find the best match if possible... easy
// -- simply replace in the matrix the value by the value plus the
@@ -230,7 +231,7 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
// 1:1: get the best discard lines and columns and iterate
// Here we basically implement ?:* because the algorithm
// picks up the best matching object above threshold for i.
- if (debug > 0) System.err.print("Storing class alignment\n");
+ logger.debug("Storing class alignment");
for ( i=0; i<nbclass1; i++ ){
boolean found = false;
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
index 39dc7813..78b76d4a 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.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 General Public License as published by
@@ -24,6 +24,9 @@ import java.net.URI;
import java.util.Properties;
import java.lang.reflect.Method;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentException;
@@ -45,6 +48,7 @@ import fr.inrialpes.exmo.align.impl.MatrixMeasure;
*/
public class StringDistAlignment extends DistanceAlignment implements AlignmentProcess {
+ final static Logger logger = LoggerFactory.getLogger( StringDistAlignment.class );
Method dissimilarity = null;
String methodName = "equalDistance";
@@ -59,14 +63,13 @@ public class StringDistAlignment extends DistanceAlignment implements AlignmentP
try {
s1 = ontology1().getEntityName( o1 );
s2 = ontology2().getEntityName( o2 );
- } catch ( Exception owex ) { // dealt with below
- if ( debug > 1 ) owex.printStackTrace();
+ } catch ( Exception owex ) {
+ logger.debug( "IGNORED (returned 1. instead)", owex );
};
// Unnamed entity = max distance
if ( s1 == null || s2 == null ) return 1.;
Object[] params = { s1.toLowerCase(), s2.toLowerCase() };
- if ( debug > 4 )
- System.err.println( "OB:"+s1+" ++ "+s2+" ==> "+dissimilarity.invoke( null, params ));
+ //logger.trace( "OB:{} ++ {} ==> {}", s1, s2, dissimilarity.invoke( null, params ) );
return ((Double)dissimilarity.invoke( null, params )).doubleValue();
}
public double classMeasure( Object cl1, Object cl2 ) throws Exception {
@@ -103,7 +106,7 @@ public class StringDistAlignment extends DistanceAlignment implements AlignmentP
Class[] mParams = { sClass, sClass };
dissimilarity = Class.forName("fr.inrialpes.exmo.ontosim.string.StringDistances").getMethod( methodName, mParams );
} catch (ClassNotFoundException e) {
- e.printStackTrace(); // never happens
+ logger.debug( "IGNORED (never happens)", e ); // never happens
} catch (NoSuchMethodException e) {
throw new AlignmentException( "Unknown method for StringDistAlignment : "+params.getProperty("stringFunction"), e );
}
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
index 05844d77..7c529114 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2004, 2007-2010
+ * Copyright (C) INRIA, 2003-2004, 2007-2010, 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
@@ -18,7 +18,6 @@
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
-
package fr.inrialpes.exmo.align.impl.method;
import java.util.Vector;
@@ -26,6 +25,9 @@ import java.util.Set;
import java.util.Properties;
import java.lang.Integer;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.Cell;
@@ -51,11 +53,12 @@ import fr.inrialpes.exmo.ontosim.string.StringDistances;
* - pia3 [ignored=0]: weigth for property domain
* - pia4 [ignored=0]: weigth for property range
*
- * @author J�r�me Euzenat
+ * @author J�r�me Euzenat
* @version $Id$
*/
public class StrucSubsDistAlignment extends DistanceAlignment implements AlignmentProcess {
+ final static Logger logger = LoggerFactory.getLogger( StrucSubsDistAlignment.class );
private HeavyLoadedOntology<Object> honto1 = null;
private HeavyLoadedOntology<Object> honto2 = null;
@@ -99,9 +102,6 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
double pia1 = 1.; // relation weight for name
double epsillon = 0.05; // stoping condition
- if ( params.getProperty("debug") != null )
- debug = Integer.parseInt( params.getProperty("debug") );
-
try {
// Create property lists and matrix
for ( Object prop : honto1.getObjectProperties() ){
@@ -133,7 +133,7 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
}
classmatrix = new double[nbclass1+1][nbclass2+1];
- if (debug > 0) System.err.println("Initializing property distances");
+ logger.debug("Initializing property distances");
for ( i=0; i<nbprop1; i++ ){
Object cl1 = proplist1.get(i);
@@ -152,7 +152,7 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
}
// Initialize class distances
- if (debug > 0) System.err.println("Initializing class distances");
+ logger.debug("Initializing class distances");
for ( i=0; i<nbclass1; i++ ){
Object cl1 = classlist1.get(i);
for ( j=0; j<nbclass2; j++ ){
@@ -171,7 +171,7 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
// Here create the best matches for property distance already
// -- FirstExp: goes directly in the alignment structure
// since it will never be refined anymore...
- if (debug > 0) System.err.print("Storing property alignment\n");
+ logger.debug("Storing property alignment");
for ( i=0; i<nbprop1; i++ ){
boolean found = false;
int best = 0;
@@ -186,7 +186,7 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
if ( found ) { addAlignCell( proplist1.get(i), proplist2.get(best), "=", 1.-max ); }
}
- if (debug > 0) System.err.print("Computing class distances\n");
+ logger.debug("Computing class distances");
// Compute classes distances
// -- for all of its attribute, find the best match if possible... easy
// -- simply replace in the matrix the value by the value plus the
@@ -242,7 +242,7 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
// 1:1: get the best discard lines and columns and iterate
// Here we basically implement ?:* because the algorithm
// picks up the best matching object above threshold for i.
- if (debug > 0) System.err.print("Storing class alignment\n");
+ logger.debug("Storing class alignment");
for ( i=0; i<nbclass1; i++ ){
boolean found = false;
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
index 8604a6d0..57551611 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/COWLMappingRendererVisitor.java
@@ -93,7 +93,7 @@ public class COWLMappingRendererVisitor extends GenericReflectiveVisitor impleme
writer.print(" <cowl:targetOntology>\n");
writer.print(" <owl:Ontology rdf:about=\""+onto2.getURI()+"\"/>\n");
writer.print(" </cowl:targetOntology>\n");
- for( Cell c : align ){
+ for( Cell c : alignment ){
c.accept( this );
} //end for
writer.print(" </cowl:Mapping>\n");
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
index ea9bd4fd..7c773f15 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2012
+ * Copyright (C) INRIA, 2012-2013
*
* 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
@@ -23,6 +23,9 @@ package fr.inrialpes.exmo.align.impl.renderer;
import java.lang.reflect.Method;
import java.lang.reflect.InvocationTargetException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.AlignmentException;
/**
@@ -34,6 +37,7 @@ import org.semanticweb.owl.align.AlignmentException;
* and Relation may be extended.
*/
public class GenericReflectiveVisitor {
+ final static Logger logger = LoggerFactory.getLogger( GenericReflectiveVisitor.class );
/**
* Finds the visit(X) method corresponding to the object class (subclass of a root class)
@@ -54,7 +58,7 @@ public class GenericReflectiveVisitor {
}
}
if ( m == null ) {//newc == Object.class ) {
- // System.out.println( "Searching for interfaces" );
+ // logger.trace( "Searching for interfaces" );
Class[] interfaces = c.getInterfaces();
for ( int i=0; i < interfaces.length; i++ ) {
if ( interfaces[i] != root ) {
@@ -83,12 +87,12 @@ public class GenericReflectiveVisitor {
method.invoke( visitor, new Object[] {o} );
return true;
} catch ( IllegalAccessException iaex ) {
- iaex.printStackTrace();
+ logger.debug( "IGNORED Exception", iaex );
} catch ( InvocationTargetException itex ) {
if ( itex.getCause() instanceof AlignmentException ) {
throw (AlignmentException)itex.getCause();
} else {
- itex.printStackTrace();
+ logger.debug( "IGNORED Exception", itex );
}
}
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/GraphPatternRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/GraphPatternRendererVisitor.java
index 2d0f4ec7..bd40289c 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/GraphPatternRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/GraphPatternRendererVisitor.java
@@ -32,6 +32,9 @@ import java.util.Iterator;
import java.util.List;
import java.util.Set;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
@@ -71,6 +74,7 @@ import fr.inrialpes.exmo.align.parser.SyntaxElement.Constructor;
// JE: create a string... problem with increment.
public abstract class GraphPatternRendererVisitor extends IndentedRendererVisitor implements EDOALVisitor {
+ final static Logger logger = LoggerFactory.getLogger( GraphPatternRendererVisitor.class );
Alignment alignment = null;
Cell cell = null;
@@ -163,7 +167,7 @@ public abstract class GraphPatternRendererVisitor extends IndentedRendererVisito
if ( out != null ) // there was at least one file
out.close();
} catch(IOException ioe) {
- System.err.println( ioe );
+ logger.debug( "IGNORED Exception", ioe );
}
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
index e6ab0b18..4506a4d6 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
@@ -25,6 +25,9 @@ import java.util.Properties;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
@@ -87,6 +90,7 @@ import fr.inrialpes.exmo.align.impl.edoal.EDOALVisitor;
*/
public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements AlignmentVisitor, EDOALVisitor {
+ final static Logger logger = LoggerFactory.getLogger( OWLAxiomsRendererVisitor.class );
boolean heterogeneous = false;
boolean edoal = false;
Alignment alignment = null;
@@ -108,6 +112,7 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
public void visit( Alignment align ) throws AlignmentException {
if ( subsumedInvocableMethod( this, align, Alignment.class ) ) return;
// default behaviour
+ //logger.trace( "Alignment: {}", align );
if ( align instanceof ObjectAlignment ) {
alignment = align;
onto1 = (LoadedOntology)((ObjectAlignment)alignment).getOntologyObject1();
@@ -139,10 +144,10 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
writer.print(" </owl:Ontology>"+NL+NL);
try {
- for( Cell c : align ){
+ for( Cell c : alignment ){
Object ob1 = c.getObject1();
Object ob2 = c.getObject2();
-
+ //logger.trace( "Rendering {} -- {}", ob1, ob2 );
if ( heterogeneous || edoal ||
( onto1.isClass( ob1 ) && onto2.isClass( ob2 ) ) ||
( onto1.isDataProperty( ob1 ) && onto2.isDataProperty( ob2 ) ) ||
@@ -154,6 +159,9 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
} catch ( OntowrapException owex ) {
throw new AlignmentException( "Error accessing ontology", owex );
}
+ //logger.trace( "Heterogeneous: {}", heterogeneous);
+ //logger.trace( "EDOAL: {}", edoal);
+ //logger.trace( "onto1: {}", onto1);
writer.print("</rdf:RDF>"+NL);
}
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
index c7433db0..59ff583e 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2010, 2012
+ * Copyright (C) INRIA, 2003-2010, 2012-2013
*
* 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
@@ -28,6 +28,9 @@ import java.util.Properties;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
@@ -87,6 +90,7 @@ import fr.inrialpes.exmo.align.impl.edoal.EDOALVisitor;
*/
public class RDFRendererVisitor extends IndentedRendererVisitor implements AlignmentVisitor,EDOALVisitor {
+ final static Logger logger = LoggerFactory.getLogger( RDFRendererVisitor.class );
Alignment alignment = null;
Cell cell = null;
@@ -111,6 +115,7 @@ public class RDFRendererVisitor extends IndentedRendererVisitor implements Align
}
public void visit( Alignment align ) throws AlignmentException {
+ //logger.trace( "Processing alignment {}", align );
if ( subsumedInvocableMethod( this, align, Alignment.class ) ) return;
// default behaviour
String extensionString = "";
@@ -224,6 +229,7 @@ public class RDFRendererVisitor extends IndentedRendererVisitor implements Align
}
public void visit( Cell cell ) throws AlignmentException {
+ //logger.trace( "Processing cell {}", cell );
if ( subsumedInvocableMethod( this, cell, Cell.class ) ) return;
// default behaviour
this.cell = cell;
@@ -242,6 +248,7 @@ public class RDFRendererVisitor extends IndentedRendererVisitor implements Align
if ( alignment.getLevel().startsWith("2EDOAL") ) {
indentedOutputln("<"+SyntaxElement.ENTITY1.print(DEF)+">");
increaseIndent();
+ //logger.trace( "Processing ob1 {}", cell.getObject1() );
((Expression)(cell.getObject1())).accept( this );
decreaseIndent();
writer.print(NL);
@@ -249,6 +256,7 @@ public class RDFRendererVisitor extends IndentedRendererVisitor implements Align
indentedOutputln("<"+SyntaxElement.ENTITY2.print(DEF)+">");
increaseIndent();
((Expression)(cell.getObject2())).accept( this );
+ //logger.trace( "Processing ob2 {}", cell.getObject2() );
decreaseIndent();
writer.print(NL);
indentedOutputln("</"+SyntaxElement.ENTITY2.print(DEF)+">");
@@ -644,7 +652,7 @@ public class RDFRendererVisitor extends IndentedRendererVisitor implements Align
indentedOutput("</"+SyntaxElement.TRANSF.print(DEF)+">");
}
- public void visit( final Datatype e ) throws AlignmentException {
+ public void visit( final Datatype e ) {
indentedOutput("<"+SyntaxElement.EDATATYPE.print(DEF)+">");
writer.print("<"+SyntaxElement.DATATYPE.print(DEF)+" "+SyntaxElement.RDF_ABOUT.print(DEF)+"=\""+e.getType()+"\"/>");
writer.print("</"+SyntaxElement.EDATATYPE.print(DEF)+">");
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SEKTMappingRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SEKTMappingRendererVisitor.java
index 2b3fe349..d24d75a9 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SEKTMappingRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SEKTMappingRendererVisitor.java
@@ -80,7 +80,7 @@ public class SEKTMappingRendererVisitor extends GenericReflectiveVisitor impleme
writer.print(" source(<\""+onto1.getURI()+"\">)\n");
writer.print(" target(<\""+onto2.getURI()+"\">)\n");
- for( Cell c : align ){
+ for( Cell c : alignment ){
c.accept( this );
} //end for
writer.print(")\n");
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLConstructRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLConstructRendererVisitor.java
index dbf00e2b..3f810dfa 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLConstructRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLConstructRendererVisitor.java
@@ -99,7 +99,7 @@ public class SPARQLConstructRendererVisitor extends GraphPatternRendererVisitor
content_Corese += "<!ENTITY rul \"http://ns.inria.fr/edelweiss/2011/rule#\">" + NL;
content_Corese += "]>" + NL;
content_Corese += "<rdf:RDF xmlns:rdfs=\"&rdfs;\" xmlns:rdf=\"&rdf;\" xmlns = \'&rul;\' >" + NL + NL + NL;
- for( Cell c : align ){ c.accept( this ); };
+ for( Cell c : alignment ){ c.accept( this ); };
content_Corese += "</rdf:RDF>" + NL;
if ( corese ) {
if( split ) {
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLSelectRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLSelectRendererVisitor.java
index 916f5688..058936d9 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLSelectRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLSelectRendererVisitor.java
@@ -80,7 +80,7 @@ public class SPARQLSelectRendererVisitor extends GraphPatternRendererVisitor imp
throw new AlignmentException("SPARQLSELECTRenderer: cannot render simple alignment. Need an EDOALAlignment", alex );
}
}
- for( Cell c : align ){ c.accept( this ); };
+ for( Cell c : alignment ){ c.accept( this ); };
}
public void visit( Cell cell ) throws AlignmentException {
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SWRLRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SWRLRendererVisitor.java
index babf4464..b4c2d42c 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SWRLRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SWRLRendererVisitor.java
@@ -25,6 +25,9 @@ import java.util.Properties;
import java.io.PrintWriter;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
@@ -47,6 +50,7 @@ import fr.inrialpes.exmo.ontowrap.OntowrapException;
*/
public class SWRLRendererVisitor extends GenericReflectiveVisitor implements AlignmentVisitor {
+ final static Logger logger = LoggerFactory.getLogger( SWRLRendererVisitor.class );
PrintWriter writer = null;
Alignment alignment = null;
LoadedOntology onto1 = null;
@@ -90,7 +94,7 @@ public class SWRLRendererVisitor extends GenericReflectiveVisitor implements Ali
}
writer.print("\n");
writer.println(" <owlx:Imports rdf:resource=\""+onto1.getURI()+"\"/>\n");
- for( Cell c : align ){
+ for( Cell c : alignment ){
c.accept( this );
}
writer.println("</swrlx:Ontology>");
@@ -104,13 +108,23 @@ public class SWRLRendererVisitor extends GenericReflectiveVisitor implements Ali
}
public void visit( EquivRelation rel ) throws AlignmentException {
- // JE: We should send warnings when dataproperties are mapped to individual properties and vice versa...
Object ob1 = cell.getObject1();
Object ob2 = cell.getObject2();
- URI uri1;
- URI uri2;
+ generateImplication( ob1, ob2 );
+ generateImplication( ob2, ob1 );
+ }
+
+ public void visit( SubsumeRelation rel ) throws AlignmentException {
+ generateImplication( cell.getObject2(), cell.getObject1() );
+ };
+ public void visit( SubsumedRelation rel ) throws AlignmentException {
+ generateImplication( cell.getObject1(), cell.getObject2() );
+ };
+
+ public void generateImplication( Object ob1, Object ob2 ) throws AlignmentException {
+ // JE: We should send warnings when dataproperties are mapped to individual properties and vice versa...
try {
- uri1 = onto1.getEntityURI( ob1 );
+ URI uri1 = onto1.getEntityURI( ob1 );
writer.println(" <ruleml:imp>");
writer.println(" <ruleml:_body>");
if ( onto1.isClass( ob1 ) ){
@@ -131,7 +145,7 @@ public class SWRLRendererVisitor extends GenericReflectiveVisitor implements Ali
}
writer.println(" </ruleml:_body>");
writer.println(" <ruleml:_head>");
- uri2 = onto2.getEntityURI( ob2 );
+ URI uri2 = onto2.getEntityURI( ob2 );
if ( onto2.isClass( ob2 ) ){
writer.println(" <swrlx:classAtom>");
writer.println(" <owllx:Class owllx:name=\""+uri2+"\"/>");
@@ -155,9 +169,66 @@ public class SWRLRendererVisitor extends GenericReflectiveVisitor implements Ali
}
}
- public void visit( SubsumeRelation rel ){};
- public void visit( SubsumedRelation rel ){};
- public void visit( IncompatRelation rel ){};
+ public void visit( IncompatRelation rel ) throws AlignmentException {
+ // JE: We should send warnings when dataproperties are mapped to individual properties and vice versa...
+ Object ob1 = cell.getObject1();
+ Object ob2 = cell.getObject2();
+ try {
+ URI uri1 = onto1.getEntityURI( ob1 );
+ URI uri2 = onto2.getEntityURI( ob2 );
+ writer.println(" <ruleml:imp>");
+ if ( onto1.isClass( ob1 ) && onto2.isClass( ob2 ) ){
+ writer.println(" <ruleml:_body>");
+ writer.println(" <swrl:classAtom>");
+ writer.println(" <owllx:Class owllx:name=\""+uri1+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" </swrl:classAtom>");
+ writer.println(" <swrlx:classAtom>");
+ writer.println(" <owllx:Class owllx:name=\""+uri2+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" </swrl:classAtom>");
+ writer.println(" </ruleml:_body>");
+ writer.println(" <ruleml:_head>");
+ writer.println(" <swrlx:classAtom>");
+ writer.println(" <owllx:Class owllx:name=\"owl:Nothing\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" </swrl:classAtom>");
+ writer.println(" </ruleml:_head>");
+ } else if ( onto1.isDataProperty( ob1 ) && onto2.isDataProperty( ob2 ) ) {
+ writer.println(" <ruleml:_body>");
+ writer.println(" <swrl:datavaluedPropertyAtom swrlx:property=\""+uri1+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" <ruleml:var>y</ruleml:var>");
+ writer.println(" <swrl:datavaluedPropertyAtom>");
+ writer.println(" <swrl:datavaluedPropertyAtom swrlx:property=\""+uri2+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" <ruleml:var>y</ruleml:var>");
+ writer.println(" </swrl:datavaluedPropertyAtom>");
+ writer.println(" </ruleml:_body>");
+ writer.println(" <ruleml:_head>");
+ writer.println(" </ruleml:_head>");
+ } else if ( onto1.isObjectProperty( ob1 ) && onto2.isObjectProperty( ob2 ) ) {
+ writer.println(" <ruleml:_body>");
+ writer.println(" <swrl:individualPropertyAtom swrlx:property=\""+uri1+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" <ruleml:var>y</ruleml:var>");
+ writer.println(" </swrl:individualPropertyAtom>");
+ writer.println(" <swrl:individualPropertyAtom swrlx:property=\""+uri2+"\"/>");
+ writer.println(" <ruleml:var>x</ruleml:var>");
+ writer.println(" <ruleml:var>y</ruleml:var>");
+ writer.println(" </swrl:individualPropertyAtom>");
+ writer.println(" </ruleml:_body>");
+ writer.println(" <ruleml:_head>");
+ writer.println(" </ruleml:_head>");
+ } else {
+ logger.warn( "Cannot generate heterogeneous rules" );
+ }
+ writer.println(" </ruleml:imp>\n");
+ } catch ( OntowrapException owex ) {
+ throw new AlignmentException( "Error accessing ontology", owex );
+ }
+ }
+
public void visit( Relation rel ) throws AlignmentException {
if ( subsumedInvocableMethod( this, rel, Relation.class ) ) return;
// default behaviour
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
index ab197073..c13dc989 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/XSLTRendererVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2004, 2006-2010, 2012
+ * Copyright (C) INRIA, 2003-2004, 2006-2010, 2012-2013
*
* 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
@@ -78,7 +78,7 @@ public class XSLTRendererVisitor extends GenericReflectiveVisitor implements Ali
onto1 = (LoadedOntology)((ObjectAlignment)align).getOntologyObject1();
onto2 = (LoadedOntology)((ObjectAlignment)align).getOntologyObject2();
}
- for( Cell c : align ){
+ for( Cell c : alignment ){
collectURIs( c );
}
alignment = align;
@@ -98,7 +98,7 @@ public class XSLTRendererVisitor extends GenericReflectiveVisitor implements Ali
}
writer.print("\n");
- for ( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
+ for ( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
Cell c = (Cell)e.nextElement();
c.accept( this );
}
@@ -136,8 +136,8 @@ public class XSLTRendererVisitor extends GenericReflectiveVisitor implements Ali
throw new AlignmentException( "Cannot find entity URI", owex );
}
} else {
- entity1URI = cell.getObject1AsURI(alignment);
- entity2URI = cell.getObject2AsURI(alignment);
+ entity1URI = cell.getObject1AsURI( alignment );
+ entity2URI = cell.getObject2AsURI( alignment );
}
if ( entity1URI != null ) {
String ns1 = entity1URI.getScheme()+":"+entity1URI.getSchemeSpecificPart()+"#";
@@ -163,8 +163,8 @@ public class XSLTRendererVisitor extends GenericReflectiveVisitor implements Ali
throw new AlignmentException( "Cannot find entity URI", owex );
}
} else {
- writer.println(" <xsl:template match=\""+namespacify(cell.getObject1AsURI(alignment))+"\">");
- writer.println(" <xsl:element name=\""+namespacify(cell.getObject2AsURI(alignment))+"\">");
+ 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/ling/JWNLAlignment.java b/src/fr/inrialpes/exmo/align/ling/JWNLAlignment.java
index 45511c63..29f07beb 100644
--- a/src/fr/inrialpes/exmo/align/ling/JWNLAlignment.java
+++ b/src/fr/inrialpes/exmo/align/ling/JWNLAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2005, 2007, 2009-2010
+ * Copyright (C) INRIA, 2003-2005, 2007, 2009-2010, 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
@@ -32,12 +32,17 @@ import org.semanticweb.owl.align.AlignmentException;
import java.util.Properties;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* This Class uses JWNLDistances to align two ontologies.
* @version $Id$
*/
public class JWNLAlignment extends DistanceAlignment implements AlignmentProcess {
+ final static Logger logger = LoggerFactory.getLogger( JWNLAlignment.class );
+
final static String WNVERS = "3.0";
final static int BASICSYNDIST = 0;
@@ -93,7 +98,7 @@ public class JWNLAlignment extends DistanceAlignment implements AlignmentProcess
return measure( pr1, pr2 );
}
public double individualMeasure( Object id1, Object id2 ) throws Exception {
- if ( debug > 4 ) System.err.println( "ID:"+id1+" -- "+id2);
+ //logger.trace( "ID: {} -- {}", id1, id2 );
return measure( id1, id2 );
}
}
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index c84d9d15..ce0a5cc4 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2005, 2007-2010, 2012
+ * Copyright (C) INRIA, 2003-2005, 2007-2010, 2012-2013
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -33,6 +33,9 @@ import java.lang.Integer;
import java.lang.Double;
import java.util.Hashtable;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.AlignmentException;
@@ -47,7 +50,7 @@ import fr.inrialpes.exmo.align.impl.Annotations;
/**
* This class allows the creation of a parser for an Alignment file.
* The class is called by:
- * AlignmentParser parser = new AlignmentParser( debugLevel );
+ * AlignmentParser parser = new AlignmentParser();
* Alignment alignment = parser.parse( input );
* input can be a URI as a String, an InputStream
* This new version (January 2004) parses the alignment description in
@@ -56,12 +59,8 @@ import fr.inrialpes.exmo.align.impl.Annotations;
*/
public class AlignmentParser {
+ final static Logger logger = LoggerFactory.getLogger( AlignmentParser.class );
- /**
- * level of debug/warning information
- */
- protected int debugMode = 0;
-
/**
* a URI to a process
*/
@@ -97,11 +96,11 @@ public class AlignmentParser {
/**
* Creates a Parser.
- * @param debugMode The value of the debug mode
+ * @param debugMode The value of the debug mode DEPRECATED
*/
- public AlignmentParser( int debugMode ) {
- this.debugMode = debugMode;
- }
+ public AlignmentParser( int debugMode ) {}
+
+ public AlignmentParser() {}
public void setEmbedded( boolean b ){
embedded = b;
@@ -129,21 +128,19 @@ public class AlignmentParser {
*/
private Alignment callParser( Object o ) throws AlignmentException {
try {
- XMLParser parser = new XMLParser( debugMode );
+ XMLParser parser = new XMLParser();
if ( embedded ) parser.setEmbedded( embedded );
//alignment = parser.parse( o );
alignment = callParser( parser, o );
} catch ( Exception e ) {
- if ( debugMode > 0 ) {
- System.err.println("XMLParser failed to parse alignment (INFO)");
- e.printStackTrace();
- }
+ logger.debug( "XMLParser failed to parse alignment (INFO)", e );
+ logger.debug( "Using RDFParser instead" );
try {
if ( !embedded ) {
- RDFParser rparser = new RDFParser( debugMode );
+ RDFParser rparser = new RDFParser();
alignment = callParser( rparser, o );
} else {
- throw new AlignmentException( "Cannot parse "+o+" (use debug>0 for more info)", e );
+ throw new AlignmentException( "Cannot parse "+o+" (use logging for more info)", e );
}
} catch ( Exception ex ) {
// JE: should contain both ex and e
diff --git a/src/fr/inrialpes/exmo/align/parser/RDFParser.java b/src/fr/inrialpes/exmo/align/parser/RDFParser.java
index 8ab22b29..c88cfe04 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, 2008-2010, 2012
+ * Copyright (C) INRIA, 2008-2010, 2012-2013
*
* 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
@@ -84,8 +84,8 @@ import java.util.HashSet;
import java.util.List;
import java.util.LinkedList;
-import java.util.logging.Logger;
-import java.util.logging.Level;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
// Yes we are relying on Jena for parsing RDF
import com.hp.hpl.jena.rdf.model.Model;
@@ -116,13 +116,10 @@ import com.hp.hpl.jena.vocabulary.RDF;
* @version $Revision: 1.7 $
*/
public class RDFParser {
-
- private static Logger logger = Logger.getLogger(RDFParser.class.toString());
+ final static Logger logger = LoggerFactory.getLogger( RDFParser.class );
private static Model rDFModel;
- private int debug = 0;
-
private boolean isPattern = false; // I contain variables
private boolean speedparse = false; // skip all checks
@@ -131,17 +128,13 @@ public class RDFParser {
/**
* Creates an RDF Parser.
*/
- public RDFParser() {
- this(0);
- }
+ public RDFParser() {}
/**
* Creates an RDF Parser.
- * @param debugMode The value of the debug mode
+ * @param debugMode The value of the debug mode (DEPRECATED)
*/
- public RDFParser( int debugMode ) {
- debug = debugMode;
- }
+ public RDFParser( int debugMode ) {}
/**
* Initialisation of the structures
@@ -172,7 +165,7 @@ public class RDFParser {
// Initialize the syntax description
initSyntax();
// Shut up logging handling
- com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler.silent = true;
+ //com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler.silent = true;
// Get the statement including alignment resource as rdf:type
StmtIterator stmtIt = rdfmodel.listStatements(null, RDF.type,(Resource)SyntaxElement.getResource("Alignment"));
// Take the first one if it exists
@@ -283,11 +276,10 @@ public class RDFParser {
stmtIt = node.listProperties((Property)SyntaxElement.MAP.resource );
while (stmtIt.hasNext()) {
Statement stmt = stmtIt.nextStatement();
- if ( debug > 0 ) System.err.println( " ---------------> "+stmt );
+ //logger.trace( " ---------------> {}", stmt );
try { alignment.addAlignCell( parseCell( stmt.getResource() ) ); }
catch ( AlignmentException ae ) {
- System.err.println( "Error "+ae );
- ae.printStackTrace();
+ logger.debug( "IGNORED Exception", ae );
}
}
@@ -394,10 +386,8 @@ public class RDFParser {
Expression s = parseExpression( entity1 );
Expression t = parseExpression( entity2 );
- if ( debug > 0 ) {
- System.err.println(" s : "+s);
- System.err.println(" t : "+t);
- }
+ //logger.trace(" s : {}", s);
+ //logger.trace(" t : {}", t);
EDOALCell cell = new EDOALCell( id, s, t, type, m );
// Parse the possible transformations
@@ -406,13 +396,11 @@ public class RDFParser {
Statement stmt = stmtIt.nextStatement();
try { cell.addTransformation( parseTransformation( stmt.getResource() ) ); }
catch ( AlignmentException ae ) {
- System.err.println( "Error "+ae );
- ae.printStackTrace();
+ logger.debug( "INGORED Exception", ae );
}
}
return cell;
} catch (Exception e) { //wrap other type exception
- logger.log(java.util.logging.Level.SEVERE, "The cell isn't correct: " + node.getLocalName() + " "+e.getMessage());
throw new AlignmentException("Cannot parse correspondence " + node.getLocalName(), e);
}
}
@@ -429,13 +417,10 @@ public class RDFParser {
Resource entity2 = node.getProperty((Property)SyntaxElement.TRENT2.resource).getResource();
ValueExpression s = parseValue( entity1 );
ValueExpression t = parseValue( entity2 );
- if ( debug > 0 ) {
- System.err.println(" (Transf)s : "+s);
- System.err.println(" (Transf)t : "+t);
- }
+ //logger.trace(" (Transf)s : {}", s);
+ //logger.trace(" (Transf)t : {}", t);
return new Transformation( type, s, t );
} catch (Exception e) { //wrap other type exception
- logger.log(java.util.logging.Level.SEVERE, "The cell isn't correct:" + node.getLocalName() + " "+e.getMessage());
throw new AlignmentException("Cannot parse transformation " + node, e);
}
}
@@ -476,10 +461,8 @@ public class RDFParser {
}
protected ClassExpression parseClass( final Resource node ) throws AlignmentException {
- if ( debug > 1 ) {
- StmtIterator it = node.listProperties();
- while ( it.hasNext() ) System.err.println( " > "+it.next() );
- }
+ //StmtIterator it = node.listProperties();
+ //while ( it.hasNext() ) logger.trace( " > {}", it.next() );
Resource rdfType = node.getProperty(RDF.type).getResource();
if ( rdfType.equals( SyntaxElement.CLASS_EXPR.resource ) ) {
URI id = getNodeId( node );
@@ -696,7 +679,7 @@ public class RDFParser {
protected Datatype parseDatatype ( final RDFNode nn ) throws AlignmentException {
String uri = null;
if ( nn.isLiteral() ) { // Legacy
- System.err.println( "Warning: datatypes must be Datatype objects ("+((Literal)nn).getString()+")" );
+ logger.warn( "Datatypes must be Datatype objects ({})", ((Literal)nn).getString() );
uri = ((Literal)nn).getString();
} else if ( nn.isResource() ) {
if ( !((Resource)nn).getProperty(RDF.type).getResource().equals( SyntaxElement.DATATYPE.resource ) )
@@ -824,7 +807,7 @@ public class RDFParser {
u = new URI( ((Resource)node).getProperty( (Property)SyntaxElement.ETYPE.resource ).getLiteral().getString() );
} catch (URISyntaxException urisex) {
//throw new AlignmentException( "Incorect URI for edoal:type : "+ ((Resource)node).getProperty( (Property)SyntaxElement.TYPE.resource ).getLiteral().getString() );
- urisex.printStackTrace();
+ logger.debug( "IGNORED Exception", urisex );
}
}
if ( u != null ) {
diff --git a/src/fr/inrialpes/exmo/align/parser/TypeCheckingVisitor.java b/src/fr/inrialpes/exmo/align/parser/TypeCheckingVisitor.java
index 7b485fbd..3a416e58 100644
--- a/src/fr/inrialpes/exmo/align/parser/TypeCheckingVisitor.java
+++ b/src/fr/inrialpes/exmo/align/parser/TypeCheckingVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2010-2012
+ * Copyright (C) INRIA, 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
@@ -24,6 +24,9 @@ import java.util.Hashtable;
import java.util.Properties;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Cell;
@@ -73,6 +76,7 @@ import fr.inrialpes.exmo.align.impl.edoal.Comparator;
*/
public class TypeCheckingVisitor {
+ final static Logger logger = LoggerFactory.getLogger( TypeCheckingVisitor.class );
public enum TYPE { CLASS, PROPERTY, RELATION, INSTANCE, VALUE, DATATYPE, ANY, ERROR };
@@ -352,7 +356,7 @@ public class TypeCheckingVisitor {
public TYPE raiseError( final URI u, TYPE expT, TYPE foundT ) {
error = true;
- if ( print ) System.err.println( "Incorrectly typed expression "+u+": Type "+foundT+" ("+expT+" expected)");
+ if ( print ) logger.error( "Incorrectly typed expression {}: Type {} ({} expected)", u, foundT, expT );
return TYPE.ERROR;
}
diff --git a/src/fr/inrialpes/exmo/align/parser/XMLParser.java b/src/fr/inrialpes/exmo/align/parser/XMLParser.java
index 2c26e142..9d48978d 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, 2007-2012
+ * Copyright (C) INRIA, 2003-2005, 2007-2013
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -43,6 +43,9 @@ import java.lang.Integer;
import java.lang.Double;
import java.util.Hashtable;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.AlignmentException;
@@ -60,7 +63,7 @@ import fr.inrialpes.exmo.align.impl.Extensions;
/**
* This class allows the creation of a parser for an Alignment file.
* The class is called by:
- * AlignmentParser parser = new AlignmentParser( debugLevel );
+ * AlignmentParser parser = new AlignmentParser();
* Alignment alignment = parser.parse( input );
* input can be a URI as a String, an InputStream
* This new version (January 2004) parses the alignment description in
@@ -69,12 +72,8 @@ import fr.inrialpes.exmo.align.impl.Extensions;
*/
public class XMLParser extends DefaultHandler {
+ final static Logger logger = LoggerFactory.getLogger( XMLParser.class );
- /**
- * level of debug/warning information
- */
- protected int debugMode = 0;
-
/**
* a URI to a process
*/
@@ -171,22 +170,22 @@ public class XMLParser extends DefaultHandler {
* Creates an XML Parser.
*/
public XMLParser() throws ParserConfigurationException, SAXException {
- this(0);
+ this(false);
}
/**
* Creates an XML Parser.
- * @param debugMode The value of the debug mode
+ * @param validate 0 if non validating, more otherwise
+ * This should become a boolean
*/
- public XMLParser( int debugMode ) throws ParserConfigurationException, SAXException {
- this.debugMode = debugMode;
+ public XMLParser( int validate ) throws ParserConfigurationException, SAXException {
+ this( (validate > 0) );
+ }
+
+ public XMLParser( boolean validate ) throws ParserConfigurationException, SAXException {
SAXParserFactory parserFactory = SAXParserFactory.newInstance();
- if (debugMode > 0) {
- parserFactory.setValidating(true);
- } else {
- parserFactory.setValidating(false);
- }
- parserFactory.setNamespaceAware(true);
+ parserFactory.setValidating( validate );
+ parserFactory.setNamespaceAware( true );
parser = parserFactory.newSAXParser();
}
@@ -264,7 +263,7 @@ public class XMLParser extends DefaultHandler {
* @param atts The attributes name of the current element
*/
public void startElement(String namespaceURI, String pName, String qname, Attributes atts) throws SAXException {
- if(debugMode > 2) System.err.println("startElement XMLParser : " + pName);
+ logger.debug( "startElement XMLParser : {}", pName );
parseLevel++;
if( namespaceURI.equals( Namespace.ALIGNMENT.uri+"#" )
|| namespaceURI.equals( Namespace.ALIGNMENT.uri ) ) {
@@ -272,16 +271,14 @@ public class XMLParser extends DefaultHandler {
} else if (pName.equals( SyntaxElement.SEMANTICS.name )) {
} else if (pName.equals( SyntaxElement.MEASURE.name )) {
} else if (pName.equals( SyntaxElement.ENTITY2.name )) {
- if(debugMode > 2)
- System.err.println(" resource = " + atts.getValue(SyntaxElement.RDF_RESOURCE.print()));
+ //logger.trace( " resource = {}", atts.getValue(SyntaxElement.RDF_RESOURCE.print()) );
try {
cl2 = new URI( atts.getValue(SyntaxElement.RDF_RESOURCE.print()) );
} catch (URISyntaxException e) {
throw new SAXException("Malformed URI: "+atts.getValue(SyntaxElement.RDF_RESOURCE.print()));
}
} else if (pName.equals( SyntaxElement.ENTITY1.name )) {
- if(debugMode > 2)
- System.err.println(" resource = " + atts.getValue(SyntaxElement.RDF_RESOURCE.print()));
+ //logger.trace(" resource = {}", atts.getValue(SyntaxElement.RDF_RESOURCE.print()));
try {
cl1 = new URI( atts.getValue( SyntaxElement.RDF_RESOURCE.print() ) );
} catch (URISyntaxException e) {
@@ -347,7 +344,7 @@ public class XMLParser extends DefaultHandler {
alignment.setExtension( Namespace.ALIGNMENT.uri, Annotations.ID, about );
};
} else {
- if ( debugMode > 0 ) System.err.println("[XMLParser] Unknown element name : "+pName);
+ logger.warn( "Unknown element name : {}", pName );
};
} else if ( namespaceURI.equals( Namespace.SOAP_ENV.prefix )) { //"http://schemas.xmlsoap.org/soap/envelope/")) {
// Ignore SOAP namespace
@@ -373,8 +370,7 @@ 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);
+ //logger.trace( "content XMLParser : {}", content );
}
*/
@@ -393,7 +389,7 @@ public class XMLParser extends DefaultHandler {
} else {
content = newContent;
}
- if ( debugMode > 2 ) System.err.println("content XMLParser : " + content);
+ logger.debug( "content XMLParser : {}", content );
}
/**
@@ -404,8 +400,7 @@ public class XMLParser extends DefaultHandler {
* @param qName The name of the current element
*/
public void endElement(String namespaceURI, String pName, String qName ) throws SAXException {
- if(debugMode > 2)
- System.err.println("endElement XMLParser : " + pName);
+ logger.debug( "endElement XMLParser : {}", pName );
if( namespaceURI.equals( Namespace.ALIGNMENT.uri+"#" )
|| namespaceURI.equals( Namespace.ALIGNMENT.uri ) ) {
try {
@@ -418,17 +413,15 @@ public class XMLParser extends DefaultHandler {
} else if (pName.equals( SyntaxElement.ENTITY2.name )) {
} else if (pName.equals( SyntaxElement.ENTITY1.name )) {
} else if (pName.equals( SyntaxElement.CELL.name )) {
- if(debugMode > 1) {
- System.err.print(" " + cl1);
- System.err.print(" " + cl2);
- System.err.print(" " + relation);
- System.err.println(" " + Double.parseDouble(measure));
- }
+ //logger.trace( " {}", cl1 );
+ //logger.trace( " {}", cl2 );
+ //logger.trace( " {}", relation);
+ //logger.trace( " {}", Double.parseDouble(measure));
if ( cl1 == null || cl2 == null ) {
// Maybe we could just print this out and fail in the end.
//throw new SAXException( "Missing entity "+cl1+" "+cl2 );
// The cell is void
- System.err.println("Warning (cell voided), missing entity "+cl1+" "+cl2 );
+ logger.warn( "(cell voided), missing entity {} {}", cl1, cl2 );
} else if ( measure == null || relation == null ){
cell = alignment.addAlignCell( cl1, cl2);
} else {
@@ -497,8 +490,8 @@ public class XMLParser extends DefaultHandler {
alignment.setExtension( namespaceURI, pName, content );
} else if ( parseLevel == 5 ) {
extensions.setExtension( namespaceURI, pName, content );
- } else //if ( debugMode > 0 )
- System.err.println("[XMLParser("+parseLevel+")] Unknown element name : "+pName);
+ } else
+ logger.warn( "("+parseLevel+") Unknown element name : {}", pName );
//throw new SAXException("[XMLParser] Unknown element name : "+pName);
};
} catch ( AlignmentException e ) { throw new SAXException("[XMLParser] Exception raised", e); };
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index ef6532ec..6bfa3735 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -248,7 +248,7 @@ public class AServProtocolManager implements Service {
Alignment al = null;
try {
//logger.trace(" Parsing alignment");
- AlignmentParser aparser = new AlignmentParser(0);
+ AlignmentParser aparser = new AlignmentParser();
al = aparser.parse( name );
//logger.trace(" Alignment parsed");
} catch (Exception e) {
diff --git a/src/fr/inrialpes/exmo/align/service/AlignmentService.java b/src/fr/inrialpes/exmo/align/service/AlignmentService.java
index 1e74ae11..152b088e 100644
--- a/src/fr/inrialpes/exmo/align/service/AlignmentService.java
+++ b/src/fr/inrialpes/exmo/align/service/AlignmentService.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2006-2009, 2010, 2013
+ * Copyright (C) INRIA, 2006-2009, 2010, 2013-2014
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -24,13 +24,15 @@ import fr.inrialpes.exmo.queryprocessor.QueryProcessor;
import fr.inrialpes.exmo.queryprocessor.Result;
import fr.inrialpes.exmo.queryprocessor.Type;
-import fr.inrialpes.exmo.align.util.NullStream;
+import fr.inrialpes.exmo.align.cli.CommonCLI;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import gnu.getopt.LongOpt;
-import gnu.getopt.Getopt;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.ParseException;
import java.util.Hashtable;
import java.util.Enumeration;
@@ -62,12 +64,12 @@ $Id$
* @author J�r�me Euzenat
*/
-public class AlignmentService {
+public class AlignmentService extends CommonCLI {
final static Logger logger = LoggerFactory.getLogger( AlignmentService.class );
public String //DBMS Parameters
DBHOST = "localhost",
- DBPORT = "3306",
+ DBPORT = null,
DBUSER = "adminAServ",
DBPASS = "aaa345",
DBBASE = "AServDB",
@@ -91,22 +93,49 @@ public class AlignmentService {
private AServProtocolManager manager;
private DBService connection;
+ public AlignmentService() {
+ super();
+ //options.addOption( OptionBuilder.withLongOpt( "load" ).hasArg().withDescription( "Load previous database image from FILE" ).withArgName("FILE").create( 'l' ) );
+ options.addOption( OptionBuilder.withLongOpt( "impl" ).hasArg().withDescription( "Launch service corresponding to CLASS" ).withArgName("CLASS").create( 'i' ) );
+ options.addOption( OptionBuilder.withLongOpt( "uriprefix" ).hasArg().withDescription( "Set alignment URIs with prefix URI" ).withArgName("URI").create( 'u' ) );
+ options.addOption( OptionBuilder.withLongOpt( "host" ).hasArg().withDescription( "Set the HOSTNAME of the server" ).withArgName("HOSTNAME").create( 'S' ) );
+
+ options.addOption( OptionBuilder.withLongOpt( "http" ).hasOptionalArg().withDescription( "Launch HTTP service (with port PORT; default "+HTML+")" ).withArgName("PORT").create( 'H' ) );
+ options.addOption( OptionBuilder.withLongOpt( "jade" ).hasOptionalArg().withDescription( "Launch JADE service (with port PORT; default "+JADE+")" ).withArgName("PORT").create( 'A' ) );
+ options.addOption( OptionBuilder.withLongOpt( "wsdl" ).hasOptionalArg().withDescription( "Launch Web service (with port PORT; default "+WSDL+")" ).withArgName("PORT").create( 'W' ) );
+ options.addOption( OptionBuilder.withLongOpt( "jxta" ).hasOptionalArg().withDescription( "Launch JXTA service (with port PORT; default "+JXTA+")" ).withArgName("PORT").create( 'X' ) );
+
+ options.addOption( "O", "oyster", false, "Register to Oyster directory" );
+ //options.addOption( "U", "uddi", false, "Register to Oyster directory" );
+ //options.addOption( OptionBuilder.withLongOpt( "params" ).hasArg().withDescription( "Read parameters from FILE" ).withArgName("FILE").create( 'p' ) );
+
+ options.addOption( OptionBuilder.withLongOpt( "dbms" ).hasArg().withDescription( "Use DBMS system (mysql,postgres; default: mysql)" ).withArgName("DBMS").create( 'B' ) );
+ options.addOption( OptionBuilder.withLongOpt( "dbmshost" ).hasArg().withDescription( "Use DBMS HOST (default: "+DBHOST+")" ).withArgName("HOST").create( 'm' ) );
+ options.addOption( OptionBuilder.withLongOpt( "dbmsport" ).hasArg().withDescription( "Use DBMS PORT (default: "+DBPORT+")" ).withArgName("PORT").create( 's' ) );
+ options.addOption( OptionBuilder.withLongOpt( "dbmsuser" ).hasArg().withDescription( "Use DBMS USER (default: scott)" ).withArgName("USER").create( 'l' ) );
+ options.addOption( OptionBuilder.withLongOpt( "dbmspass" ).hasArg().withDescription( "Use DBMS PASSword (default: tiger)" ).withArgName("PASS").create( 'p' ) );
+ options.addOption( OptionBuilder.withLongOpt( "dbmsbase" ).hasArg().withDescription( "Use DBMS BASE (default: "+DBBASE+")" ).withArgName("BASE").create( 'b' ) );
+
+ }
+
public static void main(String[] args) {
try { new AlignmentService().run( args ); }
- catch ( Exception ex ) {
- logger.error( "FATAL error", ex );
- };
+ catch ( Exception ex ) { logger.error( "FATAL error", ex ); };
}
public void run(String[] args) throws Exception {
services = new Hashtable<String,AlignmentServiceProfile>();
directories = new Hashtable<String,Directory>();
+
// Read parameters
- Properties params = readParameters( args );
- if ( outfile != null ) {
+ readParameters( args );
+
+ // In principle, this is useless
+ if ( outputfilename != null ) {
// This redirects error outout to log file given by -o
- System.setErr( new PrintStream( outfile ) );
- }
+ System.setErr( new PrintStream( outputfilename ) );
+ }
+
logger.debug("Parameter parsed");
// Shut down hook
@@ -114,37 +143,49 @@ public class AlignmentService {
public void run() { close(); } });
// Connect database
- if( DBMS.equals("postgres") ) {
+ if ( DBMS.equals("postgres") ) {
logger.debug("postgres driver");
- DBPORT = "5432";
- connection = new DBServiceImpl( "org.postgresql.Driver" , "jdbc:postgresql", DBPORT );
- } else {
+ if ( DBPORT == null ) DBPORT = "5432";
+ connection = new DBServiceImpl( "org.postgresql.Driver", "jdbc:postgresql", DBPORT );
+ } else if ( DBMS.equals("mysql") ) {
logger.debug("mysql driver");
- DBPORT = "3306";
- connection = new DBServiceImpl( "com.mysql.jdbc.Driver" , "jdbc:mysql", DBPORT );
+ if ( DBPORT == null ) DBPORT = "3306";
+ connection = new DBServiceImpl( "com.mysql.jdbc.Driver", "jdbc:mysql", DBPORT );
+ } else {
+ logger.error( "Unsupported JDBC driver: {}", DBMS );
+ usage();
+ System.exit(-1);
}
-
- connection.init();
- connection.connect( DBHOST, DBPORT, DBUSER, DBPASS, DBBASE );
+ try {
+ logger.debug("Connecting to database");
+ connection.init();
+ connection.connect( DBHOST, DBPORT, DBUSER, DBPASS, DBBASE );
+ } catch ( Exception ex ) {
+ logger.error( ex.getMessage() );
+ System.exit(-1);
+ }
+
logger.debug("Database connected");
// Create a AServProtocolManager
manager = new AServProtocolManager( directories );
- manager.init( connection, params );
+ manager.init( connection, parameters );
logger.debug("Manager created");
// Launch services
for ( AlignmentServiceProfile serv : services.values() ) {
try {
- serv.init( params, manager );
+ serv.init( parameters, manager );
} catch ( AServException ex ) { // This should rather be the job of the caller
- logger.warn( "Cannot start {} server on {}:{}", serv, params.getProperty( "host" ), params.getProperty( "http" ) );
+ logger.warn( "Cannot start {} server on {}:{}", serv, parameters.getProperty( "host" ), parameters.getProperty( "http" ) );
}
}
+ logger.debug("Services launched");
+
// Register to directories
for ( Directory dir : directories.values() ) {
try {
- dir.open( params );
+ dir.open( parameters );
logger.debug("{} connected.", dir);
} catch ( AServException ex ) {
logger.warn( "Cannot connect to {} directory", dir );
@@ -153,8 +194,10 @@ public class AlignmentService {
//directories.remove( name, dir );
}
}
+ logger.debug("Directories registered");
// Wait loop
+ logger.info("Alignment server running");
while ( true ) {
// do not exhaust CPU
Thread.sleep(1000);
@@ -181,9 +224,11 @@ public class AlignmentService {
}
// Shut down database connection
- manager.close();
+ logger.debug("Stopping manager");
+ if ( manager != null ) manager.close();
+ logger.debug("Closing database connection");
connection.close();
- logger.debug("Database connection closed");
+ logger.info("Alignment server stopped");
System.err.close();
}
@@ -192,246 +237,95 @@ public class AlignmentService {
finally { super.finalize(); }
}
- protected Object loadInstance( String className) throws ClassNotFoundException, NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
+ protected Object loadInstance( String className ) throws ClassNotFoundException, NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
Class<?> cl = Class.forName(className);
java.lang.reflect.Constructor constructor = cl.getConstructor( (Class[])null );
return constructor.newInstance( (Object[])null );
}
+ public void readParameters( String[] args ) {
+ try {
+ CommandLine line = parseCommandLine( args );
+ if ( line == null ) System.exit(1); // -help
- public Properties readParameters( String[] args ) {
- Properties params = new Properties();
- // Default values
- params.setProperty( "host", HOST );
-
- // Read parameters
+ // Default values
+ parameters.setProperty( "host", HOST );
- LongOpt[] longopts = new LongOpt[20];
- // General parameters
- longopts[0] = new LongOpt("help", LongOpt.NO_ARGUMENT, null, 'h');
- longopts[1] = new LongOpt("output", LongOpt.REQUIRED_ARGUMENT, null, 'o');
- longopts[2] = new LongOpt("debug", LongOpt.OPTIONAL_ARGUMENT, null, 'd');
- longopts[3] = new LongOpt("impl", LongOpt.REQUIRED_ARGUMENT, null, 'l');
- // Is there a way for that in LongOpt ???
- longopts[4] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
- // Service parameters
- longopts[5] = new LongOpt("html", LongOpt.OPTIONAL_ARGUMENT, null, 'H');
- longopts[6] = new LongOpt("jade", LongOpt.OPTIONAL_ARGUMENT, null, 'A');
- longopts[7] = new LongOpt("wsdl", LongOpt.OPTIONAL_ARGUMENT, null, 'W');
- longopts[8] = new LongOpt("jxta", LongOpt.OPTIONAL_ARGUMENT, null, 'P');
- longopts[9] = new LongOpt("oyster", LongOpt.OPTIONAL_ARGUMENT, null, 'O');
- longopts[10] = new LongOpt("uddi", LongOpt.OPTIONAL_ARGUMENT, null, 'U');
- // DBMS Server parameters
- longopts[11] = new LongOpt("dbmshost", LongOpt.REQUIRED_ARGUMENT, null, 'm');
- longopts[12] = new LongOpt("dbmsport", LongOpt.REQUIRED_ARGUMENT, null, 's');
- longopts[13] = new LongOpt("dbmsuser", LongOpt.REQUIRED_ARGUMENT, null, 'u');
- longopts[14] = new LongOpt("dbmspass", LongOpt.REQUIRED_ARGUMENT, null, 'p');
- longopts[15] = new LongOpt("dbmsbase", LongOpt.REQUIRED_ARGUMENT, null, 'b');
- longopts[16] = new LongOpt("dbms", LongOpt.REQUIRED_ARGUMENT, null, 'B');
- longopts[17] = new LongOpt("host", LongOpt.REQUIRED_ARGUMENT, null, 'S');
- longopts[18] = new LongOpt("serv", LongOpt.REQUIRED_ARGUMENT, null, 'i');
- longopts[19] = new LongOpt("uriprefix", LongOpt.REQUIRED_ARGUMENT, null, 'f');
-
- Getopt g = new Getopt("", args, "ho:S:l:f:d::D:H::A::W::P::O::U::m:s:u:p:b:B:i:", longopts);
- int c;
- String arg;
-
- while ((c = g.getopt()) != -1) {
- switch (c) {
- case 'h' :
- usage();
- System.exit(0);
- break;
- case 'o' :
- /* Use filename instead of stdout */
- outfile = g.getOptarg();
- break;
- case 'l' :
- /* Use the given file as a database image to load */
- filename = g.getOptarg();
- break;
- case 'd' :
- /* DEPRECATED: Debug level */
- arg = g.getOptarg();
- System.err.println( "WARNING: debug argument is deprecated, use logging" );
- System.err.println( "See http://alignapi.gforge.inria.fr/logging.html" );
- break;
- case 'i' :
- /* external service */
- arg = g.getOptarg();
+ // Here deal with command specific arguments
+
+ /* Use the given file as a database image to load */
+ //if ( line.hasOption( 'l' ) ) filename = line.getOptionValue( 'l' );
+ if ( line.hasOption( 'i' ) ) { /* external service */
+ String arg = line.getOptionValue( 'i' );
try {
services.put( arg, (AlignmentServiceProfile)loadInstance( arg ) );
} catch (Exception ex) {
logger.warn( "Cannot create service for {}", arg );
- logger.trace( "IGNORED Exception", ex );
- }
- break;
- case 'f' :
- /* Parameter definition */
- params.setProperty( "prefix", g.getOptarg() );
- break;
- case 'H' :
- /* HTTP Server + port */
- arg = g.getOptarg();
- if ( arg != null ) {
- params.setProperty( "http", arg );
- } else {
- params.setProperty( "http", HTML );
+ logger.debug( "IGNORED Exception", ex );
}
+ }
+ if ( line.hasOption( 'u' ) ) parameters.setProperty( "prefix", line.getOptionValue( 'u' ) );
+ if ( line.hasOption( 'H' ) ) {
+ parameters.setProperty( "http", line.getOptionValue( 'H', HTML ) );
// This shows that it does not work
try {
services.put( "fr.inrialpes.exmo.align.service.HTMLAServProfile", (AlignmentServiceProfile)loadInstance( "fr.inrialpes.exmo.align.service.HTMLAServProfile" ) );
} catch (Exception ex) {
logger.warn( "Cannot create service for HTMLAServProfile", ex );
}
- break;
- case 'A' :
- /* JADE Server + port */
- arg = g.getOptarg();
- if ( arg != null ) {
- params.setProperty( "jade", arg );
- } else {
- params.setProperty( "jade", JADE );
- }
+ }
+ if ( line.hasOption( 'A' ) ) {
+ parameters.setProperty( "jade", line.getOptionValue( 'A', JADE ) );
try {
services.put( "fr.inrialpes.exmo.align.service.jade.JadeFIPAAServProfile", (AlignmentServiceProfile)loadInstance( "fr.inrialpes.exmo.align.service.jade.JadeFIPAAServProfile" ) );
- } catch (Exception ex) {
+ } catch ( Exception ex ) {
logger.warn("Cannot create service for JadeFIPAAServProfile", ex);
}
- break;
- case 'W' :
- /* Web service + port */
- arg = g.getOptarg();
- if ( arg != null ) {
- params.setProperty( "wsdl", arg );
- } else {
- params.setProperty( "wsdl", WSDL );
- };
+ }
+ if ( line.hasOption( 'W' ) ) {
+ parameters.setProperty( "wsdl", line.getOptionValue( 'W', WSDL ) );
// The WSDL extension requires HTTP server (and the same one).
// Put the default port, may be overriden
- if ( params.getProperty( "http" ) == null )
- params.setProperty( "http", HTML );
+ if ( parameters.getProperty( "http" ) == null )
+ parameters.setProperty( "http", HTML );
try {
services.put( "fr.inrialpes.exmo.align.service.HTMLAServProfile", (AlignmentServiceProfile)loadInstance( "fr.inrialpes.exmo.align.service.HTMLAServProfile" ) );
- } catch (Exception ex) {
- logger.warn("Cannot create service for Web services", ex);
- }
- break;
- case 'P' :
- /* JXTA Server + port */
- arg = g.getOptarg();
- if ( arg != null ) {
- params.setProperty( "jxta", arg );
- } else {
- params.setProperty( "jxta", JXTA );
- }
- break;
- case 'S' :
- /* Server */
- params.setProperty( "host", g.getOptarg() );
- break;
- case 'O' :
- /* [JE: Currently not working]: Oyster directory + port */
- arg = g.getOptarg();
- if ( arg != null ) {
- params.setProperty( "oyster", arg );
- } else {
- params.setProperty( "oyster", JADE );
+ } catch ( Exception ex ) {
+ logger.warn( "Cannot create service for Web services", ex );
}
+ }
+ if ( line.hasOption( 'X' ) ) { parameters.setProperty( "jxta", line.getOptionValue( 'P', JXTA ) ); }
+ if ( line.hasOption( 'S' ) ) { parameters.setProperty( "host", line.getOptionValue( 'S' ) ); }
+ if ( line.hasOption( 'O' ) ) {
try {
directories.put( "fr.inrialpes.exmo.align.service.OysterDirectory", (Directory)loadInstance( "fr.inrialpes.exmo.align.service.OysterDirectory" ) );
} catch (Exception ex) {
- logger.warn("Cannot create directory for Oyster", ex);
+ logger.warn( "Cannot create directory for Oyster", ex );
}
- break;
- case 'U' :
- /* [JE: Currently not working]: UDDI directory + port */
- arg = g.getOptarg();
- if ( arg != null ) {
- params.setProperty( "uddi", arg );
- } else {
- params.setProperty( "uddi", JADE );
- }
+ }
+ /*if ( line.hasOption( 'U' ) ) {
try {
directories.put( "fr.inrialpes.exmo.align.service.UDDIDirectory", (Directory)loadInstance( "fr.inrialpes.exmo.align.service.UDDIDirectory" ) );
} catch (Exception ex) {
logger.warn("Cannot create directory for UDDI", ex);
}
- break;
- case 'm' :
- DBHOST = g.getOptarg();
- break;
- case 's' :
- DBPORT = g.getOptarg();
- break;
- case 'u' :
- DBUSER = g.getOptarg();
- break;
- case 'p' :
- DBPASS = g.getOptarg();
- break;
- case 'b' :
- DBBASE = g.getOptarg();
- break;
- case 'B' :
- arg = g.getOptarg();
- if ( arg != null ) {
- params.setProperty( "DBMS", arg );
- DBMS = arg;
- } else {
- params.setProperty( "DBMS", "mysql" );
- DBMS = "mysql";
- }
- break;
- case 'D' :
- /* Parameter definition */
- arg = g.getOptarg();
- int index = arg.indexOf('=');
- if ( index != -1 ) {
- params.setProperty( arg.substring( 0, index),
- arg.substring(index+1));
- } else {
- logger.warn("Bad parameter syntax: "+g);
- usage();
- System.exit(0);
-
- }
- break;
- }
+ }*/
+ if ( line.hasOption( 'm' ) ) { DBHOST = line.getOptionValue( 'm' ); }
+ if ( line.hasOption( 's' ) ) { DBPORT = line.getOptionValue( 's' ); }
+ if ( line.hasOption( 'l' ) ) { DBUSER = line.getOptionValue( 'l' ); }
+ if ( line.hasOption( 'p' ) ) { DBPASS = line.getOptionValue( 'p' ); }
+ if ( line.hasOption( 'b' ) ) { DBBASE = line.getOptionValue( 'b' ); }
+ if ( line.hasOption( 'B' ) ) { DBMS = line.getOptionValue( 'B' ); }
+ parameters.setProperty( "DBMS", DBMS );
+ } catch( ParseException exp ) {
+ logger.error( exp.getMessage() );
+ usage();
+ System.exit(-1);
}
-
- return params;
}
- // Really missing:
- // OUTPUT(o): what for, there is no output (maybe LOGS)
- // LOAD(l): good idea, load from file, but what kind? sql?
- // PARAMS(p is taken, P is taken): yes good as well to read parameters from file
public void usage() {
- System.err.println("usage: AlignmentService [options]");
- System.err.println("options are:");
- //System.err.println("\t--load=filename -l filename\t\tInitialize the Service with the content of this ");
- System.err.println("\t--html[=port] -H[port]\t\t\tLaunch HTTP service");
- System.err.println("\t--jade[=port] -A[port]\t\t\tLaunch Agent service");
- System.err.println("\t--wsdl[=port] -W[port]\t\t\tLaunch Web service");
- System.err.println("\t--jxta[=port] -P[port]\t\t\tLaunch P2P service");
- System.err.println("\t--oyster -O\t\t\tRegister to Oyster directory");
- //System.err.println("\t--uddi -U\t\t\tRegister to Oyster directory");
- System.err.println("\t--serv=class -i class\t\t\tLaunch service corresponding to fully qualified classname");
- //System.err.println("\t--params=filename -p filename\tReads parameters from filename");
- System.err.println("\t--output=filename -o filename\tRedirect output to filename");
- System.err.println("\t--dbmshost=host -m host\t\t\tUse DBMS host");
- System.err.println("\t--dbmsport=port -s port\t\t\tUse DBMS port");
- System.err.println("\t--dbmsuser=name -u name\t\t\tUse DBMS user name");
- System.err.println("\t--dbmspass=pwd -p pwd\t\t\tUse DBMS password");
- System.err.println("\t--dbmsbase=name -b name\t\t\tUse Database name");
- System.err.println("\t--dbms=name -B name\t\t\tUse Database Management System");
- System.err.println("\t--uriprefix=uri -f uri\t\t\tSet alignment URIs with this prefix");
- System.err.println("\t-Dparam=value\t\t\tSet parameter");
- System.err.println("\t--help -h\t\t\tPrint this message");
-
- System.err.print("\n"+AlignmentService.class.getPackage().getImplementationTitle()+" "+AlignmentService.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
+ usage( "java "+this.getClass().getName()+" [options]\nLaunch an Alignment server" );
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/DBServiceImpl.java b/src/fr/inrialpes/exmo/align/service/DBServiceImpl.java
index e411db08..08920dad 100644
--- a/src/fr/inrialpes/exmo/align/service/DBServiceImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/DBServiceImpl.java
@@ -2,7 +2,7 @@
* $Id$
*
* Copyright (C) Seungkeun Lee, 2006
- * Copyright (C) INRIA, 2007-2009, 2013
+ * Copyright (C) INRIA, 2007-2009, 2013-2014
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -81,7 +81,8 @@ public class DBServiceImpl implements DBService {
public void connect(String IPAddress, String port, String user, String password, String database ) throws SQLException {
dbpass = password;
conn = DriverManager.getConnection(driverPrefix+"://"+IPAddress+":"+port+"/"+database, user, password);
- }
+ }
+
//with "dbpass" given by "connect"
public Connection reconnect() throws SQLException {
conn = DriverManager.getConnection(driverPrefix+"://"+IPAddress+":"+port+"/"+database, user, dbpass);
@@ -96,7 +97,7 @@ public class DBServiceImpl implements DBService {
public void close() {
try {
- conn.close();
+ if ( conn != null ) conn.close();
} catch (Exception ex) {
logger.debug( "IGNORED Closing exception", ex );
}
diff --git a/src/fr/inrialpes/exmo/align/service/QueryMediator.java b/src/fr/inrialpes/exmo/align/service/QueryMediator.java
index c4fc23d7..8fedb1c8 100644
--- a/src/fr/inrialpes/exmo/align/service/QueryMediator.java
+++ b/src/fr/inrialpes/exmo/align/service/QueryMediator.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2006-2009
+ * Copyright (C) INRIA, 2006-2009, 2013
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -76,7 +76,7 @@ public class QueryMediator implements QueryProcessor {
public QueryMediator( QueryProcessor proc, String alignmentURI ) throws SAXException,ParserConfigurationException,IOException {
processor = proc;
- AlignmentParser aparser = new AlignmentParser(0);
+ AlignmentParser aparser = new AlignmentParser();
try { alignment = aparser.parse( alignmentURI ); }
catch ( Exception ex ) {
throw new ParserConfigurationException("Error on parsing");
diff --git a/src/fr/inrialpes/exmo/align/service/WSAlignment.java b/src/fr/inrialpes/exmo/align/service/WSAlignment.java
index 7b891101..0d3c94ca 100644
--- a/src/fr/inrialpes/exmo/align/service/WSAlignment.java
+++ b/src/fr/inrialpes/exmo/align/service/WSAlignment.java
@@ -177,7 +177,7 @@ public class WSAlignment extends URIAlignment implements AlignmentProcess {
//}
- AlignmentParser parser = new AlignmentParser( 0 );
+ AlignmentParser parser = new AlignmentParser();
parser.initAlignment( this );
parser.setEmbedded( true );
parser.parse( httpConn.getInputStream() );
diff --git a/src/fr/inrialpes/exmo/align/service/jade/JadeFIPAAServProfile.java b/src/fr/inrialpes/exmo/align/service/jade/JadeFIPAAServProfile.java
index 9432c97a..ba25babf 100755
--- a/src/fr/inrialpes/exmo/align/service/jade/JadeFIPAAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/jade/JadeFIPAAServProfile.java
@@ -2,7 +2,7 @@
* $Id$
*
* Copyright (C) Orange R&D, 2006-2007
- * Copyright (C) INRIA, 2006-2007, 2009-2010
+ * Copyright (C) INRIA, 2006-2007, 2009-2010, 2013
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -24,7 +24,6 @@ package fr.inrialpes.exmo.align.service.jade;
import jade.core.Profile;
import jade.core.ProfileImpl;
import jade.core.Runtime;
-import jade.util.Logger;
import jade.wrapper.AgentContainer;
import jade.wrapper.AgentController;
import jade.wrapper.ControllerException;
@@ -36,16 +35,17 @@ import fr.inrialpes.exmo.align.service.AlignmentServiceProfile;
import java.io.File;
import java.util.Properties;
-public class JadeFIPAAServProfile implements AlignmentServiceProfile {
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+public class JadeFIPAAServProfile implements AlignmentServiceProfile {
+ final static Logger logger = LoggerFactory.getLogger( JadeFIPAAServProfile.class );
private AgentContainer mc;
private AgentController algagentcontroller;
- private Logger myLogger = Logger.getMyLogger(getClass().getName());
public void init( Properties params, AServProtocolManager manager ) throws AServException {
int port = 8888;
- int debug = 0;
Object args[] = new Object[2];
//set up the manager as an argument to pass to the JADEFIPAAServiceAgent
@@ -56,8 +56,6 @@ public class JadeFIPAAServProfile implements AlignmentServiceProfile {
if ( params.getProperty( "jade" ) != null )
port = Integer.parseInt( params.getProperty( "jade" ) );
- if ( params.getProperty( "debug" ) != null )
- debug = Integer.parseInt( params.getProperty( "debug" ) ) - 1;
/**
Properties props = new Properties();
@@ -76,8 +74,7 @@ public class JadeFIPAAServProfile implements AlignmentServiceProfile {
// create a default Profile
Profile pMain = new ProfileImpl(null, port, null);
- if ( debug > 0 )
- System.out.println("Launching a whole in-process platform..."+pMain);
+ //logger.trace( "Launching a whole in-process platform... {}", pMain );
mc = rt.createMainContainer(pMain);
algagentcontroller = mc.createNewAgent("JadeFIPAAServiceAgent", JadeFIPAAServiceAgent.class.getName(), args);
algagentcontroller.start();
@@ -91,15 +88,15 @@ public class JadeFIPAAServProfile implements AlignmentServiceProfile {
try{
algagentcontroller.kill();
mc.kill();
- myLogger.log(Logger.INFO, "Agent Alignement close");
+ logger.info( "Agent Alignement closed" );
} catch (ControllerException e) {
- myLogger.log(Logger.WARNING, "Error killing the alignment agent."); }
+ logger.warn( "Error killing the alignment agent." ); }
try {
// Destroy the files please (JE)
new File("APDescription.txt").delete();
new File("MTPs-Main-Container.txt").delete();
} catch (Exception e) {
- e.printStackTrace();
+ logger.debug( "IGNORED Exception", e );
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/jade/JadeFIPAAServiceAgent.java b/src/fr/inrialpes/exmo/align/service/jade/JadeFIPAAServiceAgent.java
index 1fc9677c..3f67c5ae 100755
--- a/src/fr/inrialpes/exmo/align/service/jade/JadeFIPAAServiceAgent.java
+++ b/src/fr/inrialpes/exmo/align/service/jade/JadeFIPAAServiceAgent.java
@@ -2,7 +2,7 @@
* $Id$
*
* Copyright (C) Orange R&D, 2006
- * Copyright (C) INRIA, 2006, 2008-2009, 2011-2012
+ * Copyright (C) INRIA, 2006, 2008-2009, 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
@@ -19,12 +19,14 @@
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-
package fr.inrialpes.exmo.align.service.jade;
import java.util.Iterator;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import jade.content.ContentElement;
import jade.content.ContentManager;
import jade.content.Predicate;
@@ -40,7 +42,6 @@ import jade.domain.FIPAAgentManagement.DFAgentDescription;
import jade.domain.FIPAAgentManagement.ServiceDescription;
import jade.lang.acl.ACLMessage;
import jade.lang.acl.MessageTemplate;
-import jade.util.Logger;
import fr.inrialpes.exmo.align.service.AServProtocolManager;
import fr.inrialpes.exmo.align.service.msg.Message;
@@ -58,12 +59,12 @@ import fr.inrialpes.exmo.align.service.jade.messageontology.STORE;
import fr.inrialpes.exmo.align.service.jade.messageontology.TRANSLATE;
public class JadeFIPAAServiceAgent extends Agent {
+ final static Logger logger = LoggerFactory.getLogger( JadeFIPAAServiceAgent.class );
private static final long serialVersionUID = 330;
public static final String SERVICE_NAME = "Alignment";
public static final String SERVICE_TYPE = "Alignment-service";
- private Logger myLogger = Logger.getMyLogger(getClass().getName());
private String myId;
private String serverId;
private AServProtocolManager manager;
@@ -78,24 +79,24 @@ public class JadeFIPAAServiceAgent extends Agent {
protected void setup() {
- //myLogger.log(Logger.INFO, getAID().getName()+" started");
- super.setup();
- codec = new SLCodec();
-
- // ontology = ContextAgentManagerOntology.getInstance();
- CTmanager = this.getContentManager();
+ logger.info( "{} started", getAID().getName() );
+ super.setup();
+ codec = new SLCodec();
- //System.out.println("agent" + getAID() + " "+ getLocalName()+" is created");
+ // ontology = ContextAgentManagerOntology.getInstance();
+ CTmanager = this.getContentManager();
+
+ // logger.trace("agent {} {} is created", getAID(), getLocalName() );
- CTmanager.registerOntology(ontology);
- CTmanager.registerLanguage(codec);
+ CTmanager.registerOntology(ontology);
+ CTmanager.registerLanguage(codec);
// Read arguments
Object[] args = getArguments();
if (args != null) {
/**for (int i = 0; i < args.length; ++i) {
- myLogger.log(Logger.INFO, "Arg-"+i+" = "+args[i]);
+ logger.debug( "Arg-{} = {}", i, args[i] );
}**/
manager=(AServProtocolManager) args[0];
@@ -123,7 +124,7 @@ public class JadeFIPAAServiceAgent extends Agent {
ACLMessage msg = myAgent.receive(tpl);
if (msg != null) {
// ---------------------------------------------------------
- //myLogger.log(Logger.INFO, "Received message: "+msg.toString());
+ //logger.debug( "Received message: {}", msg.toString() );
try{
ContentElement ce = null;
@@ -141,7 +142,9 @@ public class JadeFIPAAServiceAgent extends Agent {
((Action)ce).setResult(answer.getContent());
CTmanager.fillContent(JADEanswer, ce);
myAgent.send(JADEanswer);
- }else{myLogger.log(Logger.WARNING, answer.getContent());}
+ }else{
+ logger.warn( answer.getContent() );
+ }
}else if (ce instanceof LOAD){
Message answer = manager.load(new Message(newId(), (Message)null,myId,serverId,"",params));
if(!(answer instanceof ErrorMsg)){
@@ -153,7 +156,9 @@ public class JadeFIPAAServiceAgent extends Agent {
CTmanager.fillContent(JADEanswer, ce);
//JADEanswer.setContent(answer.getContent());
myAgent.send(JADEanswer);
- }else{myLogger.log(Logger.WARNING, answer.getContent());}
+ }else{
+ logger.warn( answer.getContent() );
+ }
}else if (ce instanceof RETRIEVE){
Message answer = manager.render(new Message(newId(), (Message)null,myId,serverId,"",params));
if(!(answer instanceof ErrorMsg)){
@@ -165,7 +170,9 @@ public class JadeFIPAAServiceAgent extends Agent {
((Action)ce).setResult(answer.getContent());
CTmanager.fillContent(JADEanswer, ce);
myAgent.send(JADEanswer);
- }else{myLogger.log(Logger.WARNING, answer.getContent());}
+ }else{
+ logger.warn( answer.getContent() );
+ }
}else if (ce instanceof TRANSLATE){
//TODO
}else if (ce instanceof METADATA){
@@ -181,7 +188,9 @@ public class JadeFIPAAServiceAgent extends Agent {
((Action)ce).setResult(answer.getContent());
CTmanager.fillContent(JADEanswer, ce);
myAgent.send(JADEanswer);
- }else{myLogger.log(Logger.WARNING, answer.getContent());}
+ }else{
+ logger.warn( answer.getContent() );
+ }
}else if (ce instanceof FIND){
Message answer = manager.existingAlignments(new Message(newId(), (Message)null,myId,serverId,"",params));
if(!(answer instanceof ErrorMsg)){
@@ -193,7 +202,9 @@ public class JadeFIPAAServiceAgent extends Agent {
((Action)ce).setResult(answer.getContent());
CTmanager.fillContent(JADEanswer, ce);
myAgent.send(JADEanswer);
- }else{myLogger.log(Logger.WARNING, answer.getContent());}
+ }else{
+ logger.warn( answer.getContent() );
+ }
}else if (ce instanceof CUT){
Message answer = manager.trim(new Message(newId(), (Message)null,myId,serverId,"",params));
if(!(answer instanceof ErrorMsg)){
@@ -205,7 +216,9 @@ public class JadeFIPAAServiceAgent extends Agent {
((Action)ce).setResult(answer.getContent());
CTmanager.fillContent(JADEanswer, ce);
myAgent.send(JADEanswer);
- }else{myLogger.log(Logger.WARNING, answer.getContent());}
+ }else{
+ logger.warn( answer.getContent() );
+ }
}else {
ACLMessage JADEanswer=msg.createReply();
JADEanswer.setLanguage(codec.getName());
@@ -213,10 +226,11 @@ public class JadeFIPAAServiceAgent extends Agent {
JADEanswer.setPerformative(ACLMessage.NOT_UNDERSTOOD);
myAgent.send(JADEanswer);
}
+ } catch( CodecException ce ) {
+ logger.debug( "IGNORED Exception", ce );
+ } catch( OntologyException oe ) {
+ logger.debug( "IGNORED Exception", oe );
}
-
- catch(CodecException ce){ce.printStackTrace();}
- catch(OntologyException oe){oe.printStackTrace();}
}else {
block();
}
@@ -231,9 +245,8 @@ public class JadeFIPAAServiceAgent extends Agent {
}//end of Setup
protected void takeDown() {
-
- myLogger.log(Logger.INFO, "Agent Alignement Service close");
- this.doDelete();
+ logger.info( "Agent Alignement Service closed" );
+ this.doDelete();
}
private void registerWithDF() {
@@ -244,12 +257,12 @@ public class JadeFIPAAServiceAgent extends Agent {
sd.setType(SERVICE_TYPE);
dfd.addServices(sd);
try {
- //myLogger.log(Logger.INFO, "Registering with DF...");
- DFService.register(this, dfd);
- //myLogger.log(Logger.INFO, "Registration OK.");
+ logger.debug( "Registering with DF..." );
+ DFService.register(this, dfd);
+ logger.debug( "Registration OK." );
}
- catch (FIPAException fe) {
- myLogger.log(Logger.WARNING, "Error registering with DF.", fe);
+ catch ( FIPAException fex ) {
+ logger.warn( "Error registering with DF", fex );
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/jade/messageontology/JADEFIPAAlignmentServerOntology.java b/src/fr/inrialpes/exmo/align/service/jade/messageontology/JADEFIPAAlignmentServerOntology.java
index fd307925..fcb4c905 100644
--- a/src/fr/inrialpes/exmo/align/service/jade/messageontology/JADEFIPAAlignmentServerOntology.java
+++ b/src/fr/inrialpes/exmo/align/service/jade/messageontology/JADEFIPAAlignmentServerOntology.java
@@ -1,5 +1,29 @@
-// file: JADEFIPAAlignmentServerOntologyOntology.java generated by ontology bean generator. DO NOT EDIT, UNLESS YOU ARE REALLY SURE WHAT YOU ARE DOING!
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA, 2007, 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
+ * the Free Software Foundation; either version 2.1 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+// file: JADEFIPAAlignmentServerOntologyOntology.java generated by ontology bean generator. DO NOT EDIT, UNLESS YOU ARE REALLY SURE WHAT YOU ARE DOING!
+
package fr.inrialpes.exmo.align.service.jade.messageontology;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import jade.content.onto.*;
import jade.content.schema.*;
@@ -12,6 +36,7 @@ import jade.core.CaseInsensitiveString;
* @version 2007/03/19, 17:12:29
*/
public class JADEFIPAAlignmentServerOntology extends jade.content.onto.Ontology {
+ final static Logger logger = LoggerFactory.getLogger( JADEFIPAAlignmentServerOntology.class );
//NAME
private static final long serialVersionUID = 330;
public static final String ONTOLOGY_NAME = "JADEFIPAAlignmentServerOntology";
@@ -102,6 +127,7 @@ public class JADEFIPAAlignmentServerOntology extends jade.content.onto.Ontology
- }catch (java.lang.Exception e) {e.printStackTrace();}
+ }catch (java.lang.Exception e) {
+ logger.debug( "IGNORED Exception", e );}
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/msg/AlignmentIds.java b/src/fr/inrialpes/exmo/align/service/msg/AlignmentIds.java
index 147d0b77..cdde5684 100644
--- a/src/fr/inrialpes/exmo/align/service/msg/AlignmentIds.java
+++ b/src/fr/inrialpes/exmo/align/service/msg/AlignmentIds.java
@@ -22,11 +22,15 @@ package fr.inrialpes.exmo.align.service.msg;
import java.util.Properties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* Contains the messages that should be sent according to the protocol
*/
public class AlignmentIds extends Success {
+ final static Logger logger = LoggerFactory.getLogger( AlignmentIds.class );
String pretty = null;
@@ -45,8 +49,8 @@ public class AlignmentIds extends Success {
if ( id.length >= 1 ) {
result = "Alignment Ids: <ul>";
for ( int i = id.length-1; i >= 0; i-- ){
- //System.err.println("id["+i+"]"+id[i]);
- //result += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id[i]+"\">";
+ // logger.trace("id[{}]{}", i, id[i] );
+ // result += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id[i]+"\">";
result += "<li><a href=\""+id[i]+"\">";
result += id[i];
String pp = null;
@@ -56,7 +60,7 @@ public class AlignmentIds extends Success {
if (pp != null && !pp.equals("") && !pp.equals("null")) {
result += " ("+pp+")";
}
- //System.err.println("pid["+i+"]="+pp);
+ // logger.trace( "pid[{}]={}", i, pp );
} catch(Exception ex) {
}
}
diff --git a/src/fr/inrialpes/exmo/ontowrap/OntologyCache.java b/src/fr/inrialpes/exmo/ontowrap/OntologyCache.java
index 0c4c9b4d..6770f214 100644
--- a/src/fr/inrialpes/exmo/ontowrap/OntologyCache.java
+++ b/src/fr/inrialpes/exmo/ontowrap/OntologyCache.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2007-2008, 2010
+ * Copyright (C) INRIA, 2007-2008, 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
@@ -21,11 +21,13 @@
package fr.inrialpes.exmo.ontowrap;
-// import java classes
import java.util.Hashtable;
import java.util.Enumeration;
import java.net.URI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
/**
* This caches the loaded ontologies so that it is possible
* to share them between alignments
@@ -38,7 +40,8 @@ import java.net.URI;
*/
public class OntologyCache <O extends LoadedOntology> {
-
+ final static Logger logger = LoggerFactory.getLogger( OntologyCache.class );
+
/** The list of currently loaded ontologies as a function:
* URI --> Ontology
* This is the ontology URI, NOT its filename
@@ -73,15 +76,15 @@ public class OntologyCache <O extends LoadedOntology> {
/* debugging utility */
public void displayCache(){
- System.err.println("CACHE: "+ontologies.size()+"/"+ontologyUris.size()+" elements cached");
+ logger.trace( "CACHE: {}/{} elements cached", ontologies.size(), ontologyUris.size() );
// No way to make this iterable??
//for ( URI u : ontologies.keys() ){
for( Enumeration<URI> e = ontologies.keys(); e.hasMoreElements(); ){
- URI u = e.nextElement();
+ URI u = e.nextElement();
LoadedOntology o = ontologies.get( u );
- System.err.println( " "+u );
- System.err.println( " "+o.getURI() );
- System.err.println( " --> "+o+" ("+o.getOntology()+")" );
+ logger.trace( " {}", u );
+ logger.trace( " {}", o.getURI() );
+ logger.trace( " --> {} ({})", o, o.getOntology() );
}
};
diff --git a/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
index 4c39e881..e7a60e78 100644
--- a/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
@@ -168,11 +168,11 @@ public abstract class OntologyFactory {
*/
public LoadedOntology loadOntology( Ontology onto ) throws OntowrapException {
// logger.trace( "loading Ontology: {}", onto );
- try { // Try with URI
- return loadOntology( onto.getURI() );
+ try { // Try with file
+ return loadOntology( onto.getFile() );
} catch ( Exception ex ) {
- try { // Try with file
- return loadOntology( onto.getFile() );
+ try { // Try with URI
+ return loadOntology( onto.getURI() );
} catch ( Exception ex2 ) {
throw new OntowrapException( "Cannot load ontology "+onto );
}
diff --git a/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntology.java b/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntology.java
index f7bec973..7595929c 100644
--- a/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntology.java
+++ b/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntology.java
@@ -55,11 +55,11 @@ import fr.inrialpes.exmo.ontowrap.util.EntityFilter;
public class JENAOntology extends BasicOntology<OntModel> implements HeavyLoadedOntology<OntModel>{
- private boolean onlyLocalEntities=true;
+ private boolean onlyLocalEntities = true;
// JE: this is not very Java 1.5...
// This is because of the version of Jena we use apparently
-
+ public JENAOntology() {} // default is true
public JENAOntology(boolean onlyLocalEntities) {
this.onlyLocalEntities=onlyLocalEntities;
diff --git a/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntologyFactory.java
index 08e4286a..de57fd59 100644
--- a/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntologyFactory.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2008, 2010
+ * Copyright (C) INRIA, 2003-2008, 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
@@ -24,6 +24,9 @@ import java.net.URI;
import java.net.URISyntaxException;
import java.util.NoSuchElementException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.ontology.Ontology;
@@ -35,6 +38,7 @@ import fr.inrialpes.exmo.ontowrap.OntologyCache;
import fr.inrialpes.exmo.ontowrap.OntowrapException;
public class JENAOntologyFactory extends OntologyFactory {
+ final static Logger logger = LoggerFactory.getLogger( JENAOntologyFactory.class );
private static URI formalismUri = null;
private static String formalismId = "OWL1.0";
@@ -45,7 +49,9 @@ public class JENAOntologyFactory extends OntologyFactory {
cache = new OntologyCache<JENAOntology>();
try {
formalismUri = new URI("http://www.w3.org/2002/07/owl#");
- } catch (URISyntaxException ex) { ex.printStackTrace(); } // should not happen
+ } catch (URISyntaxException ex) {
+ logger.debug( "IGNORED (should never happen)", ex );
+ } // should not happen
}
public JENAOntology newOntology( Object ontology , boolean onlyLocalEntities ) throws OntowrapException {
diff --git a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIAnnotIt.java b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIAnnotIt.java
index dcc760a4..177cfab7 100644
--- a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIAnnotIt.java
+++ b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIAnnotIt.java
@@ -1,7 +1,7 @@
/*
* $Id: OWLAPIAnnotIt.java 896 2008-11-25 14:45:46Z jdavid $
*
- * Copyright (C) INRIA, 2007-2008, 2010
+ * Copyright (C) INRIA, 2007-2008, 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
@@ -23,6 +23,9 @@ package fr.inrialpes.exmo.ontowrap.owlapi10;
import java.util.Iterator;
import java.util.NoSuchElementException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.model.OWLAnnotationInstance;
import org.semanticweb.owl.model.OWLDataValue;
import org.semanticweb.owl.model.OWLEntity;
@@ -36,6 +39,7 @@ import org.semanticweb.owl.model.OWLOntology;
*
*/
public class OWLAPIAnnotIt implements Iterator<String> {
+ final static Logger logger = LoggerFactory.getLogger( OWLAPIAnnotIt.class );
/*private OWLOntology o;
private OWLEntity e;*/
@@ -80,7 +84,7 @@ public class OWLAPIAnnotIt implements Iterator<String> {
}
}
} catch (OWLException e) {
- e.printStackTrace();
+ logger.debug( "IGNORED Exception", e );
currentElem=null;
}
}
diff --git a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntology.java b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntology.java
index fb132c80..69bc1921 100644
--- a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntology.java
+++ b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntology.java
@@ -1,7 +1,7 @@
/*
* $Id: OWLAPIOntology.java 896 2008-11-25 14:45:46Z jdavid $
*
- * Copyright (C) INRIA, 2007-2008, 2010
+ * Copyright (C) INRIA, 2007-2008, 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
@@ -40,6 +40,9 @@ import java.util.Map;
import java.util.Set;
import java.util.HashSet;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.ontowrap.Annotation;
import fr.inrialpes.exmo.ontowrap.OntologyFactory;
import fr.inrialpes.exmo.ontowrap.HeavyLoadedOntology;
@@ -69,6 +72,7 @@ import org.semanticweb.owl.model.helper.OWLEntityCollector;
*/
public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyLoadedOntology<OWLOntology> {
+ final static Logger logger = LoggerFactory.getLogger( OWLAPIOntology.class );
/* For caching sizes */
private int nbentities = -1;
@@ -82,7 +86,9 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyL
setFormalism( "OWL1.0" );
try {
setFormURI( new URI("http://www.w3.org/2002/07/owl#") );
- } catch (Exception e) {}; // does not happen
+ } catch (Exception e) {
+ logger.debug( "IGNORED (should never happen)", e );
+ };
};
// -----------------------------------------------------------------
@@ -179,7 +185,7 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyL
try {
return new OWLAPIAnnotIt(o,e,lang,typeAnnot);
} catch (OWLException e) {
- e.printStackTrace();
+ logger.debug( "IGNORED", e );
return null;
}
}
@@ -357,7 +363,9 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyL
public void unload() {
try {
onto.getOWLConnection().notifyOntologyDeleted( onto );
- } catch (OWLException ex) { System.err.println(ex); };
+ } catch (OWLException ex) {
+ logger.debug( "IGNORED Exception", ex);
+ };
}
// -----------------------------------------------------------------
@@ -412,7 +420,9 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyL
if ( ent instanceof OWLRestriction )
prop.add( ((OWLRestriction)ent).getProperty() );
}
- } catch (OWLException e) { e.printStackTrace(); }
+ } catch (OWLException e) {
+ logger.debug( "IGNORED", e );
+ }
} else {
prop = getInheritedProperties( (OWLClass)cl );
}
diff --git a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java
index 3039bd37..2bc3cb0d 100644
--- a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntologyFactory.java
@@ -28,6 +28,9 @@ import java.util.HashSet;
import java.util.Map;
import java.util.Set;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.util.OWLConnection;
@@ -40,6 +43,7 @@ import fr.inrialpes.exmo.ontowrap.LoadedOntology;
import fr.inrialpes.exmo.ontowrap.OntowrapException;
public class OWLAPIOntologyFactory extends OntologyFactory {
+ final static Logger logger = LoggerFactory.getLogger( OWLAPIOntologyFactory.class );
private static URI formalismUri = null;
private static String formalismId = "OWL1.0";
@@ -49,7 +53,9 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
cache = new OntologyCache<OWLAPIOntology>();
try {
formalismUri = new URI("http://www.w3.org/2002/07/owl#");
- } catch (URISyntaxException ex) { ex.printStackTrace(); } // should not happen
+ } catch (URISyntaxException ex) {
+ logger.debug( "IGNORED should never happen", ex );
+ }
};
public void clearCache() throws OntowrapException {
@@ -67,7 +73,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
onto.setURI( ((OWLOntology)ontology).getLogicalURI() );
} catch (OWLException e) {
// Better put in the OntowrapException of loaded
- e.printStackTrace();
+ logger.debug( "IGNORED (ontology without URI)", e );
}
//cache.recordOntology( uri, onto );
return onto;
@@ -99,7 +105,7 @@ public class OWLAPIOntologyFactory extends OntologyFactory {
onto.setURI( ontology.getLogicalURI() );
} catch (OWLException e) {
// Better put in the OntowrapException of loaded
- e.printStackTrace();
+ logger.debug( "IGNORED Exception", e );
}
cache.recordOntology( uri, onto );
return onto;
diff --git a/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3Ontology.java b/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3Ontology.java
index 82e36865..3c3fea5d 100644
--- a/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3Ontology.java
+++ b/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3Ontology.java
@@ -93,9 +93,6 @@ public class OWLAPI3Ontology extends BasicOntology<OWLOntology> implements Heavy
//return onto.getDataPropertiesInSignature();
}
-
-
-
public Set<? extends Object> getEntities() {
//return onto.getSignature();
return new EntityFilter<OWLEntity>(onto.getSignature(),this) {
diff --git a/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3OntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3OntologyFactory.java
index 788996dc..d08caf42 100644
--- a/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3OntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3OntologyFactory.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2008-2011
+ * Copyright (C) INRIA, 2008-2011, 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
@@ -23,6 +23,9 @@ package fr.inrialpes.exmo.ontowrap.owlapi30;
import java.net.URI;
import java.net.URISyntaxException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.OWLOntology;
@@ -38,6 +41,7 @@ import fr.inrialpes.exmo.ontowrap.OntologyFactory;
import fr.inrialpes.exmo.ontowrap.HeavyLoadedOntology;
public class OWLAPI3OntologyFactory extends OntologyFactory {
+ final static Logger logger = LoggerFactory.getLogger( OWLAPI3OntologyFactory.class );
private URI formalismUri = null;
@@ -52,13 +56,13 @@ public class OWLAPI3OntologyFactory extends OntologyFactory {
try {
formalismUri = new URI("http://www.w3.org/2002/07/owl#");
manager = OWLManager.createOWLOntologyManager();
- } catch (URISyntaxException ex) { // should not happen
- ex.printStackTrace();
+ } catch (URISyntaxException ex) {
+ logger.debug( "IGNORED should never happen", ex );
}
}
@Override
- public OWLAPI3Ontology newOntology( Object ontology , boolean onlyLocalEntities) throws OntowrapException {
+ public OWLAPI3Ontology newOntology( Object ontology, boolean onlyLocalEntities) throws OntowrapException {
if ( ontology instanceof OWLOntology ) {
OWLAPI3Ontology onto = new OWLAPI3Ontology(onlyLocalEntities);
onto.setFormalism( formalismId );
@@ -74,27 +78,26 @@ public class OWLAPI3OntologyFactory extends OntologyFactory {
}
@Override
- public HeavyLoadedOntology loadOntology( URI uri , boolean onlyLocalEntities) throws OntowrapException {
+ public HeavyLoadedOntology loadOntology( URI uri, boolean onlyLocalEntities ) throws OntowrapException {
OWLAPI3Ontology onto = null;
- //System.err.println( " Loading ontology "+uri );
+ // logger.trace( " Loading ontology {}", uri );
// Cache seems to be implemented in API 3.0 anyway
// and it seems to not work well with this one
onto = cache.getOntologyFromURI( uri );
- //System.err.println( " cache1: "+onto );
+ // logger.trace( "cache1: {}", onto );
if ( onto != null ) return onto;
onto = cache.getOntology( uri );
- //System.err.println( " cache2: "+onto );
+ // logger.trace( "cache2: {}", onto );
if ( onto != null ) return onto;
// OWLAPI's own cache
IRI ontoIRI = IRI.create( uri );
OWLOntology ontology = manager.getOntology( ontoIRI );
- //System.err.println( " cache3: "+ontology );
-
+ // logger.trace( "cache3: {}", ontology );
try {
// This below does not seem to work!
//ontology = manager.loadOntologyFromOntologyDocument( IRI.create( uri ) );
if ( ontology == null ) ontology = manager.loadOntology( ontoIRI );
- //System.err.println( " loaded: "+ontology );
+ // logger.trace( "loaded: {}", ontology );
// I must retrieve it from cache and return it!
} catch ( OWLOntologyDocumentAlreadyExistsException oodaeex ) { // should never happen
// This is a cache failure
@@ -105,10 +108,9 @@ public class OWLAPI3OntologyFactory extends OntologyFactory {
if ( ontology == null )
throw new OntowrapException("Already loaded [owl cache failure] " + uri, ooaeex );
} catch ( OWLOntologyCreationException oocex ) {
- oocex.printStackTrace();
- throw new OntowrapException("Cannot load " + uri, oocex );
+ throw new OntowrapException( "Cannot load " + uri, oocex );
}
- onto = new OWLAPI3Ontology(onlyLocalEntities);
+ onto = new OWLAPI3Ontology( onlyLocalEntities );
onto.setFormalism( formalismId );
onto.setFormURI( formalismUri );
onto.setOntology( ontology );
@@ -119,10 +121,10 @@ public class OWLAPI3OntologyFactory extends OntologyFactory {
// Better put in the OntowrapException of loaded
// The ontology has no URI. In principle, it is not valid
// It may be possible to put the uri instead (now it is void)
- e.printStackTrace();
+ logger.debug( "IGNORED Exception (ontology without URI)", e );
}
cache.recordOntology( uri, onto );
- //System.err.println( " after-cache: "+cache.getOntology( uri ) );
+ // logger.trace( "after-cache: {}", cache.getOntology( uri ) );
return onto;
}
diff --git a/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSOntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSOntologyFactory.java
index fa9fdf95..312c5d88 100644
--- a/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSOntologyFactory.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2009-2010
+ * Copyright (C) INRIA, 2009-2010, 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
@@ -24,6 +24,9 @@ import java.net.URI;
import java.net.URISyntaxException;
import java.util.NoSuchElementException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.skosapibinding.SKOSManager;
import org.semanticweb.skos.SKOSCreationException;
import org.semanticweb.skos.SKOSDataset;
@@ -35,6 +38,7 @@ import fr.inrialpes.exmo.ontowrap.OntologyCache;
import fr.inrialpes.exmo.ontowrap.OntowrapException;
public class SKOSOntologyFactory extends OntologyFactory {
+ final static Logger logger = LoggerFactory.getLogger( SKOSOntologyFactory.class );
private static URI formalismUri = null;
private static String formalismId = "SKOS1.0";
@@ -47,7 +51,7 @@ public class SKOSOntologyFactory extends OntologyFactory {
cache = new OntologyCache<SKOSThesaurus>();
try {
formalismUri = new URI("http://www.w3.org/2004/02/skos/core#");
- } catch (URISyntaxException ex) { ex.printStackTrace(); } // should not happen
+ } catch (URISyntaxException ex) { logger.debug( "IGNORED should not happen", ex ); }
try {
manager = new SKOSManager();
} catch (SKOSCreationException sce) {
@@ -77,7 +81,7 @@ public class SKOSOntologyFactory extends OntologyFactory {
@Override
public SKOSThesaurus loadOntology( URI uri , boolean onlyLocalEntities) throws OntowrapException {
- //System.err.println(" Loading "+uri );
+ //logger.trace( "Loading {}", uri );
SKOSThesaurus onto = null;
onto = cache.getOntologyFromURI( uri );
if ( onto != null ) return onto;
diff --git a/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSThesaurus.java b/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSThesaurus.java
index d0fbea57..8f8ab921 100644
--- a/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSThesaurus.java
+++ b/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSThesaurus.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2009-2010, 2012
+ * Copyright (C) INRIA, 2009-2010, 2012-2013
*
* 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
@@ -27,6 +27,9 @@ import java.util.Iterator;
import java.util.Map;
import java.util.Set;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import org.semanticweb.skos.SKOSDataFactory;
import org.semanticweb.skos.SKOSDataset;
import org.semanticweb.skos.SKOSAnnotation;
@@ -45,6 +48,7 @@ import fr.inrialpes.exmo.ontowrap.HeavyLoadedOntology;
import fr.inrialpes.exmo.ontowrap.OntowrapException;
public class SKOSThesaurus extends BasicOntology<SKOSDataset> implements HeavyLoadedOntology<SKOSDataset>{
+ final static Logger logger = LoggerFactory.getLogger( SKOSThesaurus.class );
SKOSDataFactory factory;
@@ -88,7 +92,7 @@ onto.getSKOSDataRelationAssertions(concept)
assertion.getSKOSObject();
if (literal.isTyped()) {
SKOSTypedLiteral typedLiteral = literal.getAsSKOSTypedLiteral();
-System.out.println("\t\t" + assertion.getSKOSProperty().getURI().getFragment() + " " + literal.getLiteral() + " Type:" + typedLiteral.getDataType().getURI() );
+//logger.trace("\t\t {} {} Type: {}", assertion.getSKOSProperty().getURI().getFragment(), literal.getLiteral(), typedLiteral.getDataType().getURI() );
} else {
SKOSUntypedLiteral untypedLiteral = literal.getAsSKOSUntypedLiteral();
if (untypedLiteral.hasLang()) {
diff --git a/src/fr/inrialpes/exmo/ontowrap/skoslite/SKOSLiteOntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/skoslite/SKOSLiteOntologyFactory.java
index aefc3594..8c412061 100644
--- a/src/fr/inrialpes/exmo/ontowrap/skoslite/SKOSLiteOntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/skoslite/SKOSLiteOntologyFactory.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * 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
@@ -23,6 +23,9 @@ package fr.inrialpes.exmo.ontowrap.skoslite;
import java.net.URI;
import java.net.URISyntaxException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import com.hp.hpl.jena.rdf.model.Model;
import fr.inrialpes.exmo.ontowrap.OntologyCache;
@@ -30,6 +33,7 @@ import fr.inrialpes.exmo.ontowrap.OntologyFactory;
import fr.inrialpes.exmo.ontowrap.OntowrapException;
public class SKOSLiteOntologyFactory extends OntologyFactory {
+ final static Logger logger = LoggerFactory.getLogger( SKOSLiteOntologyFactory.class );
private URI formalismUri;
private final static String formalismId = "SKOS1.0";
@@ -39,8 +43,7 @@ public class SKOSLiteOntologyFactory extends OntologyFactory {
try {
formalismUri = new URI("http://www.w3.org/2004/02/skos/core#");
} catch (URISyntaxException e) {
-
- e.printStackTrace();
+ logger.trace( "IGNORED: should never been raised", e );
}
}
diff --git a/src/fr/inrialpes/exmo/ontowrap/skoslite/SKOSLiteThesaurus.java b/src/fr/inrialpes/exmo/ontowrap/skoslite/SKOSLiteThesaurus.java
index 51291e00..497726ac 100644
--- a/src/fr/inrialpes/exmo/ontowrap/skoslite/SKOSLiteThesaurus.java
+++ b/src/fr/inrialpes/exmo/ontowrap/skoslite/SKOSLiteThesaurus.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2008-2010, 2012
+ * Copyright (C) INRIA, 2008-2010, 2012-2013
*
* 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
@@ -27,6 +27,9 @@ import java.util.HashSet;
import java.util.Map;
import java.util.Set;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.rdf.model.InfModel;
import com.hp.hpl.jena.rdf.model.Model;
@@ -45,6 +48,7 @@ import fr.inrialpes.exmo.ontowrap.HeavyLoadedOntology;
import fr.inrialpes.exmo.ontowrap.OntowrapException;
public class SKOSLiteThesaurus implements HeavyLoadedOntology<Model> {
+ final static Logger logger = LoggerFactory.getLogger( SKOSLiteThesaurus.class );
protected final static String SKOS_ONTO = SKOSLiteThesaurus.class.getClassLoader().getResource("fr/inrialpes/exmo/ontowrap/skoslite/skos.rdf").toString();
@@ -150,7 +154,7 @@ public class SKOSLiteThesaurus implements HeavyLoadedOntology<Model> {
*/
public Set<? extends Object> getSubClasses(Object c, int local, int asserted, int named) {
HashSet<Object> sub = new HashSet<Object>();
- //System.out.println(c);
+ //logger.trace( "getSubClasses({})", c);
StmtIterator it =ontoInf.listStatements(null,ontoInf.getProperty(SKOS_BROADERTRANSITIVE),(Resource) c);
while ( it.hasNext() ) {
Statement st = it.next();
@@ -203,7 +207,8 @@ public class SKOSLiteThesaurus implements HeavyLoadedOntology<Model> {
try {
Object o = ontoInf.getRawModel().getResource(u.toString());
if (! ontoInf.contains((Resource) o, RDF.type, ontoInf.getResource(SKOS_CONCEPT))) {
- return null;//System.out.println(u+" : "+o);
+ //logger.trace( "getEntity({}) = {}", u, o);
+ return null;
}
return o;
@@ -224,7 +229,7 @@ public class SKOSLiteThesaurus implements HeavyLoadedOntology<Model> {
while (it.hasNext()) {
Node n = it.next().asNode();
if (n.isLiteral() && (lang==null || lang.equals(n.getLiteralLanguage()))) {
- //System.out.println(n.getLiteralLexicalForm());
+ //logger.trace( "getEntityAnnotation = {}", n.getLiteralLexicalForm() );
annots.add(n.getLiteralLexicalForm());
}
}
@@ -243,7 +248,7 @@ public class SKOSLiteThesaurus implements HeavyLoadedOntology<Model> {
while (it.hasNext()) {
Node n = it.next().asNode();
if (n.isLiteral()) {
- //System.out.println(n.getLiteralLexicalForm());
+ //logger.trace( "getEntityAnnotationsL = {}", n.getLiteralLexicalForm() );
annots.add(new Annotation(n.getLiteralLexicalForm(),n.getLiteralLanguage()));
}
}
diff --git a/src/fr/inrialpes/exmo/ontowrap/util/EntityFilter.java b/src/fr/inrialpes/exmo/ontowrap/util/EntityFilter.java
index d99f8982..2504b503 100644
--- a/src/fr/inrialpes/exmo/ontowrap/util/EntityFilter.java
+++ b/src/fr/inrialpes/exmo/ontowrap/util/EntityFilter.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2010
+ * Copyright (C) INRIA, 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
@@ -23,10 +23,14 @@ package fr.inrialpes.exmo.ontowrap.util;
import java.net.URI;
import java.util.Set;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import fr.inrialpes.exmo.ontowrap.LoadedOntology;
import fr.inrialpes.exmo.ontowrap.OntowrapException;
public class EntityFilter<T> extends FilteredSet<T> {
+ final static Logger logger = LoggerFactory.getLogger( EntityFilter.class );
private String ontoURI=null;
private LoadedOntology<?> onto=null;
@@ -43,11 +47,11 @@ public class EntityFilter<T> extends FilteredSet<T> {
protected boolean isFiltered(T obj) {
try {
URI entURI=onto.getEntityURI(obj);
- //System.out.println(entURI +" - "+ontoURI);
+ //logger.trace( "{}�- {}", entURI, ontoURI);
return (entURI.getAuthority()!=null) && (entURI==null || ontoURI.equals(entURI.toString()) || !entURI.toString().startsWith(ontoURI));
}
catch (OntowrapException e) {
- // e.printStackTrace();
+ logger.debug( "IGNORED: Entity is filtered", e );
}
return true;
}
diff --git a/src/org/semanticweb/owl/align/AlignmentException.java b/src/org/semanticweb/owl/align/AlignmentException.java
index a09da48c..f55cac7d 100644
--- a/src/org/semanticweb/owl/align/AlignmentException.java
+++ b/src/org/semanticweb/owl/align/AlignmentException.java
@@ -30,19 +30,16 @@ import java.lang.Exception;
* @version $Id$
*/
-public class AlignmentException extends Exception
-{
+public class AlignmentException extends Exception {
private static final long serialVersionUID = 330;
- public AlignmentException( String message )
- {
+ public AlignmentException( String message ) {
super( message );
}
- public AlignmentException( String message, Exception e )
- {
- super( message, e );
+ public AlignmentException( String message, Exception ex ) {
+ super( message, ex );
}
}
diff --git a/test/clitest.sh b/test/clitest.sh
new file mode 100644
index 00000000..00a4bd38
--- /dev/null
+++ b/test/clitest.sh
@@ -0,0 +1,1143 @@
+#!/bin/sh
+#
+# This long script runs commands from the
+#
+# It is highly dependent on logback and my own logback.xml
+#
+
+CWD=`pwd`
+CP=$CWD/lib/procalign.jar:$CWD/lib/slf4j/logback-core-1.0.9.jar:$CWD/lib/slf4j/logback-classic-1.0.9.jar:$CWD
+RESDIR='/tmp/clitest'
+
+########################################################################
+# ProcAlign
+########################################################################
+
+/bin/rm -rf $RESDIR
+mkdir -p $RESDIR
+
+# GOTO
+if false; then
+echo this is for avoiding some parts
+#GOTO
+fi
+
+echo "\t\tTHE -z OPTIONS RELY ON LOGBACK BEING PROPERLY DEFINED"
+echo "\t\t *** Testing Procalign ***"
+
+#-------------------
+echo "\t-z, -zzz"
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.Procalign -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with PROC-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.Procalign --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with PROC-ERR2; fi
+
+#-------------------
+echo "\t-h,--help"
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign -h &> $RESDIR/proc-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign --help &> $RESDIR/proc-help.txt
+if [ -s $RESDIR/proc-h.txt ]; then diff $RESDIR/proc-h.txt $RESDIR/proc-help.txt > $RESDIR/proc-diff-h.txt; else echo error with PROC-HELP1; fi
+if [ -s $RESDIR/proc-diff-h.txt ]; then echo error with PROC-HELP2; fi
+
+#-------------------
+echo "\t-o,--output <FILE>"
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -o $RESDIR/proc-o1.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl --output $RESDIR/proc-output1.rdf
+sed "s:<time>[^<]*</time>::" $RESDIR/proc-o1.rdf > $RESDIR/proc-o.rdf
+sed "s:<time>[^<]*</time>::" $RESDIR/proc-output1.rdf > $RESDIR/proc-output.rdf
+if [ -s $RESDIR/proc-o.rdf ]; then diff $RESDIR/proc-o.rdf $RESDIR/proc-output.rdf; else echo error with PROC-OUTPUT1; fi
+
+#-------------------
+echo "\t-a,--alignment <FILE>"
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -a examples/rdf/sample.rdf | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-a.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl --alignment examples/rdf/sample.rdf | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-align.rdf
+if [ -s $RESDIR/proc-a.rdf ]; then diff $RESDIR/proc-a.rdf $RESDIR/proc-align.rdf; else echo error with PROC-ALIGN1; fi
+
+#-------------------
+echo "\t-i <C>, --impl <C>"
+#JE: A random distance available (could try with others)
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.StrucSubsDistAlignment | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-i.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl --impl fr.inrialpes.exmo.align.impl.method.StrucSubsDistAlignment | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-impl.rdf
+if [ -s $RESDIR/proc-i.rdf ]; then diff $RESDIR/proc-i.rdf $RESDIR/proc-impl.rdf; else echo error with PROC-IMPL1; fi
+
+#-------------------
+echo "\t-Dn=v"
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-id.rdf
+if [ -s $RESDIR/proc-id.rdf ]; then diff $RESDIR/proc-i.rdf $RESDIR/proc-id.rdf | sed "s:<time>[^<]*</time>::" > $RESDIR/diff-proc.txt; else echo error with PROC-PARAM1; fi
+if [ ! -s $RESDIR/diff-proc.txt ]; then echo error with PROC-PARAM2; fi
+
+#-------------------
+echo "\t-t,--threshold <DOUBLE>"
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -t 0.4 | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-t.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance --threshold 0.4 | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-threshold.rdf
+if [ -s $RESDIR/proc-t.rdf ]; then diff $RESDIR/proc-t.rdf $RESDIR/proc-threshold.rdf; else echo error with PROC-THRES1; fi
+# test diff from previous
+diff $RESDIR/proc-t.rdf $RESDIR/proc-id.rdf > $RESDIR/diff-proc.txt
+if [ ! -s $RESDIR/diff-proc.txt ]; then echo error with PROC-THRES2; fi
+
+#-------------------
+echo "\t-T,--cutmethod <METHOD>"
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -t 0.4 -T perc | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-C.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl --impl fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -t 0.4 --cutmethod perc | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-cutmethod.rdf
+if [ -s $RESDIR/proc-C.rdf ]; then diff $RESDIR/proc-C.rdf $RESDIR/proc-cutmethod.rdf; else echo error with PROC-CUT1; fi
+# test diff from previous
+diff $RESDIR/proc-C.rdf $RESDIR/proc-t.rdf > $RESDIR/diff-proc.txt
+if [ ! -s $RESDIR/diff-proc.txt ]; then echo error with PROC-CUT2; fi
+
+#-------------------
+echo "\t-r,--renderer <CLASS>"
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor | sed "s/time: [0-9]*/time: 0/" > $RESDIR/proc-r.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl --renderer fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor | sed "s/time: [0-9]*/time: 0/" > $RESDIR/proc-render.rdf
+if [ -s $RESDIR/proc-r.rdf ]; then diff $RESDIR/proc-r.rdf $RESDIR/proc-render.rdf; else echo error with PROC-RENDER1; fi
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "<?xml version='1.0' encoding='utf-8' standalone='no'?>
+<\x21DOCTYPE properties SYSTEM \"http://java.sun.com/dtd/properties.dtd\">
+<properties>
+<entry key=\"impl\">fr.inrialpes.exmo.align.impl.method.StringDistAlignment</entry>
+<entry key=\"stringFunction\">levenshteinDistance</entry>
+</properties>" > $RESDIR/params.xml
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -P $RESDIR/params.xml | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-p.rdf
+#Will not work because we use loadFromXML
+#echo "impl=fr.inrialpes.exmo.align.impl.method.StringDistAlignment
+#stringFunction=levenshteinDistance" > $RESDIR/params.prop
+java -cp $CP fr.inrialpes.exmo.align.cli.Procalign file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl --params $RESDIR/params.xml | sed "s:<time>[^<]*</time>::" > $RESDIR/proc-params.rdf
+if [ -s $RESDIR/proc-p.rdf ]; then diff $RESDIR/proc-p.rdf $RESDIR/proc-params.rdf; else echo error with PROC-PARAMS1; fi
+diff $RESDIR/proc-p.rdf $RESDIR/proc-id.rdf
+
+########################################################################
+# ParserPrinter
+########################################################################
+
+echo "\t\t *** Testing ParserPrinter ***"
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with PARS-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with PARS-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter -h &> $RESDIR/pars-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter --help &> $RESDIR/pars-help.txt
+if [ -s $RESDIR/pars-h.txt ]; then diff $RESDIR/pars-h.txt $RESDIR/pars-help.txt; else echo error with $RESDIR/pars-h.txt; fi
+
+#-------------------
+echo "\tno-op"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf &> $RESDIR/pars-noop.rdf
+
+#-------------------
+echo "\t-e,--embedded"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf -e -o $RESDIR/pars-e.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf --embedded -o $RESDIR/pars-emb.rdf
+if [ -s $RESDIR/pars-e.rdf ]; then diff $RESDIR/pars-e.rdf $RESDIR/pars-emb.rdf; else echo error with PARS-EMB; fi
+diff $RESDIR/pars-e.rdf $RESDIR/pars-noop.rdf
+
+#-------------------
+# JE: there is no alternative parser (RDF/XML Parser are not AlignmentParsers)
+echo "\t-p,--parser <CLASS>"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter -p fr.inrialpes.exmo.align.parser.AlignmentParser file://$CWD/examples/rdf/newsample.rdf -o $RESDIR/pars-p1.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter --parser fr.inrialpes.exmo.align.parser.AlignmentParser file://$CWD/examples/rdf/newsample.rdf -o $RESDIR/pars-p2.rdf
+if [ -s $RESDIR/pars-p1.rdf ]; then diff $RESDIR/pars-p1.rdf $RESDIR/pars-p2.rdf; else echo error with PARS-PARS1; fi
+
+#-------------------
+echo "\t-o <F>, --output <F>"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf -o $RESDIR/pars-o1.rdf
+if [ -s $RESDIR/pars-o1.rdf ]; then diff $RESDIR/pars-o1.rdf $RESDIR/pars-noop.rdf; else echo error with PARS-OUTPUT0; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf --output $RESDIR/pars-output1.rdf
+diff $RESDIR/pars-o1.rdf $RESDIR/pars-output1.rdf
+
+#-------------------
+# This is for SPARQL OUTPUT
+echo "\t-c,--outputDir <DIR>"
+#java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf -w $RESDIR -o pars-o2.rdf
+#java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf --output pars-output2.rdf --outputDir $RESDIR
+#if [ -s $RESDIR/pars-o2.rdf ]; then diff $RESDIR/pars-o2.rdf $RESDIR/pars-output2.rdf; else echo error with PARS-OUTPUT2; fi
+
+#-------------------
+echo "\t-i,--inverse"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf -i -o $RESDIR/pars-i.rdf
+if [ -s $RESDIR/pars-i.rdf ]; then diff $RESDIR/pars-i.rdf $RESDIR/pars-noop.rdf > $RESDIR/diff-pars.txt; else echo error with PARS-INV1; fi
+if [ ! -s $RESDIR/diff-pars.txt ]; then echo error with PARS-INV2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf --inverse --output $RESDIR/pars-inverse.rdf
+diff $RESDIR/pars-i.rdf $RESDIR/pars-inverse.rdf
+
+#-------------------
+echo "\t-t,--threshold <DOUBLE>"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf -t .6 -o $RESDIR/pars-t1.rdf
+if [ -s $RESDIR/pars-t1.rdf ]; then diff $RESDIR/pars-t1.rdf $RESDIR/pars-noop.rdf > $RESDIR/diff-thres.txt; else echo error with PARS-THRES1; fi
+if [ ! -s $RESDIR/diff-thres.txt ]; then echo error with PARS-THRES2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf --threshold .6 --output $RESDIR/pars-thres1.rdf
+diff $RESDIR/pars-t1.rdf $RESDIR/pars-thres1.rdf
+
+#-------------------
+echo "\t-T,--cutmethod <METHOD>"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf -T best -t .6 -o $RESDIR/pars-g1.rdf
+if [ -s $RESDIR/pars-g1.rdf ]; then diff $RESDIR/pars-g1.rdf $RESDIR/pars-t1.rdf > $RESDIR/diff-gap.txt; else echo error with PARS-GAP1; fi
+if [ ! -s $RESDIR/diff-gap.txt ]; then echo error with PARS-GAP2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf --cutmethod best --threshold .6 --output $RESDIR/pars-gap1.rdf
+diff $RESDIR/pars-g1.rdf $RESDIR/pars-gap1.rdf
+
+#-------------------
+echo "\t-r,--renderer <CLASS>"
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor -o $RESDIR/pars-r1.rdf
+if [ -s $RESDIR/pars-r1.rdf ]; then diff $RESDIR/pars-r1.rdf $RESDIR/pars-o1.rdf > $RESDIR/diff-rend.txt; else echo error with PARS-RENDER1; fi
+if [ ! -s $RESDIR/diff-rend.txt ]; then echo error with PARS-RENDER2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ParserPrinter file://$CWD/examples/rdf/newsample.rdf --renderer fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor -o $RESDIR/pars-render1.rdf
+diff $RESDIR/pars-r1.rdf $RESDIR/pars-render1.rdf
+
+#-------------------
+echo "\t-Dn=v"
+echo "\t(same as Procalign)"
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign)"
+
+########################################################################
+# EvalAlign
+########################################################################
+
+echo "\t\t *** Testing EvalAlign ***"
+
+#-------------------
+echo "\t-d(<L>), --debug (<L>) DEPRECATED"
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with EVAL-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with EVAL-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign -h &> $RESDIR/eval-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign --help &> $RESDIR/eval-help.txt
+# This should be put everywhere!
+if [ -s $RESDIR/eval-h.txt ]; then diff $RESDIR/eval-h.txt $RESDIR/eval-help.txt; else echo error with EVAL-HELP1; fi
+
+#java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator html/tutorial/refalign.rdf html/tutorial/refalign.rdf -o $RESDIR/eval-i.txt
+#java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign --impl fr.inrialpes.exmo.align.impl.eval.PRecEvaluator html/tutorial/refalign.rdf html/tutorial/refalign.rdf --output $RESDIR/eval-impl.txt
+#if [ -s $RESDIR/eval-i.txt ]; then diff $RESDIR/eval-i.txt $RESDIR/eval-impl.txt; else echo error with EVAL_HELP2; fi
+
+#-------------------
+echo "\tno-op"
+java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign file://$CWD/examples/rdf/newsample.rdf file://$RESDIR/proc-o1.rdf &> $RESDIR/eval-noop.xml
+if [ ! -s $RESDIR/eval-noop.xml ]; then echo error with EVAL-NOOP; fi
+
+#-------------------
+echo "\t-o <F>, --output <F>"
+java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign file://$CWD/examples/rdf/newsample.rdf file://$RESDIR/proc-o1.rdf -o $RESDIR/eval-o1.xml
+if [ -s $RESDIR/eval-o1.xml ]; then diff $RESDIR/eval-o1.xml $RESDIR/eval-noop.xml; else echo error with EVAL-OUT1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign file://$CWD/examples/rdf/newsample.rdf file://$RESDIR/proc-o1.rdf --output $RESDIR/eval-out1.xml
+diff $RESDIR/eval-out1.xml $RESDIR/eval-o1.xml
+
+#-------------------
+echo "\t-i <C>, --impl <C>"
+java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.WeightedPREvaluator file://$CWD/examples/rdf/newsample.rdf file://$RESDIR/proc-o1.rdf -o $RESDIR/eval-i1.xml
+if [ -s $RESDIR/eval-i1.xml ]; then diff $RESDIR/eval-o1.xml $RESDIR/eval-noop.xml > $RESDIR/diff-evimpl.txt ; else echo error with EVAL-IMPL1; fi
+if [ ! -s $RESDIR/diff-rend.txt ]; then echo error with EVAL-IMPL2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.EvalAlign --impl fr.inrialpes.exmo.align.impl.eval.WeightedPREvaluator file://$CWD/examples/rdf/newsample.rdf file://$RESDIR/proc-o1.rdf -o $RESDIR/eval-impl1.xml
+diff $RESDIR/eval-impl1.xml $RESDIR/eval-i1.xml
+
+#-------------------
+echo "\t-Dn=v"
+echo "\t(same as Procalign)"
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign)"
+
+########################################################################
+# TestGen
+########################################################################
+
+echo "\t\t *** Testing TestGen ***"
+
+#java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -u http://www.example.org/mynewtest -w $RESDIR/outtestdir -DremoveClasses=.25 examples/rdf/edu.umbc.ebiquity.publication.owl
+# --> This one
+#java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -t fr.inrialpes.exmo.align.gen.BenchmarkGenerator -u http://www.example.org/mynewtest -w $RESDIR/outtestdir examples/rdf/edu.umbc.ebiquity.publication.owl
+#$JAVA -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -t fr.inrialpes.exmo.align.gen.BenchmarkGenerator -u $URI/$run/ -w $DIR/r$run $seedonto
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.TestGen -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GEN-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.TestGen --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GEN-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+java -cp $CP fr.inrialpes.exmo.align.cli.TestGen -h &> $RESDIR/test-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.TestGen --help &> $RESDIR/test-help.txt
+if [ -s $RESDIR/test-h.txt ]; then diff $RESDIR/test-h.txt $RESDIR/test-help.txt; else echo error with TEST-HELP; fi
+
+#-------------------
+echo "\t-u,--urlprefix <URI> --uriprefix"
+mkdir $RESDIR/smalltest
+mkdir $RESDIR/smalltest/gentestempty1
+cd $RESDIR/smalltest/gentestempty1
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -u http://www.example.org/mynewtest $CWD/examples/rdf/edu.umbc.ebiquity.publication.owl
+if [ ! -s refalign.rdf ]; then echo error with GEN-EMP1; fi
+if [ ! -s onto.rdf ]; then echo error with GEN-EMP2; fi
+mkdir $RESDIR/smalltest/gentestempty2
+cd $RESDIR/smalltest/gentestempty2
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen --uriprefix http://www.example.org/mynewtest2 $CWD/examples/rdf/edu.umbc.ebiquity.publication.owl
+if [ -s refalign.rdf ]; then diff refalign.rdf $RESDIR/smalltest/gentestempty1/refalign.rdf > gendiff.txt; else echo error with GEN-EMP3; fi
+if [ ! -s gendiff.txt ]; then echo error with GEN-EMP4; fi
+if [ -s onto.rdf ]; then diff onto.rdf $RESDIR/smalltest/gentestempty1/onto.rdf > gendiff.txt; else echo error with GEN-EMP5; fi
+if [ ! -s gendiff.txt ]; then echo error with GEN-EMP6; fi
+cd $CWD
+
+#-------------------
+echo "\t-w,--outdir <DIR>"
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -u http://www.example.org/mynewtest -w $RESDIR/smalltest/outtestdir1 examples/rdf/edu.umbc.ebiquity.publication.owl
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -u http://www.example.org/mynewtest --outdir $RESDIR/smalltest/outtestdir2 examples/rdf/edu.umbc.ebiquity.publication.owl
+#if [ -s $RESDIR/smalltest/outtestdir1/onto.rdf ]; then diff $RESDIR/smalltest/outtestdir1/onto.rdf $RESDIR/smalltest/outtestdir2/onto.rdf; else echo error with GEN-OUT1; fi
+if [ -s $RESDIR/smalltest/outtestdir1/refalign.rdf ]; then diff $RESDIR/smalltest/outtestdir1/refalign.rdf $RESDIR/smalltest/outtestdir2/refalign.rdf; else echo error with GEN-OUT2; fi
+
+#-------------------
+echo "\t-Dn=v"
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -u http://www.example.org/mynewtest -DremoveClasses=.25 -w $RESDIR/smalltest/outtestdir3 examples/rdf/edu.umbc.ebiquity.publication.owl
+# Here we can do with many parameters
+if [ -s $RESDIR/smalltest/outtestdir3/onto.rdf ]; then diff $RESDIR/smalltest/outtestdir1/refalign.rdf $RESDIR/smalltest/outtestdir3/refalign.rdf > $RESDIR/smalltest/outtestdir2/gendiff.txt ; else echo error with GEN-OUT3; fi
+if [ ! -s $RESDIR/smalltest/outtestdir2/gendiff.txt ]; then echo error with GEN-VAR1; fi
+
+#-------------------
+echo "\t-a,--alignname <FILE> "
+echo "\t-o,--output <FILE>"
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -u http://www.example.org/mynewtest -a myalign.rdf -o biblio.owl -w $RESDIR/outtestdir4 examples/rdf/edu.umbc.ebiquity.publication.owl
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -u http://www.example.org/mynewtest --alignname myalign.rdf --output biblio.owl -w $RESDIR/outtestdir5 examples/rdf/edu.umbc.ebiquity.publication.owl
+if [ -s $RESDIR/outtestdir4/biblio.owl ]; then diff $RESDIR/outtestdir5/biblio.owl $RESDIR/outtestdir4/biblio.owl; else echo error with GEN-OUT1; fi
+if [ -s $RESDIR/outtestdir4/myalign.rdf ]; then diff $RESDIR/outtestdir5/myalign.rdf $RESDIR/outtestdir4/myalign.rdf; else echo error with GEN-AL1; fi
+diff $RESDIR/outtestdir5/myalign.rdf $RESDIR/smalltest/outtestdir1/refalign.rdf > $RESDIR/outtestdir5/gendiff.txt
+if [ ! -s $RESDIR/outtestdir5/gendiff.txt ]; then echo error with GEN-AL2; fi
+
+#-------------------
+echo "\t-t,--testset <CLASS>"
+mkdir $RESDIR/outtestdir
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen -t fr.inrialpes.exmo.align.gen.BenchmarkGenerator -u http://www.example.org/mynewtest -w $RESDIR/outtestdir examples/rdf/edu.umbc.ebiquity.publication.owl
+mkdir $RESDIR/outtestdir9
+java -Xmx1200m -cp $CP fr.inrialpes.exmo.align.cli.TestGen --testset fr.inrialpes.exmo.align.gen.BenchmarkGenerator --uriprefix http://www.example.org/mynewtest --outdir $RESDIR/outtestdir9 examples/rdf/edu.umbc.ebiquity.publication.owl
+if [ -s $RESDIR/outtestdir9/266/onto.rdf ]; then diff $RESDIR/outtestdir/266/onto.rdf $RESDIR/outtestdir9/266/onto.rdf > $RESDIR/outtestdir9/gendiff.txt; else echo error with GEN-TSET1; fi
+if [ ! -s $RESDIR/outtestdir9/gendiff.txt ]; then echo error with GEN-TSET2; fi
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign)"
+
+########################################################################
+# GroupAlign
+########################################################################
+
+# ADJUSTED Because otherwise --alignment below does not work
+
+for i in `cd $RESDIR/smalltest/; ls -d */`
+do
+sed -i '' "s;<location>http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#</location>;<location>file://$RESDIR/smalltest/gentestempty1/onto1.rdf</location>;" $RESDIR/smalltest/${i}refalign.rdf
+sed -i '' "s;<location>http://www.example.org/mynewtest/onto.rdf#</location>;<location>file://$RESDIR/smalltest/${i}onto.rdf</location>;" $RESDIR/smalltest/${i}refalign.rdf
+sed -i '' "s;http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#;http://www.example.org/mynewtest/101/onto.rdf#;" $RESDIR/smalltest/${i}refalign.rdf
+done
+
+echo "\t\t *** Testing GroupAlign ***"
+
+cp $RESDIR/outtestdir/101/onto.rdf $RESDIR/smalltest/gentestempty1/onto1.rdf
+cp $RESDIR/outtestdir/101/onto.rdf $RESDIR/smalltest/gentestempty2/onto1.rdf
+cp $RESDIR/outtestdir/101/onto.rdf $RESDIR/smalltest/outtestdir1/onto1.rdf
+cp $RESDIR/outtestdir/101/onto.rdf $RESDIR/smalltest/outtestdir2/onto1.rdf
+cp $RESDIR/outtestdir/101/onto.rdf $RESDIR/smalltest/outtestdir3/onto1.rdf
+
+#-------------------
+echo "\tEMPTY"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GRAL-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GRAL-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -h &> $RESDIR/gral-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --help &> $RESDIR/gral-help.txt
+if [ -s $RESDIR/gral-h.txt ]; then diff $RESDIR/gral-h.txt $RESDIR/gral-help.txt; else echo error with GRAL-HELP; fi
+
+#-------------------
+echo "\t-w,--directory <DIR>"
+echo "\t-o <F>, --output <F>"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -w $RESDIR/smalltest -o streq1.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --directory $RESDIR/smalltest --output streq2.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/streq1.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/streq2.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/streq1.rdf ]; then diff $RESDIR/smalltest/gentestempty1/streq1.rdf $RESDIR/smalltest/gentestempty1/streq2.rdf > $RESDIR/smalltest/diffstreq.txt ; else echo error with GRAL-DIR1; fi
+if [ -s $RESDIR/smalltest/diffstreq.txt ]; then echo error with GRAL-DIR2; fi
+
+#-------------------
+echo "\t-i <C>, --impl <C>"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment -w $RESDIR/smalltest -o edna1.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/edna1.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/edna1.rdf ]; then diff $RESDIR/smalltest/gentestempty1/edna1.rdf $RESDIR/smalltest/gentestempty1/streq2.rdf > $RESDIR/smalltest/diffstredna.txt ; else echo error with GRAL-IMPL1; fi
+if [ ! -s $RESDIR/smalltest/diffstredna.txt ]; then echo error with GRAL-IMPL2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --impl fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment -w $RESDIR/smalltest -o edna2.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/edna2.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/edna2.rdf ]; then diff $RESDIR/smalltest/gentestempty1/edna1.rdf $RESDIR/smalltest/gentestempty1/edna2.rdf > $RESDIR/smalltest/diffedna.txt ; else echo error with GRAL-IMPL3; fi
+if [ -s $RESDIR/smalltest/diffedna.txt ]; then echo error with GRAL-IMPL4; fi
+
+#-------------------
+# This test in fact does not work because there are too many 1. values.
+# I have checked that it works independently (add a bad distance name!)
+echo "\t-Dn=v"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -w $RESDIR/smalltest -o lev1.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/lev1.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/lev1.rdf ]; then diff $RESDIR/smalltest/gentestempty1/edna1.rdf $RESDIR/smalltest/gentestempty1/lev1.rdf > $RESDIR/smalltest/diffstredna.txt ; else echo error with GRAL-DV1; fi
+if [ ! -s $RESDIR/smalltest/diffstredna.txt ]; then echo error with GRAL-DV2; fi
+
+#-------------------
+
+echo "\t-a,--alignment <FILE> "
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -a refalign.rdf -w $RESDIR/smalltest -o streq1a.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --alignment refalign.rdf --directory $RESDIR/smalltest --output streq2a.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/streq1a.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/streq2a.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/streq1a.rdf ]; then diff $RESDIR/smalltest/gentestempty1/streq1a.rdf $RESDIR/smalltest/gentestempty1/streq2a.rdf > $RESDIR/smalltest/diffstreqa.txt ; else echo error with GRAL-AL1; fi
+if [ -s $RESDIR/smalltest/diffstreqa.txt ]; then echo error with GRAL-AL2; fi
+
+#-------------------
+echo "\t-n,--name <URI>"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -n file://$RESDIR/outtestdir/101/onto.rdf -w $RESDIR/smalltest -o streq1n.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --name file://$RESDIR/outtestdir/101/onto.rdf --directory $RESDIR/smalltest --output streq2n.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/streq1n.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/streq2n.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/streq1n.rdf ]; then diff $RESDIR/smalltest/gentestempty1/streq1n.rdf $RESDIR/smalltest/gentestempty1/streq2n.rdf > $RESDIR/smalltest/diffstreqn.txt ; else echo error with GRAL-NAME1; fi
+if [ -s $RESDIR/smalltest/diffstreqn.txt ]; then echo error with GRAL-NAME2; fi
+
+#-------------------
+echo "\t-r,--renderer <CLASS>"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -r fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor -w $RESDIR/smalltest -o streq1.html
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --renderer fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor --directory $RESDIR/smalltest --output streq2.html
+sed -i '' "s;time</td><td property=\"align:time\">[^<]*;;g" $RESDIR/smalltest/gentestempty1/streq1.html
+sed -i '' "s;time</td><td property=\"align:time\">[^<]*;;g" $RESDIR/smalltest/gentestempty1/streq2.html
+if [ -s $RESDIR/smalltest/gentestempty1/streq1.html ]; then diff $RESDIR/smalltest/gentestempty1/streq1.html $RESDIR/smalltest/gentestempty1/streq2.html ; else echo error with GRAL-RENDER1; fi
+
+#-------------------
+echo "\t-s,--source <FILE>"
+echo "\t-t,--target <FILE>"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -s onto.rdf -t onto1.rdf -w $RESDIR/smalltest -o streq1x.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/streq1x.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/streq1x.rdf ]; then diff $RESDIR/smalltest/gentestempty1/streq1x.rdf $RESDIR/smalltest/gentestempty1/streq2n.rdf > $RESDIR/smalltest/diffstreqxn.txt ; else echo error with GRAL-ST1; fi
+if [ ! -s $RESDIR/smalltest/diffstreqxn.txt ]; then echo error with GRAL-ST2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --source onto.rdf --target onto1.rdf --directory $RESDIR/smalltest --output streq2x.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/streq2x.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/streq1x.rdf ]; then diff $RESDIR/smalltest/gentestempty1/streq1x.rdf $RESDIR/smalltest/gentestempty1/streq2x.rdf ; else echo error with GRAL-ST3; fi
+
+#-------------------
+echo "\t-u,--uriprefix <URI>"
+
+ln -s /tmp/clitest/smalltest /tmp/clitest/preftest
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -w $RESDIR/smalltest -u file:///tmp/clitest/preftest -o strpr1.rdf
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign --directory $RESDIR/smalltest --uriprefix file:///tmp/clitest/preftest --output strpr2.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/strpr1.rdf
+sed -i '' "s;<time>[^<]*</time>;;g" $RESDIR/smalltest/gentestempty1/strpr2.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/strpr1.rdf ]; then diff $RESDIR/smalltest/gentestempty1/strpr1.rdf $RESDIR/smalltest/gentestempty1/strpr2.rdf > $RESDIR/smalltest/diffpref.txt ; else echo error with GRAL-PR1; fi
+if [ -s $RESDIR/smalltest/diffpref.txt ]; then echo error with GRAL-PR2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -w $RESDIR/smalltest -u file:///tmp/clitest/dummy -o strpr3.rdf
+if [ -s $RESDIR/smalltest/gentestempty1/strpr3.rdf ]; then echo error with GRAL-PR3; fi
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign)"
+
+########################################################################
+# GroupEval
+########################################################################
+
+echo "\t\t *** Testing GroupEval ***"
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GREV-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GroupEval --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GREV-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -h &> $RESDIR/groupeval-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval --help &> $RESDIR/groupeval-help.txt
+if [ -s $RESDIR/groupeval-h.txt ]; then diff $RESDIR/groupeval-h.txt $RESDIR/groupeval-help.txt; else echo error with GREVAL-HELP; fi
+
+#-------------------
+echo "\t-l,--list <FILE>"
+
+cd $RESDIR/smalltest
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -l "refalign,lev1,streq1" > groupeval-l1.html
+if [ ! -s groupeval-l1.html ]; then echo error with GREV-LIST1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval --list "refalign,lev1,streq1" > groupeval-l2.html
+if [ -s groupeval-l2.html ]; then diff groupeval-l1.html groupeval-l2.html ; else echo error with GREV-LIST2; fi
+cd $CWD
+
+#-------------------
+echo "\t-w,--directory <DIR>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/groupeval-w1.html
+if [ -s $RESDIR/groupeval-w1.html ]; then diff $RESDIR/groupeval-w1.html $RESDIR/smalltest/groupeval-l1.html > $RESDIR/smalltest/diffgrev-w1.txt ; else echo error with GREV-DIR1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-w1.txt ]; then echo error with GREV-DIR2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" --directory $RESDIR/smalltest > $RESDIR/groupeval-w2.html
+if [ -s $RESDIR/groupeval-w2.html ]; then diff $RESDIR/groupeval-w1.html $RESDIR/groupeval-w2.html ; else echo error with GREV-DIR3; fi
+
+#-------------------
+echo "\t-o <F>, --output <F>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/groupeval-o1.html
+if [ -s $RESDIR/groupeval-o1.html ]; then diff $RESDIR/groupeval-o1.html $RESDIR/groupeval-w1.html ; else echo error with GREV-OUT1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest --output $RESDIR/groupeval-o2.html
+if [ -s $RESDIR/groupeval-o2.html ]; then diff $RESDIR/groupeval-o1.html $RESDIR/groupeval-o2.html ; else echo error with GREV-OUT3; fi
+
+#-------------------
+echo "\t-f,--format <MEAS>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -f f -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/groupeval-f1.html
+if [ -s $RESDIR/groupeval-f1.html ]; then diff $RESDIR/groupeval-w1.html $RESDIR/groupeval-f1.html > $RESDIR/smalltest/diffgrev-f1.txt ; else echo error with GREV-FORM1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-f1.txt ]; then echo error with GREV-FORM2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval --format f -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/groupeval-f2.html
+if [ -s $RESDIR/groupeval-f2.html ]; then diff $RESDIR/groupeval-f1.html $RESDIR/groupeval-f2.html ; else echo error with GREV-FORM3; fi
+
+#-------------------
+echo "\t-c,--color (<COLOR>)"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -c -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/groupeval-c1.html
+if [ -s $RESDIR/groupeval-c1.html ]; then diff $RESDIR/groupeval-w1.html $RESDIR/groupeval-c1.html > $RESDIR/smalltest/diffgrev-c1.txt ; else echo error with GREV-COL1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-c1.txt ]; then echo error with GREV-COL2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval --color -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/groupeval-c2.html
+if [ -s $RESDIR/groupeval-c2.html ]; then diff $RESDIR/groupeval-c1.html $RESDIR/groupeval-c2.html ; else echo error with GREV-COL3; fi
+
+#-------------------
+echo "\t-r,--reference <FILE>"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -r lev1.rdf -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/groupeval-r1.html
+if [ -s $RESDIR/groupeval-r1.html ]; then diff $RESDIR/groupeval-w1.html $RESDIR/groupeval-r1.html > $RESDIR/smalltest/diffgrev-r1.txt ; else echo error with GREV-REF1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-r1.txt ]; then echo error with GREV-REF2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval --reference lev1.rdf -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/groupeval-r2.html
+if [ -s $RESDIR/groupeval-r2.html ]; then diff $RESDIR/groupeval-r1.html $RESDIR/groupeval-r2.html ; else echo error with GREV-REF3; fi
+
+#-------------------
+echo "\t-t,--type <TYPE> Output TYPE (html|xml|tex|ascii|triangle"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -t triangle -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/groupeval-ttr1.tex
+if [ -s $RESDIR/groupeval-ttr1.tex ]; then diff $RESDIR/groupeval-w1.html $RESDIR/groupeval-ttr1.tex > $RESDIR/smalltest/diffgrev-t1.txt ; else echo error with GREV-TYP1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-t1.txt ]; then echo error with GREV-TYP2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval --type triangle -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/groupeval-ttr2.tex
+if [ -s $RESDIR/groupeval-ttr2.tex ]; then diff $RESDIR/groupeval-ttr1.tex $RESDIR/groupeval-ttr2.tex ; else echo error with GREV-TYP3; fi
+
+#-------------------
+echo "\t-Dn=v"
+echo "\t(same as Procalign; useless: no parameters involved so far)"
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign; useless: no parameters involved so far)"
+
+########################################################################
+# WGroupEval
+########################################################################
+
+echo "\t\t *** Testing WGroupEval ***"
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with WGREV-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with WGREV-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -h &> $RESDIR/wgrev-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval --help &> $RESDIR/wgrev-help.txt
+if [ -s $RESDIR/wgrev-h.txt ]; then diff $RESDIR/wgrev-h.txt $RESDIR/wgrev-help.txt; else echo error with WGREV-HELP; fi
+
+#-------------------
+echo "\t-l,--list <FILE>"
+
+cd $RESDIR/smalltest
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -l "refalign,lev1,streq1" > wgrev-l1.html
+if [ ! -s wgrev-l1.html ]; then echo error with WGREV-LIST1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval --list "refalign,lev1,streq1" > wgrev-l2.html
+if [ -s wgrev-l2.html ]; then diff wgrev-l1.html wgrev-l2.html ; else echo error with WGREV-LIST2; fi
+cd $CWD
+
+#-------------------
+echo "\t-w,--directory <DIR>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/wgrev-w1.html
+if [ -s $RESDIR/wgrev-w1.html ]; then diff $RESDIR/wgrev-w1.html $RESDIR/smalltest/wgrev-l1.html > $RESDIR/smalltest/diffgrev-w1.txt ; else echo error with WGREV-DIR1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-w1.txt ]; then echo error with WGREV-DIR2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" --directory $RESDIR/smalltest > $RESDIR/wgrev-w2.html
+if [ -s $RESDIR/wgrev-w2.html ]; then diff $RESDIR/wgrev-w1.html $RESDIR/wgrev-w2.html ; else echo error with WGREV-DIR3; fi
+
+#-------------------
+echo "\t-o <F>, --output <F>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/wgrev-o1.html
+if [ -s $RESDIR/wgrev-o1.html ]; then diff $RESDIR/wgrev-o1.html $RESDIR/wgrev-w1.html ; else echo error with WGREV-OUT1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest --output $RESDIR/wgrev-o2.html
+if [ -s $RESDIR/wgrev-o2.html ]; then diff $RESDIR/wgrev-o1.html $RESDIR/wgrev-o2.html ; else echo error with WGREV-OUT3; fi
+
+#-------------------
+echo "\t-f,--format <MEAS>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -f f -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/wgrev-f1.html
+if [ -s $RESDIR/wgrev-f1.html ]; then diff $RESDIR/wgrev-w1.html $RESDIR/wgrev-f1.html > $RESDIR/smalltest/diffgrev-f1.txt ; else echo error with WGREV-FORM1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-f1.txt ]; then echo error with WGREV-FORM2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval --format f -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/wgrev-f2.html
+if [ -s $RESDIR/wgrev-f2.html ]; then diff $RESDIR/wgrev-f1.html $RESDIR/wgrev-f2.html ; else echo error with WGREV-FORM3; fi
+
+#-------------------
+echo "\t-c,--color (<COLOR>)"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -c -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/wgrev-c1.html
+if [ -s $RESDIR/wgrev-c1.html ]; then diff $RESDIR/wgrev-w1.html $RESDIR/wgrev-c1.html > $RESDIR/smalltest/diffgrev-c1.txt ; else echo error with WGREV-COL1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-c1.txt ]; then echo error with WGREV-COL2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval --color -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/wgrev-c2.html
+if [ -s $RESDIR/wgrev-c2.html ]; then diff $RESDIR/wgrev-c1.html $RESDIR/wgrev-c2.html ; else echo error with WGREV-COL3; fi
+
+#-------------------
+echo "\t-r,--reference <FILE>"
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -r lev1.rdf -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/wgrev-r1.html
+if [ -s $RESDIR/wgrev-r1.html ]; then diff $RESDIR/wgrev-w1.html $RESDIR/wgrev-r1.html > $RESDIR/smalltest/diffgrev-r1.txt ; else echo error with WGREV-REF1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-r1.txt ]; then echo error with WGREV-REF2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval --reference lev1.rdf -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/wgrev-r2.html
+if [ -s $RESDIR/wgrev-r2.html ]; then diff $RESDIR/wgrev-r1.html $RESDIR/wgrev-r2.html ; else echo error with WGREV-REF3; fi
+
+#-------------------
+echo "\t-t,--type <TYPE> Output TYPE (html|xml|tex|ascii|triangle)"
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval -t triangle -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/wgrev-ttr1.tex
+if [ -s $RESDIR/wgrev-ttr1.tex ]; then diff $RESDIR/wgrev-w1.html $RESDIR/wgrev-ttr1.tex > $RESDIR/smalltest/diffgrev-t1.txt ; else echo error with WGREV-TYP1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-t1.txt ]; then echo error with WGREV-TYP2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.WGroupEval --type triangle -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/wgrev-ttr2.tex
+if [ -s $RESDIR/wgrev-ttr2.tex ]; then diff $RESDIR/wgrev-ttr1.tex $RESDIR/wgrev-ttr2.tex ; else echo error with WGREV-TYP3; fi
+
+#-------------------
+echo "\t-Dn=v"
+echo "\t(same as Procalign; useless: no parameters involved so far)"
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign; useless: no parameters involved so far)"
+
+########################################################################
+# ExtGroupEval
+########################################################################
+
+echo "\t\t *** Testing ExtGroupEval ***"
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with EXTGRPEV-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with EXTGRPEV-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -h &> $RESDIR/extgrpev-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval --help &> $RESDIR/extgrpev-help.txt
+if [ -s $RESDIR/extgrpev-h.txt ]; then diff $RESDIR/extgrpev-h.txt $RESDIR/extgrpev-help.txt; else echo error with EXTGRPEV-HELP; fi
+
+#-------------------
+echo "\t-l,--list <FILE>"
+
+cd $RESDIR/smalltest
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -l "refalign,lev1,streq1" > extgrpev-l1.html
+if [ ! -s extgrpev-l1.html ]; then echo error with EXTGRPEV-LIST1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval --list "refalign,lev1,streq1" > extgrpev-l2.html
+if [ -s extgrpev-l2.html ]; then diff extgrpev-l1.html extgrpev-l2.html ; else echo error with EXTGRPEV-LIST2; fi
+cd $CWD
+
+#-------------------
+echo "\t-w,--directory <DIR>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/extgrpev-w1.html
+if [ -s $RESDIR/extgrpev-w1.html ]; then diff $RESDIR/extgrpev-w1.html $RESDIR/smalltest/extgrpev-l1.html > $RESDIR/smalltest/diffgrev-w1.txt ; else echo error with EXTGRPEV-DIR1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-w1.txt ]; then echo error with EXTGRPEV-DIR2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" --directory $RESDIR/smalltest > $RESDIR/extgrpev-w2.html
+if [ -s $RESDIR/extgrpev-w2.html ]; then diff $RESDIR/extgrpev-w1.html $RESDIR/extgrpev-w2.html ; else echo error with EXTGRPEV-DIR3; fi
+
+#-------------------
+echo "\t-o <F>, --output <F>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/extgrpev-o1.html
+if [ -s $RESDIR/extgrpev-o1.html ]; then diff $RESDIR/extgrpev-o1.html $RESDIR/extgrpev-w1.html ; else echo error with EXTGRPEV-OUT1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest --output $RESDIR/extgrpev-o2.html
+if [ -s $RESDIR/extgrpev-o2.html ]; then diff $RESDIR/extgrpev-o1.html $RESDIR/extgrpev-o2.html ; else echo error with EXTGRPEV-OUT3; fi
+
+#-------------------
+echo "\t-f,--format <MEAS>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -f f -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/extgrpev-f1.html
+if [ -s $RESDIR/extgrpev-f1.html ]; then diff $RESDIR/extgrpev-w1.html $RESDIR/extgrpev-f1.html > $RESDIR/smalltest/diffgrev-f1.txt ; else echo error with EXTGRPEV-FORM1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-f1.txt ]; then echo error with EXTGRPEV-FORM2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval --format f -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/extgrpev-f2.html
+if [ -s $RESDIR/extgrpev-f2.html ]; then diff $RESDIR/extgrpev-f1.html $RESDIR/extgrpev-f2.html ; else echo error with EXTGRPEV-FORM3; fi
+
+#-------------------
+echo "\t-c,--color (<COLOR>)"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -c -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/extgrpev-c1.html
+if [ -s $RESDIR/extgrpev-c1.html ]; then diff $RESDIR/extgrpev-w1.html $RESDIR/extgrpev-c1.html > $RESDIR/smalltest/diffgrev-c1.txt ; else echo error with EXTGRPEV-COL1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-c1.txt ]; then echo error with EXTGRPEV-COL2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval --color -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest > $RESDIR/extgrpev-c2.html
+if [ -s $RESDIR/extgrpev-c2.html ]; then diff $RESDIR/extgrpev-c1.html $RESDIR/extgrpev-c2.html ; else echo error with EXTGRPEV-COL3; fi
+
+#-------------------
+echo "\t-r,--reference <FILE>"
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -r lev1.rdf -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/extgrpev-r1.html
+if [ -s $RESDIR/extgrpev-r1.html ]; then diff $RESDIR/extgrpev-o1.html $RESDIR/extgrpev-r1.html > $RESDIR/smalltest/diffgrev-r1.txt ; else echo error with EXTGRPEV-REF1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-r1.txt ]; then echo error with EXTGRPEV-REF2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval --reference lev1.rdf -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/extgrpev-r2.html
+if [ -s $RESDIR/extgrpev-r2.html ]; then diff $RESDIR/extgrpev-r1.html $RESDIR/extgrpev-r2.html ; else echo error with EXTGRPEV-REF3; fi
+
+#-------------------
+echo "\t-t,--type <TYPE> Output TYPE (html|xml|tex|ascii|triangle)"
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval -t triangle -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/extgrpev-ttr1.tex
+if [ -s $RESDIR/extgrpev-ttr1.tex ]; then diff $RESDIR/extgrpev-o1.html $RESDIR/extgrpev-ttr1.tex > $RESDIR/smalltest/diffgrev-t1.txt ; else echo error with EXTGRPEV-TYP1; fi
+# Useless: only html is available at the moment, so the diff is empty
+#if [ ! -s $RESDIR/smalltest/diffgrev-t1.txt ]; then echo error with EXTGRPEV-TYP2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.ExtGroupEval --type triangle -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/extgrpev-ttr2.tex
+if [ -s $RESDIR/extgrpev-ttr2.tex ]; then diff $RESDIR/extgrpev-ttr1.tex $RESDIR/extgrpev-ttr2.tex ; else echo error with EXTGRPEV-TYP3; fi
+
+#-------------------
+echo "\t-Dn=v"
+echo "\t(same as Procalign; useless: no parameters involved so far)"
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign; useless: no parameters involved so far)"
+
+########################################################################
+# GroupOutput
+########################################################################
+
+echo "\t\t *** Testing GroupOutput ***"
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GROUT-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GROUT-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -h &> $RESDIR/grout-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput --help &> $RESDIR/grout-help.txt
+if [ -s $RESDIR/grout-h.txt ]; then diff $RESDIR/grout-h.txt $RESDIR/grout-help.txt; else echo error with $RESDIR/grout-h.txt; fi
+diff $RESDIR/grout-h.txt $RESDIR/grout-help.txt
+
+#-------------------
+echo "\t-l,--list <FILE>"
+
+cd $RESDIR/smalltest
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" > grout-l1.tex
+if [ ! -s grout-l1.tex ]; then echo error with GROUT-LIST1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput --list "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" > grout-l2.tex
+if [ -s grout-l2.tex ]; then diff grout-l1.tex grout-l2.tex ; else echo error with GROUT-LIST2; fi
+cd $CWD
+
+#-------------------
+echo "\t-o <F>, --output <F>"
+
+cd $RESDIR/smalltest
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,lev1" -o $RESDIR/grout-o1.tex
+if [ ! -s $RESDIR/grout-o1.tex ]; then echo error with GROUT-OUT1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,lev1" --output $RESDIR/grout-o2.tex
+if [ -s $RESDIR/grout-o2.tex ]; then diff $RESDIR/grout-o1.tex $RESDIR/grout-o2.tex ; else echo error with GROUT-OUT3; fi
+cd $CWD
+
+#-------------------
+echo "\t-w,--directory <DIR>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/grout-w1.tex
+if [ -s $RESDIR/grout-w1.tex ]; then diff $RESDIR/grout-o1.tex $RESDIR/grout-w1.tex ; else echo error with GROUT-DIR1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,lev1" --directory $RESDIR/smalltest --output $RESDIR/grout-w2.tex
+if [ -s $RESDIR/grout-w2.tex ]; then diff $RESDIR/grout-o1.tex $RESDIR/grout-o2.tex ; else echo error with GROUT-DIR3; fi
+
+#-------------------
+echo "\t-v,--value"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,lev1" -v -w $RESDIR/smalltest -o $RESDIR/grout-v1.tex
+if [ -s $RESDIR/grout-v1.tex ]; then diff $RESDIR/grout-o1.tex $RESDIR/grout-v1.tex > $RESDIR/smalltest/diffgrout-v1.txt; else echo error with GROUT-VAL1; fi
+if [ ! -s $RESDIR/smalltest/diffgrout-v1.txt ]; then echo error with GROUT-VAL2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,lev1" --values --directory $RESDIR/smalltest --output $RESDIR/grout-v2.tex
+if [ -s $RESDIR/grout-v2.tex ]; then diff $RESDIR/grout-v1.tex $RESDIR/grout-v2.tex ; else echo error with GROUT-VAL3; fi
+
+#-------------------
+echo "\t-e,--labels"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,lev1" -e -w $RESDIR/smalltest -o $RESDIR/grout-e1.tex
+if [ -s $RESDIR/grout-e1.tex ]; then diff $RESDIR/grout-o1.tex $RESDIR/grout-e1.tex > $RESDIR/smalltest/diffgrout-e1.txt; else echo error with GROUT-LAB1; fi
+if [ ! -s $RESDIR/smalltest/diffgrout-e1.txt ]; then echo error with GROUT-LAB2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -l "refalign,edna1,streq1,lev1" --labels --directory $RESDIR/smalltest --output $RESDIR/grout-e2.tex
+if [ -s $RESDIR/grout-e2.tex ]; then diff $RESDIR/grout-e1.tex $RESDIR/grout-e2.tex ; else echo error with GROUT-LAB3; fi
+
+#-------------------
+echo "\t-c,--color (<COLOR>)"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -c pink -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest > $RESDIR/grout-c1.tex
+if [ -s $RESDIR/grout-c1.tex ]; then diff $RESDIR/grout-o1.tex $RESDIR/grout-c1.tex > $RESDIR/smalltest/diffgrev-c1.txt ; else echo error with GROUT-COL1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-c1.txt ]; then echo error with GROUT-COL2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput --color pink -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest > $RESDIR/grout-c2.tex
+if [ -s $RESDIR/grout-c2.tex ]; then diff $RESDIR/grout-c1.tex $RESDIR/grout-c2.tex ; else echo error with GROUT-COL3; fi
+
+#-------------------
+echo "\t-f,--format <MEAS>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -f r -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest > $RESDIR/grout-f1.tex
+if [ -s $RESDIR/grout-f1.tex ]; then diff $RESDIR/grout-w1.tex $RESDIR/grout-f1.tex > $RESDIR/smalltest/diffgrev-f1.txt ; else echo error with GROUT-FORM1; fi
+# These are always the same values, so no change with these parameters...
+#if [ ! -s $RESDIR/smalltest/diffgrev-f1.txt ]; then echo error with GROUT-FORM2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput --format r -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest > $RESDIR/grout-f2.tex
+if [ -s $RESDIR/grout-f2.tex ]; then diff $RESDIR/grout-f1.tex $RESDIR/grout-f2.tex ; else echo error with GROUT-FORM3; fi
+
+#-------------------
+echo "\t-t,--type <TYPE> Output TYPE (tex|html) / only tex available in fact"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput -t html -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/grout-t1.tex
+# The results are necessary empty with html
+#if [ -s $RESDIR/grout-t1.tex ]; then diff $RESDIR/grout-o1.tex $RESDIR/grout-t1.tex > $RESDIR/smalltest/diffgrev-t1.txt ; else echo error with GROUT-TYP1; fi
+#if [ ! -s $RESDIR/smalltest/diffgrev-t1.txt ]; then echo error with GROUT-TYP2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GroupOutput --type html -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/grout-t2.tex
+#if [ -s $RESDIR/grout-t2.tex ]; then diff $RESDIR/grout-t1.tex $RESDIR/grout-t2.tex ; else echo error with GROUT-TYP3; fi
+
+#-------------------
+echo "\t-Dn=v"
+echo "\t(same as Procalign; useless: no parameters involved so far)"
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign; useless: no parameters involved so far)"
+
+########################################################################
+# GenPlot
+########################################################################
+
+echo "\t\t *** Testing GenPlot ***"
+
+#-------------------
+echo "\t-h, --help"
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -h &> $RESDIR/genplot-h.txt
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot --help &> $RESDIR/genplot-help.txt
+if [ -s $RESDIR/genplot-h.txt ]; then diff $RESDIR/genplot-h.txt $RESDIR/genplot-help.txt; else echo error with $RESDIR/genplot-h.txt; fi
+
+#-------------------
+echo "\t-z,--zzz"
+
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GENPLOT-ERR1; fi
+java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GenPlot --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with GENPLOT-ERR2; fi
+
+#-------------------
+echo "\t-l,--list <FILE>"
+
+cd $RESDIR/smalltest
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" > genplot-l1.tex
+if [ ! -s genplot-l1.tex ]; then echo error with GENPLOT-LIST1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot --list "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" > genplot-l2.tex
+if [ -s genplot-l2.tex ]; then diff genplot-l1.tex genplot-l2.tex ; else echo error with GENPLOT-LIST2; fi
+cd $CWD
+
+#-------------------
+echo "\t-o <F>, --output <F>"
+
+cd $RESDIR/smalltest
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -l "refalign,edna1,streq1,lev1" -o $RESDIR/genplot-o1.tex
+if [ ! -s $RESDIR/genplot-o1.tex ]; then echo error with GENPLOT-OUT1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -l "refalign,edna1,streq1,lev1" --output $RESDIR/genplot-o2.tex
+if [ -s $RESDIR/genplot-o2.tex ]; then diff $RESDIR/genplot-o1.tex $RESDIR/genplot-o2.tex ; else echo error with GENPLOT-OUT3; fi
+cd $CWD
+
+#-------------------
+echo "\t-w,--directory <DIR>"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/genplot-w1.tex
+if [ -s $RESDIR/genplot-w1.tex ]; then diff $RESDIR/genplot-o1.tex $RESDIR/genplot-w1.tex ; else echo error with GENPLOT-DIR1; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -l "refalign,edna1,streq1,lev1" --directory $RESDIR/smalltest --output $RESDIR/genplot-w2.tex
+if [ -s $RESDIR/genplot-w2.tex ]; then diff $RESDIR/genplot-o1.tex $RESDIR/genplot-o2.tex ; else echo error with GENPLOT-DIR3; fi
+
+#-------------------
+echo "\t-e,--evaluator <CLASS>"
+
+mv lev1.table $RESDIR/lev1-init.table
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -e fr.inrialpes.exmo.align.impl.eval.WeightedPRecEvaluator -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/genplot-e1.tex
+if [ -s lev1.table ]; then diff $RESDIR/lev1-init.table lev1.table > $RESDIR/smalltest/diffgrev-e1.txt; else echo error with GENPLOT-EVA1; fi
+echo "--> These are the same values for both evaluators, so the error"
+if [ ! -s $RESDIR/smalltest/diffgrev-e1.txt ]; then echo error with GENPLOT-EVA2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot --evaluator fr.inrialpes.exmo.align.impl.eval.WeightedPRecEvaluator -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/genplot-e2.tex
+if [ -s $RESDIR/genplot-e2.tex ]; then diff $RESDIR/genplot-e1.tex $RESDIR/genplot-e2.tex ; else echo error with GENPLOT-EVA3; fi
+
+#-------------------
+echo "\t-g,--grapher <CLASS> "
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -g fr.inrialpes.exmo.align.impl.eval.ROCCurveEvaluator -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/genplot-g1.tex
+if [ -s $RESDIR/genplot-g1.tex ]; then diff $RESDIR/genplot-o1.tex $RESDIR/genplot-g1.tex > $RESDIR/smalltest/diffgrev-g1.txt ; else echo error with GENPLOT-GRA1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-g1.txt ]; then echo error with GENPLOT-GRA2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot --grapher fr.inrialpes.exmo.align.impl.eval.ROCCurveEvaluator -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/genplot-g2.tex
+if [ -s $RESDIR/genplot-g2.tex ]; then diff $RESDIR/genplot-g1.tex $RESDIR/genplot-g2.tex ; else echo error with GENPLOT-GRA3; fi
+
+#-------------------
+echo "\t-t,--type <TYPE> Output TYPE (tsv|tex|html(|xml))"
+
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot -t html -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/genplot-t1.html
+if [ -s $RESDIR/genplot-t1.html ]; then diff $RESDIR/genplot-o1.tex $RESDIR/genplot-t1.html > $RESDIR/smalltest/diffgrev-t1.txt ; else echo error with GENPLOT-TYP1; fi
+if [ ! -s $RESDIR/smalltest/diffgrev-t1.txt ]; then echo error with GENPLOT-TYP2; fi
+java -cp $CP fr.inrialpes.exmo.align.cli.GenPlot --type html -l "refalign,edna1,streq1,lev1" -w $RESDIR/smalltest -o $RESDIR/genplot-t2.html
+if [ -s $RESDIR/genplot-t2.html ]; then diff $RESDIR/genplot-t1.html $RESDIR/genplot-t2.html ; else echo error with GENPLOT-TYP3; fi
+
+#-------------------
+echo "\t-Dn=v"
+echo "\t(same as Procalign)"
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign)"
+
+
+########################################################################
+# AlignmentService
+########################################################################
+
+echo "\t\t *** Testing AlignmentService ***"
+echo "\tTHIS WILL ONLY WORK WITH A RUNNING MYSQL SET FOR THE SERVER"
+echo "\tTHIS IS ALSO VERY SENSITIVE TO TIMEOUTS"
+
+#-------------------
+echo "\t-z, -zzz"
+
+java -Dlog.level=INFO -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -z &> $RESDIR/zerr.txt
+grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-ERR1; fi
+java -Dlog.level=INFO -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --zzz &> $RESDIR/zzzerr.txt
+grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-ERR2; fi
+
+#-------------------
+echo "\t-h, --help"
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -h &> $RESDIR/aser-h.txt
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --help &> $RESDIR/aser-help.txt
+if [ -s $RESDIR/aser-h.txt ]; then diff $RESDIR/aser-h.txt $RESDIR/aser-help.txt; else echo error with ASERV-HELP1; fi
+
+#-------------------
+echo "\t-o <F>, --output <F>"
+java -Dlog.level=DEBUG -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -o $RESDIR/aserv.log &
+sleep 15
+if [ -s $RESDIR/aserv.log ]; then grep "Alignment server running" $RESDIR/aserv.log > $RESDIR/oerr.txt; else echo error with ASERV-OUT1; fi
+if [ ! -s $RESDIR/oerr.txt ]; then echo error with ASERV-OUT2; fi
+kill -TERM $!
+echo > $RESDIR/aserv.log
+java -Dlog.level=DEBUG -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --output $RESDIR/aserv2.log &
+sleep 15
+if [ -s $RESDIR/aserv2.log ]; then grep "Alignment server running" $RESDIR/aserv2.log > $RESDIR/oerr.txt; else echo error with ASERV-OUT3; fi
+if [ ! -s $RESDIR/oerr.txt ]; then echo error with ASERV-OUT4; fi
+kill -TERM $!
+
+#-------------------
+echo "\t-i,--impl <CLASS>"
+java -Dlog.level=WARN -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -i fr.inrialpes.exmo.align.cli.GenPlot &> $Resdir/err.txt &
+sleep 5;
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-IMPL1; else grep "Cannot create service for fr.inrialpes.exmo.align.cli.GenPlot" $RESDIR/err.txt > $RESDIR/ierr.txt; fi
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-IMPL2; fi
+kill -TERM $!
+java -Dlog.level=WARN -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --impl fr.inrialpes.exmo.align.cli.GenPlot2 &> $Resdir/err.txt &
+sleep 5;
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-IMPL3; else grep "Cannot create service for fr.inrialpes.exmo.align.cli.GenPlot2" $RESDIR/err.txt > $RESDIR/ierr.txt; fi
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-IMPL4; fi
+kill -TERM $!
+
+#-------------------
+echo "\t-A,--jade <PORT>"
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -A 5555 &> $RESDIR/err.txt &
+sleep 20;
+if [ -s $RESDIR/err.txt ]; then grep "is ready" $RESDIR/err.txt > $RESDIR/jerr.txt; else echo error with ASERV-JADE1; fi
+if [ ! -s $RESDIR/jerr.txt ]; then echo error with ASERV-JADE2; fi
+kill -TERM $!
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --jade 5555 &> $RESDIR/err.txt &
+sleep 20;
+if [ -s $RESDIR/err.txt ]; then grep "is ready" $RESDIR/err.txt > $RESDIR/jerr.txt; else echo error with ASERV-JADE3; fi
+if [ ! -s $RESDIR/jerr.txt ]; then echo error with ASERV-JADE4; fi
+kill -TERM $!
+/bin/rm -f $RESDIR/err.txt $RESDIR/jerr.txt
+
+#-------------------
+echo "\t-W,--wsdl <PORT>"
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -W 5555 &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-WSDL1; fi
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --wsdl 5555 &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-WSDL2; fi
+
+#-------------------
+echo "\t-H,--http <PORT>"
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -H 5555 &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-HTTP1; fi
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --http 5555 &> $Resdir/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-HTTP2; fi
+
+#-------------------
+echo "\t-X,--jxta <PORT>"
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -X 5555 &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-JXTA1; fi
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --jxta 5555 &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-JXTA2; fi
+
+#-------------------
+echo "\t-O,--oyster"
+echo "\t\tTO BE DEPRECATED"
+#java -cp $CP:lib/oyster/oyster.jar:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -O &> $RESDIR/err.txt &
+#sleep 5;
+#if [ -s $RESDIR/err.txt ]; then echo error with ASERV-OYSTER1; fi
+#kill -TERM $!
+#java -cp $CP:lib/oyster/oyster.jar:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --oyster &> $RESDIR/err.txt &
+#sleep 5;
+#if [ -s $RESDIR/err.txt ]; then echo error with ASERV-OYSTER2; fi
+#kill -TERM $!
+
+#-------------------
+echo "\t-S,--host <HOSTNAME>"
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -S aserv.inria.fr &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-HOST1; fi
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --host aserv.inria.fr &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-HOST2; fi
+
+#-------------------
+echo "\t-u,--uriprefix <URI>"
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -u http://www.example.org &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-URIP1; fi
+java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --uriprefix http://www.example.org &> $RESDIR/err.txt &
+sleep 5;
+kill -TERM $!
+if [ -s $RESDIR/err.txt ]; then echo error with ASERV-URIP2; fi
+
+#-------------------
+echo "\t-B,--dbms <DBMS>"
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -B postgres &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBMS1; else grep "Connection refused." $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBMS2; fi
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --dbms postgres &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBMS3; else grep "Connection refused." $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBMS4; fi
+
+#-------------------
+echo "\t-m,--dbmshost <HOST>"
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -m www.gloubi.boulga &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBHOST1; else grep "Communications link failure" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBHOST2; fi
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --dbmshost www.gloubi.boulga &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBHOST3; else grep "Communications link failure" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBHOST4; fi
+
+#-------------------
+echo "\t-s,--dbmsport <PORT>"
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -s 5555 &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBPORT1; else grep "Communications link failure" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBPORT2; fi
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --dbmsport 5555 &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBPORT3; else grep "Communications link failure" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBPORT4; fi
+
+#-------------------
+echo "\t-b,--dbmsbase <BASE>"
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -b myAlignDB &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBDB1; else grep "Access denied for user" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBDB2; fi
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --dbmsbase myAlignDB &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBDB3; else grep "Access denied for user" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBDB4; fi
+
+#-------------------
+echo "\t-l,--dbmsuser <USER>"
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -l scott &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBUSR1; else grep "Access denied for user" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBUSR2; fi
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --dbmsuser scott &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBUSR3; else grep "Access denied for user" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBUSR4; fi
+
+#-------------------
+echo "\t-p,--dbmspass <PASS>"
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -p tiger &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBPAS1; else grep "Access denied for user" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBPAS2; fi
+java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --dbmspass tiger &> $RESDIR/err.txt
+if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBPAS3; else grep "Access denied for user" $RESDIR/err.txt > $RESDIR/dberr.txt; fi
+if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBPAS4; fi
+
+#-------------------
+echo "\t-Dn=v"
+echo "\t(same as Procalign)"
+
+#-------------------
+echo "\t-P,--params <FILE>"
+echo "\t(same as Procalign)"
+
+########################################################################
+echo Evrything is fine
+
+
+
+
+
diff --git a/test/src/EDOALTest.java b/test/src/EDOALTest.java
index bf9e55b8..02a75c3c 100644
--- a/test/src/EDOALTest.java
+++ b/test/src/EDOALTest.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2008-2011
+ * Copyright (C) INRIA, 2008-2011, 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
@@ -124,7 +124,8 @@ java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter wine2
//assertEquals( wine2, stream.toString() );
}
- /* This is round triping wrt converting to URIALignment... */
+ /* This is round triping wrt converting to URIALignment...
+ // Does not work anymore, because now it would try to parse an OMWG file... which goes to loop
@Test(expectedExceptions = AlignmentException.class, groups = { "full", "omwg", "raw" }, dependsOnMethods = {"roundTripTest"})
public void anotherRoundTripTest() throws Exception {
aparser1.initAlignment( null );
@@ -137,6 +138,6 @@ java -cp ../../lib/procalign.jar fr.inrialpes.exmo.align.cli.ParserPrinter wine2
eal = EDOALAlignment.toEDOALAlignment( al ); // does not work because the ontology cannot be loaded!
assertNotNull( eal );
assertEquals( eal.nbCells(), 3 );
- }
+ } */
}
diff --git a/test/src/RendererTest.java b/test/src/RendererTest.java
index 80846e4c..512528b1 100644
--- a/test/src/RendererTest.java
+++ b/test/src/RendererTest.java
@@ -166,7 +166,7 @@ public class RendererTest {
oalignment.render( renderer ); // test error with alignment
writer.flush();
writer.close();
- assertTrue( valueSimilarTo( stream.toString().length(), 17293 ), "Rendered differently: expected "+17293+" but was "+stream.toString().length() );
+ assertTrue( valueSimilarTo( stream.toString().length(), 33811 ), "Rendered differently: expected "+33811+" but was "+stream.toString().length() );
}
@Test(groups = { "full", "impl", "raw" })
--
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