From 1867c2b5dc83905fa1ca1ce506c8f3ca33b6b861 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Tue, 15 Jan 2008 13:00:36 +0000
Subject: [PATCH] - Make plugin compile at shell level
---
plugins/build.xml | 271 ++++++++++++++++++
.../align/plugin/neontk/SWTInterface.java | 119 +++-----
2 files changed, 318 insertions(+), 72 deletions(-)
create mode 100644 plugins/build.xml
diff --git a/plugins/build.xml b/plugins/build.xml
new file mode 100644
index 00000000..4053ed4d
--- /dev/null
+++ b/plugins/build.xml
@@ -0,0 +1,271 @@
+<?xml version="1.0" encoding="iso-8859-1" ?>
+<!-- $Id: build.xml 533 2007-08-04 09:38:07Z euzenat $ -->
+
+<project name="align" default="compile" basedir=".">
+
+ <!-- tested -->
+ <target name="usage" depends="init">
+ <echo message="ant _target_ _options_"/>
+ <echo/>
+ <echo message="usage: this message"/>
+ <echo message="init: sets necessary variables"/>
+ <echo message="compile: incrementaly compiles sources"/>
+ <echo message="compileall: recompiles all sources"/>
+ <echo message="jar: archives compiled code"/>
+ <echo message="test: performs unit tests [nyi]"/>
+ <echo message="zip: creates a new zip file"/>
+ <echo message="javadoc: generates documentation"/>
+ <echo message="release: releases a new version"/>
+ <echo message="svnbranch: copy the version under svn"/>
+ <echo message="clean: clean-up before release"/>
+ <echo/>
+ <echo message=" -Dversion=${version}"/>
+ </target>
+
+ <!-- tested -->
+ <target name="init">
+ <tstamp><format locale="fr,fr" pattern="dd/MM/yyyy" property="TODAY"/></tstamp>
+ <property name="doing" value="running"/>
+ <property name="version" value="3.0"/>
+ <property name="date" value="${TODAY}"/>
+ <property name="login" value="euzenat"/>
+ <property name="email" value="Jerome.Euzenat@inrialpes.fr"/>
+ <property name="libdir" value="lib" />
+ <property name="debug" value="off"/>
+ <property name="rep" value="svn+ssh://scm.gforge.inria.fr/svn/alignapi"/>
+ <!-- This should now be handled by GForge -->
+ <property name="FTPDir" value="/Web/html/ftpexmo/software/ontoalign"/>
+
+ <property name="classpath" value="classes"/>
+
+ <filter token="DATE" value="${date}"/>
+ <filter token="VERS" value="${version}"/>
+
+ <path id="classpath">
+ <fileset dir="./lib">
+ <include name="*.jar"/>
+ </fileset>
+ <fileset dir="../lib">
+ <include name="align.jar"/>
+ <include name="procalign.jar"/>
+ </fileset>
+ </path>
+
+ </target>
+
+ <!-- tested -->
+ <target name="compile" depends="init">
+ <echo message="Compiling..."/>
+ <property name="javacargs" value="-deprecation" />
+ <javac deprecation="yes" nowarn="no" verbose="no" srcdir="src" destdir="classes">
+ <compilerarg value="${javacargs}"/>
+ <classpath refid="classpath"/>
+ </javac>
+ </target>
+
+ <!-- tested -->
+ <target name="compileall" depends="init">
+ <echo message="Erasing..."/>
+ <delete>
+ <fileset dir="classes" includes="**/*.class"/>
+ </delete>
+ <antcall target="compile"/>
+ </target>
+
+ <!-- tested -->
+ <target name="compilelint" depends="init">
+ <!-- values: all, deprecation, unchecked, fallthrough, path, serial, finally -->
+ <echo message="Setting property..."/>
+ <property name="javacargs" value="-Xlint:all" />
+ <antcall target="compileall"/>
+ </target>
+
+ <!-- tested -->
+ <target name="jar" depends="compile">
+ <echo message="Jarchiving..."/>
+ <copy file="distrib/LICENSE.TXT" tofile="classes/LICENSE.TXT" filtering="true"/>
+ <delete file="lib/align.jar"/>
+ <jar jarfile="lib/align.jar" manifest="distrib/MANIFEST.MF">
+ <fileset dir="classes" includes="org/semanticweb/owl/align/*.class"/>
+ <fileset dir="classes" includes="LICENSE.TXT"/>
+ </jar>
+ <delete file="lib/procalign.jar"/>
+ <jar jarfile="lib/procalign.jar" manifest="distrib/MANIFEST-pr.MF">
+ <fileset dir="classes" includes="org/ivml/**/*.class"/>
+ <fileset dir="classes" includes="fr/inrialpes/exmo/align/util/**/*.class"/>
+ <fileset dir="classes" includes="fr/inrialpes/exmo/align/parser/**/*.class"/>
+ <fileset dir="classes" includes="fr/inrialpes/exmo/align/impl/**/*.class"/>
+ <fileset dir="classes" includes="LICENSE.TXT"/>
+ </jar>
+ <delete file="lib/alignwn.jar"/>
+ <jar jarfile="lib/alignwn.jar" manifest="distrib/MANIFEST-wn.MF">
+ <fileset dir="classes" includes="fr/inrialpes/exmo/align/ling/**/*.class"/>
+ <fileset dir="classes" includes="LICENSE.TXT"/>
+ </jar>
+ <delete file="lib/alignsvc.jar"/>
+ <copy file="src/fr/inrialpes/exmo/align/service/aserv.wsdl" tofile="classes/fr/inrialpes/exmo/align/service/aserv.wsdl" filtering="false"/>
+ <jar jarfile="lib/alignsvc.jar" manifest="distrib/MANIFEST-svc.MF">
+ <fileset dir="classes" includes="fr/inrialpes/exmo/align/service/**/*.class"/>
+ <fileset dir="classes" includes="fr/inrialpes/exmo/align/service/**/*.wsdl"/>
+ <fileset dir="classes" includes="fr/inrialpes/exmo/queryprocessor/**/*.class"/>
+ <fileset dir="classes" includes="LICENSE.TXT"/>
+ </jar>
+ </target>
+
+ <!-- not tested -->
+ <target name="test" depends="init">
+ <echo message="Testing..."/>
+ <!-- <javac srcdir="test/fr/fluxmedia/transmorpher/graph/rules"
+ debug="on" destdir="classes">
+ <classpath refid="classpath"/>
+ </javac> -->
+ <javac srcdir="test/fr/fluxmedia/" debug="on" destdir="classes">
+ <classpath refid="classpath"/>
+ </javac>
+ <antcall target="jar"/>
+ <junit printsummary="yes" fork="yes" haltonfailure="no">
+ <batchtest todir="test/reports/xml/">
+ <fileset dir="classes/">
+ <include name="**/*Test.class"/>
+ <exclude name="**/Test.class"/>
+ </fileset>
+ <formatter type="xml"/>
+ </batchtest>
+ <classpath refid="classpath"/>
+ </junit>
+ <junitreport todir="test/reports">
+ <fileset dir="test/reports/xml/">
+ <include name="TEST-*.xml"/>
+ </fileset>
+ <report todir="test/reports/html/"/>
+ </junitreport>
+ </target>
+
+ <!-- tested -->
+ <target name="javadoc">
+ <echo message="Javadocing..."/>
+ <javadoc
+ sourcepath="src" destdir="javadoc"
+ packagenames="fr.inrialpes.*,org.semanticweb.owl.align.*,org.ivml.alimo.*"
+ Use="true" Splitindex="true" private="true"
+ Windowtitle="Ontology Alignment API"
+ Doctitle="alignmebr" Header="INRIA & friends"
+ bottom="..no bottom yet..."
+ >
+ <!--link href="http://www.inrialpes.fr/exmo/local/doc/jdk1.3-doc/api"/>
+ <link href="http://www.inrialpes.fr/exmo/local/doc/xerces-doc/apiDocs"/>
+ <link href="http://www.inrialpes.fr/exmo/local/doc/xalan-doc/apidocs"/>
+ <link href="http://www.inrialpes.fr/exmo/local/doc/SAX2-doc/javadoc"/-->
+ </javadoc>
+ </target>
+
+ <!-- tested -->
+ <target name="release" depends="init">
+ <echo message="Releasing version ${version}" />
+ <copy file="distrib/README.TXT" tofile="README.TXT" filtering="true"/>
+ <copy file="distrib/LICENSE.TXT" tofile="LICENSE.TXT" filtering="true"/>
+ <antcall target="zip"/>
+ <!-- This should now go to GForge -->
+ <!--copy file="${FTPDir}/align-${version}.zip" tofile="${WebDir}/align.zip" /-->
+ <echo message="Please upload the released file to Gforge" />
+ <echo message="svn copy svn+ssh://euzenat@scm.gforge.inria.fr/svn/alignapi/trunk svn+ssh://euzenat@scm.gforge.inria.fr/svn/alignapi/tags/version-${version} -m 'release ${version}'"/>
+ <delete file="LICENSE.TXT"/>
+ </target>
+
+ <!-- tested -->
+ <target name="zip" depends="init">
+ <echo message="Ziping..."/>
+ <!--echo message="Are you sure that everything is OK (update/ci/compile)?"/-->
+ <antcall target="clean"/>
+ <!-- Unfortunately commit is not functional -->
+ <!--antcall target="commit"/-->
+ <antcall target="compileall"/>
+ <antcall target="jar"/>
+ <antcall target="javadoc"/>
+ <!-- may be useful to change directory -->
+ <zip zipfile="${FTPDir}/align-${version}.zip">
+ <fileset dir=".">
+ <include name="**/*"/>
+ <exclude name="**/.svn"/>
+ </fileset>
+ </zip>
+ </target>
+
+<target name="svnCommit">
+ <property name="source-root" value="/usr/src"/>
+ <property name="repository.URL" value="http://sources.example.com"/>
+ <java classname="org.tmatesoft.svn.cli.SVN"
+ dir="${source-root}/TESTREPO" fork="true">
+ <arg value="commit"/>
+ <arg value="--username"/>
+ <arg value="admin"/>
+ <arg value="--password"/>
+ <arg value="admin"/>
+ <arg value="-m"/>
+ <arg value='"Testing"'/>
+ <arg value="${repository.URL}/TESTING"/>
+ <classpath>
+ <pathelement location="${antroot}/LIB/ganymed.jar" />
+ <pathelement location="${antroot}/LIB/javasvn.jar" />
+ <pathelement location="${antroot}/LIB/javasvn-cli.jar" />
+ </classpath>
+ </java>
+ </target>
+
+ <!-- This is for testing purposes, but has been found to work -->
+ <target name="status" depends="init">
+ <java classname="org.tmatesoft.svn.cli.SVN" dir="." fork="true">
+ <arg value="status" />
+ <classpath refid="classpath"/>
+ </java>
+ </target>
+
+ <!-- not tested yet -->
+ <target name="update" depends="init">
+ <java classname="org.tmatesoft.svn.cli.SVN" dir="." fork="true"
+ failonerror="true">
+ <sysproperty key="javasvn.ssh2.key"
+ value="/Volumes/Khata/.ssh/id_dsa" />
+ <!--sysproperty key="javasvn.ssh2.username" value="${login}" />
+ <sysproperty key="javasvn.ssh2.passphrase" value="aa" /-->
+ <arg value="update" />
+ <classpath refid="classpath"/>
+ </java>
+ </target>
+
+ <!-- not tested yet -->
+ <target name="commit" depends="update">
+ <java classname="org.tmatesoft.svn.cli.SVN" dir="." fork="true">
+ <arg value="commit" />
+ <arg value="--username" />
+ <arg value="${login}" />
+ <arg value="-m" />
+ <arg value='"Pre-release ${version}"' />
+ <classpath refid="classpath"/>
+ </java>
+ </target>
+
+ <!-- not tested yet -->
+ <target name="svnbranch" depends="">
+ <java classname="org.tmatesoft.svn.cli.SVN" dir="." fork="true">
+ <arg value="copy" />
+ <arg value="--username" />
+ <arg value="${login}" />
+ <arg value="${rep}/trunk" />
+ <arg value="${rep}/tags/version-${version}" />
+ <arg value="-m" />
+ <arg value='"Release ${version}"' />
+ <classpath refid="classpath"/>
+ </java>
+ </target>
+
+ <target name="clean">
+ <echo message="Cleaning..."/>
+ <delete>
+ <fileset dir="classes" includes="**/*.class"/>
+ <fileset dir="examples" includes="**/*.class"/>
+ <fileset dir="examples" includes="**/*.jar"/>
+ </delete>
+ </target>
+
+</project>
diff --git a/plugins/src/fr/inrialpes/exmo/align/plugin/neontk/SWTInterface.java b/plugins/src/fr/inrialpes/exmo/align/plugin/neontk/SWTInterface.java
index 01344286..28147bcc 100644
--- a/plugins/src/fr/inrialpes/exmo/align/plugin/neontk/SWTInterface.java
+++ b/plugins/src/fr/inrialpes/exmo/align/plugin/neontk/SWTInterface.java
@@ -1,3 +1,23 @@
+/*
+ * $Id$
+ *
+ * Copyright (C) INRIA Rhône-Alpes, 2007-2008
+ *
+ * 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
+ */
+
package fr.inrialpes.exmo.align.plugin.neontk;
import java.io.*;
@@ -21,21 +41,14 @@ import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
-//import edu.stanford.smi.protege.util.*;
-import fr.inrialpes.exmo.align.parser.*;
-import fr.inrialpes.exmo.align.util.*;
-import fr.inrialpes.exmo.align.impl.*;
-import fr.inrialpes.exmo.align.impl.method.*;
import org.semanticweb.owl.align.*;
-import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Parameters;
-import org.semanticweb.owl.util.OWLManager;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.io.owl_rdf.OWLRDFParser;
-import org.semanticweb.owl.io.owl_rdf.OWLRDFErrorHandler;
+
+import fr.inrialpes.exmo.align.impl.BasicParameters;
+import fr.inrialpes.exmo.align.impl.OntologyCache;
import fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor;
import fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor;
@@ -369,70 +382,32 @@ public class SWTInterface extends JPanel {
if(online == false) {
- OWLOntology onto1 = null;
- OWLOntology onto2 = null;
- Parameters p = new BasicParameters();
- Parameters p2 = new BasicParameters();
- AlignmentProcess A1 = null;
- AlignmentProcess A2 = null;
-
- try {
- OWLRDFParser parser = new OWLRDFParser();
- parser.setConnection(OWLManager.getOWLConnection());
- onto1 = parser.parseOntology((URI)uris.get(0));
- onto2 = parser.parseOntology((URI)uris.get(1));
+ //OWLOntology onto1 = null;
+ //OWLOntology onto2 = null;
+ Parameters p = new BasicParameters();
+ AlignmentProcess A1 = null;
+ try {
+ //OWLRDFParser parser = new OWLRDFParser();
+ //parser.setConnection(OWLManager.getOWLConnection());
+ //onto1 = parser.parseOntology((URI)uris.get(0));
+ //onto2 = parser.parseOntology((URI)uris.get(1));
- if( matching_method.equals("fr.inrialpes.exmo.align.impl.method.SubsDistNameAlignment") ) {
-
- A1 = new SubsDistNameAlignment(onto1, onto2);
- A2 = new SubsDistNameAlignment(onto1, onto2);
- A1.align((Alignment)null,p);
- A2.align((Alignment)null,p2);
- }
- else if (matching_method.equals("fr.inrialpes.exmo.align.impl.method.NameEqAlignment") ) {
- A1 = new NameEqAlignment(onto1, onto2);
- A2 = new NameEqAlignment(onto1, onto2);
- A1.align((Alignment)null,p);
- A2.align((Alignment)null,p2);
- }
- else if (matching_method.equals("fr.inrialpes.exmo.align.impl.method.StringDistAlignment") ) {
- A1 = new StringDistAlignment(onto1, onto2);
- A2 = new StringDistAlignment(onto1, onto2);
- A1.align((Alignment)null,p);
- A2.align((Alignment)null,p2);
- }
- else if (matching_method.equals("fr.inrialpes.exmo.align.impl.method.SMOANameAlignment") ) {
- A1 = new SMOANameAlignment(onto1, onto2);
- A2 = new SMOANameAlignment(onto1, onto2);
- A1.align((Alignment)null,p);
- A2.align((Alignment)null,p2);
- }
- else if (matching_method.equals("fr.inrialpes.exmo.align.impl.method.StrucSubsDistAlignment") ) {
- A1 = new StrucSubsDistAlignment(onto1, onto2);
- A2 = new StrucSubsDistAlignment(onto1, onto2);
- A1.align((Alignment)null,p);
- A2.align((Alignment)null,p2);
- }
- else if (matching_method.equals("fr.inrialpes.exmo.align.impl.method.NameAndPropertyAlignment") ) {
- A1 = new NameAndPropertyAlignment(onto1, onto2);
- A2 = new NameAndPropertyAlignment(onto1, onto2);
- A1.align((Alignment)null,p);
- A2.align((Alignment)null,p2);
- }
- else if (matching_method.equals("fr.inrialpes.exmo.align.impl.method.ClassStructAlignment") ) {
- A1 = new ClassStructAlignment(onto1, onto2);
- A2 = new ClassStructAlignment(onto1, onto2);
- A1.align((Alignment)null,p);
- A2.align((Alignment)null,p2);
- }
- else if (matching_method.equals("fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment") ) {
- A1 = new EditDistNameAlignment(onto1, onto2);
- A2 = new EditDistNameAlignment(onto1, onto2);
- A1.align((Alignment)null,p);
- A2.align((Alignment)null,p2);
+ try {
+ // Create alignment object
+ Object[] mparams = {};
+ Class alignmentClass = Class.forName(matching_method);
+ Class[] cparams = {};
+ java.lang.reflect.Constructor alignmentConstructor = alignmentClass.getConstructor(cparams);
+ A1 = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
+ A1.init( (URI)uris.get(0), (URI)uris.get(1), (OntologyCache)null );
+ } catch (Exception ex) {
+ System.err.println("Cannot create alignment "+matching_method+"\n"+ex.getMessage());
+ throw ex;
}
-
+
+ A1.align((Alignment)null,p);
+
//for storing
FileWriter owlF = new FileWriter(new File( "align.owl"));
AlignmentVisitor V = new OWLAxiomsRendererVisitor( new PrintWriter ( owlF ) );
@@ -446,7 +421,7 @@ public class SWTInterface extends JPanel {
AlignmentVisitor V1 = new HTMLRendererVisitor(
new PrintWriter ( htmlF ) );
- A2.render(V1);
+ A1.render(V1);
htmlF.close();
String htmlString = fileToString(new File ("align.html"));
--
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