diff --git a/build.xml b/build.xml index c08f76b788472b4e711d976c06f2a097f66af0e5..f4f8791c562e3e96ee71307333e92b255e03bd02 100644 --- a/build.xml +++ b/build.xml @@ -55,7 +55,7 @@ <!-- tested --> <target name="init" depends="bind"> - <property name="jarclasspath" value="owlapi30/owlapi-bin.jar ontosim/ontosim.jar getopt/getopt.jar log4j/commons-logging.jar log4j/log4j.jar align.jar ontowrap.jar procalign.jar jena/jena.jar jena/iri.jar jena/icu4j_3_4.jar xerces/xercesImpl.jar procalign.jar"/> + <property name="jarclasspath" value="owlapi30/owlapi-bin.jar ontosim/ontosim.jar getopt/getopt.jar log4j/commons-logging.jar log4j/log4j.jar log4j/slf4j-api.jar log4j/slf4j-log4j.jar jwnl/jwnl.jar align.jar ontowrap.jar procalign.jar jena/jena.jar jena/iri.jar jena/icu4j.jar xerces/xercesImpl.jar procalign.jar"/> </target> @@ -176,7 +176,7 @@ <manifest> <attribute name="Built-Date" value="${TODAY}"/> <attribute name="Main-Class" value="fr.inrialpes.exmo.align.service.AlignmentService"/> - <attribute name="Class-Path" value="procalign.jar jade/jade.jar iiop.jar jade/http.jar jdbc/mysql-connector-java-5.0.3-bin.jar jdbc/postgresql-8.3-603.jdbc3.jar servlet/servlet-api.jar jetty/jetty.jar jetty/jetty-util.jar xerces/xercesImpl.jar"/> + <attribute name="Class-Path" value="procalign.jar jade/jade.jar iiop.jar jade/http.jar jdbc/mysql-connector-java.jar jdbc/postgresql-jdbc4.jar servlet/servlet-api.jar jetty/jetty.jar jetty/jetty-util.jar xerces/xercesImpl.jar"/> <attribute name="Implementation-Title" value="Alignment server"/> <attribute name="Implementation-Version" value="${version}"/> </manifest> diff --git a/html/lib.html b/html/lib.html index 3fa37fa2d4faff772edcff9813673d213d6b36d6..c7d764cc0e3a06db69e76e40725e8f48f229a801 100644 --- a/html/lib.html +++ b/html/lib.html @@ -10,94 +10,140 @@ <h1 class="titre">Alignment API: Libraries shipped with the package (release 3.1)</h1> <p>The Alignment API uses a number of external libraries. These libraries -are shipped (in the lib directory) with the Alignment API. We provide -here the list of these libraries together with the reason why they may -be necessary within the API and some other information.</p> -<p>You may use this information for restricting the libraries to only -the one you need.</p> +are shipped (in the lib directory) with the Alignment API. Each +subdirectory of the lib directory contains version.txt and license.txt +files which indicates what version are embedded and what are its +conditions of use. +</p> +<p> +We provide here the list of these libraries together with the +reason why they may be necessary within the API and some other +information. +</p> +<p> +Some of these libraries are necessary for recompiling the Alignment +API. Some of them are only needed at runtime when invoking the +feature that uses them. You may use this information for restricting +the libraries to only the one you need. +</p> +<p> +Here is a picture of the various dependencies involved: +<center> +<img src=""/> +</center> +</p> <h2>Required for the API implementation (procalign)</h2> <dl> <dt><a href="http://www.urbanophile.com/arenn/hacking/download.html">Gnu - getopt</a>: getopt.jar [<a href="http://www.opensource.org/licenses/bsd-license.php">BSD</a>/<a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GPL</a>]</dt> + getopt</a> 1.0.13: getopt.jar + [<a href="http://www.opensource.org/licenses/bsd-license.php">BSD</a>/<a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GPL</a>] (C)</dt> <dd>Gnu library for parsing command line arguments. Required everywhere (included by OWL-API).</dd> -<dt><a href="http://logging.apache.org/log4j">Apache Log4J</a>: - log4j.jar [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>]</dt> -<dd>Required by OWL-API -- maybe used by procalign.</dd> -<!--dt><a href=""></a>: xerces.jar xml-apis.jar</dt> +<dt><a href="http://logging.apache.org/log4j">Apache Log4J</a> 1.2.15 + & <a href="http://jakarta.apache.org/commons/logging/">Jakarta + Commons Logging</a> 1.1.1: + log4j.jar commons-logging.jar + [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>] + slf4j-api.jar (1.5.6) slf4j-log4j.jar +</dt> +<dd>Required by OWL-API, jwnl, Jena for the last two ones... if someone + could clear the mess with loggers in Java, you are welcome!</dd> +<dt><a href="http://xerces.apache.org">Xerces</a> 2.9.1: xercesImpl.jar xml-apis.jar [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>]</dt> <dd>Certainly not required anymore...</dd--> </dl> -<h3>Required for the OWL-API part</h3> +<h3>Required for using EDOAL</h3> <dl> -<dt><a href="http://owl.man.ac.uk/api.shtml">OWL API</a> 1.4.3: - rdfapi.jar rdfparser.jar api.jar impl.jar io.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> -<dd>Provides parsing and API to OWL entities. Used by - OWLAPIAlignments. api.jar is required for compiling, the others are - necessary for executing parts of the Alignment API which need the - OWL API.</dd> +<dt><a href="http://jena.sourceforge.net/">Jena</a> 2.6.2: + jena.jar icu4j.jar iri.jar arq.jar [<a href="http://www.opensource.org/licenses/bsd-license.php">BSD*</a>]</dt> +<dd>Provides the RDF parser (which is also used by Pellet).</dd> </dl> -<h3>Required for the WSMO part</h3> +<h3>Required for some bundled matching methods</h3> <dl> -<dt><a href="http://www.sourceforge.net/projects/mediation">OMWG Mapping API</a>: - mappingapilite.jar [<a href="http://www.opensource.org/licenses/afl-3.0.php">AFL</a>]</dt> -<dd>Provides the implementation of an expressive alignment format which - is the basis for level 2OMWG alignments. This jarfile is generated - on purpose from the main build file of the mappingapi source - repository. It is an incomplete version of the mappingapi - (likewise, the OMWG mapping api does only contain a part of the - Alignment API).</dd> -<!--dt><a href="http://wsmo4j.sourceforge.net/">WSMO API</a> 0.6.1: - wsmo-api-0.6.1.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> -<dd>Provide the implementation of the Web Service Modelling - Organisation API.</dd--> -<dt><a href="http://jena.sourceforge.net/">Jena</a> 2.5.4: - jena.jar [<a href="http://www.opensource.org/licenses/bsd-license.php">BSD</a>]</dt> -<dd>Provides the RDF parser.</dd> +<dt><a href="">OntoSim</a> ??: ontosim.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> +<dd>The whole ontosim system requires...</dd> </dl> -<h2>Required for the WordNet addition</h2> +<h3>Required for the WordNet addition (JWNLAlignment)</h3> +<p> +In addition to OntoSim. <dl> <dt><a href="http://jwordnet.sourceforge.net/">JWordNet (JWNL)</a> - 1.3: jwnl.jar [<a href="http://www.opensource.org/licenses/bsd-license.php">BSD</a>]</dt> + 1.4rc2: jwnl.jar [<a href="http://www.opensource.org/licenses/bsd-license.php">BSD</a>]</dt> <dd>This also requires WordNet to be installed in the computer.</dd> -<dt><a href="http://jakarta.apache.org/commons/logging/">Jakarta - Commons Logging</a>: commons-logging.jar [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>]</dt> -<dd>Necessary for alignwn.</dd> +</dl> +</p> + +<h3>Required for reasoning with alignments</h3> + +<dl> +<dt><a href="">IDDL</a> 1.2: iddl.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> +<dd>In turns it requires Pellet.</dd> +<dt><a href="">Pellet</a> : pellet.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> +<dd>In turns it requires Jena, Jetty, etc.</dd> +</dl> + +<h2>Required for parsing ontologies (ontowrap)</h2> + +<p> +Ontowrap requires one of these libraries to be functional. It will +only compile if all of them are available. However, it is possible to +delete the subdirectories <tt>src/fr/inrialpes/exmo/ontowrap/xxxx</tt> +and this will compile again. +</p> +<dl> +<dt><a href="http://owlapi.sourceforge.org">OWL API</a> 3.0: + owlapi-bin.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> +<dd>Provides parsing and API to OWL entities. Used by + OWLAPIAlignments. api.jar is required for compiling, the others are + necessary for executing parts of the Alignment API which need the + OWL API.</dd> +<dt><a href="http://owl.man.ac.uk/api.shtml">OWL API</a> 1.4.3: + rdfapi.jar rdfparser.jar api.jar impl.jar io.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> +<dd>Provides parsing and API to OWL entities. Used by + OWLAPIAlignments. api.jar is required for compiling, the others are + necessary for executing parts of the Alignment API which need the + OWL API.</dd> +<dt>Jena</dt> +<dd>is also an option.</dd> </dl> -<h2>Required for the Alignment Server</h2> +<h2>Required for the Alignment server (alignsvc)</h2> <dl> <dt><a href="http://dev.mysql.com/downloads/connector/j/3.0.html">MySQL - JDBC Connectors</a> 5.0.3: mysql-connector-java-5.0.3-bin.jar [<a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GPL</a>]</dt> + 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 Postgres JDBC connectors 8.4.701</dt> <dd>This also requires MySQL to be installed. Required for alignsvc.</dd> <dt><a href="http://jetty.mortbay.org/">Jetty</a> 6.1.2rc5: jetty.jar jetty-util.jar servlet-api.jar [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>]</dt> <dd>This also requires MySQL to be installed. Required for HTML and web service part.</dd> +<dt><a href="http://jetty.mortbay.org/">Servlet API</a> 2.5: servlet-api.jar [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">??</a>]</dt> +<dd>Required and shipped with Jetty.</dd> </dl> -<h3>Required for the Agent/JADE part</h3> +<h3>Required for the Agent/JADE plug-in</h3> <dl> <dt><a href="http://jade.tilab.com/">Java Agent Development - Environment (JADE)</a> 3.3: jade.jar http.jar iiop.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> + Environment (JADE)</a> 3.7: jade.jar http.jar iiop.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt> <dd>Required by alignsvc (Agent version).</dd> </dl> -<h3>Required for the Web service part</h3> +<h3>Required for the Web service plug-in</h3> <dl> </dl> -<h3>Required for the P2P/JXTA part</h3> +<h3>Required for the P2P/JXTA plug-in</h3> <dl> </dl> diff --git a/html/relnotes.html b/html/relnotes.html index a33a5b6f45594ae6c5e9d051566c3cfbf8859f3c..f61cd39061b38483a49fd988c8bdd9a13a5ff866 100644 --- a/html/relnotes.html +++ b/html/relnotes.html @@ -75,15 +75,18 @@ likely to include: <!--h2>Version 4.1 (1xxx): xx/09/2009 - Tring</h2--> <!--h2>Version 4.0 (1310): xx/03/2010 - Rouquine carmélite</h2--> -<!--p><span style="color: red;">BEWARE (major upgrade):</span> -UPGRADE ALL LIBRARIES -</p--> -<p>The Alignment API is now compiled in Java 1.6 (older versions should still be able to run it).</p> +<p>The Alignment API is now compiled in Java 1.6 (older versions + should still be able to run it). All <a href="lib.html">imported + libraries</a> have been upgraded to their current versions. Only the + upgrade from Jena 2.5 to 2.6 required a minor change (due to + parameterised declarations: the API still works with 2.5 but needs + 2.6 to compile). +</p> <p> <ul compact="1"> <li>Integration and reengineering of OMWG alignments as the new EDOAL language (edoal)</li> <li>Separated the Alignment API from <a href="http://ontosim.gforge.inria.fr">OntoSim</a> (impl/ling)</li> -<li>Replacement of <tt>Parameters</tt> by Java <tt>Property</tt> (api/impl)</li> +<li><span style="color: red;">Replacement</span> of <tt>Parameters</tt> by Java <tt>Properties</tt> (api/impl)</li> <li>Reintegrated <tt>JWNLAlignment</tt> in implementation (procalign)</li> <li>Separated <tt>ontowrap</tt> (previously <tt>onto</tt>) as a distinct library (ontowrap)</li> <li>Migrated to <span style="color: green">OWL API 3</span> as the default Ontology implementation (ontowrap)</li> @@ -113,6 +116,7 @@ UPGRADE ALL LIBRARIES <li>Changed the signature of <tt></tt> from <tt>Enumeration</tt> to <tt>Collection<Alignment></tt> (server)</tt> <li>Reorganised the lib directory hierarchically (build)</li> +<li>Corrected missing hashCode() (bug #9680) (impl)</li> <li>Corrected a bug when the server is launched without -S (server)</li> <li>Corrected a bug in <tt>HTMLRendererVisitor</tt> that made the @@ -129,7 +133,7 @@ UPGRADE ALL LIBRARIES "stored" date of alignments (server)</li> <li>Corrected a bug in the "find" primitive of service (server)</li> <li>Corrected a bug that prevented proper search of <tt>aserv.wsdl</tt> file in all imported jars (server)</li> -<li>Corrected a bug in tests that did not forced to clean-up the state +<li>Corrected a bug in tests that did not force to clean-up the state after <tt>OntoTest</tt> (test)</li> <li>Corrected a (commented) error in the <tt>wine.xml</tt> OMWG example (edoal)</li> diff --git a/lib/getopt/version.txt b/lib/getopt/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..89680eab8d817841960f2e3ea2df161c5ce8beba --- /dev/null +++ b/lib/getopt/version.txt @@ -0,0 +1 @@ +1.0.13 (2006) diff --git a/lib/jdbc/mysql-connector-java-5.0.3-bin.jar b/lib/jdbc/mysql-connector-java-5.0.3-bin.jar deleted file mode 100644 index bd5143785583c42a3b22b4776e4683b0533e5b74..0000000000000000000000000000000000000000 Binary files a/lib/jdbc/mysql-connector-java-5.0.3-bin.jar and /dev/null differ diff --git a/lib/jdbc/mysql-connector-java.jar b/lib/jdbc/mysql-connector-java.jar new file mode 100644 index 0000000000000000000000000000000000000000..af5847eed4ccfd139427aaadbf3e9f3fbcef020d Binary files /dev/null and b/lib/jdbc/mysql-connector-java.jar differ diff --git a/lib/jdbc/postgresql-8.3-603.jdbc3.jar b/lib/jdbc/postgresql-8.3-603.jdbc3.jar deleted file mode 100644 index a9156e958b025e87e791d75f76cfceae7539334e..0000000000000000000000000000000000000000 Binary files a/lib/jdbc/postgresql-8.3-603.jdbc3.jar and /dev/null differ diff --git a/lib/jdbc/postgresql-jdbc4.jar b/lib/jdbc/postgresql-jdbc4.jar new file mode 100644 index 0000000000000000000000000000000000000000..e21beec54882a8f5b27fe277055859dd2c33fe01 Binary files /dev/null and b/lib/jdbc/postgresql-jdbc4.jar differ diff --git a/lib/jdbc/version.txt b/lib/jdbc/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..db5bd28344cba31f114ea0d5ebfd50cfbe14accb --- /dev/null +++ b/lib/jdbc/version.txt @@ -0,0 +1,2 @@ +mysql-connector-java-5.1.12-bin +postgresql-8.4-701.jdbc4 diff --git a/lib/jena/arq.jar b/lib/jena/arq.jar index 64077ddb277d658e7907403d75202e5e03865d2d..5fb8d9e904739bd4b015e9f4639dcbe1a8e48dfe 100644 Binary files a/lib/jena/arq.jar and b/lib/jena/arq.jar differ diff --git a/lib/jena/concurrent.jar b/lib/jena/concurrent.jar deleted file mode 100644 index f01955af949e55bbf672b7b53eed3bec461f7f70..0000000000000000000000000000000000000000 Binary files a/lib/jena/concurrent.jar and /dev/null differ diff --git a/lib/jena/icu4j.jar b/lib/jena/icu4j.jar new file mode 100644 index 0000000000000000000000000000000000000000..f5e8c167e7f7f3d078407859cb50b8abf23c697e Binary files /dev/null and b/lib/jena/icu4j.jar differ diff --git a/lib/jena/icu4j_3_4.jar b/lib/jena/icu4j_3_4.jar deleted file mode 100644 index d35e3c3466e601e0fe8aefc5ec043ea163e606c4..0000000000000000000000000000000000000000 Binary files a/lib/jena/icu4j_3_4.jar and /dev/null differ diff --git a/lib/jena/iri.jar b/lib/jena/iri.jar index 3a34d207562f146c28376ecf6f670305796f3d3d..811201a584c273bb723bfd6d3276748817538839 100644 Binary files a/lib/jena/iri.jar and b/lib/jena/iri.jar differ diff --git a/lib/jena/jena.jar b/lib/jena/jena.jar index 5f56285c37a7614858f919343aec0ca2cc81c6c1..796d87b367bd169c579db1c0ee209a079df15346 100644 Binary files a/lib/jena/jena.jar and b/lib/jena/jena.jar differ diff --git a/lib/jena/version.txt b/lib/jena/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..9ceb7838e058ca6380f398ab4ef45fbd0493d44b --- /dev/null +++ b/lib/jena/version.txt @@ -0,0 +1,10 @@ +jena-2.6.2 +arq-2.8.1 +icu4j-3.4.4 +iri-0.7 + +lucene-core-2.3.1 +slf4j-api-1.5.6 +slf4j-log4j12-1.5.6 +stax-api-1.0.1 +wstx-asl-3.2.9 diff --git a/lib/jetty/version.txt b/lib/jetty/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c12f2ddb04cff7848e8460534df0807df5ec525 --- /dev/null +++ b/lib/jetty/version.txt @@ -0,0 +1 @@ +6.1.2rc5 diff --git a/lib/jwnl/license.txt b/lib/jwnl/license.txt new file mode 100755 index 0000000000000000000000000000000000000000..ea3952b9e8c25956d65897c177b1a0aee335d7bb --- /dev/null +++ b/lib/jwnl/license.txt @@ -0,0 +1,22 @@ +License Information + +Copyright (C) 2000-2007 the JWNL development team (http://www.sourceforge.net/projects/jwordnet) +All rights reserved. + +Redistribution and use in source and binary forms, with or without modification, are permitted provided +that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this list of conditions and the +following disclaimer. +* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and +the following disclaimer in the documentation and/or other materials provided with the distribution. +* Neither the name of the product ("JWNL") nor the names of its contributors may be used to endorse or promote +products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, +INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE +USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/lib/jwnl/version.txt b/lib/jwnl/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..795961714356237cf446725e84f4a9296860ecb5 --- /dev/null +++ b/lib/jwnl/version.txt @@ -0,0 +1 @@ +1.4rc2 diff --git a/lib/log4j/commons-logging.jar b/lib/log4j/commons-logging.jar index b73a80fab641131e6fbe3ae833549efb3c540d17..bd4511684badd0cc710df5169b98e7b8f351858e 100644 Binary files a/lib/log4j/commons-logging.jar and b/lib/log4j/commons-logging.jar differ diff --git a/lib/log4j/log4j.jar b/lib/log4j/log4j.jar index 1595a56ef29615a8e3c77827071a03500cb32fe9..c930a6ab4d4b73c1a6feb9e929091205664bb340 100644 Binary files a/lib/log4j/log4j.jar and b/lib/log4j/log4j.jar differ diff --git a/lib/log4j/slf4j-api.jar b/lib/log4j/slf4j-api.jar new file mode 100644 index 0000000000000000000000000000000000000000..d794252336e627b38e183beaaa66c62192a97135 Binary files /dev/null and b/lib/log4j/slf4j-api.jar differ diff --git a/lib/log4j/slf4j-log4j.jar b/lib/log4j/slf4j-log4j.jar new file mode 100644 index 0000000000000000000000000000000000000000..97241bb140b80b5ed63724040694d63131cba3ee Binary files /dev/null and b/lib/log4j/slf4j-log4j.jar differ diff --git a/lib/log4j/version.txt b/lib/log4j/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..fcb9c26d291aeb9dcad6ed85c6d84051684d3af9 --- /dev/null +++ b/lib/log4j/version.txt @@ -0,0 +1,4 @@ +commons-logging-api-1.1.1 +log4j-1.2.15 +slf4j-api-1.5.6 +slf4j-log4j12-1.5.6 diff --git a/lib/owlapi10/version.txt b/lib/owlapi10/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..e4f698ef6cdf8215d1b9fec77ed456507daaa99a --- /dev/null +++ b/lib/owlapi10/version.txt @@ -0,0 +1 @@ +OWL API 1 1.4.3 diff --git a/lib/owlapi30/license.txt b/lib/owlapi30/license.txt new file mode 100644 index 0000000000000000000000000000000000000000..cca7fc278f5c81ce23a2687208f0d63a6ea44009 --- /dev/null +++ b/lib/owlapi30/license.txt @@ -0,0 +1,165 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + + This version of the GNU Lesser General Public License incorporates +the terms and conditions of version 3 of the GNU General Public +License, supplemented by the additional permissions listed below. + + 0. Additional Definitions. + + As used herein, "this License" refers to version 3 of the GNU Lesser +General Public License, and the "GNU GPL" refers to version 3 of the GNU +General Public License. + + "The Library" refers to a covered work governed by this License, +other than an Application or a Combined Work as defined below. + + An "Application" is any work that makes use of an interface provided +by the Library, but which is not otherwise based on the Library. +Defining a subclass of a class defined by the Library is deemed a mode +of using an interface provided by the Library. + + A "Combined Work" is a work produced by combining or linking an +Application with the Library. The particular version of the Library +with which the Combined Work was made is also called the "Linked +Version". + + The "Minimal Corresponding Source" for a Combined Work means the +Corresponding Source for the Combined Work, excluding any source code +for portions of the Combined Work that, considered in isolation, are +based on the Application, and not on the Linked Version. + + The "Corresponding Application Code" for a Combined Work means the +object code and/or source code for the Application, including any data +and utility programs needed for reproducing the Combined Work from the +Application, but excluding the System Libraries of the Combined Work. + + 1. Exception to Section 3 of the GNU GPL. + + You may convey a covered work under sections 3 and 4 of this License +without being bound by section 3 of the GNU GPL. + + 2. Conveying Modified Versions. + + If you modify a copy of the Library, and, in your modifications, a +facility refers to a function or data to be supplied by an Application +that uses the facility (other than as an argument passed when the +facility is invoked), then you may convey a copy of the modified +version: + + a) under this License, provided that you make a good faith effort to + ensure that, in the event an Application does not supply the + function or data, the facility still operates, and performs + whatever part of its purpose remains meaningful, or + + b) under the GNU GPL, with none of the additional permissions of + this License applicable to that copy. + + 3. Object Code Incorporating Material from Library Header Files. + + The object code form of an Application may incorporate material from +a header file that is part of the Library. You may convey such object +code under terms of your choice, provided that, if the incorporated +material is not limited to numerical parameters, data structure +layouts and accessors, or small macros, inline functions and templates +(ten or fewer lines in length), you do both of the following: + + a) Give prominent notice with each copy of the object code that the + Library is used in it and that the Library and its use are + covered by this License. + + b) Accompany the object code with a copy of the GNU GPL and this license + document. + + 4. Combined Works. + + You may convey a Combined Work under terms of your choice that, +taken together, effectively do not restrict modification of the +portions of the Library contained in the Combined Work and reverse +engineering for debugging such modifications, if you also do each of +the following: + + a) Give prominent notice with each copy of the Combined Work that + the Library is used in it and that the Library and its use are + covered by this License. + + b) Accompany the Combined Work with a copy of the GNU GPL and this license + document. + + c) For a Combined Work that displays copyright notices during + execution, include the copyright notice for the Library among + these notices, as well as a reference directing the user to the + copies of the GNU GPL and this license document. + + d) Do one of the following: + + 0) Convey the Minimal Corresponding Source under the terms of this + License, and the Corresponding Application Code in a form + suitable for, and under terms that permit, the user to + recombine or relink the Application with a modified version of + the Linked Version to produce a modified Combined Work, in the + manner specified by section 6 of the GNU GPL for conveying + Corresponding Source. + + 1) Use a suitable shared library mechanism for linking with the + Library. A suitable mechanism is one that (a) uses at run time + a copy of the Library already present on the user's computer + system, and (b) will operate properly with a modified version + of the Library that is interface-compatible with the Linked + Version. + + e) Provide Installation Information, but only if you would otherwise + be required to provide such information under section 6 of the + GNU GPL, and only to the extent that such information is + necessary to install and execute a modified version of the + Combined Work produced by recombining or relinking the + Application with a modified version of the Linked Version. (If + you use option 4d0, the Installation Information must accompany + the Minimal Corresponding Source and Corresponding Application + Code. If you use option 4d1, you must provide the Installation + Information in the manner specified by section 6 of the GNU GPL + for conveying Corresponding Source.) + + 5. Combined Libraries. + + You may place library facilities that are a work based on the +Library side by side in a single library together with other library +facilities that are not Applications and are not covered by this +License, and convey such a combined library under terms of your +choice, if you do both of the following: + + a) Accompany the combined library with a copy of the same work based + on the Library, uncombined with any other library facilities, + conveyed under the terms of this License. + + b) Give prominent notice with the combined library that part of it + is a work based on the Library, and explaining where to find the + accompanying uncombined form of the same work. + + 6. Revised Versions of the GNU Lesser General Public License. + + The Free Software Foundation may publish revised and/or new versions +of the GNU Lesser General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + + Each version is given a distinguishing version number. If the +Library as you received it specifies that a certain numbered version +of the GNU Lesser General Public License "or any later version" +applies to it, you have the option of following the terms and +conditions either of that published version or of any later version +published by the Free Software Foundation. If the Library as you +received it does not specify a version number of the GNU Lesser +General Public License, you may choose any version of the GNU Lesser +General Public License ever published by the Free Software Foundation. + + If the Library as you received it specifies that a proxy can decide +whether future versions of the GNU Lesser General Public License shall +apply, that proxy's public statement of acceptance of any version is +permanent authorization for you to choose that version for the +Library. diff --git a/lib/owlapi30/version.txt b/lib/owlapi30/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..e4f698ef6cdf8215d1b9fec77ed456507daaa99a --- /dev/null +++ b/lib/owlapi30/version.txt @@ -0,0 +1 @@ +OWL API 1 1.4.3 diff --git a/lib/servlet/version.txt b/lib/servlet/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..95e3ba8192053fb4a18be631cb8d273638ac768b --- /dev/null +++ b/lib/servlet/version.txt @@ -0,0 +1 @@ +2.5 diff --git a/lib/xerces/license.txt b/lib/xerces/license.txt new file mode 100644 index 0000000000000000000000000000000000000000..1914f856a2026b21ee0a81b2432f045025534ecc --- /dev/null +++ b/lib/xerces/license.txt @@ -0,0 +1,55 @@ +Apache License +Version 2.0, January 2004 +http://www.apache.org/licenses/ + +TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + +1. Definitions. + +"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. + +"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. + +"Legal Entity" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. + +"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License. + +"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. + +"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. + +"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). + +"Derivative Works" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. For the purposes of this License, Derivative Works shall not include works that remain separable from, or merely link (or bind by name) to the interfaces of, the Work and Derivative Works thereof. + +"Contribution" shall mean any work of authorship, including the original version of the Work and any modifications or additions to that Work or Derivative Works thereof, that is intentionally submitted to Licensor for inclusion in the Work by the copyright owner or by an individual or Legal Entity authorized to submit on behalf of the copyright owner. For the purposes of this definition, "submitted" means any form of electronic, verbal, or written communication sent to the Licensor or its representatives, including but not limited to communication on electronic mailing lists, source code control systems, and issue tracking systems that are managed by, or on behalf of, the Licensor for the purpose of discussing and improving the Work, but excluding communication that is conspicuously marked or otherwise designated in writing by the copyright owner as "Not a Contribution." + +"Contributor" shall mean Licensor and any individual or Legal Entity on behalf of whom a Contribution has been received by Licensor and subsequently incorporated within the Work. + +2. Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. + +3. Grant of Patent License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except as stated in this section) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer the Work, where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You institute patent litigation against any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the Work or a Contribution incorporated within the Work constitutes direct or contributory patent infringement, then any patent licenses granted to You under this License for that Work shall terminate as of the date such litigation is filed. + +4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions: + + 1. You must give any other recipients of the Work or Derivative Works a copy of this License; and + + 2. You must cause any modified files to carry prominent notices stating that You changed the files; and + + 3. You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and + + 4. If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License. + +You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License. + +5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions. + +6. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file. + +7. Disclaimer of Warranty. Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License. + +8. Limitation of Liability. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise, unless required by applicable law (such as deliberate and grossly negligent acts) or agreed to in writing, shall any Contributor be liable to You for damages, including any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this License or out of the use or inability to use the Work (including but not limited to damages for loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses), even if such Contributor has been advised of the possibility of such damages. + +9. Accepting Warranty or Additional Liability. While redistributing the Work or Derivative Works thereof, You may choose to offer, and charge a fee for, acceptance of support, warranty, indemnity, or other liability obligations and/or rights consistent with this License. However, in accepting such obligations, You may act only on Your own behalf and on Your sole responsibility, not on behalf of any other Contributor, and only if You agree to indemnify, defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. + +END OF TERMS AND CONDITIONS diff --git a/lib/xerces/version.txt b/lib/xerces/version.txt new file mode 100644 index 0000000000000000000000000000000000000000..dedcc7d4335da09214ca036d5fdf9473a45f1682 --- /dev/null +++ b/lib/xerces/version.txt @@ -0,0 +1 @@ +2.9.1 diff --git a/lib/xerces/xercesImpl.jar b/lib/xerces/xercesImpl.jar index eac75ae8ef63d94dfd435c7d05dc26d14115399f..8f762e1a85fc0ac9d83c24b51f520a8765e7c461 100644 Binary files a/lib/xerces/xercesImpl.jar and b/lib/xerces/xercesImpl.jar differ diff --git a/src/fr/inrialpes/exmo/ontowrap/jena25/JENAEntityIt.java b/src/fr/inrialpes/exmo/ontowrap/jena25/JENAEntityIt.java deleted file mode 100644 index ded08e09b19ac3e2820ec7303116e22bb5417fcb..0000000000000000000000000000000000000000 --- a/src/fr/inrialpes/exmo/ontowrap/jena25/JENAEntityIt.java +++ /dev/null @@ -1,70 +0,0 @@ -/* - * $Id$ - * - * Copyright (C) INRIA, 2008-2010 - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU Lesser General Public License as published by - * 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.ontowrap.jena25; - -import java.net.URI; -import java.util.AbstractSet; -import java.util.Iterator; -import java.util.NoSuchElementException; - -import com.hp.hpl.jena.ontology.OntResource; - - -public class JENAEntityIt implements Iterator<OntResource> { - - private Iterator<OntResource> it; - private OntResource current; - private URI ontURI; - - public JENAEntityIt(URI ontURI, Iterator<OntResource> entityIt) { - this.ontURI = ontURI; - this.it= entityIt; - } - - private void setNext() { - while (current==null) { - current = it.next(); - if (current.getURI()==null) {// || !current.getURI().startsWith(ontURI.toString())) { - current=null; - } - } - } - public boolean hasNext() { - try { - setNext(); - return current!=null; - } - catch (NoSuchElementException e) { - return false; - } - } - - public OntResource next() { - setNext(); - OntResource returnR = current; - current=null; - return returnR; - } - - public void remove() { - throw new UnsupportedOperationException(); - } -} diff --git a/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntology.java b/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntology.java index 3259c38b72428b17c0f2a3af53a6688e082c5166..a5e3f2bf007e28773a54afecd6d47bcf2c4f5fd8 100644 --- a/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntology.java +++ b/src/fr/inrialpes/exmo/ontowrap/jena25/JENAOntology.java @@ -25,10 +25,12 @@ import java.util.AbstractSet; import java.util.HashSet; import java.util.Iterator; import java.util.Set; +import java.util.NoSuchElementException; import com.hp.hpl.jena.ontology.DatatypeProperty; import com.hp.hpl.jena.ontology.Individual; import com.hp.hpl.jena.ontology.ObjectProperty; +import com.hp.hpl.jena.ontology.AnnotationProperty; import com.hp.hpl.jena.ontology.OntClass; import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntProperty; @@ -38,6 +40,10 @@ import com.hp.hpl.jena.rdf.model.NodeIterator; import com.hp.hpl.jena.rdf.model.Property; import com.hp.hpl.jena.rdf.model.RDFNode; +import com.hp.hpl.jena.util.iterator.ExtendedIterator; +import com.hp.hpl.jena.util.iterator.Filter; +import com.hp.hpl.jena.util.iterator.Map1; + import com.hp.hpl.jena.rdf.model.impl.LiteralImpl; import fr.inrialpes.exmo.ontowrap.BasicOntology; @@ -53,19 +59,19 @@ public class JENAOntology extends BasicOntology<OntModel> implements LoadedOntol return onto.getOntResource(u.toString()); } - public void getEntityAnnotations(Object o, Set<String> annots) throws OntowrapException { - OntResource or = (OntResource) o; - Iterator<?> z = onto.listAnnotationProperties(); + public void getEntityAnnotations( Object o, Set<String> annots ) throws OntowrapException { + // THIS SHOULD BE STATIC NOW!! + Iterator<AnnotationProperty> z = onto.listAnnotationProperties(); while (z.hasNext()) { - NodeIterator j = or.listPropertyValues((Property) z.next()); - while (j.hasNext()) { - RDFNode n = j.nextNode(); - if (n.isResource()) - getEntityAnnotations(n, annots); - else if (n.isLiteral()) { - annots.add(((Literal) n.as(Literal.class)).getLexicalForm()); - } + NodeIterator j = ((OntResource)o).listPropertyValues((Property)z.next()); + while (j.hasNext()) { + RDFNode n = j.nextNode(); + if (n.isResource()) + getEntityAnnotations(n, annots); + else if (n.isLiteral()) { + annots.add( ((Literal)n.as(Literal.class)).getLexicalForm() ); } + } } } @@ -77,11 +83,9 @@ public class JENAOntology extends BasicOntology<OntModel> implements LoadedOntol public Set<String> getEntityComments(Object o, String lang) throws OntowrapException { Set<String> comments = new HashSet<String>(); - OntResource or = (OntResource) o; - Iterator<?> i = or.listComments(lang); - while (i.hasNext()) { - String comment = ((LiteralImpl) i.next()).getLexicalForm(); - comments.add(comment); + Iterator<RDFNode> it = ((OntResource)o).listComments(lang); + while (it.hasNext()) { + comments.add( ((LiteralImpl)it.next()).getLexicalForm() ); } return comments; } @@ -129,15 +133,21 @@ public class JENAOntology extends BasicOntology<OntModel> implements LoadedOntol } } - protected Set<OntResource> getEntitySet(final Iterator<OntResource> i) { - return new AbstractSet<OntResource>() { + /** + * This strange structure, as well as the corresponding JENAEntityIt + * is there only because Jena may return unammed entities that have to + * be filtered out from the sets. + * + */ + protected <R extends OntResource> Set<R> getEntitySet(final ExtendedIterator<R> i) { + return new AbstractSet<R>() { private int size=-1; - public Iterator<OntResource> iterator() { - return new JENAEntityIt(getURI(),i); + public Iterator<R> iterator() { + return new JENAEntityIt( getURI(), i ); } public int size() { if (size==-1) { - for (OntResource r : this) + for (R r : this) size++; size++; } @@ -146,35 +156,49 @@ public class JENAOntology extends BasicOntology<OntModel> implements LoadedOntol }; } - @SuppressWarnings("unchecked") - public Set<?> getClasses() { - return getEntitySet(onto.listNamedClasses()); + public Set<OntClass> getClasses() { + return onto.listNamedClasses().toSet(); } - @SuppressWarnings("unchecked") - public Set<?> getDataProperties() { + public Set<DatatypeProperty> getDataProperties() { return getEntitySet(onto.listDatatypeProperties()); } - @SuppressWarnings("unchecked") - public Set<?> getEntities() { - return getEntitySet(onto.listObjectProperties().andThen(onto.listDatatypeProperties()). - andThen(onto.listIndividuals()).andThen(onto.listClasses())); + static Map1 myMap = new Map1 () { public OntResource map1 ( Object o ) { return (OntResource)o; } }; + + public Set<OntResource> getEntities() { + //ExtendedIterator<OntResource> a = onto.listObjectProperties(); + return getEntitySet(onto.listObjectProperties().mapWith( myMap ) + .andThen(onto.listDatatypeProperties().mapWith( myMap )) + .andThen(onto.listNamedClasses().mapWith( myMap )) + .andThen(onto.listIndividuals().mapWith( myMap )) + ); + //.andThen(((ExtendedIterator<OntResource>)(onto.listDatatypeProperties())))); + /* + return getEntitySet( onto.listOntProperties().filterKeep( new Filter () { + public boolean accept( Object o ) { return (o instanceof DatatypeProperty) || + (o instanceof ObjectProperty) || (o instanceof Individual) || (o instanceof OntClass); } + }) ); + return getEntitySet(onto.listObjectProperties()); + .andThen(onto.listDatatypeProperties()) + .andThen(onto.listIndividuals()) + .andThen(onto.listClasses())); + */ } - @SuppressWarnings("unchecked") - public Set<?> getIndividuals() { + public Set<Individual> getIndividuals() { return getEntitySet(onto.listIndividuals()); } - @SuppressWarnings("unchecked") - public Set<?> getObjectProperties() { + public Set<ObjectProperty> getObjectProperties() { return getEntitySet(onto.listObjectProperties()); } - @SuppressWarnings("unchecked") - public Set<?> getProperties() { - return getEntitySet(onto.listObjectProperties().andThen(onto.listDatatypeProperties())); + public Set<OntProperty> getProperties() { + return getEntitySet( onto.listAllOntProperties().filterDrop( new Filter () { + public boolean accept( Object o ) { return (o instanceof AnnotationProperty); } + }) ); + //return getEntitySet(onto.listObjectProperties().andThen(onto.listDatatypeProperties())); } public boolean isClass(Object o) { @@ -231,3 +255,44 @@ public class JENAOntology extends BasicOntology<OntModel> implements LoadedOntol } + +class JENAEntityIt<R extends OntResource> implements Iterator<R> { + + private ExtendedIterator<R> it; + private R current; + private URI ontURI; + + public JENAEntityIt( URI ontURI, ExtendedIterator<R> entityIt ) { + this.ontURI = ontURI; + this.it = entityIt; + } + + private void setNext() { + while (current==null) { + current = it.next(); + if (current.getURI()==null) {// || !current.getURI().startsWith(ontURI.toString())) { + current=null; + } + } + } + public boolean hasNext() { + try { + setNext(); + return current!=null; + } + catch (NoSuchElementException e) { + return false; + } + } + + public R next() { + setNext(); + R returnR = current; + current=null; + return returnR; + } + + public void remove() { + throw new UnsupportedOperationException(); + } +}