Mentions légales du service

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Commit 4380ac86 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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- genericised storage cache

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......@@ -72,18 +72,16 @@ with a warning:
<!--h2>Version 4.9 (1xxx): ??/??/201X - Al pesto</h2-->
<!--h2>Version 4.8 (1xxx): ??/??/201x - Antésine</h2-->
<!--h2>Version 4.7 (1xxx): ??/??/201x - Letraset</h2-->
<!--h2>Version 4.7 (1xxx): ??/0?/2014 - Letraset</h2-->
<p><ul compact="1">
<li><span style="color: red;">Deprecated</span> <tt>BasicAlignment.removeAlignCell()</tt>,
use <tt>remCell()</tt> instead (impl)</tt>
<li><span style="color: red;">Moved</span> <tt>QueryMediator</tt>,
from <tt>service</tt> to <tt>queryprocessor</tt> (impl)</tt>
<li>Fixed a bug in <tt>QueryMediator</tt> which doubled '#' (server)</li>
<li>Implemented <tt>translateMessage()</tt>
and <tt>rewriteQuery()</tt> in <tt>BasicAlignment</tt> (impl)</li>
<li>Enabled query translation in interface (server)</li>
<li><span style="color: red;">Deprecated</span> <tt>BasicAlignment.removeAlignCell()</tt>, use <tt>remCell()</tt> instead (impl)</tt>
<li><span style="color: red;">Moved</span> <tt>QueryMediator</tt>, from <tt>service</tt> to <tt>queryprocessor</tt> (impl)</tt>
<li>Fixed a bug in <tt>QueryMediator</tt> which doubled '#' (serv)</li>
<li>Implemented <tt>translateMessage()</tt> and <tt>rewriteQuery()</tt> in <tt>BasicAlignment</tt> (impl)</li>
<li>Enabled query translation in interface (serv)</li>
<li>Added a command-line utility for query translation (cli)</li>
<li>Added a guard forbiding to create a <tt>BasicCell</tt> with null objects (impl)</li>
<li>Genericised storage <tt>Cache</tt> (serv)</li>
</ul></p>
<h2>Version 4.6 (1875): 22/01/2014 - Da lec'h all</h2>
......@@ -91,10 +89,10 @@ with a warning:
<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>All logging and signaling is now through slf4j (impl/serv)</li>
<li>Replaced getopt by <span style="color: green">commons cli 1.2</span> 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>Declared Alignment server as an OSGi service (serv)</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>
......@@ -117,18 +115,18 @@ with a warning:
<p><ul compact="1">
<li>Added several EDOAL-SPARQL renderers (impl)</li>
<li>Added <tt>ontowrap</tt> support in database store (server)</li>
<li>Made Alignment URIs independent from URL prefix (server)</li>
<li>Added alignment selection per ontologies in list alignment interface (server)</li>
<li>Added <tt>ontowrap</tt> support in database store (serv)</li>
<li>Made Alignment URIs independent from URL prefix (serv)</li>
<li>Added alignment selection per ontologies in list alignment interface (serv)</li>
<li>Added relation sensitiveness to evaluators (impl)</li>
<li>Added generation of local <a href="maven.html">maven repository</a> in build.xml</li>
<li>Implemented transactions in database store (server)</li>
<li>Implemented transactions in database store (serv)</li>
<li>Modified evaluators needing <tt>ObjectAlignment</tt> to convert them on the fly (impl)</li>
<li>Modified renderers needing <tt>ObjectAlignment</tt> to convert them on the fly (impl)</li>
<li>Evaluators report better errors on the server (server)</li>
<li>Evaluators report better errors on the server (serv)</li>
<li>Fixed a bug in <tt>WeightedPREvaluator</tt> (can be more than 1.) (impl)</li>
<li>Fixed strong bug in the implementation of relaxed precision and recall (impl)</li>
<li>Fixed a (non manifested) bug in cache management (server)</li>
<li>Fixed a (non manifested) bug in cache management (serv)</li>
<li>Fixed a bug in displaying evaluation tables (cli)</li>
<li>Fixed a bug with subsumption statements in <tt>OWLAxiomsRendererVisitor</tt> (impl)</li>
<li>Simplified and rewritten <tt>SemPRecEvaluator</tt> (impl)</li>
......@@ -154,10 +152,10 @@ with a warning:
<li>Upgraded to <span style="color: green">SKOS API 2</span> and
<span style="color: green">OntoSim 2.3</span> (lib)</li>
<li>Added <tt>JSONRendererVisitor</tt> (impl)</li>
<li>Added <tt>corresp</tt> primitive (server)</li>
<li>Added <tt>corresp</tt> primitive (serv)</li>
<li>Added <tt>EDOALAlignment.toEDOALAlignment()</tt> (edoal)</li>
<li>Simplified <tt>TestGen</tt> options (cli)</li>
<li>Fixed server initialisation error with new log4j (server)</li>
<li>Fixed server initialisation error with new log4j (serv)</li>
<li>Fixed a float parsing bug in <tt>XMLParser</tt> (parser)</li>
<li>Fixed a display error in <tt>DiffEvaluator</tt> (impl)</li>
<li>Corrected bug with <tt>owl:inverseOf</tt> in OWL rendering (edoal)</li>
......@@ -215,13 +213,13 @@ with a warning:
<li>Added a few statistical primitives to BasicAlignment (impl)</li>
<li>Suppressed <tt>EDOALRelation</tt>: EDOAL uses <tt>BasicRelation</tt> (edoal)</li>
<li>EDOAL default printout now uses pretty relations, i.e., &lt;, &gt;, =, % (edoal)</li>
<li>Modified server answers so that namespaces are well placed in REST (server)</li>
<li>Modified server answers so that namespaces are well placed in REST (serv)</li>
<li>Changed order of display to precision/F-measure/recall (util)</li>
<li><span style="color: red;">Suppressed</span> incorrect computation of fallout (eval)</li>
<li>Corrected NaN derived measures when precision is 0. (eval)</li>
<li>Set precision to 1. when alignments are empty (eval)</li>
<li>Upgraded to <span style="color: green">OntoSim 2.2</span> (lib)</li>
<li>Minor display changes in HTML display (server)</li>
<li>Minor display changes in HTML display (serv)</li>
<li>Suppressed <tt>PreAlignment</tt> (impl)</li>
</ul></p>
......@@ -241,7 +239,7 @@ with a warning:
<li>Added a <tt>getResult()</tt> method to <tt>Evaluator</tt> (api)</li>
<li>Added a <tt>DiffAlign( al1, al2 )</tt> evaluator (impl)</li>
<li>Added an <tt>aggr.ConsensusAggregator</tt> for merging several alignments (impl)</li>
<li>Implemented online evaluation and diff (server)</li>
<li>Implemented online evaluation and diff (serv)</li>
<li>Added the possibility to drop a number of correspondences in <tt>ONetworkWeakener</tt> (util)</li>
<li>Added a google chart API display of plots <tt>GenPlot -t html</tt> (util)</li>
<li><tt>edoal:or</tt>, <tt>edoal:and</tt> and <tt>edoal:compose</tt> can be empty (edoal)</li>
......@@ -252,7 +250,7 @@ with a warning:
<li>Added <a href="tutorial/tutorial4/index.html">tutorial 4</a> Pellet action (tutorial)</li>
<li>Added <a href="tutorial/tutorial5/index.html">tutorial 5</a> about exposing matchers as web services (tutorial)</li>
<li>Fixed several problems with loading twice the same ontology in the OWL API (ontowrap)</li>
<li>Corrected an error in matching when a alignment existed without method extension (server)</li>
<li>Corrected an error in matching when a alignment existed without method extension (serv)</li>
<li>Fixed path errors in tutorials (tutorial)</li>
<li>Improved RDF Rendering layout (impl)</li>
</ul></p>
......@@ -277,14 +275,14 @@ with a warning:
<li>Implemented semantic precision and recall (impl)</li>
<li>Implemented ROC curve computing and reimplemented the plotting
structure. Now they are based on harmonic means instead of average. (eval)</li>
<li>Fully implemented <tt>find</tt> to interface (server)</li>
<li>Fully implemented <tt>find</tt> to interface (serv)</li>
<li>Completely modified the web service interface so that SOAP and
REST are fully aligned. This is
now <a href="rest.html#version4">documented</a> (serv)</li>
<li>Added a <tt>listevaluators</tt> primitive to the service interface (serv)</li>
<li>Added computation of MAP (Mean Average Precision) in <tt>PRGraphEvaluator</tt> (impl).</li>
<li>Added pretty-printing of names in server (server)</li>
<li>Added provenance tracking in server (server)</li>
<li>Added pretty-printing of names in server (serv)</li>
<li>Added provenance tracking in server (serv)</li>
<li>Added initialisation through initial alignment
in <tt>MatrixMeasure</tt> (impl)</li>
<li>Added a parameter to the <tt>OWLAxiomsRendererVisitor</tt> so that it could render
......@@ -295,26 +293,26 @@ with a warning:
<li>Suppressed <tt>OWLAPICell</tt> and <tt>OWLAPIAlignment</tt>
(deprecated since version 3.3) (impl)</li>
<li>Changed the signature of <tt></tt> from <tt>Enumeration</tt>
to <tt>Collection&lt;Alignment&gt;</tt> (server)</tt>
to <tt>Collection&lt;Alignment&gt;</tt> (serv)</tt>
<li>Reorganised the lib directory hierarchically (build)</li>
<li>Corrected missing <tt>hashCode()</tt> (bug #9680) (impl)</li>
<li>Corrected a bug when the server is launched without -S
(server)</li>
<li>Fixed error message in server (#8502: org.apache.xml.resolver.readers.CatalogReader: deprecated) by upgrading resolver.jar (server)</li>
(serv)</li>
<li>Fixed error message in server (#8502: org.apache.xml.resolver.readers.CatalogReader: deprecated) by upgrading resolver.jar (serv)</li>
<li>Corrected a bug in <tt>HTMLRendererVisitor</tt> that made the
display of alignments, especially stored, to break (server)</li>
display of alignments, especially stored, to break (serv)</li>
<li>Corrected the README.TXT of examples/wservice (serv)</li>
<li>Corrected a bug in retrieving alignments from ontologies when the
two ontologies are the same (server)</li>
two ontologies are the same (serv)</li>
<li>Corrected a bug in triming, which left one item too much (impl)</li>
<li>Corrected a bug when <tt>StringDistAlignment</tt> fails to raise
exception when unknown method is given (impl)</li>
<li>Corrected a problem due to parser reentrance which led two
alignment parsed by the same parser to go into the same alignment (parser)</li>
<li>Corrected a bug introduced in 3.6 which prevented from storing the
"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>
"stored" date of alignments (serv)</li>
<li>Corrected a bug in the "find" primitive of service (serv)</li>
<li>Corrected a bug that prevented proper search of <tt>aserv.wsdl</tt> file in all imported jars (serv)</li>
<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
......@@ -336,14 +334,14 @@ If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
<p>
<ul compact="1">
<li><tt>tokenize</tt> has been moved from <tt>JWNLDistances</tt> to <tt>StringDistances</tt> (ling)</li>
<li>Added REST interface to the HTML interface (server)</li>
<li>Added REST interface to the HTML interface (serv)</li>
<li>Addition of the notion of <tt>OntologyNetwork</tt> made of a set of
ontologies and alignments within the API (api/impl/test).</li>
<li>Added new gap based (hardgap and propgap) methods in <tt>BasicAlignment.cut()</tt> (impl)</li>
<li>Added new methods (Cosynonymy, Wu-Palmer) in JWNLDistances (ling)</li>
<li>Added tests for ling and set noling as default in build (test)</li>
<li>Added the possibility for <tt>OWLAxiomsRendererVisitor</tt> to output relations between individuals (renderer)</li>
<li>Added JDBC drivers for Postgress and improved mySQL code for genericity (server)</li>
<li>Added JDBC drivers for Postgress and improved mySQL code for genericity (serv)</li>
<li>Improved renderers with more metadata (renderer)</li>
<li>Completed individual alignment and extraction in <tt>DistanceAlignment</tt> (impl)</li>
<li>Completed matrix printing in <tt>MatrixMeasure</tt> (impl)</li>
......@@ -351,7 +349,7 @@ If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
<li>Corrected a bug in <tt>XMLMetadataRendererVisitor</tt> (renderer)</li>
<li>Corrected a bug in <tt>RDFRendererVisitor</tt> that output rdf:ID="" (renderer)</li>
<li>Corrected a bug in <tt>OWLAxiomsRendererVisitor</tt> for generating disjointWith statements (renderer)</li>
<li>Corrected a (rare) bug in server which was not able to recognise URIs (server)</li>
<li>Corrected a (rare) bug in server which was not able to recognise URIs (serv)</li>
<li>Corrected a bug in <tt>BasicAlignment.cut("best")</tt> (impl)</li>
<li>Prevented <tt>OWLAxiomsRenderer</tt> from returning equivalence
between Data and Object properties and, in general, heterogeneous equivalences (impl)</li>
......@@ -371,13 +369,13 @@ If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
<li>Completed the integration of Jena ontologies (ontowrap)</li>
<li>Implemented basic algebraic operations (impl)</li>
<li>Added diff algebraic operation (api)</li>
<li>Reengineered parameter passing for web service interface (server)</li>
<li>Reengineered parameter passing for web service interface (serv)</li>
<li>Updated <tt>SKOSRendererVisitor</tt> to work with 2008 version of
SKOS, old version can be obtained by parameter <tt>pre2008</tt> (impl)</li>
<li>Suppressed <tt>GenTriangle</tt> (util)</li>
<li>Corrected an error preventing DistanceAlignment to consider individuals (impl)</li>
<li>Corrected SWRL format missing rdf namespace (impl)</li>
<li>Corrected an error transmitting the DBMS coordinates on the web (server)</li>
<li>Corrected an error transmitting the DBMS coordinates on the web (serv)</li>
<li>Corrected a bug in <tt>SKOSRendererVisitor</tt> and <tt>XSLTRendererVisitor</tt> (impl)</li>
<li>Started to put copyright notices to INRIA instead of INRIA Rh&ocirc;ne-Alpes (misc)</li>
<li>Used Java 1.5 print Formatter instead of our printFormat (impl)</li>
......@@ -390,7 +388,7 @@ If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
<p>
<ul compact="1">
<li>Implemented WSAlignment connecting to remote web service for
matching (server)</li>
matching (serv)</li>
<li><span style="color: red;">Deprecated</span> <tt>Cell.getObjectXAsURI()</tt>
in favour of <tt>Cell.getObjectXAsURI(Alignment al)</tt> (api)</tt>
<li>Upgraded NeOn plug-in for working with <span style="color: green">NeOn toolkit 1.1</span> (plugin)</li>
......@@ -404,22 +402,22 @@ If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
<li>Added <tt>initAlignment(URIAlignment)</tt> to parser (parser)</li>
<li>Added <tt>parse(InputStream)</tt> to parser (parser)</li>
<li>Parser now ignore SOAP envelops (parser)</li>
<li>Implemented a better recovery in case of database connection loss (server)</li>
<li>Implemented cache flushing functions (server)</li>
<li>Provided better return forms in <tt>HTMLAServManager</tt> (server)</li>
<li>Catched <tt>init()</tt> errors in server (server)</li>
<li>Reorganised HTML interface (server)</li>
<li>Added indentation and namespaces in the Web service interface (server)</li>
<li>Implemented a better recovery in case of database connection loss (serv)</li>
<li>Implemented cache flushing functions (serv)</li>
<li>Provided better return forms in <tt>HTMLAServManager</tt> (serv)</li>
<li>Catched <tt>init()</tt> errors in server (serv)</li>
<li>Reorganised HTML interface (serv)</li>
<li>Added indentation and namespaces in the Web service interface (serv)</li>
<li>Implemented <a href="http://www.webcontent.fr">WebContent</a> plug-in (plugin)</li>
<li>Improved NeOn plug-in documentation (html)</li>
<li>Increased the size of relation id to 25 char (server)</li>
<li>Increased the size of relation id to 25 char (serv)</li>
<li>Corrected <tt>MyAlign</tt> example which was not adapted to the
new onto structure (examples)</li>
<li>Corrected tutorial so that it works with new code (tutorial)</li>
<li>Corrected an error of the <tt>Cell.inverse()</tt> method (impl)</li>
<li>Corrected an error in storing alignments (server)</li>
<li>Corrected an error in storing alignments (serv)</li>
<li>Corrected an error in the MANIFEST of the NeOn plug in (plugin)</li>
<li>Corrected an error that prevented the server to work on Windows (server)</li>
<li>Corrected an error that prevented the server to work on Windows (serv)</li>
</ul>
</p>
......@@ -436,8 +434,8 @@ If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
<li>Made <tt>Alignment</tt> iterable&lt;Cell&gt; (api/impl)</li>
<li>Improved NeOn plug-in and upgraded to <span style="color: green">
NeOn toolkit 1.0</span> (plugin)</li>
<li>Corrected a bug in Web service when the content was XML (server)</li>
<li>Corrected a bug when loading an alignment with id (server)</li>
<li>Corrected a bug in Web service when the content was XML (serv)</li>
<li>Corrected a bug when loading an alignment with id (serv)</li>
<li>Corrected a bug in AlignmentParser that overlooked formalism URI (parser)</li>
<li>Passed to Java 1.5 generics [incl. API modif] (dev/api)</li>
<li>Added first unit tests (TestNG) (dev)</li>
......@@ -448,18 +446,18 @@ If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
<a name="3.2"></a><h2>Version 3.2 (666): 29/02/2008 - Blejsko jezero</h2>
<p>
<ul compact="1">
<li>Connection to Oyster directory (server)</li>
<li>Added the opportunity to run matchers asynchronously (server)</li>
<li>Connection to Oyster directory (serv)</li>
<li>Added the opportunity to run matchers asynchronously (serv)</li>
<li>Made sure that http server is launched when wsdl option is chosen
(server)</li>
(serv)</li>
<li>Moved NeOn toolkit plugin in the plugins/neon (plugin)</li>
<li>Cleaned-up working NeOn plug-in for NeOn toolkit (plugin)</li>
<li>Introduced abstract directories (server)</li>
<li>Introduced abstract directories (serv)</li>
<li>Improved the WordNet interface by introducing version. 3.0 is default (ling)</li>
<li>Reinstated the possibility to use the old namespace in the parser (parser)</li>
<li>Corrected a bug that prevented to store alignments in Web service
interface (server)</li>
<li>Passed command line parameters to <tt>align()</tt> (server)</li>
interface (serv)</li>
<li>Passed command line parameters to <tt>align()</tt> (serv)</li>
<li>Created an Annotation class for storing static strings (impl)</li>
<li>Enriched Ontology objects (impl)</li>
<li>Progressed in the implementation of alignment composition (impl)</li>
......@@ -479,7 +477,7 @@ For better conforming with RDF practice, we have
<li>Modified the extension mechanism so that getExtension and
setExtension take a namespace URI as first argument (api).</li>
<li>Modified the service database extension format for recording this
URI (server).</li>
URI (serv).</li>
</ul></p>
<p>
......@@ -494,24 +492,24 @@ Other improvements include:
implementation of ontology descriptions (format/parser/impl)</li>
<li>Modified the Alignement namespace by adding a '#'(format)</li>
<li>Separated namespace from pName in extension keys</li>
<li>Added Web Service Alignment server profile (server)</li>
<li>Multithreaded matching in Services (server)</li>
<li>Added Web Service Alignment server profile (serv)</li>
<li>Multithreaded matching in Services (serv)</li>
<li>Got rid of the property file for wordnet (ling)</li>
<li>In Server/FIPA, suppressed generated files on <tt>close()</tt> (server)</li>
<li>Suppressed all printouts (Jade or Jetty logging) (server)</li>
<li>Added file logging option (server)</li>
<li>Added the inverse operation (server)</li>
<li>Completely rewritten autodetection of renderers and methods in server (server)</li>
<li>In Server/FIPA, suppressed generated files on <tt>close()</tt> (serv)</li>
<li>Suppressed all printouts (Jade or Jetty logging) (serv)</li>
<li>Added file logging option (serv)</li>
<li>Added the inverse operation (serv)</li>
<li>Completely rewritten autodetection of renderers and methods in server (serv)</li>
<li>Modified interface of embedded methods</li>
<li>Added guarantee that results displayed by <tt>GroupEval</tt> be sorted
(thanks Vassilis Spiliopoulos) (util)</li>
<li>Added namespace support in BasicAlignment (impl)</li>
<li>Forced trailing slash in HTML menu URLs (server)</li>
<li>Added fetching alignments from URIs (server)</li>
<li>Changed for Jetty as an embedded HTTP server (server)</li>
<li>Implemented alignment upload (server)</li>
<li>Forced trailing slash in HTML menu URLs (serv)</li>
<li>Added fetching alignments from URIs (serv)</li>
<li>Changed for Jetty as an embedded HTTP server (serv)</li>
<li>Implemented alignment upload (serv)</li>
<li>Corrected an error on "force"-ing alignment in Server/HTML (was
inverted) (server)</li>
inverted) (serv)</li>
<li>Corrected a bug concerning extension namespaces (impl)</li>
<li>Corrected a bug in the DistanceAlignment Hungarian method
extraction (impl)</li>
......
src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+ 8
− 10
View file @ 4380ac86
......@@ -67,8 +67,6 @@ import org.semanticweb.owl.align.Evaluator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.sql.SQLException;
import java.lang.ClassNotFoundException;
import java.lang.InstantiationException;
import java.lang.NoSuchMethodException;
......@@ -138,12 +136,12 @@ public class AServProtocolManager implements Service {
directories = dir;
}
public void init( DBService connection, Properties prop ) throws SQLException, AlignmentException {
public void init( DBService connection, Properties prop ) throws AlignmentException {
commandLineParams = prop;
serverId = prop.getProperty("prefix");
if ( serverId == null || serverId.equals("") )
serverId = "http://"+prop.getProperty("host")+":"+prop.getProperty("http");
alignmentCache = new CacheImpl( connection );
alignmentCache = new SQLCache( connection );
alignmentCache.init( prop, serverId );
renderers = implementations( "org.semanticweb.owl.align.AlignmentVisitor" );
methods = implementations( "org.semanticweb.owl.align.AlignmentProcess" );
......@@ -154,16 +152,16 @@ public class AServProtocolManager implements Service {
public void close() {
try { alignmentCache.close(); }
catch (SQLException sqle) {
logger.trace( "IGNORED SQL Exception", sqle );
catch (AlignmentException alex) {
logger.trace( "IGNORED Exception", alex );
}
}
public void reset() {
try {
alignmentCache.reset();
} catch (SQLException sqle) {
logger.trace( "IGNORED SQL Exception", sqle );
} catch (AlignmentException alex) {
logger.trace( "IGNORED Exception", alex );
}
}
......@@ -175,8 +173,8 @@ public class AServProtocolManager implements Service {
try {
alignmentCache.close();
System.exit(0);
} catch (SQLException sqle) {
logger.trace( "IGNORED SQL Exception", sqle );
} catch (AlignmentException alex) {
logger.trace( "IGNORED Exception", alex );
}
}
......
src/fr/inrialpes/exmo/align/service/Cache.java 0 → 100644
+ 114
− 0
View file @ 4380ac86
/*
* $Id$
*
* Copyright (C) INRIA, 2014
*
* 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.service;
import java.util.Enumeration;
import java.util.Collection;
import java.util.Set;
import java.util.Properties;
import java.net.URI;
import java.net.URISyntaxException;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
/**
* This interface caches the content of the alignment database.
* It may be implemented in various ways: SQL or RDF repositories
*/
public interface Cache {
/**
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
*/
public void init( Properties p, String prefix ) throws AlignmentException;
public void reset() throws AlignmentException;
public void close() throws AlignmentException;
public void flushCache();
// **********************************************************************
// LOADING FROM DATABASE
/**
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
* index them under the ontology URIs
*/
public Collection<Alignment> alignments();
public Collection<URI> ontologies();
public Collection<Alignment> alignments( URI u1, URI u2 );
//**********************************************************************
// DEALING WITH URIs
// Public because this is now used by AServProtocolManager
public String generateAlignmentUri();
//**********************************************************************
// FETCHING FROM CACHE
/**
* retrieve alignment metadata from id
* This is more difficult because we return the alignment we have
* disreagarding if it is complete o only metadata
*/
public Alignment getMetadata( String uri ) throws AlignmentException;
/**
* retrieve full alignment from id (and cache it)
*/
public Alignment getAlignment( String uri ) throws AlignmentException;
public Set<Alignment> getAlignments( URI uri );
/**
* returns the alignments between two ontologies
* if one of the ontologies is null, then return them all
*/
public Set<Alignment> getAlignments( URI uri1, URI uri2 );
//**********************************************************************
// RECORDING ALIGNMENTS
/**
* records newly created alignment
*/
public String recordNewAlignment( Alignment alignment, boolean force );
/**
* records alignment identified by id
*/
public String recordNewAlignment( String uri, Alignment al, boolean force ) throws AlignmentException;
//**********************************************************************
// STORING IN DATABASE
public boolean isAlignmentStored( Alignment alignment );
/**
* Non publicised class
*/
public void eraseAlignment( String uri, boolean eraseFromDB ) throws AlignmentException;
public void storeAlignment( String uri ) throws AlignmentException;
}
src/fr/inrialpes/exmo/align/service/DBServiceImpl.java
+ 0
− 1
View file @ 4380ac86
......@@ -46,7 +46,6 @@ public class DBServiceImpl implements DBService {
static String dbpass = null;
String driverPrefix = "jdbc:mysql";
//String driverPrefix = "jdbc:postgresql";
CacheImpl cache = null;
public DBServiceImpl() throws ClassNotFoundException, InstantiationException, IllegalAccessException {
Class.forName("com.mysql.jdbc.Driver").newInstance();
......
src/fr/inrialpes/exmo/align/service/CacheImpl.java → src/fr/inrialpes/exmo/align/service/SQLCache.java
+ 174
− 118
View file @ 4380ac86
......@@ -2,7 +2,7 @@
* $Id$
*
* Copyright (C) Seungkeun Lee, 2006
* Copyright (C) INRIA, 2006-2013
* Copyright (C) INRIA, 2006-2014
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
......@@ -60,14 +60,17 @@ import java.io.PrintStream;
import java.io.EOFException;
/**
* JE: This class and Cache should never return SQLException but AlignmentException
* JE: Maybe some methods are common with RDF storage, the rest would rather be DBService...
*
* This class caches the content of the alignment database. I.e.,
* It loads the metadata in the hash table
* It stores the alignment when requested
* It
*/
public class CacheImpl {
final static Logger logger = LoggerFactory.getLogger( CacheImpl.class );
public class SQLCache implements Cache {
final static Logger logger = LoggerFactory.getLogger( SQLCache.class );
Hashtable<String,Alignment> alignmentTable = null;
Hashtable<URI,Set<Alignment>> ontologyTable = null;
......@@ -109,7 +112,7 @@ public class CacheImpl {
//**********************************************************************
public CacheImpl( DBService serv ) {
public SQLCache( DBService serv ) {
service = serv;
try {
conn = service.getConnection();
......@@ -120,50 +123,63 @@ public class CacheImpl {
ontologyTable = new Hashtable<URI,Set<Alignment>>();
}
public void reset() throws SQLException {
public void reset() throws AlignmentException {
alignmentTable = new Hashtable<String,Alignment>();
ontologyTable = new Hashtable<URI,Set<Alignment>>();
// reload alignment descriptions
loadAlignments( true );
try {
loadAlignments( true );
} catch ( SQLException sqlex ) {
throw new AlignmentException( "SQL exception", sqlex );
}
}
/**
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
*/
public void init( Properties p, String prefix ) throws SQLException, AlignmentException {
public void init( Properties p, String prefix ) throws AlignmentException {
logger.debug( "Initializing Database cache" );
port = p.getProperty("http"); // bad idea
host = p.getProperty("host");
idprefix = prefix;
Statement st = createStatement();
// test if a database is here, otherwise create it
ResultSet rs = conn.getMetaData().getTables(null,null, "server", new String[]{"TABLE"});
if ( !rs.next() ) {
initDatabase();
} else {
updateDatabase(); // in case it is necessary to upgrade
}
String pref = p.getProperty("prefix");
if ( pref == null || pref.equals("") ) {
rs = st.executeQuery( "SELECT prefix FROM server WHERE port='port'" );
while( rs.next() ) {
idprefix = rs.getString("prefix");
try {
Statement st = createStatement();
// test if a database is here, otherwise create it
ResultSet rs = conn.getMetaData().getTables(null,null, "server", new String[]{"TABLE"});
if ( !rs.next() ) {
initDatabase();
} else {
updateDatabase(); // in case it is necessary to upgrade
}
String pref = p.getProperty("prefix");
if ( pref == null || pref.equals("") ) {
rs = st.executeQuery( "SELECT prefix FROM server WHERE port='port'" );
while( rs.next() ) {
idprefix = rs.getString("prefix");
}
}
// register by the database
registerServer( host, port, rights==1, idprefix );
// load alignment descriptions
loadAlignments( true );
st.close();
} catch (SQLException sqlex) {
throw new AlignmentException( "SQLException", sqlex );
}
st.close();
// register by the database
registerServer( host, port, rights==1, idprefix );
// load alignment descriptions
loadAlignments( true );
}
public void close() throws SQLException {
Statement st = createStatement();
// unregister by the database
st.executeUpdate( "DELETE FROM server WHERE host='"+host+"' AND port='"+port+"'" );
st.close();
conn.close();
public void close() throws AlignmentException {
try {
Statement st = createStatement();
// unregister by the database
st.executeUpdate( "DELETE FROM server WHERE host='"+host+"' AND port='"+port+"'" );
st.close();
conn.close();
} catch (SQLException sqlex) {
throw new AlignmentException( "SQL Exception", sqlex );
}
}
public Statement createStatement() throws SQLException {
......@@ -207,15 +223,15 @@ public class CacheImpl {
return alignmentTable.elements();
}
protected Collection<Alignment> alignments() {
public Collection<Alignment> alignments() {
return alignmentTable.values();
}
protected Collection<URI> ontologies() {
public Collection<URI> ontologies() {
return ontologyTable.keySet();
}
protected Collection<Alignment> alignments( URI u1, URI u2 ) {
public Collection<Alignment> alignments( URI u1, URI u2 ) {
Collection<Alignment> results = new HashSet<Alignment>();
if ( u1 != null ) {
for ( Alignment al : ontologyTable.get( u1 ) ) {
......@@ -237,7 +253,7 @@ public class CacheImpl {
return results;
}
protected void flushCache() {// throws AlignmentException
public void flushCache() {// throws AlignmentException
for ( Alignment al : alignmentTable.values() ){
if ( al.getExtension(SVCNS, CACHED ) != null &&
!al.getExtension( SVCNS, CACHED ).equals("") &&
......@@ -438,7 +454,7 @@ public class CacheImpl {
/**
* retrieve full alignment from id (and cache it)
*/
public Alignment getAlignment( String uri ) throws AlignmentException, SQLException {
public Alignment getAlignment( String uri ) throws AlignmentException {
Alignment result = null;
try {
result = alignmentTable.get( uri );
......@@ -456,8 +472,11 @@ public class CacheImpl {
if ( ( result.getExtension( SVCNS, CACHED ) == null || result.getExtension( SVCNS, CACHED ).equals("") )
&& result.getExtension(SVCNS, STORED ) != null
&& !result.getExtension(SVCNS, STORED ).equals("") ) {
try { retrieveAlignment( uri, result ); }
catch ( URISyntaxException urisex ) {
try {
retrieveAlignment( uri, result );
} catch ( SQLException sqlex ) {
throw new AlignmentException( "getAlignment: SQL exception", sqlex );
} catch ( URISyntaxException urisex ) {
logger.trace( "Cache: cannot read from DB", urisex );
throw new AlignmentException( "getAlignment: Cannot find alignment", urisex );
};
......@@ -615,16 +634,19 @@ public class CacheImpl {
!alignment.getExtension( SVCNS, STORED ).equals("") );
}
/**
* Non publicised class
*/
public void eraseAlignment( String uri, boolean eraseFromDB ) throws SQLException, AlignmentException {
public void eraseAlignment( String uri, boolean eraseFromDB ) throws AlignmentException {
Alignment alignment = getAlignment( uri );
if ( alignment != null ) {
if ( eraseFromDB ) unstoreAlignment( uri, alignment );
// Suppress it from the cache...
unRecordAlignment( alignment );
try {
if ( eraseFromDB ) unstoreAlignment( uri, alignment );
// Suppress it from the cache...
} catch (SQLException sqlex) {
throw new AlignmentException( "SQL Exception", sqlex );
}
unRecordAlignment( alignment );
}
}
......@@ -667,7 +689,17 @@ public class CacheImpl {
}
}
public void storeAlignment( String uri ) throws AlignmentException, SQLException {
/*
try {
if ( eraseFromDB ) unstoreAlignment( uri, alignment );
// Suppress it from the cache...
} catch (SQLException sqlex) {
throw new AlignmentException( "SQL Exception", sqlex );
}
unRecordAlignment( alignment );
}
*/
public void storeAlignment( String uri ) throws AlignmentException {
String query = null;
BasicAlignment alignment = (BasicAlignment)getAlignment( uri );
String id = stripAlignmentUri( uri );
......@@ -677,89 +709,92 @@ public class CacheImpl {
// We empty cached date
alignment.setExtension( SVCNS, CACHED, (String)null );
// Try to store at most 3 times.
// Otherwise, an exception EOFException will be thrown (relation with Jetty???)
// [JE2013: Can we check this?]
for( int i=0; i < 3 ; i++ ) {
st = createStatement();
try {
logger.debug( "Storing alignment {}as {}", uri, id );
conn.setAutoCommit( false );
query = "INSERT INTO alignment " +
"(id, type, level) " +
"VALUES (" +quote(id)+","+quote(alignment.getType())+","+quote(alignment.getLevel()) +")";
st.executeUpdate(query);
recordOntology( st, id, true,
alignment.getOntology1URI(),
alignment.getFile1(),
alignment.getOntologyObject1() );
recordOntology( st, id, false,
alignment.getOntology2URI(),
alignment.getFile2(),
alignment.getOntologyObject2() );
// store dependencies
for ( String[] ext : alignment.getExtensions() ) {
String turi = ext[0];
String tag = ext[1];
String val = ext[2];
query = "INSERT INTO extension " +
"(id, uri, tag, val) " +
"VALUES (" + quote(id) + "," + quote(turi) + "," + quote(tag) + "," + quote(val) + ")";
try {
// Try to store at most 3 times.
// Otherwise, an exception EOFException will be thrown (relation with Jetty???)
// [JE2013: Can we check this?]
for( int i=0; i < 3 ; i++ ) {
try {
st = createStatement();
logger.debug( "Storing alignment {}as {}", uri, id );
conn.setAutoCommit( false );
query = "INSERT INTO alignment " +
"(id, type, level) " +
"VALUES (" +quote(id)+","+quote(alignment.getType())+","+quote(alignment.getLevel()) +")";
st.executeUpdate(query);
}
for( Cell c : alignment ) {
String cellid = null;
if ( c.getObject1() != null && c.getObject2() != null ){
cellid = c.getId();
if ( cellid != null ){
if ( cellid.startsWith("#") ) {
cellid = alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ) + cellid;
}
} else if ( c.getExtensions() != null ) {
// JE: In case of extensions create an ID
cellid = generateCellId();
}
else cellid = "";
String uri1 = c.getObject1AsURI(alignment).toString();
String uri2 = c.getObject2AsURI(alignment).toString();
String strength = c.getStrength() + ""; // crazy Java
String sem;
if ( !c.getSemantics().equals("first-order") )
sem = c.getSemantics();
else sem = "";
String rel = ((BasicRelation)c.getRelation()).getRelation();
query = "INSERT INTO cell " +
"(id, cell_id, uri1, uri2, measure, semantics, relation) " +
"VALUES (" + quote(id) + "," + quote(cellid) + "," + quote(uri1) + "," + quote(uri2) + "," + quote(strength) + "," + quote(sem) + "," + quote(rel) + ")";
recordOntology( st, id, true,
alignment.getOntology1URI(),
alignment.getFile1(),
alignment.getOntologyObject1() );
recordOntology( st, id, false,
alignment.getOntology2URI(),
alignment.getFile2(),
alignment.getOntologyObject2() );
// store dependencies
for ( String[] ext : alignment.getExtensions() ) {
String turi = ext[0];
String tag = ext[1];
String val = ext[2];
query = "INSERT INTO extension " +
"(id, uri, tag, val) " +
"VALUES (" + quote(id) + "," + quote(turi) + "," + quote(tag) + "," + quote(val) + ")";
st.executeUpdate(query);
}
if ( cellid != null && !cellid.equals("") && c.getExtensions() != null ) {
// Store extensions
for ( String[] ext : c.getExtensions() ) {
String turi = ext[0];
String tag = ext[1];
String val = ext[2];
query = "INSERT INTO extension " +
"(id, uri, tag, val) " +
"VALUES (" + quote(cellid) + "," + quote(turi) + "," + quote(tag) + "," + quote(val) + ")";
for( Cell c : alignment ) {
String cellid = null;
if ( c.getObject1() != null && c.getObject2() != null ){
cellid = c.getId();
if ( cellid != null ){
if ( cellid.startsWith("#") ) {
cellid = alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ) + cellid;
}
} else if ( c.getExtensions() != null ) {
// JE: In case of extensions create an ID
cellid = generateCellId();
}
else cellid = "";
String uri1 = c.getObject1AsURI(alignment).toString();
String uri2 = c.getObject2AsURI(alignment).toString();
String strength = c.getStrength() + ""; // crazy Java
String sem;
if ( !c.getSemantics().equals("first-order") )
sem = c.getSemantics();
else sem = "";
String rel = ((BasicRelation)c.getRelation()).getRelation();
query = "INSERT INTO cell " +
"(id, cell_id, uri1, uri2, measure, semantics, relation) " +
"VALUES (" + quote(id) + "," + quote(cellid) + "," + quote(uri1) + "," + quote(uri2) + "," + quote(strength) + "," + quote(sem) + "," + quote(rel) + ")";
st.executeUpdate(query);
}
if ( cellid != null && !cellid.equals("") && c.getExtensions() != null ) {
// Store extensions
for ( String[] ext : c.getExtensions() ) {
String turi = ext[0];
String tag = ext[1];
String val = ext[2];
query = "INSERT INTO extension " +
"(id, uri, tag, val) " +
"VALUES (" + quote(cellid) + "," + quote(turi) + "," + quote(tag) + "," + quote(val) + ")";
st.executeUpdate(query);
}
}
}
st.close();
} catch ( SQLException sex ) {
logger.warn( "SQLError", sex );
conn.rollback();
throw new AlignmentException( "SQLException", sex );
} finally {
conn.setAutoCommit( true );
}
} catch ( SQLException sex ) {
logger.warn( "SQLError", sex );
conn.rollback();
throw sex;
} finally {
conn.setAutoCommit( true );
break;
}
break;
} catch (SQLException sqlex) {
throw new AlignmentException( "SQLRollBack issue", sqlex );
}
st.close();
// We reset cached date
resetCacheStamp(alignment);
}
......@@ -872,6 +907,27 @@ public class CacheImpl {
st.executeUpdate("CREATE TABLE cell(id VARCHAR(100), cell_id VARCHAR(255), uri1 VARCHAR(255), uri2 VARCHAR(255), semantics VARCHAR(30), measure VARCHAR(20), relation VARCHAR(255))");
st.executeUpdate("CREATE TABLE extension(id VARCHAR(100), uri VARCHAR(200), tag VARCHAR(50), val VARCHAR(500))");
st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), prefix VARCHAR (50), edit BOOLEAN, version VARCHAR(5))");
/*
// EDOAL
st.executeUpdate("CREATE TABLE instexpr (intid VARCHAR(50), id VARCHAR(250), var VARCHAR(250))");
st.executeUpdate("CREATE TABLE instlist (joinid VARCHAR(50), intid VARCHAR(250))"); //intid in instexpr
st.executeUpdate("CREATE TABLE classexpr (intid VARCHAR(50), type VARCHAR(10), joinid VARCHAR(250), var VARCHAR(250))");
// type=uri: joinid = uri
// type=id: joinid = uri
// type\in classconst: joinid = joinid in classlist
// type\in classrest: joinid = id in classrest
st.executeUpdate("CREATE TABLE classlist (joinid VARCHAR(50), intid VARCHAR(250))"); //intid in classexpr
st.executeUpdate("CREATE TABLE classrest (joinid VARCHAR(50), arg1 VARCHAR(250), arg2 VARCHAR(250))");
*/
st.close();
// Register *DATABASE* Because of the values (that some do not like), this is a special statement
......
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