diff --git a/html/relnotes.html b/html/relnotes.html
index 2c76d86af54e5bc58deb1d73707a032c7130d576..f5474ae812b6ebed1a7c5ee7c20dbceb6cdbefc4 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -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., <, >, =, % (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<Alignment></tt> (server)</tt>
+ to <tt>Collection<Alignment></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 Rhône-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<Cell> (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>
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 4765c00fd75f6362bdedebff83ad8390b1c4be8d..75a33ce33908cfc6b3f3314f2f6a3c17cef53cd2 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -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 );
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/Cache.java b/src/fr/inrialpes/exmo/align/service/Cache.java
new file mode 100644
index 0000000000000000000000000000000000000000..9f9178fc9a8661fd11bca53bd63475470334bd69
--- /dev/null
+++ b/src/fr/inrialpes/exmo/align/service/Cache.java
@@ -0,0 +1,114 @@
+/*
+ * $Id$
+ *
+ * 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;
+
+}
diff --git a/src/fr/inrialpes/exmo/align/service/DBServiceImpl.java b/src/fr/inrialpes/exmo/align/service/DBServiceImpl.java
index 08920dad88c4fcb758df369cb98ec5af4968a968..9008bbd22f6cf78dc4b71cbd7dcfd23a0b0b6083 100644
--- a/src/fr/inrialpes/exmo/align/service/DBServiceImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/DBServiceImpl.java
@@ -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();
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/SQLCache.java
similarity index 83%
rename from src/fr/inrialpes/exmo/align/service/CacheImpl.java
rename to src/fr/inrialpes/exmo/align/service/SQLCache.java
index d44e9e7b83640470d845a0cdee43e8e3cda75492..dacbeea645942971df99fd2962abb413102b6eb8 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/SQLCache.java
@@ -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