From 27caeeb2ff1accc448b6ebc4aee09da56375288d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Mon, 1 Jun 2009 14:10:34 +0000
Subject: [PATCH] - updated to hierarchical storage of libraries - added pretty
value management (server) - Corrected a bug when the server is launched
without -S (server)
---
build.xml | 44 +++---
html/relnotes.html | 19 ++-
.../exmo/align/impl/Annotations.java | 3 +-
.../exmo/align/impl/BasicAlignment.java | 12 +-
.../impl/renderer/HTMLRendererVisitor.java | 8 +-
.../align/service/AServProtocolManager.java | 64 +++++----
.../exmo/align/service/AlignmentId.java | 16 ++-
.../exmo/align/service/AlignmentIds.java | 13 +-
.../exmo/align/service/AlignmentService.java | 8 +-
.../exmo/align/service/CacheImpl.java | 7 +-
.../exmo/align/service/HTMLAServProfile.java | 125 +++++++++++-------
11 files changed, 207 insertions(+), 112 deletions(-)
diff --git a/build.xml b/build.xml
index b47a2455..bce786fd 100644
--- a/build.xml
+++ b/build.xml
@@ -14,22 +14,24 @@
<!-- tested -->
<target name="usage" depends="init">
- <echo message="ant _target_ _options_"/>
- <echo/>
- <echo message="usage: this message"/>
- <echo message="init: sets necessary variables"/>
- <echo message="compile: incrementaly compiles sources"/>
- <echo message="compileall: recompiles all sources"/>
- <echo message="lint: compiles all sources with bug flags on"/>
- <echo message="jar: archives compiled code"/>
- <echo message="test: performs unit tests"/>
- <echo message="zip: creates a new zip file"/>
- <echo message="javadoc: generates documentation"/>
- <echo message="release: releases a new version"/>
- <echo message="svnbranch: copy the version under svn"/>
- <echo message="clean: clean-up before release"/>
- <echo/>
- <echo message=" -Dversion=${version}"/>
+ <echo>ant _target_ _options_
+
+ usage: this message
+ init: sets necessary variables
+ upgrade: retrieve necessary libraries from other projects (local)
+ compile: incrementaly compiles sources
+ compileall: recompiles all sources
+ lint: compiles all sources with bug flags on
+ jar: archives compiled code
+ test: performs unit tests
+ zip: creates a new zip file
+ javadoc: generates documentation
+ release: releases a new version
+ svnbranch: copy the version under svn
+ clean: clean-up before release
+
+ -Dversion=${version}
+ </echo>
</target>
<!-- tested -->
@@ -54,6 +56,12 @@
</target>
+ <target name="upgrade">
+ <copy file="../ontosim/lib/ontosim.jar" todir="lib/ontosim"
+ filtering="false"/>
+ <echo message="mappingapi is only updated from its directory"/>
+ </target>
+
<!-- tested -->
<target name="compile" depends="init">
<echo message="Compiling..."/>
@@ -122,7 +130,7 @@
<manifest>
<attribute name="Built-Date" value="${TODAY}"/>
<attribute name="Main-Class" value="fr.inrialpes.exmo.align.util.Procalign"/>
- <attribute name="Class-Path" value="procalign.jar jwnl.jar"/>
+ <attribute name="Class-Path" value="procalign.jar jwnl/jwnl.jar"/>
<attribute name="Implementation-Title" value="Alignment API WordNet support"/>
<attribute name="Implementation-Version" value="${version}"/>
</manifest>
@@ -135,7 +143,7 @@
<manifest>
<attribute name="Built-Date" value="${TODAY}"/>
<attribute name="Main-Class" value="fr.inrialpes.exmo.align.service.AlignmentService"/>
- <attribute name="Class-Path" value="procalign.jar alignwn.jar jade.jar iiop.jar http.jar mysql-connector-java-5.0.3-bin.jar servlet-api.jar jetty.jar jetty-util.jar"/>
+ <attribute name="Class-Path" value="procalign.jar alignwn.jar jade/jade.jar iiop.jar jade/http.jar jdbc/mysql-connector-java-5.0.3-bin.jar servlet/servlet-api.jar jetty/jetty.jar jetty/jetty-util.jar"/>
<attribute name="Implementation-Title" value="Alignment server"/>
<attribute name="Implementation-Version" value="${version}"/>
</manifest>
diff --git a/html/relnotes.html b/html/relnotes.html
index ed81820e..c1d929c9 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -33,8 +33,6 @@ the main ruptures that will appear:
support from OMWGAlignments which are currently based on Jena, (c)
release of separated subpackages offering OWL API 1.0, OWL API 2.0,
Jena 2.5, OLGraph and SKOS. (onto)</li>
-<li>Addition of the notion of <tt>OntologyNetwork</tt> made of a set of
- ontologies and alignments within the API.</li>
<li>Creation of a different project, OntoSim, for supporting distances
and similarities across ontologies. This project will adopt several
parts of the current implementation part. It will have no impact on
@@ -46,6 +44,7 @@ Other less radical changes include:
<li>Implementation of <tt>Relation</tt> and <tt>Confidence</tt> interfaces </li>
<li>Implement <tt>onto</tt> support in database store (server)</li>
<li>Move <tt>OLgraphs</tt> as HeavyLoadedOntology (onto)</li>
+<li>Integrate OWMG as part of the Alignment API code (impl)</li>
<li>Implement database store for OMWG Language (server)</li>
</ul>
Currently the development and maintainance of 3 versions continue.
@@ -58,8 +57,6 @@ Currently the development and maintainance of 3 versions continue.
<li>Providing a <tt>DiffAlign( al1, al2 )</tt> operation and interface
(util)</li>
<li>Added get-aligned to interface (server)</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>Improve HTML interface layout and usability (server)</li>
<li>Implement metadata edition (server)</li>
<li>Implement correspondence selection (server)</li>
@@ -72,8 +69,16 @@ Currently the development and maintainance of 3 versions continue.
<h2>Current SVN trunk version</h2>
-<!--h2>Version 3.7/4.0 (95x): xx/09/2009 - Tring</h2-->
-<!--h2>Version 3.7/4.0 (95x): xx/09/2009 - Rouquine carmélite</h2-->
+<!--h2>Version 3.8/4.0/4.1 (1xxx): xx/09/2009 - Tring</h2-->
+<!--h2>Version 3.7/4.0 (1xxx): xx/09/2009 - Rouquine carmélite</h2-->
+
+<p>
+<ul compact="1">
+<li>Added pretty-printing of names in server (server)</li>
+<li>Reorganised the lib directory hierarchically (build)</li>
+<li>Corrected a bug when the server is launched without -S (server)</li>
+</ul>
+</p>
<h2>Version 3.6 (988): 27/05/2009 - Sabai sabai</h2>
@@ -89,6 +94,8 @@ If you want to stay with WordNet-2.0, you need to replace the jwnl.jar
<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>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>
diff --git a/src/fr/inrialpes/exmo/align/impl/Annotations.java b/src/fr/inrialpes/exmo/align/impl/Annotations.java
index 5c99b4c8..8b3204d1 100644
--- a/src/fr/inrialpes/exmo/align/impl/Annotations.java
+++ b/src/fr/inrialpes/exmo/align/impl/Annotations.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2008
+ * Copyright (C) INRIA, 2008-2009
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -26,6 +26,7 @@ public class Annotations {
public static String METHOD = "method";
public static String TIME = "time";
public static String ID = "id";
+ public static String PRETTY = "pretty";
/* Set to true for rejecting the use of deprecated (non deterministic) primitives */
public static boolean STRICT_IMPLEMENTATION = false;
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 030d1851..0a89a39e 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -646,11 +646,15 @@ public class BasicAlignment implements Alignment {
for ( Object ext : ((BasicParameters)extensions).getValues() ){
result.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
- String oldid = result.getExtension( Annotations.ALIGNNS, "id" );
+ String oldid = result.getExtension( Annotations.ALIGNNS, Annotations.ID );
if ( oldid != null && !oldid.equals("") ) {
result.setExtension( Annotations.ALIGNNS, "derivedFrom", oldid );
- result.getExtensions().unsetParameter( Annotations.ALIGNNS+"id" );
+ result.getExtensions().unsetParameter( Annotations.ALIGNNS+Annotations.ID );
}
+ String pretty = result.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pretty != null ){
+ result.setExtension( Annotations.ALIGNNS, Annotations.PRETTY, pretty+"/inverted" );
+ };
result.setExtension( Annotations.ALIGNNS, "method", "http://exmo.inrialpes.fr/align/impl/BasicAlignment#inverse" );
for ( Enumeration e = namespaces.getNames() ; e.hasMoreElements(); ){
String label = (String)e.nextElement();
@@ -696,10 +700,10 @@ public class BasicAlignment implements Alignment {
for ( Object ext : ((BasicParameters)extensions).getValues() ){
align.setExtension( ((String[])ext)[0], ((String[])ext)[1], ((String[])ext)[2] );
}
- String oldid = align.getExtension( Annotations.ALIGNNS, "id" );
+ String oldid = align.getExtension( Annotations.ALIGNNS, Annotations.ID );
if ( oldid != null && !oldid.equals("") ) {
align.setExtension( Annotations.ALIGNNS, "derivedFrom", oldid );
- align.getExtensions().unsetParameter( Annotations.ALIGNNS+"id" );
+ align.getExtensions().unsetParameter( Annotations.ALIGNNS+Annotations.ID );
}
align.setExtension( Annotations.ALIGNNS, "method", this.getClass().getName()+"#clone" );
for ( Enumeration e = namespaces.getNames() ; e.hasMoreElements(); ){
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
index 92d93ec0..d6d5946f 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
@@ -98,7 +98,13 @@ public class HTMLRendererVisitor implements AlignmentVisitor
writer.print("\n xmlns:"+nslist.get(k)+"='"+k+"'");
}
writer.print(">\n<head><title>Alignment</title></head>\n<body>\n");
- writer.print("<h1></h1>\n");
+ String id = align.getExtension( Annotations.ALIGNNS, Annotations.ID );
+ String pid = align.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) {
+ writer.print("<h1>"+id+"</h1>\n");
+ } else {
+ writer.print("<h1>"+id+" ("+pid+")</h1>\n");
+ }
writer.print("<div typeof=\"align:Alignment\">\n");
writer.print("<h2>Alignment metadata</h2>\n");
writer.print("<table border=\"0\">\n");
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 4f37bcc5..03e093e4 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -185,23 +185,29 @@ public class AServProtocolManager {
file = (String)params.getParameter("filename");
if ( file != null && !file.equals("") ) name = "file://"+file;
}
- //if (debgug > 0) System.err.println("Preparing for "+name);
- Alignment init = null;
+ //if ( debug > 0 ) System.err.println("Preparing for "+name);
+ Alignment al = null;
try {
- //if (debug > 0) System.err.println(" Parsing init");
+ //if (debug > 0) System.err.println(" Parsing alignment");
AlignmentParser aparser = new AlignmentParser(0);
- init = aparser.parse( name );
- //if (debug > 0) System.err.println(" Init parsed");
+ al = aparser.parse( name );
+ //if (debug > 0) System.err.println(" Alignment parsed");
} catch (Exception e) {
return new UnreachableAlignment(newId(),mess,myId,mess.getSender(),name,(Parameters)null);
}
+ // We preserve the pretty tag within the loaded ontology
+ String pretty = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pretty == null ) pretty = (String)params.getParameter("pretty");
+ if ( pretty != null ) {
+ al.setExtension( Annotations.ALIGNNS, Annotations.PRETTY, pretty );
+ }
// register it
- String id = alignmentCache.recordNewAlignment( init, true );
+ String id = alignmentCache.recordNewAlignment( al, true );
// if the file has been uploaded: discard it
- if ( init != null && file != null ) {
+ if ( al != null && al != null ) {
// try unlink
}
- return new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
+ return new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null,pretty);
}
// Implements: align
@@ -269,9 +275,11 @@ public class AServProtocolManager {
if ( alignments != null && params.getParameter("force") == null ) {
for ( Iterator it = alignments.iterator(); it.hasNext() ; ){
Alignment al = ((Alignment)it.next());
- if ( al.getExtension( Annotations.ALIGNNS, Annotations.METHOD ).equals(method) )
- return new AlignmentId(newId(),mess,myId,mess.getSender(),al.getExtension( Annotations.ALIGNNS, Annotations.ID ),(Parameters)null);
-
+ if ( al.getExtension( Annotations.ALIGNNS, Annotations.METHOD ).equals(method) ) {
+ return new AlignmentId(newId(),mess,myId,mess.getSender(),
+ al.getExtension( Annotations.ALIGNNS, Annotations.ID ),(Parameters)null,
+ al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY ) );
+ }
}
}
return (Message)null;
@@ -303,11 +311,12 @@ public class AServProtocolManager {
return new ErrorMsg(newId(),mess,myId,mess.getSender(),"MalformedURI problem",(Parameters)null);
}; //done below
String msg = "";
- for( Iterator it = alignments.iterator(); it.hasNext(); ){
- msg += ((Alignment)it.next()).getExtension( Annotations.ALIGNNS, Annotations.ID );
- msg += " ";
+ String prettys = "";
+ for ( Alignment al : alignments ) {
+ msg += al.getExtension( Annotations.ALIGNNS, Annotations.ID )+" ";
+ prettys += al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
}
- return new AlignmentIds(newId(),mess,myId,mess.getSender(),msg,(Parameters)null);
+ return new AlignmentIds(newId(),mess,myId,mess.getSender(),msg,(Parameters)null,prettys);
}
// ABSOLUTELY NOT IMPLEMENTED
@@ -430,7 +439,8 @@ public class AServProtocolManager {
}
// register by them
// Could also be an AlreadyStoredAlignment error
- return new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
+ return new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null,
+ al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY ));
} catch (Exception e) {
return new UnknownAlignment(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
}
@@ -487,8 +497,13 @@ public class AServProtocolManager {
catch (AlignmentException e) {
return new ErrorMsg(newId(),mess,myId,mess.getSender(),"dummy//",(Parameters)null);
}
+ String pretty = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pretty != null ){
+ al.setExtension( Annotations.ALIGNNS, Annotations.PRETTY, pretty+"/trimmed "+threshold );
+ };
String newId = alignmentCache.recordNewAlignment( al, true );
- return new AlignmentId(newId(),mess,myId,mess.getSender(),newId,(Parameters)null);
+ return new AlignmentId(newId(),mess,myId,mess.getSender(),newId,(Parameters)null,
+ al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY ));
}
public Message harden( Message mess ){
@@ -512,7 +527,8 @@ public class AServProtocolManager {
return new ErrorMsg(newId(),mess,myId,mess.getSender(),"dummy//",(Parameters)null);
}
String newId = alignmentCache.recordNewAlignment( al, true );
- return new AlignmentId(newId(),mess,myId,mess.getSender(),newId,(Parameters)null);
+ return new AlignmentId(newId(),mess,myId,mess.getSender(),newId,(Parameters)null,
+ al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY ));
}
public Message meet( Message mess ){
@@ -894,16 +910,15 @@ public class AServProtocolManager {
java.lang.reflect.Constructor alignmentConstructor = alignmentClass.getConstructor(cparams);
AlignmentProcess aresult = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
try {
-
aresult.init( uri1, uri2 );
-
long time = System.currentTimeMillis();
-
aresult.align( init, params ); // add opts
-
long newTime = System.currentTimeMillis();
-
aresult.setExtension( Annotations.ALIGNNS, Annotations.TIME, Long.toString(newTime - time) );
+ aresult.setExtension( Annotations.ALIGNNS, Annotations.TIME, Long.toString(newTime - time) );
+ String pretty = (String)params.getParameter( "pretty" );
+ if ( pretty != null )
+ aresult.setExtension( Annotations.ALIGNNS, Annotations.PRETTY, pretty );
} catch (AlignmentException e) {
// The unreachability test has already been done
// JE 15/1/2009: commented the unreachability test
@@ -918,7 +933,8 @@ public class AServProtocolManager {
}
// ask to store A'
alignmentCache.recordNewAlignment( id, aresult, true );
- result = new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
+ result = new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null,
+ aresult.getExtension( Annotations.ALIGNNS, Annotations.PRETTY ));
} catch (ClassNotFoundException e) {
result = new RunTimeError(newId(),mess,myId,mess.getSender(),"Class not found: "+method,(Parameters)null);
} catch (NoSuchMethodException e) {
diff --git a/src/fr/inrialpes/exmo/align/service/AlignmentId.java b/src/fr/inrialpes/exmo/align/service/AlignmentId.java
index 2b18a032..80fe7cad 100644
--- a/src/fr/inrialpes/exmo/align/service/AlignmentId.java
+++ b/src/fr/inrialpes/exmo/align/service/AlignmentId.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2006-2008
+ * Copyright (C) INRIA, 2006-2009
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -33,10 +33,16 @@ public class AlignmentId extends Success {
public AlignmentId ( int surr, Message rep, String from, String to, String cont, Parameters param ) {
super( surr, rep, from, to, cont, param );
}
+ public AlignmentId ( int surr, Message rep, String from, String to, String cont, Parameters param, String pretty ) {
+ super( surr, rep, from, to, cont, param );
+ this.pretty = pretty;
+ }
public String getPretty( String alid ) {
- // getextension "pretty"
- // if no pretty then
- return alid;
+ if ( pretty == null ) {
+ return alid;
+ } else {
+ return alid+" ("+pretty+")";
+ }
};
public String HTMLString(){
return "Alignment ID: <a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+getContent()+"\">"+getPretty(getContent())+"</a> ";
@@ -45,7 +51,7 @@ public class AlignmentId extends Success {
return "Alignment ID: <a href=\"../rest/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+getContent()+"\">"+getPretty(getContent())+"</a> ";
}
public String RESTString(){
- return "<alid>"+content+"</alid>";
+ return "<alid>"+getContent()+"</alid>";
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/AlignmentIds.java b/src/fr/inrialpes/exmo/align/service/AlignmentIds.java
index e0485e0d..a6eed356 100644
--- a/src/fr/inrialpes/exmo/align/service/AlignmentIds.java
+++ b/src/fr/inrialpes/exmo/align/service/AlignmentIds.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2006-2008
+ * Copyright (C) INRIA, 2006-2009
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -28,14 +28,23 @@ import org.semanticweb.owl.align.Parameters;
public class AlignmentIds extends Success {
+ String pretty = null;
+
public AlignmentIds ( int surr, Message rep, String from, String to, String cont, Parameters param ) {
super( surr, rep, from, to, cont, param );
}
+ public AlignmentIds ( int surr, Message rep, String from, String to, String cont, Parameters param, String pretty ) {
+ super( surr, rep, from, to, cont, param );
+ this.pretty = pretty;
+ }
public String HTMLString(){
String result = "Alignment Ids: <ul>";
String id[] = content.split(" ");
+ String pid[] = pretty.split("???");
for ( int i = id.length-1; i >= 0; i-- ){
- result += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id[i]+"\">"+id[i]+"</a></li>";
+ result += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id[i]+"\">";
+ if ( pid != null && !pid[i].equals("") ) result += " ("+pid[i]+")";
+ result += "</a></li>";
}
return result += "</ul>";
}
diff --git a/src/fr/inrialpes/exmo/align/service/AlignmentService.java b/src/fr/inrialpes/exmo/align/service/AlignmentService.java
index 5847aaad..a99d758f 100644
--- a/src/fr/inrialpes/exmo/align/service/AlignmentService.java
+++ b/src/fr/inrialpes/exmo/align/service/AlignmentService.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2006-2008
+ * Copyright (C) INRIA, 2006-2009
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -116,11 +116,11 @@ public class AlignmentService {
// Connect database
if( DBMS.equals("postgres") ) {
- System.err.println("postgres");
+ if ( debug > 0 ) System.err.println("postgres driver");
DBPORT = "5432";
connection = new DBServiceImpl( "org.postgresql.Driver" , "jdbc:postgresql", DBPORT );
} else {
- System.err.println("mysql");
+ if ( debug > 0 ) System.err.println("mysql driver");
DBPORT = "3306";
connection = new DBServiceImpl( "com.mysql.jdbc.Driver" , "jdbc:mysql", DBPORT );
}
@@ -206,6 +206,8 @@ public class AlignmentService {
public Parameters readParameters( String[] args ) {
Parameters params = new BasicParameters();
+ // Default values
+ params.setParameter( "host", HOST );
// Read parameters
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 0ebc5213..54a78af5 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -2,7 +2,7 @@
* $Id$
*
* Copyright (C) Seungkeun Lee, 2006
- * Copyright (C) INRIA Rhône-Alpes, 2006-2008
+ * Copyright (C) INRIA, 2006-2009
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -25,6 +25,7 @@ import java.util.Enumeration;
import java.util.Iterator;
import java.util.Hashtable;
import java.util.Vector;
+import java.util.Collection;
import java.util.Set;
import java.util.HashSet;
import java.util.Date;
@@ -198,6 +199,10 @@ public class CacheImpl {
return alignmentTable.elements();
}
+ protected Collection<Alignment> alignments() {
+ return alignmentTable.values();
+ }
+
protected void flushCache() {// throws AlignmentException
for ( Alignment al : alignmentTable.values() ){
if ( al.getExtension( SVCNS, CACHED ) != ""
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index 3b3e812b..465ffbb9 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -1,4 +1,4 @@
- /*
+/*
* $Id$
*
* Copyright (C) INRIA, 2006-2009.
@@ -401,29 +401,32 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
if ( perf.equals("listalignments") ){
msg = "<h1>Available alignments</h1><ul compact=\"1\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID );
- msg += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id+"\">"+id+"</a></li>";
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID );
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id+"\">"+pid+"</a></li>";
}
msg += "</ul>";
} else if ( perf.equals("listmethods") ){
msg = "<h1>Embedded classes</h1>\n<h2>Methods</h2><ul compact=\"1\">";
- for( Iterator it = manager.listmethods().iterator(); it.hasNext(); ) {
- msg += "<li>"+it.next()+"</li>";
+ for( String m : manager.listmethods() ) {
+ msg += "<li>"+m+"</li>";
}
msg += "</ul>";
msg += "<h2>Renderers</h2><ul compact=\"1\">";
- for( Iterator it = manager.listrenderers().iterator(); it.hasNext(); ) {
- msg += "<li>"+it.next()+"</li>";
+ for( String m : manager.listrenderers() ) {
+ msg += "<li>"+m+"</li>";
}
msg += "</ul>";
msg += "<h2>Services</h2><ul compact=\"1\">";
- for( Iterator it = manager.listservices().iterator(); it.hasNext(); ) {
- msg += "<li>"+it.next()+"</li>";
+ for( String m : manager.listservices() ) {
+ msg += "<li>"+m+"</li>";
}
msg += "</ul>";
msg += "<h2>Evaluators</h2><ul compact=\"1\">";
- for( Iterator it = manager.listevaluators().iterator(); it.hasNext(); ) {
- msg += "<li>"+it.next()+"</li>";
+ for( String m : manager.listevaluators() ) {
+ msg += "<li>"+m+"</li>";
}
msg += "</ul>";
} else if ( perf.equals("prmsqlquery") ){
@@ -494,7 +497,9 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
params.setParameter("id", id);
if ( !manager.storedAlignment( new Message(newId(),(Message)null,myId,serverId,"", params ) ) ){
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ String pid = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
}
msg += "</select><br />";
@@ -525,11 +530,14 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg ="<h1>Trim alignments</h1><form action=\"cut\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){
- msg += "<option selected=\"1\" value=\""+id+"\">"+id+"</option>";
+ msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
} else {
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
}
msg += "</select><br />";
@@ -550,8 +558,11 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg ="<h1>Inverse alignment</h1><form action=\"inv\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
msg += "</select><br />";
msg += "<input type=\"submit\" name=\"action\" value=\"Invert\"/><br /></form>";
@@ -572,22 +583,25 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
String readonlyOnto = "";
//Ontologies from Cupboard may be already provided here.
if((String)params.getParameter("restful") != null && ((String)params.getParameter("renderer")).equals("HTML") ){
- RESTOnto1 = (String)params.getParameter("onto1");
- RESTOnto2 = (String)params.getParameter("onto2");
- //if(RESTOnto1 != null && !RESTOnto1.equals("") && RESTOnto2 != null && !RESTOnto2.equals(""))
- readonlyOnto = "readonly=\"readonly\"";
- }
- msg ="<h1>Match ontologies</h1><form action=\"match\">Ontology 1: <input type=\"text\" name=\"onto1\" size=\"80\" value="+RESTOnto1+ " " + readonlyOnto+"> (uri)<br />Ontology 2: <input type=\"text\" name=\"onto2\" size=\"80\" value="+RESTOnto2+ " " + readonlyOnto+ "> (uri)<br /><small>These are the URL of places where to find these ontologies. They must be reachable by the server (i.e., file:// URI are acceptable if they are on the server)</small><br /><!--input type=\"submit\" name=\"action\" value=\"Find\"/><br /-->Methods: <select name=\"method\">";
- for( Iterator it = manager.listmethods().iterator(); it.hasNext(); ) {
- String id = (String)it.next();
+ RESTOnto1 = (String)params.getParameter("onto1");
+ RESTOnto2 = (String)params.getParameter("onto2");
+ //if(RESTOnto1 != null && !RESTOnto1.equals("") && RESTOnto2 != null && !RESTOnto2.equals(""))
+ readonlyOnto = "readonly=\"readonly\"";
+ }
+ msg ="<h1>Match ontologies</h1><form action=\"match\">Ontology 1: <input type=\"text\" name=\"onto1\" size=\"80\" value="+RESTOnto1+" " +readonlyOnto+"> (uri)<br />Ontology 2: <input type=\"text\" name=\"onto2\" size=\"80\" value="+RESTOnto2+" "+readonlyOnto+ "> (uri)<br /><small>These are the URL of places where to find these ontologies. They must be reachable by the server (i.e., file:// URI are acceptable if they are on the server)</small><br /><!--input type=\"submit\" name=\"action\" value=\"Find\"/><br /-->Methods: <select name=\"method\">";
+ for( String id : manager.listmethods() ) {
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br />Initial alignment id: <select name=\"id\"><option value=\"\" selected=\"1\"></option>";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
msg += "</select><br />";
+ msg += "Pretty name: <input type=\"text\" name=\"pretty\" size=\"80\"/><br />";
msg += "<input type=\"submit\" name=\"action\" value=\"Match\"/>";
msg += " <input type=\"checkbox\" name=\"force\" /> Force <input type=\"checkbox\" name=\"async\" /> Asynchronous<br />";
msg += "Additional parameters:<br /><input type=\"text\" name=\"paramn1\" size=\"15\"/> = <input type=\"text\" name=\"paramv1\" size=\"65\"/><br /><input type=\"text\" name=\"paramn2\" size=\"15\"/> = <input type=\"text\" name=\"paramv2\" size=\"65\"/><br /><input type=\"text\" name=\"paramn3\" size=\"15\"/> = <input type=\"text\" name=\"paramv3\" size=\"65\"/><br /><input type=\"text\" name=\"paramn4\" size=\"15\"/> = <input type=\"text\" name=\"paramv4\" size=\"65\"/></form>";
@@ -614,17 +628,19 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Retrieve alignment</h1><form action=\"retrieve\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){
- msg += "<option selected=\"1\" value=\""+id+"\">"+id+"</option>";
+ msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
} else {
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
}
msg += "</select><br />";
msg += "Rendering: <select name=\"method\">";
- for( Iterator it = manager.listrenderers().iterator(); it.hasNext(); ) {
- String id = (String)it.next();
+ for( String id : manager.listrenderers() ) {
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "</select><br /><input type=\"submit\" value=\"Retrieve\"/></form>";
@@ -642,8 +658,11 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Retrieve alignment metadata</h1><form action=\"metadata\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
msg += "</select><br /><input type=\"submit\" value=\"Get metadata\"/></form>";
} else if ( perf.equals("metadata") ) {
@@ -663,13 +682,14 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
// Alignment in HTML can be rendre or metadata+tuples
} else if ( perf.equals("prmload") ) {
// Should certainly be good to offer store as well
- msg = "<h1>Load an alignment</h1><form action=\"load\">Alignment URL: <input type=\"text\" name=\"url\" size=\"80\"/> (uri)<br /><small>This is the URL of the place where to find this alignment. It must be reachable by the server (i.e., file:// URI is acceptable if it is on the server).</small><br /><input type=\"submit\" value=\"Load\"/></form>";
+ msg = "<h1>Load an alignment</h1><form action=\"load\">Alignment URL: <input type=\"text\" name=\"url\" size=\"80\"/> (uri)<br /><small>This is the URL of the place where to find this alignment. It must be reachable by the server (i.e., file:// URI is acceptable if it is on the server).</small><br />Pretty name: <input type=\"text\" name=\"pretty\" size=\"80\"/><br /><input type=\"submit\" value=\"Load\"/></form>";
//msg += "Alignment file: <form ENCTYPE=\"text/xml; charset=utf-8\" action=\"loadfile\" method=\"POST\">";
msg += "Alignment file: <form enctype=\"multipart/form-data\" action=\"load\" method=\"POST\">";
- msg += " <input type=\"hidden\" name=\"MAX_FILE_SIZE\" value=\""+MAX_FILE_SIZE+"\"/>";
+ msg += "<input type=\"hidden\" name=\"MAX_FILE_SIZE\" value=\""+MAX_FILE_SIZE+"\"/>";
msg += "<input name=\"content\" type=\"file\" size=\"35\">";
msg += "<br /><small>NOTE: Max file size is "+(MAX_FILE_SIZE/1024)+"KB; this is experimental but works</small><br />";
- msg += " <input type=\"submit\" Value=\"Upload\">";
+ msg += "Pretty name: <input type=\"text\" name=\"pretty\" size=\"80\"/><br />";
+ msg += "<input type=\"submit\" Value=\"Upload\">";
msg += " </form>";
} else if ( perf.equals("load") ) {
// load
@@ -684,8 +704,11 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Translate query</h1><form action=\"translate\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
msg += "</select><br />";
msg += "SPARQL query:<br /> <textarea name=\"query\" rows=\"20\" cols=\"80\">PREFIX foaf: <http://xmlns.com/foaf/0.1/>\nSELECT *\nFROM <>\nWHERE {\n\n}</textarea> (SPARQL)<br /><small>A SPARQL query (PREFIX prefix: <uri> SELECT variables FROM <url> WHERE { triples })</small><br /><input type=\"submit\" value=\"Translate\"/></form>";
@@ -704,8 +727,11 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Retrieve alignment metadata</h1><form action=\"metadata\">";
msg += "Alignment id: <select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
msg += "</select><br /><input type=\"submit\" value=\"Get metadata\"/></form>";
} else if ( perf.equals("metadata") ) {
@@ -724,21 +750,26 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "Alignment to evaluate: ";
msg += "<select name=\"id\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
msg += "</select><br />";
msg +="Reference alignment: ";
msg += "<select name=\"ref\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
- String id = ((Alignment)e.nextElement()).getExtension( Annotations.ALIGNNS, Annotations.ID);
- msg += "<option value=\""+id+"\">"+id+"</option>";
+ Alignment al = (Alignment)e.nextElement();
+ String id = al.getExtension( Annotations.ALIGNNS, Annotations.ID);
+ String pid = al.getExtension( Annotations.ALIGNNS, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<option value=\""+id+"\">"+pid+"</option>";
}
msg += "</select><br />";
msg += "Evaluator: ";
msg += "<select name=\"method\">";
- for( Iterator it = manager.listevaluators().iterator(); it.hasNext(); ) {
- String id = (String)it.next();
+ for( String id : manager.listevaluators() ) {
msg += "<option value=\""+id+"\">"+id+"</option>";
}
msg += "<br /><input type=\"submit\" name=\"action\" value=\"Evaluate\"/>\n";
--
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