diff --git a/build.xml b/build.xml
index ccd41462e945a585c0a11a3f277f08fad3176c2c..ae3e3dbac1e0f6053d8c856f83ac0b9e1881701c 100644
--- a/build.xml
+++ b/build.xml
@@ -54,7 +54,7 @@
<target name="versionnumber" depends="bind" description="Establishes the version number">
<tstamp><format locale="fr,fr" pattern="dd/MM/yyyy" property="date"/></tstamp>
<property name="version.major" value="4"/>
- <property name="version.minor" value="4"/>
+ <property name="version.minor" value="5"/>
<property name="copyyear" value="2003-2013"/>
<!-- first attempt -->
<exec executable="svnversion" outputproperty="svn.rev" failifexecutionfails="false"/>
diff --git a/html/aserv.html b/html/aserv.html
index 3998f5995d668780a5d6c0a99531e7844a6c4bd9..14a8bece908df8fa1a5e68fd5d71e72b740e7c43 100644
--- a/html/aserv.html
+++ b/html/aserv.html
@@ -11,7 +11,7 @@
<p>An extensive presentation of the alignment API can be
found at <a href="http://gforge.inria.fr/docman/?group_id=117">http://gforge.inria.fr/docman/?group_id=117</a>. We also have
- an on-line <a href="tutorial/tutorial1/server/">tutorial</a> on using it.</p>
+ an on-line <a href="tutorial/tutorial1/server.html">tutorial</a> on using it.</p>
<h2>Requirements</h2>
@@ -70,7 +70,6 @@ The alignment server is then available through HTTP with:
The possible switches to the server launcher are:
<div class="terminal">
$ java -jar lib/alignsvc.jar -h
-usage: AlignmentService [options]
options are:
--html[=port] -H[port] Launch HTTP service
--jade[=port] -A[port] Launch Agent service
@@ -85,11 +84,11 @@ options are:
--dbmspass=pwd -p pwd Use DBMS password
--dbmsbase=name -b name Use Database name
--dbms=name -B name Use Database Management System
- --debug[=n] -d[n] Report debug info at level n
+ --uriprefix=uri -f uri Set alignment URIs with this prefix
-Dparam=value Set parameter
--help -h Print this message
-Alignment server 4.3 (1709:1716M) ($Id$)
+Alignment server 4.4 (1835M) ($Id$)
</div>
</p>
diff --git a/html/index.html b/html/index.html
index 6b975ac693810d2913b10f35bbfe87fc81cbc91c..44671d0adc0fb92a54b8f296379a2a5a3992a7de 100644
--- a/html/index.html
+++ b/html/index.html
@@ -15,7 +15,7 @@
[<a href="aserv.html">Server</a>]
<p style="background-color: yellow; text-align: center;">
-New Alignment API 4.4. <a href="http://gforge.inria.fr/frs/?group_id=117">Get it!</a>
+New Alignment API 4.5. <a href="http://gforge.inria.fr/frs/?group_id=117">Get it!</a>
</p>
<h1 class="titre">Alignment API and Alignment Server</h1>
@@ -98,7 +98,7 @@ cannot find such a paper about the Alignment API or one of its sample matcher).
</dl>
</p>
-<h2>Technical documentations</h2>
+<h2>Technical documentation</h2>
<p><dl>
<dt><a href="format.html">Alignment format</a> and
the <a href="edoal.html">Expressive and Declarative Ontology Alignment Language (EDOAL)</a></dt>
@@ -128,7 +128,8 @@ the <a href="edoal.html">Expressive and Declarative Ontology Alignment Language
<dd>Notify your bugs and request features here</dd>
<dt><a href="http://gforge.inria.fr/scm/?group_id=117">SVN access</a></dt>
<dd>You can browse and you can join.</dd>
-<dt><a href="lib.html">Included libraries and dependencies</a></dt>
+<dt><a href="lib.html">Included libraries and dependencies</a> and a
+ <a href="maven.html">small step towards Maven</a></dt>
<dd>Wonderful components that the Alignement API and server use.</dd>
<dt><a href="license.html">License</a></dt>
<dd>Basically, open source (LGPL).</dd>
diff --git a/html/lib.html b/html/lib.html
index a5846d50490efeef5cec65eb65e77198d8dc9fee..e90974a7e7c314fcfd603aa328ce002ac043b9c4 100644
--- a/html/lib.html
+++ b/html/lib.html
@@ -7,7 +7,7 @@
</head>
<body bgcolor="#ffffff">
-<h1 class="titre">Alignment API: Libraries shipped with the package (release 4.0)</h1>
+<h1 class="titre">Alignment API: Libraries shipped with the package (release 4.5)</h1>
<p>The Alignment API uses a number of external libraries. These libraries
are shipped (in the lib directory) with the Alignment API. Each
@@ -63,7 +63,7 @@ This is a simplified view: <a href="img/dependencies.png">click here
<h3>Required for some bundled matching methods</h3>
<dl>
-<dt><a href="http://ontosim.gforge.inria.fr">OntoSim</a> 2.1: ontosim.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt>
+<dt><a href="http://ontosim.gforge.inria.fr">OntoSim</a> 2.3adv: ontosim.jar [<a href="http://www.gnu.org/licenses/old-licenses/lgpl-2.1.html">LGPL</a>]</dt>
<dd>The whole ontosim system requires more libraries, including JWNL. But in our simplest behaviour, these libraries are not needed.</dd>
<dt><a href="http://lucene.apache.org/">Lucene</a> 3.0.2: lucene-core.jar [<a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache</a>]</dt>
<dd>This small part of lucene is used for WordNet matching classes.</dd>
diff --git a/html/relnotes.html b/html/relnotes.html
index 14c8d09b1aa889c8b2dd875d00042521b53e98e4..2d8d20873bc22b95ab0993ca44213decc7dc3f42 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -75,7 +75,8 @@ with a warning:
<!--h2>Version 4.8 (1xxx): ??/??/201x - Antésine</h2-->
<!--h2>Version 4.7 (1xxx): ??/??/201x - Letraset</h2-->
<!--h2>Version 4.6 (1xxx): ??/??/201X - Da lec'h all</h2-->
-<!--h2>Version 4.5 (18xx): ??/03/2013 - Building 16</h2-->
+
+<h2>Version 4.5 (18xx): ??/03/2013 - Building 16</h2>
<p><ul compact="1">
<li>Added several EDOAL-SPARQL renderers (impl)</li>
<li>Added <tt>ontowrap</tt> support in database store (server)</li>
@@ -95,7 +96,7 @@ with a warning:
<li>Simplified and rewritten <tt>SemPRecEvaluator</tt> (impl)</li>
<li>Fixed all issues but IDDL in <a href="tutorial/tutorial4/index.html">tutorial4</a> (impl)</li>
<li>Fixed display bug in <tt>HTMLMetadataRenderer</tt> (impl)</li>
-<li>Upgraded to <span style="color: green">IDDL</span> to 1.4 (lib)</li>
+<li>Upgraded to <span style="color: green">IDDL</span> to 1.5 (lib)</li>
<li>Upgraded to <span style="color: green">OWL API</span> to 3.4.2 (lib)</li>
<li>Upgraded to <span style="color: green">SLF4J</span> to 1.7.2; suppressed slf4j-log4j (lib)</li>
<li>Replaced Pellet by <span style="color: green">HermiT</span> as default reasonner (lib)</li>
diff --git a/lib/align.jar b/lib/align.jar
index 6e698530e0f6ee93f08dbd26e3c1083bcf243b0a..5c9f28a266391e70d16059ceb735cdd2ef6dae36 100644
Binary files a/lib/align.jar and b/lib/align.jar differ
diff --git a/lib/align.pom b/lib/align.pom
index 02ec47859aac64e2268568e139198bbeb4875246..6dacf412524e94078fc038c866bc9739448b6c04 100644
--- a/lib/align.pom
+++ b/lib/align.pom
@@ -17,7 +17,7 @@
<groupId>org.semanticweb.owl</groupId>
<artifactId>align</artifactId>
<version>4.4</version>
- <!-- Rev 1835M 17/03/2013 -->
+ <!-- Rev 1835:1844M 25/03/2013 -->
<name>The Alignment API</name>
<description>The Alignment API is an API for manipulating ontology alignments.</description>
<url>http://alignapi.gforge.inria.fr</url>
diff --git a/lib/alignsvc.jar b/lib/alignsvc.jar
index 6dd2c04d9e544ab058db5c1ab38fd365fc78277c..4eb50950bc121a5c749bfa44a16bcd856c60e648 100644
Binary files a/lib/alignsvc.jar and b/lib/alignsvc.jar differ
diff --git a/lib/alignsvc.pom b/lib/alignsvc.pom
index ee52ddde80f0c1e46ae46a648da2418eefa0043a..e95e402867243887fb57891e1e20e0ab9812325c 100644
--- a/lib/alignsvc.pom
+++ b/lib/alignsvc.pom
@@ -17,7 +17,7 @@
<groupId>fr.inrialpes.exmo.align</groupId>
<artifactId>alignsvc</artifactId>
<version>4.4</version>
- <!-- Rev 1835M 17/03/2013 -->
+ <!-- Rev 1835:1844M 25/03/2013 -->
<name>Alignment server</name>
<description>A server for storing and sharing ontology alignments.</description>
<url>http://alignapi.gforge.inria.fr</url>
diff --git a/lib/ontowrap.jar b/lib/ontowrap.jar
index ae316e6c1f052a469a6cbcab5eb0e58e90512c30..86ea179a112b63a9c7a9659aa894c237dacb39c1 100644
Binary files a/lib/ontowrap.jar and b/lib/ontowrap.jar differ
diff --git a/lib/ontowrap.pom b/lib/ontowrap.pom
index c0adf7f8351fe968e0bd0cdcc38992cac7cb50ab..ba871e5d3ed0b4ea9dc2dafc8ccdc4f3c7f2d810 100644
--- a/lib/ontowrap.pom
+++ b/lib/ontowrap.pom
@@ -17,7 +17,7 @@
<groupId>fr.inrialpes.exmo</groupId>
<artifactId>ontowrap</artifactId>
<version>4.4</version>
- <!-- Rev 1835M 17/03/2013 -->
+ <!-- Rev 1835:1844M 25/03/2013 -->
<name>Ontology wrapping API</name>
<description>An ontology wrapping API and library.</description>
<url>http://alignapi.gforge.inria.fr</url>
diff --git a/lib/procalign.jar b/lib/procalign.jar
index d1c62466e355dbef102eac4aa061e131e1a4e58a..cc3b2a9842274e716380e1997334a06f4e7631b5 100644
Binary files a/lib/procalign.jar and b/lib/procalign.jar differ
diff --git a/lib/procalign.pom b/lib/procalign.pom
index 0cd22f556c70a9eaa9886533ea5491f6ea948a17..3906d02811e8325b646844c2d792415a0dc0ca80 100644
--- a/lib/procalign.pom
+++ b/lib/procalign.pom
@@ -17,7 +17,7 @@
<groupId>fr.inrialpes.exmo.align</groupId>
<artifactId>procalign</artifactId>
<version>4.4</version>
- <!-- Rev 1835M 17/03/2013 -->
+ <!-- Rev 1835:1844M 25/03/2013 -->
<name>Reference implementation of the Alignment API</name>
<description>Implementation of the Alignment API for manipulating ontology alignments.</description>
<url>http://alignapi.gforge.inria.fr</url>
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 3815f78e04333a22d76376788c4b991c856e5bd6..d44e9e7b83640470d845a0cdee43e8e3cda75492 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -76,10 +76,9 @@ public class CacheImpl {
String port = null;
int rights = 1; // writing rights in the database (default is 1)
- // [JE2013:ID]
String idprefix = null;
- final int VERSION = 444; // Version of the API to be stored in the database
+ final int VERSION = 450; // Version of the API to be stored in the database
/* 300: initial database format
301: ADDED alignment id as primary key
302: ALTERd cached/stored/ouri tag forms
@@ -90,8 +89,8 @@ public class CacheImpl {
ALTERd level size to 25
ADDED cell_id as keys?
450: ADDED ontology database / reduced alignment database
- ADDED prefix in server [JE2013:ID][JE2013:ID2] I want to have only the suffix to be stored as ID
- ADDED dependency database (no action) [JE2013:DEPEND1]
+ ADDED prefix in server
+ ADDED dependency database (no action)
*/
DBService service = null;
@@ -104,14 +103,12 @@ public class CacheImpl {
static private final String SVCNS = Namespace.ALIGNSVC.getUriPrefix();
static private final String CACHED = "cached";
static private final String STORED = "stored";
- // [JE2013:ID]
static private final String ALID = "alid/";
static private final String OURI1 = "ouri1";
static private final String OURI2 = "ouri2";
//**********************************************************************
- // [JE2013:ID*done*]
public CacheImpl( DBService serv ) {
service = serv;
try {
@@ -123,7 +120,6 @@ public class CacheImpl {
ontologyTable = new Hashtable<URI,Set<Alignment>>();
}
- // [JE2013:ID*done*]
public void reset() throws SQLException {
alignmentTable = new Hashtable<String,Alignment>();
ontologyTable = new Hashtable<URI,Set<Alignment>>();
@@ -135,12 +131,10 @@ public class CacheImpl {
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
*/
- // [JE2013:ID*done*]
public void init( Properties p, String prefix ) throws SQLException, AlignmentException {
logger.debug( "Initializing Database cache" );
port = p.getProperty("http"); // bad idea
host = p.getProperty("host");
- // [JE2013:ID]
idprefix = prefix;
Statement st = createStatement();
// test if a database is here, otherwise create it
@@ -150,7 +144,6 @@ public class CacheImpl {
} else {
updateDatabase(); // in case it is necessary to upgrade
}
- // [JE2013:ID]
String pref = p.getProperty("prefix");
if ( pref == null || pref.equals("") ) {
rs = st.executeQuery( "SELECT prefix FROM server WHERE port='port'" );
@@ -165,7 +158,6 @@ public class CacheImpl {
loadAlignments( true );
}
- // [JE2013:ID*done*]
public void close() throws SQLException {
Statement st = createStatement();
// unregister by the database
@@ -174,7 +166,6 @@ public class CacheImpl {
conn.close();
}
- // [JE2013:ID*done*]
public Statement createStatement() throws SQLException {
conn = service.getConnection();
return conn.createStatement();
@@ -187,7 +178,6 @@ public class CacheImpl {
* alignmentTable hashtable
* index them under the ontology URIs
*/
- // [JE2013:ID*done*]
private void loadAlignments( boolean force ) throws SQLException {
logger.debug( "Loading alignments..." );
String id = null;
@@ -207,29 +197,24 @@ public class CacheImpl {
for( int i = 0; i < idInfo.size(); i ++ ) {
id = idInfo.get(i);
alignment = retrieveDescription( id );
- // [JE2013:ID2]
recordAlignment( recoverAlignmentUri( id ), alignment, true );
}
}
st.close();
}
- // [JE2013:ID*done*]
protected Enumeration<Alignment> listAlignments() {
return alignmentTable.elements();
}
- // [JE2013:ID*done*]
protected Collection<Alignment> alignments() {
return alignmentTable.values();
}
- // [JE2013:ID*done*]
protected Collection<URI> ontologies() {
return ontologyTable.keySet();
}
- // [JE2013:ID*done*]
protected Collection<Alignment> alignments( URI u1, URI u2 ) {
Collection<Alignment> results = new HashSet<Alignment>();
if ( u1 != null ) {
@@ -252,7 +237,6 @@ public class CacheImpl {
return results;
}
- // [JE2013:ID*done*]
protected void flushCache() {// throws AlignmentException
for ( Alignment al : alignmentTable.values() ){
if ( al.getExtension(SVCNS, CACHED ) != null &&
@@ -266,7 +250,6 @@ public class CacheImpl {
* loads the description of alignments from the database and set them
* in an alignment object
*/
- // [JE2013:ID*done*]
protected Alignment retrieveDescription( String id ){
ResultSet rs;
String tag;
@@ -274,7 +257,6 @@ public class CacheImpl {
logger.debug( "Loading alignment {}", id );
URIAlignment result = new URIAlignment();
- // [JE2013: Interestingly, the alignment does not know its id or uri]
Statement st = null;
try {
st = createStatement();
@@ -309,7 +291,7 @@ public class CacheImpl {
}
}
- // Get dependencies if necessary [JE2013:DEPEND1]
+ // Get dependencies if necessary
// Get extension metadata
rs = st.executeQuery( "SELECT * FROM extension WHERE id = '" + id + "'" );
@@ -340,7 +322,6 @@ public class CacheImpl {
* && result.getExtension(STORED) != "") {
*/
- // [JE2003:ID*done*][JE2013:cellid*done*]
protected Alignment retrieveAlignment( String uri, Alignment alignment ) throws SQLException, AlignmentException, URISyntaxException {
String id = stripAlignmentUri( uri );
URI ent1 = null, ent2 = null;
@@ -360,7 +341,7 @@ public class CacheImpl {
String cid = rs.getString( "cell_id" );
if ( cid != null && !cid.equals("") ) {
if ( !cid.startsWith("##") ) {
- cell.setId( cid ); //[JE2013:cellid*done*]
+ cell.setId( cid );
}
ResultSet rse2 = st2.executeQuery("SELECT * FROM extension WHERE id = '" + cid + "'");
while ( rse2.next() ){
@@ -386,7 +367,6 @@ public class CacheImpl {
* ( result.getExtension(CACHED) != ""
* && obviously result.getExtension(STORED) != ""
*/
- // [JE2003:ID*done*]
protected void flushAlignment( Alignment alignment ) {// throws AlignmentException
//alignment.removeAllCells();
// reset
@@ -397,19 +377,16 @@ public class CacheImpl {
// DEALING WITH URIs
// Public because this is now used by AServProtocolManager
- // [JE2013:ID*done*]
public String generateAlignmentUri() {
// Generate an id based on a URI prefix + Date + random number
return recoverAlignmentUri( generateId() );
}
- // [JE2013:ID*done*]
public String recoverAlignmentUri( String id ) {
// Recreate Alignment URI from its id
return idprefix + "/" + ALID + id;
}
- // [JE2013:ID*done*]
public String stripAlignmentUri( String alid ) {
return alid.substring( alid.indexOf( ALID )+5 );
}
@@ -430,18 +407,15 @@ public class CacheImpl {
* At alignment load-from-db time, get the id and all the
*/
- // [JE2003:ID*done*]
private String generateCellId() {
return "##"+generateId();
}
- // [JE2003:ID*done*]
private String generateId() {
// Generate an id based on Date + random number
return new Date().getTime() + "/" + randomNum();
}
- // [JE2003:ID*done*]
private int randomNum() {
Random rand = new Random(System.currentTimeMillis());
return Math.abs(rand.nextInt(1000));
@@ -454,7 +428,6 @@ public class CacheImpl {
* This is more difficult because we return the alignment we have
* disreagarding if it is complete o only metadata
*/
- // [JE2003:ID*done*]
public Alignment getMetadata( String uri ) throws AlignmentException {
Alignment result = alignmentTable.get( uri );
if ( result == null )
@@ -465,7 +438,6 @@ public class CacheImpl {
/**
* retrieve full alignment from id (and cache it)
*/
- // [JE2003:ID*done*]
public Alignment getAlignment( String uri ) throws AlignmentException, SQLException {
Alignment result = null;
try {
@@ -493,7 +465,6 @@ public class CacheImpl {
return result;
}
- // [JE2003:ID*done*]
public Set<Alignment> getAlignments( URI uri ) {
return ontologyTable.get( uri );
}
@@ -502,7 +473,6 @@ public class CacheImpl {
* returns the alignments between two ontologies
* if one of the ontologies is null, then return them all
*/
- // [JE2003:ID*done*]
public Set<Alignment> getAlignments( URI uri1, URI uri2 ) {
Set<Alignment> result;
Set<Alignment> potential = new HashSet<Alignment>();
@@ -541,9 +511,7 @@ public class CacheImpl {
/**
* records newly created alignment
*/
- // [JE2013:ID*done*]
public String recordNewAlignment( Alignment alignment, boolean force ) {
- //[JE2013:ID2]
try { return recordNewAlignment( generateAlignmentUri(), alignment, force );
} catch (AlignmentException ae) { return (String)null; }
}
@@ -551,7 +519,6 @@ public class CacheImpl {
/**
* records alignment identified by id
*/
- // [JE2013:ID*done*]
public String recordNewAlignment( String uri, Alignment al, boolean force ) throws AlignmentException {
Alignment alignment = al;
@@ -569,11 +536,9 @@ public class CacheImpl {
/**
* records alignment identified by id
*/
- // [JE2013:ID*done*]
public String recordAlignment( String uri, Alignment alignment, boolean force ) {
// record the Alignment at the corresponding Uri in tables!
alignment.setExtension( Namespace.ALIGNMENT.uri, Annotations.ID, uri );
- // [JE2013:ID2] alignment.setExtension( SVCNS, ALID, id );
// Store it
try {
@@ -604,7 +569,6 @@ public class CacheImpl {
/**
* suppresses the record for an alignment
*/
- // [JE2013:ID*done*]
public void unRecordAlignment( Alignment alignment ) {
String id = alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
try {
@@ -629,7 +593,6 @@ public class CacheImpl {
* This function is used here for protecting everything to be entered in
* the database
*/
- // [JE2013:ID*done*]
public String quote( String s ) {
if ( s == null ) return "NULL";
String result = "'";
@@ -647,7 +610,6 @@ public class CacheImpl {
return result + new String( chars, j, i-j ) + "'";
}
- // [JE2013:ID*done*]
public boolean isAlignmentStored( Alignment alignment ) {
return ( alignment.getExtension( SVCNS, STORED ) != null &&
!alignment.getExtension( SVCNS, STORED ).equals("") );
@@ -657,7 +619,6 @@ public class CacheImpl {
/**
* Non publicised class
*/
- // [JE2013:ID*done*]
public void eraseAlignment( String uri, boolean eraseFromDB ) throws SQLException, AlignmentException {
Alignment alignment = getAlignment( uri );
if ( alignment != null ) {
@@ -670,7 +631,6 @@ public class CacheImpl {
/**
* Non publicised class
*/
- // [JE2013:ID*done*]
public void unstoreAlignment( String uri ) throws SQLException, AlignmentException {
Alignment alignment = getAlignment( uri );
if ( alignment != null ) {
@@ -678,7 +638,6 @@ public class CacheImpl {
}
}
- // [JE2013:ID*done*][JE2003:cellid*done*]
public void unstoreAlignment( String uri, Alignment alignment ) throws SQLException, AlignmentException {
Statement st = createStatement();
String id = stripAlignmentUri( uri );
@@ -695,7 +654,6 @@ public class CacheImpl {
st.executeUpdate("DELETE FROM cell WHERE id='"+id+"'");
st.executeUpdate("DELETE FROM extension WHERE id='"+id+"'");
st.executeUpdate("DELETE FROM ontology WHERE id='"+id+"'");
- // [JE2013:DEPEND1*done*]
st.executeUpdate("DELETE FROM dependency WHERE id='"+id+"'");
st.executeUpdate("DELETE FROM alignment WHERE id='"+id+"'");
alignment.setExtension( SVCNS, STORED, (String)null);
@@ -709,7 +667,6 @@ public class CacheImpl {
}
}
- // [JE2013:ID*done*][JE2013:cellid*done*]
public void storeAlignment( String uri ) throws AlignmentException, SQLException {
String query = null;
BasicAlignment alignment = (BasicAlignment)getAlignment( uri );
@@ -742,7 +699,7 @@ public class CacheImpl {
alignment.getFile2(),
alignment.getOntologyObject2() );
- // [JE2013:DEPEND1] store dependencies
+ // store dependencies
for ( String[] ext : alignment.getExtensions() ) {
String turi = ext[0];
@@ -757,14 +714,14 @@ public class CacheImpl {
for( Cell c : alignment ) {
String cellid = null;
if ( c.getObject1() != null && c.getObject2() != null ){
- cellid = c.getId(); //[JE2013:cellid*done*] -This is the regular...
+ 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(); //[JE2013:cellid*done*] -setinternal, YES SO easy
+ cellid = generateCellId();
}
else cellid = "";
String uri1 = c.getObject1AsURI(alignment).toString();
@@ -808,7 +765,6 @@ public class CacheImpl {
}
// Do not add transaction here: this is handled by caller
- // [JE2013:ID*done*]
public void recordOntology( Statement st, String id, boolean source, URI uri, URI file, Ontology onto ) throws SQLException {
String sfile = "";
String suri = "";
@@ -831,12 +787,10 @@ public class CacheImpl {
//**********************************************************************
// CACHE MANAGEMENT (Not implemented yet)
- // [JE2013:ID*done*]
public void resetCacheStamp( Alignment result ){
result.setExtension(SVCNS, CACHED, new Date().toString() );
}
- // [JE2013:ID*done*]
public void cleanUpCache() {
// for each alignment in the table
// set currentDate = Date();
@@ -878,7 +832,7 @@ public class CacheImpl {
formuri varchar(255)
);
- # dependencies info [JE2013:DEPEND1*done*]
+ # dependencies info
create table dependency (
id varchar(255),
@@ -906,7 +860,6 @@ public class CacheImpl {
*/
- // [JE2013:ID*done*]
public void initDatabase() throws SQLException {
logger.info( "Initialising database" );
Statement st = createStatement();
@@ -915,11 +868,9 @@ public class CacheImpl {
// Create tables
st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), type VARCHAR(5), level VARCHAR(25), primary key (id))");
st.executeUpdate("CREATE TABLE ontology (id VARCHAR(255), source BOOLEAN, uri VARCHAR(255), formname VARCHAR(50), formuri VARCHAR(255), file VARCHAR(255), primary key (id, source))");
- //[JE2013:DEPEND1*done*]
st.executeUpdate("CREATE TABLE dependency (id VARCHAR(255), dependsOn VARCHAR(255))");
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))");
- //[JE2013:ID1]
st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), prefix VARCHAR (50), edit BOOLEAN, version VARCHAR(5))");
st.close();
@@ -934,7 +885,6 @@ public class CacheImpl {
}
}
- // [JE2013:ID*done*]
public void resetDatabase( boolean force ) throws SQLException, AlignmentException {
Statement st = createStatement();
try {
@@ -953,7 +903,6 @@ public class CacheImpl {
st.executeUpdate("DROP TABLE IF EXISTS server");
st.executeUpdate("DROP TABLE IF EXISTS alignment");
st.executeUpdate("DROP TABLE IF EXISTS ontology");
- // [JE2013:DEPEND1*done*]
st.executeUpdate("DROP TABLE IF EXISTS dependency");
st.executeUpdate("DROP TABLE IF EXISTS cell");
st.executeUpdate("DROP TABLE IF EXISTS extension");
@@ -972,16 +921,13 @@ public class CacheImpl {
}
}
- // [JE2013:ID*done*]
private void registerServer( String host, String port, Boolean writeable, String prefix ) throws SQLException {
// Register *THIS* server, etc. characteristics (incl. version name)
- //[JE2013:ID]
PreparedStatement pst = conn.prepareStatement("INSERT INTO server (host, port, edit, version, prefix) VALUES (?,?,?,?,?)");
pst.setString(1,host);
pst.setString(2,port);
pst.setBoolean(3,writeable);
pst.setString(4,VERSION+"");
- //[JE2013:ID]
pst.setString(5,idprefix);
pst.executeUpdate();
pst.close();
@@ -991,7 +937,6 @@ public class CacheImpl {
* A dummy method, since it exists just ALTER TABLE ... DROP and ALTER TABLE ... ADD in SQL Language.
* each dbms has its own language for manipulating table columns....
*/
- // [JE2013:ID*done*]
public void renameColumn(Statement st, String tableName, String oldName, String newName, String newType) throws SQLException {
try {
conn.setAutoCommit( false );
@@ -1011,7 +956,6 @@ public class CacheImpl {
* Another dummy method, since it exists just ALTER TABLE ... DROP and ALTER TABLE ... ADD in SQL Language.
* each dbms has its own language for manipulating table columns....
*/
- // [JE2013:ID*done*]
public void changeColumnType(Statement st, String tableName, String columnName, String newType) throws SQLException {
try {
conn.setAutoCommit( false );
@@ -1088,10 +1032,10 @@ public class CacheImpl {
renameColumn(st,"alignment","owlontology1","ontology1", "VARCHAR(255)");
renameColumn(st,"alignment","owlontology2","ontology2", "VARCHAR(255)");
}
- if ( version < 441 ) { // [JE2013:ID] ***** MAKE ALL 450 *****
- logger.info("Upgrading to version 4.1");
+ if ( version < 450 ) {
+ logger.info("Upgrading to version 4.5");
+ logger.info("Creating Ontology table");
st.executeUpdate("CREATE TABLE ontology (id VARCHAR(255), uri VARCHAR(255), source BOOLEAN, file VARCHAR(255), formname VARCHAR(50), formuri VARCHAR(255), primary key (id, source))");
- // Move all the data from ontologies in ontology table
ResultSet rse = st.executeQuery("SELECT * FROM alignment");
while ( rse.next() ){
Statement st2 = createStatement();
@@ -1099,25 +1043,17 @@ public class CacheImpl {
st2.executeUpdate("INSERT INTO ontology (id, uri, source, file) VALUES ('"+rse.getString("id")+"','"+rse.getString("uri1")+"','1','"+rse.getString("file1")+"')");
st2.executeUpdate("INSERT INTO ontology (id, uri, source, file) VALUES ('"+rse.getString("id")+"','"+rse.getString("uri2")+"','0','"+rse.getString("file2")+"')");
}
- }
- if ( version < 442 ) {
- logger.info("Upgrading to version 4.2");
+ logger.info("Cleaning up Alignment table");
st.executeUpdate("ALTER TABLE alignment DROP ontology1");
st.executeUpdate("ALTER TABLE alignment DROP ontology2");
st.executeUpdate("ALTER TABLE alignment DROP uri1");
st.executeUpdate("ALTER TABLE alignment DROP uri2");
st.executeUpdate("ALTER TABLE alignment DROP file1");
st.executeUpdate("ALTER TABLE alignment DROP file2");
- }
- if ( version < 443 ) {
- logger.info("Upgrading to version 4.3");
- // [JE2013:ID]
- // Add new column in server table
- logger.debug("Altering server");
+ logger.debug("Altering server table");
st.executeUpdate("ALTER TABLE server ADD prefix VARCHAR(50);");
st.executeUpdate("UPDATE server SET prefix='"+idprefix+"'");
- logger.debug("Server updated with prefix");
- // [JE2013:ID] THE REAL THING
+ logger.debug("Updating server with prefix");
Statement stmt = null;
try { // In all alignment
conn.setAutoCommit( false );
@@ -1137,7 +1073,6 @@ public class CacheImpl {
// In all ontology
st.executeUpdate("UPDATE ontology SET id='"+newid+"' WHERE id='"+oldid+"'" );
}
- // [JE2013:cellid]
// Now, for each cell, with an id,
// either recast the id ... or not
conn.commit();
@@ -1147,17 +1082,11 @@ public class CacheImpl {
if ( stmt != null ) { stmt.close(); }
conn.setAutoCommit( true );
}
- }
- if ( version < 444 ) {
- logger.info("Upgrading to version 4.4");
- // [JE2013:DEPEND1*done*]
+ logger.info("Creating dependency table");
st.executeUpdate("CREATE TABLE dependency (id VARCHAR(255), dependsOn VARCHAR(255))");
- }
- if ( version < 445 ) {
- logger.info("Upgrading to version 4.5");
- // Fixing legacy errors
+ logger.info("Fixing legacy errors in cached/stored");
st.executeUpdate( "UPDATE extension SET val=( SELECT e2.val FROM extension e2 WHERE e2.tag='cached' AND e2.id=extension.id ) WHERE tag='stored' AND val=''" );
- // We should also implement a clean up (suppress all tarting with http://)
+ // We should also implement a clean up (suppress all starting with http://)
}
// ALTER version
st.executeUpdate("UPDATE server SET version='"+VERSION+"'");