diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 811f4049d72c96852f5cde04e21dc4983d4eba4b..1fad9412ddf7f10e03d1acb372fe258582ff831b 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -1,677 +1,677 @@
-/*
- * $Id$
- *
- * Copyright (C) Seungkeun Lee, 2006
- * Copyright (C) INRIA Rhône-Alpes, 2006-2008
- *
- * 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.Iterator;
-import java.util.Hashtable;
-import java.util.Vector;
-import java.util.Set;
-import java.util.HashSet;
-import java.util.Date;
-import java.util.Random;
-import java.net.URI;
-import java.net.URISyntaxException;
-
-import java.sql.Connection;
-import java.sql.ResultSet;
-import java.sql.Statement;
-import java.sql.SQLException;
-
-import fr.inrialpes.exmo.align.impl.BasicRelation;
-import fr.inrialpes.exmo.align.impl.Annotations;
-import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.URIAlignment;
-import fr.inrialpes.exmo.align.impl.URICell;
-
-import org.semanticweb.owl.align.Alignment;
-import org.semanticweb.owl.align.AlignmentException;
-import org.semanticweb.owl.align.Cell;
-import org.semanticweb.owl.align.Parameters;
-
-/**
- * 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 {
- Hashtable<String,Alignment> alignmentTable = null;
- Hashtable<URI,Set<Alignment>> ontologyTable = null;
-
- String host = null;
- String port = null;
- int rights = 1; // writing rights in the database (default is 1)
-
- final int VERSION = 310; // Version of the API to be stored in the database
- /* 300: initial database format
- 301: added alignment id as primary key
- 302: changed cached/stored/ouri tag forms
- 310: changed extension table with added URIs and method -> val
- */
-
- Connection conn = null;
-
- final int CONNECTION_ERROR = 1;
- final int SUCCESS = 2;
- final int INIT_ERROR = 3;
-
- static public final String SVCNS = "http://exmo.inrialpes.fr/align/service#";
- static public final String CACHED = "cached";
- static public final String STORED = "stored";
- static public final String OURI1 = "ouri1";
- static public final String OURI2 = "ouri2";
-
- //**********************************************************************
- public CacheImpl( DBService service ) {
- try {
- this.conn = service.getConnection();
- } catch(Exception e) {
- // Rather raise an exception
- System.err.println(e.toString());
- }
- alignmentTable = new Hashtable<String,Alignment>();
- ontologyTable = new Hashtable<URI,Set<Alignment>>();
- }
-
- /**
- * loads the alignment descriptions from the database and put them in the
- * alignmentTable hashtable
- */
- public void init( Parameters p ) throws SQLException, AlignmentException {
- port = (String)p.getParameter("http"); // bad idea
- host = (String)p.getParameter("host");
- Statement st = (Statement) conn.createStatement();
- // test if a database is here, otherwise create it
- ResultSet rs = (ResultSet)st.executeQuery("SHOW TABLES LIKE 'server'");
- if ( !rs.next() ) {
- initDatabase();
- } else {
- updateDatabase(); // in case it is necessart to upgrade
- }
- // register by the database
- st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('"+host+"','"+port+"','"+rights+"',"+VERSION+")");
- // load alignment descriptions
- loadAlignments( true );
- }
-
- public void close() throws SQLException {
- Statement st = (Statement) conn.createStatement();
- // unregister by the database
- st.executeUpdate("DELETE FROM server WHERE host='"+host+"' AND port='"+port+"'");
- }
-
- // **********************************************************************
- // LOADING FROM DATABASE
- /**
- * loads the alignment descriptions from the database and put them in the
- * alignmentTable hashtable
- * index them under the ontology URIs
- */
- private void loadAlignments( boolean force ) throws SQLException {
- String query = null;
- String id = null;
- Alignment alignment = null;
- Vector<String> idInfo = new Vector<String>();
- Statement st = (Statement) conn.createStatement();
-
- if (force) {
- // Retrieve the alignment ids
- ResultSet rs = (ResultSet) st.executeQuery("SELECT id FROM alignment");
- while(rs.next()) {
- id = rs.getString("id");
- idInfo.add(id);
- }
-
- // For each alignment id store metadata
- for( int i = 0; i < idInfo.size(); i ++ ) {
- id = idInfo.get(i);
- alignment = retrieveDescription( id );
- recordAlignment( id, alignment, true );
- }
- }
- }
-
- protected Enumeration<Alignment> listAlignments() {
- return alignmentTable.elements();
- }
-
- /**
- * loads the description of alignments from the database and set them
- * in an alignment object
- *
- * Beware, the Alignment API has two attributes:
- * onto1 is the Ontology object
- * uri1 is the URI object from which loading the ontologies
- * In the database we store:
- * owlontology1 the URI string of the ontology
- * file1 the URI string from which loading the ontologies
- * uri1 which should be the same as the last one...
- * Since alignments are indexed by the URI of the ontologies, we use
- * the "ouri1" temporary extension to contain this URI.
- */
- protected Alignment retrieveDescription( String id ){
- String query;
- ResultSet rs;
- String tag;
- String value;
-
- URIAlignment result = new URIAlignment();
-
- try {
- Statement st = (Statement) conn.createStatement();
- // Get basic ontology metadata
- query = "SELECT * FROM alignment WHERE id = '" + id +"'";
- rs = (ResultSet) st.executeQuery(query);
- while(rs.next()) {
- // Either uri1 or file1
- result.setFile1( new URI( rs.getString("file1") ) );
- result.setFile2( new URI( rs.getString("file2") ) );
- result.getOntologyObject1().setURI( new URI(rs.getString("owlontology1")) );
- result.getOntologyObject2().setURI( new URI(rs.getString("owlontology2")) );
- result.setExtension( SVCNS, OURI1, rs.getString("owlontology1") );
- result.setExtension( SVCNS, OURI2, rs.getString("owlontology2") );
- result.setLevel(rs.getString("level"));
- result.setType(rs.getString("type"));
- }
-
- // Get extension metadata
- query = "SELECT * FROM extension WHERE id = '" + id + "'";
- rs = (ResultSet) st.executeQuery(query);
- while(rs.next()) {
- tag = rs.getString("tag");
- value = rs.getString("val");
- result.setExtension( rs.getString("uri"), tag, value);
- }
- } catch (Exception e) { // URI exception that should not occur
- System.err.println("Unlikely URI exception!");
- e.printStackTrace();
- return null;
- }
- // should be there
- //result.setExtension( SVCNS, STORED, "DATE");
- // not yet cached
- result.setExtension(SVCNS, CACHED, "");
- return result;
- }
-
- /**
- * loads the full alignments from the database and put them in the
- * alignmentTable hastable
- *
- * should be invoked when:
- * ( result.getExtension(CACHED) == ""
- * && result.getExtension(STORED) != "") {
-
- */
- protected Alignment retrieveAlignment( String id, Alignment alignment ) throws SQLException, AlignmentException, URISyntaxException {
- String query;
- URI ent1 = null, ent2 = null;
- Cell cell = null;
-
- Statement st = (Statement) conn.createStatement();
-
- alignment.setOntology1( new URI( alignment.getExtension( SVCNS, OURI1 ) ) );
- alignment.setOntology2( new URI( alignment.getExtension( SVCNS, OURI2 ) ) );
-
- // Get cells
- query = "SELECT * FROM cell WHERE id = '" + id + "'";
- ResultSet rs = (ResultSet) st.executeQuery(query);
- while(rs.next()) {
- ent1 = new URI(rs.getString("uri1"));
- ent2 = new URI(rs.getString("uri2"));
- if(ent1 == null || ent2 == null) break;
- cell = alignment.addAlignCell(ent1, ent2, rs.getString("relation"), Double.parseDouble(rs.getString("measure")));
- cell.setId(rs.getString("cell_id"));
- cell.setSemantics(rs.getString("semantics"));
-
- }
-
- // JE: I must now retrieve all the extensions
- for( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
- cell = (Cell)e.nextElement();
- String cid = cell.getId();
- if ( cid != null && !cid.equals("") ){
- query = "SELECT * FROM extension WHERE id = '" + cid + "'";
- ResultSet rse = (ResultSet) st.executeQuery(query);
- while ( rse.next() ){
- cell.setExtension( rse.getString("uri"),
- rse.getString("tag"),
- rse.getString("val") );
- }
- }
- }
- // reset
- resetCacheStamp(alignment);
-
- return alignment;
- }
-
- // Public because this is now used by AServProtocolManager
- public String generateAlignmentId() {
- // Generate an id based on a URI prefix + Date + random number
- return "http://"+host+":"+port+"/alid/" + new Date().getTime() + "/" + randomNum();
- }
-
- private String generateCellId( String alId ) {
- // Generate an id based on a URI prefix + Date + random number
- int end = alId.indexOf("/alid/");
- if ( end == -1 || alId.indexOf( '#' ) != -1 ) {
- return "http://"+host+":"+port+"/cellid/" + new Date().getTime() + "/" + randomNum();
- } else {
- return alId + "#" + randomNum();
- }
- }
-
- private int randomNum() {
- Random rand = new Random(System.currentTimeMillis());
- return Math.abs(rand.nextInt(1000));
- }
-
- //**********************************************************************
- // 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 id ) throws Exception {
- Alignment result = alignmentTable.get( id );
- if ( result == null )
- throw new Exception("getMetadata: Cannot find alignment");
- return result;
- }
-
- /**
- * retrieve full alignment from id (and cache it)
- */
- public Alignment getAlignment( String id ) throws Exception {
- Alignment result = alignmentTable.get( id );
-
- if ( result == null )
- throw new Exception("getAlignment: Cannot find alignment");
-
- // If not cached, retrieve it now
- if ( result.getExtension( SVCNS, CACHED) == ""
- && result.getExtension(SVCNS, STORED) != "") {
- retrieveAlignment( id, result );
- }
-
- return result;
- }
-
- public Set<Alignment> getAlignments( URI uri ) {
- return ontologyTable.get( uri );
- }
-
- public Set<Alignment> getAlignments( URI uri1, URI uri2 ) {
- // Create the set and compare
- Set<Alignment> result = new HashSet<Alignment>();
- Set<Alignment> potentials = ontologyTable.get( uri1 );
- if ( potentials != null ) {
- String uri2String = uri2.toString();
- for( Iterator it = potentials.iterator(); it.hasNext(); ) {
- Alignment al = (Alignment)it.next();
- // This is not the best because URI are not resolved here...
- if ( al.getExtension(SVCNS, OURI2).equals( uri2String ) ) result.add( al );
- }
- }
- return result;
- }
-
- //**********************************************************************
- // RECORDING ALIGNMENTS
- /**
- * records newly created alignment
- */
- public String recordNewAlignment( Alignment alignment, boolean force ) {
- try { return recordNewAlignment( generateAlignmentId(), alignment, force );
- } catch (AlignmentException ae) { return (String)null; }
- }
-
- /**
- * records alignment identified by id
- */
- public String recordNewAlignment( String id, Alignment al, boolean force ) throws AlignmentException {
+/*
+ * $Id$
+ *
+ * Copyright (C) Seungkeun Lee, 2006
+ * Copyright (C) INRIA Rhône-Alpes, 2006-2008
+ *
+ * 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.Iterator;
+import java.util.Hashtable;
+import java.util.Vector;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.Date;
+import java.util.Random;
+import java.net.URI;
+import java.net.URISyntaxException;
+
+import java.sql.Connection;
+import java.sql.ResultSet;
+import java.sql.Statement;
+import java.sql.SQLException;
+
+import fr.inrialpes.exmo.align.impl.BasicRelation;
+import fr.inrialpes.exmo.align.impl.Annotations;
+import fr.inrialpes.exmo.align.impl.BasicParameters;
+import fr.inrialpes.exmo.align.impl.URIAlignment;
+import fr.inrialpes.exmo.align.impl.URICell;
+
+import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.Cell;
+import org.semanticweb.owl.align.Parameters;
+
+/**
+ * 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 {
+ Hashtable<String,Alignment> alignmentTable = null;
+ Hashtable<URI,Set<Alignment>> ontologyTable = null;
+
+ String host = null;
+ String port = null;
+ int rights = 1; // writing rights in the database (default is 1)
+
+ final int VERSION = 310; // Version of the API to be stored in the database
+ /* 300: initial database format
+ 301: added alignment id as primary key
+ 302: changed cached/stored/ouri tag forms
+ 310: changed extension table with added URIs and method -> val
+ */
+
+ Connection conn = null;
+
+ final int CONNECTION_ERROR = 1;
+ final int SUCCESS = 2;
+ final int INIT_ERROR = 3;
+
+ static public final String SVCNS = "http://exmo.inrialpes.fr/align/service#";
+ static public final String CACHED = "cached";
+ static public final String STORED = "stored";
+ static public final String OURI1 = "ouri1";
+ static public final String OURI2 = "ouri2";
+
+ //**********************************************************************
+ public CacheImpl( DBService service ) {
+ try {
+ this.conn = service.getConnection();
+ } catch(Exception e) {
+ // Rather raise an exception
+ System.err.println(e.toString());
+ }
+ alignmentTable = new Hashtable<String,Alignment>();
+ ontologyTable = new Hashtable<URI,Set<Alignment>>();
+ }
+
+ /**
+ * loads the alignment descriptions from the database and put them in the
+ * alignmentTable hashtable
+ */
+ public void init( Parameters p ) throws SQLException, AlignmentException {
+ port = (String)p.getParameter("http"); // bad idea
+ host = (String)p.getParameter("host");
+ Statement st = (Statement) conn.createStatement();
+ // test if a database is here, otherwise create it
+ ResultSet rs = (ResultSet)st.executeQuery("SHOW TABLES LIKE 'server'");
+ if ( !rs.next() ) {
+ initDatabase();
+ } else {
+ updateDatabase(); // in case it is necessart to upgrade
+ }
+ // register by the database
+ st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('"+host+"','"+port+"','"+rights+"',"+VERSION+")");
+ // load alignment descriptions
+ loadAlignments( true );
+ }
+
+ public void close() throws SQLException {
+ Statement st = (Statement) conn.createStatement();
+ // unregister by the database
+ st.executeUpdate("DELETE FROM server WHERE host='"+host+"' AND port='"+port+"'");
+ }
+
+ // **********************************************************************
+ // LOADING FROM DATABASE
+ /**
+ * loads the alignment descriptions from the database and put them in the
+ * alignmentTable hashtable
+ * index them under the ontology URIs
+ */
+ private void loadAlignments( boolean force ) throws SQLException {
+ String query = null;
+ String id = null;
+ Alignment alignment = null;
+ Vector<String> idInfo = new Vector<String>();
+ Statement st = (Statement) conn.createStatement();
+
+ if (force) {
+ // Retrieve the alignment ids
+ ResultSet rs = (ResultSet) st.executeQuery("SELECT id FROM alignment");
+ while(rs.next()) {
+ id = rs.getString("id");
+ idInfo.add(id);
+ }
+
+ // For each alignment id store metadata
+ for( int i = 0; i < idInfo.size(); i ++ ) {
+ id = idInfo.get(i);
+ alignment = retrieveDescription( id );
+ recordAlignment( id, alignment, true );
+ }
+ }
+ }
+
+ protected Enumeration<Alignment> listAlignments() {
+ return alignmentTable.elements();
+ }
+
+ /**
+ * loads the description of alignments from the database and set them
+ * in an alignment object
+ *
+ * Beware, the Alignment API has two attributes:
+ * onto1 is the Ontology object
+ * uri1 is the URI object from which loading the ontologies
+ * In the database we store:
+ * owlontology1 the URI string of the ontology
+ * file1 the URI string from which loading the ontologies
+ * uri1 which should be the same as the last one...
+ * Since alignments are indexed by the URI of the ontologies, we use
+ * the "ouri1" temporary extension to contain this URI.
+ */
+ protected Alignment retrieveDescription( String id ){
+ String query;
+ ResultSet rs;
+ String tag;
+ String value;
+
+ URIAlignment result = new URIAlignment();
+
+ try {
+ Statement st = (Statement) conn.createStatement();
+ // Get basic ontology metadata
+ query = "SELECT * FROM alignment WHERE id = '" + id +"'";
+ rs = (ResultSet) st.executeQuery(query);
+ while(rs.next()) {
+ // Either uri1 or file1
+ result.setFile1( new URI( rs.getString("file1") ) );
+ result.setFile2( new URI( rs.getString("file2") ) );
+ result.getOntologyObject1().setURI( new URI(rs.getString("owlontology1")) );
+ result.getOntologyObject2().setURI( new URI(rs.getString("owlontology2")) );
+ result.setExtension( SVCNS, OURI1, rs.getString("owlontology1") );
+ result.setExtension( SVCNS, OURI2, rs.getString("owlontology2") );
+ result.setLevel(rs.getString("level"));
+ result.setType(rs.getString("type"));
+ }
+
+ // Get extension metadata
+ query = "SELECT * FROM extension WHERE id = '" + id + "'";
+ rs = (ResultSet) st.executeQuery(query);
+ while(rs.next()) {
+ tag = rs.getString("tag");
+ value = rs.getString("val");
+ result.setExtension( rs.getString("uri"), tag, value);
+ }
+ } catch (Exception e) { // URI exception that should not occur
+ System.err.println("Unlikely URI exception!");
+ e.printStackTrace();
+ return null;
+ }
+ // should be there
+ //result.setExtension( SVCNS, STORED, "DATE");
+ // not yet cached
+ result.setExtension(SVCNS, CACHED, "");
+ return result;
+ }
+
+ /**
+ * loads the full alignments from the database and put them in the
+ * alignmentTable hastable
+ *
+ * should be invoked when:
+ * ( result.getExtension(CACHED) == ""
+ * && result.getExtension(STORED) != "") {
+
+ */
+ protected Alignment retrieveAlignment( String id, Alignment alignment ) throws SQLException, AlignmentException, URISyntaxException {
+ String query;
+ URI ent1 = null, ent2 = null;
+ Cell cell = null;
+
+ Statement st = (Statement) conn.createStatement();
+
+ alignment.setOntology1( new URI( alignment.getExtension( SVCNS, OURI1 ) ) );
+ alignment.setOntology2( new URI( alignment.getExtension( SVCNS, OURI2 ) ) );
+
+ // Get cells
+ query = "SELECT * FROM cell WHERE id = '" + id + "'";
+ ResultSet rs = (ResultSet) st.executeQuery(query);
+ while(rs.next()) {
+ ent1 = new URI(rs.getString("uri1"));
+ ent2 = new URI(rs.getString("uri2"));
+ if(ent1 == null || ent2 == null) break;
+ cell = alignment.addAlignCell(ent1, ent2, rs.getString("relation"), Double.parseDouble(rs.getString("measure")));
+ cell.setId(rs.getString("cell_id"));
+ cell.setSemantics(rs.getString("semantics"));
+
+ }
+
+ // JE: I must now retrieve all the extensions
+ for( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
+ cell = (Cell)e.nextElement();
+ String cid = cell.getId();
+ if ( cid != null && !cid.equals("") ){
+ query = "SELECT * FROM extension WHERE id = '" + cid + "'";
+ ResultSet rse = (ResultSet) st.executeQuery(query);
+ while ( rse.next() ){
+ cell.setExtension( rse.getString("uri"),
+ rse.getString("tag"),
+ rse.getString("val") );
+ }
+ }
+ }
+ // reset
+ resetCacheStamp(alignment);
+
+ return alignment;
+ }
+
+ // Public because this is now used by AServProtocolManager
+ public String generateAlignmentId() {
+ // Generate an id based on a URI prefix + Date + random number
+ return "http://"+host+":"+port+"/alid/" + new Date().getTime() + "/" + randomNum();
+ }
+
+ private String generateCellId( String alId ) {
+ // Generate an id based on a URI prefix + Date + random number
+ int end = alId.indexOf("/alid/");
+ if ( end == -1 || alId.indexOf( '#' ) != -1 ) {
+ return "http://"+host+":"+port+"/cellid/" + new Date().getTime() + "/" + randomNum();
+ } else {
+ return alId + "#" + randomNum();
+ }
+ }
+
+ private int randomNum() {
+ Random rand = new Random(System.currentTimeMillis());
+ return Math.abs(rand.nextInt(1000));
+ }
+
+ //**********************************************************************
+ // 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 id ) throws Exception {
+ Alignment result = alignmentTable.get( id );
+ if ( result == null )
+ throw new Exception("getMetadata: Cannot find alignment");
+ return result;
+ }
+
+ /**
+ * retrieve full alignment from id (and cache it)
+ */
+ public Alignment getAlignment( String id ) throws Exception {
+ Alignment result = alignmentTable.get( id );
+
+ if ( result == null )
+ throw new Exception("getAlignment: Cannot find alignment");
+
+ // If not cached, retrieve it now
+ if ( result.getExtension( SVCNS, CACHED) == ""
+ && result.getExtension(SVCNS, STORED) != "") {
+ retrieveAlignment( id, result );
+ }
+
+ return result;
+ }
+
+ public Set<Alignment> getAlignments( URI uri ) {
+ return ontologyTable.get( uri );
+ }
+
+ public Set<Alignment> getAlignments( URI uri1, URI uri2 ) {
+ // Create the set and compare
+ Set<Alignment> result = new HashSet<Alignment>();
+ Set<Alignment> potentials = ontologyTable.get( uri1 );
+ if ( potentials != null ) {
+ String uri2String = uri2.toString();
+ for( Iterator it = potentials.iterator(); it.hasNext(); ) {
+ Alignment al = (Alignment)it.next();
+ // This is not the best because URI are not resolved here...
+ if ( al.getExtension(SVCNS, OURI2).equals( uri2String ) ) result.add( al );
+ }
+ }
+ return result;
+ }
+
+ //**********************************************************************
+ // RECORDING ALIGNMENTS
+ /**
+ * records newly created alignment
+ */
+ public String recordNewAlignment( Alignment alignment, boolean force ) {
+ try { return recordNewAlignment( generateAlignmentId(), alignment, force );
+ } catch (AlignmentException ae) { return (String)null; }
+ }
+
+ /**
+ * records alignment identified by id
+ */
+ public String recordNewAlignment( String id, Alignment al, boolean force ) throws AlignmentException {
Alignment alignment = al;
-
- alignment.setExtension(SVCNS, OURI1, alignment.getOntology1URI().toString());
- alignment.setExtension(SVCNS, OURI2, alignment.getOntology2URI().toString());
- // Index
- recordAlignment( id, alignment, force );
- // Not yet stored
- alignment.setExtension(SVCNS, STORED, "");
- // Cached now
- resetCacheStamp(alignment);
- return id;
- }
-
- /**
- * records alignment identified by id
- */
- public String recordAlignment( String id, Alignment alignment, boolean force ){
+
+ alignment.setExtension(SVCNS, OURI1, alignment.getOntology1URI().toString());
+ alignment.setExtension(SVCNS, OURI2, alignment.getOntology2URI().toString());
+ // Index
+ recordAlignment( id, alignment, force );
+ // Not yet stored
+ alignment.setExtension(SVCNS, STORED, "");
+ // Cached now
+ resetCacheStamp(alignment);
+ return id;
+ }
+
+ /**
+ * records alignment identified by id
+ */
+ public String recordAlignment( String id, Alignment alignment, boolean force ){
// record the Id!
- //CLD put in comment this line for allowing to create a new ID for any alignment
- //if ( alignment.getExtension( Annotations.ALIGNNS, Annotations.ID ) == null )
+ //CLD put in comment this line for allowing to create a new ID for any alignment
+ //if ( alignment.getExtension( Annotations.ALIGNNS, Annotations.ID ) == null )
alignment.setExtension( Annotations.ALIGNNS, Annotations.ID, id );
-
- // Store it
- try {
- URI ouri1 = new URI( alignment.getExtension( SVCNS, OURI1) );
- URI ouri2 = new URI( alignment.getExtension( SVCNS, OURI2) );
- if ( force || alignmentTable.get( id ) == null ) {
- Set<Alignment> s1 = ontologyTable.get( ouri1 );
- if ( s1 == null ) {
- s1 = new HashSet<Alignment>();
- ontologyTable.put( ouri1, s1 );
- }
- s1.add( alignment );
- Set<Alignment> s2 = ontologyTable.get( ouri2 );
- if ( s2 == null ) {
- s2 = new HashSet<Alignment>();
- ontologyTable.put( ouri2, s2 );
- }
+
+ // Store it
+ try {
+ URI ouri1 = new URI( alignment.getExtension( SVCNS, OURI1) );
+ URI ouri2 = new URI( alignment.getExtension( SVCNS, OURI2) );
+ if ( force || alignmentTable.get( id ) == null ) {
+ Set<Alignment> s1 = ontologyTable.get( ouri1 );
+ if ( s1 == null ) {
+ s1 = new HashSet<Alignment>();
+ ontologyTable.put( ouri1, s1 );
+ }
+ s1.add( alignment );
+ Set<Alignment> s2 = ontologyTable.get( ouri2 );
+ if ( s2 == null ) {
+ s2 = new HashSet<Alignment>();
+ ontologyTable.put( ouri2, s2 );
+ }
s2.add( alignment );
-
+
alignmentTable.put( id, alignment );
-
- }
- return id;
- } catch (Exception e) {
- //System.err.println("Unlikely URI exception!");
- e.printStackTrace();
- return null;
- }
- }
-
- //**********************************************************************
- // STORING IN DATABASE
- /**
- * quote:
- * Prepare a string to be used in SQL queries by preceeding occurences of
- * "'", """, and "\" by a "\".
- * This should be implemented at a lower level within Java itself
- * (or the sql package).
- * This function is used here for protecting everything to be entered in
- * the database
- */
- public String quote( String s ) {
- String result = null;
- char[] chars = s.toCharArray();
- int j = 0;
- int i = 0;
- char c;
- for ( ; i < chars.length; i++ ){
- c = chars[i];
- if ( c == '\'' || c == '"' || c == '\\' ) {
- result += new String( chars, j, i-j ) + "\\" + c;
- j = i+1;
- };
- }
- if ( result != null ) {
- return result + new String( chars, j, i-j );
- } else {
- return s;
- }
- }
-
- public boolean isAlignmentStored( Alignment alignment ) {
- if ( alignment.getExtension( SVCNS, STORED ) != null &&
- !alignment.getExtension( SVCNS, STORED ).equals("") )
- return false;
- else return true;
- }
-
- public void storeAlignment( String id ) throws Exception {
- String query = null;
- Alignment alignment = getAlignment( id );
- Statement st = (Statement) conn.createStatement();
-
- // We store stored date
- alignment.setExtension( SVCNS, STORED, new Date().toString());
- // We empty cached date
- alignment.setExtension( SVCNS, CACHED, "");
-
- try {
- String s_O1 = alignment.getExtension(SVCNS, OURI1);
- String s_O2 = alignment.getExtension(SVCNS, OURI2);
-
- // file attribute
- String s_File1 = null;
- String s_File2 = null;
- if (alignment.getFile1() != null)
- s_File1 = alignment.getFile1().toString();
- if (alignment.getFile2() != null)
- s_File2 = alignment.getFile2().toString();
-
- // uri attribute
- String s_uri1 = alignment.getOntology1URI().toString();
- String s_uri2 = alignment.getOntology2URI().toString();
-
- String type = alignment.getType();
- String level = alignment.getLevel();
-
- query = "INSERT INTO alignment " +
- "(id, owlontology1, owlontology2, type, level, file1, file2, uri1, uri2) " +
- "VALUES ('" + quote(id) + "','" + quote(s_O1) + "','" + quote(s_O2) + "','" + quote(type) + "','" + quote(level) + "','" + quote(s_File1) + "','" + quote(s_File2) + "','" + quote(s_uri1) + "','" + quote(s_uri2) + "')";
- st.executeUpdate(query);
- for ( Object ext : ((BasicParameters)alignment.getExtensions()).getValues() ){
- String uri = ((String[])ext)[0];
- String tag = ((String[])ext)[1];
- String val = ((String[])ext)[2];
- query = "INSERT INTO extension " +
- "(id, uri, tag, val) " +
- "VALUES ('" + quote(id) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
- st.executeUpdate(query);
- }
-
- for( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
- Cell c = (Cell)e.nextElement();
- String cellid = null;
- if ( c.getObject1() != null && c.getObject2() != null ){
- cellid = c.getId();
- if ( cellid != null ){
- if ( cellid.startsWith("#") ) {
- cellid = alignment.getExtension( Annotations.ALIGNNS, Annotations.ID ) + cellid;
- }
- } else if ( c.getExtensions() != null ) {
- // JE: In case of extensions create an ID
- c.setId( generateCellId( id ) );
- cellid = c.getId();
- }
- else cellid = "";
- String uri1 = c.getObject1AsURI().toString();
- String uri2 = c.getObject2AsURI().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 ) {
- // JE: I must now store all the extensions
- // JE:EXT
- for ( Object ext : ((BasicParameters)c.getExtensions()).getValues() ){
- String uri = ((String[])ext)[0];
- String tag = ((String[])ext)[1];
- String val = ((String[])ext)[2];
- query = "INSERT INTO extension " +
- "(id, uri, tag, val) " +
- "VALUES ('" + quote(cellid) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
- st.executeUpdate(query);
- }
- }
- }
- } catch (Exception e) { e.printStackTrace(); };
- // We reset cached date
- resetCacheStamp(alignment);
- }
-
- //**********************************************************************
- // CACHE MANAGEMENT (Not implemented yet)
- public void resetCacheStamp( Alignment result ){
- result.setExtension(SVCNS, CACHED, new Date().toString() );
- }
-
- public void cleanUpCache() {
- // for each alignment in the table
- // set currentDate = Date();
- // if ( DateFormat.parse( result.getExtension(SVCNS, CACHED) ).before( ) ) {
- // - for each ontology if no other alignment => unload
- // - clean up cells
- // }
- }
-
- // **********************************************************************
- // DATABASE CREATION AND UPDATING
- /*
- # server info
-
- create table server (
- host varchar(50),
- port varchar(5),
- edit varchar(5)
- );
-
-
- # alignment info
-
- create table alignment (
- id varchar(100),
- owlontology1 varchar(250),
- owlontology2 varchar(250),
- type varchar(5),
- level varchar(1),
- file1 varchar(250),
- file2 varchar(250),
- uri1 varchar(250),
- uri2 varchar(250),
- primary key (id));
-
- # cell info
-
- create table cell(
- id varchar(100),
- cell_id varchar(250),
- uri1 varchar(250),
- uri2 varchar(250),
- semantics varchar(30),
- measure varchar(20),
- relation varchar(5));
-
- # extension info
-
- create table extension(
- id varchar(100),
- uri varchar(200),
- tag varchar(50),
- val varchar(500));
-
- */
-
- public void initDatabase() throws SQLException {
- Statement st = (Statement) conn.createStatement();
- // Create tables
- st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), owlontology1 VARCHAR(250), owlontology2 VARCHAR(250), type VARCHAR(5), level VARCHAR(1), file1 VARCHAR(250), file2 VARCHAR(250), uri1 VARCHAR(250), uri2 VARCHAR(250), primary key (id))");
- st.executeUpdate("CREATE TABLE cell(id VARCHAR(100), cell_id VARCHAR(250), uri1 VARCHAR(250), uri2 VARCHAR(250), semantics VARCHAR(30), measure VARCHAR(20), relation VARCHAR(5))");
- 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), edit BOOLEAN, version VARCHAR(5))");
- st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('dbms', 'port', 0, '"+VERSION+"')");
- }
-
- public void resetDatabase( boolean force ) throws SQLException, AlignmentException {
- Statement st = (Statement) conn.createStatement();
- // Check that no one else is connected...
- if ( force != true ){
- ResultSet rs = (ResultSet) st.executeQuery("SELECT COUNT(*) AS rowcount FROM server WHERE edit=1");
- rs.next();
- int count = rs.getInt("rowcount") ;
- rs.close() ;
- if ( count > 1 ) {
- throw new AlignmentException("Cannot init database: other processes use it");
- }
- }
- // Suppress old database if exists
- st.executeUpdate("DROP TABLE IF EXISTS server");
- st.executeUpdate("DROP TABLE IF EXISTS alignment");
- st.executeUpdate("DROP TABLE IF EXISTS cell");
- st.executeUpdate("DROP TABLE IF EXISTS extension");
- // Redo it
- initDatabase();
- // Register this server, etc. characteristics (incl. version name)
- st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('"+host+"','"+port+"','"+rights+"',"+VERSION+")");
- }
-
- public void updateDatabase( ) throws SQLException, AlignmentException {
- Statement st = (Statement) conn.createStatement();
- // get the version number
- ResultSet rs = (ResultSet) st.executeQuery("SELECT version FROM server WHERE port='port'");
- rs.next();
- int version = rs.getInt("version") ;
- if ( version < VERSION ) {
- if ( version >= 302 ) {
- // Change database
- st.executeUpdate("ALTER TABLE extension CHANGE method val VARCHAR(500)");
- st.executeUpdate("ALTER TABLE extension ADD uri VARCHAR(200);");
- // Modify extensions
- ResultSet rse = (ResultSet) st.executeQuery("SELECT * FROM extension");
- Statement st2 = (Statement) conn.createStatement();
- while ( rse.next() ){
- String tag = rse.getString("tag");
- System.err.println(" Treating tag "+tag+" of "+rse.getString("id"));
- if ( !tag.equals("") ){
- int pos;
- String ns;
- String name;
- if ( (pos = tag.lastIndexOf('#')) != -1 ) {
- ns = tag.substring( 0, pos );
- name = tag.substring( pos+1 );
- } else if ( (pos = tag.lastIndexOf(':')) != -1 && pos > 5 ) {
- ns = tag.substring( 0, pos )+"#";
- name = tag.substring( pos+1 );
- } else if ( (pos = tag.lastIndexOf('/')) != -1 ) {
- ns = tag.substring( 0, pos+1 );
- name = tag.substring( pos+1 );
- } else {
- ns = Annotations.ALIGNNS;
- name = tag;
- }
- System.err.println(" >> "+ns+" : "+name);
- st2.executeUpdate("UPDATE extension SET tag='"+name+"', uri='"+ns+"' WHERE id='"+rse.getString("id")+"' AND tag='"+tag+"'");
- }
- }
- // Change version
- st.executeUpdate("UPDATE server SET version='"+VERSION+"' WHERE port='port'");
- } else {
- throw new AlignmentException("Database must be upgraded ("+version+" -> "+VERSION+")");
- }
- }
- }
-
-}
+
+ }
+ return id;
+ } catch (Exception e) {
+ //System.err.println("Unlikely URI exception!");
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ //**********************************************************************
+ // STORING IN DATABASE
+ /**
+ * quote:
+ * Prepare a string to be used in SQL queries by preceeding occurences of
+ * "'", """, and "\" by a "\".
+ * This should be implemented at a lower level within Java itself
+ * (or the sql package).
+ * This function is used here for protecting everything to be entered in
+ * the database
+ */
+ public String quote( String s ) {
+ String result = null;
+ char[] chars = s.toCharArray();
+ int j = 0;
+ int i = 0;
+ char c;
+ for ( ; i < chars.length; i++ ){
+ c = chars[i];
+ if ( c == '\'' || c == '"' || c == '\\' ) {
+ result += new String( chars, j, i-j ) + "\\" + c;
+ j = i+1;
+ };
+ }
+ if ( result != null ) {
+ return result + new String( chars, j, i-j );
+ } else {
+ return s;
+ }
+ }
+
+ public boolean isAlignmentStored( Alignment alignment ) {
+ if ( alignment.getExtension( SVCNS, STORED ) != null &&
+ !alignment.getExtension( SVCNS, STORED ).equals("") )
+ return false;
+ else return true;
+ }
+
+ public void storeAlignment( String id ) throws Exception {
+ String query = null;
+ Alignment alignment = getAlignment( id );
+ Statement st = (Statement) conn.createStatement();
+
+ // We store stored date
+ alignment.setExtension( SVCNS, STORED, new Date().toString());
+ // We empty cached date
+ alignment.setExtension( SVCNS, CACHED, "");
+
+ try {
+ String s_O1 = alignment.getExtension(SVCNS, OURI1);
+ String s_O2 = alignment.getExtension(SVCNS, OURI2);
+
+ // file attribute
+ String s_File1 = null;
+ String s_File2 = null;
+ if (alignment.getFile1() != null)
+ s_File1 = alignment.getFile1().toString();
+ if (alignment.getFile2() != null)
+ s_File2 = alignment.getFile2().toString();
+
+ // uri attribute
+ String s_uri1 = alignment.getOntology1URI().toString();
+ String s_uri2 = alignment.getOntology2URI().toString();
+
+ String type = alignment.getType();
+ String level = alignment.getLevel();
+
+ query = "INSERT INTO alignment " +
+ "(id, owlontology1, owlontology2, type, level, file1, file2, uri1, uri2) " +
+ "VALUES ('" + quote(id) + "','" + quote(s_O1) + "','" + quote(s_O2) + "','" + quote(type) + "','" + quote(level) + "','" + quote(s_File1) + "','" + quote(s_File2) + "','" + quote(s_uri1) + "','" + quote(s_uri2) + "')";
+ st.executeUpdate(query);
+ for ( Object ext : ((BasicParameters)alignment.getExtensions()).getValues() ){
+ String uri = ((String[])ext)[0];
+ String tag = ((String[])ext)[1];
+ String val = ((String[])ext)[2];
+ query = "INSERT INTO extension " +
+ "(id, uri, tag, val) " +
+ "VALUES ('" + quote(id) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
+ st.executeUpdate(query);
+ }
+
+ for( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
+ Cell c = (Cell)e.nextElement();
+ String cellid = null;
+ if ( c.getObject1() != null && c.getObject2() != null ){
+ cellid = c.getId();
+ if ( cellid != null ){
+ if ( cellid.startsWith("#") ) {
+ cellid = alignment.getExtension( Annotations.ALIGNNS, Annotations.ID ) + cellid;
+ }
+ } else if ( c.getExtensions() != null ) {
+ // JE: In case of extensions create an ID
+ c.setId( generateCellId( id ) );
+ cellid = c.getId();
+ }
+ else cellid = "";
+ String uri1 = c.getObject1AsURI().toString();
+ String uri2 = c.getObject2AsURI().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 ) {
+ // JE: I must now store all the extensions
+ // JE:EXT
+ for ( Object ext : ((BasicParameters)c.getExtensions()).getValues() ){
+ String uri = ((String[])ext)[0];
+ String tag = ((String[])ext)[1];
+ String val = ((String[])ext)[2];
+ query = "INSERT INTO extension " +
+ "(id, uri, tag, val) " +
+ "VALUES ('" + quote(cellid) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
+ st.executeUpdate(query);
+ }
+ }
+ }
+ } catch (Exception e) { e.printStackTrace(); };
+ // We reset cached date
+ resetCacheStamp(alignment);
+ }
+
+ //**********************************************************************
+ // CACHE MANAGEMENT (Not implemented yet)
+ public void resetCacheStamp( Alignment result ){
+ result.setExtension(SVCNS, CACHED, new Date().toString() );
+ }
+
+ public void cleanUpCache() {
+ // for each alignment in the table
+ // set currentDate = Date();
+ // if ( DateFormat.parse( result.getExtension(SVCNS, CACHED) ).before( ) ) {
+ // - for each ontology if no other alignment => unload
+ // - clean up cells
+ // }
+ }
+
+ // **********************************************************************
+ // DATABASE CREATION AND UPDATING
+ /*
+ # server info
+
+ create table server (
+ host varchar(50),
+ port varchar(5),
+ edit varchar(5)
+ );
+
+
+ # alignment info
+
+ create table alignment (
+ id varchar(100),
+ owlontology1 varchar(250),
+ owlontology2 varchar(250),
+ type varchar(5),
+ level varchar(1),
+ file1 varchar(250),
+ file2 varchar(250),
+ uri1 varchar(250),
+ uri2 varchar(250),
+ primary key (id));
+
+ # cell info
+
+ create table cell(
+ id varchar(100),
+ cell_id varchar(250),
+ uri1 varchar(250),
+ uri2 varchar(250),
+ semantics varchar(30),
+ measure varchar(20),
+ relation varchar(5));
+
+ # extension info
+
+ create table extension(
+ id varchar(100),
+ uri varchar(200),
+ tag varchar(50),
+ val varchar(500));
+
+ */
+
+ public void initDatabase() throws SQLException {
+ Statement st = (Statement) conn.createStatement();
+ // Create tables
+ st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), owlontology1 VARCHAR(250), owlontology2 VARCHAR(250), type VARCHAR(5), level VARCHAR(1), file1 VARCHAR(250), file2 VARCHAR(250), uri1 VARCHAR(250), uri2 VARCHAR(250), primary key (id))");
+ st.executeUpdate("CREATE TABLE cell(id VARCHAR(100), cell_id VARCHAR(250), uri1 VARCHAR(250), uri2 VARCHAR(250), semantics VARCHAR(30), measure VARCHAR(20), relation VARCHAR(5))");
+ 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), edit BOOLEAN, version VARCHAR(5))");
+ st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('dbms', 'port', 0, '"+VERSION+"')");
+ }
+
+ public void resetDatabase( boolean force ) throws SQLException, AlignmentException {
+ Statement st = (Statement) conn.createStatement();
+ // Check that no one else is connected...
+ if ( force != true ){
+ ResultSet rs = (ResultSet) st.executeQuery("SELECT COUNT(*) AS rowcount FROM server WHERE edit=1");
+ rs.next();
+ int count = rs.getInt("rowcount") ;
+ rs.close() ;
+ if ( count > 1 ) {
+ throw new AlignmentException("Cannot init database: other processes use it");
+ }
+ }
+ // Suppress old database if exists
+ st.executeUpdate("DROP TABLE IF EXISTS server");
+ st.executeUpdate("DROP TABLE IF EXISTS alignment");
+ st.executeUpdate("DROP TABLE IF EXISTS cell");
+ st.executeUpdate("DROP TABLE IF EXISTS extension");
+ // Redo it
+ initDatabase();
+ // Register this server, etc. characteristics (incl. version name)
+ st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('"+host+"','"+port+"','"+rights+"',"+VERSION+")");
+ }
+
+ public void updateDatabase( ) throws SQLException, AlignmentException {
+ Statement st = (Statement) conn.createStatement();
+ // get the version number
+ ResultSet rs = (ResultSet) st.executeQuery("SELECT version FROM server WHERE port='port'");
+ rs.next();
+ int version = rs.getInt("version") ;
+ if ( version < VERSION ) {
+ if ( version >= 302 ) {
+ // Change database
+ st.executeUpdate("ALTER TABLE extension CHANGE method val VARCHAR(500)");
+ st.executeUpdate("ALTER TABLE extension ADD uri VARCHAR(200);");
+ // Modify extensions
+ ResultSet rse = (ResultSet) st.executeQuery("SELECT * FROM extension");
+ Statement st2 = (Statement) conn.createStatement();
+ while ( rse.next() ){
+ String tag = rse.getString("tag");
+ System.err.println(" Treating tag "+tag+" of "+rse.getString("id"));
+ if ( !tag.equals("") ){
+ int pos;
+ String ns;
+ String name;
+ if ( (pos = tag.lastIndexOf('#')) != -1 ) {
+ ns = tag.substring( 0, pos );
+ name = tag.substring( pos+1 );
+ } else if ( (pos = tag.lastIndexOf(':')) != -1 && pos > 5 ) {
+ ns = tag.substring( 0, pos )+"#";
+ name = tag.substring( pos+1 );
+ } else if ( (pos = tag.lastIndexOf('/')) != -1 ) {
+ ns = tag.substring( 0, pos+1 );
+ name = tag.substring( pos+1 );
+ } else {
+ ns = Annotations.ALIGNNS;
+ name = tag;
+ }
+ System.err.println(" >> "+ns+" : "+name);
+ st2.executeUpdate("UPDATE extension SET tag='"+name+"', uri='"+ns+"' WHERE id='"+rse.getString("id")+"' AND tag='"+tag+"'");
+ }
+ }
+ // Change version
+ st.executeUpdate("UPDATE server SET version='"+VERSION+"' WHERE port='port'");
+ } else {
+ throw new AlignmentException("Database must be upgraded ("+version+" -> "+VERSION+")");
+ }
+ }
+ }
+
+}