diff --git a/html/relnotes.html b/html/relnotes.html
index 26d5dc83160a0d88daaffcdf6448f22ee0ca4411..a2934090e0d7dab58224d87c36cbbf16aa6be5e5 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -37,16 +37,19 @@ The development of 4 versions continues.
<h2>Under development (you can contribute)</h2>
<p><ul compact="1">
-<li>Implement <tt>ontowrap</tt> support in database store (server [4.5])</li>
+
<li>Make URIs dependent on a urlprefix (server [4.5])</li>
<li>Provide several URIs for the same alignment (server [4.5])</li>
-<li>Add a <tt>dependsOn</tt> alignment property (api [4.6])</li>
-<li>Consolidate alignment based on <tt>dependsOn</tt> (loop checking,
- cell ingestion) (impl [4.6])</li>
+
<li>Implement database store for EDOAL (server [4.6])</li>
+<li>Add simple "harder" test generator (gen [4.6])</li>
+<li>Add simple "hidden" test generator (gen [4.6])</li>
+<li>Add a <tt>dependsOn</tt> alignment property (api [4.6])</li>
+<li>Consolidate alignment based on <tt>dependsOn</tt> (loop checking, cell ingestion) (impl [4.6])</li>
+
<li>Add a JSON interface (server)</li>
-<li>Integrate tests from generator</li>
-<li>Integrate some basic reasoning.</li>
+<li>Integrate tests from generator (test)</li>
+<li>Integrate some basic reasoning (impl).</li>
<li>Complete tutorial4 with distributed reasoning.</li>
<li>Genericize evaluators in <tt>GraphEvaluator</tt> and <tt>GenPlot</tt> (eval)</li>
<li>Implementation of a provenance metadata tag (server/impl)</li>
@@ -74,11 +77,17 @@ with a warning:
<!--h2>Version 4.6 (1xxx): ??/??/2012 - Da lec'h all</h2-->
<!--h2>Version 4.5 (17xx): ??/??/2012 - Metro</h2-->
<p><ul compact="1">
-<!--li>Upgraded to <span style="color: green"></span> (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">IDDL</span> to 1.4 (lib)</li>
+<li>Replaced Pellet by <span style="color: green">HermiT</span> as default reasonner (lib)</li>
+<li>Added <tt>ontowrap</tt> support in database store (server)</li>
<li>Added several EDOAL-SPARQL renderers (impl)</li>
<li>Added alignment selection per ontologies in list alignment interface (server)</li>
+<li>Implemented transactions in database store (server)</li>
<li>Fixed a (non manifested) bug in cache management (server)</li>
+<li>Fixed a bug in displaying evaluation tables (cli)</li>
<li>Fixed a bug with subsumption statements in <tt>OWLAxiomsRendererVisitor</tt> (impl)</li>
+<li>Simplified <tt>SemPRecEvaluator</tt> when an ontology is inconsistent (impl)</li>
</ul></p>
<h2>Version 4.4 (1754): 17/07/2012 - Casa Cirilo</h2>
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 5925c7d51650497eedcacf55dd2413a90195410d..549650eaa26036e516d5da5c2f811911d87277ff 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, 2006-2012
+ * Copyright (C) INRIA, 2006-2013
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -48,6 +48,8 @@ import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.URICell;
import fr.inrialpes.exmo.align.impl.Namespace;
+import fr.inrialpes.exmo.ontowrap.Ontology;
+
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
@@ -69,16 +71,23 @@ public class CacheImpl {
String port = null;
int rights = 1; // writing rights in the database (default is 1)
- final int VERSION = 400; // Version of the API to be stored in the database
+ // [JE2012:ID] This should now be a local identifier
+ // Only Date/random should be stored.
+ String idprefix = null;
+
+ final int VERSION = 420; // Version of the API to be stored in the database
/* 300: initial database format
- 301: added alignment id as primary key
+ 301: ADDED alignment id as primary key
302: ALTERd cached/stored/ouri tag forms
310: ALTERd extension table with added URIs and method -> val
340: ALTERd size of relation in cell table (5 -> 25)
400: ALTERd size of relation in cell table (5 -> 255 because of URIs)
ALTERd all URI size to 255
ALTERd level size to 25
- added cell_id as keys?
+ ADDED cell_id as keys?
+ 450: ADDED ontology database / reduced alignment database [JE2012:ONTO]
+ ADDED prefix in server [JE2012:ID] I want to have only the suffix to be stored as ID
+ ADDED dependency database [JE2012:DEPEND]
*/
DBService service = null;
@@ -92,6 +101,7 @@ public class CacheImpl {
static private final String SVCNS = Namespace.ALIGNSVC.getUriPrefix();
static private final String CACHED = "cached";
static private final String STORED = "stored";
+ // [JE2012:ID][JE2013]static private final String ALID = "alid";
static private final String OURI1 = "ouri1";
static private final String OURI2 = "ouri2";
@@ -123,6 +133,9 @@ public class CacheImpl {
public void init( Properties p ) throws SQLException, AlignmentException {
port = p.getProperty("http"); // bad idea
host = p.getProperty("host");
+ // [JE2012:ID]
+ idprefix = p.getProperty("uriprefix");
+ if ( idprefix == null || idprefix.equals("") ) idprefix = "http://"+host+":"+port;
Statement st = createStatement();
// test if a database is here, otherwise create it
ResultSet rs = conn.getMetaData().getTables(null,null, "server", new String[]{"TABLE"});
@@ -133,6 +146,7 @@ public class CacheImpl {
}
// register by the database
st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('"+host+"','"+port+"','"+rights+"',"+VERSION+")");
+ // [JE2012:ID][JE2013] st.executeUpdate("INSERT INTO server (host, port, prefix, edit, version) VALUES ('"+host+"','"+port+"','"+idprefix+"','"+rights+"',"+VERSION+")");
st.close();
// load alignment descriptions
loadAlignments( true );
@@ -230,6 +244,7 @@ public class CacheImpl {
* in an alignment object
*
* Beware, the Alignment API has two attributes:
+ * [JE2012:ONTO] TO BE REVISED
* onto1 is the Ontology object
* uri1 is the URI object from which loading the ontologies
* In the database we store:
@@ -253,6 +268,7 @@ public class CacheImpl {
query = "SELECT * FROM alignment WHERE id = '" + id +"'";
rs = st.executeQuery(query);
while(rs.next()) {
+ /*
// Either uri1 or file1
result.setFile1( new URI( rs.getString("file1") ) );
result.setFile2( new URI( rs.getString("file2") ) );
@@ -260,10 +276,38 @@ public class CacheImpl {
result.getOntologyObject2().setURI( new URI(rs.getString("ontology2")) );
result.setExtension( SVCNS, OURI1, rs.getString("ontology1") );
result.setExtension( SVCNS, OURI2, rs.getString("ontology2") );
+ //result.getOntologyObject1().setURI( new URI(rs.getString("ontology1")) );
+ //result.getOntologyObject2().setURI( new URI(rs.getString("ontology2")) );
+ */
result.setLevel(rs.getString("level"));
result.setType(rs.getString("type"));
}
+ // Get ontologies [JE2012:ONTO]
+ query = "SELECT * FROM ontology WHERE id = '" + id +"'";
+ rs = st.executeQuery(query);
+ while(rs.next()) {
+ if ( rs.getBoolean("source") ) {
+ result.getOntologyObject1().setURI( new URI(rs.getString("uri")) );
+ if ( rs.getString("file") != null )
+ result.setFile1( new URI( rs.getString("file") ) );
+ if ( rs.getString("formuri") != null )
+ result.getOntologyObject1().setFormURI( new URI(rs.getString("formuri")) );
+ if ( rs.getString("formname") != null )
+ result.getOntologyObject1().setFormalism( rs.getString("formname") );
+ result.setExtension( SVCNS, OURI1, rs.getString("uri") );
+ } else {
+ result.getOntologyObject2().setURI( new URI(rs.getString("uri")) );
+ if ( rs.getString("file") != null )
+ result.setFile2( new URI( rs.getString("file") ) );
+ if ( rs.getString("formuri") != null )
+ result.getOntologyObject2().setFormURI( new URI(rs.getString("formuri")) );
+ if ( rs.getString("formname") != null )
+ result.getOntologyObject2().setFormalism( rs.getString("formname") );
+ result.setExtension( SVCNS, OURI2, rs.getString("uri") );
+ }
+ }
+
// Get extension metadata
query = "SELECT * FROM extension WHERE id = '" + id + "'";
rs = st.executeQuery(query);
@@ -287,7 +331,7 @@ public class CacheImpl {
}
/**
- * loads the full alignments from the database and put them in the
+ * loads the full alignment from the database and put it in the
* alignmentTable hastable
*
* should be invoked when:
@@ -351,6 +395,17 @@ public class CacheImpl {
}
// Public because this is now used by AServProtocolManager
+ public String generateAlignmentUri() {
+ // Generate an id based on a URI prefix + Date + random number
+ return idprefix + "/alid/" + generateId();
+ }
+
+ private String generateId() {
+ // Generate an id based on Date + random number
+ return new Date().getTime() + "/" + randomNum();
+ }
+
+ // Public because this is now used by AServProtocolManager [JE2012:ID][JE2013] useless
public String generateAlignmentId() {
// Generate an id based on a URI prefix + Date + random number
return "http://"+host+":"+port+"/alid/" + new Date().getTime() + "/" + randomNum();
@@ -403,8 +458,9 @@ public class CacheImpl {
}
// If not cached, retrieve it now
- if ( result.getExtension( SVCNS, CACHED) == ""
- && result.getExtension(SVCNS, STORED) != "") {
+ if ( ( result.getExtension( SVCNS, CACHED) == null || result.getExtension( SVCNS, CACHED).equals("") )
+ && result.getExtension(SVCNS, STORED) != null
+ && !result.getExtension(SVCNS, STORED).equals("") ) {
try { retrieveAlignment( id, result ); }
catch (URISyntaxException urisex) {
System.err.println("Cache: cannot read from DB");
@@ -462,6 +518,7 @@ public class CacheImpl {
*/
public String recordNewAlignment( Alignment alignment, boolean force ) {
try { return recordNewAlignment( generateAlignmentId(), alignment, force );
+ //[JE2012:ID][2013]try { return recordNewAlignment( generateAlignmentUri(), alignment, force );
} catch (AlignmentException ae) { return (String)null; }
}
@@ -490,7 +547,9 @@ public class CacheImpl {
//CLD put in comment this line for allowing to create a new ID for any alignment
//if ( alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ) == null )
alignment.setExtension( Namespace.ALIGNMENT.uri, Annotations.ID, id );
-
+ // [JE2012:ID] set only the suffix, please!!
+ // [JE2012:ID][JE2013]alignment.setExtension( SVCNS, ALID, id );
+
// Store it
try {
URI ouri1 = new URI( alignment.getExtension( SVCNS, OURI1) );
@@ -597,40 +656,51 @@ public class CacheImpl {
public void unstoreAlignment( String id, Alignment alignment ) throws SQLException, AlignmentException {
Statement st = createStatement();
- String query = null;
- for ( Cell c : alignment ) {
- String cellid = c.getId();
- if ( cellid != null && !cellid.equals("") ) {
- query = "DELETE FROM extension WHERE id='"+cellid+"'";
- st.executeUpdate(query);
+ try {
+ conn.setAutoCommit( false );
+ String query = null;
+ for ( Cell c : alignment ) {
+ String cellid = c.getId();
+ if ( cellid != null && !cellid.equals("") ) {
+ query = "DELETE FROM extension WHERE id='"+cellid+"'";
+ st.executeUpdate(query);
+ }
}
+ st.executeUpdate("DELETE FROM cell WHERE id='"+id+"'");
+ st.executeUpdate("DELETE FROM extension WHERE id='"+id+"'");
+ // [JE2012:ONTO]
+ st.executeUpdate("DELETE FROM ontology WHERE id='"+id+"'");
+ // [JE2012:DEPEND] certainly something to do with dependencies
+ //st.executeUpdate("DELETE FROM dependencies WHERE id='"+id+"'");
+ st.executeUpdate("DELETE FROM alignment WHERE id='"+id+"'");
+ alignment.setExtension( SVCNS, STORED, (String)null);
+ } catch ( SQLException sex ) {
+ conn.rollback();
+ throw sex;
+ } finally {
+ conn.setAutoCommit( false );
+ st.close();
}
- query = "DELETE FROM cell WHERE id='"+id+"'";
- st.executeUpdate(query);
- query = "DELETE FROM extension WHERE id='"+id+"'";
- st.executeUpdate(query);
- query = "DELETE FROM alignment WHERE id='"+id+"'";
- st.executeUpdate(query);
- alignment.setExtension( SVCNS, STORED, (String)null);
- st.close();
}
- public void storeAlignment( String id ) throws AlignmentException, SQLException {
+ public void storeAlignment( String id ) throws AlignmentException, SQLException {
String query = null;
- Alignment alignment = getAlignment( id );
+ BasicAlignment alignment = (BasicAlignment)getAlignment( id );
+ //[2013]-Alignment alignment = getAlignment( id );
Statement st = null;
// We store stored date
alignment.setExtension( SVCNS, STORED, new Date().toString());
// We empty cached date
alignment.setExtension( SVCNS, CACHED, "");
- //Try to store at most 3 times. Otherwise, an exception EOFException will be thrown.
- for(int i=0; i < 3 ; i++) {
+ // Try to store at most 3 times. Otherwise, an exception EOFException will be thrown.
+ // [JE2013: Can we check this?]
+ for( int i=0; i < 3 ; i++ ) {
st = createStatement();
- try {
+ try { //-[JE2013] Suppressed below
+ /*
String s_O1 = alignment.getExtension(SVCNS, OURI1);
String s_O2 = alignment.getExtension(SVCNS, OURI2);
-
// file attribute
String s_File1 = null;
String s_File2 = null;
@@ -638,70 +708,92 @@ public class CacheImpl {
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, ontology1, ontology2, 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 ( String[] ext : alignment.getExtensions() ) {
- String uri = ext[0];
- String tag = ext[1];
- String val = ext[2];
- query = "INSERT INTO extension " +
- "(id, uri, tag, val) " +
- "VALUES ('" + quote(id) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
+ // [JE2013] Suppressed until here */
+
+ // [JE2012:ONTO]
+ try {
+ conn.setAutoCommit( false );
+ query = "INSERT INTO alignment " +
+ "(id, type, level) " +
+ "VALUES ('"+quote(id)+"','"+quote(alignment.getType())+"','"+quote(alignment.getLevel()) +"')";
+ //query = "INSERT INTO alignment " +
+ // "(id, ontology1, ontology2, 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( Cell c : alignment ) {
- String cellid = null;
- if ( c.getObject1() != null && c.getObject2() != null ){
- cellid = c.getId();
- if ( cellid != null ){
- if ( cellid.startsWith("#") ) {
- cellid = alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ) + cellid;
- }
- } else if ( c.getExtensions() != null ) {
- // JE: In case of extensions create an ID
- c.setId( generateCellId( id ) );
- cellid = c.getId();
- }
- else cellid = "";
- String uri1 = c.getObject1AsURI(alignment).toString();
- String uri2 = c.getObject2AsURI(alignment).toString();
- String strength = c.getStrength() + ""; // crazy Java
- String sem;
- if ( !c.getSemantics().equals("first-order") )
- sem = c.getSemantics();
- else sem = "";
- String rel = ((BasicRelation)c.getRelation()).getRelation();
- query = "INSERT INTO cell " +
- "(id, cell_id, uri1, uri2, measure, semantics, relation) " +
- "VALUES ('" + quote(id) + "','" + quote(cellid) + "','" + quote(uri1) + "','" + quote(uri2) + "','" + quote(strength) + "','" + quote(sem) + "','" + quote(rel) + "')";
+
+ // [JE2012:ONTO]
+ recordOntology( st, id, true,
+ alignment.getOntology1URI().toString(),
+ alignment.getFile1(),
+ alignment.getOntologyObject1() );
+ recordOntology( st, id, false,
+ alignment.getOntology2URI().toString(),
+ alignment.getFile2(),
+ alignment.getOntologyObject2() );
+
+ // [JE2012:DEPEND] store dependencies
+ for ( String[] ext : alignment.getExtensions() ) {
+ String uri = ext[0];
+ String tag = ext[1];
+ String val = ext[2];
+ query = "INSERT INTO extension " +
+ "(id, uri, tag, val) " +
+ "VALUES ('" + quote(id) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
st.executeUpdate(query);
}
- if ( cellid != null && !cellid.equals("") && c.getExtensions() != null ) {
- // Store extensions
- for ( String[] ext : c.getExtensions() ) {
- String uri = ext[0];
- String tag = ext[1];
- String val = ext[2];
- query = "INSERT INTO extension " +
- "(id, uri, tag, val) " +
- "VALUES ('" + quote(cellid) + "','" + quote(uri) + "','" + quote(tag) + "','" + quote(val) + "')";
+
+ for( Cell c : alignment ) {
+ String cellid = null;
+ if ( c.getObject1() != null && c.getObject2() != null ){
+ cellid = c.getId();
+ if ( cellid != null ){
+ if ( cellid.startsWith("#") ) {
+ cellid = alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ) + cellid;
+ }
+ } else if ( c.getExtensions() != null ) {
+ // JE: In case of extensions create an ID
+ c.setId( generateCellId( id ) );
+ cellid = c.getId();
+ }
+ else cellid = "";
+ String uri1 = c.getObject1AsURI(alignment).toString();
+ String uri2 = c.getObject2AsURI(alignment).toString();
+ String strength = c.getStrength() + ""; // crazy Java
+ String sem;
+ if ( !c.getSemantics().equals("first-order") )
+ sem = c.getSemantics();
+ else sem = "";
+ String rel = ((BasicRelation)c.getRelation()).getRelation();
+ query = "INSERT INTO cell " +
+ "(id, cell_id, uri1, uri2, measure, semantics, relation) " +
+ "VALUES ('" + quote(id) + "','" + quote(cellid) + "','" + quote(uri1) + "','" + quote(uri2) + "','" + quote(strength) + "','" + quote(sem) + "','" + quote(rel) + "')";
st.executeUpdate(query);
}
+ if ( cellid != null && !cellid.equals("") && c.getExtensions() != null ) {
+ // Store extensions
+ for ( String[] ext : c.getExtensions() ) {
+ String uri = ext[0];
+ String tag = ext[1];
+ String val = 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) {
- // We should cancel this... IF NOT STORED!
+ } catch ( SQLException sex ) {
+ conn.rollback();
+ throw sex;
+ } finally {
+ conn.setAutoCommit( true );
+ }
+ } catch ( Exception e ) {
//System.err.println("Cannot store id=" + id );
alignment.setExtension( SVCNS, STORED, (String)null );
e.printStackTrace();
@@ -714,6 +806,26 @@ public class CacheImpl {
resetCacheStamp(alignment);
}
+ // [JE2012:ONTO]
+ // Do not add transaction here (only one action+this is handled by caller)
+ public void recordOntology( Statement st, String id, boolean source, String uri, URI file, Ontology onto ) throws SQLException {
+ String sfile = "";
+ if ( file != null ) sfile = file.toString();
+ String query = null;
+
+ if ( onto != null ) {
+ // JE2013: One of the two getOnt may be null
+ query = "INSERT INTO ontology " +
+ "(id, uri, file, source, formname, formuri) " +
+ "VALUES ('"+quote(id)+"','"+ quote(uri)+"','"+quote(sfile)+"','" +(source?'1':'0')+"','"+quote(onto.getFormalism())+"','"+quote(onto.getFormURI().toString())+"')";
+ } else {
+ query = "INSERT INTO ontology " +
+ "(id, uri, file, source) " +
+ "VALUES ('"+quote(id)+"','"+ quote(uri)+"','"+quote(sfile)+"','" +(source?'1':'0')+"')";
+ }
+ st.executeUpdate(query);
+ }
+
//**********************************************************************
// CACHE MANAGEMENT (Not implemented yet)
public void resetCacheStamp( Alignment result ){
@@ -737,6 +849,7 @@ public class CacheImpl {
create table server (
host varchar(50),
port varchar(5),
+ [JE2012:ID]prefix varchar(50),
edit varchar(5)
);
@@ -745,16 +858,28 @@ public class CacheImpl {
create table alignment (
id varchar(100),
- ontology1 varchar(255),
- ontology2 varchar(255),
type varchar(5),
level varchar(25),
- file1 varchar(255),
- file2 varchar(255),
- uri1 varchar(255),
- uri2 varchar(255),
primary key (id));
+ # ontology info
+
+ create table ontology (
+ id varchar(255),
+ uri varchar(255),
+ file varchar(255),
+ source boolean,
+ formname varchar(50),
+ formuri varchar(255)
+ );
+
+ # dependencies info [JE2012:DEPEND]
+
+ create table dependencies (
+ id varchar(255),
+ dependsOn varchar(255)
+ );
+
# cell info
create table cell(
@@ -777,51 +902,81 @@ public class CacheImpl {
*/
public void initDatabase() throws SQLException {
+ System.err.println ( "Initialising database" );
Statement st = createStatement();
- // Create tables
- st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), ontology1 VARCHAR(255), ontology2 VARCHAR(255), type VARCHAR(5), level VARCHAR(25), file1 VARCHAR(255), file2 VARCHAR(255), uri1 VARCHAR(255), uri2 VARCHAR(255), primary key (id))");
- st.executeUpdate("CREATE TABLE cell(id VARCHAR(100), cell_id VARCHAR(255), uri1 VARCHAR(255), uri2 VARCHAR(255), semantics VARCHAR(30), measure VARCHAR(20), relation VARCHAR(255))");
- st.executeUpdate("CREATE TABLE extension(id VARCHAR(100), uri VARCHAR(200), tag VARCHAR(50), val VARCHAR(500))");
- st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), edit BOOLEAN, version VARCHAR(5))");
- st.close();
+ try {
+ conn.setAutoCommit( false );
+ // Create tables
+ //[JE2012:ONTO]
+ st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), type VARCHAR(5), level VARCHAR(25), primary key (id))");
+ //-[JE2013]st.executeUpdate("CREATE TABLE alignment (id VARCHAR(100), ontology1 VARCHAR(255), ontology2 VARCHAR(255), type VARCHAR(5), level VARCHAR(25), file1 VARCHAR(255), file2 VARCHAR(255), uri1 VARCHAR(255), uri2 VARCHAR(255), 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))");
+ //[JE2012:DEPEND][JE2013]st.executeUpdate("CREATE TABLE dependencies (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))");
+ st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), edit BOOLEAN, version VARCHAR(5))");
+ //[JE2012:ID][JE2013]st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), prefix VARCHAR (50), edit BOOLEAN, version VARCHAR(5))");
+ st.close();
- // Because of the values (that some do not like, this is a special statement
- PreparedStatement pst = conn.prepareStatement("INSERT INTO server (host, port, edit, version) VALUES ('dbms','port',?,?)");
- pst.setBoolean(1,false);
- pst.setString(2,VERSION+"");
- pst.executeUpdate();
- pst.close();
+ // Because of the values (that some do not like), this is a special statement
+ PreparedStatement pst = conn.prepareStatement("INSERT INTO server (host, port, edit, version) VALUES ('dbms','port',?,?)");
+ //[JE2012:ID][JE2013]PreparedStatement pst = conn.prepareStatement("INSERT INTO server (host, port, prefix, edit, version) VALUES ('dbms','port','idprefix',?,?)");
+ pst.setBoolean(1,false);
+ pst.setString(2,VERSION+"");
+ pst.executeUpdate();
+ pst.close();
+ } catch ( SQLException sex ) {
+ conn.rollback();
+ throw sex;
+ } finally {
+ conn.setAutoCommit( true );
+ }
}
public void resetDatabase( boolean force ) throws SQLException, AlignmentException {
Statement st = createStatement();
- // Check that no one else is connected...
- if ( force != true ){
- ResultSet rs = 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");
+ try {
+ conn.setAutoCommit( false );
+ // Check that no one else is connected...
+ if ( force != true ){
+ ResultSet rs = 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 ontology");
+ st.executeUpdate("DROP TABLE IF EXISTS dependencies");
+ 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)
+ PreparedStatement pst = conn.prepareStatement("INSERT INTO server (host, port, edit, version) VALUES (?,?,?,?)");
+ //[JE2012:ID][JE2013]PreparedStatement pst = conn.prepareStatement("INSERT INTO server (host, port, prefix, edit, version) VALUES (?,?,?,?,?)");
+ pst.setString(1,host);
+ pst.setString(2,port);
+ pst.setBoolean(3,rights==1);
+ pst.setString(4,VERSION+"");
+ /*[JE2012:ID][JE2013]
+ pst.setString(3,idprefix);
+ pst.setBoolean(4,rights==1);
+ pst.setString(5,VERSION+"");*/
+ pst.executeUpdate();
+ pst.close();
+ } catch ( SQLException sex ) {
+ conn.rollback();
+ throw sex;
+ } finally {
+ st.close();
+ conn.setAutoCommit( true );
}
- // 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();
- st.close();
-
- // Register this server, etc. characteristics (incl. version name)
- PreparedStatement pst = conn.prepareStatement("INSERT INTO server (host, port, edit, version) VALUES (?,?,?,?)");
- pst.setString(1,host);
- pst.setString(2,port);
- pst.setBoolean(3,rights==1);
- pst.setString(4,VERSION+"");
- pst.executeUpdate();
- pst.close();
}
/*
@@ -829,9 +984,17 @@ public class CacheImpl {
* each dbms has its own language for manipulating table columns....
*/
public void renameColumn(Statement st, String tableName, String oldName, String newName, String newType) throws SQLException {
- st.executeUpdate("ALTER TABLE "+tableName+" ADD "+newName+" "+newType);
- st.executeUpdate("UPDATE "+tableName+" SET "+newName+"="+oldName);
- st.executeUpdate("ALTER TABLE "+tableName+" DROP "+oldName);
+ try {
+ conn.setAutoCommit( false );
+ st.executeUpdate("ALTER TABLE "+tableName+" ADD "+newName+" "+newType);
+ st.executeUpdate("UPDATE "+tableName+" SET "+newName+"="+oldName);
+ st.executeUpdate("ALTER TABLE "+tableName+" DROP "+oldName);
+ } catch ( SQLException sex ) {
+ conn.rollback();
+ throw sex;
+ } finally {
+ conn.setAutoCommit( true );
+ }
}
/*
@@ -839,20 +1002,29 @@ public class CacheImpl {
* each dbms has its own language for manipulating table columns....
*/
public void changeColumnType(Statement st, String tableName, String columnName, String newType) throws SQLException {
- String tempName = columnName+"temp";
- renameColumn(st,tableName,columnName,tempName,newType);
- renameColumn(st,tableName,tempName,columnName,newType);
+ try {
+ conn.setAutoCommit( false );
+ String tempName = columnName+"temp";
+ renameColumn(st,tableName,columnName,tempName,newType);
+ renameColumn(st,tableName,tempName,columnName,newType);
+ } catch ( SQLException sex ) {
+ conn.rollback();
+ throw sex;
+ } finally {
+ conn.setAutoCommit( true );
+ }
}
public void updateDatabase() throws SQLException, AlignmentException {
Statement st = createStatement();
- // get the version number
+ // get the version number (port is the entry which is always here)
ResultSet rs = st.executeQuery("SELECT version FROM server WHERE port='port'");
rs.next();
int version = rs.getInt("version") ;
if ( version < VERSION ) {
if ( version >= 302 ) {
if ( version < 310 ) {
+ System.err.println ( "Upgrading to version 3.1" );
// ALTER database
renameColumn(st,"extension","method","val","VARCHAR(500)");
// case mysql
@@ -889,19 +1061,8 @@ public class CacheImpl {
}
// Nothing to do with 340: subsumed by 400
if ( version < 400 ) {
- // ALTER database
- /*
- st.executeUpdate("ALTER TABLE cell CHANGE relation relation VARCHAR(255)");
- st.executeUpdate("ALTER TABLE cell CHANGE uri1 uri1 VARCHAR(255)");
- st.executeUpdate("ALTER TABLE cell CHANGE uri2 uri2 VARCHAR(255)");
- st.executeUpdate("ALTER TABLE alignment CHANGE level level VARCHAR(25)");
- st.executeUpdate("ALTER TABLE alignment CHANGE uri1 uri1 VARCHAR(255)");
- st.executeUpdate("ALTER TABLE alignment CHANGE uri2 uri2 VARCHAR(255)");
- st.executeUpdate("ALTER TABLE alignment CHANGE file1 file1 VARCHAR(255)");
- st.executeUpdate("ALTER TABLE alignment CHANGE file2 file2 VARCHAR(255)");
- st.executeUpdate("ALTER TABLE alignment CHANGE owlontology1 ontology1 VARCHAR(255)");
- st.executeUpdate("ALTER TABLE alignment CHANGE owlontology2 ontology2 VARCHAR(255)");
- */
+ System.err.println("Upgrading to version 4.0");
+ // ALTER database
changeColumnType(st,"cell","relation", "VARCHAR(255)");
changeColumnType(st,"cell","uri1", "VARCHAR(255)");
changeColumnType(st,"cell","uri2", "VARCHAR(255)");
@@ -914,11 +1075,46 @@ public class CacheImpl {
renameColumn(st,"alignment","owlontology1","ontology1", "VARCHAR(255)");
renameColumn(st,"alignment","owlontology2","ontology2", "VARCHAR(255)");
-
-
-
+ }
+ if ( version < 410 ) {
+ System.err.println("Upgrading to version 4.1");
+ // [JE2012:ONTO]
+ 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();
+ // No Ontology _type_ available then
+ 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 < 430 ) {
+ System.err.println("Upgrading to version 4.2");
+ // [JE2012:ID][JE2013:this works]
+ // Add new column in server table
+ //st.executeUpdate("ALTER TABLE server ADD prefix VARCHAR(50);");
+ //st.executeUpdate("UPDATE server SET prefix='"+idprefix+"'");
+ // Reset id in Alignment to suffix
+ // TODO...
+ }
+ if ( version < 440 ) {
+ System.err.println("Upgrading to version 4.3");
+ // [JE2012:DEPEND][JE2013:this works]
+ //st.executeUpdate("CREATE TABLE dependencies (id VARCHAR(255), dependsOn VARCHAR(255))");
+ }
+ if ( version < 420 ) {
+ System.err.println("Upgrading to version 4.4");
+ // [JE2012:ONTO]
+ 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");
}
// ALTER version
+ // [JE2013: better alter it everywere]
st.executeUpdate("UPDATE server SET version='"+VERSION+"' WHERE port='port'");
} else {
throw new AlignmentException("Database must be upgraded ("+version+" -> "+VERSION+")");