Mentions légales du service

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Commit 8079c4b8 authored by Jérôme Euzenat's avatar Jérôme Euzenat
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- reengineered the Database/Cache interface separation 

- improved the Cache implementation by separating ontology/alignment (real cache)
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src/fr/inrialpes/exmo/align/service/Cache.java
+ 9
− 5
View file @ 8079c4b8
......@@ -21,12 +21,16 @@
package fr.inrialpes.exmo.align.service;
import java.net.URI;
import java.util.Vector;
import java.util.Set;
import java.sql.SQLException;
import org.semanticweb.owl.align.Alignment;
public interface Cache {
int loading();
Alignment get(long id);
Vector get(URI uri);
Vector get(URI uri1, URI uri2);
void init() throws SQLException;
Alignment getMetadata( String id );
Alignment getAlignment( String id ) throws Exception;
Set getAlignments( URI uri );
Set getAlignments( URI uri1, URI uri2 );
void recordAlignment( Alignment alignment, boolean force );
void storeAlignment( String id ) throws Exception;
}
src/fr/inrialpes/exmo/align/service/CacheImpl.java
+ 316
− 183
View file @ 8079c4b8
......@@ -20,218 +20,351 @@
package fr.inrialpes.exmo.align.service;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Vector;
import java.util.Set;
import java.util.HashSet;
import java.net.URI;
import java.net.URISyntaxException;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.Statement;
import java.util.Hashtable;
import java.util.Vector;
import java.sql.SQLException;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.io.owl_rdf.OWLRDFParser;
import org.semanticweb.owl.util.OWLManager;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLException;
import org.semanticweb.owl.util.OWLManager;
import fr.inrialpes.exmo.align.impl.BasicRelation;
import fr.inrialpes.exmo.align.impl.BasicAlignment;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLException;
/**
* 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 implements Cache {
Hashtable alignmentTable = null;
Hashtable alignmentTable = null;
Hashtable ontologyTable = null;
Statement st = null;
ResultSet rs = null;
Connection conn = null;
Statement st = null;
ResultSet rs = null;
Connection conn = null;
final int CONNECTION_ERROR = 1;
final int SUCCESS = 2;
final int INIT_ERROR = 3;
final int CONNECTION_ERROR = 1;
final int SUCCESS = 2;
final int INIT_ERROR = 3;
public CacheImpl(Connection conn) {
try {
this.conn = conn;
st = (Statement) conn.createStatement();
} catch(Exception e) {System.out.println(e.toString());}
//**********************************************************************
public CacheImpl( DBService service ) {
try {
this.conn = service.getConnection();
st = (Statement) conn.createStatement();
} catch(Exception e) {
// Rather raise an exception
System.err.println(e.toString());
}
alignmentTable = new Hashtable();
ontologyTable = new Hashtable();
}
/**
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
*/
public void init() throws SQLException {
loadAlignments( true );
}
//**********************************************************************
/**
* 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 idInfo = new Vector();
public int loading() {
alignmentTable = new Hashtable();
if(loadAlignment(true)) return SUCCESS;
else return INIT_ERROR;
if (force) {
// Retrieve the alignment ids
query = "select id " + "from alignment";
rs = (ResultSet) st.executeQuery(query);
//System.err.println("1234");
while(rs.next()) {
id = rs.getString("id");
idInfo.add(id);
//System.err.println(id);
}
// For each alignment id store metadata
for( int i = 0; i < idInfo.size(); i ++ ) {
id = (String)idInfo.get(i);
alignment = retrieveDescription( id );
recordAlignment( id, alignment, true );
}
}
}
/**
* loads the description of alignments from the database and set them
* in an alignment object
*/
protected Alignment retrieveDescription( String id ){
String query;
String tag;
String method;
OWLEntity ent1 = null, ent2 = null;
Cell cell = null;
Alignment result = new BasicAlignment();
private boolean loadAlignment(boolean force){
String query = null;
String id = null;
Alignment alignment = null;
Vector idInfo = new Vector();
if (force) {
try {
query = "select id " + "from alignment";
rs = (ResultSet) st.executeQuery(query);
System.out.println("1234");
while(rs.next()) {
id = rs.getString("id");
idInfo.add(id);
System.out.println(id);
}
for( int i = 0; i < idInfo.size(); i ++ ) {
id = (String) idInfo.get(i);
alignment = retrieve(Long.parseLong(id));
alignmentTable.put(id, alignment);
}
} catch (Exception e) {System.out.println("Hashtable loading error1");}
return true;
}
else return false;
try {
// Get basic ontology metadata
query = "select * "+"from alignment "+"where id = " + id;
rs = (ResultSet) st.executeQuery(query);
while(rs.next()) {
result.setFile1(new URI(rs.getString("uri1")));
result.setFile2(new URI(rs.getString("uri2")));
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");
method = rs.getString("method");
result.setExtension(tag, method);
}
} catch (Exception e) {
System.err.println("No problem");
System.err.println(e.toString());
return null;
}
result.setExtension("fr.inrialpes.exmo.align.service.stored", "DATE");
result.setExtension("fr.inrialpes.exmo.align.service.cached", "");
return result;
}
/**
* loads the full alignments from the database and put them in the
* alignmentTable hastable
*
* should be invoked when:
* ( result.getExtension("fr.inrialpes.exmo.align.service.cached") == ""
* && result.getExtension("fr.inrialpes.exmo.align.service.stored") != "") {
*/
protected Alignment retrieveAlignment( String id, Alignment result ) throws SQLException, AlignmentException, URISyntaxException, OWLException {
OWLOntology o1 = null;
OWLOntology o2 = null;
String query;
String tag;
String method;
OWLEntity ent1 = null, ent2 = null;
Cell cell = null;
// Load the ontologies
o1 = loadOntology(result.getFile1());
o2 = loadOntology(result.getFile2());
result.setOntology1(o1);
result.setOntology1(o2);
protected Alignment retrieve(long id){
OWLOntology o1 = null;
OWLOntology o2 = null;
String query;
String tag;
String method;
OWLEntity ent1 = null, ent2 = null;
Cell cell = null;
Alignment result = new BasicAlignment();
try {
query = "select * " +
"from alignment " +
"where id = " + id;
rs = (ResultSet) st.executeQuery(query);
while(rs.next()) {
o1 = loadOntology(new URI(rs.getString("uri1")));
o2 = loadOntology(new URI(rs.getString("uri2")));
result.setLevel(rs.getString("level"));
result.setType(rs.getString("type"));
result.setOntology1(o1);
result.setOntology2(o2);
}
query = "select * " +
"from extension " +
"where id = " + id;
rs = (ResultSet) st.executeQuery(query);
while(rs.next()) {
tag = rs.getString("tag");
method = rs.getString("method");
result.setExtension(tag, method);
}
query = "select * " +
"from cell " +
"where id = " + id;
rs = (ResultSet) st.executeQuery(query);
while(rs.next()) {
ent1 = (OWLEntity) o1.getClass(new URI(rs.getString("uri1")));
ent2 = (OWLEntity) o2.getClass(new URI(rs.getString("uri2")));
if(ent1 == null || ent2 == null) break;
cell = result.addAlignCell(ent1, ent2, rs.getString("relation"), Double.parseDouble(rs.getString("measure")));
cell.setId(rs.getString("cell_id"));
cell.setSemantics(rs.getString("semantics"));
}
} catch (Exception e) {
System.out.println("No problem");
System.out.println(e.toString());
return null;
}
return result;
// Get extension metadata
query = "select * "+"from extension "+"where id = " + id;
rs = (ResultSet) st.executeQuery(query);
while(rs.next()) {
tag = rs.getString("tag");
method = rs.getString("method");
result.setExtension(tag, method);
}
private boolean loadOne(long id, Alignment alignment, boolean force){
if (force) {
try {
alignmentTable.put(Long.toString(id), alignment);
} catch (Exception e) {System.out.println("Hashtable loading error2");}
return true;
}
else return false;
}
public Alignment get(long id) {
Alignment result = null;
String query = null;
try {
result = (Alignment) alignmentTable.get(Long.toString(id));
if (result == null) {
query = "select id " + "from alignment " + "where id = " + id;
rs = (ResultSet) st.executeQuery(query);
if(rs == null) return null;
else {
while (rs.next()) {
result = retrieve(id);
loadOne(id, result, true);
}
}
}
} catch (Exception e) {System.out.println("Alignment Finding Exception1");}
return result;
// Get cells
query = "select * "+"from cell "+"where id = " + id;
rs = (ResultSet) st.executeQuery(query);
while(rs.next()) {
ent1 = (OWLEntity) o1.getClass(new URI(rs.getString("uri1")));
ent2 = (OWLEntity) o2.getClass(new URI(rs.getString("uri2")));
if(ent1 == null || ent2 == null) break;
cell = result.addAlignCell(ent1, ent2, rs.getString("relation"), Double.parseDouble(rs.getString("measure")));
cell.setId(rs.getString("cell_id"));
cell.setSemantics(rs.getString("semantics"));
}
result.setExtension("fr.inrialpes.exmo.align.service.stored", "DATE");
// Put the date here
result.setExtension("fr.inrialpes.exmo.align.service.cached", "DATE");
return result;
}
private String generateAlignmentId() {
// Generate an id based on a URI prefix + Date + random number
return "http://blavlacestmoi";
}
//**********************************************************************
/**
* retrieve alignment metadata from id
*/
public Alignment getMetadata( String id ) {
Alignment result = null;
String query = null;
public Vector get(URI uri) {
Vector result = new Vector();
result = (Alignment)alignmentTable.get( id );
Alignment temp = null;
String query = null;
try {
query = "select id " + "from alignment " + "where uri1 = \'" + uri + "\' OR uri2 = \'" + uri + "\'";
System.out.println(query);
rs = (ResultSet) st.executeQuery(query);
if(rs == null) return null;
else {
while (rs.next()) {
System.out.println("1234");
temp = get(Long.parseLong(rs.getString("id")));
result.add(temp);
}
}
} catch (Exception e) {System.out.println("Alignment Finding Exception2");}
return result;
}
// Raise an exception if no result
return result;
}
/**
* retrieve full alignment from id (and cache it)
*/
public Alignment getAlignment( String id ) throws Exception {
Alignment result = null;
String query = null;
public Vector get(URI uri1, URI uri2) {
Vector result = new Vector();
result = (Alignment)alignmentTable.get( id );
Alignment temp = null;
String query = null;
try {
query = "select id " + "from alignment " + "where uri1 = \'" + uri1 + "\' AND uri2 = \'" + uri2 + "\'";
rs = (ResultSet) st.executeQuery(query);
if(rs == null) return null;
else {
while (rs.next()) {
temp = get(Long.parseLong(rs.getString("id")));
result.add(temp);
}
}
} catch (Exception e) {System.out.println("Alignment Finding Exception3");}
return result;
if ( result.getExtension("fr.inrialpes.exmo.align.service.cached") == "" && result.getExtension("fr.inrialpes.exmo.align.service.stored") != "") {
retrieveAlignment( id, result );
}
// Raise an exception if no result
return result;
}
public static OWLOntology loadOntology(URI uri) throws Exception {
OWLRDFParser parser = new OWLRDFParser();
parser.setConnection(OWLManager.getOWLConnection());
return parser.parseOntology(uri);
//**********************************************************************
public Set getAlignments( URI uri ) {
return (Set)ontologyTable.get( uri );
}
public Set getAlignments( URI uri1, URI uri2 ) {
// Crete the set and compare
return (Set)ontologyTable.get( uri1 );
}
/**
* records newly created alignment
*/
public void recordAlignment( Alignment alignment, boolean force ){
recordAlignment( generateAlignmentId(), alignment, force );
}
/**
* records alignment identified by id
*/
public void recordAlignment( String id, Alignment alignment, boolean force ){
if ( force || alignmentTable.get( id ) == null ) {
Set s1 = (Set)ontologyTable.get( alignment.getFile1() );
if ( s1 == null ) {
s1 = new HashSet();
ontologyTable.put( alignment.getFile1(), s1 );
}
s1.add( alignment );
Set s2 = (Set)ontologyTable.get( alignment.getFile2() );
if ( s2 == null ) {
s2 = new HashSet();
ontologyTable.put( alignment.getFile1(), s2 );
}
s2.add( alignment );
alignmentTable.put( id, alignment );
}
}
//**********************************************************************
public void storeAlignment( String id ) throws Exception {
String query = null;
Alignment alignment = null;
alignment = getAlignment( id );
try {
OWLOntology O1 = (OWLOntology)alignment.getOntology1();
OWLOntology O2 = (OWLOntology)alignment.getOntology2();
String s_O1 = O1.getLogicalURI().toString();
String s_O2 = O2.getLogicalURI().toString();
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();
String s_uri1 = O1.getPhysicalURI().toString();
String s_uri2 = O2.getPhysicalURI().toString();
String type = alignment.getType();
String level = alignment.getLevel();
query = "insert into alignment " +
"(id, owlontology1, owlontology2, type, level, file1, file2, uri1, uri2) " +
"values (" + id + ",'" + s_O1 + "','" + s_O2 + "','" + type + "','" + level + "','" + s_File1 + "','" + s_File2 + "','" + s_uri1 + "','" + s_uri2 + "')";
st.executeUpdate(query);
for( Enumeration e = alignment.getExtensions().getNames() ; e.hasMoreElements() ; ){
String tag = (String)e.nextElement();
String s_method = alignment.getExtension(tag);
query = "insert into extension " +
"(id, tag, method) " +
"values (" + id + ",'" + tag + "','" + s_method + "')";
st.executeUpdate(query);
}
for( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
Cell c = (Cell)e.nextElement();
String temp[] = new String[10];
try {
if ( ((OWLEntity)c.getObject1()).getURI() != null && ((OWLEntity)c.getObject2()).getURI() != null ){
if ( c.getId() != null ){
temp[0] = c.getId();
}
else temp[0] = "";
temp[1] = ((OWLEntity)c.getObject1()).getURI().toString();
temp[2] = ((OWLEntity)c.getObject2()).getURI().toString();
temp[3] = c.getStrength() + "";
if ( !c.getSemantics().equals("first-order") )
temp[4] = c.getSemantics();
else temp[4] = "";
temp[5] = ((BasicRelation)c.getRelation()).getRelation();
query = "insert into cell " +
"(id, cell_id, uri1, uri2, measure, semantics, relation) " +
"values (" + id + ",'" + temp[0] + "','" + temp[1] + "','" + temp[2] + "','" + temp[3] + "','" + temp[4] + "','" + temp[5] + "')";
st.executeUpdate(query);
}
} catch ( OWLException ex) {
// Raise an exception
System.err.println( "getURI problem" + ex.toString() ); }
}
} catch (Exception e) {
System.err.println(e.toString());
}
}
//**********************************************************************
public static OWLOntology loadOntology( URI uri ) throws OWLException {
OWLRDFParser parser = new OWLRDFParser();
parser.setConnection(OWLManager.getOWLConnection());
return parser.parseOntology(uri);
}
}
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