From 8079c4b8be5d41e30a4dfba9f07b0b7f194e4bc5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Sat, 21 Oct 2006 07:15:27 +0000
Subject: [PATCH] - reengineered the Database/Cache interface separation -
improved the Cache implementation by separating ontology/alignment (real
cache)
---
.../inrialpes/exmo/align/service/Cache.java | 14 +-
.../exmo/align/service/CacheImpl.java | 499 +++++++++++-------
2 files changed, 325 insertions(+), 188 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/service/Cache.java b/src/fr/inrialpes/exmo/align/service/Cache.java
index 58851e03..1587a5ff 100644
--- a/src/fr/inrialpes/exmo/align/service/Cache.java
+++ b/src/fr/inrialpes/exmo/align/service/Cache.java
@@ -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;
}
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index a3f77a63..dae4cbe7 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -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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