diff --git a/src/fr/inrialpes/exmo/align/impl/BasicCell.java b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
index ad3c9fdfcce1e383384e987af8b146686f11972d..165192d2714a4d84598b2f91226362bb0322e70c 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicCell.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
@@ -22,16 +22,15 @@
package fr.inrialpes.exmo.align.impl;
import java.net.URI;
+import java.util.Enumeration;
import org.xml.sax.ContentHandler;
-//*/3.0
-//import org.semanticweb.owl.model.OWLEntity;
-
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
+import org.semanticweb.owl.align.Parameters;
/**
* Represents an ontology alignment correspondence.
@@ -45,32 +44,15 @@ public class BasicCell implements Cell, Comparable {
visitor.visit( this );
}
- String id = null;
- String semantics = null;
- //*/3.0
- //OWLEntity object1 = null;
- //OWLEntity object2 = null;
- Object object1 = null;
- Object object2 = null;
- Relation relation = null;
- double strength = 0;
+ protected String id = null;
+ protected String semantics = null;
+ protected Object object1 = null;
+ protected Object object2 = null;
+ protected Relation relation = null;
+ protected double strength = 0;
+ protected Parameters extensions = null;
/** Creation **/
- // public BasicCell( Object ob1, Object ob2 ) throws AlignmentException {
- // new BasicCell( (String)null, ob1, ob2, "=", 0 );
- // };
-
-//*/3.0
-// public BasicCell( Object ob1, Object ob2, String rel, double m ) throws AlignmentException {
-// throw new AlignmentException("BasicCell: must take two OWLEntity as argument");
-// }
-// public BasicCell( OWLEntity ob1, OWLEntity ob2, String rel, double m ) throws AlignmentException {
-// public BasicCell( String id, Object ob1, Object ob2, String rel, double m ) throws AlignmentException {
-// new BasicCell( id, ob1, ob2, BasicRelation.createRelation(rel), m );
-// };
-
-//*/3.0
-// public BasicCell( OWLEntity ob1, OWLEntity ob2, Relation rel, double m ) throws AlignmentException {
public BasicCell( String id, Object ob1, Object ob2, Relation rel, double m ) throws AlignmentException {
setId( id );
object1 = ob1;
@@ -78,6 +60,7 @@ public class BasicCell implements Cell, Comparable {
relation = rel;
// No exception, just keep 0?
if ( m >= 0 && m <= 1 ) strength = m;
+ // extensions is only created on demand, otherwise, it is too expensive
};
// the strength must be compared with regard to abstract types
@@ -124,21 +107,9 @@ public class BasicCell implements Cell, Comparable {
}
}
public void setObject1( Object ob ) throws AlignmentException {
-//*/3.0
-// if ( ob instanceof OWLEntity ) {
-// object1 = (OWLEntity)ob;
-// } else {
-// throw new AlignmentException("BasicCell.setObject1: must have an OWLEntity as argument");
-// }
object1 = ob;
}
public void setObject2( Object ob ) throws AlignmentException {
-//*/3.0
-// if ( ob instanceof OWLEntity ) {
-// object2 = (OWLEntity)ob;
-// } else {
-// throw new AlignmentException("BasicCell.setObject2: must have an OWLEntity as argument");
-// }
object2 = ob;
}
public Relation getRelation(){ return relation; };
@@ -146,9 +117,36 @@ public class BasicCell implements Cell, Comparable {
public double getStrength(){ return strength; };
public void setStrength( double m ){ strength = m; };
+ public Parameters getExtensions(){ return extensions; }
+ public void setExtensions( Parameters p ){
+ extensions = p;
+ }
+
+ public void setExtension( String label, String value ) {
+ if ( extensions == null )
+ extensions = new BasicParameters();
+ extensions.setParameter( label, value );
+ };
+
+ public String getExtension( String label ) {
+ if ( extensions != null ) {
+ return (String)extensions.getParameter( label );
+ } else {
+ return (String)null;
+ }
+ };
+
public Cell inverse() throws AlignmentException {
- return (Cell)new BasicCell( (String)null, object2, object1, relation.inverse(), strength );
+ Cell result = (Cell)new BasicCell( (String)null, object2, object1, relation.inverse(), strength );
+ if ( extensions != null ) {
+ for ( Enumeration e = extensions.getNames() ; e.hasMoreElements(); ){
+ String label = (String)e.nextElement();
+ result.setExtension( label, getExtension( label ) );
+ }
+ }
+ result.getExtensions().unsetParameter( "id" );
// The sae should be done for the measure
+ return result;
}
/** Housekeeping **/
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
index 4331283a9e8a51b117c85e276cb9b73c695b3645..255ba11eee68fa092e519b8f3734f849be064409 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
@@ -52,7 +52,7 @@ public class HTMLRendererVisitor implements AlignmentVisitor
}
public void visit( Alignment align ) throws AlignmentException {
- //alignment = align;
+ alignment = align;
writer.print("<html>\n<head></head>\n<body>\n");
writer.print("<h1></h1>\n");
writer.print("<h2>Alignment metadata</h2>\n");
@@ -72,7 +72,7 @@ public class HTMLRendererVisitor implements AlignmentVisitor
}
writer.print("</table>\n");
writer.print("<h2>Correspondences</h2>\n");
- writer.print("<table><tr><td>Id</td><td>object1</td><td>relation</td><td>strength</td><td>object2</td></tr>\n");
+ writer.print("<table><tr><td>object1</td><td>relation</td><td>strength</td><td>object2</td><td>Id</td></tr>\n");
for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
Cell c = (Cell)e.nextElement();
c.accept( this );
@@ -80,17 +80,26 @@ public class HTMLRendererVisitor implements AlignmentVisitor
writer.print("</table>\n");
writer.print("</body>\n</html>\n");
}
+
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
writer.print(" <tr>");
- if ( cell.getId() != null ) writer.print("<td>"+cell.getId()+"</td>");
- else writer.print("<td></td>");
writer.print("<td>"+cell.getObject1AsURI().toString()+"</td><td>");
cell.getRelation().accept( this );
writer.print("</td><td>"+cell.getStrength()+"</td>");
- writer.print("<td>"+cell.getObject2AsURI().toString()+"</td></tr>");
+ writer.print("<td>"+cell.getObject2AsURI().toString()+"</td>");
+ if ( cell.getId() != null ) {
+ String id = cell.getId();
+ // Would be useful to test for the Alignment URI
+ if ( id.startsWith( (String)alignment.getExtension( "id" ) ) ){
+ writer.print("<td>"+id.substring( id.indexOf( '#' ) )+"</td>");
+ } else {
+ writer.print("<td>"+id+"</td>");
+ }
+ } else writer.print("<td></td>");
//if ( !cell.getSemantics().equals("first-order") )
// writer.print(" <semantics>"+cell.getSemantics()+"</semantics>\n");
+ writer.println("</tr>");
}
public void visit( Relation rel ) {
rel.write( writer );
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
index 56a94e6303f2802b73c267db44b76248e4a2448d..6a1b16d5534a47b8ba2be9ab6b67237891d12e5d 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
@@ -23,11 +23,6 @@ package fr.inrialpes.exmo.align.impl.renderer;
import java.util.Enumeration;
import java.io.PrintWriter;
-//*/3.0
-//import org.semanticweb.owl.model.OWLOntology;
-//import org.semanticweb.owl.model.OWLEntity;
-//import org.semanticweb.owl.model.OWLException;
-
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
@@ -68,51 +63,56 @@ public class RDFRendererVisitor implements AlignmentVisitor
String tag = (String)e.nextElement();
writer.print(" <"+tag+">"+align.getExtension(tag)+"</"+tag+">\n");
}
- // try {
- if ( align.getFile1() != null )
- writer.print(" <onto1>"+align.getFile1().toString()+"</onto1>\n");
- if ( align.getFile2() != null )
- writer.print(" <onto2>"+align.getFile2().toString()+"</onto2>\n");
- writer.print(" <uri1>");
- writer.print( align.getOntology1URI().toString() );
- writer.print("</uri1>\n");
- writer.print(" <uri2>");
- writer.print( align.getOntology2URI().toString() );
- writer.print("</uri2>\n");
+ if ( align.getFile1() != null )
+ writer.print(" <onto1>"+align.getFile1().toString()+"</onto1>\n");
+ if ( align.getFile2() != null )
+ writer.print(" <onto2>"+align.getFile2().toString()+"</onto2>\n");
+ writer.print(" <uri1>");
+ writer.print( align.getOntology1URI().toString() );
+ writer.print("</uri1>\n");
+ writer.print(" <uri2>");
+ writer.print( align.getOntology2URI().toString() );
+ writer.print("</uri2>\n");
- for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
- Cell c = (Cell)e.nextElement();
- c.accept( this );
- } //end for
- // } catch (OWLException ex) { throw new AlignmentException( "getURI problem", ex); }
+ for( Enumeration e = align.getElements() ; e.hasMoreElements(); ){
+ Cell c = (Cell)e.nextElement();
+ c.accept( this );
+ } //end for
writer.print("</Alignment>\n");
writer.print("</rdf:RDF>\n");
}
public void visit( Cell cell ) throws AlignmentException {
this.cell = cell;
- //OWLOntology onto1 = (OWLOntology)alignment.getOntology1();
- // try {
if ( cell.getObject1AsURI() != null &&
cell.getObject2AsURI() != null ){
writer.print(" <map>\n");
writer.print(" <Cell");
if ( cell.getId() != null ){
- writer.print(" rdf:about=\"#"+cell.getId()+"\"");
+ writer.print(" rdf:about=\""+cell.getId()+"\"");
}
writer.print(">\n <entity1 rdf:resource='");
writer.print( cell.getObject1AsURI().toString() );
writer.print("'/>\n <entity2 rdf:resource='");
writer.print( cell.getObject2AsURI().toString() );
- writer.print("'/>\n <measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>");
+ writer.print("'/>\n <relation>");
+ cell.getRelation().accept( this );
+ writer.print("</relation>\n");
+ writer.print(" <measure rdf:datatype='http://www.w3.org/2001/XMLSchema#float'>");
writer.print( cell.getStrength() );
writer.print("</measure>\n");
- if ( !cell.getSemantics().equals("first-order") )
+ if ( cell.getSemantics() != null &&
+ !cell.getSemantics().equals("") &&
+ !cell.getSemantics().equals("first-order") )
writer.print(" <semantics>"+cell.getSemantics()+"</semantics>\n");
- writer.print(" <relation>");
- cell.getRelation().accept( this );
- writer.print("</relation>\n </Cell>\n </map>\n");
}
- // } catch ( OWLException e) { throw new AlignmentException( "getURI problem", e ); }
+ if ( cell.getExtensions() != null ) {
+ // could certainly be done better
+ for ( Enumeration e = cell.getExtensions().getNames() ; e.hasMoreElements(); ){
+ String label = (String)e.nextElement();
+ writer.print(" <"+label+">"+cell.getExtension(label)+"</"+label+">\n");
+ }
+ }
+ writer.print(" </Cell>\n </map>\n");
}
public void visit( Relation rel ) {
rel.write( writer );
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index 80c18e9e54064d6b5d809819ffdd609268030dfc..eaa380bc14e8f42b1e5692d0a58b4e76a1044a26 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -38,18 +38,13 @@ import java.lang.Integer;
import java.lang.Double;
import java.util.Hashtable;
-//*/3.0
-//import org.semanticweb.owl.util.OWLManager;
-//import org.semanticweb.owl.model.OWLOntology;
-//import org.semanticweb.owl.model.OWLEntity;
-//import org.semanticweb.owl.model.OWLException;
-//import org.semanticweb.owl.io.owl_rdf.OWLRDFParser;
-//import org.semanticweb.owl.io.owl_rdf.OWLRDFErrorHandler;
-
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.Parameters;
+
import fr.inrialpes.exmo.align.impl.URIAlignment;
+import fr.inrialpes.exmo.align.impl.BasicParameters;
/**
* This class allows the creation of a parser for an Alignment file.
@@ -75,15 +70,11 @@ public class AlignmentParser extends DefaultHandler {
/**
* the first Ontology
*/
- //*/3.0
- // OWLOntology onto1 = null;
Object onto1 = null;
/**
* the second Ontology
*/
- //*/3.0
- // OWLOntology onto2 = null;
Object onto2 = null;
/**
@@ -97,8 +88,6 @@ public class AlignmentParser extends DefaultHandler {
* This is a pitty but the idea of creating a particular alignment
* is not in accordance with using an interface.
*/
- //*/3.0
- //protected BasicAlignment alignment = null;
protected URIAlignment alignment = null;
/**
@@ -109,15 +98,11 @@ public class AlignmentParser extends DefaultHandler {
/**
* the first entity of a cell
*/
- //*/3.0
- //protected OWLEntity cl1 = null;
protected Object cl1 = null;
/**
* the second entity of a cell
*/
- //*/3.0
- //protected OWLEntity cl2 = null;
protected Object cl2 = null;
/**
@@ -140,6 +125,11 @@ public class AlignmentParser extends DefaultHandler {
*/
protected String sem = null;
+ /**
+ * Cell extensions (default null)
+ */
+ protected Parameters extensions = null;
+
/**
* the measure content as text...
*/
@@ -151,7 +141,8 @@ public class AlignmentParser extends DefaultHandler {
protected SAXParser parser = null;
/**
- * The parsing level, if equal to 2 we are in the Alignment
+ * The parsing level, if equal to 3 we are in the Alignment
+ * if equal to 5 we are in a cell
* and can find metadata
*/
protected int parselevel = 0;
@@ -211,82 +202,58 @@ public class AlignmentParser extends DefaultHandler {
System.err.println("startElement AlignmentParser : " + pName);
parselevel++;
if(namespaceURI.equals("http://knowledgeweb.semanticweb.org/heterogeneity/alignment")) {
- //*/3.0
- //try {
- if (pName.equals("relation")) {
- } else if (pName.equals("semantics")) {
- } else if (pName.equals("measure")) {
- } else if (pName.equals("entity2")) {
- if(debugMode > 2)
- System.err.println(" resource = " + atts.getValue("rdf:resource"));
- //*/3.0
- //cl2 = (OWLEntity)getEntity( onto2, atts.getValue("rdf:resource") );
- try {
- cl2 = new URI( atts.getValue("rdf:resource") );
- } catch (URISyntaxException e) {
- throw new SAXException("Malformed URI: "+atts.getValue("rdf:resource"));
- }
- } else if (pName.equals("entity1")) {
- if(debugMode > 2)
- System.err.println(" resource = " + atts.getValue("rdf:resource"));
- //*/3.0
- //cl1 = (OWLEntity)getEntity( onto1, atts.getValue("rdf:resource") );
- try {
- cl1 = new URI( atts.getValue("rdf:resource") );
- } catch (URISyntaxException e) {
- throw new SAXException("Malformed URI: "+atts.getValue("rdf:resource"));
- }
- } else if (pName.equals("Cell")) {
- if ( alignment == null )
- { throw new SAXException("No alignment provided"); };
- if ( atts.getValue("rdf:ID") != null ){
- id = atts.getValue("rdf:ID");
- } else if ( atts.getValue("rdf:about") != null ){
- id = atts.getValue("rdf:about");
- }
- sem = null;
- measure = null;
- relation = null;
- cl1 = null;
- cl2 = null;
- } else if (pName.equals("map")) {
- try {
- //*/3.0
- //if ( onto2 == null ){
- // onto2 = loadOntology( alignment.getFile2() );
- // if ( onto2 == null ) {
- // throw new SAXException("Cannot find ontology"+alignment.getFile2());
- // }
- //}
- alignment.setOntology2( onto2 );
- //*/3.0
- //if ( onto1 == null ){
- // onto1 = loadOntology( alignment.getFile1() );
- // if ( onto1 == null ) {
- // throw new SAXException("Cannot find ontology"+alignment.getFile1());
- // }
- //}
- alignment.setOntology1( onto1 );
- } catch ( AlignmentException e ) {
- throw new SAXException("Catched alignment exception", e );
- }
- } else if (pName.equals("onto2")) {
- } else if (pName.equals("onto1")) {
- } else if (pName.equals("uri2")) {
- } else if (pName.equals("uri1")) {
- } else if (pName.equals("type")) {
- } else if (pName.equals("level")) {
- } else if (pName.equals("xml")) {
- } else if (pName.equals("Alignment")) {
- //*/3.0
- //alignment = new BasicAlignment();
- alignment = new URIAlignment();
- } else {
- if ( debugMode > 0 ) System.err.println("[AlignmentParser] Unknown element name : "+pName);
- //throw new SAXException("[AlignmentParser] Unknown element name : "+pName);
- };
- //*/3.0
- //} catch ( OWLException e ) { throw new SAXException("[AlignmentParser] OWLException raised"); };
+ if (pName.equals("relation")) {
+ } else if (pName.equals("semantics")) {
+ } else if (pName.equals("measure")) {
+ } else if (pName.equals("entity2")) {
+ if(debugMode > 2)
+ System.err.println(" resource = " + atts.getValue("rdf:resource"));
+ try {
+ cl2 = new URI( atts.getValue("rdf:resource") );
+ } catch (URISyntaxException e) {
+ throw new SAXException("Malformed URI: "+atts.getValue("rdf:resource"));
+ }
+ } else if (pName.equals("entity1")) {
+ if(debugMode > 2)
+ System.err.println(" resource = " + atts.getValue("rdf:resource"));
+ try {
+ cl1 = new URI( atts.getValue("rdf:resource") );
+ } catch (URISyntaxException e) {
+ throw new SAXException("Malformed URI: "+atts.getValue("rdf:resource"));
+ }
+ } else if (pName.equals("Cell")) {
+ if ( alignment == null )
+ { throw new SAXException("No alignment provided"); };
+ if ( atts.getValue("rdf:ID") != null ){
+ id = atts.getValue("rdf:ID");
+ } else if ( atts.getValue("rdf:about") != null ){
+ id = atts.getValue("rdf:about");
+ }
+ sem = null;
+ measure = null;
+ relation = null;
+ extensions = null;
+ cl1 = null;
+ cl2 = null;
+ } else if (pName.equals("map")) {
+ try {
+ alignment.setOntology2( onto2 );
+ alignment.setOntology1( onto1 );
+ } catch ( AlignmentException e ) {
+ throw new SAXException("Catched alignment exception", e );
+ }
+ } else if (pName.equals("onto2")) {
+ } else if (pName.equals("onto1")) {
+ } else if (pName.equals("uri2")) {
+ } else if (pName.equals("uri1")) {
+ } else if (pName.equals("type")) {
+ } else if (pName.equals("level")) {
+ } else if (pName.equals("xml")) {
+ } else if (pName.equals("Alignment")) {
+ alignment = new URIAlignment();
+ } else {
+ if ( debugMode > 0 ) System.err.println("[AlignmentParser] Unknown element name : "+pName);
+ };
} else if(namespaceURI.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#")) {
if ( !pName.equals("RDF") ) {
throw new SAXException("[AlignmentParser] unknown element name: "+pName); };
@@ -295,21 +262,10 @@ public class AlignmentParser extends DefaultHandler {
}
}
- //*/3.0
- //private OWLEntity getEntity( OWLOntology ontology, String name ) throws OWLException, SAXException {
private Object getEntity( Object ontology, String name ) throws SAXException {
- URI uri = null;
-
- try { uri = new URI(name);}
- catch (URISyntaxException e) {throw new SAXException("[AlignmentParser] bad URI syntax : "+name);}
-
- //*/3.0
- //OWLEntity result = (OWLEntity)ontology.getClass( uri );
- //if ( result == null ) result = (OWLEntity)ontology.getDataProperty( uri );
- //if ( result == null ) result = (OWLEntity)ontology.getObjectProperty( uri );
- //if ( result == null ) result = (OWLEntity)ontology.getIndividual( uri );
- //return result;
- return uri;
+ try { return new URI( name );}
+ catch (URISyntaxException e) {
+ throw new SAXException("[AlignmentParser] bad URI syntax : "+name);}
}
/**
@@ -322,7 +278,7 @@ public class AlignmentParser extends DefaultHandler {
}
/*
- // Change proposed by Sabine Massmann
+ // Patch proposed by Sabine Massmann
// If to be integrated, then put it in the proper place
// There is no reasons to test for Double in characters
public void characters(char ch[], int start, int length) {
@@ -385,18 +341,15 @@ public class AlignmentParser extends DefaultHandler {
cell = alignment.addAlignCell( cl1, cl2, relation, Double.parseDouble(measure) );}
if ( id != null ) cell.setId( id );
if ( sem != null ) cell.setSemantics( sem );
+ if ( extensions != null ) cell.setExtensions( extensions );
} else if (pName.equals("map")) {
} else if (pName.equals("uri1")) {
- //*/3.0
- //onto1 = (OWLOntology)ontologies.get( content );
try {
onto1 = new URI( content );
} catch (URISyntaxException e) {
throw new SAXException("uri1: malformed URI");
}
} else if (pName.equals("uri2")) {
- //*/3.0
- //onto2 = (OWLOntology)ontologies.get( content );
try {
onto2 = new URI( content );
} catch (URISyntaxException e) {
@@ -421,54 +374,33 @@ public class AlignmentParser extends DefaultHandler {
// { throw new SAXException("Non parseable alignment"); }
} else if (pName.equals("Alignment")) {
} else {
- if ( debugMode > 0 )
+ if ( parselevel == 3 ){
+ alignment.setExtension( pName, content );
+ } else if ( parselevel == 5 ) {
+ if ( extensions == null ) extensions = new BasicParameters();
+ //cell.setExtension( pName, content );
+ extensions.setParameter( pName, content );
+ } else //if ( debugMode > 0 )
System.err.println("[AlignmentParser] Unknown element name : "+pName);
//throw new SAXException("[AlignmentParser] Unknown element name : "+pName);
};
- //*/3.0
} catch ( AlignmentException e ) { throw new SAXException("[AlignmentParser] OWLException raised"); };
} else if(namespaceURI.equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#")) {
if ( !pName.equals("RDF") ) {
throw new SAXException("[AlignmentParser] unknown element name: "+pName); };
} else {
- if ( parselevel == 2 ){
+ if ( parselevel == 3 ){
alignment.setExtension( pName, content );
+ } else if ( parselevel == 5 ) {
+ if ( extensions == null ) extensions = new BasicParameters();
+ //cell.setExtension( pName, content );
+ extensions.setParameter( pName, content );
} else throw new SAXException("[AlignmentParser] Unknown namespace : "+namespaceURI);
}
parselevel--;
} //end endElement
/** Can be used for loading the ontology if it is not available **/
- //*/3.0
- /*
- private OWLOntology loadOntology( URI ref ) throws SAXException, OWLException {
- OWLOntology parsedOnt = null;
- OWLRDFParser parser = new OWLRDFParser();
- OWLRDFErrorHandler handler = new OWLRDFErrorHandler(){
- public void owlFullConstruct( int code, String message )
- throws SAXException {
- }
- public void owlFullConstruct(int code, String message, Object o)
- throws SAXException {
- }
- public void error( String message ) throws SAXException {
- throw new SAXException( message.toString() );
- }
- public void warning( String message ) throws SAXException {
- System.out.println("WARNING: " + message);
- }
- };
- parser.setOWLRDFErrorHandler( handler );
- parser.setConnection( OWLManager.getOWLConnection() );
- try {
- parsedOnt = parser.parseOntology( ref );
- ontologies.put( ref.toString(), parsedOnt );
- return parsedOnt;
- } catch ( Exception e ) {
- throw new SAXException("[AlignmentParser] Error during parsing : "+ref);
- }
- }
-*/
}//end class
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 162d3c776076a07fdf3e4b09b55ec30abcb8776d..40ddf0deb013f7513c9b3822e178deb691b7b889 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -181,7 +181,12 @@ public class AServProtocolManager {
return alignmentCache.listAlignments();
}
- /*********************************************************************
+ public String query( String query ){
+ //return alignmentCache.query( query );
+ return "Not available yet";
+ }
+
+ /*********************************************************************
* Basic protocol primitives
*********************************************************************/
@@ -447,6 +452,7 @@ public class AServProtocolManager {
} catch (Exception e) {
return new UnknownAlignment(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
}
+ // JE: Other possibility is to render the metadata through XMLMetadataRendererVisitor into content...
// Put all the local metadata in parameters
Parameters params = new BasicParameters();
params.setParameter( "file1", al.getFile1() );
@@ -531,6 +537,22 @@ public class AServProtocolManager {
return new AlignmentId(newId(),mess,myId,mess.getSender(),"dummy//",(Parameters)null);
}
+ public boolean storedAlignment( Message mess ) {
+ // Retrieve the alignment
+ String id = (String)mess.getParameters().getParameter("id");
+ Alignment al = null;
+ try {
+ al = alignmentCache.getAlignment( id );
+ } catch (Exception e) {
+ return false;
+ }
+ if ( al.getExtension("fr.inrialpes.exmo.align.service.stored") != null && al.getExtension("fr.inrialpes.exmo.align.service.stored") != "" ) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
/*********************************************************************
* Network of alignment server implementation
*********************************************************************/
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 650b4abdb89370320a8fc419148a4bf28b434f72..96be7d29008c5196831acc9ae1373dc7c310e3eb 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -62,15 +62,23 @@ public class CacheImpl implements Cache {
String port = null;
int rights = 1; // writing rights in the database (default is 1)
- final int VERSION = 300; // Version of the API to be stored in the database
+ final int VERSION = 302; // 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
+ */
- Statement st = null;
- ResultSet rs = null;
+ Statement st = null; // JE: not sure that this should persist
Connection conn = null;
final int CONNECTION_ERROR = 1;
final int SUCCESS = 2;
final int INIT_ERROR = 3;
+
+ final String CACHED = "http://exmo.inrialpes.fr/align/service:cached";
+ final String STORED = "http://exmo.inrialpes.fr/align/service:stored";
+ final String OURI1 = "http://exmo.inrialpes.fr/align/service:ouri1";
+ final String OURI2 = "http://exmo.inrialpes.fr/align/service:ouri2";
//**********************************************************************
public CacheImpl( DBService service ) {
@@ -93,7 +101,7 @@ public class CacheImpl implements Cache {
port = (String)p.getParameter("http"); // bad idea
host = (String)p.getParameter("host");
// test if a database is here, otherwise create it
- rs = (ResultSet)st.executeQuery("SHOW TABLES LIKE 'server'");
+ ResultSet rs = (ResultSet)st.executeQuery("SHOW TABLES LIKE 'server'");
if ( !rs.next() ) initDatabase();
// register by the database
st.executeUpdate("INSERT INTO server (host, port, edit, version) VALUES ('"+host+"','"+port+"','"+rights+"',"+VERSION+")");
@@ -131,7 +139,7 @@ public class CacheImpl implements Cache {
if (force) {
// Retrieve the alignment ids
- rs = (ResultSet) st.executeQuery("SELECT id FROM alignment");
+ ResultSet rs = (ResultSet) st.executeQuery("SELECT id FROM alignment");
while(rs.next()) {
id = rs.getString("id");
idInfo.add(id);
@@ -156,6 +164,7 @@ public class CacheImpl implements Cache {
*/
protected Alignment retrieveDescription( String id ){
String query;
+ ResultSet rs;
String tag;
String method;
@@ -169,8 +178,8 @@ public class CacheImpl implements Cache {
// Either uri1 or file1
result.setFile1( new URI( rs.getString("file1") ) );
result.setFile2( new URI( rs.getString("file2") ) );
- result.setExtension( "ouri1", rs.getString("owlontology1") );
- result.setExtension( "ouri2", rs.getString("owlontology2") );
+ result.setExtension( OURI1, rs.getString("owlontology1") );
+ result.setExtension( OURI2, rs.getString("owlontology2") );
result.setLevel(rs.getString("level"));
result.setType(rs.getString("type"));
}
@@ -189,9 +198,9 @@ public class CacheImpl implements Cache {
return null;
}
// should be there
- //result.setExtension("fr.inrialpes.exmo.align.service.stored", "DATE");
+ //result.setExtension(STORED, "DATE");
// not yet cached
- result.setExtension("fr.inrialpes.exmo.align.service.cached", "");
+ result.setExtension(CACHED, "");
return result;
}
@@ -200,35 +209,48 @@ public class CacheImpl implements Cache {
* alignmentTable hastable
*
* should be invoked when:
- * ( result.getExtension("fr.inrialpes.exmo.align.service.cached") == ""
- * && result.getExtension("fr.inrialpes.exmo.align.service.stored") != "") {
+ * ( result.getExtension(CACHED) == ""
+ * && result.getExtension(STORED) != "") {
*/
- protected Alignment retrieveAlignment( String id, Alignment result ) throws SQLException, AlignmentException, URISyntaxException {
+ protected Alignment retrieveAlignment( String id, Alignment alignment ) throws SQLException, AlignmentException, URISyntaxException {
String query;
URI ent1 = null, ent2 = null;
Cell cell = null;
- result.setOntology1( new URI( result.getExtension( "ouri1" ) ) );
- result.setOntology2( new URI( result.getExtension( "ouri2" ) ) );
+ alignment.setOntology1( new URI( alignment.getExtension( OURI1 ) ) );
+ alignment.setOntology2( new URI( alignment.getExtension( OURI2 ) ) );
// Get cells
query = "SELECT * FROM cell WHERE id = '" + id + "'";
- rs = (ResultSet) st.executeQuery(query);
+ 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 = result.addAlignCell(ent1, ent2, rs.getString("relation"), Double.parseDouble(rs.getString("measure")));
+ 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("tag"),
+ rse.getString("method") );
+ }
+ }
}
- // It is here
- //result.setExtension("fr.inrialpes.exmo.align.service.stored", "DATE");
// reset
- resetCacheStamp(result);
+ resetCacheStamp(alignment);
- return result;
+ return alignment;
}
private String generateAlignmentId() {
@@ -236,6 +258,16 @@ public class CacheImpl implements Cache {
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));
@@ -265,8 +297,8 @@ public class CacheImpl implements Cache {
throw new Exception("getAlignment: Cannot find alignment");
// If not cached, retrieve it now
- if ( result.getExtension("fr.inrialpes.exmo.align.service.cached") == ""
- && result.getExtension("fr.inrialpes.exmo.align.service.stored") != "") {
+ if ( result.getExtension(CACHED) == ""
+ && result.getExtension(STORED) != "") {
retrieveAlignment( id, result );
}
@@ -285,7 +317,7 @@ public class CacheImpl implements Cache {
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("ouri2").equals( uri2.toString() ) ) result.add( al );
+ if ( al.getExtension(OURI2).equals( uri2.toString() ) ) result.add( al );
}
}
return result;
@@ -306,12 +338,12 @@ public class CacheImpl implements Cache {
*/
public String recordNewAlignment( String id, Alignment al, boolean force ) throws AlignmentException {
Alignment alignment = al;
- alignment.setExtension("ouri1", alignment.getOntology1URI().toString());
- alignment.setExtension("ouri2", alignment.getOntology2URI().toString());
+ alignment.setExtension(OURI1, alignment.getOntology1URI().toString());
+ alignment.setExtension(OURI2, alignment.getOntology2URI().toString());
// Index
recordAlignment( id, alignment, force );
// Not yet stored
- alignment.setExtension("fr.inrialpes.exmo.align.service.stored", "");
+ alignment.setExtension(STORED, "");
// Cached now
resetCacheStamp(alignment);
return id;
@@ -326,8 +358,8 @@ public class CacheImpl implements Cache {
alignment.setExtension( "id", id );
// Store it
try {
- URI ouri1 = new URI( alignment.getExtension("ouri1") );
- URI ouri2 = new URI( alignment.getExtension("ouri2") );
+ URI ouri1 = new URI( alignment.getExtension(OURI1) );
+ URI ouri2 = new URI( alignment.getExtension(OURI2) );
if ( force || alignmentTable.get( id ) == null ) {
Set s1 = (Set)ontologyTable.get( ouri1 );
if ( s1 == null ) {
@@ -389,13 +421,13 @@ public class CacheImpl implements Cache {
alignment = getAlignment( id );
// We store stored date
- alignment.setExtension("fr.inrialpes.exmo.align.service.stored", new Date().toString());
+ alignment.setExtension(STORED, new Date().toString());
// We empty cached date
- alignment.setExtension("fr.inrialpes.exmo.align.service.cached", "");
+ alignment.setExtension(CACHED, "");
try {
- String s_O1 = alignment.getExtension("ouri1");
- String s_O2 = alignment.getExtension("ouri2");
+ String s_O1 = alignment.getExtension(OURI1);
+ String s_O2 = alignment.getExtension(OURI2);
// file attribute
String s_File1 = null;
@@ -427,24 +459,43 @@ public class CacheImpl implements Cache {
for( Enumeration e = alignment.getElements() ; e.hasMoreElements(); ){
Cell c = (Cell)e.nextElement();
- String temp[] = new String[10];
- if ( c.getObject1() != null && c.getObject2() != null ){
- if ( c.getId() != null ){
- temp[0] = c.getId();
- }
- else temp[0] = "";
- temp[1] = c.getObject1AsURI().toString();
- temp[2] = c.getObject2AsURI().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 ('" + quote(id) + "','" + quote(temp[0]) + "','" + quote(temp[1]) + "','" + quote(temp[2]) + "','" + quote(temp[3]) + "','" + quote(temp[4]) + "','" + quote(temp[5]) + "')";
+ String cellid = null;
+ if ( c.getObject1() != null && c.getObject2() != null ){
+ cellid = c.getId();
+ if ( cellid != null ){
+ if ( cellid.startsWith("#") ) {
+ cellid = alignment.getExtension("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("") ) {
+ // JE: I must now store all the extensions
+ for( Enumeration e2 = c.getExtensions().getNames() ; e2.hasMoreElements() ; ){
+ String tag = (String)e2.nextElement();
+ String s_method = c.getExtension(tag);
+ query = "INSERT INTO extension " +
+ "(id, tag, method) " +
+ "VALUES ('" + quote(cellid) + "','" + quote(tag) + "','" + quote(s_method) + "')";
st.executeUpdate(query);
}
+ }
}
} catch (Exception e) { e.printStackTrace(); };
// We reset cached date
@@ -454,13 +505,13 @@ public class CacheImpl implements Cache {
//**********************************************************************
// CACHE MANAGEMENT (Not implemented yet)
public void resetCacheStamp( Alignment result ){
- result.setExtension("fr.inrialpes.exmo.align.service.cached", new Date().toString() );
+ result.setExtension(CACHED, new Date().toString() );
}
public void cleanUpCache() {
// for each alignment in the table
// set currentDate = Date();
- // if ( DateFormat.parse( result.getExtension("fr.inrialpes.exmo.align.service.cached") ).before( ) ) {
+ // if ( DateFormat.parse( result.getExtension(CACHED) ).before( ) ) {
// - for each ontology if no other alignment => unload
// - clean up cells
// }
@@ -489,7 +540,8 @@ public class CacheImpl implements Cache {
file1 varchar(250),
file2 varchar(250),
uri1 varchar(250),
- uri2 varchar(250));
+ uri2 varchar(250),
+ primary key (id));
# cell info
@@ -513,7 +565,7 @@ public class CacheImpl implements Cache {
public void initDatabase() throws SQLException {
// 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))");
+ 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), tag VARCHAR(100), method VARCHAR(500))");
st.executeUpdate("CREATE TABLE server (host VARCHAR(50), port VARCHAR(5), edit BOOLEAN, version VARCHAR(5))");
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index 0d001cef2d9cc1a4c106c6153fd72c7f0ed4c948..1bce196e5753dd94084be4e0d995ba63aea1ecbe 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -247,7 +247,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
if ( debug > 0 ) System.err.println("ADMIN["+perf+"]");
String msg = "";
if ( perf.equals("listalignments") ){
- msg = "<h1>Stored alignments</h1><ul compact=\"1\">";
+ msg = "<h1>Available alignments</h1><ul compact=\"1\">";
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
String id = ((Alignment)e.nextElement()).getExtension("id");
msg += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id+"\">"+id+"</a></li>";
@@ -272,9 +272,10 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
}
msg += "</ul>";
} else if ( perf.equals("prmsqlquery") ){
- msg = "<h1>SQL query</h1><form action=\"sqlquery\">Provide an id: <input type=\"textarea\" name=\"id\" size=\"60\"/> (sql)<br /><small>An SQL SELECT query</small><br /><input type=\"submit\" value=\"Query\"/></form>";
+ msg = "<h1>SQL query</h1><form action=\"sqlquery\">Query: <input type=\"textarea\" name=\"query\" rows=\"8\"size=\"60\"/> (sql)<br /><small>An SQL SELECT query</small><br /><input type=\"submit\" value=\"Query\"/></form>";
} else if ( perf.equals("sqlquery") ){
- msg = "Not available yet";
+ String answer = manager.query( (String)params.getParameter("query") );
+ msg = "<pre>"+answer+"</pre>";
} else if ( perf.equals("about") ){
msg = about();
} else if ( perf.equals("shutdown") ){
@@ -282,6 +283,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "Server shut down";
} else if ( perf.equals("prmreset") ){
msg = perf;
+ } else if ( perf.equals("prmflush") ){
+ msg = perf;
} else if ( perf.equals("addservice") ){
msg = perf;
} else if ( perf.equals("addmethod") ){
@@ -297,6 +300,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<li><form action=\"listrenderers\"><input type=\"submit\" value=\"Available renderers\"/></form></li>";
msg += "<li><form action=\"listservices\"><input type=\"submit\" value=\"Available services\"/></form></li>";
msg += "<li><form action=\"prmsqlquery\"><input type=\"submit\" value=\"SQL Query\"/></form></li>";
+ msg += "<li><form action=\"prmflush\"><input type=\"submit\" value=\"Flush caches\"/></form></li>";
msg += "<li><form action=\"prmreset\"><input type=\"submit\" value=\"Reset server\"/></form></li>";
msg += "<li><form action=\"shutdown\"><input type=\"submit\" value=\"Shutdown\"/></form></li>";
msg += "<li><form action=\"..\"><input type=\"submit\" value=\"About\"/></form></li>";
@@ -321,7 +325,10 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
// JE: only those non stored please (retrieve metadata + stored)
for( Enumeration e = manager.alignments(); e.hasMoreElements(); ){
String id = ((Alignment)e.nextElement()).getExtension("id");
+ params.setParameter("id", id);
+ if ( !manager.storedAlignment( new Message(newId(),(Message)null,myId,serverId,"", params ) ) ){
msg += "<option value=\""+id+"\">"+id+"</option>";
+ }
}
msg += "</select><br />";
msg += "<input type=\"submit\" value=\"Store\"/></form>";
@@ -430,12 +437,6 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
String id = ((Alignment)e.nextElement()).getExtension("id");
msg += "<option value=\""+id+"\">"+id+"</option>";
}
- msg += "</select><br />";
- msg += "Rendering: <select name=\"method\">";
- for( Iterator it = manager.listrenderers().iterator(); it.hasNext(); ) {
- String id = (String)it.next();
- msg += "<option value=\""+id+"\">"+id+"</option>";
- }
msg += "</select><br /><input type=\"submit\" value=\"Get metadata\"/></form>";
} else if ( perf.equals("metadata") ) {
Message answer = manager.render( new Message(newId(),(Message)null,myId,serverId,"", params) );
diff --git a/src/org/semanticweb/owl/align/Cell.java b/src/org/semanticweb/owl/align/Cell.java
index ec011f1f3dbd3f74f9fe2165fcf07e5a8429f492..3ae02ee60259489d04a29beeccb08ba30c0837d7 100644
--- a/src/org/semanticweb/owl/align/Cell.java
+++ b/src/org/semanticweb/owl/align/Cell.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rhône-Alpes, 2003-2005
+ * Copyright (C) INRIA Rhône-Alpes, 2003-2005, 2007
*
* 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
@@ -62,6 +62,15 @@ public interface Cell
public void setStrength( double m );
public boolean equals( Cell c );
+ /**
+ * Extensions are a way to read and add other information (metadata)
+ * to the Cell structure itself.
+ */
+ public Parameters getExtensions();
+ public void setExtensions( Parameters param );
+ public String getExtension( String label );
+ public void setExtension( String label, String value );
+
public Cell inverse() throws AlignmentException;
/** Housekeeping **/