diff --git a/build.xml b/build.xml
index 10ed0390e42759abf687252cd96d990f2156e07f..0f2c0b409112c29923febf8ba86d694d657dc50f 100644
--- a/build.xml
+++ b/build.xml
@@ -11,6 +11,7 @@
<echo message="init: sets necessary variables"/>
<echo message="compile: incrementaly compiles sources"/>
<echo message="compileall: recompiles all sources"/>
+ <echo message="lint: compiles all sources with bug flags on"/>
<echo message="jar: archives compiled code"/>
<echo message="test: performs unit tests [nyi]"/>
<echo message="zip: creates a new zip file"/>
@@ -104,6 +105,7 @@
</manifest>
<fileset dir="classes" includes="org/ivml/**/*.class"/>
<fileset dir="classes" includes="fr/inrialpes/exmo/align/util/**/*.class"/>
+ <fileset dir="classes" includes="fr/inrialpes/exmo/align/onto/**/*.class"/>
<fileset dir="classes" includes="fr/inrialpes/exmo/align/parser/**/*.class"/>
<fileset dir="classes" includes="fr/inrialpes/exmo/align/impl/**/*.class"/>
<fileset dir="classes" includes="LICENSE.TXT"/>
diff --git a/html/relnotes.html b/html/relnotes.html
index 4942418bb8a98397e1e6fca62ea41a2a0e5d29f8..59134f5c21e65bc7e3d9628dda63ead1183fb5e8 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -22,6 +22,7 @@
<li>Restructuring language dependent alignments (impl)</li>
<li>Implementing database store for OMWG Language (server)</li>
<li>Replacing <tt>Parameters</tt> with Java <tt>Property</tt> (api/impl)</li>
+<li>Implement debug options with log4j</li>
<li>Use more for-each Java 1.5 construct</li>
</ul></p>
@@ -30,6 +31,7 @@
<!--h2>Version 3.3 (): xx/yy/2008 - O sole mio</h2-->
<p><ul compact="1">
+<li>Added an abstract ontology interface (impl)</li>
<li>Passed to Java 1.5 generics [incl. API modif] (dev/api)</li>
<li>Passed all code through lint (dev)</li>
</ul></p>
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 90738ec7ea39d50ee08c7ddcf027f2b39c7b7546..a51155bb567342a6de7a2e63590ca26f9c8cf359 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -41,6 +41,9 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
import org.semanticweb.owl.align.Parameters;
+import fr.inrialpes.exmo.align.onto.Ontology;
+import fr.inrialpes.exmo.align.onto.BasicOntology;
+
/**
* Represents a basic ontology alignment, i.e., a fully functionnal alignment
* for wich the type of aligned objects is not known.
@@ -61,8 +64,8 @@ public class BasicAlignment implements Alignment {
visitor.visit(this);
}
- protected Ontology onto1 = null;
- protected Ontology onto2 = null;
+ protected Ontology<Object> onto1 = null;
+ protected Ontology<Object> onto2 = null;
protected int debug = 0;
@@ -80,26 +83,21 @@ public class BasicAlignment implements Alignment {
protected Parameters namespaces = null;
- /**
- * This is the URI of the place from which the ontology has been loaded!
- * This is NOT the Ontology URI which can be obtained by
- * getOntology1URI()
- */
-
public BasicAlignment() {
hash1 = new Hashtable<Object,Set<Cell>>();
hash2 = new Hashtable<Object,Set<Cell>>();
extensions = new BasicParameters();
namespaces = new BasicParameters();
if ( this instanceof AlignmentProcess ) setExtension( Annotations.ALIGNNS, Annotations.METHOD, getClass().getName() );
- onto1 = new Ontology();
- onto2 = new Ontology();
+ onto1 = new BasicOntology<Object>();
+ onto2 = new BasicOntology<Object>();
}
public void init( Object onto1, Object onto2, Object cache ) throws AlignmentException {
+ // JE: Onto I am not sure this works
if ( onto1 instanceof Ontology ) {
- this.onto1 = (Ontology)onto1;
- this.onto2 = (Ontology)onto2;
+ this.onto1 = (Ontology<Object>)onto1;
+ this.onto2 = (Ontology<Object>)onto2;
} else {
this.onto1.setOntology( onto1 );
this.onto2.setOntology( onto2 );
@@ -139,22 +137,12 @@ public class BasicAlignment implements Alignment {
return onto2;
};
- public URI getOntology1URI() throws AlignmentException {
- Object ontology = onto1.getOntology();
- if ( ontology != null && ontology instanceof URI ) {
- return (URI)ontology;
- } else {
- throw new AlignmentException( "Cannot find URI for "+onto1 );
- }
+ public URI getOntology1URI() {
+ return onto1.getURI();
};
- public URI getOntology2URI() throws AlignmentException {
- Object ontology = onto2.getOntology();
- if ( ontology != null && ontology instanceof URI ) {
- return (URI)ontology;
- } else {
- throw new AlignmentException( "Cannot find URI for "+onto2 );
- }
+ public URI getOntology2URI() {
+ return onto2.getURI();
};
public void setOntology1(Object ontology) throws AlignmentException {
diff --git a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
index c605b49d031f4d4117c0f7dd589a3b7e0c71323d..e2e2a6cb71e4d52c07c2743ac6c89db1469cf249 100644
--- a/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/OWLAPIAlignment.java
@@ -35,11 +35,6 @@ import org.xml.sax.SAXException;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLEntity;
import org.semanticweb.owl.model.OWLException;
-import org.semanticweb.owl.util.OWLManager;
-import org.semanticweb.owl.util.OWLConnection;
-import org.semanticweb.owl.io.owl_rdf.OWLRDFParser;
-import org.semanticweb.owl.io.owl_rdf.OWLConsumer;
-import org.semanticweb.owl.io.owl_rdf.OWLRDFErrorHandler;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
@@ -48,6 +43,11 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
import org.semanticweb.owl.align.Parameters;
+import fr.inrialpes.exmo.align.onto.OntologyFactory;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
+import fr.inrialpes.exmo.align.onto.Ontology;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
+
/**
* Represents an OWL ontology alignment. An ontology comprises a number of
* collections. Each ontology has a number of classes, properties and
@@ -72,34 +72,13 @@ public class OWLAPIAlignment extends BasicAlignment {
OntologyCache cache = null;
if ( ontologies instanceof OntologyCache ) cache = (OntologyCache)ontologies;
else cache = (OntologyCache)null;
+ // JE: why should this happen now? Never?
if ( (o1 instanceof OWLOntology && o2 instanceof OWLOntology)
|| (o1 instanceof Ontology && o2 instanceof Ontology) ){
super.init( o1, o2, ontologies );
} else if ( o1 instanceof URI && o2 instanceof URI ) {
- // The URI is set below
- setFile1( (URI)o1 );
- setFile2( (URI)o2 );
- // JE: newOnto ---
- ((Ontology)onto1).setFormalism( "OWL1.0" );
- ((Ontology)onto2).setFormalism( "OWL1.0" );
- // JE: newOnto ---
- try {
- URI u = new URI("http://www.w3.org/2002/07/owl#");
- ((Ontology)onto1).setFormURI( u );
- ((Ontology)onto2).setFormURI( u );
- } catch (Exception e) {}; // does not happen
- try {
- super.init( loadOntology( (URI)o1, cache ),
- loadOntology( (URI)o2, cache ) );
- // Not sure it should be here or in super.init()
- onto1.setURI( ((OWLOntology)(onto1.getOntology())).getLogicalURI() );
- onto2.setURI( ((OWLOntology)(onto2.getOntology())).getLogicalURI() );
- } catch (OWLException e) {
- throw new AlignmentException( "Cannot load ontologies", e );
- } catch (SAXException e) {
- throw new AlignmentException( "Cannot load ontologies", e );
- }
- // We should set the URI to that of the ontologies
+ super.init( loadOntology( (URI)o1, cache ),
+ loadOntology( (URI)o2, cache ) );
} else {
throw new AlignmentException("arguments must be OWLOntology or URI");
};
@@ -119,50 +98,9 @@ public class OWLAPIAlignment extends BasicAlignment {
}
}
- // JE: --- post-3.1
- public URI getOntology1URI() //throws AlignmentException
-{
- //try {
- // JE: OWMG1
- //return ((OWLOntology)(onto1.getOntology())).getLogicalURI();
- return onto1.getURI();
- //} catch ( OWLException e ) {
- //throw new AlignmentException( "URI conversion error for "+onto1, e );
- //}
- };
+ public URI getOntology1URI() { return onto1.getURI(); };
- // JE: --- post-3.1
- public URI getOntology2URI() //throws AlignmentException
- {
- //try {
- // JE: OWMG1
- //return ((OWLOntology)(onto2.getOntology())).getLogicalURI();
- return onto2.getURI();
- //} catch ( OWLException e ) {
- //throw new AlignmentException( "URI conversion error for "+onto2, e );
- //}
- };
-
- // JE: --- post-3.1
- //public void setOntology1(Object ontology) throws AlignmentException {
- //if ( ontology instanceof OWLOntology ){
- //super.setOntology1( ontology );
- //onto1.setOntology( ontology );
- //} else {
- //throw new AlignmentException("arguments must be OWLOntology");
- //};
- //};
-
- // JE: --- post-3.1
- //public void setOntology2(Object ontology) throws AlignmentException {
- // JE: tonewOnto
- //if ( ontology instanceof OWLOntology ){
- //super.setOntology2( ontology );
- //onto2.setOntology( ontology );
- //} else {
- //throw new AlignmentException("arguments must be OWLOntology");
- //};
- //};
+ public URI getOntology2URI() { return onto2.getURI(); };
/** Cell methods **/
public Cell addAlignCell(String id, Object ob1, Object ob2, Relation relation, double measure, Parameters extensions ) throws AlignmentException {
@@ -285,9 +223,6 @@ public class OWLAPIAlignment extends BasicAlignment {
// Here it becomes necessary to load OWL
static public OWLAPIAlignment toOWLAPIAlignment( URIAlignment al, OntologyCache ontologies ) throws AlignmentException, SAXException, OWLException {
OWLAPIAlignment alignment = new OWLAPIAlignment();
- //alignment.setFile1( al.getFile1() );
- //alignment.setFile2( al.getFile2() );
- //System.err.println( "TOA: " + al.getFile1()+ " -- " + al.getFile2());
alignment.init( al.getFile1(), al.getFile2(), ontologies );
alignment.setType( al.getType() );
alignment.setLevel( al.getLevel() );
@@ -311,7 +246,14 @@ public class OWLAPIAlignment extends BasicAlignment {
return alignment;
}
- // JE: newOnto ---
+ private static LoadedOntology loadOntology( URI ref, OntologyCache ontologies ) {
+ OntologyFactory factory = OntologyFactory.newInstance();
+ LoadedOntology onto = factory.loadOntology( ref );
+ if ( ontologies != null ) ontologies.recordOntology( ref, onto );
+ return onto;
+ }
+
+ // JE: newOnto --- Onto: should be discarded
private static OWLEntity getEntity( OWLOntology ontology, URI uri ) throws OWLException, SAXException {
OWLEntity result = (OWLEntity)ontology.getClass( uri );
if ( result == null ) result = (OWLEntity)ontology.getDataProperty( uri );
@@ -320,8 +262,9 @@ public class OWLAPIAlignment extends BasicAlignment {
return result;
}
- // JE: newOnto ---
+ // JE: newOnto --- Onto: should be discarded
/** Can be used for loading the ontology if it is not available **/
+ /*
//private static OWLOntology loadOntology( URI ref, Hashtable ontologies ) throws SAXException, OWLException {
private static OWLOntology loadOntology( URI ref, OntologyCache ontologies ) throws SAXException, OWLException {
if ( (ontologies != null) && ( ontologies.getOntology( ref ) != null ) ) {
@@ -355,6 +298,6 @@ public class OWLAPIAlignment extends BasicAlignment {
return parsedOnt;
}
}
-
+ */
}
diff --git a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
index a7fe1b87c2609dc82860d10eab98085077d48d8d..77f28707ec6800930c44f0b0a589e0c6b36eb930 100644
--- a/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/URIAlignment.java
@@ -44,6 +44,8 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
import org.semanticweb.owl.align.Parameters;
+import fr.inrialpes.exmo.align.onto.Ontology;
+
/**
* Represents an ontology alignment relating entities identified by their URIs
*
@@ -53,8 +55,6 @@ import org.semanticweb.owl.align.Parameters;
public class URIAlignment extends BasicAlignment {
- public URIAlignment() {}
-
// JE: OMWG1, not sure it works...
public void init(Object o1, Object o2) throws AlignmentException {
if ( o1 instanceof Ontology && o2 instanceof Ontology ){
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
index dba5a84bf9c772182c01d38d25adcdcb308ad247..7ac511a0399cbc9753858fa109d98a6d2ae1616c 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/HTMLRendererVisitor.java
@@ -60,12 +60,12 @@ public class HTMLRendererVisitor implements AlignmentVisitor
writer.print("<h1></h1>\n");
writer.print("<h2>Alignment metadata</h2>\n");
writer.print("<table border=\"0\">\n");
- writer.print("<tr><td>uri1</td><td>"+align.getOntology1URI().toString()+"</td></tr>\n" );
- writer.print("<tr><td>uri2</td><td>"+align.getOntology2URI().toString()+"</td></tr>\n" );
+ writer.print("<tr><td>uri1</td><td>"+align.getOntology1URI()+"</td></tr>\n" );
+ writer.print("<tr><td>uri2</td><td>"+align.getOntology2URI()+"</td></tr>\n" );
if ( align.getFile1() != null )
- writer.print("<tr><td>ontofile1</td><td><a href=\""+align.getFile1().toString()+"\">"+align.getFile1().toString()+"</a></td></tr>\n" );
+ writer.print("<tr><td>ontofile1</td><td><a href=\""+align.getFile1()+"\">"+align.getFile1()+"</a></td></tr>\n" );
if ( align.getFile2() != null )
- writer.print("<tr><td>ontofile2</td><td><a href=\""+align.getFile2().toString()+"\">"+align.getFile2().toString()+"</a></td></tr>\n" );
+ writer.print("<tr><td>ontofile2</td><td><a href=\""+align.getFile2()+"\">"+align.getFile2()+"</a></td></tr>\n" );
writer.print("<tr><td>level</td><td>"+align.getLevel()+"</td></tr>\n" );
writer.print("<tr><td>type</td><td>"+align.getType()+"</td></tr>\n" );
// Get the keys of the parameter
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index 0640f4982ba9fcc4b6c0058d84032dc5f0fff378..e638a0151876159964215eaff0cc9903c3e5941f 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -51,7 +51,9 @@ import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Parameters;
-import fr.inrialpes.exmo.align.impl.Ontology;
+import fr.inrialpes.exmo.align.onto.Ontology;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
+import fr.inrialpes.exmo.align.onto.BasicOntology;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.BasicParameters;
import fr.inrialpes.exmo.align.impl.Annotations;
@@ -67,8 +69,6 @@ import fr.inrialpes.exmo.align.impl.Annotations;
public class AlignmentParser extends DefaultHandler {
- private static String ALIGNNS = "http://knowledgeweb.semanticweb.org/heterogeneity/alignment#";
-
/**
* level of debug/warning information
*/
@@ -231,7 +231,7 @@ public class AlignmentParser extends DefaultHandler {
System.err.println("startElement AlignmentParser : " + pName);
parselevel++;
if( namespaceURI.equals("http://knowledgeweb.semanticweb.org/heterogeneity/alignment")
- || namespaceURI.equals(ALIGNNS) ) {
+ || namespaceURI.equals(Annotations.ALIGNNS) ) {
if (pName.equals("relation")) {
} else if (pName.equals("semantics")) {
} else if (pName.equals("measure")) {
@@ -282,7 +282,8 @@ public class AlignmentParser extends DefaultHandler {
} else if (pName.equals("Ontology")) {
if ( atts.getValue("rdf:about") != null && !atts.getValue("rdf:about").equals("") ) {
try {
- curronto.setOntology( new URI( atts.getValue("rdf:about") ) );
+ // JE: Onto
+ //curronto.setOntology( new URI( atts.getValue("rdf:about") ) );
curronto.setURI( new URI( atts.getValue("rdf:about") ) );
} catch (URISyntaxException e) {
throw new SAXException("onto2: malformed URI");
@@ -299,8 +300,9 @@ public class AlignmentParser extends DefaultHandler {
} else if (pName.equals("xml")) {
} else if (pName.equals("Alignment")) {
alignment = new URIAlignment();
- onto1 = new Ontology();
- onto2 = new Ontology();
+ onto1 = ((URIAlignment)alignment).getOntologyObject1();
+ onto2 = ((URIAlignment)alignment).getOntologyObject2();
+ System.err.println(">>>>>>> "+onto1);
if ( atts.getValue("rdf:about") != null && !atts.getValue("rdf:about").equals("") ) {
alignment.setExtension( Annotations.ALIGNNS, Annotations.ID, atts.getValue("rdf:about") );
};
@@ -367,7 +369,7 @@ public class AlignmentParser extends DefaultHandler {
if(debugMode > 2)
System.err.println("endElement AlignmentParser : " + pName);
if( namespaceURI.equals("http://knowledgeweb.semanticweb.org/heterogeneity/alignment")
- || namespaceURI.equals(ALIGNNS) ) {
+ || namespaceURI.equals(Annotations.ALIGNNS) ) {
try {
if (pName.equals("relation")) {
relation = content;
@@ -398,20 +400,22 @@ public class AlignmentParser extends DefaultHandler {
if ( extensions != null ) cell.setExtensions( extensions );
} else if (pName.equals("map")) {
} else if (pName.equals("uri1")) {
- if ( onto1.getOntology() == null ){
+ if ( onto1.getURI() == null ){//JE: Onto
try {
URI u = new URI( content );
- onto1.setOntology( u );
+ // JE: Onto
+ //onto1.setOntology( u );
onto1.setURI( u );
} catch (URISyntaxException e) {
throw new SAXException("uri1: malformed URI");
}
}
} else if (pName.equals("uri2")) {
- if ( onto2.getOntology() == null ){
+ if ( onto2.getURI() == null ){//JE: Onto
try {
URI u = new URI( content );
- onto2.setOntology( u );
+ // JE: Onto
+ //onto2.setOntology( u );
onto2.setURI( u );
} catch (URISyntaxException e) {
throw new SAXException("uri2: malformed URI");
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 9c171cb123f3b90e7801f736e040c132b1131f58..c2dcc6f8fdfd71e4e78fc92b0fccd5e22209a76f 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -25,7 +25,10 @@ import fr.inrialpes.exmo.align.parser.AlignmentParser;
import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicParameters;
import fr.inrialpes.exmo.align.impl.BasicAlignment;
-import fr.inrialpes.exmo.align.impl.OntologyCache;
+import fr.inrialpes.exmo.align.onto.OntologyFactory;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
+import fr.inrialpes.exmo.align.onto.Ontology;
+import fr.inrialpes.exmo.align.onto.LoadedOntology;
import org.semanticweb.owl.align.Parameters;
import org.semanticweb.owl.align.Alignment;
@@ -33,14 +36,6 @@ import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
-import org.semanticweb.owl.util.OWLManager;
-import org.semanticweb.owl.model.OWLOntology;
-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.io.ParserException;
-
-import org.xml.sax.SAXException;
import java.sql.SQLException;
import java.lang.ClassNotFoundException;
@@ -88,7 +83,6 @@ public class AServProtocolManager {
Set<String> services = null;
OntologyCache loadedOntologies = null;
- OWLRDFErrorHandler handler = null;
Hashtable<String,Directory> directories = null;
// This should be stored somewhere
@@ -113,20 +107,6 @@ public class AServProtocolManager {
methods.remove("fr.inrialpes.exmo.align.impl.DistanceAlignment"); // this one is generic
services = implementations( "fr.inrialpes.exmo.align.service.AlignmentServiceProfile" );
loadedOntologies = new OntologyCache();
- 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.err.println("WARNING: " + message);
- }
- };
}
public void close() {
@@ -235,8 +215,8 @@ public class AServProtocolManager {
// find and access o, o'
URI uri1 = null;
URI uri2 = null;
- OWLOntology onto1 = null;
- OWLOntology onto2 = null;
+ Ontology onto1 = null;
+ Ontology onto2 = null;
try {
uri1 = new URI((String)params.getParameter("onto1"));
uri2 = new URI((String)params.getParameter("onto2"));
@@ -249,13 +229,7 @@ public class AServProtocolManager {
return new UnreachableOntology(newId(),mess,myId,mess.getSender(),(String)params.getParameter("onto2"),(Parameters)null);
}
// Try to retrieve first
- Set alignments = null;
- try {
- // This is OWLAPI specific but there is no other way...
- alignments = alignmentCache.getAlignments( onto1.getLogicalURI(), onto2.getLogicalURI() );
- } catch (OWLException e) {
- // Unexpected OWLException!
- }
+ Set alignments = alignmentCache.getAlignments( onto1.getURI(), onto2.getURI() );
if ( alignments != null && params.getParameter("force") == null ) {
for ( Iterator it = alignments.iterator(); it.hasNext() ; ){
Alignment al = ((Alignment)it.next());
@@ -380,24 +354,25 @@ public class AServProtocolManager {
public Message store( Message mess ){
String id = mess.getContent();
try {
- alignmentCache.storeAlignment( id );
- } catch (Exception e) {
- return new UnknownAlignment(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
- }
- // Retrieve the alignment
- Alignment al = null;
- try { al = alignmentCache.getAlignment( id );
+ Alignment al = alignmentCache.getAlignment( id );
+ // Be sure it is not already stored
+ if ( !alignmentCache.isAlignmentStored( al ) ){
+ alignmentCache.storeAlignment( id );
+ // Retrieve the alignment again
+ al = alignmentCache.getAlignment( id );
+ // for all directories...
+ for ( Directory d : directories.values() ){
+ // Declare the alignment in the directory
+ try { d.register( al ); }
+ catch (AServException e) { e.printStackTrace(); }// ignore
+ }
+ }
+ // register by them
+ // Could also be an AlreadyStoredAlignment error
+ return new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
} catch (Exception e) {
return new UnknownAlignment(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
}
- // for all directories...
- for ( Directory d : directories.values() ){
- // Declare the alignment in the directory
- try { d.register( al ); }
- catch (AServException e) { e.printStackTrace(); }// ignore
- }
- // register by them
- return new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
}
/*
@@ -573,24 +548,21 @@ public class AServProtocolManager {
* Utilities: reaching and loading ontologies
*********************************************************************/
- public OWLOntology reachable( URI uri ){
+ public LoadedOntology reachable( URI uri ){
try { return loadOntology( uri ); }
catch (Exception e) {
e.printStackTrace();
- return (OWLOntology)null;
+ return null;
}
}
- public OWLOntology loadOntology( URI uri ) throws ParserException, OWLException {
+ public LoadedOntology loadOntology( URI uri ) {
// Test if not loaded...
- OWLOntology parsedOnt = null;
- OWLRDFParser parser = new OWLRDFParser();
- parser.setOWLRDFErrorHandler(handler);
- parser.setConnection(OWLManager.getOWLConnection());
- parsedOnt = parser.parseOntology( uri );
+ OntologyFactory factory = OntologyFactory.newInstance();
+ LoadedOntology onto = factory.loadOntology( uri );
if ( loadedOntologies != null )
- loadedOntologies.recordOntology( uri, parsedOnt );
- return parsedOnt;
+ loadedOntologies.recordOntology( uri, onto );
+ return onto;
}
/*********************************************************************
@@ -748,8 +720,6 @@ public class AServProtocolManager {
// find and access o, o'
URI uri1 = null;
URI uri2 = null;
- OWLOntology onto1 = null;
- OWLOntology onto2 = null;
try {
uri1 = new URI((String)params.getParameter("onto1"));
@@ -811,7 +781,6 @@ public class AServProtocolManager {
} catch (AlignmentException e) {
result = new NonConformParameters(newId(),mess,myId,mess.getSender(),"nonconform/params/",(Parameters)null);
}
- // JE: In non OWL-API-based version, here unload ontologies
loadedOntologies.clear(); // not always necessary
result = new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Parameters)null);
}
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index 9a538f45f08b75f38bd830303a7e084fecb41002..ed58e2bc074fb11714b98abd2037845a8ae1f4b3 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -127,16 +127,6 @@ public class CacheImpl {
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
* index them under the ontology URIs
- *
- * Beware, the Alignment API has two attributes:
- * onto1 is the OWLOntology object
- * uri1 is the URI object from which loading the ontologies
- * In the database we store:
- * owlontology1 the URI string of the ontology
- * file1 the URI string from which loading the ontologies
- * uri1 which should be the same as the last one...
- * Since alignments are indexed by the URI of the ontologies, we use
- * the "ouri1" temporary extension to contain this URI.
*/
private void loadAlignments( boolean force ) throws SQLException {
String query = null;
@@ -169,6 +159,16 @@ public class CacheImpl {
/**
* loads the description of alignments from the database and set them
* in an alignment object
+ *
+ * Beware, the Alignment API has two attributes:
+ * onto1 is the OWLOntology object
+ * uri1 is the URI object from which loading the ontologies
+ * In the database we store:
+ * owlontology1 the URI string of the ontology
+ * file1 the URI string from which loading the ontologies
+ * uri1 which should be the same as the last one...
+ * Since alignments are indexed by the URI of the ontologies, we use
+ * the "ouri1" temporary extension to contain this URI.
*/
protected Alignment retrieveDescription( String id ){
String query;
@@ -176,7 +176,7 @@ public class CacheImpl {
String tag;
String value;
- Alignment result = new URIAlignment();
+ URIAlignment result = new URIAlignment();
try {
Statement st = (Statement) conn.createStatement();
@@ -187,6 +187,8 @@ public class CacheImpl {
// Either uri1 or file1
result.setFile1( new URI( rs.getString("file1") ) );
result.setFile2( new URI( rs.getString("file2") ) );
+ result.getOntologyObject1().setURI( new URI(rs.getString("owlontology1")) );
+ result.getOntologyObject2().setURI( new URI(rs.getString("owlontology2")) );
result.setExtension( SVCNS, OURI1, rs.getString("owlontology1") );
result.setExtension( SVCNS, OURI2, rs.getString("owlontology2") );
result.setLevel(rs.getString("level"));
@@ -428,6 +430,13 @@ public class CacheImpl {
}
}
+ public boolean isAlignmentStored( Alignment alignment ) {
+ if ( alignment.getExtension( SVCNS, STORED ) != null &&
+ !alignment.getExtension( SVCNS, STORED ).equals("") )
+ return false;
+ else return true;
+ }
+
public void storeAlignment( String id ) throws Exception {
String query = null;
Alignment alignment = getAlignment( id );
diff --git a/src/fr/inrialpes/exmo/align/service/OysterDirectory.java b/src/fr/inrialpes/exmo/align/service/OysterDirectory.java
index 5bb6a0a640902557844af697abbddff221d8bd99..dbbd5882e35c08b6973eb08ddfd4b6850502e7b1 100644
--- a/src/fr/inrialpes/exmo/align/service/OysterDirectory.java
+++ b/src/fr/inrialpes/exmo/align/service/OysterDirectory.java
@@ -27,7 +27,8 @@ import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
import fr.inrialpes.exmo.align.impl.Annotations;
-import fr.inrialpes.exmo.align.impl.Ontology;
+
+import fr.inrialpes.exmo.align.onto.Ontology;
import org.neon_toolkit.registry.api.Oyster2Manager;
import org.neon_toolkit.registry.api.Oyster2Connection;
diff --git a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java b/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
index 479f688782bdb1edcdb9a0a62bf13af59e8b970a..3a5b7274903a1bef214b73caac306ae620fe6b22 100644
--- a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
@@ -33,10 +33,11 @@ import org.semanticweb.owl.align.Parameters;
import org.semanticweb.owl.align.Evaluator;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.OntologyCache;
import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.eval.ExtPREvaluator;
+import fr.inrialpes.exmo.align.parser.AlignmentParser;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
import java.io.File;
import java.io.PrintStream;
@@ -52,8 +53,6 @@ import org.xml.sax.SAXException;
import gnu.getopt.LongOpt;
import gnu.getopt.Getopt;
-import fr.inrialpes.exmo.align.parser.AlignmentParser;
-
/** A basic class for synthesizing the results of a set of alignments provided
by different algorithms. The output is a table showing various generalisations
of precision and recall for each test and for each algorithm.
diff --git a/src/fr/inrialpes/exmo/align/util/GenTriangle.java b/src/fr/inrialpes/exmo/align/util/GenTriangle.java
index fec1d3c832948c30536e48b7a1193dfefefc6cf5..bf6cece475084279c0eb33d61c5b6940d5378c8b 100644
--- a/src/fr/inrialpes/exmo/align/util/GenTriangle.java
+++ b/src/fr/inrialpes/exmo/align/util/GenTriangle.java
@@ -31,8 +31,8 @@ import org.semanticweb.owl.align.Parameters;
import org.semanticweb.owl.align.Evaluator;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.OntologyCache;
import fr.inrialpes.exmo.align.impl.eval.PRecEvaluator;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
import java.io.File;
import java.io.PrintStream;
diff --git a/src/fr/inrialpes/exmo/align/util/GroupAlign.java b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
index a2d69a11db828e78f7222ba513ec8ec8a338c1f2..c9e699d4ff5c47e1236239e2258ba0fca3eea12c 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupAlign.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
@@ -38,8 +38,8 @@ import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.OntologyCache;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
import java.io.File;
import java.io.FileOutputStream;
diff --git a/src/fr/inrialpes/exmo/align/util/GroupEval.java b/src/fr/inrialpes/exmo/align/util/GroupEval.java
index ac9c5f95c3f082f8f434ba5b864a262eca4ff43f..1fab84473ea6de216397eeaa23ea965812a4bb58 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupEval.java
@@ -31,8 +31,8 @@ import org.semanticweb.owl.align.Parameters;
import org.semanticweb.owl.align.Evaluator;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.OntologyCache;
import fr.inrialpes.exmo.align.impl.eval.PRecEvaluator;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
import java.io.File;
import java.io.PrintStream;
diff --git a/src/fr/inrialpes/exmo/align/util/GroupOutput.java b/src/fr/inrialpes/exmo/align/util/GroupOutput.java
index fa3751b0282fd4d7317b101864d49dba6347d4f2..dbf7e80ac56822797e255c6140e4e6e8a441e9dd 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupOutput.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupOutput.java
@@ -33,8 +33,8 @@ import org.semanticweb.owl.align.Parameters;
import org.semanticweb.owl.align.Evaluator;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.OntologyCache;
import fr.inrialpes.exmo.align.impl.eval.PRecEvaluator;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
import java.io.File;
import java.io.FileOutputStream;
diff --git a/src/fr/inrialpes/exmo/align/util/ParserPrinter.java b/src/fr/inrialpes/exmo/align/util/ParserPrinter.java
index 611689551b434a57a10df2b38665a9477ac485e4..09fe449c104535c02af6f7c16bd8786708ab7ea2 100644
--- a/src/fr/inrialpes/exmo/align/util/ParserPrinter.java
+++ b/src/fr/inrialpes/exmo/align/util/ParserPrinter.java
@@ -33,8 +33,8 @@ import org.semanticweb.owl.align.AlignmentException;
import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
-import fr.inrialpes.exmo.align.impl.OntologyCache;
import fr.inrialpes.exmo.align.impl.URIAlignment;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
import java.io.OutputStream;
import java.io.FileOutputStream;
diff --git a/src/fr/inrialpes/exmo/align/util/Procalign.java b/src/fr/inrialpes/exmo/align/util/Procalign.java
index c507f707b1197e1ed6e1240542ff315798cbc59d..0613657a50e58bf0af142f82722bc7ca9c819125 100644
--- a/src/fr/inrialpes/exmo/align/util/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/util/Procalign.java
@@ -34,7 +34,7 @@ import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-import fr.inrialpes.exmo.align.impl.OntologyCache;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
import java.io.OutputStream;
import java.io.FileOutputStream;
@@ -218,7 +218,7 @@ public class Procalign {
System.exit(0);
}
- if (debug > 0) System.err.println(" Handler set");
+ if (debug > 0) System.err.println(" Ready");
try {
if (initName != null) {