Thread: [Jason-developers] SF.net SVN: jason: [1155] trunk/applications/jasdl-owlapi

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Revision: 1155
          http://jason.svn.sourceforge.net/jason/?rev=1155&view=rev
Author:   tomklapiscak
Date:     2008-03-16 10:44:47 -0700 (Sun, 16 Mar 2008)

Log Message:
-----------
Run-time class definition implemented. Switched to use the OWL-API Manchester OWL Syntax parser as opposed to Clexer. Additionally, class-definitions now include namespace prefixes for entities and can span any entity from any ontology known to the agent.
Dropped "origin" annotation -> run-time defined classes are distinguished inherently now since they "reside" in an agent's "personal" ontology. Individuals defined at run-time also reside in this ontology.
Further work on semantically-enriched knowledge sharing. Switched to using OWL-API Manchester OWL Syntax renderer for generation of class expressions to be shared.

Modified Paths:
--------------
    trunk/applications/jasdl-owlapi/examples/travel_agent/config.mas2j
    trunk/applications/jasdl-owlapi/examples/travel_agent/customer.asl
    trunk/applications/jasdl-owlapi/examples/travel_agent/ontologies/travel.owl
    trunk/applications/jasdl-owlapi/examples/travel_agent/travel_agent.asl
    trunk/applications/jasdl-owlapi/src/jasdl/architecture/IncomingPropContProcessingStrategy.java
    trunk/applications/jasdl-owlapi/src/jasdl/architecture/JasdlAgArch.java
    trunk/applications/jasdl-owlapi/src/jasdl/architecture/OutgoingPropContProcessingStrategy.java
    trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlAgent.java
    trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlConfigurator.java
    trunk/applications/jasdl-owlapi/src/jasdl/bridge/MappingManager.java
    trunk/applications/jasdl-owlapi/src/jasdl/bridge/seliteral/SELiteral.java
    trunk/applications/jasdl-owlapi/src/jasdl/bridge/seliteral/SELiteralFactory.java

Added Paths:
-----------
    trunk/applications/jasdl-owlapi/examples/travel_agent/ontologies/places.owl
    trunk/applications/jasdl-owlapi/src/jasdl/bridge/label/OntologyURIManager.java
    trunk/applications/jasdl-owlapi/src/jasdl/ia/
    trunk/applications/jasdl-owlapi/src/jasdl/ia/define_class.java

Removed Paths:
-------------
    trunk/applications/jasdl-owlapi/src/jasdl/bridge/label/PhysicalURIManager.java

Modified: trunk/applications/jasdl-owlapi/examples/travel_agent/config.mas2j
===================================================================

--- trunk/applications/jasdl-owlapi/examples/travel_agent/config.mas2j	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/examples/travel_agent/config.mas2j	2008-03-16 17:44:47 UTC (rev 1155)
@@ -33,11 +33,14 @@
 	       travel_agent 
        	   travel_agent.asl
 	       [				
-	       	jasdl_ontologies="travel",
+	       	jasdl_ontologies="travel,places",
 			jasdl_travel_uri="http://www.dur.ac.uk/t.g.klapiscak/onts/travel.owl",
 			jasdl_travel_mapping_strategies="jasdl.bridge.alias.DecapitaliseMappingStrategy",
-			jasdl_travel_mapping_manual="small_beach=beach"
+			jasdl_travel_mapping_manual="small_beach=beach",
 			
+			jasdl_places_uri="http://www.dur.ac.uk/t.g.klapiscak/onts/places.owl",
+			jasdl_places_mapping_strategies="jasdl.bridge.alias.DecapitaliseMappingStrategy"
+			
 			//,jasdl_aktors_uri="http://www.aktors.org/ontology/portal.owl",
 			//jasdl_aktors_mapping_strategies="jasdl.bridge.alias.DecapitaliseMappingStrategy"
 	       ]
@@ -50,8 +53,8 @@
        	   customer.asl
 	       [		   
 	       	jasdl_ontologies="holidays",
+			//jasdl_holidays_uri="file:///home/tom/Desktop/Project/workspace/jason/applications/jasdl-owlapi/examples/travel_agent/ontologies/travel.owl",
 			jasdl_holidays_uri="http://www.dur.ac.uk/t.g.klapiscak/onts/travel.owl",
-			//jasdl_holidays_uri="file:///home/tom/Desktop/Project/workspace/jason/applications/jasdl-owlapi/examples/travel_agent/ontologies/travel.owl",
 			jasdl_holidays_mapping_strategies="jasdl.bridge.alias.DecapitaliseMappingStrategy",
 			jasdl_holidays_mapping_manual="small_beach=beach, luxuriousHotel=LuxuryHotel" // arbitrary primitive mappings handled correctly
 			

Modified: trunk/applications/jasdl-owlapi/examples/travel_agent/customer.asl
===================================================================
--- trunk/applications/jasdl-owlapi/examples/travel_agent/customer.asl	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/examples/travel_agent/customer.asl	2008-03-16 17:44:47 UTC (rev 1155)
@@ -21,12 +21,12 @@
 +luxuriousHotel(L)[o(holidays), source(Source)]
 	<-
 	/* 1 */ .print("The ", L, " luxurious hotel is available");
-	/* 2 */ jasdl.ia.define_class(query, "city and hasAccommodation value ", L, holidays);
+	/* 2 */ jasdl.ia.define_class(query, "city and hasAccommodation value ", L);
 	/* 3 */ .send(Source, askOne, query(City)[o(holidays)], query(City)[o(holidays)]);
 	/* 4 */ .print(L, " is located in the city ", City);	
 	
 	// check given hotel is located in a destination that has some museums
-	jasdl.ia.define_class(q2, "{",L,"} and isLocatedAt some (hasActivity some museums)", holidays);
+	jasdl.ia.define_class(q2, "{",L,"} and isLocatedAt some (hasActivity some museums)");
 	.send(Source, askOne, q2(Hotel)[o(holidays)], q2(Hotel)[o(holidays)]);
 	.print(Hotel, " is located in a city with some museums");
 	

Added: trunk/applications/jasdl-owlapi/examples/travel_agent/ontologies/places.owl
===================================================================
--- trunk/applications/jasdl-owlapi/examples/travel_agent/ontologies/places.owl	                        (rev 0)
+++ trunk/applications/jasdl-owlapi/examples/travel_agent/ontologies/places.owl	2008-03-16 17:44:47 UTC (rev 1155)
@@ -0,0 +1,58 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+    <!ENTITY owl11 "http://www.w3.org/2006/12/owl11#" >
+    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+    <!ENTITY owl11xml "http://www.w3.org/2006/12/owl11-xml#" >
+    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+    <!ENTITY places "http://www.dur.ac.uk/t.g.klapiscak/ontologies/places.owl#" >
+]>
+
+
+<rdf:RDF xmlns="http://www.dur.ac.uk/t.g.klapiscak/ontologies/places.owl#"
+     xml:base="http://www.dur.ac.uk/t.g.klapiscak/ontologies/places.owl"
+     xmlns:places="http://www.dur.ac.uk/t.g.klapiscak/ontologies/places.owl#"
+     xmlns:owl11="http://www.w3.org/2006/12/owl11#"
+     xmlns:owl11xml="http://www.w3.org/2006/12/owl11-xml#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#">
+    <owl:Ontology rdf:about=""/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.dur.ac.uk/t.g.klapiscak/ontologies/places.owl#Building -->
+
+    <owl:Class rdf:about="#Building">
+        <rdfs:subClassOf rdf:resource="#Place"/>
+    </owl:Class>
+    
+
+
+    <!-- http://www.dur.ac.uk/t.g.klapiscak/ontologies/places.owl#Place -->
+
+    <owl:Class rdf:about="#Place">
+        <rdfs:subClassOf rdf:resource="&owl;Thing"/>
+    </owl:Class>
+    
+
+
+    <!-- http://www.w3.org/2002/07/owl#Thing -->
+
+    <owl:Class rdf:about="&owl;Thing"/>
+</rdf:RDF>

Modified: trunk/applications/jasdl-owlapi/examples/travel_agent/ontologies/travel.owl
===================================================================
--- trunk/applications/jasdl-owlapi/examples/travel_agent/ontologies/travel.owl	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/examples/travel_agent/ontologies/travel.owl	2008-03-16 17:44:47 UTC (rev 1155)
@@ -323,9 +323,6 @@
         <rdfs:subClassOf rdf:resource="#Destination"/>
     </owl:Class>
     
-    <owl:Class rdf:about="#beach">
-        <rdfs:subClassOf rdf:resource="#Destination"/>
-    </owl:Class>
 
 
     <!-- http://www.owl-ontologies.com/travel.owl#BedAndBreakfast -->
@@ -677,6 +674,14 @@
     
 
 
+    <!-- http://www.owl-ontologies.com/travel.owl#beach -->
+
+    <owl:Class rdf:about="#beach">
+        <rdfs:subClassOf rdf:resource="#Destination"/>
+    </owl:Class>
+    
+
+
     <!-- http://www.w3.org/2002/07/owl#Thing -->
 
     <owl:Class rdf:about="&owl;Thing"/>
@@ -709,9 +714,9 @@
     <!-- http://www.owl-ontologies.com/travel.owl#TwoStarRating -->
 
     <AccommodationRating rdf:about="#TwoStarRating"/>
+    
 
 
-
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //

Modified: trunk/applications/jasdl-owlapi/examples/travel_agent/travel_agent.asl
===================================================================
--- trunk/applications/jasdl-owlapi/examples/travel_agent/travel_agent.asl	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/examples/travel_agent/travel_agent.asl	2008-03-16 17:44:47 UTC (rev 1155)
@@ -45,6 +45,15 @@
 	+hasActivity(london, scienceMuseum)[o(travel)];	
 	+hotel(travel_lodge)[o(travel)];
 	
+	+building(hilton)[o(places)];
+	
+	?place(Place)[o(places)];
+	.print(Place);
+	
+	jasdl.ia.define_class(q2, "(places:place and places:building) and travel:hotel");
+	?q2(X)[o(self)];
+	.print(X);
+	
 	.print("Completed: Updating Belief Base 1").
 
 
@@ -121,11 +130,11 @@
 	+hasActivity(butlins, butlins_yoga)[o(travel)];
 	+hasActivity(butlins, butlins_sunbathing)[o(travel)];	
 	//jasdl.ia.all_different([butlins_yoga, butlins_sunbathing], travel);	- DEPRECATED (see below)
-	+all_different([butlins_yoga, butlins_sunbathing])[o(travel), something]; // all_different now represented as an se-literal. We can now query, inspect and send these assertions
+	+all_different([butlins_yoga, butlins_sunbathing])[o(self), something]; // all_different now represented as an se-literal. We can now query, inspect and send these assertions
 	// Query below will not succeed unless butlins_yoga and butlins_sunbathing are different individuals since family destination requires min 2 *different* activities.
 	// Note: OWL doesn't make UNA and since these individuals do not belong to disjoint classes, therefore they must be explicitly asserted as different.
 	?familyDestination(butlins)[o(travel)];
-	?all_different([butlins_yoga, butlins_sunbathing, hilton])[o(travel)];
+	?all_different([butlins_yoga, butlins_sunbathing, hilton])[o(self)];
 	/* ?all_different([hilton, fourSeasons])[o(travel)]; */  // Will fail, since hilton and fourSeasons cannot be established as distinct
 	.print("Completed: all_different assertion").
 		

Modified: trunk/applications/jasdl-owlapi/src/jasdl/architecture/IncomingPropContProcessingStrategy.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/architecture/IncomingPropContProcessingStrategy.java	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/src/jasdl/architecture/IncomingPropContProcessingStrategy.java	2008-03-16 17:44:47 UTC (rev 1155)
@@ -19,6 +19,8 @@
  */
 package jasdl.architecture;
 
+import static jasdl.architecture.JasdlAgArch.NAMED_ANNOTATION_FUNCTOR;
+import static jasdl.architecture.JasdlAgArch.ANON_ANNOTATION_FUNCTOR;
 import jasdl.asSemantics.JasdlAgent;
 import jasdl.bridge.seliteral.SELiteral;
 import jasdl.util.JasdlException;

Modified: trunk/applications/jasdl-owlapi/src/jasdl/architecture/JasdlAgArch.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/architecture/JasdlAgArch.java	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/src/jasdl/architecture/JasdlAgArch.java	2008-03-16 17:44:47 UTC (rev 1155)
@@ -36,6 +36,8 @@
 
 public class JasdlAgArch extends AgArch {
 	
+	public static String NAMED_ANNOTATION_FUNCTOR = "named";
+	public static String ANON_ANNOTATION_FUNCTOR = "anon";
 	
 	IncomingPropContProcessingStrategy incomingStrategy = new IncomingPropContProcessingStrategy();
 	OutgoingPropContProcessingStrategy outgoingStrategy = new OutgoingPropContProcessingStrategy();

Modified: trunk/applications/jasdl-owlapi/src/jasdl/architecture/OutgoingPropContProcessingStrategy.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/architecture/OutgoingPropContProcessingStrategy.java	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/src/jasdl/architecture/OutgoingPropContProcessingStrategy.java	2008-03-16 17:44:47 UTC (rev 1155)
@@ -19,14 +19,27 @@
  */
 package jasdl.architecture;
 
+import static jasdl.architecture.JasdlAgArch.ANON_ANNOTATION_FUNCTOR;
+import static jasdl.architecture.JasdlAgArch.NAMED_ANNOTATION_FUNCTOR;
 import jasdl.asSemantics.JasdlAgent;
+import jasdl.bridge.alias.Alias;
 import jasdl.bridge.seliteral.SELiteral;
 import jasdl.util.JasdlException;
 import jasdl.util.NotEnrichedException;
+import jason.asSyntax.ListTerm;
+import jason.asSyntax.ListTermImpl;
 import jason.asSyntax.Literal;
+import jason.asSyntax.StringTerm;
 import jason.asSyntax.StringTermImpl;
 import jason.asSyntax.Structure;
 
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.semanticweb.owl.model.OWLOntology;
+
 public class OutgoingPropContProcessingStrategy implements PropContProcessingStrategy {
 
 	
@@ -40,13 +53,52 @@
 	 */
 	public Literal process(Literal l, JasdlAgent agent) throws JasdlException {
 		try{
-			SELiteral sl = new SELiteral(l, agent); // note, l might not (yet) be a valid se-literal (mappings may be performed below) so factory cannot be used	
-			sl.qualifyOntologyAnnotation();
+			SELiteral sl = new SELiteral(l, agent);	
 			
-			Structure expr = new Structure("expr");			
-			expr.addTerm(new StringTermImpl( agent.getManchesterObjectRenderer().render(sl.toOWLObject()) ));			
-			sl.addAnnot(expr);
+			StringTerm expression = new StringTermImpl( agent.getManchesterObjectRenderer().render(sl.toOWLObject()));
 			
+			
+			Alias alias = sl.toAlias();
+			if(alias.getLabel().equals(agent.getPersonalOntologyLabel())){ // do we have an anonymous run-time defined class?				
+				
+				Structure anon = new Structure(ANON_ANNOTATION_FUNCTOR);
+				anon.addTerm(expression);				
+				
+				// add set of prerequisite ontologies
+				Set<OWLOntology> prereqs = new HashSet<OWLOntology>();
+				String[] tokens = expression.toString().split(" ");
+				for(String token : tokens){
+					try {
+						URI entityURI = new URI(token);
+						URI ontologyURI = new URI(entityURI.getScheme(), entityURI.getSchemeSpecificPart(), null);
+						prereqs.add(agent.getLogicalURIManager().getLeft(ontologyURI));
+					} catch (URISyntaxException e) {	
+						// do nothing, probably a keyword
+					}
+				}
+				ListTerm list = new ListTermImpl();
+				for(OWLOntology prereq : prereqs){
+					list.add(agent.getLabelManager().getLeft(prereq));
+				}
+				anon.addTerm(list);
+				
+				l.addAnnot(anon);				
+				
+				// drop o, not needed
+				sl.dropOntologyAnnotation();				
+				
+			}else{
+				// qualify o
+				sl.qualifyOntologyAnnotation();
+				
+				// unambiguously refer to named entity
+				Structure named = new Structure(NAMED_ANNOTATION_FUNCTOR);			
+				named.addTerm(expression);			
+				sl.addAnnot(named);
+			}
+			
+			
+			
 			return sl;
 		}catch(NotEnrichedException e){
 			// do nothing

Modified: trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlAgent.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlAgent.java	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlAgent.java	2008-03-16 17:44:47 UTC (rev 1155)
@@ -4,11 +4,14 @@
 import jasdl.bb.JasdlBeliefBase;
 import jasdl.bridge.ToAxiomConverter;
 import jasdl.bridge.ToSELiteralConverter;
+import jasdl.bridge.alias.Alias;
+import jasdl.bridge.alias.AliasFactory;
 import jasdl.bridge.alias.AliasManager;
 import jasdl.bridge.label.LabelManager;
-import jasdl.bridge.label.PhysicalURIManager;
+import jasdl.bridge.label.OntologyURIManager;
 import jasdl.bridge.seliteral.SELiteralFactory;
 import jasdl.util.JasdlException;
+import jasdl.util.UnknownMappingException;
 import jason.JasonException;
 import jason.architecture.AgArch;
 import jason.asSemantics.TransitionSystem;
@@ -17,19 +20,32 @@
 import jason.runtime.Settings;
 
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.Set;
 
 import jmca.asSemantics.JmcaAgent;
 
+import org.coode.manchesterowlsyntax.ManchesterOWLSyntaxDescriptionParser;
 import org.mindswap.pellet.PelletOptions;
 import org.mindswap.pellet.owlapi.Reasoner;
 import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.expression.OWLEntityChecker;
+import org.semanticweb.owl.model.OWLClass;
+import org.semanticweb.owl.model.OWLDataProperty;
+import org.semanticweb.owl.model.OWLDataType;
+import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owl.model.OWLEntity;
+import org.semanticweb.owl.model.OWLIndividual;
+import org.semanticweb.owl.model.OWLObject;
+import org.semanticweb.owl.model.OWLObjectProperty;
 import org.semanticweb.owl.model.OWLOntology;
 import org.semanticweb.owl.model.OWLOntologyCreationException;
 import org.semanticweb.owl.model.OWLOntologyManager;
+import org.semanticweb.owl.model.OWLRuntimeException;
+import org.semanticweb.owl.util.ShortFormProvider;
 
+import uk.ac.manchester.cs.owl.OWLClassImpl;
 import uk.ac.manchester.cs.owl.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
-import uk.ac.manchester.cs.owl.mansyntaxrenderer.ManchesterOWLSyntaxObjectRenderer;
 
 public class JasdlAgent extends JmcaAgent {	
 	private OWLOntologyManager ontologyManager;
@@ -39,23 +55,38 @@
 	private SELiteralFactory seLiteralFactory;
 	private ToSELiteralConverter toSELiteralConverter;	
 	private ToAxiomConverter toAxiomConverter;
-	private PhysicalURIManager physicalURIManager;
+	private OntologyURIManager logicalURIManager;
+	private OntologyURIManager physicalURIManager;
 	private ManchesterOWLSyntaxOWLObjectRendererImpl manchesterObjectRenderer;
+	private ManchesterOWLSyntaxDescriptionParser manchesterDescriptionParser;
 	
+
+	
 	public JasdlAgent(){
 		super();
 		// instantiate managers
 		aliasManager = new AliasManager();
 		labelManager = new LabelManager();
 		ontologyManager = OWLManager.createOWLOntologyManager();
-		physicalURIManager = new PhysicalURIManager();
+		physicalURIManager = new OntologyURIManager();
+		logicalURIManager = new OntologyURIManager();
+		
 		seLiteralFactory = new SELiteralFactory(this);
 		toAxiomConverter = new ToAxiomConverter(this);
 		toSELiteralConverter = new ToSELiteralConverter(this);
 		
 		manchesterObjectRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
+		manchesterObjectRenderer.setShortFormProvider(new ShortFormProvider(){
+			public void dispose() {			
+			}
+			public String getShortForm(OWLEntity entity) {
+				return entity.getURI().toString();
+			}			
+		}); // we want fully qualified entity references
 		
+		manchesterDescriptionParser = new ManchesterOWLSyntaxDescriptionParser(ontologyManager.getOWLDataFactory(), new NSPrefixEntityChecker(this));
 		
+		
 		// instantiate (Pellet) reasoner
 		PelletOptions.USE_TRACING = true;
 		reasoner = new Reasoner(ontologyManager);
@@ -78,7 +109,7 @@
 		
 		// load .mas2j JASDL configuration
 		JasdlConfigurator config = new JasdlConfigurator(this);
-		config.configure(stts);
+			config.configure(stts);
 		return super.initAg(arch, bb, src, stts);
 	}
 
@@ -97,13 +128,54 @@
 			reasoner.classify();
 			labelManager.put(label, ontology);
 			physicalURIManager.put(ontology, uri);
+			logicalURIManager.put(ontology, ontology.getURI());
 		}catch(OWLOntologyCreationException e){
 			throw new JasdlException("Error loading ontology "+uri+". Reason: "+e);
 		}		
 	}
+	
+	
+	public void createOntology(Atom label, URI uri) throws JasdlException{
+		try{
+			OWLOntology ontology = getOntologyManager().createOntology( uri );
+			getLabelManager().put(label, ontology);
+			getPhysicalURIManager().put(ontology, uri);
+			getLogicalURIManager().put(ontology, uri);
+			getReasoner().loadOntology(ontology);			
+		} catch (OWLOntologyCreationException e) {
+			throw new JasdlException("Error instantiating OWL ontology. Reason: "+e);
+		}		
+	}
+	
+	public Atom getPersonalOntologyLabel(){
+		return new Atom("self");		
+	}
+	
 
 
+	public URI getPersonalOntologyURI() {
+		return URI.create("http://www.dur.ac.uk/t.g.klapiscak/"+getPersonalOntologyLabel()+".owl");
+	}	
+	
+	
+	
+	public OWLDescription defineClass(Atom functor, String expression) throws JasdlException{
+		OWLDescription desc;
+		try{
+    		desc = getManchesterDescriptionParser().parse(expression);       
+    	}catch(Exception e){
+    		e.printStackTrace();
+    		throw new JasdlException("Could not parse expression "+expression+". Reason: "+e);
+    	}
+    	
+    	Alias alias = AliasFactory.INSTANCE.create(functor, getPersonalOntologyLabel());
+    	getAliasManager().put(alias, desc); 
+    	
+    	return desc;    	
+	}
 
+
+
 	public AliasManager getAliasManager() {
 		return aliasManager;
 	}
@@ -124,12 +196,19 @@
 
 
 
-	public PhysicalURIManager getPhysicalURIManager() {
+	public OntologyURIManager getPhysicalURIManager() {
 		return physicalURIManager;
 	}
 
+	
+	
 
+	public OntologyURIManager getLogicalURIManager() {
+		return logicalURIManager;
+	}
 
+
+
 	public Reasoner getReasoner() {
 		return reasoner;
 	}
@@ -164,11 +243,135 @@
 	public ManchesterOWLSyntaxOWLObjectRendererImpl getManchesterObjectRenderer() {
 		return manchesterObjectRenderer;
 	}
+
+
+
+	public ManchesterOWLSyntaxDescriptionParser getManchesterDescriptionParser() {
+		return manchesterDescriptionParser;
+	}
 	
 	
+	/**
+	 * Convenience method to (polymorphically) create an entity from resource URI (if known).
+	 * TODO: where should this sit?
+	 * @param uri	URI of resource to create entity from
+	 * @return		entity identified by URI
+	 * @throws UnknownReferenceException	if OWLObject not known
+	 */
+	public OWLEntity toEntity(URI uri) throws JasdlException{
+		URI ontURI;
+		try {
+			ontURI = new URI(uri.getScheme(), uri.getSchemeSpecificPart(), null);
+		} catch (URISyntaxException e) {
+			throw new JasdlException("Invalid entity URI "+uri);
+		}
+		OWLOntology ontology = getLogicalURIManager().getLeft(ontURI);;
+		
+		// clumsy approach, but I can't find any way of achieving this polymorphically (i.e. retrieve an OWLObject from a URI) using OWL-API
+		OWLEntity entity;
+		if(ontology.containsClassReference(uri)){
+			entity = getOntologyManager().getOWLDataFactory().getOWLClass(uri);
+		}else if (ontology.containsObjectPropertyReference(uri)){	
+			entity = getOntologyManager().getOWLDataFactory().getOWLObjectProperty(uri);
+		}else if (ontology.containsDataPropertyReference(uri)){	
+			entity = getOntologyManager().getOWLDataFactory().getOWLDataProperty(uri);
+		}else if (ontology.containsIndividualReference(uri)){
+			entity = getOntologyManager().getOWLDataFactory().getOWLIndividual(uri);
+		}else{
+			throw new UnknownMappingException("Unknown ontology resource URI: "+uri);
+		}
+		return entity;
+	}	
 	
+	
+	
+	
+	private class NSPrefixEntityChecker implements OWLEntityChecker{
+		
+		private JasdlAgent agent;
 
+		public NSPrefixEntityChecker(JasdlAgent agent){
+			this.agent = agent;
+		}
 
+		public OWLClass getOWLClass(String name) {			
+			OWLEntity entity = convert(name);
+			if(entity == null){
+				return null;
+			}
+			if(entity.isOWLClass()){
+				return entity.asOWLClass();
+			}else{
+				return null;
+			}
+		}
 
+		public OWLDataProperty getOWLDataProperty(String name) {
+			OWLEntity entity = convert(name);
+			if(entity == null){
+				return null;
+			}
+			if(entity.isOWLDataProperty()){
+				return entity.asOWLDataProperty();
+			}else{
+				return null;
+			}
+		}
 
+		public OWLDataType getOWLDataType(String name) {
+			OWLEntity entity = convert(name);
+			if(entity == null){
+				return null;
+			}
+			if(entity.isOWLDataType()){
+				return entity.asOWLDataType();
+			}else{
+				return null;
+			}
+		}
+
+		public OWLIndividual getOWLIndividual(String name) {
+			OWLEntity entity = convert(name);
+			if(entity == null){
+				return null;
+			}
+			if(entity.isOWLIndividual()){
+				return entity.asOWLIndividual();
+			}else{
+				return null;
+			}
+		}
+
+		public OWLObjectProperty getOWLObjectProperty(String name) {
+			OWLEntity entity = convert(name);
+			if(entity == null){
+				return null;
+			}
+			if(entity.isOWLObjectProperty()){
+				return entity.asOWLObjectProperty();
+			}else{
+				return null;
+			}
+		}
+		
+		private OWLEntity convert(String name){
+			String[] tokens = name.split(":");
+			try {
+				Atom functor = new Atom(tokens[1]);
+				Atom label = new Atom(tokens[0]);
+				Alias alias = AliasFactory.INSTANCE.create(functor, label);
+				return (OWLEntity)agent.getAliasManager().getRight(alias); // guaranteed to be an entity? Not for anonymous classes!
+			} catch (Exception e) {
+				return null;
+			}			
+		}
+		
+		
+	}
+
+
+
+
+
+
 }

Modified: trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlConfigurator.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlConfigurator.java	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlConfigurator.java	2008-03-16 17:44:47 UTC (rev 1155)
@@ -14,6 +14,7 @@
 
 import java.lang.reflect.Constructor;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.List;
 import java.util.Set;
 import java.util.Vector;
@@ -76,7 +77,7 @@
 				if(split.length == 2){
 					Alias alias = AliasFactory.INSTANCE.create(new Atom(split[0].trim()), label);
 					URI uri = URI.create(ontology.getURI() + "#" + split[1].trim());
-					OWLEntity entity = toEntity(ontology, uri);
+					OWLEntity entity = agent.toEntity(uri);
 					agent.getAliasManager().put(alias, entity);
 				}
 			}
@@ -147,18 +148,11 @@
 	 */
 	private void applyMiscMappings() throws JasdlException{
 		
-		
 		// create a "placeholder" ontology so we can safely map thing and nothing without actually loading the ontology
-		try {
-			URI uri = URI.create("http://www.w3.org/2002/07/owl");
-			OWLOntology ontology = agent.getOntologyManager().createOntology( uri );
-			agent.getLabelManager().put(AliasFactory.OWL_THING.getLabel(), ontology);
-			agent.getPhysicalURIManager().put(ontology, uri);
-			agent.getReasoner().loadOntology(ontology);
+		agent.createOntology(AliasFactory.OWL_THING.getLabel(), URI.create("http://www.w3.org/2002/07/owl"));
 		
-		} catch (OWLOntologyCreationException e) {
-			throw new JasdlException("Error instantiating blank OWL ontology placeholder. Reason: "+e);
-		}
+		// create a personal ontology for (axioms that reference) run-time defined class
+		agent.createOntology(agent.getPersonalOntologyLabel(), agent.getPersonalOntologyURI());
 		
 		agent.getAliasManager().put( AliasFactory.OWL_THING, agent.getOntologyManager().getOWLDataFactory().getOWLThing());
 		agent.getAliasManager().put( AliasFactory.OWL_NOTHING, agent.getOntologyManager().getOWLDataFactory().getOWLNothing());
@@ -217,38 +211,5 @@
 	
 	
 	
-	/**
-	 * Convenience method to (polymorphically) create an entity from resource URI (if known).
-	 * TODO: where should this sit?
-	 * @param uri	URI of resource to create entity from
-	 * @return		entity identified by URI
-	 * @throws UnknownReferenceException	if OWLObject not known
-	 */
-	private OWLEntity toEntity(OWLOntology ontology, URI uri) throws UnknownMappingException{
-		// clumsy approach, but I can't find any way of achieving this polymorphically (i.e. retrieve an OWLObject from a URI) using OWL-API
-		OWLEntity entity;
-		
-		/*
-		// TODO: make from uri only version once OWLOntologyManager#getOntology(URI) is fixed
-		URI ns = URI.create(uri.getScheme() + uri.getSchemeSpecificPart());		
-		OWLOntology ontology;
-		try {
-			ontology = ontologyManager.getOntology(ns);
-		} catch (UnknownOWLOntologyException e) {
-			throw new UnknownMappingException("Unknown ontology URI "+ns);
-		}
-		*/
-		if(ontology.containsClassReference(uri)){
-			entity = agent.getOntologyManager().getOWLDataFactory().getOWLClass(uri);
-		}else if (ontology.containsObjectPropertyReference(uri)){	
-			entity = agent.getOntologyManager().getOWLDataFactory().getOWLObjectProperty(uri);
-		}else if (ontology.containsDataPropertyReference(uri)){	
-			entity = agent.getOntologyManager().getOWLDataFactory().getOWLDataProperty(uri);
-		}else if (ontology.containsIndividualReference(uri)){
-			entity = agent.getOntologyManager().getOWLDataFactory().getOWLIndividual(uri);
-		}else{
-			throw new UnknownMappingException("Unknown ontology resource URI: "+uri);
-		}
-		return entity;
-	}			
+			
 }

Modified: trunk/applications/jasdl-owlapi/src/jasdl/bridge/MappingManager.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/bridge/MappingManager.java	2008-03-16 16:43:27 UTC (rev 1154)
+++ trunk/applications/jasdl-owlapi/src/jasdl/bridge/MappingManager.java	2008-03-16 17:44:47 UTC (rev 1155)
@@ -35,6 +35,7 @@
 	 * @throws DuplicateMappingException	if either alias or entity is already mapped (thus breaking 1 <-> 1 constraint)
 	 */
 	public void put(X x, Y y) throws DuplicateMappingException{
+		logger.fine("mapping "+x+" <-> "+y);
 		
 		if(isKnownLeft(x)){
 			throw new DuplicateMappingException("Duplicate mapping on "+x);
@@ -72,7 +73,7 @@
 	public Y getRight(X x) throws UnknownMappingException{
 		Y y = xToYMap.get(x);
 		if(y == null){
-			throw new UnknownMappingException("Unknown mapping "+y);
+			throw new UnknownMappingException("Unknown mapping "+x);
 		}
 		return y;
 	}

Copied: trunk/applications/jasdl-owlapi/src/jasdl/bridge/label/OntologyURIManager.java (from rev 1147, trunk/applications/jasdl-owlapi/src/jasdl/bridge/label/PhysicalURIManager.java)
================...
 
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Thread: [Jason-developers] SF.net SVN: jason: [1155] trunk/applications/jasdl-owlapi

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