[Jason-developers] SF.net SVN: jason: [1202] trunk/applications/jasdl-owlapi

[<tom...@us...>]

Revision: 1202
          http://jason.svn.sourceforge.net/jason/?rev=1202&view=rev
Author:   tomklapiscak
Date:     2008-04-02 18:24:25 -0700 (Wed, 02 Apr 2008)

Log Message:
-----------
Implemented experimental annotation gathering functionality (using Bebops library). Disabled by default, can be enabled in .mas2j (jasdl_useAnnotationGathering="true").

Implemented jasdl.ia.is_annotation_gathering_enabled and jasdl_ia.is_belief_revision_enabled internal actions to test status of experiemental features.

Implemented jasdl.ia.set_annotation_gathering_enabled and jasdl.ia.set_belief_revision_enabled internal actions to complement .mas2j settings.

Implemented workaround for strange behaviour when using Pellets isConsistent(OWLOntology) method (with agent.isBBConsistent() method).

Modified Paths:
--------------
    trunk/applications/jasdl-owlapi/build.xml
    trunk/applications/jasdl-owlapi/examples/travel_agent/config.mas2j
    trunk/applications/jasdl-owlapi/examples/travel_agent/travel_agent.asl
    trunk/applications/jasdl-owlapi/lib/bebops.jar
    trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlAgent.java
    trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlConfigurator.java
    trunk/applications/jasdl-owlapi/src/jasdl/bb/JasdlBeliefBase.java
    trunk/applications/jasdl-owlapi/src/jasdl/bb/JasdlIncisionFunction.java
    trunk/applications/jasdl-owlapi/src/jasdl/bridge/factory/AxiomToSELiteralConverter.java
    trunk/applications/jasdl-owlapi/src/jasdl/test/JasdlBeliefBaseTest.java
    trunk/applications/jasdl-owlapi/src/jasdl/util/exception/JasdlException.java

Added Paths:
-----------
    trunk/applications/jasdl-owlapi/src/jasdl/ia/is_annotation_gathering_enabled.java
    trunk/applications/jasdl-owlapi/src/jasdl/ia/is_belief_revision_enabled.java
    trunk/applications/jasdl-owlapi/src/jasdl/ia/set_annotation_gathering_enabled.java
    trunk/applications/jasdl-owlapi/src/jasdl/ia/set_belief_revision_enabled.java

Modified: trunk/applications/jasdl-owlapi/build.xml
===================================================================
--- trunk/applications/jasdl-owlapi/build.xml	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/build.xml	2008-04-03 01:24:25 UTC (rev 1202)
@@ -2,12 +2,16 @@
 	<property name="jason.dir" 	value="../.."/>
 	<property name="apps.dir"	value="${jason.dir}/applications"/>
 	<property name="jmca.dir" 	value="${apps.dir}/jmca"/>
+	<property name="bebops.dir" 	value="${apps.dir}/bebops"/>
+	<property name="bebops.jar" 	value="${bebops.dir}/lib/bebops.jar"/>
 	<property name="asunit.dir" 	value="${apps.dir}/as-unit-test"/>
 	<property name="source.dir" 	value="${basedir}/src" />
 	<property name="build.dir" 	value="${basedir}/bin" />
 	<property name="apidocs.dir" 	value="${basedir}/doc/api" />
-	<property name="jar.file" 	value="${basedir}/lib/jasdl.jar" />
+	<property name="lib.dir" 	value="${basedir}/lib" />
+	<property name="jasdl.jar" 	value="${lib.dir}/jasdl.jar" />
 	
+	
 
 	<path id="project.classpath">
 		<pathelement location="${jason.dir}/lib/jason.jar"/>
@@ -26,21 +30,27 @@
 	<target name="init">
 		<tstamp/>
 		<mkdir dir="${build.dir}"/>
+		<available file="${bebops.dir}" type="dir" property="bebops.available"/>
 	</target>
 
-	<target name="compile" depends="init">
+	<target name="bebops" depends="init" if="bebops.available">
+		<ant dir="${bebops.dir}" inheritAll="false"/>
+		<copy file="${bebops.jar}" todir="${lib.dir}"/>
+	</target>
+
+	<target name="compile" depends="init, bebops">
 		<javac srcdir="src" destdir="${build.dir}" debug="true" deprecation="true" optimize="true" nowarn="true" source="1.5" target="1.5">
 			<classpath refid="project.classpath" />
 		</javac>
 	</target>
 
 	<target name="jar" depends="compile">
-		<jar destfile="${jar.file}" basedir="./bin" includes="**/*.class"/>
+		<jar destfile="${jasdl.jar}" basedir="./bin" includes="**/*.class"/>
 	</target>
 
 	<target name="clean">
 		<delete dir="${build.dir}"/>
-		<delete file="${jar.file}"/>
+		<delete file="${jasdl.jar}"/>
 		<delete dir="${apidocs.dir}"/>
 	</target>
 

Modified: trunk/applications/jasdl-owlapi/examples/travel_agent/config.mas2j
===================================================================
--- trunk/applications/jasdl-owlapi/examples/travel_agent/config.mas2j	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/examples/travel_agent/config.mas2j	2008-04-03 01:24:25 UTC (rev 1202)
@@ -32,6 +32,7 @@
        	   travel_agent.asl
 	       [			
 			jasdl_useBeliefRevision = "true", // use experimental DL-based belief revision mechanism
+			jasdl_useAnnotationGathering = "true", // use experimental annotation gathering mechanism
 			
 			/*
 			 * To use FaCT++, set the below. Must have libFaCTPlusPlusJNI.so in /usr/lib (or the equivalent for Mac or Windows)

Modified: trunk/applications/jasdl-owlapi/examples/travel_agent/travel_agent.asl
===================================================================
--- trunk/applications/jasdl-owlapi/examples/travel_agent/travel_agent.asl	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/examples/travel_agent/travel_agent.asl	2008-04-03 01:24:25 UTC (rev 1202)
@@ -19,12 +19,12 @@
  */
 
 !start(total).
-!start(ubb1).!example_UBB_1.!end(ubb1).
-!start(ubb2).!example_UBB_2.!end(ubb2).
+!start(ubb1).!example_UBB.!end(ubb1).
+!start(ubb2).!example_brf.!end(ubb2).
 !start(qbb).!example_QBB.!end(qbb).
 !start(rpp).!example_RPP.!end(rpp).
 !start(all_different).!example_all_different.!end(all_different).
-//!example_annotation_gathering.
+!start(annnotation_gathering).!example_annotation_gathering.!end(annnotation_gathering).
 !start(ksaa).!example_KSAA.!end(ksaa).
 //!end(total) is within example_KSAA_complete to allow inter-agent communication to finish
 
@@ -42,9 +42,9 @@
 	.print("Execution time for counter ",A,": ",TotalTime,"s").
 
 @example_ubb_1[atomic]
-+!example_UBB_1
++!example_UBB
 	<-
-	.print("Example: Updating Belief Base 1");
+	.print("Example: Updating Belief Base");
 	+hotel(hilton)[o(travel)];						// hilton is a hotel
 	+hasRating(hilton, threeStarRating)[o(travel)];	// hilton has three-star rating
 	+town(london)[o(travel)];
@@ -58,12 +58,23 @@
 	+museums(scienceMuseum)[o(travel)];
 	+hasActivity(london, scienceMuseum)[o(travel)];	
 	+hotel(travel_lodge)[o(travel)];
-	.print("Completed: Updating Belief Base 1").
+	.print("Completed: Updating Belief Base").
+
+@example_brf[atomic]
++!example_brf
+	<-
+	jasdl.ia.is_belief_revision_enabled(true);
+	!example_brf_continue.
 	
-@example_ubb_2[atomic]
-+!example_UBB_2
+@example_brf_fail[atomic]
+-!example_brf
+	<-
+	.print("Belief revision feature disabled, skipping").
+	
+@example_brf_continue[atomic]
++!example_brf_continue
 	<-	
-	.print("Example: Updating Belief Base 2");	
+	.print("Example: Belief Revision");	
 	
 	jasdl.ia.define_class(tiny, "travel:urbanArea and travel:hasActivity max 1 travel:activity");
 	+tiny(newcastle)[o(self), source(tom)];	
@@ -83,25 +94,19 @@
 	+ruralArea(somewhere)[o(travel), source(tom)];
 	?ruralArea(somewhere)[o(travel)];
 	
-	
-	
-	
-	.print("DL-based belief revision is enabled"); // without, the above test-goal will fail, since legacy mechanism simply removes incoming inconsistent beliefs
-	
-	
 	// since the classes destination and and contact are disjoint (and ruralArea is a subclass of destination),
 	// and since we trust ben less than tom, the belief addition below will fail (and tom's assertion above will persist),
 	// thus failing the whole plan.
 	+contact(somewhere)[o(travel), source(ben)];
 	
-	.print("Failed: Updating Belief Base 2").
+	.print("Failed: Belief Revision").
 
-@example_UBB_2_failure[atomic]
--!example_UBB_2
+@example_brf_continue_fail[atomic]
+-!example_brf_continue
 	<-
 	// Notice this does not hold, since belief revision rejected the less trusted assertion made by ben.
 	?~contact(somewhere)[o(travel)];
-	.print("Completed: Updating Belief Base 2").
+	.print("Completed: Belief Revision").
 	
 @example_qbb[atomic, breakpoint]
 +!example_QBB
@@ -157,18 +162,22 @@
 @example_all_different[atomic]
 +!example_all_different
 	<-
-	.print("Example: all_different assertion");	
+	
+	
+	.print("Example: all_different assertion");
 	+destination(butlins)[o(travel)];
 	+hotel(butlins_hotel)[o(travel)];
 	+hasAccommodation(butlins, butlins_hotel)[o(travel)];	
 	+yoga(butlins_yoga)[o(travel)];
-	+sunbathing(butlins_sunbathing)[o(travel)];		
+	+sunbathing(butlins_sunbathing)[o(travel)];	
 	+hasActivity(butlins, butlins_yoga)[o(travel)];
+	//jasdl.ia.all_different([butlins_yoga, butlins_sunbathing], travel);	- DEPRECATED (see below)	
 	+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(self), 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)]; // 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(self)];
 	/* ?all_different([hilton, fourSeasons])[o(travel)]; */  // Will fail, since hilton and fourSeasons cannot be established as distinct
@@ -178,6 +187,17 @@
 @example_annotation_gathering[atomic]
 +!example_annotation_gathering
 	<-
+	jasdl.ia.is_annotation_gathering_enabled(true); // why does True not fail immediately? possible Jason bug?
+	!example_annotation_gathering_continue.
+	
+@example_annotation_gathering_fail[atomic]
+-!example_annotation_gathering
+	<-
+	.print("Annotation gathering feature disabled, skipping").
+
+@example_annotation_gathering_continue[atomic]
++!example_annotation_gathering_continue
+	<-
 	.print("Example: annotation gathering");
 	+ruralArea(kingsworthy)[o(travel), annotation];
 	?destination(kingsworthy)[o(travel), annotation];
@@ -190,9 +210,10 @@
 	+urbanArea(x)[o(travel), source(tom)];
 	+ruralArea(y)[o(travel), source(ben)];
 	// because knowledge from tom and ben contributed to the inference that x and y are distinct
-	?all_different([x,y])[o(travel), source(tom), source(ben)]; 
+	?all_different([x,y])[o(self), source(tom), source(ben)]; 
 	
 	// notice "something" annotation is gathered (added in !example_all_different) here since it all_different assertion contributes to this inference
+	+all_different([butlins_yoga, butlins_sunbathing])[o(self), something];
 	?familyDestination(butlins)[o(travel), something]; 
 	
 	.print("Complete: annotation gathering").

Modified: trunk/applications/jasdl-owlapi/lib/bebops.jar
===================================================================
(Binary files differ)

Modified: trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlAgent.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlAgent.java	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlAgent.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -98,10 +98,12 @@
 	private HashMap<Atom, Float> trustMap;
 	
 	private boolean beliefRevisionEnabled;
+	private boolean annotationGatheringEnabled;
 	private List<MappingStrategy> defaultMappingStrategies = JasdlConfigurator.DEFAULT_MAPPING_STRATEGIES;
 
 	
-	public JasdlAgent(){
+	
+	public JasdlAgent() throws Exception{
 		super();
 		
 		// instantiate managers
@@ -160,7 +162,7 @@
 	public List<Literal> getABoxState() throws JasdlException{
 		List<Literal> bels = new Vector<Literal>();		
 		for(OWLOntology ontology : ontologyManager.getOntologies()){
-			for(OWLIndividualAxiom axiom : ontology.getIndividualAxioms()){				
+			for(OWLIndividualAxiom axiom : ontology.getIndividualAxioms()){	
 				Literal l = axiomToSELiteralConverter.convert(axiom).getLiteral();			
 				bels.add(l);	
 			}
@@ -184,10 +186,12 @@
 
 	public List<Literal>[] brf(Literal beliefToAdd, Literal beliefToDel, Intention i)  throws RevisionFailedException {
 		// TODO: what annotations should revision contractions contain? all! (or none? - same effect)
+		
 		// No! the same. -a[x] only undermines assertions leading to a[x]!
 		// if we are performing belief-revision all annotations will be gathered (shortcut - use none?) ensuring axiom will be obliterated
 		// annotations never solely lead to conflicts.
 		
+		// TODO: these is a bug hiding in this somewhere. Using below causes strange failures
 		if(!isBeliefRevisionEnabled()){ // if experimental feature is disabled
 			return super.brf(beliefToAdd, beliefToDel, i);
 		}
@@ -210,13 +214,19 @@
 				BeliefBaseSemiRevisor bbrev = new BeliefBaseSemiRevisor(axiomToAdd, getOntologyManager(), new JasdlReasonerFactory(), getLogger());
 				List<OWLAxiom> contractList = bbrev.revise(new TBoxAxiomKernelsetFilter(), new JasdlIncisionFunction(this, sl));
 				
-				// will only have reached here if new belief is accepted.
-				addList.add(beliefToAdd);
+				
 				for(OWLAxiom contract : contractList){
 					removeList.add(axiomToSELiteralConverter.convert((OWLIndividualAxiom)contract).getLiteral());
 				}
-				revisionApplied = true;
+				if(!removeList.isEmpty()){
+					getLogger().info("brf: contracted "+removeList);
+					revisionApplied = true;						
+				}
+				
+				addList.add(beliefToAdd); // will only reach here if belief accepted (or bef is disabled)
+				
 			}catch(BebopsRevisionFailedException e){
+				getLogger().info("brf: rejected "+e.getMessage());
 				throw new RevisionFailedException(); // propagate upwards
 			}catch(NotEnrichedException e){
 				// can't perform DL-based belief revision on SN-Literals
@@ -233,6 +243,7 @@
 		
 		// Need to perform removals before additions so our ontology instance never becomes inconsistent		
 		for(Literal removed : removeList){
+			
 			boolean ok = false;
 			if(revisionApplied){
 				ok = true;
@@ -246,7 +257,8 @@
 	            }
 	            ok = believes(removed, u);
 	            if(ok) removed.apply(u);
-			}			
+			}	
+				
             if(ok){	
 				if(getBB().remove(removed)){
 					if(toReturn == null){
@@ -545,7 +557,8 @@
 			}
 		} catch (OWLReasonerException e) {
 			throw new JasdlException("Unable to refresh reasoner. Reason: "+e);
-		}
+		}			
+
 	}
 	
 	
@@ -561,9 +574,25 @@
 			Log4JLogger kb_logger = (Log4JLogger)pellet.getKB().log;
 			kb_logger.getLogger().setLevel(level);
 		}
-	}	
+	}
 	
 	/**
+	 *  For some reason, use of pellet's isConsistent(OWLOntology) method causes strange behaviour.
+	 *  So we wrap it's isConsistent() method here.
+	 *  TODO: resolve this issue properly
+	 * @return
+	 * @throws JasdlException
+	 */
+	public boolean isBBConsistent() throws JasdlException{
+		if(getReasoner() instanceof org.mindswap.pellet.owlapi.Reasoner){
+			return((org.mindswap.pellet.owlapi.Reasoner)getReasoner()).isConsistent();
+		}else{
+			//TODO: FaCT++
+			throw new JasdlException("isBBConsistent not implemented for FaCT++ reasoner");
+		}
+	}
+	
+	/**
 	 * *Must* be unique within society!
 	 * @return
 	 */
@@ -676,7 +705,20 @@
 		return trustMap.get(name);
 	}
 
+
+
+	public boolean isAnnotationGatheringEnabled() {
+		return annotationGatheringEnabled;
+	}
+
+
+
+	public void setAnnotationGatheringEnabled(boolean annotationGatheringEnabled) {
+		this.annotationGatheringEnabled = annotationGatheringEnabled;
+	}
+
 	
 	
+	
 
 }

Modified: trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlConfigurator.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlConfigurator.java	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/src/jasdl/asSemantics/JasdlConfigurator.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -20,6 +20,7 @@
 import java.util.Vector;
 import java.util.logging.Level;
 
+import org.mindswap.pellet.PelletOptions;
 import org.semanticweb.owl.inference.OWLReasoner;
 import org.semanticweb.owl.model.OWLEntity;
 import org.semanticweb.owl.model.OWLOntology;
@@ -34,14 +35,15 @@
 	public static String MAS2J_TRUSTRATING				= "_trustRating";
 	public static String MAS2J_KNOWNAGENTS				= "_knownAgents";
 	public static String MAS2J_USEBELIEFREVISION		= "_useBeliefRevision";
+	public static String MAS2J_USEANNOTATIONGATHERING	= "_useAnnotationGathering";
 	public static String MAS2J_REASONERCLASS			= "_reasonerClass";
 	
 	public static List<MappingStrategy> DEFAULT_MAPPING_STRATEGIES = Arrays.asList( new MappingStrategy[] { new DecapitaliseMappingStrategy()} );
 	public static String DEFAULT_REASONER_CLASS = "org.mindswap.pellet.owlapi.Reasoner";
 	public static boolean DEFAULT_USEBELIEFREVISION = false;
+	public static boolean DEFAULT_USEANNOTATIONGATHERING = false;
 	
 	
-	
 	/**
 	 * List of reserved ontology labels. Currently:
 	 * <ul>
@@ -65,6 +67,7 @@
 		loadReasoner(stts);
 		loadDefaultMappingStrategies(stts);
 		setUseBeliefRevision(stts);			
+		setUseAnnotationGathering(stts);
 		loadOntologies(stts);
 		applyManualMappings(stts);
 		loadKnownAgents(stts);
@@ -108,7 +111,17 @@
 		}
 	}
 	
+	private void setUseAnnotationGathering(Settings stts) throws JasdlException{
+		try{
+			// set whether to use belief revision or not
+			String useAnnotationGathering = prepareUserParameter(stts, MAS2J_PREFIX + MAS2J_USEANNOTATIONGATHERING);
+			agent.setAnnotationGatheringEnabled(Boolean.parseBoolean(useAnnotationGathering));
+		}catch(JasdlConfigurationException e){
+			agent.setAnnotationGatheringEnabled(DEFAULT_USEANNOTATIONGATHERING);
+		}
+	}	
 	
+	
 	/**
 	 * Load ontologies as specified in .mas2j settings
 	 * @param stts	.mas2j settings

Modified: trunk/applications/jasdl-owlapi/src/jasdl/bb/JasdlBeliefBase.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/bb/JasdlBeliefBase.java	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/src/jasdl/bb/JasdlBeliefBase.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -45,7 +45,8 @@
 						
 			boolean containsAxiom = ontology.containsAxiom(axiom);
 			if(!containsAxiom){
-				agent.getOntologyManager().applyChange(new AddAxiom(ontology, axiom));	
+				agent.getOntologyManager().applyChange(new AddAxiom(ontology, axiom));
+				agent.refreshReasoner();
 			}
 			
 			boolean containsAllAnnots = true;
@@ -55,13 +56,16 @@
 				if(!ontology.containsAxiom(annotAxiom)){
 					containsAllAnnots = false;
 					agent.getOntologyManager().applyChange(new AddAxiom(ontology, annotAxiom));
+					agent.refreshReasoner();
 				}
-			}			
+			}
 			
-			if(!containsAxiom || !containsAllAnnots){
-				agent.refreshReasoner();			
-				if(!agent.isBeliefRevisionEnabled()){ // if brf disabled, resort to legacy consistency maintenance mechanism 
-					if(!agent.getReasoner().isConsistent(ontology)){
+			
+			
+			if(!containsAxiom || !containsAllAnnots){				
+				if(!agent.isBeliefRevisionEnabled()){ // if brf disabled, resort to legacy consistency maintenance mechanism 					
+					if(!agent.isBBConsistent()){
+						getLogger().info("legacy consistency assurance: rejected "+axiom);
 						RemoveAxiom rem = new RemoveAxiom(ontology, axiom);
 						agent.getOntologyManager().applyChange(rem);
 						agent.refreshReasoner();
@@ -192,6 +196,8 @@
 		
 		getLogger().fine("Getting relevancies for "+l);
 		
+		
+		
 		Set<Literal> relevant = new HashSet<Literal>();
 		try{			
 			SELiteral sl = agent.getSELiteralFactory().construct(l);

Modified: trunk/applications/jasdl-owlapi/src/jasdl/bb/JasdlIncisionFunction.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/bb/JasdlIncisionFunction.java	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/src/jasdl/bb/JasdlIncisionFunction.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -15,7 +15,7 @@
 
 import bebops.common.IncisionFunction;
 
-public class JasdlIncisionFunction implements IncisionFunction{	
+public class JasdlIncisionFunction extends IncisionFunction{	
 	
 
 	private JasdlAgent agent;
@@ -39,23 +39,21 @@
 	 * Currently calculated using ASSERTED source annotations only.
 	 * No source annotation is taken as trust = 0;
 	 */
-	public Set<OWLAxiom> apply(Set<Set<OWLAxiom>> kernelset) {
+	public Set<OWLAxiom> applyToOne(Set<OWLAxiom> akernel){
 		try{
 			Set<OWLAxiom> chosen = new HashSet<OWLAxiom>();
-			for(Set<OWLAxiom> akernel : kernelset){			
-				if(!akernel.isEmpty()){
-					OWLAxiom leastTrusted = null; // guaranteed to take a value 
-					float minTrustRating = 1f;					
-					for(OWLAxiom axiom : akernel){
-						float trustRating = getTrustRating(axiom);
-						agent.getLogger().finest("Trust rating of "+axiom+"="+trustRating);
-						if(trustRating <= minTrustRating){
-							minTrustRating = trustRating;
-							leastTrusted = axiom;
-						}
+			if(!akernel.isEmpty()){
+				OWLAxiom leastTrusted = null; // guaranteed to take a value 
+				float minTrustRating = 1f;					
+				for(OWLAxiom axiom : akernel){
+					float trustRating = getTrustRating(axiom);
+					agent.getLogger().finest("Trust rating of "+axiom+"="+trustRating);
+					if(trustRating <= minTrustRating){
+						minTrustRating = trustRating;
+						leastTrusted = axiom;
 					}
-					chosen.add(leastTrusted);
-				}				
+				}
+				chosen.add(leastTrusted);
 			}
 			return chosen;
 		}catch(Exception e){
@@ -66,6 +64,7 @@
 	
 	/**
 	 * Currently returns the trust rating of the most trusted source. Future work will look at better ways of calculating this.
+	 * TODO: Essentially duplicating work here. Annotation gathering (performed by AxiomToSELiteralConverter) requires axiom-pinponting - so does contraction.
 	 * @param axiom
 	 * @return
 	 * @throws JasdlException

Modified: trunk/applications/jasdl-owlapi/src/jasdl/bridge/factory/AxiomToSELiteralConverter.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/bridge/factory/AxiomToSELiteralConverter.java	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/src/jasdl/bridge/factory/AxiomToSELiteralConverter.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -1,6 +1,8 @@
 package jasdl.bridge.factory;
 
 import jasdl.asSemantics.JasdlAgent;
+import jasdl.bb.JasdlReasonerFactory;
+import jasdl.bb.TBoxAxiomKernelsetFilter;
 import jasdl.bridge.mapping.aliasing.Alias;
 import jasdl.bridge.mapping.aliasing.AllDifferentPlaceholder;
 import jasdl.bridge.seliteral.SELiteral;
@@ -17,20 +19,27 @@
 import java.util.List;
 import java.util.Set;
 import java.util.Vector;
+import java.util.logging.Logger;
 
+import org.semanticweb.owl.inference.OWLReasonerException;
 import org.semanticweb.owl.model.OWLAxiom;
 import org.semanticweb.owl.model.OWLAxiomAnnotationAxiom;
 import org.semanticweb.owl.model.OWLClassAssertionAxiom;
 import org.semanticweb.owl.model.OWLConstant;
 import org.semanticweb.owl.model.OWLDataPropertyAssertionAxiom;
 import org.semanticweb.owl.model.OWLDifferentIndividualsAxiom;
+import org.semanticweb.owl.model.OWLException;
 import org.semanticweb.owl.model.OWLIndividual;
 import org.semanticweb.owl.model.OWLIndividualAxiom;
 import org.semanticweb.owl.model.OWLObjectPropertyAssertionAxiom;
 import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyChangeException;
+import org.semanticweb.owl.model.OWLOntologyCreationException;
 import org.semanticweb.owl.model.OWLTypedConstant;
 
+import bebops.pinpointing.KernelOperator;
 
+
 /**
  * Accepts an arbitrary OWLIndividualAxiom and, depending on its type, creates a SE-Literal encoding of it.
  * Will always result in a ground SELiteral (since OWLIndividualAxioms must always be ground)<p>
@@ -50,7 +59,8 @@
 	 */
 	private JasdlAgent agent;
 	
-	public AxiomToSELiteralConverter(JasdlAgent agent){
+	
+	public AxiomToSELiteralConverter(JasdlAgent agent) throws OWLReasonerException, OWLOntologyCreationException, OWLOntologyChangeException{
 		this.agent = agent;
 	}
 	
@@ -59,19 +69,53 @@
 	 * TODO: Shift to a factory?
 	 * @param sl
 	 */
-	public static List<Term> getAssertedAnnotations(OWLAxiom axiom, OWLOntology ontology){
+	public List<Term> getAssertedAnnotations(OWLAxiom axiom){
 		List<Term> result = new Vector<Term>();
-		// get annotations
-		Set<OWLAxiomAnnotationAxiom> annotAxioms = axiom.getAnnotationAxioms(ontology);
-		for(OWLAxiomAnnotationAxiom annotAxiom : annotAxioms){ // remember, possibly semantically-naive payload!
-			Term annot = Literal.parse(annotAxiom.getAnnotation().getAnnotationValueAsConstant().getLiteral());
-			result.add(annot);
+		// get annotations from all known ontologies
+		for(OWLOntology ontology : agent.getOntologyManager().getOntologies()){
+			Set<OWLAxiomAnnotationAxiom> annotAxioms = axiom.getAnnotationAxioms(ontology);
+			for(OWLAxiomAnnotationAxiom annotAxiom : annotAxioms){ // remember, possibly semantically-naive payload!
+				Term annot = Literal.parse(annotAxiom.getAnnotation().getAnnotationValueAsConstant().getLiteral());
+				result.add(annot);
+			}
 		}
 		return result;
 	}
 	
+	public List<Term> getInferredAnnotations(OWLAxiom axiom) throws JasdlException{
+		try {
+			List<Term> annots = new Vector<Term>();
+			KernelOperator kernelOperator = new KernelOperator(agent.getOntologyManager(), new JasdlReasonerFactory());			
+			//Set<OWLAxiom> supportingAxioms = OWLReasonerAdapter.flattenSetOfSets((kernelOperator.apply(axiom, true)));
+			Set<OWLAxiom> supportingAxioms = (new TBoxAxiomKernelsetFilter()).applyToOne((kernelOperator.applySingle(axiom, true)));
+			getLogger().finest("Explanation for "+axiom+": "+supportingAxioms);
+			for(OWLAxiom supportingAxiom : supportingAxioms){
+				annots.addAll(getAssertedAnnotations(supportingAxiom));
+			}
+			getLogger().finest("Annotations: "+annots);
+			return annots;
+		} catch (OWLException e) {
+			throw new JasdlException("Annotation gathering failed for "+axiom, e);
+		}
+	}
 	
+	
 	/**
+	 * Utility method to get the annotations of an axiom as an array of terms within the ontology referenced by alias
+	 * @param alias
+	 * @param axiom
+	 * @return
+	 * @throws UnknownMappingException
+	 */
+	private Term[] getAnnots(Alias alias, OWLAxiom axiom) throws JasdlException{	
+		List<Term> annots = getAssertedAnnotations(axiom);
+		if(agent.isAnnotationGatheringEnabled()) annots.addAll(getInferredAnnotations(axiom)); // optional, experimental feature
+		return (Term[])annots.toArray(new Term[annots.size()]);
+	}		
+	
+	
+	
+	/**
 	 * Polymorphically applies appropriate factory method depending on specialisation of axiom
 	 * @param axiom
 	 * @return
@@ -176,18 +220,10 @@
 		return agent.getSELiteralFactory().construct(alias, is, getAnnots(alias, axiom));
 	}
 	
-	/**
-	 * Utility method to get the annotations of an axiom as an array of terms within the ontology referenced by alias
-	 * @param alias
-	 * @param axiom
-	 * @return
-	 * @throws UnknownMappingException
-	 */
-	private Term[] getAnnots(Alias alias, OWLAxiom axiom) throws UnknownMappingException{
-		OWLOntology ontology = agent.getLabelManager().getRight(alias.getLabel());	
-		List<Term> collection = getAssertedAnnotations(axiom, ontology);
-		return (Term[])collection.toArray(new Term[collection.size()]);
-	}	
+	public Logger getLogger(){
+		return agent.getLogger();
+	}
+
 	
 
 }

Added: trunk/applications/jasdl-owlapi/src/jasdl/ia/is_annotation_gathering_enabled.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/ia/is_annotation_gathering_enabled.java	                        (rev 0)
+++ trunk/applications/jasdl-owlapi/src/jasdl/ia/is_annotation_gathering_enabled.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -0,0 +1,61 @@
+/* 
+ *  Copyright (C) 2008 Thomas Klapiscak (t.g...@du...)
+ *  
+ *  This file is part of JASDL.
+ *
+ *  JASDL is free software: you can redistribute it and/or modify
+ *  it under the terms of the Lesser GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  JASDL is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  Lesser GNU General Public License for more details.
+ *
+ *  You should have received a copy of the Lesser GNU General Public License
+ *  along with JASDL.  If not, see <http://www.gnu.org/licenses/>.
+ *  
+ */
+package jasdl.ia;
+
+import jasdl.asSemantics.JasdlAgent;
+import jason.asSemantics.DefaultInternalAction;
+import jason.asSemantics.TransitionSystem;
+import jason.asSemantics.Unifier;
+import jason.asSyntax.Literal;
+import jason.asSyntax.Term;
+
+import java.util.logging.Logger;
+
+/**
+ * @author Tom Klapiscak
+ * 
+ * Usage jasdl.ia.define_class(classname, classexpr, label), where:
+ * 	- classname is an atomic name used to refer to this class in future. Must begin with a lowercase letter and not clash with any AgentSpeak keyword
+ *  - classexpr is a expression defining this class
+ *  
+ *  Changed class name to atom only - forces valid alias syntax
+ *
+ */
+public class is_annotation_gathering_enabled extends DefaultInternalAction {
+
+
+    private Logger logger = Logger.getLogger("jasdl."+is_annotation_gathering_enabled.class.getName());
+
+    @Override
+    public Object execute(TransitionSystem ts, Unifier un, Term[] args) throws Exception {
+        try { 
+        	JasdlAgent agent = (JasdlAgent)ts.getAg();
+        	Literal res = agent.isAnnotationGatheringEnabled() ? Literal.LTrue : Literal.LFalse;
+        	return un.unifies(args[0], res); 
+        } catch (Exception e) {
+        	logger.warning("Error in internal action 'jasdl.ia.is_annotation_gathering_enabled'! Reason:");
+        	e.printStackTrace();            
+            return false;
+        }       
+    }
+    
+    
+    
+}
\ No newline at end of file

Added: trunk/applications/jasdl-owlapi/src/jasdl/ia/is_belief_revision_enabled.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/ia/is_belief_revision_enabled.java	                        (rev 0)
+++ trunk/applications/jasdl-owlapi/src/jasdl/ia/is_belief_revision_enabled.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -0,0 +1,61 @@
+/* 
+ *  Copyright (C) 2008 Thomas Klapiscak (t.g...@du...)
+ *  
+ *  This file is part of JASDL.
+ *
+ *  JASDL is free software: you can redistribute it and/or modify
+ *  it under the terms of the Lesser GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  JASDL is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  Lesser GNU General Public License for more details.
+ *
+ *  You should have received a copy of the Lesser GNU General Public License
+ *  along with JASDL.  If not, see <http://www.gnu.org/licenses/>.
+ *  
+ */
+package jasdl.ia;
+
+import jasdl.asSemantics.JasdlAgent;
+import jason.asSemantics.DefaultInternalAction;
+import jason.asSemantics.TransitionSystem;
+import jason.asSemantics.Unifier;
+import jason.asSyntax.Literal;
+import jason.asSyntax.Term;
+
+import java.util.logging.Logger;
+
+/**
+ * @author Tom Klapiscak
+ * 
+ * Usage jasdl.ia.define_class(classname, classexpr, label), where:
+ * 	- classname is an atomic name used to refer to this class in future. Must begin with a lowercase letter and not clash with any AgentSpeak keyword
+ *  - classexpr is a expression defining this class
+ *  
+ *  Changed class name to atom only - forces valid alias syntax
+ *
+ */
+public class is_belief_revision_enabled extends DefaultInternalAction {
+
+
+    private Logger logger = Logger.getLogger("jasdl."+is_belief_revision_enabled.class.getName());
+
+    @Override
+    public Object execute(TransitionSystem ts, Unifier un, Term[] args) throws Exception {
+        try { 
+        	JasdlAgent agent = (JasdlAgent)ts.getAg();
+        	Literal res = agent.isBeliefRevisionEnabled() ? Literal.LTrue : Literal.LFalse;
+        	return un.unifies(args[0], res); 
+        } catch (Exception e) {
+        	logger.warning("Error in internal action 'jasdl.ia.is_belief_revision_enabled'! Reason:");
+        	e.printStackTrace();            
+            return false;
+        }       
+    }
+    
+    
+    
+}
\ No newline at end of file

Added: trunk/applications/jasdl-owlapi/src/jasdl/ia/set_annotation_gathering_enabled.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/ia/set_annotation_gathering_enabled.java	                        (rev 0)
+++ trunk/applications/jasdl-owlapi/src/jasdl/ia/set_annotation_gathering_enabled.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -0,0 +1,67 @@
+/* 
+ *  Copyright (C) 2008 Thomas Klapiscak (t.g...@du...)
+ *  
+ *  This file is part of JASDL.
+ *
+ *  JASDL is free software: you can redistribute it and/or modify
+ *  it under the terms of the Lesser GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  JASDL is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  Lesser GNU General Public License for more details.
+ *
+ *  You should have received a copy of the Lesser GNU General Public License
+ *  along with JASDL.  If not, see <http://www.gnu.org/licenses/>.
+ *  
+ */
+package jasdl.ia;
+
+import jasdl.asSemantics.JasdlAgent;
+import jason.asSemantics.DefaultInternalAction;
+import jason.asSemantics.TransitionSystem;
+import jason.asSemantics.Unifier;
+import jason.asSyntax.Literal;
+import jason.asSyntax.Term;
+
+import java.util.logging.Logger;
+
+/**
+ * @author Tom Klapiscak
+ * 
+ * Usage jasdl.ia.define_class(classname, classexpr, label), where:
+ * 	- classname is an atomic name used to refer to this class in future. Must begin with a lowercase letter and not clash with any AgentSpeak keyword
+ *  - classexpr is a expression defining this class
+ *  
+ *  Changed class name to atom only - forces valid alias syntax
+ *
+ */
+public class set_annotation_gathering_enabled extends DefaultInternalAction {
+
+
+    private Logger logger = Logger.getLogger("jasdl."+set_annotation_gathering_enabled.class.getName());
+
+    @Override
+    public Object execute(TransitionSystem ts, Unifier un, Term[] args) throws Exception {
+        try {
+        	JasdlAgent agent = (JasdlAgent)ts.getAg();
+        	if(args[0].equals(Literal.LTrue)){
+        		agent.setAnnotationGatheringEnabled((true));
+        	}else if(args[0].equals(Literal.LFalse)){
+        		agent.setAnnotationGatheringEnabled(false);
+        	}else{
+        		throw new Exception("Argument must be boolean");
+        	}
+        	return true; 
+        } catch (Exception e) {
+        	logger.warning("Error in internal action 'jasdl.ia.set_annotation_gathering_enabled'! Reason:");
+        	e.printStackTrace();            
+            return false;
+        }       
+    }
+    
+    
+    
+}
\ No newline at end of file

Added: trunk/applications/jasdl-owlapi/src/jasdl/ia/set_belief_revision_enabled.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/ia/set_belief_revision_enabled.java	                        (rev 0)
+++ trunk/applications/jasdl-owlapi/src/jasdl/ia/set_belief_revision_enabled.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -0,0 +1,67 @@
+/* 
+ *  Copyright (C) 2008 Thomas Klapiscak (t.g...@du...)
+ *  
+ *  This file is part of JASDL.
+ *
+ *  JASDL is free software: you can redistribute it and/or modify
+ *  it under the terms of the Lesser GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  JASDL is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  Lesser GNU General Public License for more details.
+ *
+ *  You should have received a copy of the Lesser GNU General Public License
+ *  along with JASDL.  If not, see <http://www.gnu.org/licenses/>.
+ *  
+ */
+package jasdl.ia;
+
+import jasdl.asSemantics.JasdlAgent;
+import jason.asSemantics.DefaultInternalAction;
+import jason.asSemantics.TransitionSystem;
+import jason.asSemantics.Unifier;
+import jason.asSyntax.Literal;
+import jason.asSyntax.Term;
+
+import java.util.logging.Logger;
+
+/**
+ * @author Tom Klapiscak
+ * 
+ * Usage jasdl.ia.define_class(classname, classexpr, label), where:
+ * 	- classname is an atomic name used to refer to this class in future. Must begin with a lowercase letter and not clash with any AgentSpeak keyword
+ *  - classexpr is a expression defining this class
+ *  
+ *  Changed class name to atom only - forces valid alias syntax
+ *
+ */
+public class set_belief_revision_enabled extends DefaultInternalAction {
+
+
+    private Logger logger = Logger.getLogger("jasdl."+set_belief_revision_enabled.class.getName());
+
+    @Override
+    public Object execute(TransitionSystem ts, Unifier un, Term[] args) throws Exception {
+        try {
+        	JasdlAgent agent = (JasdlAgent)ts.getAg();
+        	if(args[0].equals(Literal.LTrue)){
+        		agent.setBeliefRevisionEnabled(true);
+        	}else if(args[0].equals(Literal.LFalse)){
+        		agent.setBeliefRevisionEnabled(false);
+        	}else{
+        		throw new Exception("Argument must be boolean");
+        	}
+        	return true; 
+        } catch (Exception e) {
+        	logger.warning("Error in internal action 'jasdl.ia.set_belief_revision_enabled'! Reason:");
+        	e.printStackTrace();            
+            return false;
+        }       
+    }
+    
+    
+    
+}
\ No newline at end of file

Modified: trunk/applications/jasdl-owlapi/src/jasdl/test/JasdlBeliefBaseTest.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/test/JasdlBeliefBaseTest.java	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/src/jasdl/test/JasdlBeliefBaseTest.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -165,7 +165,10 @@
 	 */
 	private static int NUM_ENTITIES_TEST_ADD = 3;
 	@Test
-	public void testAddLiteral() throws Exception{		
+	public void testAddLiteral() throws Exception{
+		// ensure annotation gathering disabled for this test - we are only checking handling of annotation additions is correct
+		agent.setAnnotationGatheringEnabled(false);
+		
 		Atom[][] annotSets = new Atom[][] {new Atom[]{}, new Atom[] {new Atom("x")}, new Atom[] {new Atom("x"), new Atom("y")} }; // TODO: No real reason to check annotation handling for ALL types of entity - exactly the same code is used
 		for(OWLOntology ontology : agent.getOntologyManager().getOntologies()){	// test against all known ontologies
 			for(int run=0; run<=1; run++){	// run twice to ensure duplicate additions are rejected

Modified: trunk/applications/jasdl-owlapi/src/jasdl/util/exception/JasdlException.java
===================================================================
--- trunk/applications/jasdl-owlapi/src/jasdl/util/exception/JasdlException.java	2008-04-02 21:13:50 UTC (rev 1201)
+++ trunk/applications/jasdl-owlapi/src/jasdl/util/exception/JasdlException.java	2008-04-03 01:24:25 UTC (rev 1202)
@@ -23,6 +23,11 @@
 
 
 public class JasdlException extends JasonException {
+	
+	public JasdlException(String msg, Exception cause) {
+		super(msg, cause);
+	}
+
 	public JasdlException(String message){
 		super(message);
 	}


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