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HermiT is reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more.
This is the maven build of HermiT and is designed for people who wish to use HermiT from within the OWL API. It is now versioned in the main HermiT version repository, although not officially supported by the HermiT developers.
The version number of this package is a composite of the HermiT version and a value representing the OWLAPI release it is compatible with. Note that the group id for the upstream HermiT is com.hermit-reasoner, while this fork is released under net.sourceforge.owlapi.
This fork exists to allow HermiT users to use newer OWLAPI versions than the ones supported by the original HermiT codebase.
This package includes the Jautomata library (http://jautomata.sourceforge.net/), and builds with it directly. This library appears to be no longer under active development, and so a "fork" seems appropriate. No development is intended or anticipated on this code base.
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/* Copyright 2008, 2009, 2010 by the Oxford University Computing Laboratory
This file is part of HermiT.
HermiT is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
HermiT 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
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with HermiT. If not, see m_elements;
protected final Graph m_knownSubsumptions;
protected final Graph m_possibleSubsumptions;
/**
* @param tableau tableau
* @param progressMonitor progressMonitor
* @param topElement topElement
* @param bottomElement bottomElement
* @param elements elements
*/
public QuasiOrderClassification(Tableau tableau,ClassificationProgressMonitor progressMonitor,AtomicConcept topElement,AtomicConcept bottomElement,Set elements) {
m_tableau=tableau;
m_progressMonitor=progressMonitor;
m_topElement=topElement;
m_bottomElement=bottomElement;
m_elements=elements;
m_knownSubsumptions=new Graph<>();
m_possibleSubsumptions=new Graph<>();
}
/**
* @return classified hierarchy
*/
public Hierarchy classify() {
return buildHierarchy(this::classifyDoesSubsume);
}
private boolean classifyDoesSubsume(AtomicConcept parent,AtomicConcept child) {
Set allKnownSubsumers=getAllKnownSubsumers(child);
if (allKnownSubsumers.contains(parent))
return true;
else if (!m_possibleSubsumptions.getSuccessors(child).contains(parent))
return false;
Individual freshIndividual=Individual.createAnonymous("fresh-individual");
Map checkedNode=new HashMap<>();
checkedNode.put(freshIndividual,null);
boolean isSubsumedBy=!m_tableau.isSatisfiable(true,Collections.singleton(Atom.create(child,freshIndividual)),null,null,Collections.singleton(Atom.create(parent,freshIndividual)),checkedNode,getSubsumptionTestDescription(child,parent));
if (!isSubsumedBy)
prunePossibleSubsumers();
readKnownSubsumersFromRootNode(child, checkedNode.get(freshIndividual));
m_possibleSubsumptions.getSuccessors(child).removeAll(getAllKnownSubsumers(child));
return isSubsumedBy;
}
protected Hierarchy buildHierarchy(Relation hierarchyRelation) {
double totalNumberOfTasks=m_elements.size();
makeConceptUnsatisfiable(m_bottomElement);
initialiseKnownSubsumptionsUsingToldSubsumers();
double tasksPerformed=updateSubsumptionsUsingLeafNodeStrategy(totalNumberOfTasks);
// Unlike Rob's paper our set of possible subsumptions P would only keep unknown possible subsumptions and not known subsumptions as well.
Set unclassifiedElements=new HashSet<>();
for (AtomicConcept element : m_elements) {
if (!isUnsatisfiable(element)) {
m_possibleSubsumptions.getSuccessors(element).removeAll(getAllKnownSubsumers(element));
if (!m_possibleSubsumptions.getSuccessors(element).isEmpty()) {
unclassifiedElements.add(element);
continue;
}
}
}
Set classifiedElements=new HashSet<>();
while (!unclassifiedElements.isEmpty()) {
AtomicConcept unclassifiedElement=null;
for (AtomicConcept element : unclassifiedElements) {
m_possibleSubsumptions.getSuccessors(element).removeAll(getAllKnownSubsumers(element));
if (!m_possibleSubsumptions.getSuccessors(element).isEmpty()) {
unclassifiedElement=element;
break;
}
classifiedElements.add(element);
while (unclassifiedElements.size()<(totalNumberOfTasks-tasksPerformed)) {
m_progressMonitor.elementClassified(element);
tasksPerformed++;
}
}
unclassifiedElements.removeAll(classifiedElements);
if (unclassifiedElements.isEmpty())
break;
Set unknownPossibleSubsumers=m_possibleSubsumptions.getSuccessors(unclassifiedElement);
if (!isEveryPossibleSubsumerNonSubsumer(unknownPossibleSubsumers,unclassifiedElement,2,7) && !unknownPossibleSubsumers.isEmpty()) {
Hierarchy smallHierarchy=buildHierarchyOfUnknownPossible(unknownPossibleSubsumers);
checkUnknownSubsumersUsingEnhancedTraversal(hierarchyRelation,smallHierarchy.getTopNode(),unclassifiedElement);
}
unknownPossibleSubsumers.clear();
}
return buildTransitivelyReducedHierarchy(m_knownSubsumptions,m_elements);
}
protected Hierarchy buildHierarchyOfUnknownPossible(Set unknownSubsumers) {
Graph smallKnownSubsumptions=new Graph<>();
for (AtomicConcept unknownSubsumer0 : unknownSubsumers) {
smallKnownSubsumptions.addEdge(m_bottomElement,unknownSubsumer0);
smallKnownSubsumptions.addEdge(unknownSubsumer0,m_topElement);
Set knownSubsumersOfElement=getAllKnownSubsumers(unknownSubsumer0);
for (AtomicConcept unknownSubsumer1 : unknownSubsumers)
if (knownSubsumersOfElement.contains(unknownSubsumer1))
smallKnownSubsumptions.addEdge(unknownSubsumer0,unknownSubsumer1);
}
Set unknownSubsumersWithTopBottom = new HashSet<>(unknownSubsumers);
unknownSubsumersWithTopBottom.add(m_bottomElement);
unknownSubsumersWithTopBottom.add(m_topElement);
return buildTransitivelyReducedHierarchy(smallKnownSubsumptions,unknownSubsumersWithTopBottom);
}
protected double updateSubsumptionsUsingLeafNodeStrategy(double totalNumberOfTasks) {
double conceptsProcessed = 0;
Hierarchy hierarchy=buildTransitivelyReducedHierarchy(m_knownSubsumptions,m_elements);
LinkedList> toProcess=new LinkedList<>();
toProcess.addAll(hierarchy.getBottomNode().getParentNodes());
Set> unsatHierarchyNodes=new HashSet<>();
while (!toProcess.isEmpty()) {
HierarchyNode currentHierarchyElement=toProcess.pop();
AtomicConcept currentHierarchyConcept=currentHierarchyElement.getRepresentative();
if (conceptsProcessed < Math.ceil(totalNumberOfTasks*0.85)) {
m_progressMonitor.elementClassified(currentHierarchyConcept);
conceptsProcessed++;
}
if (!conceptHasBeenProcessedAlready(currentHierarchyConcept)) {
Node rootNodeOfModel=buildModelForConcept(currentHierarchyConcept);
// If the leaf was unsatisfable we go up to explore its parents, until a satisfiable parent is discovered. Each time a node is unsat this information is propagated downwards.
if (rootNodeOfModel==null) {
makeConceptUnsatisfiable(currentHierarchyConcept);
unsatHierarchyNodes.add(currentHierarchyElement);
toProcess.addAll(currentHierarchyElement.getParentNodes());
Set> visited=new HashSet<>();
Queue> toVisit=new LinkedList<>(currentHierarchyElement.getChildNodes());
while (!toVisit.isEmpty()) {
HierarchyNode current=toVisit.poll();
if (visited.add(current) && !unsatHierarchyNodes.contains(current)) {
toVisit.addAll(current.getChildNodes());
unsatHierarchyNodes.add(current);
makeConceptUnsatisfiable(current.getRepresentative());
toProcess.remove(current);
for (HierarchyNode parentOfRemovedConcept : current.getParentNodes())
if (!conceptHasBeenProcessedAlready(parentOfRemovedConcept.getRepresentative()))
toProcess.add(parentOfRemovedConcept);
}
}
}
else {
// We cannot do rootNodeOfModel.getCanonicalNode() here. This is done
// in readKnownSubsumersFromRootNode(), but only if rootNodeOfModel
// has not been merged into another node, or if the merge was deterministic.
readKnownSubsumersFromRootNode(currentHierarchyConcept,rootNodeOfModel);
updatePossibleSubsumers();
}
}
}
return conceptsProcessed;
}
private boolean conceptHasBeenProcessedAlready(AtomicConcept atConcept) {
return !m_possibleSubsumptions.getSuccessors(atConcept).isEmpty() || isUnsatisfiable(atConcept);
}
protected Node buildModelForConcept(AtomicConcept concept) {
Individual freshIndividual=Individual.createAnonymous("fresh-individual");
Map checkedNode=new HashMap<>();
checkedNode.put(freshIndividual,null);
if (m_tableau.isSatisfiable(false,Collections.singleton(Atom.create(concept,freshIndividual)),null,null,null,checkedNode,getSatTestDescription(concept)))
return checkedNode.get(freshIndividual);
else
return null;
}
protected void makeConceptUnsatisfiable(AtomicConcept concept) {
addKnownSubsumption(concept,m_bottomElement);
m_possibleSubsumptions.getSuccessors(concept).clear();
}
protected boolean isUnsatisfiable(AtomicConcept concept) {
return m_knownSubsumptions.getSuccessors(concept).contains(m_bottomElement);
}
protected void readKnownSubsumersFromRootNode(AtomicConcept subconcept,Node _checkedNode) {
Node checkedNode=_checkedNode;
if (checkedNode.getCanonicalNodeDependencySet().isEmpty()) {
checkedNode=checkedNode.getCanonicalNode();
ExtensionTable.Retrieval retrieval=m_tableau.getExtensionManager().getBinaryExtensionTable().createRetrieval(new boolean[] { false,true },ExtensionTable.View.TOTAL);
retrieval.getBindingsBuffer()[1]=checkedNode;
retrieval.open();
while (!retrieval.afterLast()) {
Object conceptObject=retrieval.getTupleBuffer()[0];
if (conceptObject instanceof AtomicConcept && retrieval.getDependencySet().isEmpty() && m_elements.contains(conceptObject))
addKnownSubsumption(subconcept,(AtomicConcept)conceptObject);
retrieval.next();
}
}
}
protected void updatePossibleSubsumers() {
ExtensionTable.Retrieval retrieval=m_tableau.getExtensionManager().getBinaryExtensionTable().createRetrieval(new boolean[] { false,false },ExtensionTable.View.TOTAL);
retrieval.open();
Object[] tupleBuffer=retrieval.getTupleBuffer();
while (!retrieval.afterLast()) {
Object conceptObject=tupleBuffer[0];
if (conceptObject instanceof AtomicConcept && m_elements.contains(conceptObject)) {
AtomicConcept atomicConcept=(AtomicConcept)conceptObject;
Node node=(Node)tupleBuffer[1];
if (node.isActive() && !node.isBlocked()) {
if (m_possibleSubsumptions.getSuccessors(atomicConcept).isEmpty())
readPossibleSubsumersFromNodeLabel(atomicConcept,node);
else
prunePossibleSubsumersOfConcept(atomicConcept,node);
}
}
retrieval.next();
}
}
protected void prunePossibleSubsumers() {
ExtensionTable.Retrieval retrieval=m_tableau.getExtensionManager().getBinaryExtensionTable().createRetrieval(new boolean[] { false,false },ExtensionTable.View.TOTAL);
retrieval.open();
Object[] tupleBuffer=retrieval.getTupleBuffer();
while (!retrieval.afterLast()) {
Object conceptObject=tupleBuffer[0];
if (conceptObject instanceof AtomicConcept && m_elements.contains(conceptObject)) {
Node node=(Node)tupleBuffer[1];
if (node.isActive() && !node.isBlocked())
prunePossibleSubsumersOfConcept((AtomicConcept)conceptObject,node);
}
retrieval.next();
}
}
protected void prunePossibleSubsumersOfConcept(AtomicConcept atomicConcept,Node node) {
List possibleSubsumersOfConcept=new ArrayList<>(m_possibleSubsumptions.getSuccessors(atomicConcept));
for (AtomicConcept atomicCon : possibleSubsumersOfConcept)
if (!m_tableau.getExtensionManager().containsConceptAssertion(atomicCon,node))
m_possibleSubsumptions.getSuccessors(atomicConcept).remove(atomicCon);
}
protected void readPossibleSubsumersFromNodeLabel(AtomicConcept atomicConcept,Node node) {
ExtensionTable.Retrieval retrieval=m_tableau.getExtensionManager().getBinaryExtensionTable().createRetrieval(new boolean[] { false,true },ExtensionTable.View.TOTAL);
retrieval.getBindingsBuffer()[1]=node;
retrieval.open();
while (!retrieval.afterLast()) {
Object concept=retrieval.getTupleBuffer()[0];
if (concept instanceof AtomicConcept && m_elements.contains(concept))
addPossibleSubsumption(atomicConcept,(AtomicConcept)concept);
retrieval.next();
}
}
protected Hierarchy buildTransitivelyReducedHierarchy(Graph knownSubsumptions,Set elements) {
final Map> allSubsumers=new HashMap<>();
for (AtomicConcept element : elements) {
Set extendedSubs = new HashSet<>(knownSubsumptions.getSuccessors(element));
extendedSubs.add(m_topElement);
extendedSubs.add(element);
allSubsumers.put(element,new GraphNode<>(element,extendedSubs));
}
allSubsumers.put(m_bottomElement,new GraphNode<>(m_bottomElement,elements));
return DeterministicClassification.buildHierarchy(m_topElement,m_bottomElement,allSubsumers);
}
protected void initialiseKnownSubsumptionsUsingToldSubsumers() {
initialiseKnownSubsumptionsUsingToldSubsumers(m_tableau.getPermanentDLOntology().getDLClauses());
}
protected void initialiseKnownSubsumptionsUsingToldSubsumers(Collection dlClauses) {
for (DLClause dlClause : dlClauses) {
if (dlClause.getHeadLength()==1 && dlClause.getBodyLength()==1) {
DLPredicate headPredicate=dlClause.getHeadAtom(0).getDLPredicate();
DLPredicate bodyPredicate=dlClause.getBodyAtom(0).getDLPredicate();
if (headPredicate instanceof AtomicConcept && bodyPredicate instanceof AtomicConcept) {
AtomicConcept headConcept=(AtomicConcept)headPredicate;
AtomicConcept bodyConcept=(AtomicConcept)bodyPredicate;
if (m_elements.contains(headConcept) && m_elements.contains(bodyConcept))
addKnownSubsumption(bodyConcept,headConcept);
}
}
}
}
protected void checkUnknownSubsumersUsingEnhancedTraversal(Relation hierarchyRelation,HierarchyNode startNode,AtomicConcept pickedElement) {
Set> startSearch=Collections.singleton(startNode);
Set> visited=new HashSet<>(startSearch);
Queue> toProcess=new LinkedList<>(startSearch);
while (!toProcess.isEmpty()) {
HierarchyNode current=toProcess.remove();
Set> subordinateElements=current.getChildNodes();
for (HierarchyNode subordinateElement : subordinateElements) {
AtomicConcept element=subordinateElement.getRepresentative();
if (visited.contains(subordinateElement))
continue;
if (hierarchyRelation.doesSubsume(element,pickedElement)) {
addKnownSubsumption(pickedElement,element);
addKnownSubsumptions(pickedElement,subordinateElement.getEquivalentElements());
if (visited.add(subordinateElement))
toProcess.add(subordinateElement);
}
visited.add(subordinateElement);
}
}
}
protected boolean isEveryPossibleSubsumerNonSubsumer(Set unknownPossibleSubsumers,AtomicConcept pickedElement,int lowerBound,int upperBound) {
if (unknownPossibleSubsumers.size()>lowerBound && unknownPossibleSubsumers.size() superconceptAssertions=new HashSet<>();
Object[] superconcepts=new Object[unknownPossibleSubsumers.size()];
int index=0;
for (AtomicConcept unknownSupNode : unknownPossibleSubsumers) {
Atom atom = Atom.create(unknownSupNode,freshIndividual);
superconceptAssertions.add(atom);
superconcepts[index++]=atom.getDLPredicate();
}
Map checkedNode=new HashMap<>();
checkedNode.put(freshIndividual,null);
boolean isSubsumedBy=!m_tableau.isSatisfiable(false,Collections.singleton(subconceptAssertion),null,null,superconceptAssertions,checkedNode,getSubsumedByListTestDescription(pickedElement,superconcepts));
if (!isSubsumedBy)
prunePossibleSubsumers();
else {
readKnownSubsumersFromRootNode(pickedElement, checkedNode.get(freshIndividual));
m_possibleSubsumptions.getSuccessors(pickedElement).removeAll(getAllKnownSubsumers(pickedElement));
}
return !isSubsumedBy;
}
return false;
}
protected Set getAllKnownSubsumers(AtomicConcept child) {
return m_knownSubsumptions.getReachableSuccessors(child);
}
protected void addKnownSubsumption(AtomicConcept subConcept,AtomicConcept superConcept) {
m_knownSubsumptions.addEdge(subConcept,superConcept);
}
protected void addKnownSubsumptions(AtomicConcept subConcept,Set superConcepts) {
m_knownSubsumptions.addEdges(subConcept,superConcepts);
}
protected void addPossibleSubsumption(AtomicConcept subConcept,AtomicConcept superConcept) {
m_possibleSubsumptions.addEdge(subConcept,superConcept);
}
protected ReasoningTaskDescription getSatTestDescription(AtomicConcept atomicConcept) {
return ReasoningTaskDescription.isConceptSatisfiable(atomicConcept);
}
protected ReasoningTaskDescription getSubsumptionTestDescription(AtomicConcept subConcept,AtomicConcept superConcept) {
return ReasoningTaskDescription.isConceptSubsumedBy(subConcept,superConcept);
}
protected ReasoningTaskDescription getSubsumedByListTestDescription(AtomicConcept subConcept,Object[] superconcepts) {
return ReasoningTaskDescription.isConceptSubsumedByList(subConcept,superconcepts);
}
}