protected boolean isSuccessorRepresented(
DomainNode<?> from, DomainNode<?> to, OWLObjectProperty property) {
if (from.getId() instanceof OWLClassExpression && to.getId() instanceof OWLClassExpression) {
Set<DomainNode<?>> successors = from.getSuccessors(property);
// StatStore.getInstance().enterValue("subclass accessing", 1.0);
// NodeSet<OWLClass> subClasses =
// m_ontologyOperator.getReasoner().getSubClasses((OWLClass)to.getId(), false);
NodeSet<OWLClass> subClasses = currentIdSubClasses;
Node<OWLClass> eqClasses = currentIdEqClasses;
for (DomainNode<?> succ : successors) {
// only compare successors to other class domain elements
if (succ.getId() instanceof OWLClass) {
// if(succ.getInstantiators().containsAll(to.getInstantiators())){ // could be done
// with reasoner
if (m_useBuffer) {
if (m_subClassBuffer.get((OWLClass) to.getId()).contains((OWLClass) succ.getId())
|| m_equivalentClassBuffer
.get((OWLClass) to.getId())
.contains((OWLClass) succ.getId())) {
return true;
}
} else {
if (subClasses.containsEntity((OWLClass) succ.getId())
|| eqClasses.contains(
(OWLClass)
succ.getId())) { // if there exists a successors more (or equally) specific
// than the new one
return true;
}
}
}
}
}
return false;
}
private void addEntailedKBSuccessors(OWLObjectSomeValuesFrom some) {
TRACKER.start(StaticValues.TIME_KB_SUCCESSORS, BlockOutputMode.COMPLETE, true);
// add all role-successors entailed by the TBox
addEntailedTBoxSuccessors(some, m_normalize); // for KB mode only normalize TBox contained roles
DomainNode<?> toNode = getDomainElement(some.getFiller());
OWLClass someClass = m_ontologyOperator.getFlatteningTransformer().getIntermediary(some);
long start = System.currentTimeMillis();
// StatStore.getInstance().enterValue("instance accessing", 1.0);
NodeSet<OWLNamedIndividual> instances =
m_ontologyOperator.getReasoner().getInstances(someClass, false);
sum += System.currentTimeMillis() - start;
// NodeSet<OWLNamedIndividual> instances =
// m_ontologyOperator.getReasoner().getInstances(getClassRepresentation(some), false);
// LOG.fine(" creating successors to " + some + " from instances: " + instances.toString());
Iterator<Node<OWLNamedIndividual>> it1 = instances.iterator();
while (it1.hasNext()) {
Iterator<OWLNamedIndividual> it2 = it1.next().iterator();
while (it2.hasNext()) {
DomainNode<?> from = m_domain.getDomainNode(it2.next());
if (from != null) {
// if(!isSuccessorRepresented(from, getDomainElement(some.getFiller()),
// (OWLObjectProperty)some.getProperty())){
from.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
// }
}
}
}
TRACKER.stop(StaticValues.TIME_KB_SUCCESSORS);
}
public Set<OWLNamedIndividual> getInstances(String classExpressionString, boolean direct) {
if (classExpressionString.trim().length() == 0) {
return Collections.emptySet();
}
OWLClassExpression classExpression = parser.parseClassExpression(classExpressionString);
NodeSet<OWLNamedIndividual> individuals = reasoner.getInstances(classExpression, direct);
return individuals.getFlattened();
}
public Set<OWLClass> getSubClasses(String classExpressionString, boolean direct) {
if (classExpressionString.trim().length() == 0) {
return Collections.emptySet();
}
OWLClassExpression classExpression = parser.parseClassExpression(classExpressionString);
NodeSet<OWLClass> subClasses = reasoner.getSubClasses(classExpression, direct);
return subClasses.getFlattened();
}
/**
* Gather information about all Activities. Individuals are placed in a HashMap (individualsHM:
* Key=URI, value = PROVIndividual)
*/
public void addActivity(OWLNamedIndividual ind) {
// Add list of Object Property values associated with ind.
addAllActivityOPs(ind);
// Add list of Data Property values associated with ind.
addAllActivityDPs(ind);
// get Types
NodeSet<OWLClass> types = PROVGraph.reasoner.getTypes(ind, true);
OWLClass[] typesArray = types.getFlattened().toArray(new OWLClass[0]);
setTypes(typesArray);
}
/**
* Adds Object Properties to the current Individual, and adds corresponding predicate to the list
* (parallel arraylists)
*/
public void addObjectPropertiesByPredicateType(String predicateURI, OWLNamedIndividual ind) {
OWLObjectProperty objectProp =
PROVGraph.manager.getOWLDataFactory().getOWLObjectProperty(IRI.create(predicateURI));
NodeSet<OWLNamedIndividual> owlObjectIndividuals =
PROVGraph.reasoner.getObjectPropertyValues(ind, objectProp);
System.out.println(predicateURI + " Nodes: " + owlObjectIndividuals.getNodes().size());
for (Node<OWLNamedIndividual> owlSameInd : owlObjectIndividuals) {
OWLNamedIndividual currInd = owlSameInd.getRepresentativeElement();
if (currInd != null) {
String owlIndURI = currInd.toStringID();
System.out.println("owlIndURI: " + owlIndURI);
// if the target individual has been previously created, point to that PROVIndividual object
if (PROVGraph.individualsHM.containsKey(owlIndURI)) {
PROVIndividual targetProvInd =
PROVGraph.individualsHM.get(owlSameInd.getRepresentativeElement().toStringID());
OPconnectionObjectInds.add(targetProvInd);
OPconnections.add(predicateURI);
} else // otherwise create a new object with the URI, and add it to the pool of collected
// PROVIndividuals
{
PROVIndividual targetProvInd =
new PROVIndividual(owlSameInd.getRepresentativeElement().toStringID());
PROVGraph.individualsHM.put(targetProvInd.uri, targetProvInd);
OPconnectionObjectInds.add(targetProvInd);
OPconnections.add(predicateURI);
}
} else {
PROVIndividual anonProvInd = new PROVIndividual("Anonymous Individual " + (++anonIndsCntr));
// **anonProvInd.uri not unique
PROVGraph.individualsHM.put(anonProvInd.uri, anonProvInd);
OPconnectionObjectInds.add(anonProvInd);
OPconnections.add(predicateURI);
}
}
}
protected Set<DomainNode<OWLClassExpression>> removeIncludedSuccessors(
OWLObjectProperty property, DomainNode<?> d, OWLClassExpression newSucc) {
Set<DomainNode<OWLClassExpression>> removed = new HashSet<DomainNode<OWLClassExpression>>();
Set<DomainNode<?>> successors = d.getSuccessors(property);
// StatStore.getInstance().enterValue("superclass accessing", 1.0);
// NodeSet<OWLClass> superClasses = m_ontologyOperator.getReasoner().getSuperClasses(newSucc,
// false);
// Node<OWLClass> eqClasses = m_ontologyOperator.getReasoner().getEquivalentClasses(newSucc);
NodeSet<OWLClass> superClasses = currentIdSuperClasses;
if (successors != null) {
// Set<DomainNode<?>> mark_removed = new HashSet<DomainNode<?>>();
Iterator<DomainNode<?>> it = successors.iterator();
// for(DomainNode<?> succ : successors){
while (it.hasNext()) {
DomainNode<?> succ = it.next();
if (succ.getId() instanceof OWLClassExpression) { // only inspect class to class relations
OWLClass succClass = getClassRepresentation((OWLClassExpression) succ.getId());
// if newSucc is more specific than succ, remove succ
if (m_useBuffer) {
if (m_superClassBuffer.get(newSucc).contains(succClass)) {
it.remove();
removed.add(m_domain.getDomainNode((OWLClassExpression) succ.getId()));
}
} else {
if (superClasses.containsEntity(succClass)) {
it.remove();
removed.add(m_domain.getDomainNode((OWLClassExpression) succ.getId()));
// mark_removed.add(succ);
}
}
} // else what about individual domain elements
}
// successors.removeAll(mark_removed);
}
return removed;
}
public static void main(String[] args) {
try {
// Create our ontology manager in the usual way.
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
// Load a copy of the people+pets ontology. We'll load the ontology from the web (it's
// acutally located
// in the TONES ontology repository).
IRI docIRI = IRI.create(DOCUMENT_IRI);
// We load the ontology from a document - our IRI points to it directly
OWLOntology ont = manager.loadOntologyFromOntologyDocument(docIRI);
System.out.println("Loaded " + ont.getOntologyID());
// We need to create an instance of OWLReasoner. An OWLReasoner provides the basic
// query functionality that we need, for example the ability obtain the subclasses
// of a class etc. To do this we use a reasoner factory.
// Create a reasoner factory. In this case, we will use HermiT, but we could also
// use FaCT++ (http://code.google.com/p/factplusplus/) or
// Pellet(http://clarkparsia.com/pellet)
// Note that (as of 03 Feb 2010) FaCT++ and Pellet OWL API 3.0.0 compatible libraries are
// expected to be available in the near future).
// For now, we'll use HermiT
// HermiT can be downloaded from http://hermit-reasoner.com
// Make sure you get the HermiT library and add it to your class path. You can then
// instantiate the HermiT reasoner factory:
// Comment out the first line below and uncomment the second line below to instantiate
// the HermiT reasoner factory. You'll also need to import the
// org.semanticweb.HermiT.Reasoner
// package.
OWLReasonerFactory reasonerFactory = null;
// OWLReasonerFactory reasonerFactory = new Reasoner.ReasonerFactory();
// We'll now create an instance of an OWLReasoner (the implementation being provided by HermiT
// as
// we're using the HermiT reasoner factory). The are two categories of reasoner, Buffering
// and
// NonBuffering. In our case, we'll create the buffering reasoner, which is the default kind
// of reasoner.
// We'll also attach a progress monitor to the reasoner. To do this we set up a configuration
// that
// knows about a progress monitor.
// Create a console progress monitor. This will print the reasoner progress out to the
// console.
ConsoleProgressMonitor progressMonitor = new ConsoleProgressMonitor();
// Specify the progress monitor via a configuration. We could also specify other setup
// parameters in
// the configuration, and different reasoners may accept their own defined parameters this
// way.
OWLReasonerConfiguration config = new SimpleConfiguration(progressMonitor);
// Create a reasoner that will reason over our ontology and its imports closure. Pass in the
// configuration.
OWLReasoner reasoner = reasonerFactory.createReasoner(ont, config);
// Ask the reasoner to do all the necessary work now
reasoner.precomputeInferences();
// We can determine if the ontology is actually consistent (in this case, it should be).
boolean consistent = reasoner.isConsistent();
System.out.println("Consistent: " + consistent);
System.out.println("\n");
// We can easily get a list of unsatisfiable classes. (A class is unsatisfiable if it
// can't possibly have any instances). Note that the getUnsatisfiableClasses method
// is really just a convenience method for obtaining the classes that are equivalent
// to owl:Nothing. In our case there should be just one unsatisfiable class - "mad_cow"
// We ask the reasoner for the unsatisfiable classes, which returns the bottom node
// in the class hierarchy (an unsatisfiable class is a subclass of every class).
Node<OWLClass> bottomNode = reasoner.getUnsatisfiableClasses();
// This node contains owl:Nothing and all the classes that are equivalent to owl:Nothing -
// i.e. the unsatisfiable classes.
// We just want to print out the unsatisfiable classes excluding owl:Nothing, and we can
// used a convenience method on the node to get these
Set<OWLClass> unsatisfiable = bottomNode.getEntitiesMinusBottom();
if (!unsatisfiable.isEmpty()) {
System.out.println("The following classes are unsatisfiable: ");
for (OWLClass cls : unsatisfiable) {
System.out.println(" " + cls);
}
} else {
System.out.println("There are no unsatisfiable classes");
}
System.out.println("\n");
// Now we want to query the reasoner for all descendants of vegetarian. Vegetarians are
// defined in the
// ontology to be animals that don't eat animals or parts of animals.
OWLDataFactory fac = manager.getOWLDataFactory();
// Get a reference to the vegetarian class so that we can as the reasoner about it.
// The full IRI of this class happens to be:
// <http://owl.man.ac.uk/2005/07/sssw/people#vegetarian>
OWLClass vegPizza =
fac.getOWLClass(IRI.create("http://owl.man.ac.uk/2005/07/sssw/people#vegetarian"));
// Now use the reasoner to obtain the subclasses of vegetarian.
// We can ask for the direct subclasses of vegetarian or all of the (proper) subclasses of
// vegetarian.
// In this case we just want the direct ones (which we specify by the "true" flag).
NodeSet<OWLClass> subClses = reasoner.getSubClasses(vegPizza, true);
// The reasoner returns a NodeSet, which represents a set of Nodes.
// Each node in the set represents a subclass of vegetarian pizza. A node of classes contains
// classes,
// where each class in the node is equivalent. For example, if we asked for the
// subclasses of some class A and got back a NodeSet containing two nodes {B, C} and {D}, then
// A would have
// two proper subclasses. One of these subclasses would be equivalent to the class D, and the
// other would
// be the class that is equivalent to class B and class C.
// In this case, we don't particularly care about the equivalences, so we will flatten this
// set of sets and print the result
Set<OWLClass> clses = subClses.getFlattened();
System.out.println("Subclasses of vegetarian: ");
for (OWLClass cls : clses) {
System.out.println(" " + cls);
}
System.out.println("\n");
// In this case, we should find that the classes, cow, sheep and giraffe are vegetarian. Note
// that in this
// ontology only the class cow had been stated to be a subclass of vegetarian. The fact that
// sheep and
// giraffe are subclasses of vegetarian was implicit in the ontology (through other things we
// had said)
// and this illustrates why it is important to use a reasoner for querying an ontology.
// We can easily retrieve the instances of a class. In this example we'll obtain the
// instances of
// the class pet. This class has a full IRI of <http://owl.man.ac.uk/2005/07/sssw/people#pet>
// We need to obtain a reference to this class so that we can ask the reasoner about it.
OWLClass country =
fac.getOWLClass(IRI.create("http://owl.man.ac.uk/2005/07/sssw/people#pet"));
// Ask the reasoner for the instances of pet
NodeSet<OWLNamedIndividual> individualsNodeSet = reasoner.getInstances(country, true);
// The reasoner returns a NodeSet again. This time the NodeSet contains individuals.
// Again, we just want the individuals, so get a flattened set.
Set<OWLNamedIndividual> individuals = individualsNodeSet.getFlattened();
System.out.println("Instances of pet: ");
for (OWLNamedIndividual ind : individuals) {
System.out.println(" " + ind);
}
System.out.println("\n");
// Again, it's worth noting that not all of the individuals that are returned were explicitly
// stated
// to be pets.
// Finally, we can ask for the property values (property assertions in OWL speak) for a given
// individual
// and property.
// Let's get the property values for the individual Mick, the full IRI of which is
// <http://owl.man.ac.uk/2005/07/sssw/people#Mick>
// Get a reference to the individual Mick
OWLNamedIndividual mick =
fac.getOWLNamedIndividual(IRI.create("http://owl.man.ac.uk/2005/07/sssw/people#Mick"));
// Let's get the pets of Mick
// Get hold of the has_pet property which has a full IRI of
// <http://owl.man.ac.uk/2005/07/sssw/people#has_pet>
OWLObjectProperty hasPet =
fac.getOWLObjectProperty(IRI.create("http://owl.man.ac.uk/2005/07/sssw/people#has_pet"));
// Now ask the reasoner for the has_pet property values for Mick
NodeSet<OWLNamedIndividual> petValuesNodeSet = reasoner.getObjectPropertyValues(mick, hasPet);
Set<OWLNamedIndividual> values = petValuesNodeSet.getFlattened();
System.out.println("The has_pet property values for Mick are: ");
for (OWLNamedIndividual ind : values) {
System.out.println(" " + ind);
}
// Notice that Mick has a pet Rex, which wasn't asserted in the ontology.
// Finally, let's print out the class hierarchy.
// Get hold of the top node in the class hierarchy (containing owl:Thing)
// Now print the hierarchy out
Node<OWLClass> topNode = reasoner.getTopClassNode();
print(topNode, reasoner, 0);
} catch (UnsupportedOperationException exception) {
System.out.println("Unsupported reasoner operation.");
} catch (OWLOntologyCreationException e) {
System.out.println("Could not load the pizza ontology: " + e.getMessage());
}
}
private void addEntailedTBoxSuccessors(OWLObjectSomeValuesFrom some, boolean doNormalizing) {
// StatStore.getInstance().enterValue("lookup " + some.getFiller(), 1.0);
// StatStore.getInstance().enterValue("restrictions handled", 1.0);
TRACKER.start(StaticValues.TIME_TBOX_SUCCESSORS, BlockOutputMode.COMPLETE, true);
// TRACKER.start("fetch domain element and intermediary", BlockOutputMode.COMPLETE, true);
DomainNode<?> toNode = getDomainElement(some.getFiller());
// the super class, intermediary stands for (some r B)
OWLClass superClass = m_ontologyOperator.getFlatteningTransformer().getIntermediary(some);
// TRACKER.stop("fetch domain element and intermediary");
// add successors from all
// TRACKER.start("query elk", BlockOutputMode.COMPLETE, true);
// StatStore.getInstance().enterValue("subclass accessing", 1.0);
NodeSet<OWLClass> classes = m_ontologyOperator.getReasoner().getSubClasses(superClass, false);
// fill current class relations from Id
// StatStore.getInstance().enterValue("subclass accessing", 1.0);
currentIdSubClasses = m_ontologyOperator.getReasoner().getSubClasses(some.getFiller(), false);
// StatStore.getInstance().enterValue("superclass accessing", 1.0);
currentIdSuperClasses =
m_ontologyOperator.getReasoner().getSuperClasses(some.getFiller(), false);
// StatStore.getInstance().enterValue("equivalent classes accessing", 1.0);
currentIdEqClasses = m_ontologyOperator.getReasoner().getEquivalentClasses(some.getFiller());
// TRACKER.stop("query elk");
// LOG.fine(" creating successors to " + some + ": " + classes.toString());
Iterator<Node<OWLClass>> nodeIt = classes.iterator();
while (nodeIt.hasNext()) {
Iterator<OWLClass> it = nodeIt.next().iterator();
while (it.hasNext()) {
DomainNode<?> node = m_domain.getDomainNode(it.next());
// if it.next() yields no domain node, there exists an ABox identity for it
// and this case is covered by addEntailedKBSuccessors
if (node != null) {
if (doNormalizing) {
// if(!isSuccessorRepresented(node, (OWLObjectProperty)some.getProperty(),
// some.getFiller())){
TRACKER.start("normalizing and adding", BlockOutputMode.COMPLETE, true);
if (!isSuccessorRepresented(node, toNode, (OWLObjectProperty) some.getProperty())) {
removeIncludedSuccessors(
(OWLObjectProperty) some.getProperty(), node, some.getFiller());
node.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
}
TRACKER.stop("normalizing and adding");
} else {
node.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
}
}
}
}
// add all equivalent class successors
// TRACKER.start("query elk", BlockOutputMode.COMPLETE, true);
Iterator<OWLClass> cIt =
m_ontologyOperator.getReasoner().getEquivalentClasses(superClass).iterator();
// TRACKER.stop("query elk");
while (cIt.hasNext()) {
DomainNode<?> node = m_domain.getDomainNode(cIt.next());
if (node != null) {
if (doNormalizing) {
// if(!isSuccessorRepresented(node, (OWLObjectProperty)some.getProperty(),
// some.getFiller())){
TRACKER.start("normalizing and adding", BlockOutputMode.COMPLETE, true);
if (!isSuccessorRepresented(node, toNode, (OWLObjectProperty) some.getProperty())) {
removeIncludedSuccessors(
(OWLObjectProperty) some.getProperty(), node, some.getFiller());
node.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
}
TRACKER.stop("normalizing and adding");
} else {
node.addSuccessor((OWLObjectProperty) some.getProperty(), toNode);
}
}
}
TRACKER.stop(StaticValues.TIME_TBOX_SUCCESSORS);
}
