protected void refillInferred() {
getOWLModelManager()
.getReasonerPreferences()
.executeTask(
OptionalInferenceTask.SHOW_INFERRED_EQUIVALENT_OBJECT_PROPERTIES,
() -> {
if (!getOWLModelManager().getReasoner().isConsistent()) {
return;
}
Node<OWLObjectPropertyExpression> equivalentObjectProperties =
getReasoner().getEquivalentObjectProperties(getRootObject());
if (!equivalentObjectProperties.getEntitiesMinus(getRootObject()).isEmpty()) {
OWLEquivalentObjectPropertiesAxiom ax =
getOWLDataFactory()
.getOWLEquivalentObjectPropertiesAxiom(
equivalentObjectProperties.getEntities());
if (!added.contains(ax)) {
addInferredRowIfNontrivial(
new OWLEquivalentObjectPropertiesAxiomFrameSectionRow(
getOWLEditorKit(),
OWLEquivalentObjectPropertiesAxiomFrameSection.this,
null,
getRootObject(),
ax));
}
}
});
}
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;
}
public Set<OWLClass> getEquivalentClasses(String classExpressionString) {
if (classExpressionString.trim().length() == 0) {
return Collections.emptySet();
}
OWLClassExpression classExpression = parser.parseClassExpression(classExpressionString);
Node<OWLClass> equivalentClasses = reasoner.getEquivalentClasses(classExpression);
Set<OWLClass> result = null;
if (classExpression.isAnonymous()) {
result = equivalentClasses.getEntities();
} else {
result = equivalentClasses.getEntitiesMinus(classExpression.asOWLClass());
}
return result;
}
private static void print(Node<OWLClass> parent, OWLReasoner reasoner, int depth) {
// We don't want to print out the bottom node (containing owl:Nothing and unsatisfiable classes)
// because this would appear as a leaf node everywhere
if (parent.isBottomNode()) {
return;
}
// Print an indent to denote parent-child relationships
printIndent(depth);
// Now print the node (containing the child classes)
printNode(parent);
for (Node<OWLClass> child : reasoner.getSubClasses(parent.getRepresentativeElement(), true)) {
// Recurse to do the children. Note that we don't have to worry about cycles as there
// are non in the inferred class hierarchy graph - a cycle gets collapsed into a single
// node since each class in the cycle is equivalent.
print(child, reasoner, depth + 1);
}
}
/**
* 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);
}
}
}
private static void printNode(Node<OWLClass> node) {
// Print out a node as a list of class names in curly brackets
System.out.print("{");
for (Iterator<OWLClass> it = node.getEntities().iterator(); it.hasNext(); ) {
OWLClass cls = it.next();
// User a prefix manager to provide a slightly nicer shorter name
System.out.print(pm.getShortForm(cls));
if (it.hasNext()) {
System.out.print(" ");
}
}
System.out.println("}");
}
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());
}
}
@Test
public void shouldGetBottomDataPropertyNode() {
Node<OWLDataProperty> node = reasoner.getBottomDataPropertyNode();
assertThat(node.getEntities(), is(Collections.singleton(owlBottomDataProperty)));
}
@Test
public void shouldGetTopObjectPropertyNode() {
Node<OWLObjectPropertyExpression> node = reasoner.getTopObjectPropertyNode();
assertThat(node.getEntities(), is(Collections.singleton(owlTopObjectProperty)));
}
@Test
public void shouldGetBottomClassNode() {
Node<OWLClass> node = reasoner.getBottomClassNode();
assertThat(node.getEntities(), is(Collections.singleton(owlNothing)));
}
@Override
public String getRenderName() {
return CommandInterpreter.getRenderName(ticker.getRepresentativeElement());
}