public Set<OWLNamedIndividual> getEntities() {
Set<OWLNamedIndividual> entities = new HashSet<OWLNamedIndividual>();
for (OWLOntology ont : ontologies) {
entities.addAll(ont.getIndividualsInSignature());
}
return entities;
}
/**
* Finds all individuals where more than one type is asserted, which is disallowed by Cirm team
* convention. Except: Protected is allowed as second class, but will still be returned from this
* method.
*
* @return
*/
public List<Pair<OWLNamedIndividual, Set<OWLClassExpression>>>
getIndividualsWithMoreThanOneTypeAsserted() {
List<Pair<OWLNamedIndividual, Set<OWLClassExpression>>> errors =
new LinkedList<Pair<OWLNamedIndividual, Set<OWLClassExpression>>>();
if (DBG)
System.out.println("Start CirmOntologyValidator::getIndividualsWithMoreThanOneTypeAsserted");
Set<OWLOntology> owlOntologies = OWL.ontologies();
for (OWLOntology owlOntology : owlOntologies) {
if (DBG) System.out.println("Getting individuals in signature of Ontology " + owlOntology);
Set<OWLNamedIndividual> s = owlOntology.getIndividualsInSignature(false);
if (DBG) System.out.println("...done.");
for (OWLNamedIndividual owlNamedIndividual : s) {
Set<OWLClassExpression> types = owlNamedIndividual.getTypes(owlOntologies);
if (types.size() > 1) {
Pair<OWLNamedIndividual, Set<OWLClassExpression>> error =
new Pair<OWLNamedIndividual, Set<OWLClassExpression>>(owlNamedIndividual, types);
errors.add(error);
if (DBG) {
System.out.println("Found " + types.size() + " types for " + owlNamedIndividual);
for (OWLClassExpression owlClassExpression : types) {
System.out.println(owlClassExpression);
}
}
}
} // for (OWLNamedIndividual
} // for (OWLOntology
if (DBG) System.out.println("Total Individuals not passing validation: " + errors.size());
return errors;
}
@SuppressWarnings({"unchecked", "rawtypes"})
private OWLReasoner createModuleReasoner() throws OWLOntologyCreationException {
LOG.info("Creating module reasoner for module: " + modelId);
ModuleType mtype = ModuleType.BOT;
OWLOntologyManager m =
OWLManager.createOWLOntologyManager(
aboxOntology.getOWLOntologyManager().getOWLDataFactory());
SyntacticLocalityModuleExtractor sme =
new SyntacticLocalityModuleExtractor(m, aboxOntology, mtype);
Set<OWLEntity> seeds = (Set) aboxOntology.getIndividualsInSignature();
OWLOntology module = sme.extractAsOntology(seeds, IRI.generateDocumentIRI());
OWLReasoner reasoner = reasonerFactory.createReasoner(module);
LOG.info("Done creating module reasoner module: " + modelId);
return reasoner;
}
public void writeOntology() throws OWLRendererException {
if (ontologies.size() != 1) {
throw new OWLRuntimeException("Can only render one ontology");
}
OWLOntology ontology = getOntologies().iterator().next();
writePrefixMap();
writeNewLine();
writeOntologyHeader(ontology);
for (OWLAnnotationProperty prop : ontology.getAnnotationPropertiesInSignature()) {
write(prop);
}
for (OWLDatatype datatype : ontology.getDatatypesInSignature()) {
write(datatype);
}
for (OWLObjectProperty prop : ontology.getObjectPropertiesInSignature()) {
write(prop);
OWLObjectPropertyExpression invProp = prop.getInverseProperty();
if (!ontology.getAxioms(invProp).isEmpty()) {
write(invProp);
}
}
for (OWLDataProperty prop : ontology.getDataPropertiesInSignature()) {
write(prop);
}
for (OWLClass cls : ontology.getClassesInSignature()) {
write(cls);
}
for (OWLNamedIndividual ind : ontology.getIndividualsInSignature()) {
write(ind);
}
for (OWLAnonymousIndividual ind : ontology.getReferencedAnonymousIndividuals()) {
write(ind);
}
// Nary disjoint classes axioms
event = new RendererEvent(this, ontology);
for (OWLDisjointClassesAxiom ax : ontology.getAxioms(AxiomType.DISJOINT_CLASSES)) {
if (ax.getClassExpressions().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getClassExpressions(), ax);
writeSection(DISJOINT_CLASSES, map, ",", false, ontology);
}
}
// Nary equivalent classes axioms
for (OWLEquivalentClassesAxiom ax : ontology.getAxioms(AxiomType.EQUIVALENT_CLASSES)) {
if (ax.getClassExpressions().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getClassExpressions(), ax);
writeSection(EQUIVALENT_CLASSES, map, ",", false, ontology);
}
}
// Nary disjoint properties
for (OWLDisjointObjectPropertiesAxiom ax :
ontology.getAxioms(AxiomType.DISJOINT_OBJECT_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(DISJOINT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary equivlant properties
for (OWLEquivalentObjectPropertiesAxiom ax :
ontology.getAxioms(AxiomType.EQUIVALENT_OBJECT_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(EQUIVALENT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary disjoint properties
for (OWLDisjointDataPropertiesAxiom ax :
ontology.getAxioms(AxiomType.DISJOINT_DATA_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(DISJOINT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary equivalent properties
for (OWLEquivalentDataPropertiesAxiom ax :
ontology.getAxioms(AxiomType.EQUIVALENT_DATA_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(EQUIVALENT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary different individuals
for (OWLDifferentIndividualsAxiom ax : ontology.getAxioms(AxiomType.DIFFERENT_INDIVIDUALS)) {
if (ax.getIndividuals().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getIndividuals(), ax);
writeSection(DIFFERENT_INDIVIDUALS, map, ",", false, ontology);
}
}
for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
writeSection(RULE, Collections.singleton(rule), ", ", false);
}
flush();
}
private OWLOntology parseWithReasoner(OWLOntologyManager manager, OWLOntology ontology) {
try {
PelletOptions.load(new URL("http://" + cssLocation + "pellet.properties"));
PelletReasoner reasoner = PelletReasonerFactory.getInstance().createReasoner(ontology);
reasoner.getKB().prepare();
List<InferredAxiomGenerator<? extends OWLAxiom>> generators =
new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
generators.add(new InferredSubClassAxiomGenerator());
generators.add(new InferredClassAssertionAxiomGenerator());
generators.add(new InferredDisjointClassesAxiomGenerator());
generators.add(new InferredEquivalentClassAxiomGenerator());
generators.add(new InferredEquivalentDataPropertiesAxiomGenerator());
generators.add(new InferredEquivalentObjectPropertyAxiomGenerator());
generators.add(new InferredInverseObjectPropertiesAxiomGenerator());
generators.add(new InferredPropertyAssertionGenerator());
generators.add(new InferredSubDataPropertyAxiomGenerator());
generators.add(new InferredSubObjectPropertyAxiomGenerator());
InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, generators);
OWLOntologyID id = ontology.getOntologyID();
Set<OWLImportsDeclaration> declarations = ontology.getImportsDeclarations();
Set<OWLAnnotation> annotations = ontology.getAnnotations();
Map<OWLEntity, Set<OWLAnnotationAssertionAxiom>> entityAnnotations =
new HashMap<OWLEntity, Set<OWLAnnotationAssertionAxiom>>();
for (OWLClass aEntity : ontology.getClassesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLObjectProperty aEntity : ontology.getObjectPropertiesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLDataProperty aEntity : ontology.getDataPropertiesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLNamedIndividual aEntity : ontology.getIndividualsInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLAnnotationProperty aEntity : ontology.getAnnotationPropertiesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
for (OWLDatatype aEntity : ontology.getDatatypesInSignature()) {
entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology));
}
manager.removeOntology(ontology);
OWLOntology inferred = manager.createOntology(id);
iog.fillOntology(manager, inferred);
for (OWLImportsDeclaration decl : declarations) {
manager.applyChange(new AddImport(inferred, decl));
}
for (OWLAnnotation ann : annotations) {
manager.applyChange(new AddOntologyAnnotation(inferred, ann));
}
for (OWLClass aEntity : inferred.getClassesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLObjectProperty aEntity : inferred.getObjectPropertiesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLDataProperty aEntity : inferred.getDataPropertiesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLNamedIndividual aEntity : inferred.getIndividualsInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLAnnotationProperty aEntity : inferred.getAnnotationPropertiesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
for (OWLDatatype aEntity : inferred.getDatatypesInSignature()) {
applyAnnotations(aEntity, entityAnnotations, manager, inferred);
}
return inferred;
} catch (FileNotFoundException e1) {
return ontology;
} catch (MalformedURLException e1) {
return ontology;
} catch (IOException e1) {
return ontology;
} catch (OWLOntologyCreationException e) {
return ontology;
}
}
private void rearrangeAndCompareResults(
OWLOntology ontology,
OWLReasoner reasoner,
Jedis resultStore,
Jedis resultStore2,
Jedis idReader)
throws Exception {
new ResultRearranger().initializeAndRearrange();
Set<OWLClass> classes = ontology.getClassesInSignature();
// rearranged results are in DB-1
resultStore.select(1);
double classCount = 0;
int multiplier = 1;
int missCount = 0;
String bottomID = Util.getPackedID(Constants.BOTTOM_ID, EntityType.CLASS);
System.out.println("Comparing Classes... " + classes.size());
OWLClass owlThing = ontology.getOWLOntologyManager().getOWLDataFactory().getOWLThing();
for (OWLClass cl : classes) {
String classID = conceptToID(cl.toString(), idReader);
// REL/Pellet doesn't consider individuals i.e. {a} \sqsubseteq \bottom
// so skipping checking bottom
if (classID.equals(bottomID)) continue;
classCount++;
Set<OWLClass> reasonerSuperClasses = reasoner.getSuperClasses(cl, false).getFlattened();
// add cl itself to S(X) computed by reasoner. That is missing
// in its result.
reasonerSuperClasses.add(cl);
reasonerSuperClasses.add(owlThing);
// adding equivalent classes -- they are not considered if asked for superclasses
Iterator<OWLClass> iterator = reasoner.getEquivalentClasses(cl).iterator();
while (iterator.hasNext()) reasonerSuperClasses.add(iterator.next());
Set<String> superClasses = resultStore.smembers(classID);
if (superClasses.size() == reasonerSuperClasses.size()) {
compareAndPrintEqualSizedClasses(cl, reasonerSuperClasses, superClasses, idReader);
} else {
System.out.println(
"\n"
+ cl.toString()
+ " -- "
+ superClasses.size()
+ ", "
+ reasonerSuperClasses.size());
for (OWLClass scl : reasonerSuperClasses) {
String sclID = conceptToID(scl.toString(), idReader);
if (!superClasses.contains(sclID)) {
System.out.print(cl.toString() + " -ne- " + scl.toString());
System.out.print(" , ");
}
superClasses.remove(sclID);
}
for (String s : superClasses)
System.out.println("\t -- " + Util.idToConcept(s, idReader) + "(" + s + ")");
System.out.println();
missCount++;
}
}
System.out.println("No of classes not equal: " + missCount);
Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
System.out.println("Rearranging individuals...");
System.out.println("Individuals: " + individuals.size());
System.out.println("Not checking for individuals...");
/*
rearrangeIndividuals(individuals, resultStore, resultStore2, idReader);
int cnt = 0;
for(OWLClass cl : classes) {
Set<OWLNamedIndividual> instances =
reasoner.getInstances(cl, false).getFlattened();
Set<String> computedInstances = resultStore2.smembers(
conceptToID(cl.toString(), idReader));
if(computedInstances.size() == instances.size()) {
compareAndPrintEqualSizedIndividuals(cl, instances, computedInstances, idReader);
}
else {
System.out.println(cl.toString() + " -- " +
computedInstances.size() + " , " + instances.size());
compareAndPrintUnEqualSizedIndividuals(cl, instances, computedInstances, idReader);
cnt++;
}
}
System.out.println("No of classes for which individuals didn't match: " + cnt);
*/
resultStore.select(0);
}
@Override
protected Set<OWLNamedIndividual> getEntities(OWLOntology ont) {
return ont.getIndividualsInSignature();
}