private void populateResultUsingVisitor(List<OWLAxiom> result, OWLAxiomToTurtleVisitor visitor) {
if (result != null) {
for (OWLAxiom axiom : result) {
axiom.accept(visitor);
}
}
}
@Override
public void removeDataProperty(String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLAxiom axiom = factory.getOWLDeclarationAxiom(dataProperty);
axiom = changeManager.getAnnotatedAxiom(axiom);
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
for (OWLAxiom ax : localContext.getReferencingAxioms(dataProperty)) {
ax = ax.getAxiomWithoutAnnotations();
ax = changeManager.getAnnotatedAxiom(ax);
changes.add(new RemoveAxiom(localContext, ax));
}
try {
synchronized (this) {
changeManager.validateRemovalChange(axiom);
manager.applyChanges(changes);
}
} catch (RemovalException ex) {
logger.severe(
ex.getMessage()
+ "Data property not defined in Ontology or not defined by "
+ "this application. Change ( removeDataProperty"
+ dataPropertyName
+ ") will not be applied. ");
}
}
public Integer visit(OWLOntology ontology) {
int max = _0;
for (OWLAxiom axiom : ontology.getLogicalAxioms()) {
int depth = axiom.accept(this);
if (depth > max) {
max = depth;
}
}
return max;
}
public void visit(OWLOntology ontology) {
checkOccurrence(ontology.getAnnotations());
for (AxiomType<?> t : AxiomType.AXIOM_TYPES) {
for (OWLAxiom ax : ontology.getAxioms(t)) {
checkOccurrence(ax.getAnnotations());
ax.accept(this);
}
}
singleAppearance.clear();
}
private List<Construct> getOrderedConstructs() {
constructs.clear();
constructs.add(AL);
for (OWLOntology ont : ontologies) {
for (OWLAxiom ax : ont.getLogicalAxioms()) {
ax.accept(this);
}
}
pruneConstructs();
List<Construct> cons = new ArrayList<Construct>(constructs);
Collections.sort(cons, new ConstructComparator());
return cons;
}
private Set<OWLAnnotation> duplicateAxiomAnnotations(OWLAxiom axiom) {
Set<OWLAnnotation> duplicatedAnnos = new HashSet<OWLAnnotation>();
for (OWLAnnotation anno : axiom.getAnnotations()) {
anno.accept(this);
duplicatedAnnos.add((OWLAnnotation) obj);
}
return duplicatedAnnos;
}
/**
* Convert.
*
* @param axiom axiom to convert
* @return converted class expression
*/
public OWLClassExpression convert(OWLAxiom axiom) {
converter.reset();
axiom.accept(converter);
OWLClassExpression result = converter.getResult();
if (result == null) {
throw new RuntimeException("Not supported yet");
}
return result;
}
/**
* <b>Motivation</b>: OWL reasoners do not return superclass expressions If we want to find all
* class expressions that may hold for a class then we must pre-coordinate all possible
* expressions within the subset of OWL we care about. <br>
* This class generates all satisfiable class expressions of the form r some c (for the
* cross-product of R x C), as well as all class expressions that have been used (which may
* include nested expressions)
*
* <p>The results are stored in queryClassMap
*
* @param precomputePropertyClassCombinations
*/
@Deprecated
private void generateQueryOntology(boolean precomputePropertyClassCombinations) {
queryClassMap = new HashMap<OWLClass, OWLClassExpression>();
getReasoner().flush();
if (precomputePropertyClassCombinations) {
LOG.debug("Precomputing all OP x Class combos");
// cross-product of P x C
// TODO - reflexivity and local reflexivity?
for (OWLObjectProperty p : tboxOntology.getObjectPropertiesInSignature(true)) {
LOG.debug(" materializing P some C for P=:" + p);
for (OWLClass c : tboxOntology.getClassesInSignature(true)) {
OWLObjectSomeValuesFrom r = getOWLDataFactory().getOWLObjectSomeValuesFrom(p, c);
// LOG.debug(" QMAP:"+r);
addClassExpressionToQueryMap(r);
}
}
}
// all expressions used in ontology
for (OWLOntology ont : tboxOntology.getImportsClosure()) {
LOG.debug("Finding all nested anonymous expressions");
for (OWLAxiom ax : ont.getAxioms()) {
// TODO - check if this is the nest closure. ie (r some (r2 some (r3 some ...)))
for (OWLClassExpression x : ax.getNestedClassExpressions()) {
if (x.isAnonymous()) {
// LOG.debug(" QMAP+:"+x);
addClassExpressionToQueryMap(x);
}
}
}
}
if (LOG.isDebugEnabled()) {
for (OWLOntology ont : collectedAxioms.keySet()) {
LOG.debug("TOTAL axioms in QMAP: " + collectedAxioms.get(ont).size());
}
}
LOG.debug("Adding collected axioms");
addCollectedAxioms();
LOG.debug("Flushing reasoner...");
reasoner.flush();
LOG.debug("Flushed reasoner");
}
private void reload(OWLOntology ontology, OWLOntologyFormat format) throws Exception {
Set<OWLAxiom> annotationAxioms = new HashSet<OWLAxiom>();
for (OWLAxiom ax : ontology.getAxioms()) {
if (ax.isAnnotationAxiom()) {
annotationAxioms.add(ax);
}
}
OWLOntologyLoaderConfiguration withAnnosConfig = new OWLOntologyLoaderConfiguration();
OWLOntology reloadedWithAnnoAxioms = reload(ontology, format, withAnnosConfig);
assertEquals(ontology.getAxioms(), reloadedWithAnnoAxioms.getAxioms());
//
OWLOntologyLoaderConfiguration withoutAnnosConfig =
new OWLOntologyLoaderConfiguration().setLoadAnnotationAxioms(false);
OWLOntology reloadedWithoutAnnoAxioms = reload(ontology, format, withoutAnnosConfig);
assertFalse(ontology.getAxioms().equals(reloadedWithoutAnnoAxioms.getAxioms()));
Set<OWLAxiom> axiomsMinusAnnotationAxioms = new HashSet<OWLAxiom>(ontology.getAxioms());
axiomsMinusAnnotationAxioms.removeAll(annotationAxioms);
assertEquals(axiomsMinusAnnotationAxioms, reloadedWithoutAnnoAxioms.getAxioms());
}
@Override
public boolean compare(JSONObject jsonObject, OWLClass owlClass, OWLOntology owlOntology) {
Set<OWLClass> allClassesInAxiomsRelated = new HashSet<OWLClass>();
JSONArray jsonAnnotationsArray = (JSONArray) jsonObject.get("annotations");
Set<OWLAxiom> owlAxiomSet = owlClass.getReferencingAxioms(owlOntology);
Iterator<OWLAxiom> owlAxiomSetIterator = owlAxiomSet.iterator();
while (owlAxiomSetIterator.hasNext()) {
OWLAxiom owlAxiom = owlAxiomSetIterator.next();
Set<OWLClass> owlClassesInAxiom = owlAxiom.getClassesInSignature();
allClassesInAxiomsRelated.addAll(owlClassesInAxiom);
}
Set<String> owlClassesIds = new HashSet<String>();
Iterator<OWLClass> allClassesInAxiomsRelatedIterator = allClassesInAxiomsRelated.iterator();
while (allClassesInAxiomsRelatedIterator.hasNext()) {
OWLClass currentClass = allClassesInAxiomsRelatedIterator.next();
owlClassesIds.add(
OwlDataExtrators.getAttribute("id", currentClass, owlOntology).replace(":", "_"));
}
Set<String> jsonAnnotationsIdsSet = new HashSet<String>();
Iterator<JSONObject> jsonAnnotationsArrayIterator = jsonAnnotationsArray.iterator();
while (jsonAnnotationsArrayIterator.hasNext()) {
JSONObject jsonAnnottation = jsonAnnotationsArrayIterator.next();
String jsonAnnotationIdentifier = (String) jsonAnnottation.get("identifier");
jsonAnnotationsIdsSet.add(jsonAnnotationIdentifier);
}
Set<Set<String>> jsonAnnotationsIdPowerSet = SetsOperations.powerSet(jsonAnnotationsIdsSet);
Iterator<Set<String>> jsonAnnotationsIdPowerSetIterator = jsonAnnotationsIdPowerSet.iterator();
while (jsonAnnotationsIdPowerSetIterator.hasNext()) {
Set<String> idsSet = jsonAnnotationsIdPowerSetIterator.next();
if (idsSet.containsAll(owlClassesIds)) {
return true;
}
}
return false;
}
public Object getRelationshipType(Object parentObject, Object childObject) {
AxiomEdge edge = new AxiomEdge(childObject, parentObject);
OWLObject edgeObject = edgeMap.get(edge);
if (edgeObject != null) {
edgeNameGenerator.reset();
if (edgeObject instanceof OWLClassExpression) {
((OWLClassExpression) edgeObject).accept(edgeNameGenerator);
} else {
((OWLAxiom) edgeObject).accept(edgeNameGenerator);
}
return edgeNameGenerator.edgeName;
} else {
return null;
}
}
public int getRelationshipDirection(Object parentObject, Object childObject) {
AxiomEdge edge = new AxiomEdge(childObject, parentObject);
OWLObject edgeObject = edgeMap.get(edge);
if (edgeObject != null) {
edgeNameGenerator.reset();
if (edgeObject instanceof OWLAxiom) {
((OWLAxiom) edgeObject).accept(edgeNameGenerator);
} else {
((OWLClassExpression) edgeObject).accept(edgeNameGenerator);
}
return edgeNameGenerator.direction;
}
return -1; // if no edge found, negative direction for handling in
// DefaultEdgeFactory
}
private boolean isOBOAxiom(OWLAxiom axiom) {
return axiom.accept(checker);
}
public AxiomType<?> getAxiomType(OWLAxiom axiom) {
axiom.accept(this);
return axiomType;
}
// ////////////////////////////////////////////////////////////////////////////////////////////
//
// Axiom Visitor stuff
//
// ////////////////////////////////////////////////////////////////////////////////////////////
protected void processAxiomAnnotations(OWLAxiom ax) {
// default behavior: iterate over the annotations outside the axiom
for (OWLAnnotation anno : ax.getAnnotations()) {
anno.accept(this);
}
}
/**
* This method clears all the map (invokes the clearMaps-method) at first. Then it iterates over
* all axioms and invokes their accept-Method with "this" as parameter.
*
* @param axioms The axioms to visualize
*/
public void addAndClearAxioms(Set<OWLAxiom> axioms) {
this.clearMaps();
for (OWLAxiom ax : axioms) {
ax.accept(this);
}
}