protected void importDataProperty(OWLOntology o, OWLDataProperty dataTypeProperty) {
String propertyIRI = dataTypeProperty.getIRI().toString();
String propertyDisplayName = getLabel(o, dataTypeProperty);
PropertyType propertyType = getPropertyType(o, dataTypeProperty);
boolean userVisible = getUserVisible(o, dataTypeProperty);
boolean searchable = getSearchable(o, dataTypeProperty);
Boolean displayTime = getDisplayTime(o, dataTypeProperty);
Double boost = getBoost(o, dataTypeProperty);
if (propertyType == null) {
throw new LumifyException("Could not get property type on data property " + propertyIRI);
}
for (OWLClassExpression domainClassExpr : dataTypeProperty.getDomains(o)) {
OWLClass domainClass = domainClassExpr.asOWLClass();
String domainClassUri = domainClass.getIRI().toString();
Concept domainConcept = getConceptByIRI(domainClassUri);
checkNotNull(domainConcept, "Could not find class with uri: " + domainClassUri);
LOGGER.info("Adding data property " + propertyIRI + " to class " + domainConcept.getTitle());
ArrayList<PossibleValueType> possibleValues = getPossibleValues(o, dataTypeProperty);
Collection<TextIndexHint> textIndexHints = getTextIndexHints(o, dataTypeProperty);
addPropertyTo(
domainConcept,
propertyIRI,
propertyDisplayName,
propertyType,
possibleValues,
textIndexHints,
userVisible,
searchable,
displayTime,
boost);
}
}
/**
* Возвращает IRI типа данных, которое связано с этим свойством. Т.е. само ограничение
* игнорируется.
*
* @param prpExp ограничение на свойство, которое определяет неименованный класс
* @return
* @deprecated
*/
public OWLDatatype getDataPrpopertyRestrictionRANGE(OWLClassExpression prpExp) {
OWLDataProperty prp = (OWLDataProperty) ((OWLRestriction) prpExp).getProperty();
// для каждого свойства находим его RANGE - берем оттуда типы
OWLDatatype datatype = OWLont.getOWLont().getDatatypeFromRange(prp.getIRI().toString());
return datatype;
}
// TODO necessary method??
public String getDataRetriavablePropertyFragments() {
for (OWLDataProperty prop : _ontology.getDataPropertiesInSignature()) {
if (isKeywordSearchable(prop)) {
return prop.getIRI().getRemainder().get();
}
}
return null;
}
private void runWithSeparateFiles() {
if (owlFile == null) {
throw new NullPointerException("You have to specify an ontology file!");
}
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = null;
OBDADataFactory obdaDataFactory = OBDADataFactoryImpl.getInstance();
try {
ontology = manager.loadOntologyFromOntologyDocument((new File(owlFile)));
if (disableReasoning) {
/*
* when reasoning is disabled, we extract only the declaration assertions for the vocabulary
*/
ontology = extractDeclarations(manager, ontology);
}
Collection<Predicate> predicates = new ArrayList<>();
for (OWLClass owlClass : ontology.getClassesInSignature()) {
Predicate predicate = obdaDataFactory.getClassPredicate(owlClass.getIRI().toString());
predicates.add(predicate);
}
for (OWLDataProperty owlDataProperty : ontology.getDataPropertiesInSignature()) {
Predicate predicate =
obdaDataFactory.getDataPropertyPredicate(owlDataProperty.getIRI().toString());
predicates.add(predicate);
}
for (OWLObjectProperty owlObjectProperty : ontology.getObjectPropertiesInSignature()) {
Predicate predicate =
obdaDataFactory.getObjectPropertyPredicate(owlObjectProperty.getIRI().toString());
predicates.add(predicate);
}
OBDAModel obdaModel = loadMappingFile(mappingFile);
Ontology inputOntology = OWLAPI3TranslatorUtility.translate(ontology);
obdaModel.declareAll(inputOntology.getVocabulary());
int numPredicates = predicates.size();
int i = 1;
for (Predicate predicate : predicates) {
System.err.println(String.format("Materializing %s (%d/%d)", predicate, i, numPredicates));
serializePredicate(ontology, inputOntology, obdaModel, predicate, outputFile, format);
i++;
}
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* This method makes sure is used to setup a new/fresh OBDA model. This is done by replacing the
* instance this.obdacontroller (the OBDA model) with a new object. On creation listeners for the
* datasources, mappings and queries are setup so that changes in these trigger and ontology
* change.
*
* <p>Additionally, this method configures all available OBDAOWLReasonerFacotry objects to have a
* reference to the newly created OBDA model and to the global preference object. This is
* necessary so that the factories are able to pass the OBDA model to the reasoner instances when
* they are created.
*/
private void setupNewOBDAModel() {
OBDAModel activeOBDAModel = getActiveOBDAModel();
if (activeOBDAModel != null) {
return;
}
activeOBDAModel = dfac.getOBDAModel();
activeOBDAModel.addSourcesListener(dlistener);
activeOBDAModel.addMappingsListener(mlistener);
queryController.addListener(qlistener);
OWLModelManager mmgr = owlEditorKit.getOWLWorkspace().getOWLModelManager();
Set<OWLOntology> ontologies = mmgr.getOntologies();
for (OWLOntology ontology : ontologies) {
// Setup the entity declarations
for (OWLClass c : ontology.getClassesInSignature()) {
OClass pred = ofac.createClass(c.getIRI().toString());
activeOBDAModel.declareClass(pred);
}
for (OWLObjectProperty r : ontology.getObjectPropertiesInSignature()) {
ObjectPropertyExpression pred = ofac.createObjectProperty(r.getIRI().toString());
activeOBDAModel.declareObjectProperty(pred);
}
for (OWLDataProperty p : ontology.getDataPropertiesInSignature()) {
DataPropertyExpression pred = ofac.createDataProperty(p.getIRI().toString());
activeOBDAModel.declareDataProperty(pred);
}
}
// Setup the prefixes
PrefixOWLOntologyFormat prefixManager =
PrefixUtilities.getPrefixOWLOntologyFormat(mmgr.getActiveOntology());
// addOBDACommonPrefixes(prefixManager);
PrefixManagerWrapper prefixwrapper = new PrefixManagerWrapper(prefixManager);
activeOBDAModel.setPrefixManager(prefixwrapper);
OWLOntology activeOntology = mmgr.getActiveOntology();
String defaultPrefix = prefixManager.getDefaultPrefix();
if (defaultPrefix == null) {
OWLOntologyID ontologyID = activeOntology.getOntologyID();
defaultPrefix = ontologyID.getOntologyIRI().toURI().toString();
}
activeOBDAModel.getPrefixManager().addPrefix(PrefixManager.DEFAULT_PREFIX, defaultPrefix);
// Add the model
URI modelUri = activeOntology.getOntologyID().getOntologyIRI().toURI();
obdamodels.put(modelUri, activeOBDAModel);
}
@Test
public void testBadDataproperty() throws Exception {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.createOntology(IRI.create(NS));
OWLClassExpression restriction =
factory.getOWLDataSomeValuesFrom(
P, factory.getOWLDatatype(XSDVocabulary.DURATION.getIRI()));
OWLAxiom axiom = factory.getOWLSubClassOfAxiom(A, restriction);
manager.addAxiom(ontology, axiom);
assertTrue(ontology.containsDataPropertyInSignature(P.getIRI()));
StringDocumentTarget t = new StringDocumentTarget();
manager.saveOntology(ontology, new RDFXMLOntologyFormat(), t);
manager.removeOntology(ontology);
ontology = manager.loadOntologyFromOntologyDocument(new StringDocumentSource(t.toString()));
assertTrue(ontology.containsDataPropertyInSignature(P.getIRI()));
}
protected PropertyType getPropertyType(OWLOntology o, OWLDataProperty dataTypeProperty) {
Set<OWLDataRange> ranges = dataTypeProperty.getRanges(o);
if (ranges.size() == 0) {
return null;
}
if (ranges.size() > 1) {
throw new LumifyException(
"Unexpected number of ranges on data property " + dataTypeProperty.getIRI().toString());
}
for (OWLDataRange range : ranges) {
if (range instanceof OWLDatatype) {
OWLDatatype datatype = (OWLDatatype) range;
return getPropertyType(datatype.getIRI().toString());
}
}
throw new LumifyException(
"Could not find range on data property " + dataTypeProperty.getIRI().toString());
}
public boolean isDomainOfDataProperty(OWLClass clase, OWLDataProperty prop) {
for (OWLClass owlClass1 : _reasoner.getDataPropertyDomains(prop, false).getFlattened()) {
if (owlClass1.getIRI().equals(clase.getIRI())) {
Log.d(
TAG,
"<idDomainOfDataProperty> "
+ clase.getIRI().getRemainder().get()
+ " dominio de "
+ prop.getIRI().getRemainder().get()
+ "? SI!");
return true;
}
}
Log.d(
TAG,
"<isDomainOfDataProperty> "
+ clase.getIRI().getRemainder().get()
+ " dominio de "
+ prop.getIRI().getRemainder().get()
+ "? NO");
return false;
}
// this method retrieves all the geometric properties that have been
// pre-designated as "house setable" or "room setable",
// that is, if a geometric property is available for houses, it has been
// annotated as "houseSetable", for rooms, "roomSetable" and for both it
// has been designated with both annotations.
public void retrieveGeometricPropertiesMaps() {
OWLDataProperty geometricProperty =
OWLFactory.getOWLDataProperty(":GeometricProperty", topIxPrefixManager);
OWLAnnotationProperty propertyID =
OWLFactory.getOWLAnnotationProperty(":propertyID", topIxPrefixManager);
logger.info(propertyID);
OWLAnnotationProperty houseSetable =
OWLFactory.getOWLAnnotationProperty(":houseSetable", topIxPrefixManager);
OWLAnnotationProperty roomSetable =
OWLFactory.getOWLAnnotationProperty(":roomSetable", topIxPrefixManager);
Set<OWLSubDataPropertyOfAxiom> tempGeometricDataPropertiesSet =
topIxOnt.getDataSubPropertyAxiomsForSuperProperty(geometricProperty);
for (OWLSubDataPropertyOfAxiom tempGeomPropAxiom : tempGeometricDataPropertiesSet) {
OWLDataProperty tempDataProperty = tempGeomPropAxiom.getSubProperty().asOWLDataProperty();
// the following two local vars will become an entry for geometricPropertiesMap
String tempString = tempDataProperty.getAnnotations(topIxOnt, propertyID).toString();
tempString = tempString.substring(tempString.indexOf('"') + 1, tempString.indexOf("^") - 1);
IRI tempIRI = tempGeomPropAxiom.getSubProperty().asOWLDataProperty().getIRI();
geometricPropertiesMap.put(tempString, tempIRI);
// the following code decides whether the above entry should also be contained
// in the houseSetableGeometricPropertiesMap
Set<OWLAnnotation> tempDataPropAnnotationSet = tempDataProperty.getAnnotations(topIxOnt);
for (OWLAnnotation tempDataPropAnnotation : tempDataPropAnnotationSet) {
if (tempDataPropAnnotation.getProperty() == houseSetable
&& tempDataPropAnnotation.getValue().toString().equals("\"true\"^^xsd:boolean")) {
houseSetableGeometricPropertiesMap.put(tempString, tempIRI);
}
if (tempDataPropAnnotation.getProperty() == roomSetable
&& tempDataPropAnnotation.getValue().toString().equals("\"true\"^^xsd:boolean")) {
roomSetableGeometricPropertiesMap.put(tempString, tempIRI);
}
}
}
}
@Override
public void visit(OWLDataProperty property) {
handleObject(property);
property.getIRI().accept(this);
}
@Override
public void ontologiesChanged(List<? extends OWLOntologyChange> changes) throws OWLException {
Map<OWLEntity, OWLEntity> renamings = new HashMap<OWLEntity, OWLEntity>();
Set<OWLEntity> removals = new HashSet<OWLEntity>();
for (int idx = 0; idx < changes.size(); idx++) {
OWLOntologyChange change = changes.get(idx);
if (change instanceof SetOntologyID) {
IRI newiri = ((SetOntologyID) change).getNewOntologyID().getOntologyIRI();
if (newiri == null) continue;
IRI oldiri = ((SetOntologyID) change).getOriginalOntologyID().getOntologyIRI();
log.debug("Ontology ID changed");
log.debug("Old ID: {}", oldiri);
log.debug("New ID: {}", newiri);
OBDAModel model = obdamodels.get(oldiri.toURI());
if (model == null) {
setupNewOBDAModel();
model = getActiveOBDAModel();
}
PrefixManager prefixManager = model.getPrefixManager();
prefixManager.addPrefix(PrefixManager.DEFAULT_PREFIX, newiri.toURI().toString());
obdamodels.remove(oldiri.toURI());
obdamodels.put(newiri.toURI(), model);
continue;
} else if (change instanceof AddAxiom) {
OWLAxiom axiom = change.getAxiom();
if (axiom instanceof OWLDeclarationAxiom) {
OWLEntity entity = ((OWLDeclarationAxiom) axiom).getEntity();
OBDAModel activeOBDAModel = getActiveOBDAModel();
if (entity instanceof OWLClass) {
OWLClass oc = (OWLClass) entity;
OClass c = ofac.createClass(oc.getIRI().toString());
activeOBDAModel.declareClass(c);
} else if (entity instanceof OWLObjectProperty) {
OWLObjectProperty or = (OWLObjectProperty) entity;
ObjectPropertyExpression r = ofac.createObjectProperty(or.getIRI().toString());
activeOBDAModel.declareObjectProperty(r);
} else if (entity instanceof OWLDataProperty) {
OWLDataProperty op = (OWLDataProperty) entity;
DataPropertyExpression p = ofac.createDataProperty(op.getIRI().toString());
activeOBDAModel.declareDataProperty(p);
}
}
} else if (change instanceof RemoveAxiom) {
OWLAxiom axiom = change.getAxiom();
if (axiom instanceof OWLDeclarationAxiom) {
OWLEntity entity = ((OWLDeclarationAxiom) axiom).getEntity();
OBDAModel activeOBDAModel = getActiveOBDAModel();
if (entity instanceof OWLClass) {
OWLClass oc = (OWLClass) entity;
OClass c = ofac.createClass(oc.getIRI().toString());
activeOBDAModel.unDeclareClass(c);
} else if (entity instanceof OWLObjectProperty) {
OWLObjectProperty or = (OWLObjectProperty) entity;
ObjectPropertyExpression r = ofac.createObjectProperty(or.getIRI().toString());
activeOBDAModel.unDeclareObjectProperty(r);
} else if (entity instanceof OWLDataProperty) {
OWLDataProperty op = (OWLDataProperty) entity;
DataPropertyExpression p = ofac.createDataProperty(op.getIRI().toString());
activeOBDAModel.unDeclareDataProperty(p);
}
}
}
if (idx + 1 >= changes.size()) {
continue;
}
if (change instanceof RemoveAxiom && changes.get(idx + 1) instanceof AddAxiom) {
// Found the pattern of a renaming refactoring
RemoveAxiom remove = (RemoveAxiom) change;
AddAxiom add = (AddAxiom) changes.get(idx + 1);
if (!(remove.getAxiom() instanceof OWLDeclarationAxiom
&& add.getAxiom() instanceof OWLDeclarationAxiom)) {
continue;
}
// Found the patter we are looking for, a remove and add of
// declaration axioms
OWLEntity olde = ((OWLDeclarationAxiom) remove.getAxiom()).getEntity();
OWLEntity newe = ((OWLDeclarationAxiom) add.getAxiom()).getEntity();
renamings.put(olde, newe);
} else if (change instanceof RemoveAxiom
&& ((RemoveAxiom) change).getAxiom() instanceof OWLDeclarationAxiom) {
// Found the pattern of a deletion
OWLDeclarationAxiom declaration = (OWLDeclarationAxiom) ((RemoveAxiom) change).getAxiom();
OWLEntity removedEntity = declaration.getEntity();
removals.add(removedEntity);
}
}
// Applying the renaming to the OBDA model
OBDAModel obdamodel = getActiveOBDAModel();
for (OWLEntity olde : renamings.keySet()) {
OWLEntity removedEntity = olde;
OWLEntity newEntity = renamings.get(removedEntity);
// This set of changes appears to be a "renaming" operation,
// hence we will modify the OBDA model accordingly
Predicate removedPredicate = getPredicate(removedEntity);
Predicate newPredicate = getPredicate(newEntity);
obdamodel.renamePredicate(removedPredicate, newPredicate);
}
// Applying the deletions to the obda model
for (OWLEntity removede : removals) {
Predicate removedPredicate = getPredicate(removede);
obdamodel.deletePredicate(removedPredicate);
}
}
/*
* (non-Javadoc)
*
* @seeorg.semanticweb.owlapi.model.OWLPropertyExpressionVisitor#visit(org.
* semanticweb.owlapi.model.OWLDataProperty)
*/
@Override
public void visit(OWLDataProperty data) {
sb.append(print(data.toString()));
}
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;
}
}
@Override
protected void writeDataPropertyComment(OWLDataProperty prop) {
writeComment(prop.getIRI().toString());
}
