protected Concept getParentConcept(
OWLOntology o, OWLClass ontologyClass, File inDir, Authorizations authorizations)
throws IOException {
Set<OWLClassExpression> superClasses = ontologyClass.getSuperClasses(o);
if (superClasses.size() == 0) {
return getEntityConcept();
} else if (superClasses.size() == 1) {
OWLClassExpression superClassExpr = superClasses.iterator().next();
OWLClass superClass = superClassExpr.asOWLClass();
String superClassUri = superClass.getIRI().toString();
Concept parent = getConceptByIRI(superClassUri);
if (parent != null) {
return parent;
}
parent = importOntologyClass(o, superClass, inDir, authorizations);
if (parent == null) {
throw new LumifyException("Could not find or create parent: " + superClass);
}
return parent;
} else {
throw new LumifyException(
"Unhandled multiple super classes. Found " + superClasses.size() + ", expected 0 or 1.");
}
}
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);
}
}
public boolean contains(OWLClass cls) {
if (cls.equals(owlOntologyManager.getOWLDataFactory().getOWLThing())) {
return true;
} else if (cls.equals(owlOntologyManager.getOWLDataFactory().getOWLNothing())) {
return true;
}
return owlClass2ClassPointerMap.containsKey(cls);
}
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();
}
}
/**
* filters the result of e.g. getSubclasses which is Set<Set<OWLClass>> To Set<OWLClass>
*
* @param original
* @return
* @throws OWLReasonerException
*/
protected Set<OWLClass> filterClasses(Set<Set<OWLClass>> original) throws OWLReasonerException {
Set<OWLClass> result = new HashSet<OWLClass>();
for (Set<OWLClass> set : original) {
for (Iterator<OWLClass> it = set.iterator(); it.hasNext(); ) {
OWLClass cls = it.next();
if (cls.getURI().equals(OWLRDFVocabulary.OWL_NOTHING)) {
it.remove();
} else {
result.add(cls);
}
}
}
return result;
}
private Iterable<Concept> getDomainsConcepts(OWLOntology o, OWLObjectProperty objectProperty) {
String uri = objectProperty.getIRI().toString();
if (objectProperty.getDomains(o).size() == 0) {
throw new LumifyException("Invalid number of domain properties on " + uri);
}
List<Concept> domains = new ArrayList<Concept>();
for (OWLClassExpression rangeClassExpr : objectProperty.getDomains(o)) {
OWLClass rangeClass = rangeClassExpr.asOWLClass();
String rangeClassUri = rangeClass.getIRI().toString();
Concept ontologyClass = getConceptByIRI(rangeClassUri);
checkNotNull(ontologyClass, "Could not find class with uri: " + rangeClassUri);
domains.add(ontologyClass);
}
return domains;
}
public void visit(OWLClass owlClass) {
try {
lastClassPointer = owlClass2ClassPointerMap.get(owlClass);
// Cache if not in map
if (lastClassPointer == null) {
if (owlClass.getURI().equals(OWLRDFVocabulary.OWL_THING.getURI())) {
lastClassPointer = faCTPlusPlus.getThing();
} else if (owlClass.getURI().equals(OWLRDFVocabulary.OWL_NOTHING.getURI())) {
lastClassPointer = faCTPlusPlus.getNothing();
} else {
lastClassPointer = faCTPlusPlus.getNamedClass(owlClass.getURI().toString());
}
classPointerMap.put(lastClassPointer, owlClass);
owlClass2ClassPointerMap.put(owlClass, lastClassPointer);
}
} catch (Exception e) {
throw new FaCTPlusPlusRuntimeException(e);
}
}
/**
* Gets OWL class by given name
*
* @param className
* @return
* @throws OWLReasonerException
*/
public OWLClass getNamedClass(String className) {
if (classnameCache == null) {
classnameCache = new HashMap<String, URI>();
for (OWLOntology ont : reasoner.getLoadedOntologies()) {
for (OWLClass cls : ont.getReferencedClasses()) {
classnameCache.put(cls.toString(), cls.getURI());
}
}
}
OWLClass namedCls = null;
URI uri = classnameCache.get(className);
if (uri != null) {
namedCls = manager.getOWLDataFactory().getOWLClass(uri);
} else {
System.err.println("Cannot find class: " + className + " in loaded ontologies");
}
return namedCls;
}
protected Concept importOntologyClass(
OWLOntology o, OWLClass ontologyClass, File inDir, Authorizations authorizations)
throws IOException {
String uri = ontologyClass.getIRI().toString();
if ("http://www.w3.org/2002/07/owl#Thing".equals(uri)) {
return getEntityConcept();
}
String label = getLabel(o, ontologyClass);
checkNotNull(label, "label cannot be null or empty: " + uri);
LOGGER.info("Importing ontology class " + uri + " (label: " + label + ")");
Concept parent = getParentConcept(o, ontologyClass, inDir, authorizations);
Concept result = getOrCreateConcept(parent, uri, label);
String color = getColor(o, ontologyClass);
if (color != null) {
result.setProperty(
OntologyLumifyProperties.COLOR.getPropertyName(),
color,
OntologyRepository.VISIBILITY.getVisibility(),
authorizations);
}
String displayType = getDisplayType(o, ontologyClass);
if (displayType != null) {
result.setProperty(
OntologyLumifyProperties.DISPLAY_TYPE.getPropertyName(),
displayType,
OntologyRepository.VISIBILITY.getVisibility(),
authorizations);
}
String titleFormula = getTitleFormula(o, ontologyClass);
if (titleFormula != null) {
result.setProperty(
OntologyLumifyProperties.TITLE_FORMULA.getPropertyName(),
titleFormula,
OntologyRepository.VISIBILITY.getVisibility(),
authorizations);
}
String subtitleFormula = getSubtitleFormula(o, ontologyClass);
if (subtitleFormula != null) {
result.setProperty(
OntologyLumifyProperties.SUBTITLE_FORMULA.getPropertyName(),
subtitleFormula,
OntologyRepository.VISIBILITY.getVisibility(),
authorizations);
}
String timeFormula = getTimeFormula(o, ontologyClass);
if (timeFormula != null) {
result.setProperty(
OntologyLumifyProperties.TIME_FORMULA.getPropertyName(),
timeFormula,
OntologyRepository.VISIBILITY.getVisibility(),
authorizations);
}
boolean userVisible = getUserVisible(o, ontologyClass);
result.setProperty(
OntologyLumifyProperties.USER_VISIBLE.getPropertyName(),
userVisible,
OntologyRepository.VISIBILITY.getVisibility(),
authorizations);
String glyphIconFileName = getGlyphIconFileName(o, ontologyClass);
setIconProperty(
result,
inDir,
glyphIconFileName,
LumifyProperties.GLYPH_ICON.getPropertyName(),
authorizations);
String mapGlyphIconFileName = getMapGlyphIconFileName(o, ontologyClass);
setIconProperty(
result,
inDir,
mapGlyphIconFileName,
LumifyProperties.MAP_GLYPH_ICON.getPropertyName(),
authorizations);
return result;
}
/**
* Gets the main temperature categories. This actually returns the direct named subclasses of the
* Temperature class.
*
* @return A <code>Collection</code> of <code>OWLNamedClasses</code>
*/
public Collection getTemperatureCategories() throws OWLReasonerException {
OWLClass temperatureCls = this.getNamedClass(PREFERENCES.getTemperatureClassName());
return temperatureCls.getSubClasses(ontology);
}
/**
* Gets the main base categories. This actually returns the direct named subclasses of the Bases
* class.
*
* @return A <code>Collection</code> of <code>OWLNamedClasses</code>
*/
public Collection getCoffeeBasesCategories() throws OWLReasonerException {
OWLClass basesCls = this.getNamedClass(PREFERENCES.getBaseClassName());
return basesCls.getSubClasses(ontology);
}
