public boolean contains(OWLDataProperty prop) {
if (prop.equals(owlOntologyManager.getOWLDataFactory().getOWLThing())) {
return true;
} else if (prop.equals(owlOntologyManager.getOWLDataFactory().getOWLNothing())) {
return true;
}
return owlDataProperty2DataPropertyPointerMap.containsKey(prop);
}
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 OWLDescription createIncludeCoffeeDescription(Set<OWLClass> includeExtras) {
OWLObjectProperty prop =
this.getNamedObjectProperty(PREFERENCES.getExtrasPropertyName()); // has_extras
Set<OWLDescription> classes = new HashSet<OWLDescription>();
classes.add(getCoffeeClass()); // get OWL class for Coffee
for (OWLClass extra : includeExtras) {
classes.add(manager.getOWLDataFactory().getOWLObjectSomeRestriction(prop, extra));
}
return manager.getOWLDataFactory().getOWLObjectIntersectionOf(classes);
}
private OWLDescription createExcludeCoffeeDescription(Set<OWLClass> excludeExtras) {
OWLObjectProperty prop =
this.getNamedObjectProperty(PREFERENCES.getExtrasPropertyName()); // has_extras
Set<OWLDescription> classes = new HashSet<OWLDescription>();
// Everything must be a coffee
for (OWLClass extra : excludeExtras) {
classes.add(manager.getOWLDataFactory().getOWLObjectSomeRestriction(prop, extra));
}
// are looking for.
return manager.getOWLDataFactory().getOWLObjectUnionOf(classes);
}
protected boolean isEntailed(
OWLOntologyManager manager, OWLOntology premise, OWLOntology conclusion)
throws OWLReasonerException {
OWLReasoner reasoner = JcelReasonerManager.getInstance().getJcelReasoner(manager);
this.reasoner = reasoner;
reasoner.clearOntologies();
reasoner.loadOntologies(Collections.singleton(premise));
reasoner.classify();
JcelEntailmentChecker checker =
new JcelEntailmentChecker(reasoner, manager.getOWLDataFactory());
boolean ret = true;
for (Iterator<OWLLogicalAxiom> it = conclusion.getLogicalAxioms().iterator();
ret && it.hasNext(); ) {
OWLLogicalAxiom axiom = it.next();
if (!checker.isEntailed(axiom)) {
ret = false;
}
}
return ret;
}
/**
* Creates OWLDescription (query) by given included extras and excluded extras
*
* @param includeExtras
* @param excludeExtras
* @return
*/
private OWLDescription createCoffeeDescription(
Set<OWLClass> includeExtras, Set<OWLClass> excludeExtras) {
// Include means existential restrictions
// Exclude means negated existential restrictions
OWLObjectProperty prop =
this.getNamedObjectProperty(PREFERENCES.getExtrasPropertyName()); // has_extras
// Create a hash set to store the components (existential restrictions)
// of our description
Set<OWLDescription> classes = new HashSet<OWLDescription>();
// Everything must be a coffee
classes.add(getCoffeeClass()); // get OWL class for Coffee
// Create the existential restrictions that represent the extras
// that we want to include.
for (OWLClass extra : includeExtras) {
// e.g. hasExtras some ex_A , hasExtras some ex_B
classes.add(manager.getOWLDataFactory().getOWLObjectSomeRestriction(prop, extra));
}
// Create the negated existential restrictions of the extras that we
// want to exclude
for (OWLClass excludeExtra : excludeExtras) {
// has_topping some topping_A
OWLDescription restriction =
manager.getOWLDataFactory().getOWLObjectSomeRestriction(prop, excludeExtra);
// not (has_topping some topping_A)
OWLObjectComplementOf neg = manager.getOWLDataFactory().getOWLObjectComplementOf(restriction);
classes.add(neg);
}
// Bind the whole thing up in an intersection class
// to create a concept description of the coffee we
// are looking for.
return manager.getOWLDataFactory().getOWLObjectIntersectionOf(classes);
}
public void visit(OWLUntypedConstant node) {
try {
lastDataValuePointer = owlConstant2DataValuePointerMap.get(node);
if (lastDataValuePointer == null) {
owlOntologyManager
.getOWLDataFactory()
.getOWLDataType(XSDVocabulary.STRING.getURI())
.accept((OWLDataVisitor) this);
lastDataValuePointer =
faCTPlusPlus.getDataValue(node.getLiteral(), getLastDataTypePointer());
owlConstant2DataValuePointerMap.put(node, lastDataValuePointer);
dataValuePointerMap.put(lastDataValuePointer, node);
}
} catch (Exception e) {
throw new FaCTPlusPlusRuntimeException(e);
}
}
public void visit(OWLDataType dataType) {
try {
lastDataTypeExpressionPointer = null;
lastDataTypePointer =
(DataTypePointer) owlDataRange2DataTypeExpressionPointerMap.get(dataType);
if (lastDataTypePointer == null) {
if (owlOntologyManager.getOWLDataFactory().getTopDataType().equals(dataType)) {
lastDataTypePointer = faCTPlusPlus.getDataTop();
} else {
lastDataTypePointer = faCTPlusPlus.getBuiltInDataType(dataType.getURI().toString());
}
owlDataRange2DataTypeExpressionPointerMap.put(dataType, lastDataTypePointer);
dataTypeExpressionPointerMap.put(lastDataTypePointer, dataType);
}
} catch (Exception e) {
throw new FaCTPlusPlusRuntimeException(e);
}
}
/**
* Gets the property by given name, e.g. has_topping
*
* @param propName
* @return
*/
public OWLObjectProperty getNamedObjectProperty(String propName) {
if (objPropNameCache == null) {
objPropNameCache = new HashMap<String, URI>();
for (OWLOntology ont : reasoner.getLoadedOntologies()) {
for (OWLObjectProperty prop : ont.getReferencedObjectProperties()) {
objPropNameCache.put(prop.toString(), prop.getURI());
}
}
}
// search the HashMap
OWLObjectProperty namedProp = null;
URI uri = objPropNameCache.get(propName);
if (uri != null) {
namedProp = manager.getOWLDataFactory().getOWLObjectProperty(uri);
} else {
System.err.println("Cannot find object property: " + propName + " in loaded ontologies");
}
return namedProp;
}
/**
* 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;
}
private void _createNewOntology() throws Exception {
assert namespace.matches(".*(/|#)");
String baseUri = namespace.replaceAll("(/|#)+$", ""); // removing any trailing slash/hash
manager = new SKOSManager();
if (namespace.endsWith("#")) {
// Ok, OWLAPI v2 works fine with hash separator:
dataset = manager.createSKOSDataset(URI.create(baseUri));
} else {
/////////////////////////////////////////////////////////////////////////////////////////////
// TODO NOTE: workaround for bug in OWLAPI v2:
// Instead of using a baseUri without separator,
// use the namespace itself (ie, w/ fragment separator):
dataset = manager.createSKOSDataset(URI.create(namespace));
// In this way, the resulting ontology looks OK except that the xml:base is
// written with the separator:
//
// <rdf:RDF xmlns="http://mmisw.org/ont/mmi/cf/parameter/"
// xml:base="http://mmisw.org/ont/mmi/cf/parameter/" <<<--- WITH trailing slash
// xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
// xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
// xmlns:owl2="http://www.w3.org/2006/12/owl2#"
// xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
// xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
// xmlns:owl="http://www.w3.org/2002/07/owl#"
// xmlns:skos="http://www.w3.org/2004/02/skos/core#">
// <owl:Ontology rdf:about=""/>
// ...
// <!-- http://mmisw.org/ont/mmi/cf/parameter/CfStdName -->
//
// <skos:ConceptScheme rdf:about="CfStdName"/>
//
//
// <!-- http://mmisw.org/ont/mmi/cf/parameter/age_of_stratospheric_air -->
//
// <skos:Concept rdf:about="age_of_stratospheric_air">
// <skos:inScheme rdf:resource="CfStdName"/>
// </skos:Concept>
//
//
// <!-- http://mmisw.org/ont/mmi/cf/parameter/air_density -->
//
// <skos:Concept rdf:about="air_density">
// <skos:inScheme rdf:resource="CfStdName"/>
// </skos:Concept>
//
// ...
/////////////////////////////////////////////////////////////////////////////////////////////
}
SAXBuilder builder = new SAXBuilder();
Document document = builder.build(new StringReader(inputContents));
standard_name_table = document.getRootElement();
_getProperty(standard_name_table, "version_number");
_getProperty(standard_name_table, "last_modified");
_getProperty(standard_name_table, "institution");
_getProperty(standard_name_table, "contact");
// TODO assign version_number, last_modified as some properties to the ontology itself.
dataFactory = manager.getSKOSDataFactory();
allEntities = new ArrayList<SKOSEntity>();
conceptScheme = dataFactory.getSKOSConceptScheme(URI.create(namespace + CONCEPT_SCHEME));
concepts = new HashSet<SKOSConcept>();
URI topConceptUri = URI.create(namespace + TOP_CONCEPT);
topConcept = dataFactory.getSKOSConcept(topConceptUri);
concepts.add(topConcept);
objectRelationAssertions = new ArrayList<SKOSObjectRelationAssertion>();
dataRelationAssertions = new ArrayList<SKOSDataRelationAssertion>();
// skos:hasTopConcept
objectRelationAssertions.add(
dataFactory.getSKOSObjectRelationAssertion(
conceptScheme, dataFactory.getSKOSHasTopConceptProperty(), topConcept));
/////////////////////////////////////////////////
// OWL API stuff
owlManager = manager.getOWLManger();
owlOntology = owlManager.getOntology(URI.create(namespace));
owlDataFactory = owlManager.getOWLDataFactory();
canonicalUnitsProp =
owlDataFactory.getOWLDataProperty(URI.create(namespace + "canonical_units"));
gribProp = owlDataFactory.getOWLDataProperty(URI.create(namespace + "grib"));
amipProp = owlDataFactory.getOWLDataProperty(URI.create(namespace + "amip"));
rdfsLabel =
owlDataFactory.getOWLDataProperty(URI.create("http://www.w3.org/2000/01/rdf-schema#label"));
rdfsComment =
owlDataFactory.getOWLDataProperty(
URI.create("http://www.w3.org/2000/01/rdf-schema#comment"));
owlChanges = new ArrayList<AddAxiom>();
_addOwlChange(topConceptUri, TOP_CONCEPT.replace('_', ' '), "", null, null, null);
}
