edu.stanford.smi.protegex.owl.jena
Class JenaNormalizer

java.lang.Object
  edu.stanford.smi.protegex.owl.jena.JenaNormalizer

public class JenaNormalizer

extends Object

A class that is able to normalize a given OntModel. Normalizing makes sure that a given OWL file (edited outside of Protege) fulfills some syntactic constraints. This process does the following:

• Converts named class expressions (enumerations, boolean classes and restrictions) into normal named classes with the expression as equivalent class.
• Turns all absolute class, property and individual names into local names, so that they get the default namespace.
• Converts multiple domain statements into a single intersectionOf

This code could clearly be optimized (generalized) to better exploit the RDF structure. However, we try to make use the of the Ontology API wherever possible, so that we could easier copy this functionality into other OWL APIs.

Author:

Holger Knublauch

Field Summary

private static boolean	logging Indicates whether logging is turned on or not
private static String	LOGGING Set this to "true" in protege.properties to enable logging
private com.hp.hpl.jena.ontology.OntModel	ontModel
private com.hp.hpl.jena.rdf.model.Model	owlFullModel

Constructor Summary

JenaNormalizer(com.hp.hpl.jena.ontology.OntModel ontModel, com.hp.hpl.jena.rdf.model.Model owlFullModel, NamespaceManager namespaceManager)

Method Summary

private void	alignPrefixes(com.hp.hpl.jena.ontology.OntModel ontModel, NamespaceManager nsm)
private void	assignNamesToAnonymousIndividuals(com.hp.hpl.jena.ontology.OntModel ontModel, String defaultNamespace)
private void	assignNamesToAnonymousTopLevelClasses(com.hp.hpl.jena.ontology.OntModel ontModel, String defaultNamespace)
static void	assignRDFTypesToMetaclassInstances(com.hp.hpl.jena.ontology.OntModel ontModel, com.hp.hpl.jena.rdf.model.Model owlFullModel)
private void	convertCyclicPropertyInheritance()
private void	convertCyclicPropertyInheritance(com.hp.hpl.jena.util.iterator.ExtendedIterator it, List errors)
private void	convertCyclicPropertyInheritance(com.hp.hpl.jena.ontology.OntProperty start, com.hp.hpl.jena.ontology.OntProperty ontProperty, Set visited, Collection errors)
private void	convertMultipleDomainsIntoIntersection(Iterator ontProperties)
private void	convertMultipleDomainsIntoIntersection(com.hp.hpl.jena.ontology.OntModel ontModel)
private void	convertMultipleRangesIntoIntersection(Iterator ontProperties)
private void	convertMultipleRangesIntoIntersection(com.hp.hpl.jena.ontology.OntModel ontModel)
private void	convertNamedClassExpressions()
private com.hp.hpl.jena.ontology.AllValuesFromRestriction	createAllValuesFromRestriction(com.hp.hpl.jena.ontology.AllValuesFromRestriction base)
private com.hp.hpl.jena.ontology.CardinalityRestriction	createCardinalityRestriction(com.hp.hpl.jena.ontology.CardinalityRestriction base)
private com.hp.hpl.jena.ontology.ComplementClass	createComplementClass(com.hp.hpl.jena.ontology.ComplementClass base)
private com.hp.hpl.jena.ontology.EnumeratedClass	createEnumeratedClass(com.hp.hpl.jena.ontology.OntClass enumeratedClass)
private com.hp.hpl.jena.ontology.HasValueRestriction	createHasValueRestriction(com.hp.hpl.jena.ontology.HasValueRestriction base)
private String	createImportURI(com.hp.hpl.jena.ontology.OntModel ontModel)
private com.hp.hpl.jena.ontology.IntersectionClass	createIntersectionClass(com.hp.hpl.jena.ontology.IntersectionClass intersectionClass)
private com.hp.hpl.jena.ontology.MaxCardinalityRestriction	createMaxCardinalityRestriction(com.hp.hpl.jena.ontology.MaxCardinalityRestriction base)
private com.hp.hpl.jena.ontology.MinCardinalityRestriction	createMinCardinalityRestriction(com.hp.hpl.jena.ontology.MinCardinalityRestriction base)
private void	createPrefixesForImports(com.hp.hpl.jena.ontology.OntModel ontModel, NamespaceManager nsm) Makes sure that there is a prefix for all non-anonymous owl:Ontologies.
private com.hp.hpl.jena.ontology.Restriction	createRestriction(com.hp.hpl.jena.ontology.Restriction restriction)
private com.hp.hpl.jena.ontology.SomeValuesFromRestriction	createSomeValuesFromRestriction(com.hp.hpl.jena.ontology.SomeValuesFromRestriction base)
private com.hp.hpl.jena.ontology.UnionClass	createUnionClass(com.hp.hpl.jena.ontology.UnionClass unionClass)
private void	ensureAnnotationPropertiesHaveRange()
private void	ensureDeprecatedClassesAreOntClasses(com.hp.hpl.jena.rdf.model.Model owlFullModel)
private void	ensureDeprecatedPropertiesAreOntProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)
private void	ensureFunctionalPropertiesAreOntProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)
private static boolean	ensureRDFType(com.hp.hpl.jena.ontology.OntResource individual, com.hp.hpl.jena.rdf.model.Resource type, com.hp.hpl.jena.rdf.model.Model owlFullModel)
private void	ensureSuperclassesAreRDFSClasses(com.hp.hpl.jena.rdf.model.Model owlFullModel) Needed for pure RDF files that define subclasses of classes that are not imported.
private void	ensureSuperPropertiesAreRDFProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel) Needed for pure RDF files that define sub-properties of properties that are not imported.
private void	ensureSymmetricPropertiesAreOntProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)
private void	ensureTransitivePropertiesAreOntProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)
private com.hp.hpl.jena.graph.Graph	getHomeGraph(com.hp.hpl.jena.ontology.OntResource resource)
private boolean	hasValidPropertyType(com.hp.hpl.jena.rdf.model.Property property)
static Iterator	listAnonTopLevelClasses(com.hp.hpl.jena.ontology.OntModel m)
private static void	log(String message)
private void	mergeOntologies()
private void	removeRedundantDomains(Iterator it)
private static com.hp.hpl.jena.rdf.model.Resource	setResourceNamespace(com.hp.hpl.jena.rdf.model.Resource resource, String newNamespace)
static void	standardizePrefixes(com.hp.hpl.jena.ontology.OntModel ontModel)
static void	unifyNamespace(com.hp.hpl.jena.ontology.OntModel ontModel, String oldNamespace, String newNamespace)
private static void	unifyNamespaceOfIndividuals(com.hp.hpl.jena.ontology.OntModel ontModel, String oldNamespace, String newNamespace)
private static void	unifyNamespaceOfNamedClasses(com.hp.hpl.jena.ontology.OntModel ontModel, String oldNamespace, String newNamespace)
private static void	unifyNamespaceOfOntologies(com.hp.hpl.jena.ontology.OntModel ontModel, String oldNamespace, String newNamespace)
private static void	unifyNamespaceOfProperties(com.hp.hpl.jena.ontology.OntModel ontModel, String oldNamespace, String newNamespace)
private static void	unifyNamespaceOfResources(Iterator it, String oldNamespace, String newNamespace)
private static void	updateLoggingStatus()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logging

private static boolean logging

Indicates whether logging is turned on or not

LOGGING

private static String LOGGING

Set this to "true" in protege.properties to enable logging

ontModel

private com.hp.hpl.jena.ontology.OntModel ontModel

owlFullModel

private com.hp.hpl.jena.rdf.model.Model owlFullModel

Constructor Detail

JenaNormalizer

public JenaNormalizer(com.hp.hpl.jena.ontology.OntModel ontModel,
                      com.hp.hpl.jena.rdf.model.Model owlFullModel,
                      NamespaceManager namespaceManager)

Method Detail

createPrefixesForImports

private void createPrefixesForImports(com.hp.hpl.jena.ontology.OntModel ontModel,
                                      NamespaceManager nsm)

Makes sure that there is a prefix for all non-anonymous owl:Ontologies. Otherwise the system runs into problems with import statements

Parameters:

ontModel -

createImportURI

private String createImportURI(com.hp.hpl.jena.ontology.OntModel ontModel)

alignPrefixes

private void alignPrefixes(com.hp.hpl.jena.ontology.OntModel ontModel,
                           NamespaceManager nsm)

ensureDeprecatedClassesAreOntClasses

private void ensureDeprecatedClassesAreOntClasses(com.hp.hpl.jena.rdf.model.Model owlFullModel)

ensureDeprecatedPropertiesAreOntProperties

private void ensureDeprecatedPropertiesAreOntProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)

ensureFunctionalPropertiesAreOntProperties

private void ensureFunctionalPropertiesAreOntProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)

hasValidPropertyType

private boolean hasValidPropertyType(com.hp.hpl.jena.rdf.model.Property property)

ensureSuperclassesAreRDFSClasses

private void ensureSuperclassesAreRDFSClasses(com.hp.hpl.jena.rdf.model.Model owlFullModel)

Needed for pure RDF files that define subclasses of classes that are not imported. This method will make these superclasses rdfs:Classes.

Parameters:

owlFullModel - the Model to write the additional rdf:type triples to

ensureSuperPropertiesAreRDFProperties

private void ensureSuperPropertiesAreRDFProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)

Needed for pure RDF files that define sub-properties of properties that are not imported. This method will make these superclasses rdf:Property.

Parameters:

owlFullModel - the Model to write the additional rdf:type triples to

ensureSymmetricPropertiesAreOntProperties

private void ensureSymmetricPropertiesAreOntProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)

ensureTransitivePropertiesAreOntProperties

private void ensureTransitivePropertiesAreOntProperties(com.hp.hpl.jena.rdf.model.Model owlFullModel)

assignNamesToAnonymousIndividuals

private void assignNamesToAnonymousIndividuals(com.hp.hpl.jena.ontology.OntModel ontModel,
                                               String defaultNamespace)

assignNamesToAnonymousTopLevelClasses

private void assignNamesToAnonymousTopLevelClasses(com.hp.hpl.jena.ontology.OntModel ontModel,
                                                   String defaultNamespace)

assignRDFTypesToMetaclassInstances

public static void assignRDFTypesToMetaclassInstances(com.hp.hpl.jena.ontology.OntModel ontModel,
                                                      com.hp.hpl.jena.rdf.model.Model owlFullModel)

convertCyclicPropertyInheritance

private void convertCyclicPropertyInheritance()

convertCyclicPropertyInheritance

private void convertCyclicPropertyInheritance(com.hp.hpl.jena.util.iterator.ExtendedIterator it,
                                              List errors)

convertCyclicPropertyInheritance

private void convertCyclicPropertyInheritance(com.hp.hpl.jena.ontology.OntProperty start,
                                              com.hp.hpl.jena.ontology.OntProperty ontProperty,
                                              Set visited,
                                              Collection errors)

convertMultipleDomainsIntoIntersection

private void convertMultipleDomainsIntoIntersection(com.hp.hpl.jena.ontology.OntModel ontModel)

convertMultipleDomainsIntoIntersection

private void convertMultipleDomainsIntoIntersection(Iterator ontProperties)

convertMultipleRangesIntoIntersection

private void convertMultipleRangesIntoIntersection(com.hp.hpl.jena.ontology.OntModel ontModel)

convertMultipleRangesIntoIntersection

private void convertMultipleRangesIntoIntersection(Iterator ontProperties)

convertNamedClassExpressions

private void convertNamedClassExpressions()

createAllValuesFromRestriction

private com.hp.hpl.jena.ontology.AllValuesFromRestriction createAllValuesFromRestriction(com.hp.hpl.jena.ontology.AllValuesFromRestriction base)

createCardinalityRestriction

private com.hp.hpl.jena.ontology.CardinalityRestriction createCardinalityRestriction(com.hp.hpl.jena.ontology.CardinalityRestriction base)

createComplementClass

private com.hp.hpl.jena.ontology.ComplementClass createComplementClass(com.hp.hpl.jena.ontology.ComplementClass base)

createEnumeratedClass

private com.hp.hpl.jena.ontology.EnumeratedClass createEnumeratedClass(com.hp.hpl.jena.ontology.OntClass enumeratedClass)

createHasValueRestriction

private com.hp.hpl.jena.ontology.HasValueRestriction createHasValueRestriction(com.hp.hpl.jena.ontology.HasValueRestriction base)

createIntersectionClass

private com.hp.hpl.jena.ontology.IntersectionClass createIntersectionClass(com.hp.hpl.jena.ontology.IntersectionClass intersectionClass)

createMaxCardinalityRestriction

private com.hp.hpl.jena.ontology.MaxCardinalityRestriction createMaxCardinalityRestriction(com.hp.hpl.jena.ontology.MaxCardinalityRestriction base)

createMinCardinalityRestriction

private com.hp.hpl.jena.ontology.MinCardinalityRestriction createMinCardinalityRestriction(com.hp.hpl.jena.ontology.MinCardinalityRestriction base)

createRestriction

private com.hp.hpl.jena.ontology.Restriction createRestriction(com.hp.hpl.jena.ontology.Restriction restriction)

createSomeValuesFromRestriction

private com.hp.hpl.jena.ontology.SomeValuesFromRestriction createSomeValuesFromRestriction(com.hp.hpl.jena.ontology.SomeValuesFromRestriction base)

createUnionClass

private com.hp.hpl.jena.ontology.UnionClass createUnionClass(com.hp.hpl.jena.ontology.UnionClass unionClass)

ensureAnnotationPropertiesHaveRange

private void ensureAnnotationPropertiesHaveRange()

ensureRDFType

private static boolean ensureRDFType(com.hp.hpl.jena.ontology.OntResource individual,
                                     com.hp.hpl.jena.rdf.model.Resource type,
                                     com.hp.hpl.jena.rdf.model.Model owlFullModel)

getHomeGraph

private com.hp.hpl.jena.graph.Graph getHomeGraph(com.hp.hpl.jena.ontology.OntResource resource)

listAnonTopLevelClasses

public static Iterator listAnonTopLevelClasses(com.hp.hpl.jena.ontology.OntModel m)

log

private static void log(String message)

mergeOntologies

private void mergeOntologies()

removeRedundantDomains

private void removeRedundantDomains(Iterator it)

setResourceNamespace

private static com.hp.hpl.jena.rdf.model.Resource setResourceNamespace(com.hp.hpl.jena.rdf.model.Resource resource,
                                                                       String newNamespace)

standardizePrefixes

public static void standardizePrefixes(com.hp.hpl.jena.ontology.OntModel ontModel)

unifyNamespace

public static void unifyNamespace(com.hp.hpl.jena.ontology.OntModel ontModel,
                                  String oldNamespace,
                                  String newNamespace)

unifyNamespaceOfIndividuals

private static void unifyNamespaceOfIndividuals(com.hp.hpl.jena.ontology.OntModel ontModel,
                                                String oldNamespace,
                                                String newNamespace)

unifyNamespaceOfResources

private static void unifyNamespaceOfResources(Iterator it,
                                              String oldNamespace,
                                              String newNamespace)

unifyNamespaceOfNamedClasses

private static void unifyNamespaceOfNamedClasses(com.hp.hpl.jena.ontology.OntModel ontModel,
                                                 String oldNamespace,
                                                 String newNamespace)

unifyNamespaceOfOntologies

private static void unifyNamespaceOfOntologies(com.hp.hpl.jena.ontology.OntModel ontModel,
                                               String oldNamespace,
                                               String newNamespace)

unifyNamespaceOfProperties

private static void unifyNamespaceOfProperties(com.hp.hpl.jena.ontology.OntModel ontModel,
                                               String oldNamespace,
                                               String newNamespace)

updateLoggingStatus

private static void updateLoggingStatus()