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org.protege.editor.owl.model.entity.CustomOWLEntityFactory Maven / Gradle / Ivy
package org.protege.editor.owl.model.entity;
/*
* Copyright (C) 2007, University of Manchester
*
*
*/
import org.protege.editor.owl.model.OWLModelManager;
import org.protege.editor.owl.model.annotation.EntityCreationMetadataPreferences;
import org.protege.editor.owl.model.annotation.EntityCreationMetadataPreferencesManager;
import org.protege.editor.owl.model.annotation.EntityCreationMetadataProvider;
import org.protege.editor.owl.model.annotation.PreferencesBasedEntityCreationMetadataProviderFactory;
import org.protege.editor.owl.model.user.OrcidPreferencesManager;
import org.protege.editor.owl.model.user.UserNamePreferencesManager;
import org.protege.editor.owl.model.user.UserPreferences;
import org.semanticweb.owlapi.model.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.*;
/**
* Author: drummond T getOWLEntity(OWLDataFactory factory, Class type, IRI iri) {
if (OWLClass.class.isAssignableFrom(type)){
return type.cast(factory.getOWLClass(iri));
}
else if (OWLObjectProperty.class.isAssignableFrom(type)){
return type.cast(factory.getOWLObjectProperty(iri));
}
else if (OWLDataProperty.class.isAssignableFrom(type)){
return type.cast(factory.getOWLDataProperty(iri));
}
else if (OWLNamedIndividual.class.isAssignableFrom(type)){
return type.cast(factory.getOWLNamedIndividual(iri));
}
else if (OWLAnnotationProperty.class.isAssignableFrom(type)){
return type.cast(factory.getOWLAnnotationProperty(iri));
}
else if (OWLDatatype.class.isAssignableFrom(type)){
return type.cast(factory.getOWLDatatype(iri));
}
throw new RuntimeException("Missing branch for entity type: " + type.getSimpleName());
}
public OWLEntityCreationSet createOWLClass(String shortName, IRI baseIRI) throws OWLEntityCreationException {
return createOWLEntity(OWLClass.class, shortName, baseIRI);
}
public OWLEntityCreationSet createOWLObjectProperty(String shortName, IRI baseURI) throws OWLEntityCreationException {
return createOWLEntity(OWLObjectProperty.class, shortName, baseURI);
}
public OWLEntityCreationSet createOWLDataProperty(String shortName, IRI baseURI) throws OWLEntityCreationException {
return createOWLEntity(OWLDataProperty.class, shortName, baseURI);
}
public OWLEntityCreationSet createOWLAnnotationProperty(String shortName, IRI baseURI) throws OWLEntityCreationException {
return createOWLEntity(OWLAnnotationProperty.class, shortName, baseURI);
}
public OWLEntityCreationSet createOWLIndividual(String shortName, IRI baseURI) throws OWLEntityCreationException {
return createOWLEntity(OWLNamedIndividual.class, shortName, baseURI);
}
public OWLEntityCreationSet createOWLDatatype(String shortName, IRI baseIRI) throws OWLEntityCreationException {
return createOWLEntity(OWLDatatype.class, shortName, baseIRI);
}
public OWLEntityCreationSet createOWLEntity(Class type, String shortName, IRI baseURI) throws OWLEntityCreationException {
try {
EntityNameInfo name = generateName(type, shortName, baseURI);
T entity = getOWLEntity(mngr.getOWLDataFactory(), type, name.getIri());
List changes = getChanges(entity, name);
return new OWLEntityCreationSet<>(entity, changes);
}
catch (URISyntaxException | AutoIDException e) {
throw new OWLEntityCreationException(e);
}
}
public OWLEntityCreationSet preview(Class type, String shortName, IRI base) throws OWLEntityCreationException {
// There is probably a better way round this.
if (getAutoIDGenerator() instanceof Revertable){
((Revertable)getAutoIDGenerator()).checkpoint();
}
try{
return createOWLEntity(type, shortName, base);
}
catch(OWLEntityCreationException e){
throw e;
}
finally{
if (getAutoIDGenerator() instanceof Revertable){
((Revertable)getAutoIDGenerator()).revert();
}
}
}
protected EntityNameInfo generateName(Class type, String shortName, IRI baseURI) throws AutoIDException, URISyntaxException, OWLEntityCreationException {
if (baseURI == null){
if (useDefaultBaseIRI() || mngr.getActiveOntology().getOntologyID().isAnonymous()){
baseURI = getDefaultBaseIRI();
}
else{
baseURI = mngr.getActiveOntology().getOntologyID().getOntologyIRI().get();
}
}
IRI iri;
String id = null;
if (isFragmentAutoGenerated()){
Set tried = new HashSet<>();
do{
id = getAutoIDGenerator().getNextID(type);
iri = createIRI(id, baseURI);
if (!tried.contains(iri)) {
tried.add(iri);
}
else {
throw new AutoIDException("Auto id generator ran out of new ids - fix this in the new entity preferences");
}
} while (isIRIAlreadyUsed(iri)); // don't pun unnecessarily
}
else {
iri = createIRI(shortName, baseURI);
if (isIRIAlreadyUsed(type, iri)){
throw new OWLEntityCreationException("Entity already exists: " + iri);
}
if (isGenerateIDLabel()){
id = getAutoIDGenerator().getNextID(type); // critical it is unique?
}
}
return new EntityNameInfo(iri, id, shortName);
}
protected List getChanges(T entity, EntityNameInfo name) {
List changes = new ArrayList<>();
if (isGenerateIDLabel() && name.getId() != null) {
changes.addAll(createLabel(entity, name.getId()));
}
if (isGenerateNameLabel() && name.getShortName() != null) {
changes.addAll(createLabel(entity, name.getShortName()));
}
OWLDataFactory df = mngr.getOWLDataFactory();
OWLAxiom ax = df.getOWLDeclarationAxiom(entity);
changes.add(new AddAxiom(mngr.getActiveOntology(), ax));
changes.addAll(getEntityCreationMetadataChanges(entity));
return changes;
}
private List getEntityCreationMetadataChanges(T entity) {
EntityCreationMetadataProvider metadataProvider = getEntityCreationMetadataProvider();
return metadataProvider.getEntityCreationMetadataChanges(entity, mngr.getActiveOntology(), mngr.getOWLDataFactory());
}
private EntityCreationMetadataProvider getEntityCreationMetadataProvider() {
PreferencesBasedEntityCreationMetadataProviderFactory factory = new PreferencesBasedEntityCreationMetadataProviderFactory(
mngr,
new UserNamePreferencesManager(UserPreferences.get()),
new OrcidPreferencesManager(UserPreferences.get()),
new EntityCreationMetadataPreferencesManager(EntityCreationMetadataPreferences.get())
);
return factory.getProvider();
}
protected IRI createIRI(String fragment, IRI baseIRI) throws URISyntaxException {
fragment = fragment.replace(" ", "_");
if (baseIRI == null){
if (useDefaultBaseIRI()){
baseIRI = EntityCreationPreferences.getDefaultBaseIRI();
}
else{
baseIRI = mngr.getActiveOntology().getOntologyID().getOntologyIRI().get();
}
}
String base = baseIRI.toString().replace(" ", "_");
if (!base.endsWith("#") && !base.endsWith("/")) {
base += EntityCreationPreferences.getDefaultSeparator();
}
return IRI.create(new URI(base + fragment));
}
private List createLabel(OWLEntity owlEntity, String value) {
LabelDescriptor descr = getLabelDescriptor();
IRI iri = descr.getIRI();
String lang = descr.getLanguage();
OWLDataFactory df = mngr.getOWLDataFactory();
OWLLiteral con = df.getOWLLiteral(value, lang);
OWLAnnotationProperty prop = df.getOWLAnnotationProperty(iri);
OWLAxiom ax = df.getOWLAnnotationAssertionAxiom(prop, owlEntity.getIRI(), con);
return Collections.singletonList(new AddAxiom(mngr.getActiveOntology(), ax));
}
private LabelDescriptor getLabelDescriptor() {
Class cls = EntityCreationPreferences.getLabelDescriptorClass();
if (labelDescriptor == null || !cls.equals(labelDescriptor.getClass())){
try {
labelDescriptor = cls.newInstance();
}
catch (InstantiationException | IllegalAccessException e) {
logger.error("Cannot create label descriptor", e);
}
}
return labelDescriptor;
}
private AutoIDGenerator getAutoIDGenerator() {
final Class prefAutoIDClass = EntityCreationPreferences.getAutoIDGeneratorClass();
if (autoIDGenerator == null || !prefAutoIDClass.equals(autoIDGenerator.getClass())){
try {
autoIDGenerator = prefAutoIDClass.newInstance();
}
catch (InstantiationException | IllegalAccessException e) {
logger.error("Cannot create auto ID generator", e);
}
}
return autoIDGenerator;
}
private boolean isIRIAlreadyUsed(Class type, IRI iri) {
for (OWLOntology ont : mngr.getActiveOntologies()){
if ((OWLClass.class.isAssignableFrom(type) && ont.containsClassInSignature(iri)) ||
(OWLObjectProperty.class.isAssignableFrom(type) && ont.containsObjectPropertyInSignature(iri)) ||
(OWLDataProperty.class.isAssignableFrom(type) && ont.containsDataPropertyInSignature(iri)) ||
(OWLIndividual.class.isAssignableFrom(type) && ont.containsIndividualInSignature(iri)) ||
(OWLAnnotationProperty.class.isAssignableFrom(type) && ont.containsAnnotationPropertyInSignature(iri)) ||
(OWLDatatype.class.isAssignableFrom(type) && ont.containsDatatypeInSignature(iri))){
return true;
}
}
return false;
}
private boolean isIRIAlreadyUsed(IRI iri) {
for (OWLOntology ont : mngr.getOntologies()){
if (ont.containsEntityInSignature(iri)){
return true;
}
}
return false;
}
protected boolean useDefaultBaseIRI() {
return EntityCreationPreferences.useDefaultBaseIRI();
}
protected boolean isFragmentAutoGenerated() {
return EntityCreationPreferences.isFragmentAutoGenerated();
}
protected boolean isGenerateNameLabel() {
return EntityCreationPreferences.isGenerateNameLabel();
}
protected boolean isGenerateIDLabel() {
return EntityCreationPreferences.isGenerateIDLabel();
}
protected IRI getDefaultBaseIRI() {
return EntityCreationPreferences.getDefaultBaseIRI();
}
public static class EntityNameInfo {
private IRI iri;
private String id;
private String shortName;
public EntityNameInfo(IRI iri, String id, String shortName) {
this.iri = iri;
this.id = id;
this.shortName = shortName;
}
public IRI getIri() {
return iri;
}
public String getId() {
return id;
}
public String getShortName() {
return shortName;
}
}
}
