@Override public Stream<OWLAnnotationProperty> annotationPropertiesInSignature(Imports imports) { return withReadLock(() -> delegate.annotationPropertiesInSignature(imports)); }
@Override public Stream<OWLAnnotationProperty> annotationPropertiesInSignature(Imports imports) { return withReadLock(() -> delegate.annotationPropertiesInSignature(imports)); }
@Override public Stream<OWLAnnotationProperty> annotationPropertiesInSignature(Imports imports) { return withReadLock(() -> delegate.annotationPropertiesInSignature(imports)); }
@Override public Stream<OWLAnnotationProperty> annotationPropertiesInSignature(Imports imports) { return withReadLock(() -> delegate.annotationPropertiesInSignature(imports)); }
private void renameObjects(final OWLOntology o) { final OWLOntologyManager m = o.getOWLOntologyManager(); final OWLEntityRenamer renamer = new OWLEntityRenamer(m, Collections.singleton(o)); final Map<OWLEntity, IRI> entity2IRIMap = new HashMap<>(); final AtomicInteger ai = new AtomicInteger(); o.individualsInSignature().forEach(toRename -> entity2IRIMap.put(toRename, IRI.create("x:ind/" + ai.getAndIncrement()))); o.classesInSignature().forEach(toRename -> entity2IRIMap.put(toRename, IRI.create("x:cls/" + ai.getAndIncrement()))); o.annotationPropertiesInSignature().forEach(toRename -> entity2IRIMap.put(toRename, IRI.create("x:ap/" + ai.getAndIncrement()))); o.dataPropertiesInSignature().forEach(toRename -> entity2IRIMap.put(toRename, IRI.create("x:dp/" + ai.getAndIncrement()))); o.objectPropertiesInSignature().forEach(toRename -> entity2IRIMap.put(toRename, IRI.create("x:op/" + ai.getAndIncrement()))); o.applyChanges(renamer.changeIRI(entity2IRIMap)); }
@Override protected Set<OWLEntity> getEntitiesThatRequireNamespaces() { return asUnorderedSet( Stream.of( getOntology().axioms(AxiomType.OBJECT_PROPERTY_ASSERTION).flatMap( ax -> ax.getProperty().objectPropertiesInSignature()), getOntology().axioms(AxiomType.DATA_PROPERTY_ASSERTION) .map(ax -> ax.getProperty().asOWLDataProperty()), getOntology().annotationPropertiesInSignature(Imports.INCLUDED)).flatMap(x -> x)); }
@Override protected Set<OWLEntity> getEntitiesThatRequireNamespaces() { return asUnorderedSet( Stream.of( getOntology().axioms(AxiomType.OBJECT_PROPERTY_ASSERTION).flatMap( ax -> ax.getProperty().objectPropertiesInSignature()), getOntology().axioms(AxiomType.DATA_PROPERTY_ASSERTION) .map(ax -> ax.getProperty().asOWLDataProperty()), getOntology().annotationPropertiesInSignature(Imports.INCLUDED)).flatMap(x -> x)); }
@Override protected Set<OWLEntity> getEntitiesThatRequireNamespaces() { return asUnorderedSet( Stream.of( getOntology().axioms(AxiomType.OBJECT_PROPERTY_ASSERTION).flatMap( ax -> ax.getProperty().objectPropertiesInSignature()), getOntology().axioms(AxiomType.DATA_PROPERTY_ASSERTION) .map(ax -> ax.getProperty().asOWLDataProperty()), getOntology().annotationPropertiesInSignature(Imports.INCLUDED)).flatMap(x -> x)); }
@Override protected Set<OWLEntity> getEntitiesThatRequireNamespaces() { return asUnorderedSet( Stream.of( getOntology().axioms(AxiomType.OBJECT_PROPERTY_ASSERTION).flatMap( ax -> ax.getProperty().objectPropertiesInSignature()), getOntology().axioms(AxiomType.DATA_PROPERTY_ASSERTION) .map(ax -> ax.getProperty().asOWLDataProperty()), getOntology().annotationPropertiesInSignature(Imports.INCLUDED)).flatMap(x -> x)); }
@SuppressWarnings("null") protected AbstractMacroExpansionVisitor(OWLOntology o) { df = o.getOWLOntologyManager().getOWLDataFactory(); expandExpressionMap = new HashMap<>(); expandAssertionToMap = new HashMap<>(); OWLAnnotationProperty ap424 = df.getOWLAnnotationProperty(IRI_IAO_0000424.getIRI()); o.objectPropertiesInSignature() .forEach(p -> getAnnotationObjects(p, o.importsClosure(), ap424).forEach( a -> mapToExpand(p, a))); o.annotationPropertiesInSignature().forEach(p -> expandAssertions(o, p)); OIO_ISEXPANSION = df.getOWLAnnotationProperty( IRI.create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, "is_expansion")); expansionMarkerAnnotation = df.getOWLAnnotation(OIO_ISEXPANSION, df.getOWLLiteral(true)); }
@SuppressWarnings("null") protected AbstractMacroExpansionVisitor(OWLOntology o) { df = o.getOWLOntologyManager().getOWLDataFactory(); expandExpressionMap = new HashMap<>(); expandAssertionToMap = new HashMap<>(); OWLAnnotationProperty ap424 = df.getOWLAnnotationProperty(IRI_IAO_0000424.getIRI()); o.objectPropertiesInSignature() .forEach(p -> getAnnotationObjects(p, o.importsClosure(), ap424).forEach( a -> mapToExpand(p, a))); o.annotationPropertiesInSignature().forEach(p -> expandAssertions(o, p)); OIO_ISEXPANSION = df.getOWLAnnotationProperty( IRI.create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, "is_expansion")); expansionMarkerAnnotation = df.getOWLAnnotation(OIO_ISEXPANSION, df.getOWLLiteral(true)); }
@SuppressWarnings("null") protected AbstractMacroExpansionVisitor(OWLOntology o) { df = o.getOWLOntologyManager().getOWLDataFactory(); expandExpressionMap = new HashMap<>(); expandAssertionToMap = new HashMap<>(); OWLAnnotationProperty ap424 = df.getOWLAnnotationProperty(IRI_IAO_0000424.getIRI()); o.objectPropertiesInSignature() .forEach(p -> getAnnotationObjects(p, o.importsClosure(), ap424).forEach( a -> mapToExpand(p, a))); o.annotationPropertiesInSignature().forEach(p -> expandAssertions(o, p)); OIO_ISEXPANSION = df.getOWLAnnotationProperty( IRI.create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX, "is_expansion")); expansionMarkerAnnotation = df.getOWLAnnotation(OIO_ISEXPANSION, df.getOWLLiteral(true)); }
protected Set<OWLEntity> getEntitiesThatRequireNamespaces() { Set<OWLEntity> result = new HashSet<>(); add(result, ontology.classesInSignature()); add(result, ontology.objectPropertiesInSignature()); add(result, ontology.dataPropertiesInSignature()); add(result, ontology.individualsInSignature()); add(result, ontology.annotationPropertiesInSignature()); return result; }
protected Set<OWLEntity> getEntitiesThatRequireNamespaces() { Set<OWLEntity> result = new HashSet<>(); add(result, ontology.classesInSignature()); add(result, ontology.objectPropertiesInSignature()); add(result, ontology.dataPropertiesInSignature()); add(result, ontology.individualsInSignature()); add(result, ontology.annotationPropertiesInSignature()); return result; }
protected Set<OWLEntity> getEntitiesThatRequireNamespaces() { Set<OWLEntity> result = new HashSet<>(); add(result, ontology.classesInSignature()); add(result, ontology.objectPropertiesInSignature()); add(result, ontology.dataPropertiesInSignature()); add(result, ontology.individualsInSignature()); add(result, ontology.annotationPropertiesInSignature()); return result; }
protected Set<OWLEntity> getEntitiesThatRequireNamespaces() { Set<OWLEntity> result = new HashSet<>(); add(result, ontology.classesInSignature()); add(result, ontology.objectPropertiesInSignature()); add(result, ontology.dataPropertiesInSignature()); add(result, ontology.individualsInSignature()); add(result, ontology.annotationPropertiesInSignature()); return result; }
private void renderInOntologySignatureEntities(Collection<IRI> illegalPuns) { renderEntities(ontology.annotationPropertiesInSignature(), ANNOTATION_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.datatypesInSignature(), DATATYPES_BANNER_TEXT, illegalPuns); renderEntities(ontology.objectPropertiesInSignature(), OBJECT_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.dataPropertiesInSignature(), DATA_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.classesInSignature(), CLASSES_BANNER_TEXT, illegalPuns); renderEntities(ontology.individualsInSignature(), INDIVIDUALS_BANNER_TEXT, illegalPuns); }
private void renderInOntologySignatureEntities(Collection<IRI> illegalPuns) { renderEntities(ontology.annotationPropertiesInSignature(), ANNOTATION_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.datatypesInSignature(), DATATYPES_BANNER_TEXT, illegalPuns); renderEntities(ontology.objectPropertiesInSignature(), OBJECT_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.dataPropertiesInSignature(), DATA_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.classesInSignature(), CLASSES_BANNER_TEXT, illegalPuns); renderEntities(ontology.individualsInSignature(), INDIVIDUALS_BANNER_TEXT, illegalPuns); }
private void renderInOntologySignatureEntities(Collection<IRI> illegalPuns) { renderEntities(ontology.annotationPropertiesInSignature(), ANNOTATION_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.datatypesInSignature(), DATATYPES_BANNER_TEXT, illegalPuns); renderEntities(ontology.objectPropertiesInSignature(), OBJECT_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.dataPropertiesInSignature(), DATA_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.classesInSignature(), CLASSES_BANNER_TEXT, illegalPuns); renderEntities(ontology.individualsInSignature(), INDIVIDUALS_BANNER_TEXT, illegalPuns); }
private void renderInOntologySignatureEntities(Collection<IRI> illegalPuns) { renderEntities(ontology.annotationPropertiesInSignature(), ANNOTATION_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.datatypesInSignature(), DATATYPES_BANNER_TEXT, illegalPuns); renderEntities(ontology.objectPropertiesInSignature(), OBJECT_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.dataPropertiesInSignature(), DATA_PROPERTIES_BANNER_TEXT, illegalPuns); renderEntities(ontology.classesInSignature(), CLASSES_BANNER_TEXT, illegalPuns); renderEntities(ontology.individualsInSignature(), INDIVIDUALS_BANNER_TEXT, illegalPuns); }