Examples with FixedChangeListGenerator edu.stanford.bmir.protege.web.server.change.FixedChangeListGenerator used on opensource projects

Example 1 with FixedChangeListGenerator

use of edu.stanford.bmir.protege.web.server.change.FixedChangeListGenerator in project webprotege by protegeproject.

the class SetOntologyAnnotationsActionHandler method getChangeListGenerator.

@Override
protected ChangeListGenerator<Set<OWLAnnotation>> getChangeListGenerator(SetOntologyAnnotationsAction action, ExecutionContext executionContext) {
    final Set<PropertyAnnotationValue> fromAnnotations = action.getFromAnnotations();
    final Set<PropertyAnnotationValue> toAnnotations = action.getToAnnotations();
    List<OWLOntologyChange> changeList = new ArrayList<>();
    OWLDataFactory dataFactory = rootOntology.getOWLOntologyManager().getOWLDataFactory();
    for (PropertyAnnotationValue annotation : fromAnnotations) {
        if (!toAnnotations.contains(annotation)) {
            annotation.getValue().asAnnotationValue().ifPresent(av -> {
                changeList.add(new RemoveOntologyAnnotation(rootOntology, dataFactory.getOWLAnnotation(annotation.getProperty().getEntity().asOWLAnnotationProperty(), av)));
            });
        }
    }
    for (PropertyAnnotationValue annotation : toAnnotations) {
        if (!fromAnnotations.contains(annotation)) {
            annotation.getValue().asAnnotationValue().ifPresent(av -> {
                changeList.add(new AddOntologyAnnotation(rootOntology, dataFactory.getOWLAnnotation(annotation.getProperty().getEntity().asOWLAnnotationProperty(), av)));
            });
        }
    }
    return new FixedChangeListGenerator<Set<OWLAnnotation>>(changeList, Collections.emptySet(), "Edited ontology annotations") {

        @Override
        public Set<OWLAnnotation> getRenamedResult(Set<OWLAnnotation> result, RenameMap renameMap) {
            return super.getRenamedResult(result, renameMap);
        }
    };
}

Example 2 with FixedChangeListGenerator

use of edu.stanford.bmir.protege.web.server.change.FixedChangeListGenerator in project webprotege by protegeproject.

the class TermSynonymsManager method setSynonyms.

public void setSynonyms(@Nonnull UserId userId, @Nonnull OWLEntity term, @Nonnull Collection<OBOTermSynonym> synonyms) {
    List<OWLOntologyChange> changes = new ArrayList<>();
    rootOntology.getAnnotationAssertionAxioms(term.getIRI()).stream().filter(ax -> getSynonymScope(ax) != null).map(ax -> new RemoveAxiom(rootOntology, ax)).forEach(changes::add);
    for (OBOTermSynonym synonym : synonyms) {
        OWLAnnotationProperty synonymProperty = getSynonymAnnoationProperty(df, synonym.getScope());
        OWLLiteral synonymNameLiteral = df.getOWLLiteral(synonym.getName());
        Set<OWLAnnotation> synonymXRefs = synonym.getXRefs().stream().filter(x -> !x.isEmpty()).map(xRefConverter::toAnnotation).collect(Collectors.toSet());
        OWLAnnotationAssertionAxiom synonymAnnotationAssertion = df.getOWLAnnotationAssertionAxiom(synonymProperty, term.getIRI(), synonymNameLiteral, synonymXRefs);
        changes.add(new AddAxiom(rootOntology, synonymAnnotationAssertion));
    }
    if (!changes.isEmpty()) {
        changeManager.applyChanges(userId, new FixedChangeListGenerator<>(changes, term, "Edited term synonyms"));
    }
}