public String getDatasourceName() {
if (annotationProvenanceTemplate != null) {
return annotationProvenanceTemplate.getSource().getName();
} else {
return null;
}
}
@Override
public AnnotationProvenance getOrCreateAnnotationProvenance(
String annotator, Date annotationDate) {
if (annotationProvenanceCache != null) {
if (annotationProvenanceCache.getAnnotator() != null
&& annotationProvenanceCache.getAnnotator().equals(annotator)) {
if (annotationProvenanceCache.getAnnotationDate() != null
&& annotationProvenanceCache.getAnnotationDate().equals(annotationDate)) {
return annotationProvenanceCache;
}
}
}
annotationProvenanceCache =
annotationProvenanceTemplate
.annotatorIs(annotator)
.annotationDateIs(annotationDate)
.build();
return annotationProvenanceCache;
}
@Override
public Collection<Annotation> updatePreviousAnnotations(
Collection<Annotation> annotationsToUpdate, AnnotationUpdate update)
throws ZoomaUpdateException {
List<Annotation> annotationsList = new ArrayList<>(annotationsToUpdate);
Collections.sort(
annotationsList,
new Comparator<Annotation>() {
@Override
public int compare(Annotation o1, Annotation o2) {
return o1.getProvenance()
.getSource()
.getURI()
.compareTo(o2.getProvenance().getSource().getURI());
}
});
Collection<Annotation> newAnnotations = new HashSet<>();
try {
AnnotationSource currentSource = annotationsList.get(0).getProvenance().getSource();
getAnnotationFactory().acquire(currentSource);
for (Annotation previousAnnotation : annotationsList) {
if (!previousAnnotation
.getProvenance()
.getSource()
.getURI()
.equals(currentSource.getURI())) {
getAnnotationFactory().release();
currentSource = previousAnnotation.getProvenance().getSource();
getAnnotationFactory().acquire(currentSource);
}
Property newProperty;
if (update.getPropertyType() != null && update.getPropertyValue() != null) {
// both fields have changed
newProperty =
new SimpleTypedProperty(update.getPropertyType(), update.getPropertyValue());
} else if (update.getPropertyType() != null && update.getPropertyValue() == null) {
// if just the property type has changed
newProperty =
new SimpleTypedProperty(
update.getPropertyType(),
previousAnnotation.getAnnotatedProperty().getPropertyValue());
} else if (update.getPropertyValue() != null) {
// if just the property has changed, get the old property value
newProperty =
previousAnnotation.getAnnotatedProperty() instanceof TypedProperty
? new SimpleTypedProperty(
((TypedProperty) previousAnnotation.getAnnotatedProperty()).getPropertyType(),
update.getPropertyValue())
: new SimpleUntypedProperty(update.getPropertyValue());
} else {
// if both are null, use the old property as it is
newProperty = previousAnnotation.getAnnotatedProperty();
}
Collection<URI> semanticTags = new HashSet<>();
if (update.isRetainSemanticTags() && previousAnnotation.getSemanticTags() != null) {
semanticTags.addAll(previousAnnotation.getSemanticTags());
}
if (update.getSemanticTags() != null) {
semanticTags.addAll(update.getSemanticTags());
}
AnnotationProvenanceTemplate template =
getAnnotationFactory()
.getAnnotationLoadingSession()
.getAnnotationProvenanceTemplate()
.annotatorIs(ZoomaUsers.getAuthenticatedUser().getFullName())
.annotationDateIs(new Date());
Annotation newAnnotation =
getAnnotationFactory()
.createAnnotation(
previousAnnotation.getAnnotatedBiologicalEntities(),
newProperty,
template.build(),
semanticTags,
Collections.singleton(previousAnnotation.getURI()));
newAnnotations.add(newAnnotation);
crossLinkAnnotations(previousAnnotation, newAnnotation);
}
// save new and update old
try {
getAnnotationDAO().create(newAnnotations);
getAnnotationDAO().update(annotationsToUpdate);
} catch (ResourceAlreadyExistsException e) {
throw new ZoomaUpdateException(
"Couldn't create new annotation as the annotation URI already existed", e);
}
} catch (InterruptedException e) {
throw new ZoomaUpdateException("Update previous annotation operation was interrupted", e);
} catch (AnonymousUserNotAllowedException e) {
throw new ZoomaUpdateException("You must be authenticated to perform update operations", e);
} finally {
getAnnotationFactory().release();
}
return newAnnotations;
}
@Override
public Collection<Annotation> saveAnnotations(Collection<Annotation> annotations)
throws ZoomaUpdateException {
List<Annotation> annotationsList = new ArrayList<>(annotations);
Collections.sort(
annotationsList,
new Comparator<Annotation>() {
@Override
public int compare(Annotation o1, Annotation o2) {
return o1.getProvenance()
.getSource()
.getURI()
.compareTo(o2.getProvenance().getSource().getURI());
}
});
Collection<Annotation> newAnnotations = new HashSet<>();
Collection<Annotation> previousAnnotations = new HashSet<>();
try {
AnnotationSource currentSource = annotationsList.get(0).getProvenance().getSource();
getAnnotationFactory().acquire(currentSource);
for (Annotation annotation : annotationsList) {
if (!annotation.getProvenance().getSource().getURI().equals(currentSource.getURI())) {
getAnnotationFactory().release();
currentSource = annotation.getProvenance().getSource();
getAnnotationFactory().acquire(currentSource);
}
String username;
ZoomaUser user = ZoomaUsers.getAuthenticatedUser();
if (annotation.getProvenance().getAnnotator() != null) {
username = annotation.getProvenance().getAnnotator();
} else {
username = user.getFullName();
}
AnnotationProvenanceTemplate template =
getAnnotationFactory()
.getAnnotationLoadingSession()
.getAnnotationProvenanceTemplate()
.annotatorIs(username)
.annotationDateIs(new Date());
Annotation newAnnotation =
getAnnotationFactory()
.createAnnotation(
annotation.getAnnotatedBiologicalEntities(),
annotation.getAnnotatedProperty(),
template.build(),
annotation.getSemanticTags(),
annotation.getReplaces());
newAnnotations.add(newAnnotation);
for (URI previousAnnotationUri : annotation.getReplaces()) {
Annotation previousAnnotation = getAnnotationDAO().read(previousAnnotationUri);
crossLinkAnnotations(previousAnnotation, newAnnotation);
previousAnnotations.add(previousAnnotation);
}
}
// save new and update old
try {
getAnnotationDAO().create(newAnnotations);
getAnnotationDAO().update(previousAnnotations);
} catch (ResourceAlreadyExistsException e) {
throw new ZoomaUpdateException(
"Couldn't create new annotation as the annotation URI already existed", e);
}
} catch (InterruptedException e) {
throw new ZoomaUpdateException("Update previous annotation operation was interrupted", e);
} finally {
getAnnotationFactory().release();
}
return newAnnotations;
}