def get_target_list(self, annotation):
target_list = annotation.get_targets_info()
deeper_targets = []
for target in target_list:
if self.is_annotation(target):
if target["id"] == annotation.id:
raise AnnotationError(
message="Annotation cannot target itself")
if self.is_deleted(target["id"]):
continue
target_annotation = self.get_annotation_es(target['id'],
params={
"username":
None,
"action":
"traverse"
})
deeper_targets += self.get_target_list(
Annotation(target_annotation))
target_ids = [target["id"] for target in target_list]
for target in deeper_targets:
if target not in target_ids:
target_list += [target]
target_ids += [target["id"]]
return target_list
def add_annotation_to_collection_es(self, annotation_id, collection_id,
params):
# check that user is allowed to edit collection
collection = self.get_from_index_if_allowed(
collection_id,
username=params["username"],
action="edit",
annotation_type="AnnotationCollection")
# check if collection contains annotation
if collection.has_annotation(annotation_id):
raise AnnotationError(
message="Collection already contains this annotation")
# check that user is allowed to see annotation
self.get_from_index_if_allowed(annotation_id,
username=params["username"],
action="see",
annotation_type="Annotation")
# add annotation
collection.add_annotation(annotation_id)
# add permissions for access (see) and update (edit)
permissions.add_permissions(collection, params)
self.update_in_index(collection.to_json(), "AnnotationCollection")
# set index needs refresh before next GET
self.set_index_needs_refresh()
# return collection metadata
return collection.to_clean_json(params)
def remove_annotation(self, annotation_id):
try:
self.items.remove(annotation_id)
except ValueError:
raise AnnotationError(
message=
"Annotation Collection does not contain annotation with id %s"
% (annotation_id))
self.modified = datetime.datetime.now(pytz.utc).isoformat()
def should_not_exist(self, annotation_id, annotation_type="_all"):
if self.es.exists(index=self.es_index,
doc_type=annotation_type,
id=annotation_id):
raise AnnotationError(
message="Annotation with id %s already exists" %
(annotation_id))
else:
return True
def should_exist(self, annotation_id, annotation_type="_all"):
if self.es.exists(index=self.es_index,
doc_type=annotation_type,
id=annotation_id):
if not self.is_deleted(annotation_id, annotation_type):
return True
raise AnnotationError(message="Annotation with id %s does not exist" %
(annotation_id),
status_code=404)
def should_have_target_list(self, annotation):
if "status" in annotation and annotation["status"] == "deleted":
return False
if annotation["type"] == "AnnotationCollection":
return False
if "target_list" not in annotation or not annotation["target_list"]:
raise AnnotationError(message="{t} should have target list".format(
t=annotation["type"]))
return True
def set_container_content(self, data, total):
data_json = self.make_json(data)
if self.is_annotation_collection(data_json):
self.items = data_json["items"]
self.generate_metadata_from_collection(data_json)
elif self.is_annotation_list(data_json):
self.items = data_json
self.generate_metadata_from_annotations(data_json, total)
else:
raise AnnotationError(message="data should be an AnnotationCollection or a list of Annotations")
def make_json(self, data):
if isinstance(data, AnnotationCollection):
return data.to_json()
if isinstance(data, Annotation):
return data.data
elif isinstance(data, list):
return [self.make_json(item) for item in data]
elif isinstance(data, dict) and "type" in data:
return data
else:
raise AnnotationError(message="data should be an AnnotationCollection or a list of Annotations")
def set_view(self, view):
if view == "PreferMinimalContainer":
self.view = self.viewMinimalContainer
self.iris=1
elif view == "PreferContainedIRIs":
self.view = self.viewContainedIRIs
self.iris=1
elif view == "PreferContainedDescriptions":
self.view = self.viewContainedDescriptions
self.iris=0
else:
raise AnnotationError(message="%s is not a valid container option. Value MUST be one of PreferMinimalContainer, PreferContainedIRIs, PreferContainedDescriptions" % (view))
self.base_url = self.update_url(self.base_url, {"iris": self.iris})
def update_chained_annotations(self, annotation_id):
# first refresh the index
self.es.indices.refresh(index=self.es_index)
chain_annotations = self.get_from_index_by_target(
{"id": annotation_id})
for chain_annotation in chain_annotations:
if chain_annotation["id"] == annotation_id:
raise AnnotationError(
message="Annotation cannot target itself")
chain_annotation["target_list"] = self.get_target_list(
Annotation(chain_annotation))
# don't use permission parameters for chained annotations
self.update_annotation_es(chain_annotation,
params={
"username": None,
"action": "traverse"
})
def remove_annotation_from_collection_es(self, annotation_id,
collection_id, params):
# check that user is allowed to edit collection
collection = self.get_from_index_if_allowed(
collection_id,
username=params["username"],
action="edit",
annotation_type="AnnotationCollection")
# check if collection contains annotation
if not collection.has_annotation(annotation_id):
raise AnnotationError(
message="Collection doesn't contain this annotation")
# check that user is allowed to see annotation
self.get_from_index_if_allowed(annotation_id,
username=params["username"],
action="see",
annotation_type="Annotation")
# remove annotation
collection.remove_annotation(annotation_id)
self.update_in_index(collection.to_json(), "AnnotationCollection")
# return collection metadata
return collection.to_json()
def view_page(self, page=0):
if not isinstance(page, int) or page < 0:
raise AnnotationError(message="Parameter page must be non-negative integer")
return self.generate_page_metadata(page)
def set_page_size(self, page_size):
if type(page_size) != int or page_size < 1:
raise AnnotationError(message='page_size must be a positive integer value')
self.page_size = page_size