def get_tag_to_uuid(dataset: str,
annotation_type: str,
tag: str,
user: User = Depends(get_user)):
""" Returns the corresponding dvid UUID of the given tag for the given scope.
Returns:
A string of the uuid corresponding to the tag, e.g., "74ea83"
"""
if not user.can_read(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to read annotations on dataset {dataset}")
tag_to_uuid = cache.get_value(collection_path=[CLIO_ANNOTATIONS_GLOBAL],
document='metadata',
path=['neurons', 'VNC', 'tag_to_uuid'])
if not tag_to_uuid:
raise HTTPException(
status_code=404,
detail=
f"Could not find any tag_to_uuid for annotation type {annotation_type} in dataset {dataset}"
)
if tag not in tag_to_uuid:
raise HTTPException(
status_code=404,
detail=
f"Could not find tag {tag} for annotation type {annotation_type} in dataset {dataset}"
)
return tag_to_uuid[tag]
def get_uuid_to_tag(dataset: str,
annotation_type: str,
uuid: str,
user: User = Depends(get_user)):
""" Returns the corresponding string tag for the given dvid UUID for the given scope.
Returns:
A string of the tag corresponding to the uuid, e.g., "v0.3.32"
"""
if not user.can_read(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to read annotations on dataset {dataset}")
uuid_to_tag = cache.get_value(collection_path=[CLIO_ANNOTATIONS_GLOBAL],
document='metadata',
path=['neurons', 'VNC', 'uuid_to_tag'])
if not uuid_to_tag:
raise HTTPException(
status_code=404,
detail=
f"Could not find any uuid_to_tag for annotation type {annotation_type} in dataset {dataset}"
)
found_tag = None
num_found = 0
for stored_uuid in uuid_to_tag:
if len(stored_uuid) < len(uuid) and uuid.startswith(stored_uuid):
num_found += 1
found_tag = uuid_to_tag[stored_uuid]
if len(stored_uuid) >= len(uuid) and stored_uuid.startswith(uuid):
num_found += 1
found_tag = uuid_to_tag[stored_uuid]
if num_found > 1:
raise HTTPException(
status_code=400,
detail=
f"uuid {uuid} is ambiguous because more than one hit for annotation type {annotation_type} in dataset {dataset}"
)
if not found_tag:
raise HTTPException(
status_code=404,
detail=
f"Could not find uuid {uuid} for annotation type {annotation_type} in dataset {dataset}"
)
return found_tag
def write_annotation(collection, data: dict, replace: bool, id_field: str,
conditional: List[str], version: str, user: User):
""" Write annotation transactionally, modifying HEAD and archiving old annotation """
if not id_field in data:
raise HTTPException(
status_code=400,
detail=
f'the id field "{id_field}" must be included in every annotation: {data}'
)
id = data[id_field]
head_key = f'id{id}'
data["_timestamp"] = time.time()
data["_user"] = user.email
new_fields = False
fields = cache.get_value(collection_path=[CLIO_ANNOTATIONS_GLOBAL],
document='metadata',
path=['neurons', 'VNC', 'fields'])
for cur_field in data:
if not cur_field.startswith('_'):
if cur_field not in fields:
fields.append(cur_field)
new_fields = True
if new_fields:
cache.set_value(collection_path=[CLIO_ANNOTATIONS_GLOBAL],
document='metadata',
value=fields,
path=['neurons', 'VNC', 'fields'])
try:
transaction = firestore.db.transaction()
head_ref = collection.document(head_key)
archived_ref = collection.document()
update_in_transaction(transaction, head_ref, archived_ref, data,
conditional, version, replace)
except Exception as e:
print(e)
raise HTTPException(
status_code=400,
detail=
f"error in writing annotation to version {version}: {e}\n Data: {data}"
)
def get_head_uuid(dataset: str,
annotation_type: str,
user: User = Depends(get_user)):
""" Returns the head version uuid for the given scope.
Returns:
A string of the HEAD version uuid, e.g., "74ea83"
"""
if not user.can_read(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to read annotations on dataset {dataset}")
head_uuid = cache.get_value(collection_path=[CLIO_ANNOTATIONS_GLOBAL],
document='metadata',
path=['neurons', 'VNC', 'head_uuid'])
if not head_uuid:
raise HTTPException(
status_code=404,
detail=
f"Could not find any head_uuid for annotation type {annotation_type} in dataset {dataset}"
)
return head_uuid
def get_versions(dataset: str,
annotation_type: str,
user: User = Depends(get_user)):
""" Returns the versions for the given scope.
Returns:
A dict with tag keys and corresponding dvid UUIDs as value.
"""
if not user.can_read(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to read annotations on dataset {dataset}")
tag_to_uuid = cache.get_value(collection_path=[CLIO_ANNOTATIONS_GLOBAL],
document='metadata',
path=['neurons', 'VNC', 'tag_to_uuid'])
if not tag_to_uuid:
raise HTTPException(
status_code=404,
detail=
f"Could not find any tag_to_uuid for annotation type {annotation_type} in dataset {dataset}"
)
return tag_to_uuid
def get_fields(dataset: str,
annotation_type: str,
user: User = Depends(get_user)):
""" Returns all fields within annotations for the given scope.
Returns:
A JSON list of the fields present in at least one annotation.
"""
if not user.can_read(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to read annotations on dataset {dataset}")
fields = cache.get_value(collection_path=[CLIO_ANNOTATIONS_GLOBAL],
document='metadata',
path=['neurons', 'VNC', 'fields'])
if not fields:
raise HTTPException(
status_code=404,
detail=
f"Could not find any fields for annotation type {annotation_type} in dataset {dataset}"
)
return fields