def delete_atlas(dataset: str,
x: int,
y: int,
z: int,
user: User = Depends(get_user)):
if not user.can_write_own(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to delete annotations in dataset {dataset}")
try:
# delete only supported from interface
# (delete by dataset + user name + xyz)
collection = firestore.get_collection(
[CLIO_ANNOTATIONS, "ATLAS", "annotations"])
match_list = collection.where("user", "==", user.email).where(
"locationkey", "==", f"{x}_{y}_{z}").where("dataset", "==",
dataset).get()
for match in match_list:
match.reference.delete()
except Exception as e:
print(e)
raise HTTPException(
status_code=400,
detail=
f"error in deleting annotation ({x},{y},{z}) for dataset {dataset}"
)
def delete_annotation(dataset: str,
key: str,
user_email: str = "",
user: User = Depends(get_user)):
""" Delete an annotation based on the key supplied in the URL. If the client has proper authorization,
annotations for another user can be deleted by supplying the query string '[email protected]'.
"""
if user_email == "":
user_email = user.email
authorized = (user_email == user.email and user.can_write_own(dataset)) or \
(user_email != user.email and user.can_write_others(dataset))
if not authorized:
raise HTTPException(
status_code=401,
detail=
f"no permission to delete annotation for user {user_email} on dataset {dataset}"
)
try:
collection = firestore.get_collection(
[CLIO_ANNOTATIONS_V2, dataset, user_email])
collection.document(key).delete()
except Exception as e:
print(e)
raise HTTPException(
status_code=400,
detail=
f"error in deleting annotation with key {key} for dataset {dataset}"
)
def write_annotation(dataset: str,
annotation: Annotation,
user: User,
move_key: str = "") -> str:
if annotation.user is None:
annotation.user = user.email
authorized = (annotation.user == user.email and user.can_write_own(dataset)) or \
(annotation.user != user.email and user.can_write_others(dataset))
if not authorized:
raise HTTPException(
status_code=401,
detail=
f"no permission to add annotation for user {annotation.user} on dataset {dataset}"
)
try:
collection = firestore.get_collection(
[CLIO_ANNOTATIONS_V2, dataset, annotation.user])
annotation_json = jsonable_encoder(annotation, exclude_unset=True)
key = annotation.key()
collection.document(key).set(annotation_json)
if move_key != "" and move_key != key:
collection.document(move_key).delete()
return key
except Exception as e:
print(e)
raise HTTPException(
status_code=400,
detail=f"error in put annotation for dataset {dataset}")
def submit_subvol(dataset: str, payload: dict, user: User = Depends(get_user)):
"""
Stores reference to an edited neuroglancer subvolume.
"""
if not user.can_write_own(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to submit subvolume in dataset {dataset}")
try:
payload["_timestamp"] = time.time()
collection = firestore.get_collection(
[CLIO_SUBVOL, user.email, "submissions"])
collection.document().set(payload)
except Exception as e:
print(e)
raise HTTPException(
status_code=400,
detail=f"error submitting subvolume for dataset {dataset}: {e}")
def edit_subvol(dataset: str,
subvol: SubVolume,
user: User = Depends(get_user)):
"""
Creates a neuroglancer precomputed subvolume cutout given bounding box. Returns
python script that can be downloaded and used to open and then submit change to Clio store.
"""
if not user.can_read(dataset) or not user.can_write_own(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to edit subvolume in dataset {dataset}")
try:
dataset_obj = get_dataset(dataset)
# cv = CloudVolume(dataset_obj.location)
# vol_dest = subvol.destination(user.email)
# vol_bounds = subvol.bbox()
# cv.transfer_to(vol_dest, vol_bounds)
except Exception as e:
print(e)
raise HTTPException(
status_code=400,
detail=f"error editing subvolume for dataset {dataset}: {e}")
def post_atlas(dataset: str,
x: int,
y: int,
z: int,
payload: dict,
user: User = Depends(get_user)) -> dict:
if "title" not in payload or "user" not in payload:
raise HTTPException(
status_code=400,
detail=f"POSTed object must include 'title' and 'user' properties")
if not user.can_write_own(dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to write annotations in dataset {dataset}")
if payload["user"] != user.email and not user.can_write_others(dataset):
raise HTTPException(
status_code=401,
detail=
f"no permission to write others' annotations in dataset {dataset}")
if "verified" in payload and payload["verified"] and not user.has_role(
"clio_write", dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to set verified status in dataset {dataset}"
)
try:
location_key = f"{x}_{y}_{z}"
collection = firestore.get_collection(
[CLIO_ANNOTATIONS, "ATLAS", "annotations"])
annotations = collection.where("user", "==", payload["user"]) \
.where("dataset", "==", dataset) \
.where("locationkey", "==", f"{x}_{y}_{z}").get()
payload["timestamp"] = time.time()
payload["dataset"] = dataset
payload["location"] = [x, y, z]
payload["locationkey"] = location_key
if len(annotations) == 0:
new_ref = collection.document()
payload["id"] = new_ref.id
if "verified" in payload:
if payload["verified"] and not user.has_role(
"clio_write", dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to set verified atlas pt")
else:
payload["verified"] = False
new_ref.set(payload)
else:
first = True
for annotation in annotations:
if first:
current = annotation.to_dict()
if "verified" in current and current[
"verified"] and not user.has_role(
"clio_write", dataset):
raise HTTPException(
status_code=401,
detail=f"no permission to modify verified atlas pt"
)
payload["id"] = annotation.id
annotation.reference.set(payload)
first = False
else: # shouldn't happen unless legacy bad points.
print(
f"deleted duplicate atlas annotation point: {annotation}"
)
annotation.reference.delete()
return payload
except HTTPException as e:
raise e
except Exception as e:
print(e)
raise HTTPException(
status_code=400,
detail=
f"error in put annotation ({x},{y},{z}) for dataset {dataset}: {e}"
)