def post(self, aligned_volume_name: str):
"""Create a new annotation table"""
check_aligned_volume(aligned_volume_name)
data = request.parsed_obj
db = get_db(aligned_volume_name)
metadata_dict = data.get("metadata")
logging.info(metadata_dict)
description = metadata_dict.get("description")
if metadata_dict.get("user_id", None) is None:
metadata_dict["user_id"] = str(g.auth_user["id"])
if description is None:
msg = "Table description required"
abort(404, msg)
else:
table_name = data.get("table_name")
headers = None
if not table_name.islower():
headers = {
"Warning":
f'201 - "Table name "{table_name}" needs to be lower case. Table will be posted to the database as "{table_name.lower()}"'
}
table_name = table_name.lower()
schema_type = data.get("schema_type")
table_name = table_name.lower().replace(" ", "_")
try:
table_info = db.create_annotation_table(
table_name, schema_type, **metadata_dict)
except (TableAlreadyExists):
abort(400, f"Table {table_name} already exists")
return Response(table_info, headers=headers)
def delete(self, aligned_volume_name: str, table_name: str, **kwargs):
"""Delete annotations"""
check_aligned_volume(aligned_volume_name)
db = get_db(aligned_volume_name)
metadata = db.get_table_metadata(table_name)
if metadata["user_id"] != str(g.auth_user["id"]):
resp = Response("Unauthorized: You did not create this table", 401)
return resp
data = request.parsed_obj
ids = data.get("annotation_ids")
db = get_db(aligned_volume_name)
deleted_ids = db.delete_annotation(table_name, ids)
if deleted_ids is None:
return f"annotation_id {ids} not in table {table_name}", 404
return deleted_ids, 200
def get(self, aligned_volume_name: str, table_name: str, **kwargs):
"""Get annotations by list of IDs"""
check_aligned_volume(aligned_volume_name)
args = annotation_parser.parse_args()
annotation_ids = args["annotation_ids"]
db = get_db(aligned_volume_name)
annotations = db.get_annotations(table_name, annotation_ids)
if annotations is None:
msg = f"annotation_id {annotation_ids} not in {table_name}"
abort(404, msg)
return annotations, 200
def put(self, aligned_volume_name: str, table_name: str, **kwargs):
"""Update annotations"""
check_aligned_volume(aligned_volume_name)
db = get_db(aligned_volume_name)
metadata = db.get_table_metadata(table_name)
if metadata["user_id"] != str(g.auth_user["id"]):
resp = Response("Unauthorized: You did not create this table", 401)
return resp
data = request.parsed_obj
annotations = data.get("annotations")
new_ids = []
for annotation in annotations:
updated_id = db.update_annotation(table_name, annotation)
new_ids.append(updated_id)
return new_ids, 200
def post(self, aligned_volume_name: str, table_name: str, **kwargs):
"""Insert annotations"""
check_aligned_volume(aligned_volume_name)
db = get_db(aligned_volume_name)
metadata = db.get_table_metadata(table_name)
if metadata["user_id"] != str(g.auth_user["id"]):
resp = Response("Unauthorized: You did not create this table", 401)
return resp
data = request.parsed_obj
annotations = data.get("annotations")
try:
inserted_ids = db.insert_annotations(table_name, annotations)
except AnnotationInsertLimitExceeded as limit_error:
logging.error(f"INSERT LIMIT EXCEEDED {limit_error}")
abort(413, limit_error)
except Exception as error:
logging.error(f"INSERT FAILED {annotations}")
abort(404, error)
return inserted_ids, 200
def get(self, aligned_volume_name: str, table_name: str) -> int:
"""Get count of rows of an annotation table"""
check_aligned_volume(aligned_volume_name)
db = get_db(aligned_volume_name)
return db.get_annotation_table_size(table_name), 200
def delete(self, aligned_volume_name: str, table_name: str) -> bool:
"""Delete an annotation table (marks for deletion, will suspend materialization, admin only)"""
check_aligned_volume(aligned_volume_name)
db = get_db(aligned_volume_name)
is_deleted = db.delete_table(table_name)
return is_deleted, 200
def get(self, aligned_volume_name: str,
table_name: str) -> FullMetadataSchema:
"""Get metadata for a given table"""
check_aligned_volume(aligned_volume_name)
db = get_db(aligned_volume_name)
return db.get_table_metadata(table_name), 200
def get(self, aligned_volume_name: str):
"""Get list of annotation tables for a aligned_volume"""
check_aligned_volume(aligned_volume_name)
db = get_db(aligned_volume_name)
tables = db._get_existing_table_names()
return tables, 200
def test_create_db(app_config, mocker):
with app_config.app_context():
db = get_db("test_aligned_volume")
logging.info(db.__dict__)
assert db.__dict__["aligned_volume"] == "test_aligned_volume"