mirror of
https://github.com/Novartis/cellxgene-gateway.git
synced 2026-09-23 19:58:12 +08:00
Alok Saldanha
c03098af17
Due to issue with opening annotation files with "-" in the name, this doesn't quite work.
59 lines
2.1 KiB
Python
59 lines
2.1 KiB
Python
# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
|
|
# under the Apache License, Version 2.0 (the "License"); you may not use
|
|
# this file except in compliance with the License. You may obtain a copy
|
|
# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
|
|
# required by applicable law or agreed to in writing, software distributed
|
|
# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
|
|
# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
|
|
# the specific language governing permissions and limitations under the License.
|
|
|
|
import os
|
|
|
|
from flask_api import status
|
|
|
|
from cellxgene_gateway import env
|
|
from cellxgene_gateway.cellxgene_exception import CellxgeneException
|
|
|
|
|
|
def is_subdir(full_path, parent_path):
|
|
subdir = os.path.realpath(full_path)
|
|
parent = os.path.realpath(parent_path)
|
|
return subdir.startswith(parent)
|
|
|
|
|
|
def create_dir(parent_path, dir_name):
|
|
full_path = os.path.join(parent_path, dir_name)
|
|
|
|
if "/" in dir_name:
|
|
raise CellxgeneException(
|
|
"Please have no slashes in the intended directory.",
|
|
status.HTTP_400_BAD_REQUEST,
|
|
)
|
|
elif not os.path.exists(parent_path):
|
|
raise CellxgeneException(
|
|
"The selected User directory does not exist.",
|
|
status.HTTP_400_BAD_REQUEST,
|
|
)
|
|
elif os.path.exists(full_path):
|
|
raise CellxgeneException(
|
|
"The provided subdirectory already exists within Directory.",
|
|
status.HTTP_400_BAD_REQUEST,
|
|
)
|
|
elif not is_subdir(full_path, parent_path):
|
|
raise CellxgeneException(
|
|
"The directory must be a subdirectory of the parent path.",
|
|
status.HTTP_400_BAD_REQUEST,
|
|
)
|
|
elif not os.path.isdir(parent_path):
|
|
raise CellxgeneException(
|
|
"The parent is not a directory.", status.HTTP_400_BAD_REQUEST
|
|
)
|
|
else:
|
|
os.mkdir(full_path)
|
|
|
|
annotations_suffix = '_annotations'
|
|
def make_h5ad(el):
|
|
return el[:-len(annotations_suffix)]+'.h5ad'
|
|
def make_annotations(el):
|
|
return el[:-5]+annotations_suffix
|