diff --git a/cellxgene_gateway/dir_util.py b/cellxgene_gateway/dir_util.py index 84aa9b0..4358376 100644 --- a/cellxgene_gateway/dir_util.py +++ b/cellxgene_gateway/dir_util.py @@ -14,44 +14,6 @@ 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" h5ad_suffix = ".h5ad" diff --git a/cellxgene_gateway/gateway.py b/cellxgene_gateway/gateway.py index 56620fb..bcb68bb 100644 --- a/cellxgene_gateway/gateway.py +++ b/cellxgene_gateway/gateway.py @@ -31,7 +31,6 @@ from cellxgene_gateway.backend_cache import BackendCache from cellxgene_gateway.cache_entry import CacheEntryStatus from cellxgene_gateway.cache_key import CacheKey from cellxgene_gateway.cellxgene_exception import CellxgeneException -from cellxgene_gateway.dir_util import create_dir, is_subdir from cellxgene_gateway.extra_scripts import get_extra_scripts from cellxgene_gateway.filecrawl import render_item_source from cellxgene_gateway.process_exception import ProcessException diff --git a/cellxgene_gateway/path_util.py b/cellxgene_gateway/path_util.py deleted file mode 100644 index 42ded92..0000000 --- a/cellxgene_gateway/path_util.py +++ /dev/null @@ -1,41 +0,0 @@ -# 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.cache_key import CacheKey -from cellxgene_gateway.cellxgene_exception import CellxgeneException -from cellxgene_gateway.dir_util import make_h5ad - - -def validate_exists(file_path): - if not os.path.exists(file_path): - raise CellxgeneException( - "File does not exist: " + file_path, status.HTTP_400_BAD_REQUEST - ) - - -def validate_is_file(file_path): - validate_exists(file_path) - if not os.path.isfile(file_path): - raise CellxgeneException( - "Path is not file: " + file_path, status.HTTP_400_BAD_REQUEST - ) - return - - -def validate_is_dir(file_path): - validate_exists(file_path) - if not os.path.isdir(file_path): - raise CellxgeneException( - "Path is not dir: " + file_path, status.HTTP_400_BAD_REQUEST - ) - return