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# Copyright (c) 2016. Mount Sinai School of Medicine
#
# 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.
"""
Manage local downloaded data.
"""
from __future__ import (
print_function,
division,
absolute_import,
)
import logging
import yaml
from os.path import join, exists
from pipes import quote
from os import environ
from collections import OrderedDict
from appdirs import user_data_dir
from pkg_resources import resource_string
ENVIRONMENT_VARIABLES = [
"MHCFLURRY_DATA_DIR",
"MHCFLURRY_DOWNLOADS_CURRENT_RELEASE",
"MHCFLURRY_DOWNLOADS_DIR",
]
_DOWNLOADS_DIR = None
_CURRENT_RELEASE = None
_METADATA = None
def get_downloads_dir():
"""
Return the path to local downloaded data
"""
return _DOWNLOADS_DIR
def get_current_release():
"""
Return the current downloaded data release
"""
return _CURRENT_RELEASE
def get_downloads_metadata():
"""
Return the contents of downloads.yml as a dict
"""
global _METADATA
if _METADATA is None:
_METADATA = yaml.load(resource_string(__name__, "downloads.yml"))
return _METADATA
def get_current_release_downloads():
"""
Return a dict of all available downloads in the current release.
The dict keys are the names of the downloads. The values are a dict
with entries:
downloaded : bool
Whether the download is currently available locally
metadata : dict
Info about the download from downloads.yml such as URL
"""
downloads = (
get_downloads_metadata()
['releases']
[get_current_release()]
['downloads'])
return OrderedDict(
(download["name"], {
'downloaded': exists(join(get_downloads_dir(), download["name"])),
'metadata': download,
}) for download in downloads
)
def get_path(download_name, filename='', test_exists=True):
"""
Get the local path to a file in a MHCflurry download
Parameters
-----------
download_name : string
filename : string
Relative path within the download to the file of interest
test_exists : boolean
If True (default) throw an error telling the user how to download the
data if the file does not exist
Returns
-----------
string giving local absolute path
"""
assert '/' not in download_name, "Invalid download: %s" % download_name
path = join(get_downloads_dir(), download_name, filename)
if test_exists and not exists(path):
raise RuntimeError(
"Missing MHCflurry downloadable file: %s. "
"To download this data, run:\n\tmhcflurry-downloads fetch %s\n"
"in a shell."
% (quote(path), download_name))
return path
def configure():
"""
Setup various global variables based on environment variables.
"""
global _DOWNLOADS_DIR
global _CURRENT_RELEASE
_CURRENT_RELEASE = None
_DOWNLOADS_DIR = environ.get("MHCFLURRY_DOWNLOADS_DIR")
if not _DOWNLOADS_DIR:
metadata = get_downloads_metadata()
_CURRENT_RELEASE = environ.get("MHCFLURRY_DOWNLOADS_CURRENT_RELEASE")
if not _CURRENT_RELEASE:
_CURRENT_RELEASE = metadata['current-release']
current_release_compatability = (
metadata["releases"][_CURRENT_RELEASE]["compatibility-version"])
current_compatability = metadata["current-compatibility-version"]
if current_release_compatability != current_compatability:
logging.warn(
"The specified downloads are not compatible with this version "
"of the MHCflurry codebase. Downloads: release %s, "
"compatability version: %d. Code compatability version: %d" % (
_CURRENT_RELEASE,
current_release_compatability,
current_compatability))
data_dir = environ.get("MHCFLURRY_DATA_DIR")
if not data_dir:
# increase the version every time we make a breaking change in
# how the data is organized. For changes to e.g. just model
# serialization, the downloads release numbers should be used.
data_dir = user_data_dir("mhcflurry", version="4")
_DOWNLOADS_DIR = join(data_dir, _CURRENT_RELEASE)
logging.debug("Configured MHCFLURRY_DOWNLOADS_DIR: %s" % _DOWNLOADS_DIR)
configure()