[1fc74a]: / BioSeqNet / resnest / utils.py

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##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
## Created by: Hang Zhang
## Email: zhanghang0704@gmail.com
## Copyright (c) 2020
##
## LICENSE file in the root directory of this source tree
##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
import os
from pathlib import Path
import requests
import errno
import shutil
import hashlib
import zipfile
import logging
from tqdm import tqdm
logger = logging.getLogger(__name__)
__all__ = ['unzip', 'download', 'mkdir', 'check_sha1', 'raise_num_file']
def unzip(zip_file_path, root=os.path.expanduser('./')):
"""Unzips files located at `zip_file_path` into parent directory specified by `root`.
"""
folders = []
with zipfile.ZipFile(zip_file_path) as zf:
zf.extractall(root)
for name in zf.namelist():
folder = Path(name).parts[0]
if folder not in folders:
folders.append(folder)
folders = folders[0] if len(folders) == 1 else tuple(folders)
return folders
def download(url, path=None, overwrite=False, sha1_hash=None):
"""Download files from a given URL.
Parameters
----------
url : str
URL where file is located
path : str, optional
Destination path to store downloaded file. By default stores to the
current directory with same name as in url.
overwrite : bool, optional
Whether to overwrite destination file if one already exists at this location.
sha1_hash : str, optional
Expected sha1 hash in hexadecimal digits (will ignore existing file when hash is specified
but doesn't match).
Returns
-------
str
The file path of the downloaded file.
"""
if path is None:
fname = url.split('/')[-1]
else:
path = os.path.expanduser(path)
if os.path.isdir(path):
fname = os.path.join(path, url.split('/')[-1])
else:
fname = path
if overwrite or not os.path.exists(fname) or (sha1_hash and not check_sha1(fname, sha1_hash)):
dirname = os.path.dirname(os.path.abspath(os.path.expanduser(fname)))
if not os.path.exists(dirname):
os.makedirs(dirname)
logger.info('Downloading %s from %s...'%(fname, url))
r = requests.get(url, stream=True)
if r.status_code != 200:
raise RuntimeError("Failed downloading url %s"%url)
total_length = r.headers.get('content-length')
with open(fname, 'wb') as f:
if total_length is None: # no content length header
for chunk in r.iter_content(chunk_size=1024):
if chunk: # filter out keep-alive new chunks
f.write(chunk)
else:
total_length = int(total_length)
for chunk in tqdm(r.iter_content(chunk_size=1024),
total=int(total_length / 1024. + 0.5),
unit='KB', unit_scale=False, dynamic_ncols=True):
f.write(chunk)
if sha1_hash and not check_sha1(fname, sha1_hash):
raise UserWarning('File {} is downloaded but the content hash does not match. ' \
'The repo may be outdated or download may be incomplete. ' \
'If the "repo_url" is overridden, consider switching to ' \
'the default repo.'.format(fname))
return fname
def check_sha1(filename, sha1_hash):
"""Check whether the sha1 hash of the file content matches the expected hash.
Parameters
----------
filename : str
Path to the file.
sha1_hash : str
Expected sha1 hash in hexadecimal digits.
Returns
-------
bool
Whether the file content matches the expected hash.
"""
sha1 = hashlib.sha1()
with open(filename, 'rb') as f:
while True:
data = f.read(1048576)
if not data:
break
sha1.update(data)
return sha1.hexdigest() == sha1_hash
def mkdir(path):
"""Make directory at the specified local path with special error handling.
"""
try:
os.makedirs(path)
except OSError as exc: # Python >2.5
if exc.errno == errno.EEXIST and os.path.isdir(path):
pass
else:
raise