93 lines
3.4 KiB
Python
93 lines
3.4 KiB
Python
# Copyright (c) 2019 NVIDIA CORPORATION. All rights reserved.
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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import bz2
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import glob
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import gzip
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import os
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import urllib.request
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import shutil
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import sys
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class PubMedDownloader:
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def __init__(self, subset, save_path):
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self.subset = subset
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# Modifying self.save_path in two steps to handle creation of subdirectories
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self.save_path = save_path + '/pubmed' + '/'
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if not os.path.exists(self.save_path):
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os.makedirs(self.save_path)
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self.save_path = self.save_path + '/' + subset
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if not os.path.exists(self.save_path):
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os.makedirs(self.save_path)
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self.download_urls = {
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'baseline' : 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/',
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'daily_update' : 'ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/',
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'fulltext' : 'ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/',
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'open_access' : 'ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/'
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}
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def download(self):
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print('subset:', self.subset)
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url = self.download_urls[self.subset]
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self.download_files(url)
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self.extract_files()
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def download_files(self, url):
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url = self.download_urls[self.subset]
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output = os.popen('curl ' + url).read()
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if self.subset == 'fulltext' or self.subset == 'open_access':
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line_split = 'comm_use' if self.subset == 'fulltext' else 'non_comm_use'
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for line in output.splitlines():
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if line[-10:] == 'xml.tar.gz' and \
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line.split(' ')[-1].split('.')[0] == line_split:
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file = os.path.join(self.save_path, line.split(' ')[-1])
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if not os.path.isfile(file):
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print('Downloading', file)
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response = urllib.request.urlopen(url + line.split(' ')[-1])
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with open(file, "wb") as handle:
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handle.write(response.read())
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elif self.subset == 'baseline' or self.subset == 'daily_update':
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for line in output.splitlines():
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if line[-3:] == '.gz':
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file = os.path.join(self.save_path, line.split(' ')[-1])
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if not os.path.isfile(file):
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print('Downloading', file)
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response = urllib.request.urlopen(url + line.split(' ')[-1])
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with open(file, "wb") as handle:
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handle.write(response.read())
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else:
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assert False, 'Invalid PubMed dataset/subset specified.'
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def extract_files(self):
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files = glob.glob(self.save_path + '/*.xml.gz')
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for file in files:
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print('file:', file)
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input = gzip.GzipFile(file, mode='rb')
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s = input.read()
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input.close()
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out = open(file[:-3], mode='wb')
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out.write(s)
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out.close()
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