forked from GoogleCloudPlatform/cloudml-samples
-
Notifications
You must be signed in to change notification settings - Fork 0
/
data-extractor.py
175 lines (142 loc) · 5.45 KB
/
data-extractor.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
#!/usr/bin/env python
# Copyright 2019 Google Inc. All Rights Reserved. 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.
# This tool downloads SDF files from an FTP source.
from __future__ import absolute_import
import argparse
import ftplib
import multiprocessing as mp
import os
import re
import signal
import tempfile
import tensorflow as tf
import zlib
from io import BytesIO
# Regular expressions to parse an FTP URI.
_USER_RE = r'''(?P<user>[^:@]+|'[^']+'|"[^"]+")'''
_PASSWORD_RE = r'''(?P<password>[^@]+|'[^']+'|"[^"]+")'''
_CREDS_RE = r'{}(?::{})?'.format(_USER_RE, _PASSWORD_RE)
FTP_RE = re.compile(r'^ftp://(?:{}@)?(?P<abs_path>.*)$'.format(_CREDS_RE))
# Good for debugging.
FORCE_DISABLE_MULTIPROCESSING = False
def _function_wrapper(args_tuple):
"""Function wrapper to call from multiprocessing."""
function, args = args_tuple
return function(*args)
def parallel_map(function, iterable):
"""Calls a function for every element in an iterable using multiple cores."""
if FORCE_DISABLE_MULTIPROCESSING:
return [function(*args) for args in iterable]
original_sigint_handler = signal.signal(signal.SIGINT, signal.SIG_IGN)
num_threads = mp.cpu_count() * 2
pool = mp.Pool(processes=num_threads)
signal.signal(signal.SIGINT, original_sigint_handler)
p = pool.map_async(_function_wrapper, ((function, args) for args in iterable))
try:
results = p.get(0xFFFFFFFF)
except KeyboardInterrupt:
pool.terminate()
raise
pool.close()
return results
def extract_data_file(ftp_file, data_dir):
"""Function to extract a single PubChem data file."""
user = ftp_file['user']
password = ftp_file['password']
server = ftp_file['server']
path = ftp_file['path']
basename = os.path.basename(path)
sdf_file = os.path.join(data_dir, os.path.splitext(basename)[0])
if not tf.gfile.Exists(sdf_file):
# The `ftp` object cannot be pickled for multithreading, so we open a
# new connection here
memfile = BytesIO()
ftp = ftplib.FTP(server, user, password)
ftp.retrbinary('RETR ' + path, memfile.write)
ftp.quit()
memfile.seek(0)
with tf.gfile.Open(sdf_file, 'w') as f:
gzip_wbits_format = zlib.MAX_WBITS | 16
contents = zlib.decompress(memfile.getvalue(), gzip_wbits_format)
f.write(contents)
print('Extracted {}'.format(sdf_file))
else:
print('Found {}'.format(sdf_file))
def run(data_sources, filter_regex, max_data_files, data_dir):
"""Extracts the specified number of data files in parallel."""
if not tf.gfile.Exists(data_dir):
tf.gfile.MakeDirs(data_dir)
# Get available data files
filter_re = re.compile(filter_regex)
ftp_files = []
for source in data_sources:
m = FTP_RE.search(source)
if not m:
raise ValueError('malformed FTP URI')
user = m.group('user') or 'anonymous'
password = m.group('password') or 'guest'
server, path_dir = m.group('abs_path').split('/', 1)
uri_prefix = 'ftp://{}:{}@{}/'.format(user, password, server)
ftp = ftplib.FTP(server, user, password)
ftp_files += [{
'user': user,
'password': password,
'server': server,
'path': path,
} for path in ftp.nlst(path_dir)
if filter_re.search(uri_prefix + path)]
ftp.quit()
# Extract data files in parallel
if not max_data_files:
max_data_files = len(ftp_files)
assert max_data_files >= 1
print('Found {} files, using {}'.format(len(ftp_files), max_data_files))
ftp_files = ftp_files[:max_data_files]
print('Extracting data files...')
parallel_map(
extract_data_file, ((ftp_file, data_dir) for ftp_file in ftp_files))
if __name__ == '__main__':
"""Main function"""
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
'--work-dir',
required=True,
help='Directory for staging and working files. '
'This can be a Google Cloud Storage path.')
parser.add_argument(
'--data-sources',
nargs='+',
default=['ftp://anonymous:[email protected]/'
'pubchem/Compound_3D/01_conf_per_cmpd/SDF'],
help='Data source location where SDF file(s) are stored. '
'Paths can be local, ftp://<path>, or gcs://<path>. '
'Examples: '
'ftp://hostname/path '
'ftp://username:password@hostname/path')
parser.add_argument(
'--filter-regex',
default=r'\.sdf',
help='Regular expression to filter which files to use. '
'The regular expression will be searched on the full absolute path. '
'Every match will be kept.')
parser.add_argument(
'--max-data-files',
type=int,
required=True,
help='Maximum number of data files for every file pattern expansion. '
'Set to -1 to use all files.')
args = parser.parse_args()
max_data_files = args.max_data_files
if args.max_data_files == -1:
max_data_files = None
data_dir = os.path.join(args.work_dir, 'data')
run(args.data_sources, args.filter_regex, max_data_files, data_dir)