-
Notifications
You must be signed in to change notification settings - Fork 5
/
awsdownload.py
300 lines (238 loc) · 10.5 KB
/
awsdownload.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
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
# pip install git+https://github.com/NDAR/nda_aws_token_generator.git#egg=nda-aws-token-generator&subdirectory=python
# cd ~/nda_aws_token_generator/python/
# sudo python setup.py install
from __future__ import with_statement
from __future__ import absolute_import
import sys
IS_PY2 = sys.version_info < (3, 0)
if IS_PY2:
from Queue import Queue
else:
from queue import Queue
import argparse
import os
from getpass import getpass
from nda_aws_token_generator import *
import csv
from threading import Thread
import boto3
import botocore
import datetime
import requests
import xml.etree.ElementTree as ET
from boto3.s3.transfer import S3Transfer
import multiprocessing
class Worker(Thread):
""" Thread executing tasks from a given tasks queue """
def __init__(self, tasks):
Thread.__init__(self)
self.tasks = tasks
self.daemon = True
self.start()
def run(self):
while True:
func, args, kargs = self.tasks.get()
try:
func(*args, **kargs)
except Exception as e:
# An exception happened in this thread
print(e)
finally:
# Mark this task as done, whether an exception happened or not
self.tasks.task_done()
class ThreadPool:
""" Pool of threads consuming tasks from a queue """
def __init__(self, num_threads):
self.tasks = Queue(num_threads)
for _ in range(num_threads):
Worker(self.tasks)
def add_task(self, func, *args, **kargs):
""" Add a task to the queue """
self.tasks.put((func, args, kargs))
def map(self, func, args_list):
""" Add a list of tasks to the queue """
for args in args_list:
self.add_task(func, args)
def wait_completion(self):
""" Wait for completion of all the tasks in the queue """
self.tasks.join()
class Download:
def __init__(self, directory):
if args.username:
self.username = args.username[0]
else:
self.username = input('Enter your NIMH Data Archives username:')
if args.password:
self.password = args.password[0]
else:
self.password = getpass('Enter your NIMH Data Archives password:')
self.url = 'https://ndar.nih.gov/DataManager/dataManager'
self.directory = directory
self.download_queue = Queue()
self.path_list = set()
self.access_key = None
self.secret_key = None
self.session = None
def useDataManager(self):
""" Download package files (not associated files) """
payload = ('<?xml version="1.0" ?>\n' +
'<S:Envelope xmlns:S="http://schemas.xmlsoap.org/soap/envelope/">\n' +
'<S:Body> <ns3:QueryPackageFileElement\n' +
'xmlns:ns4="http://dataManagerService"\n' +
'xmlns:ns3="http://gov/nih/ndar/ws/datamanager/server/bean/jaxb"\n' +
'xmlns:ns2="http://dataManager/transfer/model">\n' +
'<packageId>' + self.package + '</packageId>\n' +
'<associated>true</associated>\n' +
'</ns3:QueryPackageFileElement>\n' +
'</S:Body>\n' +
'</S:Envelope>')
headers = {
'Content-Type': "text/xml"
}
r = requests.request("POST", self.url, data=payload, headers=headers)
root = ET.fromstring(r.text)
packageFiles = root.findall(".//queryPackageFiles")
for element in packageFiles:
associated = element.findall(".//isAssociated")
path = element.findall(".//path")
for a in associated:
if a.text == 'false':
for p in path:
file = 's3:/' + p.text
self.path_list.add(file)
print('Downloading package files for package {}.'.format(self.package))
def searchForDataStructure(self):
""" Download associated files listed in data structures """
all_paths = self.path_list
self.path_list = set()
for path in all_paths:
if 'Package_{}'.format(self.package) in path:
file = path.split('/')[-1]
shortName = file.split('.')[0]
try:
ddr = requests.request("GET", "https://ndar.nih.gov/api/datadictionary/v2/datastructure/{}".format(shortName))
ddr.raise_for_status()
dataStructureFile = path.split('gpop/')[1]
dataStructureFile = os.path.join(self.directory, dataStructureFile)
self.dataStructure = dataStructureFile
self.useDataStructure()
except requests.exceptions.HTTPError as e:
if e.response.status_code == 404:
continue
def useDataStructure(self):
with open(self.dataStructure) as tsv_file:
tsv = csv.reader(tsv_file, delimiter="\t")
for row in tsv:
for element in row:
if element.startswith('s3://'):
self.path_list.add(element)
def get_links(self):
if args.packageNumber:
self.package = args.paths[0]
self.useDataManager()
elif args.datastructure:
self.dataStructure = args.paths[0]
self.useDataStructure()
elif args.txt:
with open(args.paths[0]) as tsv_file:
tsv = csv.reader(tsv_file, delimiter="\t")
for row in tsv:
self.path_list.add(row[0])
else:
self.path_list = args.paths
def check_time(self):
now_time = datetime.datetime.now()
if now_time >= self.refresh_time:
self.get_tokens()
def get_tokens(self):
start_time = datetime.datetime.now()
generator = NDATokenGenerator(self.url)
self.token = generator.generate_token(self.username, self.password)
self.refresh_time = start_time + datetime.timedelta(hours=23, minutes=55)
self.access_key = self.token.access_key
self.secret_key = self.token.secret_key
self.session = self.token.session
def download_path(self, path):
filename = path.split('/')
self.filename = filename[3:]
key = '/'.join(self.filename)
bucket = filename[2]
self.newdir = filename[3:-1]
self.newdir = '/'.join(self.newdir)
self.newdir = os.path.join(self.directory, self.newdir)
local_filename = os.path.join(self.directory, key)
downloaded = False
# check previous downloads
if args.resume:
prev_directory = args.resume[0]
prev_local_filename = os.path.join(prev_directory, key)
if os.path.isfile(prev_local_filename):
# print(prev_local_filename, 'is already downloaded.')
downloaded = True
if not downloaded:
try:
os.makedirs(self.newdir)
except OSError as e:
pass
# check tokens
self.check_time()
session = boto3.session.Session(self.access_key, self.secret_key, self.session)
s3client = session.client('s3')
s3transfer = S3Transfer(s3client)
try:
s3transfer.download_file(bucket, key, local_filename)
print('downloaded: ', path)
except botocore.exceptions.ClientError as e:
# If a client error is thrown, then check that it was a 404 error.
# If it was a 404 error, then the bucket does not exist.
error_code = int(e.response['Error']['Code'])
if error_code == 404:
print('This path is incorrect:', path, 'Please try again.\n')
pass
if error_code == 403:
print('This is a private bucket. Please contact NDAR for help:', path, '\n')
pass
def parse_args():
parser = argparse.ArgumentParser(
description='This application allows you to enter a list of aws S3 paths and will download the files to your local drive '
'in your home folder. Alternatively, you may enter an NDAR data structure file, and the client will download '
'all associated files from S3 listed in the text file.',
usage='%(prog)s <S3_path_list>')
parser.add_argument('paths', metavar='<S3_path_list>', type=str, nargs='+', action='store',
help='Will download all S3 files to your local drive')
parser.add_argument('-n', '--packageNumber', action='store_true',
help='Flags to download all S3 files in package.')
parser.add_argument('-t', '--txt', action='store_true',
help='Flags that a text file has been entered from where to download S3 files.')
parser.add_argument('-s', '--datastructure', action='store_true',
help='Flags that a data structure text file has been entered from where to download S3 files.')
parser.add_argument('-r', '--resume', metavar='<arg>', type=str, nargs=1, action='store',
help='Flags to restart a download process. If you already have some files downloaded, you must enter the directory where they are saved.')
parser.add_argument('-u', '--username', metavar='<arg>', type=str, nargs=1, action='store',
help='NDA username')
parser.add_argument('-p', '--password', metavar='<arg>', type=str, nargs=1, action='store',
help='NDA password')
parser.add_argument('-d', '--directory', metavar='<arg>', type=str, nargs=1, action='store',
help='Enter an alternate full directory path where you would like your files to be saved.')
args = parser.parse_args()
return args
if __name__ == "__main__":
args = parse_args()
if args.directory:
dir = args.directory[0]
else:
dir = os.path.join(os.path.expanduser('~'), 'AWS_downloads')
s3Download = Download(dir)
s3Download.get_links()
s3Download.get_tokens()
# Function to be executed in a thread
def download(path):
s3Download.download_path(path)
# Instantiate a thread pool with i worker threads
i = multiprocessing.cpu_count()
if i > 1:
i -= 1
pool = ThreadPool(i)
# Add the jobs in bulk to the thread pool
pool.map(download, s3Download.path_list)
pool.wait_completion()