Mercurial > repos > iuc > data_manager_fetch_busco

comparison data_manager/data_manager.py @ 0:53eec20e8fb6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author iuc
date Thu, 19 Oct 2017 15:56:20 -0400
parents
children 15b97817550a
comparison
equal deleted inserted replaced
-1:000000000000 0:53eec20e8fb6
1 import argparse
2 import datetime
3 import json
4 import os
5 import shutil
6 import tarfile
7 import zipfile
8 try:
9 # For Python 3.0 and later
10 from urllib.request import Request, urlopen
11 except ImportError:
12 # Fall back to Python 2 imports
13 from urllib2 import Request, urlopen
14
15
16 def url_download(url, workdir):
17 file_path = os.path.join(workdir, 'download.dat')
18 if not os.path.exists(workdir):
19 os.makedirs(workdir)
20 src = None
21 dst = None
22 try:
23 req = Request(url)
24 src = urlopen(req)
25 with open(file_path, 'wb') as dst:
26 while True:
27 chunk = src.read(2**10)
28 if chunk:
29 dst.write(chunk)
30 else:
31 break
32 finally:
33 if src:
34 src.close()
35 if tarfile.is_tarfile(file_path):
36 fh = tarfile.open(file_path, 'r:*')
37 elif zipfile.is_zipfile(file_path):
38 fh = zipfile.ZipFile(file_path, 'r')
39 else:
40 return
41 fh.extractall(workdir)
42 os.remove(file_path)
43
44
45 def main(args):
46 workdir = os.path.join(os.getcwd(), 'busco')
47 url_download(args.url, workdir)
48 data_manager_entry = {}
49 data_manager_entry['value'] = args.name.lower()
50 data_manager_entry['name'] = args.name
51 data_manager_entry['path'] = '.'
52 data_manager_json = dict(data_tables=dict(busco=data_manager_entry))
53 params = json.loads(open(args.output).read())
54 target_directory = params['output_data'][0]['extra_files_path']
55 os.mkdir(target_directory)
56 output_path = os.path.abspath(os.path.join(os.getcwd(), 'busco'))
57 for filename in os.listdir(workdir):
58 shutil.move(os.path.join(output_path, filename), target_directory)
59 file(args.output, 'w').write(json.dumps(data_manager_json))
60
61
62 if __name__ == '__main__':
63 parser = argparse.ArgumentParser(description='Create data manager json.')
64 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
65 parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID')
66 parser.add_argument('--url', dest='url', action='store', help='Download URL')
67 args = parser.parse_args()
68
69 main(args)