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comparison data_manager/data_manager_genomic_super_signature_ravmodels.py @ 0:b5bca6d58e4c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_genomic_super_signature_ravmodels commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
author iuc
date Wed, 12 Jan 2022 19:07:19 +0000
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-1:000000000000 0:b5bca6d58e4c
1 #!/usr/bin/env python
2 # Dan Blankenberg
3
4
5 import argparse
6 import json
7 import os
8 import re
9 import shutil
10 import urllib.request
11
12
13 OUTPUT_BASE_NAME = 'RAVmodel.rds'
14
15 BUCKET_NAME = "genomic_super_signature"
16 RAVMODEL_NAME = "RAVmodel_{prior}.rds"
17 PRIOR_URL = "https://storage.googleapis.com/{bucket_name}/{prior_filename}"
18
19
20 def get_prior_url(prior):
21 return PRIOR_URL.format(bucket_name=BUCKET_NAME, prior_filename=RAVMODEL_NAME.format(prior=prior))
22
23
24 def clean(text):
25 return re.sub(r'[^\w\-_\.]', '-', text)
26
27
28 def main():
29 parser = argparse.ArgumentParser()
30 parser.add_argument('--output', dest='output', action='store', type=str, default=None)
31 parser.add_argument('--json', dest='json', action='store', type=str, default=None)
32 parser.add_argument('--dbkey', dest='dbkey', action='store', type=str, default=None, help='dbkey')
33 parser.add_argument('--name', dest='name', action='store', type=str, default=None)
34 parser.add_argument('--id', dest='id', action='store', type=str, default=None)
35 parser.add_argument('--prior', dest='prior', action='store', type=str, default=None)
36 parser.add_argument('--url', dest='url', action='store', type=str, default=None)
37 parser.add_argument('--input', dest='input', action='store', type=str, default=None)
38 parser.add_argument('--symlink', dest='symlink', action='store_true', default=False)
39 parser.add_argument('--version', dest='version', action='store', type=str, default="0")
40 parser.add_argument('--tablename', dest='tablename', action='store', type=str, default="genomic_super_signature_ravmodels")
41 args = parser.parse_args()
42
43 os.makedirs(args.output, exist_ok=True)
44 output_filename = os.path.join(args.output, OUTPUT_BASE_NAME)
45 if args.symlink:
46 assert args.input, "You must provide a filename when using symlink functionality."
47 os.symlink(args.input, output_filename)
48 else:
49 url = args.url
50 if args.prior:
51 url = get_prior_url(args.prior)
52 if url:
53 urllib.request.urlretrieve(url, output_filename)
54 else:
55 assert args.input, "You must provide a filename, prior, or URL."
56 shutil.copyfile(args.input, output_filename)
57 data_manager_dict = {'data_tables': {args.tablename: [dict(value=clean(args.id), dbkey=args.dbkey, version=args.version, name=args.name, path=OUTPUT_BASE_NAME)]}}
58
59 with open(args.json, 'w') as fh:
60 json.dump(data_manager_dict, fh, sort_keys=True)
61
62
63 if __name__ == "__main__":
64 main()