Mercurial > repos > iuc > ncbi_eutils_esummary
comparison esearch.py @ 3:254f40d3ae2b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author | iuc |
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date | Wed, 23 Sep 2020 09:50:11 +0000 |
parents | c8d4ea6376a7 |
children |
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2:cb5a0fe9e036 | 3:254f40d3ae2b |
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1 #!/usr/bin/env python | 1 #!/usr/bin/env python |
2 from __future__ import print_function | |
3 | 2 |
4 import argparse | 3 import argparse |
5 import json | 4 import json |
5 import logging | |
6 | |
6 | 7 |
7 import eutils | 8 import eutils |
9 | |
10 | |
11 logging.basicConfig(level=logging.INFO) | |
8 | 12 |
9 | 13 |
10 if __name__ == '__main__': | 14 if __name__ == '__main__': |
11 parser = argparse.ArgumentParser(description='ESearch', epilog='') | 15 parser = argparse.ArgumentParser(description='ESearch', epilog='') |
12 parser.add_argument('db', help='Database to use') | 16 parser.add_argument('db', help='Database to use') |
15 parser.add_argument('--datetype', help='Date type') | 19 parser.add_argument('--datetype', help='Date type') |
16 parser.add_argument('--reldate', help='In past N days') | 20 parser.add_argument('--reldate', help='In past N days') |
17 parser.add_argument('--mindate', help='Minimum date') | 21 parser.add_argument('--mindate', help='Minimum date') |
18 parser.add_argument('--maxdate', help='maximum date') | 22 parser.add_argument('--maxdate', help='maximum date') |
19 # History | 23 # History |
20 parser.add_argument('--history_out', type=argparse.FileType('w'), | 24 parser.add_argument('--history_out', action="store_true", help='Output history file') |
21 help='Output history file') | |
22 parser.add_argument('--user_email', help="User email") | 25 parser.add_argument('--user_email', help="User email") |
23 parser.add_argument('--admin_email', help="Admin email") | 26 parser.add_argument('--admin_email', help="Admin email") |
27 | |
28 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)') | |
29 | |
30 # Output | |
31 parser.add_argument('--retmode', help='Retmode') | |
32 parser.add_argument('--rettype', help='Rettype') | |
33 parser.add_argument('--retstart', type=int, default=0, help='Retstart - Starting rec number (0)') | |
34 parser.add_argument('--retmax', type=int, default=20, help='Retmax - max number of recs returned (20, max 100000)') | |
35 | |
24 args = parser.parse_args() | 36 args = parser.parse_args() |
25 | 37 |
26 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) | 38 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) |
27 | 39 |
40 max_retmax = 100000 | |
41 min_retmax = 1 | |
42 max = max(min(args.retmax, max_retmax), min_retmax) | |
43 | |
28 payload = { | 44 payload = { |
29 'db': args.db, | 45 'db': args.db, |
30 'term': args.term, | 46 'term': args.term, |
31 'retstart': 0, | |
32 'retmax': 20, | |
33 # hmmm @ retmax | |
34 } | 47 } |
35 if args.history_file is not None: | 48 if args.history_file is not None: |
36 payload.update(c.get_history()) | 49 payload.update(c.get_history()) |
37 if args.history_out is not None: | 50 |
51 # if args.history_out is not None: | |
52 if args.history_out: | |
38 payload['usehistory'] = 'y' | 53 payload['usehistory'] = 'y' |
39 | 54 |
40 for attr in ('datetype', 'reldate', 'mindate', 'maxdate'): | 55 payload['retmode'] = args.retmode |
56 | |
57 for attr in ('datetype', 'reldate', 'mindate', 'maxdate', 'rettype', 'retmax', 'retstart'): | |
41 if getattr(args, attr, None) is not None: | 58 if getattr(args, attr, None) is not None: |
42 payload[attr] = getattr(args, attr) | 59 payload[attr] = getattr(args, attr) |
43 | 60 |
61 logging.info("Payload used for query:" + json.dumps(payload, indent=4)) | |
62 | |
44 results = c.search(**payload) | 63 results = c.search(**payload) |
45 | 64 |
46 if args.history_out is not None: | 65 # We're going to infer that rettype being uilist means convert to text format (which esearch does not do) |
47 history = c.extract_history(results) | 66 if args.retmode == 'text': |
48 args.history_out.write(json.dumps(history, indent=4)) | 67 ids = c.xmlstring2UIlist(results) |
49 | 68 for id in ids: |
50 print(results) | 69 print(id) |
70 elif args.retmode == 'json': | |
71 json_data = c.jsonstring2jsondata(results) | |
72 print(json.dumps(json_data, indent=4)) | |
73 else: | |
74 print(results) |