Mercurial > repos > iuc > ncbi_eutils_esearch
diff esearch.py @ 0:c8a84e910e6b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author | iuc |
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date | Thu, 07 Jul 2016 02:40:48 -0400 |
parents | |
children | 30150bd36c9a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/esearch.py Thu Jul 07 02:40:48 2016 -0400 @@ -0,0 +1,47 @@ +#!/usr/bin/env python +import json +import argparse +import eutils + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='ESearch', epilog='') + parser.add_argument('db', help='Database to use') + parser.add_argument('term', help='Query') + parser.add_argument('--history_file', help='Filter existing history') + parser.add_argument('--datetype', help='Date type') + parser.add_argument('--reldate', help='In past N days') + parser.add_argument('--mindate', help='Minimum date') + parser.add_argument('--maxdate', help='maximum date') + # History + parser.add_argument('--history_out', type=argparse.FileType('w'), + help='Output history file') + parser.add_argument('--user_email', help="User email") + parser.add_argument('--admin_email', help="Admin email") + args = parser.parse_args() + + c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) + + payload = { + 'db': args.db, + 'term': args.term, + 'retstart': 0, + 'retmax': 20, + # hmmm @ retmax + } + if args.history_file is not None: + payload.update(c.get_history()) + if args.history_out is not None: + payload['usehistory'] = 'y' + + for attr in ('datetype', 'reldate', 'mindate', 'maxdate'): + if getattr(args, attr, None) is not None: + payload[attr] = getattr(args, attr) + + results = c.search(**payload) + + if args.history_out is not None: + history = c.extract_history(results) + args.history_out.write(json.dumps(history, indent=4)) + + print results