Mercurial > repos > iuc > ncbi_eutils_esearch
view 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 (2016-07-07) |
parents | |
children | 30150bd36c9a |
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#!/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