Mercurial > repos > iuc > ncbi_eutils_efetch
view epost.py @ 4:2180fafdfe60 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 25545b698cffc9999cde0079b3be176f55e17803"
author | iuc |
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date | Mon, 04 Jan 2021 11:42:45 +0000 |
parents | c09fcbe4b16a |
children |
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#!/usr/bin/env python import argparse import eutils if __name__ == '__main__': parser = argparse.ArgumentParser(description='EPost', epilog='') parser.add_argument('db', help='Database to use') parser.add_argument('--user_email', help="User email") parser.add_argument('--admin_email', help="Admin email") parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)') # ID source parser.add_argument('--id_list', help='list of ids') parser.add_argument('--id', help='Comma separated individual IDs') parser.add_argument('--id_json', help='list of ids in a json file as returned by esearch or elink') parser.add_argument('--id_xml', help='list of ids in an xml file as returned by esearch or elink') # Target history parser.add_argument('--history_xml', help='Post to new QueryKey in an existing WebEnv (XML)') parser.add_argument('--history_file', help='Post to new QueryKey in an existing WebEnv (JSON)') parser.add_argument('--webenv', help='Post to new WebEnv (History ID)') args = parser.parse_args() c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) payload = {} if args.history_file is not None: hist = c.get_history() payload['WebEnv'] = hist['WebEnv'] elif args.history_xml is not None: hist = c.extract_history_from_xml_file(args.history_xml) payload['WebEnv'] = hist['WebEnv'] elif args.webenv is not None: payload['WebEnv'] = args.webenv merged_ids = c.parse_ids(args.id_list, args.id, None, args.id_xml, args.id_json) payload['id'] = ','.join(merged_ids) print(c.post(args.db, **payload))