Mercurial > repos > iuc > ncbi_eutils_esearch
diff epost.py @ 3:e267701c187b 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 09:48:26 +0000 |
parents | 30150bd36c9a |
children |
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--- a/epost.py Wed Mar 11 04:03:14 2020 -0400 +++ b/epost.py Wed Sep 23 09:48:26 2020 +0000 @@ -1,5 +1,4 @@ #!/usr/bin/env python -from __future__ import print_function import argparse @@ -9,22 +8,37 @@ 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('--history_file', help='Post to new QueryKey in an existing WebEnv') - parser.add_argument('--user_email', help="User email") - parser.add_argument('--admin_email', help="Admin email") + 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) - merged_ids = c.parse_ids(args.id_list, args.id, args.history_file) payload = {} if args.history_file is not None: - payload.update(c.get_history()) - else: - payload['id'] = ','.join(merged_ids) - payload['WebEnv'] = '' + 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))