annotate elink.py @ 2:0977ec0f3ba8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"

#!/usr/bin/env python
from __future__ import print_function

import argparse
import json

import eutils


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='EFetch', epilog='')
    parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)')
    parser.add_argument('dbfrom', help='Database containing input UIDs')
    parser.add_argument('cmd', choices=['neighbor', 'neighbor_score',
                                        'neighbor_history', 'acheck', 'ncheck', 'lcheck',
                                        'llinks', 'llinkslib', 'prlinks'],
                        help='ELink command mode')
    # Only used in case of neighbor_history
    parser.add_argument('--history_out', type=argparse.FileType('w'),
                        help='Output history file', default='-')

    parser.add_argument('--user_email', help="User email")
    parser.add_argument('--admin_email', help="Admin email")
    # ID Sources
    parser.add_argument('--id_list', help='list of ids')
    parser.add_argument('--id', help='Comma separated individual IDs')
    parser.add_argument('--history_file', help='Fetch results from previous query')

    # TODO: dates, linkname, term, holding
    # neighbor or neighbor_history and dbfrom is pubmed
    # 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')

    # Output
    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 = {
        'dbfrom': args.dbfrom,
        'cmd': args.cmd,
    }
    if args.history_file is not None:
        payload.update(c.get_history())
    else:
        payload['id'] = ','.join(merged_ids)

    # DB can be 'none' in a few cases.
    if args.db != "none":
        payload['db'] = args.db

    results = c.link(**payload)

    if args.cmd == "neighbor_history":
        history = c.extract_history(results)
        args.history_out.write(json.dumps(history, indent=4))

    print(results)