Mercurial > repos > iuc > ncbi_eutils_esummary
diff esearch.py @ 3:254f40d3ae2b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author | iuc |
---|---|
date | Wed, 23 Sep 2020 09:50:11 +0000 |
parents | c8d4ea6376a7 |
children |
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--- a/esearch.py Wed Mar 11 04:01:46 2020 -0400 +++ b/esearch.py Wed Sep 23 09:50:11 2020 +0000 @@ -1,12 +1,16 @@ #!/usr/bin/env python -from __future__ import print_function import argparse import json +import logging + import eutils +logging.basicConfig(level=logging.INFO) + + if __name__ == '__main__': parser = argparse.ArgumentParser(description='ESearch', epilog='') parser.add_argument('db', help='Database to use') @@ -17,34 +21,54 @@ 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('--history_out', action="store_true", help='Output history file') 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)') + + # Output + parser.add_argument('--retmode', help='Retmode') + parser.add_argument('--rettype', help='Rettype') + parser.add_argument('--retstart', type=int, default=0, help='Retstart - Starting rec number (0)') + parser.add_argument('--retmax', type=int, default=20, help='Retmax - max number of recs returned (20, max 100000)') + args = parser.parse_args() c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email) + max_retmax = 100000 + min_retmax = 1 + max = max(min(args.retmax, max_retmax), min_retmax) + 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: + + # if args.history_out is not None: + if args.history_out: payload['usehistory'] = 'y' - for attr in ('datetype', 'reldate', 'mindate', 'maxdate'): + payload['retmode'] = args.retmode + + for attr in ('datetype', 'reldate', 'mindate', 'maxdate', 'rettype', 'retmax', 'retstart'): if getattr(args, attr, None) is not None: payload[attr] = getattr(args, attr) + logging.info("Payload used for query:" + json.dumps(payload, indent=4)) + 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) + # We're going to infer that rettype being uilist means convert to text format (which esearch does not do) + if args.retmode == 'text': + ids = c.xmlstring2UIlist(results) + for id in ids: + print(id) + elif args.retmode == 'json': + json_data = c.jsonstring2jsondata(results) + print(json.dumps(json_data, indent=4)) + else: + print(results)