annotate 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
date Wed, 23 Sep 2020 09:48:26 +0000
parents 30150bd36c9a
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c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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1 #!/usr/bin/env python
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3 import argparse
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5 import eutils
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8 if __name__ == '__main__':
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9 parser = argparse.ArgumentParser(description='EPost', epilog='')
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10 parser.add_argument('db', help='Database to use')
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11 parser.add_argument('--user_email', help="User email")
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12 parser.add_argument('--admin_email', help="Admin email")
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14 parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)')
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16 # ID source
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17 parser.add_argument('--id_list', help='list of ids')
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18 parser.add_argument('--id', help='Comma separated individual IDs')
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19 parser.add_argument('--id_json', help='list of ids in a json file as returned by esearch or elink')
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20 parser.add_argument('--id_xml', help='list of ids in an xml file as returned by esearch or elink')
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22 # Target history
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23 parser.add_argument('--history_xml', help='Post to new QueryKey in an existing WebEnv (XML)')
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24 parser.add_argument('--history_file', help='Post to new QueryKey in an existing WebEnv (JSON)')
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25 parser.add_argument('--webenv', help='Post to new WebEnv (History ID)')
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27 args = parser.parse_args()
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29 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
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31 payload = {}
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32 if args.history_file is not None:
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33 hist = c.get_history()
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34 payload['WebEnv'] = hist['WebEnv']
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35 elif args.history_xml is not None:
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36 hist = c.extract_history_from_xml_file(args.history_xml)
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37 payload['WebEnv'] = hist['WebEnv']
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38 elif args.webenv is not None:
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39 payload['WebEnv'] = args.webenv
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41 merged_ids = c.parse_ids(args.id_list, args.id, None, args.id_xml, args.id_json)
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42 payload['id'] = ','.join(merged_ids)
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44 print(c.post(args.db, **payload))