Mercurial > repos > iuc > ncbi_eutils_efetch

annotate esearch.py @ 1:0fc65a60436f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 19:08:30 -0400
parents 71bcf87a7031
children c09fcbe4b16a
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71bcf87a7031 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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2 from __future__ import print_function
0fc65a60436f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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4 import argparse
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5 import json
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0fc65a60436f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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7 import eutils
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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10 if __name__ == '__main__':
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11 parser = argparse.ArgumentParser(description='ESearch', epilog='')
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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12 parser.add_argument('db', help='Database to use')
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13 parser.add_argument('term', help='Query')
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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14 parser.add_argument('--history_file', help='Filter existing history')
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15 parser.add_argument('--datetype', help='Date type')
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16 parser.add_argument('--reldate', help='In past N days')
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17 parser.add_argument('--mindate', help='Minimum date')
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18 parser.add_argument('--maxdate', help='maximum date')
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19 # History
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20 parser.add_argument('--history_out', type=argparse.FileType('w'),
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21 help='Output history file')
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22 parser.add_argument('--user_email', help="User email")
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23 parser.add_argument('--admin_email', help="Admin email")
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24 args = parser.parse_args()
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26 c = eutils.Client(history_file=args.history_file, user_email=args.user_email, admin_email=args.admin_email)
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28 payload = {
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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29 'db': args.db,
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30 'term': args.term,
71bcf87a7031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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31 'retstart': 0,
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32 'retmax': 20,
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33 # hmmm @ retmax
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34 }
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35 if args.history_file is not None:
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36 payload.update(c.get_history())
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37 if args.history_out is not None:
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38 payload['usehistory'] = 'y'
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40 for attr in ('datetype', 'reldate', 'mindate', 'maxdate'):
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41 if getattr(args, attr, None) is not None:
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42 payload[attr] = getattr(args, attr)
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44 results = c.search(**payload)
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46 if args.history_out is not None:
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47 history = c.extract_history(results)
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48 args.history_out.write(json.dumps(history, indent=4))
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50 print(results)