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3
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1 '''
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2 '''
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3
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4 import argparse, csv, sys
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5
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6 from bl.vl.kb import KnowledgeBase as KB
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7 import bl.vl.utils.ome_utils as vlu
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8 from bl.vl.utils import get_logger, LOG_LEVELS
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9
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10
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11 def make_parser():
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12 parser = argparse.ArgumentParser(description='retrieve studies details')
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13 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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14 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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15 help='logging level (default=INFO)', default='INFO')
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16 parser.add_argument('-H', '--host', type=str, help='omero hostname')
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17 parser.add_argument('-U', '--user', type=str, help='omero user')
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18 parser.add_argument('-P', '--passwd', type=str, help='omero passwd')
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19 parser.add_argument('--out_file', type=str, required=True,
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20 help='output file with studies details')
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21 return parser
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22
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23
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24 def main(argv):
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25 parser = make_parser()
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26 args = parser.parse_args(argv)
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27
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28 logger = get_logger('get_studies', level=args.loglevel,
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29 filename=args.logfile)
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30
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31 try:
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32 host = args.host or vlu.ome_host()
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33 user = args.user or vlu.ome_user()
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34 passwd = args.passwd or vlu.ome_passwd()
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35 except ValueError, ve:
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36 logger.critical(ve)
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37 sys.exit(ve)
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38
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39 kb = KB(driver='omero')(host, user, passwd)
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40
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41 logger.info('Retrieving studies')
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42 studies = kb.get_objects(kb.Study)
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43 logger.info('Retrieved {} studies'.format(len(studies)))
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44 records = []
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45 for s in studies:
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46 enr = kb.get_enrolled(s)
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47 rec = {'label': s.label,
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48 'description': s.description,
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49 'enrolled': len(enr)}
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50 records.append(rec)
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51
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52 with open(args.out_file, 'w') as outfile:
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53 writer = csv.DictWriter(outfile, ['label', 'description', 'enrolled'],
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54 delimiter='\t')
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55 # writer.writeheader()
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56 writer.writerows(sorted(records, key=lambda key: key['label']))
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57
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58 if __name__ == '__main__':
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59 main(sys.argv[1:])
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