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1 import logging, csv, argparse, sys, os
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2
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3 from bl.vl.kb import KnowledgeBase as KB
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4 import bl.vl.kb.drivers.omero.utils as vlu
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5
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6 LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s'
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7 LOG_DATEFMT = '%Y-%m-%d %H:%M:%S'
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8 LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
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9
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10 CSV_FIELDS = ['label', 'barcode', 'rows', 'columns', 'plate_status']
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11
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12 def make_parser():
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13 parser = argparse.ArgumentParser(description='dump all TiterPlate objects to a TSV file')
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14 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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15 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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16 help='logging level', default='INFO')
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17 parser.add_argument('-H', '--host', type=str, help='omero hostname')
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18 parser.add_argument('-U', '--user', type=str, help='omero user')
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19 parser.add_argument('-P', '--passwd', type=str, help='omero password')
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20 parser.add_argument('--ofile', type=str, help='output file',
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21 required=True)
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22 return parser
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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 log_level = getattr(logging, args.loglevel)
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29 kwargs = {'format' : LOG_FORMAT,
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30 'datefmt' : LOG_DATEFMT,
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31 'level' : log_level}
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32 if args.logfile:
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33 kwargs['filename'] = args.logfile
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34 logging.basicConfig(**kwargs)
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35 logger = logging.getLogger()
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36
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37 try:
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38 host = args.host or vlu.ome_host()
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39 user = args.user or vlu.ome_user()
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40 passwd = args.passwd or vlu.ome_passwd
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41 except ValueError, ve:
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42 logger.critical(ve)
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43 sys.exit(ve)
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44
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45 kb = KB(driver='omero')(host, user, passwd)
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46 logging.info('Loading TiterPlate objects')
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47 plates = kb.get_objects(kb.TiterPlate)
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48 logging.info('Loaded %d objects' % len(plates))
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49
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50 with open(args.ofile, 'w') as ofile:
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51 writer = csv.DictWriter(ofile, CSV_FIELDS, delimiter='\t')
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52 writer.writeheader()
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53 for pl in plates:
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54 logger.debug('Dumping plate %d/%d' % (plates.index(pl) + 1,
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55 len(plates)))
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56 writer.writerow({'label' : pl.label,
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57 'barcode' : pl.barcode,
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58 'rows' : pl.rows,
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59 'columns' : pl.columns,
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60 'plate_status' : pl.status.enum_label()})
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61 logger.info('Job done')
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62
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63
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64
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65
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66 if __name__ == '__main__':
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67 main(sys.argv[1:])
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