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3
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1 import argparse, sys
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2
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3 from bl.vl.kb import KnowledgeBase as KB
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4 from bl.vl.utils import get_logger, LOG_LEVELS
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5 import bl.vl.utils.ome_utils as vlu
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6
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7
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8 def make_parser():
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9 parser = argparse.ArgumentParser(description='remove datasamples connected to a specific sample of a flowcell')
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10 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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11 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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12 help='logging level (default=INFO)', default='INFO')
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13 parser.add_argument('-H', '--host', type=str, help='omero server hostname')
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14 parser.add_argument('-U', '--user', type=str, help='omero user')
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15 parser.add_argument('-P', '--passwd', type=str, help='omero password')
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16 parser.add_argument('--flowcell-label', type=str, required=True,
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17 help='flowcell label')
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18 parser.add_argument('--sample-label', type=str, required=True,
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19 help='sample label')
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20 parser.add_argument('--dry-run', action='store_true',
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21 help='run a simulation, don\'t delete anything')
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22 return parser
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23
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24
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25 def get_flowcell_samples_map(flowcell, kb, logger):
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26 fc = kb.get_by_label(kb.FlowCell, flowcell)
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27 if not fc:
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28 logger.info('No flowcell with label %s', flowcell)
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29 sys.exit(0)
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30 logger.info('Loading data for flowcell %s', flowcell)
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31 dsamples = kb.dt.get_connected(fc, aklass = kb.SeqDataSample)
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32 dsamples_map = {}
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33 for ds in dsamples:
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34 if ds.sample:
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35 dsamples_map.setdefault(ds.sample.label, []).append(ds)
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36 else:
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37 dsamples_map.setdefault('NO_SAMPLE', []).append(ds)
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38 return dsamples_map
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39
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40
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41 def print_report(dsamples_map, sample_label, kb, logger):
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42 dsamples = dsamples_map.get(sample_label)
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43 if not dsamples:
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44 logger.info('No sample with label %s is related to the flowcell', sample_label)
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45 sys.exit(0)
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46 for ds in dsamples:
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47 dobjs = kb.get_data_objects(ds)
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48 logger.info('## data sample: %s', ds.label)
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49 for dob in dobjs:
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50 logger.info('### data object: %s --- mimetype: %s', dob.path, dob.mimetype)
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51
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52
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53 def delete(dsamples_map, sample_label, kb, logger):
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54 for ds in dsamples_map[sample_label]:
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55 # this is a hack specific for the automator workflow
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56 if not ds.label.startswith('stage1'):
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57 logger.info('Deleting data for %s', ds.label)
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58 dobjs = kb.get_data_objects(ds)
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59 for d in dobjs:
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60 kb.delete(d)
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61 a = ds.action
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62 kb.delete(ds)
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63 try:
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64 kb.delete(a)
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65 except:
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66 pass
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67
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68
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69 def main(argv):
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70 parser = make_parser()
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71 args = parser.parse_args(argv)
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72
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73 logger = get_logger('delete_flowcell_results', level=args.loglevel,
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74 filename=args.logfile)
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75
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76 try:
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77 host = args.host or vlu.ome_host()
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78 user = args.user or vlu.ome_user()
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79 passwd = args.passwd or vlu.ome_passwd()
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80 except ValueError, ve:
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81 logger.critical(ve)
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82 sys.exit(ve)
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83
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84 kb = KB(driver='omero')(host, user, passwd)
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85
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86 dsamples_map = get_flowcell_samples_map(args.flowcell_label, kb, logger)
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87 print_report(dsamples_map, args.sample_label, kb, logger)
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88 if not args.dry_run:
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89 delete(dsamples_map, args.sample_label, kb. logger)
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90 pass
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91 else:
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92 logger.debug('SIMULATION, exit now')
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93 logger.info('Job completed')
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94
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95
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96 if __name__ == '__main__':
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97 main(sys.argv[1:])
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