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1 import argparse, sys
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2 from collections import Counter
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3
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4 from bl.vl.kb import KnowledgeBase as KB
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5 import bl.vl.utils.ome_utils as vlu
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6 from bl.vl.utils import get_logger, LOG_LEVELS
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7 from bl.vl.kb.drivers.omero.sequencing import SeqDataSample, SequencerOutput
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8
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9
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10 def make_parser():
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11 parser = argparse.ArgumentParser(description='delete all items related to the given flowcell')
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12 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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13 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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14 help='logging level (default=INFO)', default='INFO')
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15 parser.add_argument('-H', '--host', type=str, help='omero hostname')
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16 parser.add_argument('-U', '--user', type=str, help='omero user')
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17 parser.add_argument('-P', '--passwd', type=str, help='omero password')
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18 parser.add_argument('--flowcell-label', type=str, required=True,
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19 help='flowcell label')
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20 parser.add_argument('--datasets-only', action='store_true',
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21 help='delete only data samples and data objects related to the given flowcell')
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22 return parser
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23
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24
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25 def get_sources(objs):
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26 sources = set()
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27 for x in objs:
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28 try:
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29 sources.add(x.action.target)
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30 except AttributeError:
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31 # Action has no "target" attribute, no source for item x
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32 pass
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33 return sources
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34
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35
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36 def delete_objects(objs, kb, logger, max_retries = 3):
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37 retry_ct = Counter()
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38 while len(objs) > 0:
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39 o = objs.pop(0)
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40 if type(o) in [SeqDataSample, SequencerOutput]:
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41 logger.info('Loading DataObjects for %s:%s' % (o.__class__.__name__,
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42 o.label))
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43 dobjs = kb.get_data_objects(o)
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44 logger.info('%d DataObjects loaded' % len(dobjs))
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45 for d in dobjs:
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46 logger.info('Deleting %s:%s' % (d.__class__.__name__,
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47 d.path))
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48 kb.delete(d)
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49 try:
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50 logger.info('Deleting %s:%s' % (o.__class__.__name__,
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51 o.id))
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52 act = o.action
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53 kb.delete(o)
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54 try:
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55 logger.info('Deleting source action %s:%s' % (act.__class__.__name__,
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56 act.id))
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57 kb.delete(act)
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58 except:
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59 logger.info('Can\'t delete action')
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60 except:
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61 logger.info('Can\'t delete, putting back into objects list')
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62 if retry_ct['%s:%s' % (type(o), o.id)] < max_retries:
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63 objs.append(o)
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64 retry_ct['%s:%s' % (type(o), o.id)] += 1
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65 else:
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66 logger.info('Reached maximum retry limit for the object, skipping')
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67
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68 def main(argv):
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69 parser = make_parser()
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70 args = parser.parse_args(argv)
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71
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72 logger = get_logger('drop_flowcell_related_items', level=args.loglevel,
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73 filename=args.logfile)
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74
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75 try:
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76 host = args.host or vlu.ome_host()
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77 user = args.user or vlu.ome_user()
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78 passwd = args.passwd or vlu.ome_passwd()
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79 except ValueError, ve:
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80 logger.critical(ve)
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81 sys.exit(ve)
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82
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83 kb = KB(driver='omero')(host, user, passwd)
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84
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85 logger.info('Retrieving flowcell with label %s' % args.flowcell_label)
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86 query = 'SELECT fc FROM FlowCell fc WHERE fc.label = :fc_label'
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87 results = kb.find_all_by_query(query, {'fc_label' : args.flowcell_label})
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88 if len(results) == 0:
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89 logger.info('No FlowCell with label %s in the database' % args.flowcell_label)
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90 sys.exit(0)
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91 fc = results[0]
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92 logger.info('Loaded FlowCell with ID %s' % fc.id)
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93 logger.info('Loading related Lanes')
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94 lanes = list(kb.get_lanes_by_flowcell(fc))
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95 logger.info('%d Lanes loaded' % len(lanes))
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96 logger.info('Loading related LaneSlots')
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97 lane_slots = []
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98 for l in lanes:
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99 lane_slots += list(kb.get_laneslots_by_lane(l))
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100 logger.info('%d LaneSlots loaded' % len(lane_slots))
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101 logger.info('Loading related Tubes')
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102 sub_samples = get_sources(lane_slots)
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103 samples = get_sources(sub_samples)
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104 logger.info('%d Tubes loaded' % (len(sub_samples) + len(samples)))
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105 logger.info('Loading related SequencerOutputs')
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106 seq_out = kb.dt.get_connected(fc, aklass = kb.SequencerOutput, direction = kb.dt.DIRECTION_OUTGOING)
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107 logger.info('%d SequencerOutputs loaded' % len(seq_out))
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108 logger.info('Loading related SeqDataSamples')
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109 seq_dsamples = kb.dt.get_connected(fc, aklass = kb.SeqDataSample, direction = kb.dt.DIRECTION_OUTGOING)
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110 logger.info('%d SeqDataSamples loaded' % len(seq_dsamples))
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111
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112 if args.datasets_only:
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113 delete_items = [seq_dsamples]
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114 else:
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115 delete_items = [seq_dsamples, seq_out, lane_slots, lanes,
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116 [fc], list(sub_samples), list(samples)]
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117 for items in delete_items:
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118 delete_objects(items, kb, logger)
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119
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120 logger.info('Job completed')
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121
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122
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123 if __name__ == '__main__':
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124 main(sys.argv[1:])
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