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3
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1 import sys, csv, argparse, os
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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 LOG_LEVELS, get_logger
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7
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8
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9 def make_parser():
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10 parser = argparse.ArgumentParser(description='check data that will be passed to the merge_individuals tool')
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11 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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12 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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13 help='logging level (default=INFO)', default='INFO')
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14 parser.add_argument('-H', '--host', type=str, help='omero hostname')
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15 parser.add_argument('-U', '--user', type=str, help='omero user')
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16 parser.add_argument('-P', '--passwd', type=str, help='omero password')
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17 parser.add_argument('--in_file', type=str, required=True,
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18 help='input file')
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19 parser.add_argument('--out_file', type=str, required=True,
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20 help='output file')
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21 return parser
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22
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23
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24 def get_invalid_vids(records, logger):
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25 records_map = {}
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26 invalid_vids = []
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27
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28 for rec in records:
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29 for k,v in rec.iteritems():
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30 records_map.setdefault(k, []).append(v)
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31 # Check for duplicated sources
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32 ct = Counter()
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33 for x in records_map['source']:
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34 ct[x] += 1
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35 for k, v in ct.iteritems():
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36 if v > 1:
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37 logger.error('ID %s appears %d times as source, this ID has been marked as invalid' % (k, v))
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38 invalid_vids.append(k)
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39 # Check for VIDs that appear bots in 'source' and 'target' fields
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40 sources = set(records_map['source'])
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41 targets = set(records_map['target'])
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42 commons = sources.intersection(targets)
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43 for c in commons:
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44 logger.error('ID %s appears both in \'source\' and \'target\' columns, this ID has been marked as invalid' % c)
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45 invalid_vids.append(c)
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46
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47 return set(invalid_vids)
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48
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49
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50 def check_row(row, individuals, logger):
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51 try:
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52 source = individuals[row['source']]
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53 logger.debug('%s is a valid Individual ID' % source.id)
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54 target = individuals[row['target']]
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55 logger.debug('%s is a valid Individual ID' % target.id)
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56 return True
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57 except KeyError, ke:
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58 logger.error('%s is not a valid Individual ID' % ke)
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59 return False
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60
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61
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62 def main(argv):
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63 parser = make_parser()
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64 args = parser.parse_args(argv)
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65
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66 logger = get_logger('check_merge_individuals', level=args.loglevel,
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67 filename=args.logfile)
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68
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69 try:
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70 host = args.host or vlu.ome_host()
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71 user = args.user or vlu.ome_user()
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72 passwd = args.passwd or vlu.ome_passwd()
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73 except ValueError, ve:
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74 logger.critical(ve)
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75 sys.exit(ve)
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76
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77 kb = KB(driver='omero')(host, user, passwd)
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78
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79 logger.info('Preloading all individuals')
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80 inds = kb.get_objects(kb.Individual)
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81 logger.info('Loaded %d individuals' % len(inds))
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82 inds_map = {}
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83 for i in inds:
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84 inds_map[i.id] = i
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85
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86 with open(args.in_file) as infile, open(args.out_file, 'w') as outfile:
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87 reader = csv.DictReader(infile, delimiter='\t')
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88 records = [row for row in reader]
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89 invalid_vids = get_invalid_vids(records, logger)
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90
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91 writer = csv.DictWriter(outfile, reader.fieldnames, delimiter='\t')
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92 writer.writeheader()
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93
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94 for record in records:
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95 if record['source'] in invalid_vids or record['target'] in invalid_vids:
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96 logger.error('Skipping record %r because at least one ID was marked as invalid' % record)
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97 else:
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98 if check_row(record, inds_map, logger):
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99 writer.writerow(record)
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100 logger.debug('Record %r written in output file' % record)
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101
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102
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103 if __name__ == '__main__':
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104 main(sys.argv[1:])
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