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