kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
try:
host = args.host or vlu.ome_host()
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
kb = KB(driver='omero')(host, user, passwd)
logger.info('Start preloading dependency tree')
kb.update_dependency_tree()
logger.info('Dependency tree loaded')
with open(args.out_file, 'w') as ofile:
writer = csv.DictWriter(ofile, ['target', 'new_source_type',
'new_source', 'old_source'],
delimiter='\t')
writer.writeheader()
logger.info('Loading wells data')
for w in kb.get_objects(kb.PlateWell):
if type(w.action.target) == kb.Individual:
tubes = list(kb.dt.get_connected(w, kb.Tube))
if len(tubes) == 1:
record = {'target' : '%s:%s' % (w.container.label,
w.label),
'new_source_type' : tubes[0].__class__.__name__,
try:
host = args.host or vlu.ome_host()
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
kb = KB(driver='omero')(host, user, passwd)
plates = get_omniexpress_plates(kb)
logger.info('Retrieved %d OMNIEXPRESS related plates' % len(plates))
logger.info('Calculating dependency tree')
kb.update_dependency_tree()
logger.info('Dependency tree loaded')
with open(args.ofile, 'w') as ofile:
writer = csv.DictWriter(ofile, ['source', 'study', 'label'],
delimiter='\t')
writer.writeheader()
inds = []
oe_index = get_first_index(kb, logger)
for pl in plates:
wells = list(kb.get_wells_by_plate(pl))
logger.info('Loaded %d wells for plate %s' %
(len(wells), pl.barcode))
for w in wells:
