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: