def main(argv): parser = make_parser() args = parser.parse_args(argv) log_level = getattr(logging, args.loglevel) kwargs = {"format": LOG_FORMAT, "datefmt": LOG_DATEFMT, "level": log_level} if args.logfile: kwargs["filename"] = args.logfile logging.basicConfig(**kwargs) logger = logging.getLogger() with nested(open(args.input_file), open(args.output_file, "w")) as (f, fo): reader = csv.DictReader(f, delimiter="\t") writer = csv.DictWriter(fo, reader.fieldnames, delimiter="\t", lineterminator=os.linesep) writer.writeheader() 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) vid_mapper = VidMapper(host, user, passwd, logger, args.study) counter = Counter() for r in reader: counter["input_lines"] += 1 try: vid_mapper.map_vid(r) except ValueError: counter["skipped_lines"] += 1 continue else: counter["output_lines"] += 1 writer.writerow(r) for k, v in counter.iteritems(): logger.info("%s: %d" % (k, v))
def __init__(self, **kwargs): omero_host = vlu.ome_host() omero_user = vlu.ome_user() omero_passwd = vlu.ome_passwd() self.kb = KB(driver='omero')(omero_host, omero_user, omero_passwd) super(UniverseApplication, self).__init__(**kwargs) self.config.omero_default_host = kwargs.get('omero_default_host') self.config.omero_default_user = kwargs.get('omero_default_user') self.config.omero_default_passwd = kwargs.get('omero_default_passwd') self.config.vl_loglevel = kwargs.get('vl_loglevel', 'INFO') self.config.vl_import_enabled_users = kwargs.get('vl_import_enabled_users')
def main(argv=None): app = App() parser = app.make_parser() args = parser.parse_args(argv) loglevel = getattr(logging, args.loglevel) kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': loglevel} if args.logfile: 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)
def main(argv): parser = make_parser() args = parser.parse_args(argv) log_level = getattr(logging, args.loglevel) kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': log_level} if args.logfile: 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)
def main(argv): parser = make_parser() args = parser.parse_args(argv) log_level = getattr(logging, args.loglevel) kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': log_level} if args.logfile: kwargs['filename'] = args.logfile logging.basicConfig(**kwargs) logger = logging.getLogger() with nested(open(args.input_file), open(args.output_file, "w")) as (f, fo): reader = csv.DictReader(f, delimiter="\t") writer = csv.DictWriter(fo, reader.fieldnames, delimiter="\t", lineterminator=os.linesep) writer.writeheader() 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) vid_mapper = VidMapper(host, user, passwd, logger, args.study) counter = Counter() for r in reader: counter["input_lines"] += 1 try: vid_mapper.map_vid(r) except ValueError: counter["skipped_lines"] += 1 continue else: counter["output_lines"] += 1 writer.writerow(r) for k, v in counter.iteritems(): logger.info("%s: %d" % (k, v))