def root(context, config, database, verbose, log_file): """Clinical sequencing coverage analysis tool.""" # setup logging loglevel = LEVELS.get(min(verbose, 2), 'WARNING') init_log(logging.getLogger(), loglevel=loglevel, filename=log_file) logger.info("version {0}".format(__version__)) # avoid setting global defaults in Click options, do it below when # updating the config object context.obj = Config(config, markup=markup) context.obj['database'] = (database or context.obj.get( 'database', 'coverage.sqlite3')) # update the context with new defaults from the config file context.default_map = context.obj
def root(context, config, database, verbose, log_file): """Clinical sequencing coverage analysis tool.""" # setup logging loglevel = LEVELS.get(min(verbose, 2), 'WARNING') init_log(logging.getLogger(), loglevel=loglevel, filename=log_file) logger.info("version {0}".format(__version__)) # avoid setting global defaults in Click options, do it below when # updating the config object context.obj = Config(config, markup=markup) context.obj['database'] = (database or context.obj.get('database', 'coverage.sqlite3')) # update the context with new defaults from the config file context.default_map = context.obj
def root(context, config, database, log_level, log_file): """Clinical sequencing coverage analysis tool.""" init_log(logging.getLogger(), loglevel=log_level, filename=log_file) logger.debug("version {0}".format(__version__)) # avoid setting global defaults in Click options, do it below when if os.path.exists(config): with open(config) as conf_handle: context.obj = yaml.load(conf_handle) else: context.obj = {} context.obj['database'] = (database or context.obj.get('database')) # update the context with new defaults from the config file context.default_map = context.obj