def setUp(self): #chdir('work/') token = environ.get('KB_AUTH_TOKEN', None) config_file = environ.get('KB_DEPLOYMENT_CONFIG', None) config = {} config_p = ConfigParser() config_p.read(config_file) for nameval in config_p.items('Trimmomatic'): config[nameval[0]] = nameval[1] #wsURL = config['workspace-url'] #wsClient = workspaceService(wsURL, token=token) self.token=token self.cc = Trimmomatic(config)
def get_config(): if not get_config_file(): return None retconfig = {} config = ConfigParser() config.read(get_config_file()) for nameval in config.items(get_service_name() or 'Trimmomatic'): retconfig[nameval[0]] = nameval[1] return retconfig config = get_config() from Trimmomatic.TrimmomaticImpl import Trimmomatic impl_Trimmomatic = Trimmomatic(config) class JSONObjectEncoder(json.JSONEncoder): def default(self, obj): if isinstance(obj, set): return list(obj) if isinstance(obj, frozenset): return list(obj) if hasattr(obj, 'toJSONable'): return obj.toJSONable() return json.JSONEncoder.default(self, obj) sync_methods = {} async_run_methods = {}