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 = {}
