def __init__(self):
submod = get_service_name() or 'ExpressionUtils'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_ExpressionUtils.upload_expression,
name='ExpressionUtils.upload_expression',
types=[dict])
self.method_authentication['ExpressionUtils.upload_expression'] = 'required' # noqa
self.rpc_service.add(impl_ExpressionUtils.download_expression,
name='ExpressionUtils.download_expression',
types=[dict])
self.method_authentication['ExpressionUtils.download_expression'] = 'required' # noqa
self.rpc_service.add(impl_ExpressionUtils.export_expression,
name='ExpressionUtils.export_expression',
types=[dict])
self.method_authentication['ExpressionUtils.export_expression'] = 'required' # noqa
self.rpc_service.add(impl_ExpressionUtils.get_expressionMatrix,
name='ExpressionUtils.get_expressionMatrix',
types=[dict])
self.method_authentication['ExpressionUtils.get_expressionMatrix'] = 'required' # noqa
self.rpc_service.add(impl_ExpressionUtils.status,
name='ExpressionUtils.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def setUpClass(cls):
cls.token = environ.get('KB_AUTH_TOKEN', None)
cls.callbackURL = environ.get('SDK_CALLBACK_URL')
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('ExpressionUtils'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(cls.token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({
'token':
cls.token,
'user_id':
user_id,
'provenance': [{
'service': 'ExpressionUtils',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.shockURL = cls.cfg['shock-url']
cls.wsURL = cls.cfg['workspace-url']
cls.service_wizard_url = cls.cfg['srv-wiz-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.ws = Workspace(cls.wsURL, token=cls.token)
cls.hs = HandleService(url=cls.cfg['handle-service-url'],
token=cls.token)
# create workspace
wssuffix = int(time.time() * 1000)
wsname = "test_expression_" + str(wssuffix)
cls.wsinfo = cls.wsClient.create_workspace({'workspace': wsname})
print('created workspace ' + cls.getWsName())
cls.serviceImpl = ExpressionUtils(cls.cfg)
cls.readUtils = ReadsUtils(cls.callbackURL)
cls.dfu = DataFileUtil(cls.callbackURL, service_ver='dev')
cls.dfu.ws_name_to_id(wsname)
cls.assemblyUtil = AssemblyUtil(cls.callbackURL)
cls.gfu = GenomeFileUtil(cls.callbackURL)
cls.gaAPI = GenomeAnnotationAPI(cls.service_wizard_url)
cls.rau = ReadsAlignmentUtils(cls.callbackURL)
cls.scratch = cls.cfg['scratch']
cls.staged = {}
cls.nodes_to_delete = []
cls.handles_to_delete = []
cls.setupTestData()
def setUpClass(cls):
cls.__LOGGER = logging.getLogger('ExpressionUtils_test')
cls.__LOGGER.setLevel(logging.INFO)
streamHandler = logging.StreamHandler(sys.stdout)
formatter = logging.Formatter(
"%(asctime)s - %(filename)s - %(lineno)d - %(levelname)s - %(message)s"
)
formatter.converter = time.gmtime
streamHandler.setFormatter(formatter)
cls.__LOGGER.addHandler(streamHandler)
cls.__LOGGER.info("Logger was set")
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('ExpressionUtils'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({
'token':
token,
'user_id':
user_id,
'provenance': [{
'service': 'ExpressionUtils',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.cfg['SDK_CALLBACK_URL'] = cls.callback_url
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = ExpressionUtils(cls.cfg)
cls.scratch = cls.cfg['scratch']
def setUpClass(cls):
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('ExpressionUtils'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
# authServiceUrlAllowInsecure = cls.cfg['auth_service_url_allow_insecure']
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
# WARNING: don't call any logging methods on the context object,
# it'll result in a NoneType error
cls.ctx = MethodContext(None)
cls.ctx.update({
'token':
token,
'user_id':
user_id,
'provenance': [{
'service': 'ExpressionUtils',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = ExpressionUtils(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.dfu = DataFileUtil(cls.callback_url)
cls.gfu = GenomeFileUtil(cls.callback_url)
suffix = int(time.time() * 1000)
cls.wsName = "test_exprMatrixUtils_" + str(suffix)
cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.setupdata()