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('kb_cufflinks'):
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': 'kb_cufflinks',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = kb_cufflinks(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
def __init__(self):
submod = get_service_name() or 'kb_cufflinks'
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_kb_cufflinks.run_cufflinks,
name='kb_cufflinks.run_cufflinks',
types=[dict])
self.method_authentication[
'kb_cufflinks.run_cufflinks'] = 'required' # noqa
self.rpc_service.add(impl_kb_cufflinks.run_Cuffdiff,
name='kb_cufflinks.run_Cuffdiff',
types=[dict])
self.method_authentication[
'kb_cufflinks.run_Cuffdiff'] = 'required' # noqa
self.rpc_service.add(impl_kb_cufflinks.status,
name='kb_cufflinks.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
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('kb_cufflinks'):
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': 'kb_cufflinks',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = Workspace(url=cls.wsURL, token=token)
cls.serviceImpl = kb_cufflinks(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = environ.get('SDK_CALLBACK_URL')
cls.srv_wiz_url = cls.cfg['srv-wiz-url']
# cls.wsName = 'cufflinks_test_' + user_id # reuse existing workspace
suffix = int(time.time() * 1000)
cls.wsName = "test_kb_cufflinks_" + str(suffix)
print('workspace_name: ' + cls.wsName)
try:
# reuse existing (previously torn down) workspace
cls.wsClient.undelete_workspace({'workspace': cls.wsName})
print('reusing old workspace...')
except BaseException:
try:
# create if workspace does not exist
cls.wsClient.create_workspace({'workspace': cls.wsName})
except BaseException:
# get workspace if it exists and was not previously deleted (previously
# not torn down)
ws_info = cls.wsClient.get_workspace_info({'workspace': cls.wsName})
print("creating new workspace: " + str(ws_info))
cls.dfu = DataFileUtil(cls.callback_url)
cls.gfu = GenomeFileUtil(cls.callback_url)
cls.ru = ReadsUtils(cls.callback_url)
cls.rau = ReadsAlignmentUtils(cls.callback_url)
cls.set_api = SetAPI(cls.srv_wiz_url, service_ver='dev')
cls.cufflinks_runner = CufflinksUtils(cls.cfg)
cls.prepare_data()
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('kb_cufflinks'):
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': 'kb_cufflinks',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = kb_cufflinks(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.gfu = GenomeFileUtil(cls.callback_url)
cls.dfu = DataFileUtil(cls.callback_url)
cls.ru = ReadsUtils(cls.callback_url)
cls.rau = ReadsAlignmentUtils(cls.callback_url)
cls.deu = DifferentialExpressionUtils(cls.callback_url,
service_ver='beta')
suffix = int(time.time() * 1000)
cls.wsName = "test_cuffdiff_" + str(suffix)
cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.upload_genome()