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('AssemblyUtil'):
cls.cfg[nameval[0]] = nameval[1]
authServiceUrl = cls.cfg.get('auth-service-url',
'https://kbase.us/services/authorization/Sessions/Login')
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': 'AssemblyUtil',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL, token=token)
cls.serviceImpl = AssemblyUtil(cls.cfg)
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('AssemblyUtil'):
cls.cfg[nameval[0]] = nameval[1]
authServiceUrl = cls.cfg.get(
'auth-service-url',
'https://kbase.us/services/authorization/Sessions/Login')
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': 'AssemblyUtil',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL, token=token)
cls.serviceImpl = AssemblyUtil(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
def __init__(self):
submod = get_service_name() or 'AssemblyUtil'
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_AssemblyUtil.get_assembly_as_fasta,
name='AssemblyUtil.get_assembly_as_fasta',
types=[dict])
self.method_authentication['AssemblyUtil.get_assembly_as_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.export_assembly_as_fasta,
name='AssemblyUtil.export_assembly_as_fasta',
types=[dict])
self.method_authentication['AssemblyUtil.export_assembly_as_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.save_assembly_from_fasta,
name='AssemblyUtil.save_assembly_from_fasta',
types=[dict])
self.method_authentication['AssemblyUtil.save_assembly_from_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.status,
name='AssemblyUtil.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def setUpClass(cls):
token = os.environ.get('KB_AUTH_TOKEN', None)
config_file = os.environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('AssemblyUtil'):
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': 'AssemblyUtil',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = Workspace(cls.wsURL)
cls.serviceImpl = AssemblyUtil(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
shutil.copy2('data/NC_021490.fasta', cls.scratch)
def __init__(self):
submod = get_service_name() or 'AssemblyUtil'
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_AssemblyUtil.get_assembly_as_fasta,
name='AssemblyUtil.get_assembly_as_fasta',
types=[dict])
self.method_authentication[
'AssemblyUtil.get_assembly_as_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.get_fastas,
name='AssemblyUtil.get_fastas',
types=[dict])
self.method_authentication[
'AssemblyUtil.get_fastas'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.export_assembly_as_fasta,
name='AssemblyUtil.export_assembly_as_fasta',
types=[dict])
self.method_authentication[
'AssemblyUtil.export_assembly_as_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.save_assembly_from_fasta,
name='AssemblyUtil.save_assembly_from_fasta',
types=[dict])
self.method_authentication[
'AssemblyUtil.save_assembly_from_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.status,
name='AssemblyUtil.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
#!/usr/bin/env python
from ConfigParser import ConfigParser
from os import environ
from AssemblyUtil.authclient import KBaseAuth as _KBaseAuth
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', '/kb/module/deploy.cfg')
cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('AssemblyRAST'):
cfg[nameval[0]] = nameval[1]
authServiceUrl = cfg.get('auth-service-url', "https://kbase.us/services/authorization/Sessions/Login")
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
print user_id
#!/usr/bin/env python
from ConfigParser import ConfigParser
from os import environ
from AssemblyUtil.authclient import KBaseAuth as _KBaseAuth
token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', '/kb/module/deploy.cfg')
cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('AssemblyRAST'):
cfg[nameval[0]] = nameval[1]
authServiceUrl = cfg.get(
'auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(token)
print user_id