def __init__(self):
submod = get_service_name() or 'sample_uploader'
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_sample_uploader.import_samples,
name='sample_uploader.import_samples',
types=[dict])
self.method_authentication[
'sample_uploader.import_samples'] = 'required' # noqa
self.rpc_service.add(impl_sample_uploader.import_samples_from_IGSN,
name='sample_uploader.import_samples_from_IGSN',
types=[dict])
self.method_authentication[
'sample_uploader.import_samples_from_IGSN'] = 'required' # noqa
self.rpc_service.add(impl_sample_uploader.import_samples_from_NCBI,
name='sample_uploader.import_samples_from_NCBI',
types=[dict])
self.method_authentication[
'sample_uploader.import_samples_from_NCBI'] = 'required' # noqa
self.rpc_service.add(impl_sample_uploader.generate_OTU_sheet,
name='sample_uploader.generate_OTU_sheet',
types=[dict])
self.method_authentication[
'sample_uploader.generate_OTU_sheet'] = 'required' # noqa
self.rpc_service.add(impl_sample_uploader.update_sample_set_acls,
name='sample_uploader.update_sample_set_acls',
types=[dict])
self.method_authentication[
'sample_uploader.update_sample_set_acls'] = 'required' # noqa
self.rpc_service.add(impl_sample_uploader.export_samples,
name='sample_uploader.export_samples',
types=[dict])
self.method_authentication[
'sample_uploader.export_samples'] = 'required' # noqa
self.rpc_service.add(impl_sample_uploader.link_reads,
name='sample_uploader.link_reads',
types=[dict])
self.method_authentication[
'sample_uploader.link_reads'] = 'required' # noqa
self.rpc_service.add(impl_sample_uploader.status,
name='sample_uploader.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def setUpClass(cls):
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('sample_uploader'):
cls.cfg[nameval[0]] = nameval[1]
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
cls.username = auth_client.get_user(cls.token)
cls.test_dir = os.path.dirname(
os.path.dirname(os.path.realpath(__file__)))
sample_server = cls.cfg.get('sample-server', 'sampleservice')
cls.sample_url = cls.cfg['kbase-endpoint'] + '/{}'.format(
sample_server)
cls.workspace_url = cls.cfg['workspace-url']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
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('sample_uploader'):
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': 'sample_uploader',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.curr_dir = os.path.dirname(os.path.realpath(__file__))
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = Workspace(cls.wsURL, token=token)
cls.serviceImpl = sample_uploader(cls.cfg)
# cls.curr_dir = os.path.dirname(os.path.realpath(__file__))
cls.scratch = cls.cfg['scratch']
# cls.wiz_url = cls.cfg['srv-wiz-url']
cls.sample_url = cls.cfg['kbase-endpoint'] + '/sampleservice'
cls.callback_url = os.environ['SDK_CALLBACK_URL']
suffix = int(time.time() * 1000)
cls.wsName = "test_ContigFilter_" + str(suffix)
ret = cls.wsClient.create_workspace({'workspace': cls.wsName}) # noqa
cls.wsID = ret[0]
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('sample_uploader'):
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': 'sample_uploader',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = Workspace(cls.wsURL, token=token)
cls.serviceImpl = sample_uploader(cls.cfg)
cls.curr_dir = os.path.dirname(os.path.realpath(__file__))
cls.scratch = cls.cfg['scratch']
cls.wiz_url = cls.cfg['srv-wiz-url']
cls.sample_url = cls.cfg['kbase-endpoint'] + '/sampleservice'
cls.callback_url = os.environ['SDK_CALLBACK_URL']
suffix = int(time.time() * 1000)
cls.wsName = "test_sample_uploader_" + str(suffix)
ret = cls.wsClient.create_workspace({'workspace': cls.wsName}) # noqa
cls.wsID = ret[0]
cls.sesar_sample_file = os.path.join(cls.curr_dir, "data",
"fake_samples.tsv")
cls.sample_set_name = "test_sample_set_1"
params = {
'workspace_name': cls.wsName,
'workspace_id': cls.wsID,
'sample_file': cls.sesar_sample_file,
'file_format': "sesar",
'header_row_index': 2,
'set_name': cls.sample_set_name,
'description': "this is a test sample set.",
'output_format': "",
'name_field': "test name field",
'incl_input_in_output': 1,
'share_within_workspace': 1,
}
ret = cls.serviceImpl.import_samples(cls.ctx, params)[0]
cls.sample_set = ret['sample_set']
cls.a_sample_id = ret['sample_set']['samples'][0]['id']
cls.sample_set_ref = ret['sample_set_ref']
# add new user to test permissions
cls.wsClient.set_permissions({
"id": cls.wsID,
"new_permission": "w",
"users": ["psdehal"]
})
