def __init__(self):
submod = get_service_name() or 'PanGenomeAPI'
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_PanGenomeAPI.search_orthologs_from_pangenome,
name='PanGenomeAPI.search_orthologs_from_pangenome',
types=[dict])
self.method_authentication[
'PanGenomeAPI.search_orthologs_from_pangenome'] = 'optional' # noqa
self.rpc_service.add(
impl_PanGenomeAPI.search_families_from_comparison_genome,
name='PanGenomeAPI.search_families_from_comparison_genome',
types=[dict])
self.method_authentication[
'PanGenomeAPI.search_families_from_comparison_genome'] = 'optional' # noqa
self.rpc_service.add(
impl_PanGenomeAPI.search_functions_from_comparison_genome,
name='PanGenomeAPI.search_functions_from_comparison_genome',
types=[dict])
self.method_authentication[
'PanGenomeAPI.search_functions_from_comparison_genome'] = 'optional' # noqa
self.rpc_service.add(
impl_PanGenomeAPI.search_comparison_genome_from_comparison_genome,
name='PanGenomeAPI.search_comparison_genome_from_comparison_genome',
types=[dict])
self.method_authentication[
'PanGenomeAPI.search_comparison_genome_from_comparison_genome'] = 'optional' # noqa
self.rpc_service.add(
impl_PanGenomeAPI.compute_summary_from_pangenome,
name='PanGenomeAPI.compute_summary_from_pangenome',
types=[dict])
self.method_authentication[
'PanGenomeAPI.compute_summary_from_pangenome'] = 'optional' # noqa
self.rpc_service.add(impl_PanGenomeAPI.status,
name='PanGenomeAPI.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('PanGenomeAPI'):
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': 'PanGenomeAPI',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = PanGenomeAPI(cls.cfg)
cls.scratch = cls.cfg['scratch']
shutil.rmtree(cls.scratch)
os.mkdir(cls.scratch)
cls.callback_url = os.environ['SDK_CALLBACK_URL']
suffix = int(time.time() * 1000)
wsName = "test_pangenome_api_" + str(suffix)
cls.ws_info = cls.wsClient.create_workspace({'workspace': wsName})
cls.gcs = GenomeComparisonSDK(cls.callback_url)
cls.gaa = GenomeAnnotationAPI(cls.callback_url)
cls.prepare_data()