def setUpClass(cls):
# logging.basicConfig(level=logging.info)
token = environ.get('KB_AUTH_TOKEN', None)
# 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,
'provenance': [{
'service': 'GenomeFileUtil',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('GenomeFileUtil'):
cls.cfg[nameval[0]] = nameval[1]
cls.wsURL = cls.cfg['workspace-url']
cls.ws = workspaceService(cls.wsURL, token=token)
cls.serviceImpl = GenomeFileUtil(cls.cfg)
gi_config = SDKConfig(cls.cfg)
cls.genome_interface = GenomeInterface(gi_config)
def setUpClass(cls):
cls.token = environ.get('KB_AUTH_TOKEN', None)
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file) # type: ignore
for nameval in config.items('GenomeFileUtil'):
cls.cfg[nameval[0]] = nameval[1]
authServiceUrl = cls.cfg.get(
'auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
auth_client = _KBaseAuth(authServiceUrl)
cls.user_id = auth_client.get_user(cls.token)
cls.ctx = MethodContext(None)
cls.ctx.update({
'token':
cls.token,
'user_id':
cls.user_id,
'provenance': [{
'service': 'GenomeFileUtil',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL, token=cls.token)
cls.serviceImpl = GenomeFileUtil(cls.cfg)
cls.dfu = DataFileUtil(os.environ['SDK_CALLBACK_URL'], token=cls.token)
cls.scratch = cls.cfg['scratch']
cls.shockURL = cls.cfg['shock-url']
cls.gfu_cfg = SDKConfig(cls.cfg)
cls.prepare_data()
def setUpClass(cls):
token = environ.get('KB_AUTH_TOKEN', None)
# 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,
'provenance': [
{'service': 'GenomeFileUtil',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
config_file = environ.get('KB_DEPLOYMENT_CONFIG', None)
cls.cfg = {}
config = ConfigParser()
config.read(config_file)
for nameval in config.items('GenomeFileUtil'):
cls.cfg[nameval[0]] = nameval[1]
cls.wsURL = cls.cfg['workspace-url']
cls.ws = workspaceService(cls.wsURL, token=token)
cls.serviceImpl = GenomeFileUtil(cls.cfg)
gi_config = SDKConfig(cls.cfg)
cls.genome_interface = GenomeInterface(gi_config)
# create one WS for all tests
suffix = int(time.time() * 1000)
wsName = "test_GenomeAnnotationAPI_" + str(suffix)
cls.ws.create_workspace({'workspace': wsName})
cls.wsName = wsName
# save new genome
assembly_file_path = os.path.join(cls.cfg['scratch'],
'Rhodo_SPAdes_assembly.fa')
shutil.copy('data/Rhodo_SPAdes_assembly.fa', assembly_file_path)
au = AssemblyUtil(os.environ['SDK_CALLBACK_URL'])
cls.assembly_ref = au.save_assembly_from_fasta({
'workspace_name': cls.wsName,
'assembly_name': 'ecoli.assembly',
'file': {'path': assembly_file_path}
})
rhodobacter_contigs = json.load(open('data/rhodobacter_contigs.json'))
save_info = {
'workspace': cls.wsName,
'objects': [{
'type': 'KBaseGenomes.ContigSet',
'data': rhodobacter_contigs,
'name': 'rhodobacter_contigs'
}]
}
cls.contigset_ref = cls.ws.save_objects(save_info)
def setUpClass(cls):
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('GenomeFileUtil'):
cls.cfg[nameval[0]] = nameval[1]
# Getting username from Auth profile for token
authServiceUrl = cls.cfg['auth-service-url']
auth_client = _KBaseAuth(authServiceUrl)
cls.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': cls.user_id,
'provenance': [
{'service': 'kb_ke_util',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
cls.shockURL = cls.cfg['shock-url']
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL)
cls.serviceImpl = GenomeFileUtil(cls.cfg)
cls.scratch = cls.cfg['scratch']
cls.callback_url = os.environ['SDK_CALLBACK_URL']
cls.dfu = DataFileUtil(cls.callback_url)
cls.cfg['KB_AUTH_TOKEN'] = cls.token
# build genome interface instance
gi_config = SDKConfig(cls.cfg)
cls.genome_interface = GenomeInterface(gi_config)
# second user
test_cfg_file = '/kb/module/work/test.cfg'
test_cfg_text = "[test]\n"
with open(test_cfg_file, "r") as f:
test_cfg_text += f.read()
config = ConfigParser()
config.readfp(io.StringIO(test_cfg_text))
test_cfg_dict = dict(config.items("test"))
if ('test_token2' not in test_cfg_dict):
raise ValueError("Configuration in <module>/test_local/test.cfg file should " +
"include second user credentials ('test_token2')")
token2 = test_cfg_dict['test_token2']
user2 = auth_client.get_user(token2)
cls.ctx2 = MethodContext(None)
cls.ctx2.update({'token': token2,
'user_id': user2,
'provenance': [
{'service': 'NarrativeService',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated': 1})
suffix = int(time.time() * 1000)
cls.wsName = "test_SaveGenomeTest_" + str(suffix)
cls.wsClient.create_workspace({'workspace': cls.wsName})
cls.nodes_to_delete = []
cls.prepare_data()