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('NarrativeService'):
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(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':
cls.user_id,
'provenance': [{
'service': 'NarrativeService',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.nmsURL = cls.cfg['narrative-method-store']
cls.catalogURL = cls.cfg['catalog-url']
cls.wsURL = cls.cfg['workspace-url']
cls.serviceImpl = NarrativeService(cls.cfg)
def setUpClass(cls):
token = os.environ.get("KB_AUTH_TOKEN")
config_file = os.environ.get("KB_DEPLOYMENT_CONFIG")
cls.cfg = dict()
config = ConfigParser()
config.read(config_file)
for nameval in config.items("NarrativeService"):
cls.cfg[nameval[0]] = nameval[1]
if "auth-service-url" not in cls.cfg:
raise RuntimeError("Missing auth-service-url from config")
auth_client = KBaseAuth(cls.cfg["auth-service-url"])
user_id = auth_client.get_user(token)
cls.ctx = MethodContext(None)
cls.ctx.update({
"token":
token,
"user_id":
user_id,
"provenance": [{
"service": "NarrativeService",
"method": "please_never_use_it_in_producation",
"method_params": []
}],
"authenticated":
1
})
cls.service_impl = NarrativeService(cls.cfg)
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('NarrativeService'):
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': 'NarrativeService',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
# Set up test Workspace
cls.ws_url = cls.cfg['workspace-url']
cls.ws_client = Workspace(cls.ws_url, token=token)
cls.test_ws_info = cls._make_workspace()
cls.test_ws_name = cls.test_ws_info[1]
# Build test data stuff.
# 1. Make a fake reads object - test for report (should be null)
cls.fake_reads_upa = cls._make_fake_reads(cls.test_ws_name,
"FakeReads")
# 2. Make a report, give it that reads object - test for report, should find it
cls.fake_report_upa = cls._make_fake_report(cls.fake_reads_upa,
cls.test_ws_name)
cls.service_impl = NarrativeService(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('NarrativeService'):
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': 'NarrativeService',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.serviceWizardURL = cls.cfg['service-wizard']
cls.wsClient1 = Workspace(cls.wsURL, token=token)
cls.serviceImpl = NarrativeService(cls.cfg)
cls.SetAPI_version = cls.cfg['setapi-version']
cls.DataPalette_version = cls.cfg['datapaletteservice-version']
cls.intro_text_file = cls.cfg['intro-markdown-file']
# 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(StringIO.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' key)")
token2 = test_cfg_dict['test_token2']
user2 = auth_client.get_user(token2)
print("Test user2: " + user2)
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
})
cls.wsClient2 = Workspace(cls.wsURL, token=token2)
cls.wsClients = [cls.wsClient1, cls.wsClient2]
cls.createdWorkspaces = [[], []]
# Example objects:
cls.example_ws_name = cls.createWsStatic(0)
# Reads
cls.example_reads_name = "example_reads.1"
foft = FakeObjectsForTests(os.environ['SDK_CALLBACK_URL'])
info1 = foft.create_fake_reads({
'ws_name': cls.example_ws_name,
'obj_names': [cls.example_reads_name]
})[0]
cls.example_reads_ref = str(info1[6]) + '/' + str(
info1[0]) + '/' + str(info1[4])
# Genome
cls.example_genome_name = "example_genome.1"
foft = FakeObjectsForTests(os.environ['SDK_CALLBACK_URL'])
info2 = foft.create_fake_genomes({
'ws_name': cls.example_ws_name,
'obj_names': [cls.example_genome_name]
})[0]
cls.example_genome_ref = str(info2[6]) + '/' + str(
info2[0]) + '/' + str(info2[4])
# Other objects
foft.create_any_objects({
'ws_name':
cls.example_ws_name,
'obj_names': ['any_obj_' + str(i) for i in range(0, 30)]
})
def get_config():
if not get_config_file():
return None
retconfig = {}
config = ConfigParser()
config.read(get_config_file())
for nameval in config.items(get_service_name() or 'NarrativeService'):
retconfig[nameval[0]] = nameval[1]
return retconfig
config = get_config()
from NarrativeService.NarrativeServiceImpl import NarrativeService # noqa @IgnorePep8
impl_NarrativeService = NarrativeService(config)
class JSONObjectEncoder(json.JSONEncoder):
def default(self, obj):
if isinstance(obj, set):
return list(obj)
if isinstance(obj, frozenset):
return list(obj)
if hasattr(obj, 'toJSONable'):
return obj.toJSONable()
return json.JSONEncoder.default(self, obj)
class JSONRPCServiceCustom(JSONRPCService):
def call(self, ctx, jsondata):