def test_startups(self):
#Test normal startup, should work
self.cUtil.setUp()
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertTrue(semantic_version.validate(catalog.version(self.cUtil.anonymous_ctx())[0]))
#Test empty startup without DB version should work
self.cUtil.setUpEmpty()
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertTrue(semantic_version.validate(catalog.version(self.cUtil.anonymous_ctx())[0]))
#Test empty startup with several different valid versions should work
self.cUtil.setUpEmpty(db_version=3)
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertTrue(semantic_version.validate(catalog.version(self.cUtil.anonymous_ctx())[0]))
self.cUtil.setUpEmpty(db_version=4)
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertTrue(semantic_version.validate(catalog.version(self.cUtil.anonymous_ctx())[0]))
#Startup with version that is too high should fail
self.cUtil.setUpEmpty(db_version=2525)
catalog = None
with self.assertRaises(IOError) as e:
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertEqual(str(e.exception),
'Incompatible DB versions. Expecting DB V4, found DV V2525. You are probably running an old version of the service. Start up failed.');
def setUpClass(cls):
print('++++++++++++ RUNNING secure_config_params.py +++++++++++')
cls.cUtil = CatalogTestUtil(
'.') # TODO: pass in test directory from outside
cls.cUtil.setUp()
cls.catalog = Catalog(cls.cUtil.getCatalogConfig())
print('ready')
def setUpClass(cls):
print('++++++++++++ RUNNING admin_methods_test.py +++++++++++')
cls.cUtil = CatalogTestUtil(
'.') # TODO: pass in test directory from outside
cls.cUtil.setUp()
cls.catalog = Catalog(cls.cUtil.getCatalogConfig())
print('ready')
def setUpClass(cls):
print('++++++++++++ RUNNING core_registration_test.py +++++++++++')
# hack for testing!! remove when docker and NMS components can be tested
from biokbase.catalog.registrar import Registrar
Registrar._TEST_WITHOUT_DOCKER = True
cls.cUtil = CatalogTestUtil(
'.') # TODO: pass in test directory from outside
cls.cUtil.setUp()
cls.catalog = Catalog(cls.cUtil.getCatalogConfig())
# approve developers we will use
cls.catalog.approve_developer(cls.cUtil.admin_ctx(),
cls.cUtil.admin_ctx()['user_id'])
cls.catalog.approve_developer(cls.cUtil.admin_ctx(),
cls.cUtil.user_ctx()['user_id'])
cls.nms = NarrativeMethodStore(cls.cUtil.getCatalogConfig()['nms-url'])
def test_startups(self):
# Test normal startup, should work
self.cUtil.setUp()
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertTrue(semantic_version.validate(catalog.version(self.cUtil.anonymous_ctx())[0]))
# Test empty startup without DB version should work
self.cUtil.setUpEmpty()
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertTrue(semantic_version.validate(catalog.version(self.cUtil.anonymous_ctx())[0]))
# Test empty startup with several different valid versions should work
self.cUtil.setUpEmpty(db_version=3)
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertTrue(semantic_version.validate(catalog.version(self.cUtil.anonymous_ctx())[0]))
self.cUtil.setUpEmpty(db_version=4)
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertTrue(semantic_version.validate(catalog.version(self.cUtil.anonymous_ctx())[0]))
# Startup with version that is too high should fail
self.cUtil.setUpEmpty(db_version=2525)
catalog = None
with self.assertRaises(IOError) as e:
catalog = Catalog(self.cUtil.getCatalogConfig())
self.assertEqual(str(e.exception),
'Incompatible DB versions. Expecting DB V4, found DV V2525. You are '
'probably running an old version of the service. Start up failed.')
def setUpClass(cls):
print('++++++++++++ RUNNING basic_catalog_test.py +++++++++++')
cls.cUtil = CatalogTestUtil(
'.') # TODO: pass in test directory from outside
cls.cUtil.setUp()
cls.catalog = Catalog(cls.cUtil.getCatalogConfig())
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 'Catalog'):
retconfig[nameval[0]] = nameval[1]
return retconfig
config = get_config()
from biokbase.catalog.Impl import Catalog # noqa @IgnorePep8
impl_Catalog = Catalog(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):