Split out the local backend (#2052)

This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
This commit is contained in:
Marcus Kinsella
2021-02-18 12:58:22 -08:00
committed by GitHub
parent 036b5f8c0f
commit fb61bd6e9c
153 changed files with 14027 additions and 46 deletions

View File

@@ -240,7 +240,7 @@ class DatasetResource(Resource):
class SchemaAPI(DatasetResource):
# TODO @mdunitz separate dataset schema and user schema
@cache_control(no_store=True)
@cache_control(public=True, max_age=ONE_WEEK)
@rest_get_data_adaptor
def get(self, data_adaptor):
return common_rest.schema_get(data_adaptor)
@@ -261,7 +261,7 @@ class UserInfoAPI(DatasetResource):
class AnnotationsObsAPI(DatasetResource):
@cache_control(public=True, no_store=True)
@cache_control(public=True, max_age=ONE_WEEK)
@rest_get_data_adaptor
def get(self, data_adaptor):
return common_rest.annotations_obs_get(request, data_adaptor)

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@@ -42,6 +42,9 @@ class ServerConfig(BaseConfig):
self.app__web_base_url = default_config["app"]["web_base_url"]
self.authentication__type = default_config["authentication"]["type"]
self.authentication__insecure_test_environment = default_config["authentication"][
"insecure_test_environment"
]
self.authentication__params_oauth__oauth_api_base_url = default_config["authentication"]["params_oauth"][
"oauth_api_base_url"
]
@@ -168,6 +171,10 @@ class ServerConfig(BaseConfig):
def handle_authentication(self):
self.validate_correct_type_of_configuration_attribute("authentication__type", (type(None), str))
self.validate_correct_type_of_configuration_attribute("authentication__insecure_test_environment", bool)
if self.authentication__type == "test" and not self.authentication__insecure_test_environment:
raise ConfigurationError("Test auth can only be used in an insecure test environment")
# oauth
ptypes = str if self.authentication__type == "oauth" else (type(None), str)

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@@ -34,6 +34,7 @@ server:
# session: A session based userid is automatically generated. (no params needed)
# oauth: oauth2 is used for authentication; parameters are defined in params_oauth.
type: session
insecure_test_environment: false
params_oauth:
# url to the oauth server

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@@ -34,7 +34,10 @@ def data_with_tmp_tiledb_annotations(ext: MatrixDataType):
data_locator = DataLocator(fname)
config = AppConfig()
config.update_server_config(
app__flask_secret_key="secret", multi_dataset__dataroot=data_locator.path, authentication__type="test",
app__flask_secret_key="secret",
multi_dataset__dataroot=data_locator.path,
authentication__type="test",
authentication__insecure_test_environment=True,
)
config.update_default_dataset_config(
embeddings__names=["umap"],

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@@ -14,6 +14,7 @@ f"""server:
web_base_url: {web_base_url}
authentication:
type: {auth_type}
insecure_test_environment: {insecure_test_environment}
params_oauth:
oauth_api_base_url: {oauth_api_base_url}
client_id: {client_id}

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@@ -45,6 +45,7 @@ class AuthTest(unittest.TestCase):
app_config = AppConfig()
app_config.update_server_config(app__flask_secret_key="secret")
app_config.update_server_config(authentication__type="test")
app_config.update_server_config(authentication__insecure_test_environment=True)
app_config.update_server_config(
multi_dataset__dataroot=dict(
a1=dict(dataroot=self.dataset_dataroot, base_url="auth"),
@@ -116,6 +117,7 @@ class AuthTest(unittest.TestCase):
app_config.update_server_config(
authentication__type="test", single_dataset__datapath=f"{self.dataset_dataroot}/pbmc3k.cxg"
)
app_config.update_server_config(authentication__insecure_test_environment=True)
app_config.complete_config()

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@@ -38,6 +38,7 @@ class ConfigTests(unittest.TestCase):
api_base_url="null",
web_base_url="null",
auth_type="session",
insecure_test_environment="false",
oauth_api_base_url="null",
client_id="null",
client_secret="null",

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@@ -53,7 +53,7 @@ class TestServerConfig(ConfigTests):
def test_complete_config_checks_all_attr(self, mock_check_attrs):
mock_check_attrs.side_effect = BaseConfig.validate_correct_type_of_configuration_attribute()
self.server_config.complete_config(self.context)
self.assertEqual(mock_check_attrs.call_count, 40)
self.assertEqual(mock_check_attrs.call_count, 41)
def test_handle_app__throws_error_if_port_doesnt_exist(self):
config = self.get_config(port=99999999)
@@ -312,3 +312,12 @@ class TestServerConfig(ConfigTests):
mock_tiledb_context.assert_called_once_with(
{"sm.tile_cache_size": 10, "sm.num_reader_threads": 2, "vfs.s3.region": "us-east-1"}
)
def test_test_auth_only_in_insecure(self):
config = self.get_config(auth_type="test")
with self.assertRaises(ConfigurationError):
config.complete_config()
config.update_server_config(authentication__insecure_test_environment=True)
config.complete_config()