import os import unittest from unittest import mock from unittest.mock import patch from server.common.config.base_config import BaseConfig from server.common.utils.utils import find_available_port from server.test import PROJECT_ROOT, FIXTURES_ROOT import requests from server.common.config.app_config import AppConfig from server.common.errors import ConfigurationError from server.test import test_server from server.test.unit.common.config import ConfigTests def mockenv(**envvars): return mock.patch.dict(os.environ, envvars) class TestServerConfig(ConfigTests): def setUp(self): self.config_file_name = f"{unittest.TestCase.id(self).split('.')[-1]}.yml" self.config = AppConfig() self.config.update_server_config(app__flask_secret_key="secret") self.config.update_server_config(multi_dataset__dataroot=FIXTURES_ROOT) self.server_config = self.config.server_config self.config.complete_config() message_list = [] def noop(message): message_list.append(message) messagefn = noop self.context = dict(messagefn=messagefn, messages=message_list) def get_config(self, **kwargs): file_name = self.custom_app_config( dataroot=f"{FIXTURES_ROOT}", config_file_name=self.config_file_name, **kwargs ) config = AppConfig() config.update_from_config_file(file_name) return config def test_init_raises_error_if_default_config_is_invalid(self): invalid_config = self.get_config(port="not_valid") with self.assertRaises(ConfigurationError): invalid_config.complete_config() @patch("server.common.config.server_config.BaseConfig.validate_correct_type_of_configuration_attribute") 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) def test_handle_app__throws_error_if_port_doesnt_exist(self): config = self.get_config(port=99999999) with self.assertRaises(ConfigurationError): config.server_config.handle_app(self.context) @patch("server.common.config.server_config.discover_s3_region_name") def test_handle_data_locator_works_for_default_types(self, mock_discover_region_name): mock_discover_region_name.return_value = None # Default config self.assertEqual(self.config.server_config.data_locator__s3__region_name, None) # hard coded config = self.get_config() self.assertEqual(config.server_config.data_locator__s3__region_name, "us-east-1") # incorrectly formatted dataroot = { "d1": {"base_url": "set1", "dataroot": "/path/to/set1_datasets/"}, "d2": {"base_url": "set2/subdir", "dataroot": "s3://shouldnt/work"}, } file_name = self.custom_app_config( dataroot=dataroot, config_file_name=self.config_file_name, data_locater_region_name="true" ) config = AppConfig() config.update_from_config_file(file_name) with self.assertRaises(ConfigurationError): config.server_config.handle_data_locator() @patch("server.common.config.server_config.discover_s3_region_name") def test_handle_data_locator_can_read_from_dataroot(self, mock_discover_region_name): mock_discover_region_name.return_value = "us-west-2" dataroot = { "d1": {"base_url": "set1", "dataroot": "/path/to/set1_datasets/"}, "d2": {"base_url": "set2/subdir", "dataroot": "s3://hosted-cellxgene-dev"}, } file_name = self.custom_app_config( dataroot=dataroot, config_file_name=self.config_file_name, data_locater_region_name="true" ) config = AppConfig() config.update_from_config_file(file_name) config.server_config.handle_data_locator() self.assertEqual(config.server_config.data_locator__s3__region_name, "us-west-2") mock_discover_region_name.assert_called_once_with("s3://hosted-cellxgene-dev") def test_handle_app___can_use_envar_port(self): config = self.get_config(port=24) self.assertEqual(config.server_config.app__port, 24) # Note if the port is set in the config file it will NOT be overwritten by a different envvar os.environ["CXG_SERVER_PORT"] = "4008" self.config = AppConfig() self.config.update_server_config(app__flask_secret_key="secret") self.config.server_config.handle_app(self.context) self.assertEqual(self.config.server_config.app__port, 4008) del os.environ["CXG_SERVER_PORT"] def test_handle_app__can_get_secret_key_from_envvar_or_config_file_with_envvar_given_preference(self): config = self.get_config(flask_secret_key="KEY_FROM_FILE") self.assertEqual(config.server_config.app__flask_secret_key, "KEY_FROM_FILE") os.environ["CXG_SECRET_KEY"] = "KEY_FROM_ENV" config.external_config.handle_environment(self.context) self.assertEqual(config.server_config.app__flask_secret_key, "KEY_FROM_ENV") def test_handle_app__sets_web_base_url(self): config = self.get_config(web_base_url="anything.com") self.assertEqual(config.server_config.app__web_base_url, "anything.com") def test_handle_auth__gets_client_secret_from_envvars_or_config_with_envvars_given_preference(self): config = self.get_config(client_secret="KEY_FROM_FILE") config.server_config.handle_authentication() self.assertEqual(config.server_config.authentication__params_oauth__client_secret, "KEY_FROM_FILE") os.environ["CXG_OAUTH_CLIENT_SECRET"] = "KEY_FROM_ENV" config.external_config.handle_environment(self.context) self.assertEqual(config.server_config.authentication__params_oauth__client_secret, "KEY_FROM_ENV") def test_handle_data_source__errors_when_passed_zero_or_two_dataroots(self): file_name = self.custom_app_config( dataroot=f"{FIXTURES_ROOT}", config_file_name="two_data_roots.yml", dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", ) config = AppConfig() config.update_from_config_file(file_name) with self.assertRaises(ConfigurationError): config.server_config.handle_data_source() file_name = self.custom_app_config(config_file_name="zero_roots.yml") config = AppConfig() config.update_from_config_file(file_name) with self.assertRaises(ConfigurationError): config.server_config.handle_data_source() def test_get_api_base_url_works(self): # test the api_base_url feature, and that it can contain a path config = AppConfig() backend_port = find_available_port("localhost", 10000) config.update_server_config( app__flask_secret_key="secret", app__api_base_url=f"http://localhost:{backend_port}/additional/path", multi_dataset__dataroot=f"{PROJECT_ROOT}/example-dataset", ) config.complete_config() with test_server(["-p", str(backend_port)], app_config=config) as server: session = requests.Session() self.assertEqual(server, f"http://localhost:{backend_port}") response = session.get(f"{server}/additional/path/d/pbmc3k.h5ad/api/v0.2/config") self.assertEqual(response.status_code, 200) data_config = response.json() self.assertEqual(data_config["config"]["displayNames"]["dataset"], "pbmc3k") # test the health check at the correct url response = session.get(f"{server}/additional/path/health") assert response.json()["status"] == "pass" def test_get_web_base_url_works(self): config = self.get_config(web_base_url="www.thisisawebsite.com") web_base_url = config.server_config.get_web_base_url() self.assertEqual(web_base_url, "www.thisisawebsite.com") config = self.get_config(web_base_url="local", port=12) web_base_url = config.server_config.get_web_base_url() self.assertEqual(web_base_url, "http://localhost:12") config = self.get_config(web_base_url="www.thisisawebsite.com/") web_base_url = config.server_config.get_web_base_url() self.assertEqual(web_base_url, "www.thisisawebsite.com") config = self.get_config(api_base_url="www.api_base.com/") web_base_url = config.server_config.get_web_base_url() self.assertEqual(web_base_url, "www.api_base.com") def test_config_for_single_dataset(self): file_name = self.custom_app_config( config_file_name="single_dataset.yml", dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k.cxg" ) config = AppConfig() config.update_from_config_file(file_name) config.server_config.handle_single_dataset(self.context) self.assertIsNotNone(config.server_config.matrix_data_cache_manager) file_name = self.custom_app_config( config_file_name="single_dataset_with_about.yml", about="www.cziscience.com", dataset_datapath=f"{FIXTURES_ROOT}/pbmc3k.cxg", ) config = AppConfig() config.update_from_config_file(file_name) with self.assertRaises(ConfigurationError): config.server_config.handle_single_dataset(self.context) def test_multi_dataset_raises_error_for_illegal_routes(self): # test for illegal url_dataroots for illegal in ("../b", "!$*", "\\n", "", "(bad)"): self.config.update_server_config( multi_dataset__dataroot={"tag": {"base_url": illegal, "dataroot": f"{PROJECT_ROOT}/example-dataset"}} ) with self.assertRaises(ConfigurationError): self.config.complete_config() def test_multidataset_works_for_legal_routes(self): # test for legal url_dataroots for legal in ("d", "this.is-okay_", "a/b"): self.config.update_server_config( multi_dataset__dataroot={"tag": {"base_url": legal, "dataroot": f"{PROJECT_ROOT}/example-dataset"}} ) self.config.complete_config() def test_mulitdatasets_work_e2e(self): # test that multi dataroots work end to end self.config.update_server_config( multi_dataset__dataroot=dict( s1=dict(dataroot=f"{PROJECT_ROOT}/example-dataset", base_url="set1/1/2"), s2=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set2"), s3=dict(dataroot=f"{FIXTURES_ROOT}", base_url="set3"), ) ) # Change this default to test if the dataroot overrides below work. self.config.update_default_dataset_config(app__about_legal_tos="tos_default.html") # specialize the configs for set1 self.config.add_dataroot_config( "s1", user_annotations__enable=False, diffexp__enable=True, app__about_legal_tos="tos_set1.html" ) # specialize the configs for set2 self.config.add_dataroot_config( "s2", user_annotations__enable=True, diffexp__enable=False, app__about_legal_tos="tos_set2.html" ) # no specializations for set3 (they get the default dataset config) self.config.complete_config() with test_server(app_config=self.config) as server: session = requests.Session() response = session.get(f"{server}/set1/1/2/pbmc3k.h5ad/api/v0.2/config") data_config = response.json() assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k" assert data_config["config"]["parameters"]["annotations"] is False assert data_config["config"]["parameters"]["disable-diffexp"] is False assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set1.html" response = session.get(f"{server}/set2/pbmc3k.cxg/api/v0.2/config") data_config = response.json() assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k" assert data_config["config"]["parameters"]["annotations"] is True assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set2.html" response = session.get(f"{server}/set3/pbmc3k.cxg/api/v0.2/config") data_config = response.json() assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k" assert data_config["config"]["parameters"]["annotations"] is True assert data_config["config"]["parameters"]["disable-diffexp"] is False assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_default.html" response = session.get(f"{server}/health") assert response.json()["status"] == "pass" # access a dataset (no slash) response = session.get(f"{server}/set2/pbmc3k.cxg") self.assertEqual(response.status_code, 200) # access a dataset (with slash) response = session.get(f"{server}/set2/pbmc3k.cxg/") self.assertEqual(response.status_code, 200) @patch("server.common.config.server_config.diffexp_tiledb.set_config") def test_handle_diffexp(self, mock_tiledb_config): custom_config_file = self.custom_app_config( dataroot=f"{FIXTURES_ROOT}", cpu_multiplier=3, diffexp_max_workers=1, target_workunit=4, config_file_name=self.config_file_name, ) config = AppConfig() config.update_from_config_file(custom_config_file) config.server_config.handle_diffexp() # called with the min of diffexp_max_workers and cpus*cpu_multiplier mock_tiledb_config.assert_called_once_with(1, 4) @patch("server.data_cxg.cxg_adaptor.CxgAdaptor.set_tiledb_context") def test_handle_adaptor(self, mock_tiledb_context): custom_config = self.custom_app_config( dataroot=f"{FIXTURES_ROOT}", cxg_tile_cache_size=10, cxg_num_reader_threads=2 ) config = AppConfig() config.update_from_config_file(custom_config) config.server_config.handle_adaptor() mock_tiledb_context.assert_called_once_with( {"sm.tile_cache_size": 10, "sm.num_reader_threads": 2, "vfs.s3.region": "us-east-1"} )