def test_posix_file(self):
locator = DataLocator("../../example-dataset/pbmc3k.h5ad")
config = self.get_basic_config()
config.update_server_config(single_dataset__datapath=locator.path)
config.complete_config()
data = AnndataAdaptor(locator, config)
self.stdAsserts(data)
def setUp(self):
self.data_locator = DataLocator(f"{FIXTURES_ROOT}/nan.h5ad")
self.config = app_config(self.data_locator.path)
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=UserWarning)
self.data = AnndataAdaptor(self.data_locator, self.config)
self.data._create_schema()
def setUp(self):
self.data_file = DataLocator(
f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
config = AppConfig()
config.update_server_config(
single_dataset__datapath=self.data_file.path)
config.update_server_config(app__flask_secret_key="secret")
config.complete_config()
self.data = AnndataAdaptor(self.data_file, config)
def test_load(self):
with self.assertLogs(level="WARN") as logger:
self.data = AnndataAdaptor(self.data_locator, self.config)
self.assertTrue(logger.output)
def test_url_http(self):
url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/main/example-dataset/pbmc3k.h5ad"
locator = DataLocator(url)
config = self.get_basic_config()
data = AnndataAdaptor(locator, config)
self.stdAsserts(data)
def setUp(self):
config = app_config(self.data_locator, self.backed)
self.data = AnndataAdaptor(DataLocator(self.data_locator), config)