def setUp(self):
self.data_locator = DataLocator(f"{PROJECT_ROOT}/server/test/test_datasets/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 convert_pbmc3k(self, **kwargs):
rand_str = random_string(8)
data_locator = f"/tmp/test_{rand_str}.cxg"
self.fixtures.append(data_locator)
source_h5ad = anndata.read_h5ad(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
write_cxg(adata=source_h5ad, container=data_locator, title="pbmc3k", **kwargs)
config = app_config(data_locator)
return CxgAdaptor(DataLocator(data_locator), config)
def load_dataset(self,
path,
extra_server_config={},
extra_dataset_config={}):
config = app_config(path,
extra_server_config=extra_server_config,
extra_dataset_config=extra_dataset_config)
loader = MatrixDataLoader(path)
adaptor = loader.open(config)
return adaptor
def convert_pbmc3k(self, **kwargs):
random_string = "".join(
random.choice(string.ascii_letters) for _ in range(8))
data_locator = f"/tmp/test_{random_string}.cxg"
self.fixtures.append(data_locator)
source_h5ad = anndata.read_h5ad(
f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
write_cxg(adata=source_h5ad,
container=data_locator,
title="pbmc3k",
**kwargs)
config = app_config(data_locator)
return CxgAdaptor(DataLocator(data_locator), config)
def setUp(self):
config = app_config(self.data_locator, self.backed)
self.data = AnndataAdaptor(DataLocator(self.data_locator), config)
def get_data(self, fixture):
data_locator = f"{PROJECT_ROOT}/server/test/test_datasets/{fixture}"
config = app_config(data_locator)
return CxgAdaptor(DataLocator(data_locator), config)
def get_data(self, fixture):
data_locator = f"{FIXTURES_ROOT}/{fixture}"
config = app_config(data_locator)
return CxgAdaptor(DataLocator(data_locator), config)
def setUp(self):
data_locator = f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg"
config = app_config(data_locator)
self.data = CxgAdaptor(DataLocator(data_locator), config)