def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False):
tmp_dir = tempfile.mkdtemp()
annotations_file = path.join(tmp_dir, "test_annotations.csv")
if annotations_fixture:
shutil.copyfile(
f"{PROJECT_ROOT}/server/test/fixtures/pbmc3k-annotations.csv",
annotations_file)
fname = {
MatrixDataType.H5AD: f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
MatrixDataType.CXG: "test/fixtures/pbmc3k.cxg",
}[ext]
data_locator = DataLocator(fname)
config = AppConfig()
config.update_server_config(
app__flask_secret_key="secret",
single_dataset__obs_names=None,
single_dataset__var_names=None,
single_dataset__datapath=data_locator.path,
)
config.update_default_dataset_config(
embeddings__names=["umap"],
presentation__max_categories=100,
diffexp__lfc_cutoff=0.01,
)
config.complete_config()
data = MatrixDataLoader(data_locator.abspath()).open(config)
annotations = AnnotationsLocalFile(None, annotations_file)
return data, tmp_dir, annotations
def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False):
tmp_dir = tempfile.mkdtemp()
annotations_file = path.join(tmp_dir, "test_annotations.csv")
if annotations_fixture:
shutil.copyfile(
f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-annotations.csv",
annotations_file)
args = {
"embeddings__names": ["umap"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
"diffexp__lfc_cutoff": 0.01,
}
fname = {
MatrixDataType.H5AD: f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
MatrixDataType.CXG: "test/test_datasets/pbmc3k.cxg",
}[ext]
data_locator = DataLocator(fname)
config = AppConfig()
config.update(**args)
config.update(single_dataset__datapath=data_locator.path)
config.complete_config()
data = MatrixDataLoader(data_locator.abspath()).open(config)
annotations = AnnotationsLocalFile(None, annotations_file)
return data, tmp_dir, annotations
def data_with_tmp_tiledb_annotations(ext: MatrixDataType):
tmp_dir = tempfile.mkdtemp()
fname = {
MatrixDataType.H5AD: f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
MatrixDataType.CXG: "test/fixtures/pbmc3k.cxg",
}[ext]
data_locator = DataLocator(fname)
config = AppConfig()
config.update_server_config(
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"],
presentation__max_categories=100,
diffexp__lfc_cutoff=0.01,
user_annotations__type="hosted_tiledb_array",
user_annotations__hosted_tiledb_array__db_uri=
"postgresql://*****:*****@localhost:5432",
user_annotations__hosted_tiledb_array__hosted_file_directory=tmp_dir,
)
config.complete_config()
data = MatrixDataLoader(data_locator.abspath()).open(config)
annotations = AnnotationsHostedTileDB(
tmp_dir,
DbUtils("postgresql://*****:*****@localhost:5432"),
)
return data, tmp_dir, annotations