def _is_accessible(path, config):
if path is None:
return True
try:
dl = DataLocator(path,
region_name=config.data_locator__s3__region_name)
return dl.exists()
except RuntimeError:
return False
class MatrixDataLoader(object):
def __init__(self, location, matrix_data_type=None, app_config=None):
""" location can be a string or DataLocator """
region_name = None if app_config is None else app_config.server_config.data_locator__s3__region_name
self.location = DataLocator(location, region_name=region_name)
if not self.location.exists():
raise DatasetAccessError("Dataset does not exist.",
HTTPStatus.NOT_FOUND)
# matrix_data_type is an enum value of type MatrixDataType
self.matrix_data_type = matrix_data_type
# matrix_type is a DataAdaptor type, which corresonds to the matrix_data_type
self.matrix_type = None
if matrix_data_type is None:
self.matrix_data_type = self.__matrix_data_type()
if not self.__matrix_data_type_allowed(app_config):
raise DatasetAccessError("Dataset does not have an allowed type.")
if self.matrix_data_type == MatrixDataType.H5AD:
from local_server.data_anndata.anndata_adaptor import AnndataAdaptor
self.matrix_type = AnndataAdaptor
def __matrix_data_type(self):
if self.location.path.endswith(".h5ad"):
return MatrixDataType.H5AD
else:
return MatrixDataType.UNKNOWN
def __matrix_data_type_allowed(self, app_config):
return self.matrix_data_type != MatrixDataType.UNKNOWN
def pre_load_validation(self):
if self.matrix_data_type == MatrixDataType.UNKNOWN:
raise DatasetAccessError(
"Dataset does not have a recognized type: .h5ad")
self.matrix_type.pre_load_validation(self.location)
def file_size(self):
return self.matrix_type.file_size(self.location)
def open(self, app_config, dataset_config=None):
# create and return a DataAdaptor object
return self.matrix_type.open(self.location, app_config, dataset_config)