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3ebbb0ccbf
* move common code into server, update tests and makefile remove backend directory, refactor update smoke tests
57 lines
2.1 KiB
Python
57 lines
2.1 KiB
Python
from enum import Enum
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from server.common.utils.data_locator import DataLocator
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from server.common.errors import DatasetAccessError
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from http import HTTPStatus
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class MatrixDataType(Enum):
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H5AD = "h5ad"
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UNKNOWN = "unknown"
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class MatrixDataLoader(object):
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def __init__(self, location, matrix_data_type=None, app_config=None):
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""" location can be a string or DataLocator """
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region_name = None if app_config is None else app_config.server_config.data_locator__s3__region_name
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self.location = DataLocator(location, region_name=region_name)
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if not self.location.exists():
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raise DatasetAccessError("Dataset does not exist.", HTTPStatus.NOT_FOUND)
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# matrix_data_type is an enum value of type MatrixDataType
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self.matrix_data_type = matrix_data_type
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# matrix_type is a DataAdaptor type, which corresonds to the matrix_data_type
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self.matrix_type = None
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if matrix_data_type is None:
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self.matrix_data_type = self.__matrix_data_type()
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if not self.__matrix_data_type_allowed(app_config):
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raise DatasetAccessError("Dataset does not have an allowed type.")
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if self.matrix_data_type == MatrixDataType.H5AD:
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from server.data_anndata.anndata_adaptor import AnndataAdaptor
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self.matrix_type = AnndataAdaptor
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def __matrix_data_type(self):
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if self.location.path.endswith(".h5ad"):
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return MatrixDataType.H5AD
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else:
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return MatrixDataType.UNKNOWN
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def __matrix_data_type_allowed(self, app_config):
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return self.matrix_data_type != MatrixDataType.UNKNOWN
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def pre_load_validation(self):
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if self.matrix_data_type == MatrixDataType.UNKNOWN:
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raise DatasetAccessError("Dataset does not have a recognized type: .h5ad")
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self.matrix_type.pre_load_validation(self.location)
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def file_size(self):
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return self.matrix_type.file_size(self.location)
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def open(self, app_config, dataset_config=None):
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# create and return a DataAdaptor object
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return self.matrix_type.open(self.location, app_config, dataset_config)
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