move common code into server, update tests and makefile (#2425)

* move common code into server, update tests and makefile

remove backend directory, refactor

update smoke tests

server/data_common/matrix_loader.py

@@ -0,0 +1,56 @@
+from enum import Enum
+
+from server.common.utils.data_locator import DataLocator
+from server.common.errors import DatasetAccessError
+from http import HTTPStatus
+
+
+class MatrixDataType(Enum):
+    H5AD = "h5ad"
+    UNKNOWN = "unknown"
+
+
+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 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)