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Enhance the AppConfig with external config sources. (#1904)

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* Enhance the AppConfig with external config sources.

The external config sources are currently environment variables
and AWS secrets manager.

The config file can be augmented with a section describing how
environmen variables and secrets can update config parameters.

benefits:
 - it will enable the config to draw from more than one secret.  This is useful
   for shared secrets between cellxgene and data portal, as well as auth0 secrets.
 - it will make it very straightforward to check the config before a deployment.

 Part of #1859
This commit is contained in:
bmccandless
2020-10-07 15:38:42 -07:00
committed by GitHub
parent 1c4c501c43
commit 6c1756f852
14 changed files with 632 additions and 55 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/common/config/dataset_config.py
+10 -14
View File
@@ -30,22 +30,18 @@ class DatasetConfig(BaseConfig):
self.user_annotations__type = default_config["user_annotations"]["type"]
self.user_annotations__local_file_csv__directory = default_config["user_annotations"]["local_file_csv"][
"directory"
] # noqa E501
]
self.user_annotations__local_file_csv__file = default_config["user_annotations"]["local_file_csv"]["file"]
self.user_annotations__ontology__enable = default_config["user_annotations"]["ontology"]["enable"]
self.user_annotations__ontology__obo_location = default_config["user_annotations"]["ontology"][
"obo_location"
] # noqa E501
]
self.user_annotations__hosted_tiledb_array__db_uri = default_config["user_annotations"][
"hosted_tiledb_array"
][
"db_uri"
] # noqa E501
]["db_uri"]
self.user_annotations__hosted_tiledb_array__hosted_file_directory = default_config["user_annotations"][
"hosted_tiledb_array"
][
"hosted_file_directory"
] # noqa E501
]["hosted_file_directory"]
self.embeddings__names = default_config["embeddings"]["names"]
self.embeddings__enable_reembedding = default_config["embeddings"]["enable_reembedding"]
@@ -98,20 +94,20 @@ class DatasetConfig(BaseConfig):
self.validate_correct_type_of_configuration_attribute("user_annotations__type", str)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__local_file_csv__directory", (type(None), str)
) # noqa E501
)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__local_file_csv__file", (type(None), str)
) # noqa E501
)
self.validate_correct_type_of_configuration_attribute("user_annotations__ontology__enable", bool)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__ontology__obo_location", (type(None), str)
) # noqa E501
)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__hosted_tiledb_array__db_uri", (type(None), str)
) # noqa E501
)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__hosted_tiledb_array__hosted_file_directory", (type(None), str)
) # noqa E501
)
if self.user_annotations__enable:
server_config = self.app_config.server_config
if not self.app__authentication_enable:
@@ -166,7 +162,7 @@ class DatasetConfig(BaseConfig):
self.validate_correct_type_of_configuration_attribute("user_annotations__hosted_tiledb_array__db_uri", str)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__hosted_tiledb_array__hosted_file_directory", str
) # noqa E501
)
self.user_annotations = AnnotationsHostedTileDB(
directory_path=self.user_annotations__hosted_tiledb_array__hosted_file_directory,
db=DbUtils(self.user_annotations__hosted_tiledb_array__db_uri),