Added a config hook for secret key into the app. (#1304)

* Added a config hook for secret key into the app.

the server first looks in an environment variable,
then looks in a config file.

For the cellxgene launch app, a default key is used if none is provided.
For the eb app, a secret key must be provided.

server/app/app.py

@@ -207,8 +207,8 @@ class Server:
         self.app.permanent_session_lifetime = datetime.timedelta(days=50 * 365)
 
         # Config
-        SECRET_KEY = os.environ.get("CXG_SECRET_KEY", default="SparkleAndShine")
-        self.app.config.update(SECRET_KEY=SECRET_KEY)
+        secret_key = app_config.server__flask_secret_key
+        self.app.config.update(SECRET_KEY=secret_key)
 
         self.app.register_blueprint(webbp)
 

server/cli/launch.py

@@ -275,6 +275,7 @@ class CliLaunchServer(Server):
     """
     the CLI runs a local web server, and needs to enable a few more features.
     """
+
     def __init__(self, matrix_data_cache_manager, annotations, app_config):
         super().__init__(matrix_data_cache_manager, annotations, app_config)
 
@@ -394,6 +395,10 @@ def launch(
 
         app_config.complete_config(matrix_data_cache_manager, messagefn)
 
+        # Use a default secret if one is not provided
+        if not app_config.server__flask_secret_key:
+            app_config.server__flask_secret_key = "SparkleAndShine"
+
     except (ConfigurationError, DatasetAccessError) as e:
         raise click.ClickException(e)
 

server/common/app_config.py

@@ -65,28 +65,37 @@ class AppConfig(object):
             self.server__about_legal_tos = dc["server"]["about_legal_tos"]
             self.server__about_legal_privacy = dc["server"]["about_legal_privacy"]
             self.server__force_https = dc["server"]["force_https"]
+            self.server__flask_secret_key = dc["server"]["flask_secret_key"]
+
             self.multi_dataset__dataroot = dc["multi_dataset"]["dataroot"]
             self.multi_dataset__index = dc["multi_dataset"]["index"]
             self.multi_dataset__allowed_matrix_types = dc["multi_dataset"]["allowed_matrix_types"]
             self.multi_dataset__matrix_cache__max_datasets = dc["multi_dataset"]["matrix_cache"]["max_datasets"]
+
             self.single_dataset__datapath = dc["single_dataset"]["datapath"]
             self.single_dataset__obs_names = dc["single_dataset"]["obs_names"]
             self.single_dataset__var_names = dc["single_dataset"]["var_names"]
             self.single_dataset__about = dc["single_dataset"]["about"]
             self.single_dataset__title = dc["single_dataset"]["title"]
+
             self.user_annotations__enable = dc["user_annotations"]["enable"]
             self.user_annotations__type = dc["user_annotations"]["type"]
             self.user_annotations__local_file_csv__directory = dc["user_annotations"]["local_file_csv"]["directory"]
             self.user_annotations__local_file_csv__file = dc["user_annotations"]["local_file_csv"]["file"]
             self.user_annotations__ontology__enable = dc["user_annotations"]["ontology"]["enable"]
             self.user_annotations__ontology__obo_location = dc["user_annotations"]["ontology"]["obo_location"]
+
             self.presentation__max_categories = dc["presentation"]["max_categories"]
+
             self.embeddings__names = dc["embeddings"]["names"]
             self.embeddings__enable_reembedding = dc["embeddings"]["enable_reembedding"]
+
             self.diffexp__enable = dc["diffexp"]["enable"]
             self.diffexp__lfc_cutoff = dc["diffexp"]["lfc_cutoff"]
+
             self.adaptor__cxg_adaptor__tiledb_ctx = dc["adaptor"]["cxg_adaptor"]["tiledb_ctx"]
             self.adaptor__anndata_adaptor__backed = dc["adaptor"]["anndata_adaptor"]["backed"]
+
         except KeyError as e:
             raise ConfigurationError(f"Unexpected config: {str(e)}")
 
@@ -184,6 +193,8 @@ class AppConfig(object):
         self.__check_attr("server__port", (type(None), int))
         self.__check_attr("server__scripts", (list, tuple))
         self.__check_attr("server__open_browser", bool)
+        self.__check_attr("server__force_https", bool)
+        self.__check_attr("server__flask_secret_key", (type(None), str))
 
         if self.server__port:
             if not is_port_available(self.server__host, self.server__port):
@@ -203,6 +214,11 @@ class AppConfig(object):
         if not self.server__verbose:
             sys.tracebacklimit = 0
 
+        # secret key:
+        #   first, from CXG_SECRET_KEY environment variable
+        #   second, from config file
+        self.server__flask_secret_key = environ.get("CXG_SECRET_KEY", self.server__flask_secret_key)
+
     def handle_presentation(self, context):
         self.__check_attr("presentation__max_categories", int)
 

server/common/default_config.py

@@ -13,6 +13,7 @@ server:
   about_legal_tos: null
   about_legal_privacy: null
   force_https: false
+  flask_secret_key: null
 
 presentation:
   max_categories: 1000

server/eb/app.py

@@ -77,6 +77,13 @@ try:
 
     matrix_data_cache_manager = MatrixDataCacheManager()
     app_config.complete_config(matrix_data_cache_manager, logging.info)
+
+    if not app_config.server__flask_secret_key:
+        logging.critical(
+            f"flask_secret_key is not provided.  Either set in config file, or in CXG_SECRET_KEY environment variable"
+        )
+        sys.exit(1)
+
     user_annotations = app_config.user_annotations
 
     server = WSGIServer(matrix_data_cache_manager, user_annotations, app_config)