Update for app config (#1369)

fixes an issue with "cellxgene launch" which had a bad interaction between
command line parameters and config file parameters.
Now, the config files are applied first, followed by the parameters that
were provided in the command line.

There is also now a check that each of the config attributes is type checked.

server/cli/launch.py

@@ -358,7 +358,10 @@ def launch(
         if config_file:
             app_config.update_from_config_file(config_file)
 
-        app_config.update(
+        # Determine which config options were give on the command line.
+        # Those will override the ones provided in the config file (if provided).
+        cli_config = AppConfig()
+        cli_config.update(
             server__verbose=verbose,
             server__debug=debug,
             server__host=host,
@@ -383,6 +386,11 @@ def launch(
             diffexp__lfc_cutoff=diffexp_lfc_cutoff,
             adaptor__anndata_adaptor__backed=backed,
         )
+        diff = cli_config.changes_from_default()
+        changes = {}
+        for key, val, defval in diff:
+            changes[key] = val
+        app_config.update(**changes)
 
         # process the configuration
         #  any errors will be thrown as an exception.
@@ -391,11 +399,11 @@ def launch(
         def messagefn(message):
             click.echo("[cellxgene] " + message)
 
-        app_config.complete_config(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"
+            app_config.update(server__flask_secret_key="SparkleAndShine")
+
+        app_config.complete_config(messagefn)
 
     except (ConfigurationError, DatasetAccessError) as e:
         raise click.ClickException(e)