Remove use of instance path in configurations.

1 files changed, 13 insertions, 12 deletions

diff --git a/qc_app/__init__.py b/qc_app/__init__.py
index 1215954..045572c 100644
--- a/qc_app/__init__.py
+++ b/qc_app/__init__.py
@@ -11,22 +11,23 @@ from .samples import samples
 from .dbinsert import dbinsertbp
 from .errors import register_error_handlers
 
-def instance_path():
-    """Retrieve the `instance_path`. Raise an exception if not defined."""
-    path = os.getenv("QCAPP_INSTANCE_PATH", None)
-    if path is None:
-        raise Exception((
-            "Configuration Error: Set the `QCAPP_INSTANCE_PATH` environment "
-            "variable."))
-
-    return path
+def override_settings_with_envvars(
+        app: Flask, ignore: tuple[str, ...]=tuple()) -> None:
+    """Override settings in `app` with those in ENVVARS"""
+    for setting in (key for key in app.config if key not in ignore):
+        app.config[setting] = os.environ.get(setting) or app.config[setting]
 
 def create_app(instance_dir):
     """The application factory"""
-    app = Flask(
-        __name__, instance_path=instance_dir, instance_relative_config=True)
+    app = Flask(__name__)
     app.config.from_pyfile(os.path.join(os.getcwd(), "etc/default_config.py"))
-    app.config.from_pyfile("config.py") # Override defaults with instance path
+    if "QCAPP_CONF" in os.environ:
+        app.config.from_envvar("QCAPP_CONF") # Override defaults with instance path
+
+    override_settings_with_envvars(app, ignore=tuple())
+
+    if "QCAPP_SECRETS" in os.environ:
+        app.config.from_envvar("QCAPP_SECRETS")
 
     # setup blueprints
     app.register_blueprint(entrybp, url_prefix="/")