Added custom flask app wrapper to consume foca as config

foca/api/register_openapi.py

@@ -67,7 +67,7 @@ def register_openapi(
                 # OpenAPI 3
                 sec_schemes = spec_parsed.get(
                     'components', {'securitySchemes': {}}
-                ).get('securitySchemes', {})  # type: ignore
+                ).get('securitySchemes', {})
                 for sec_scheme in sec_schemes.values():
                     sec_scheme[key] = val
             logger.debug(f"Added security fields: {spec.add_security_fields}")

foca/config/config_parser.py

@@ -4,7 +4,7 @@
 import logging
 from logging.config import dictConfig
 from pathlib import Path
-from typing import (Dict, Optional)
+from typing import (Dict, Optional, Callable)
 
 from addict import Dict as Addict
 from pydantic import BaseModel
@@ -157,7 +157,10 @@ def parse_custom_config(self, model: str) -> BaseModel:
         module = Path(model).stem
         model_class = Path(model).suffix[1:]
         try:
-            model_class = getattr(import_module(module), model_class)
+            model_class_instance: Callable = getattr(
+                import_module(module),
+                model_class
+            )
         except ModuleNotFoundError:
             raise ValueError(
                 f"failed validating custom configuration: module '{module}' "
@@ -169,8 +172,7 @@ def parse_custom_config(self, model: str) -> BaseModel:
                 f"has no class {model_class} or could not be imported"
             )
         try:
-            custom_config = model_class(  # type: ignore[operator]
-                **self.config.custom)  # type: ignore[attr-defined]
+            custom_config = model_class_instance(**self.config.custom)
         except Exception as exc:
             raise ValueError(
                 "failed validating custom configuration: provided custom "

foca/errors/exceptions.py

@@ -211,7 +211,8 @@ def _problem_handler_json(exception: Exception) -> Response:
         JSON-formatted error response.
     """
     # Look up exception & get status code
-    conf = current_app.config.foca.exceptions  # type: ignore[attr-defined]
+    foca_conf = getattr(current_app.config, 'foca')
+    conf = foca_conf.exceptions
     exc = type(exception)
     if exc not in conf.mapping:
         exc = Exception

foca/factories/celery_app.py

@@ -3,14 +3,14 @@
 from inspect import stack
 import logging
 
-from flask import Flask
+from connexion import FlaskApp
 from celery import Celery
 
 # Get logger instance
 logger = logging.getLogger(__name__)
 
 
-def create_celery_app(app: Flask) -> Celery:
+def create_celery_app(app: FlaskApp) -> Celery:
     """Create and configure Celery application instance.
 
     Args:
@@ -19,7 +19,7 @@ def create_celery_app(app: Flask) -> Celery:
     Returns:
         Celery application instance.
     """
-    conf = app.config.foca.jobs  # type: ignore[attr-defined]
+    conf = app.config.foca.jobs
 
     # Instantiate Celery app
     celery = Celery(
@@ -32,7 +32,7 @@ def create_celery_app(app: Flask) -> Celery:
     logger.debug(f"Celery app created from '{calling_module}'.")
 
     # Update Celery app configuration with Flask app configuration
-    setattr(celery.conf, 'foca', app.config.foca)  # type: ignore[attr-defined]
+    setattr(celery.conf, 'foca', app.config.foca)
     logger.debug('Celery app configured.')
 
     class ContextTask(celery.Task):  # type: ignore

foca/factories/connexion_app.py

@@ -7,6 +7,7 @@
 from connexion import App
 
 from foca.models.config import Config
+from foca.factories.flask_app import create_flask_app
 
 # Get logger instance
 logger = logging.getLogger(__name__)
@@ -26,6 +27,7 @@ def create_connexion_app(config: Optional[Config] = None) -> App:
         __name__,
         skip_error_handlers=True,
     )
+    app.app = create_flask_app()
 
     calling_module = ':'.join([stack()[1].filename, stack()[1].function])
     logger.debug(f"Connexion app created from '{calling_module}'.")
@@ -71,7 +73,7 @@ def __add_config_to_connexion_app(
         logger.debug('* {}: {}'.format(key, value))
 
     # Add user configuration to Flask app config
-    setattr(app.app.config, 'foca', config)
+    app.app.config.foca = config
 
     logger.debug('Connexion app configured.')
     return app

foca/factories/flask_app.py

@@ -0,0 +1,35 @@
+"""Factory for creating and configuring Connexion application instances."""
+
+from flask import Config, Flask
+from inspect import stack
+import logging
+from typing import Optional
+
+from foca.models.config import Config as FocaConfig
+
+# Get logger instance
+logger = logging.getLogger(__name__)
+
+
+class FocaFlaskAppConfig(Config):
+    """Custom config class wrapper to include foca as an attribute
+    within config.
+    """
+    foca: Optional[FocaConfig]
+
+
+def create_flask_app() -> Flask:
+    """Create and configure Flask application instance for connexion
+    context.
+
+    Returns:
+        Flask application with custom foca config configured.
+    """
+
+    flask_app = Flask(__name__)
+    flask_app.config.from_object(FocaFlaskAppConfig)
+
+    calling_module = ':'.join([stack()[1].filename, stack()[1].function])
+    logger.debug(f"Flask app created from '{calling_module}'.")
+
+    return flask_app

foca/models/config.py

@@ -52,7 +52,7 @@ def _get_by_path(
     Returns:
         Value of innermost key.
     """
-    return reduce(operator.getitem, key_sequence, obj)  # type: ignore
+    return reduce(operator.getitem, key_sequence, obj)
 
 
 class ExceptionLoggingEnum(Enum):
@@ -1200,6 +1200,7 @@ class Config(FOCABaseConfig):
         db: Database config parameters.
         jobs: Background job config parameters.
         log: Logger config parameters.
+        custom: Custom config parameters. (Added by consumers)
 
     Attributes:
         server: Server config parameters.
@@ -1209,6 +1210,7 @@ class Config(FOCABaseConfig):
         db: Database config parameters.
         jobs: Background job config parameters.
         log: Logger config parameters.
+        custom: Custom config parameters. (Added by consumers)
 
     Raises:
         pydantic.ValidationError: The class was instantianted with an illegal
@@ -1248,7 +1250,7 @@ class 'werkzeug.exceptions.BadGateway'>: {'title': 'Bad Gateway', 'status': 50\
 time}: {levelname:<8}] {message} [{name}]')}, handlers={'console': LogHandlerC\
 onfig(class_handler='logging.StreamHandler', level=20, formatter='standard', s\
 tream='ext://sys.stderr')}, root=LogRootConfig(level=10, handlers=['console'])\
-))
+custom=None))
     """
     server: ServerConfig = ServerConfig()
     exceptions: ExceptionConfig = ExceptionConfig()
@@ -1257,6 +1259,7 @@ class 'werkzeug.exceptions.BadGateway'>: {'title': 'Bad Gateway', 'status': 50\
     db: Optional[MongoConfig] = None
     jobs: Optional[JobsConfig] = None
     log: LogConfig = LogConfig()
+    custom: Any = None
 
     class Config:
         """Configuration for Pydantic model class."""

foca/security/access_control/access_control_server.py

@@ -10,6 +10,7 @@
 
 from foca.utils.logging import log_traffic
 from foca.errors.exceptions import BadRequest
+from foca.models.config import AccessControlConfig
 
 logger = logging.getLogger(__name__)
 
@@ -62,16 +63,13 @@ def putPermission(
     """
     request_json = request.json
     if isinstance(request_json, dict):
-        app_config = current_app.config
+        foca_conf = getattr(current_app.config, 'foca')
         try:
-            security_conf = \
-                app_config.foca.security  # type: ignore[attr-defined]
-            access_control_config = \
-                security_conf.access_control  # type: ignore[attr-defined]
+            access_control_conf: AccessControlConfig = \
+                foca_conf.security.access_control
             db_coll_permission: Collection = (
-                app_config.foca.db.dbs[  # type: ignore[attr-defined]
-                    access_control_config.db_name]
-                .collections[access_control_config.collection_name].client
+                foca_conf.db.dbs[access_control_conf.db_name]
+                .collections[access_control_conf.collection_name].client
             )
 
             permission_data = request_json.get("rule", {})
@@ -102,11 +100,10 @@ def getAllPermissions(limit=None) -> List[Dict]:
     Returns:
         List of permission dicts.
     """
-    app_config = current_app.config
-    access_control_config = \
-        app_config.foca.security.access_control  # type: ignore[attr-defined]
+    foca_conf = getattr(current_app.config, 'foca')
+    access_control_config = foca_conf.security.access_control
     db_coll_permission: Collection = (
-        app_config.foca.db.dbs[  # type: ignore[attr-defined]
+        foca_conf.db.dbs[
             access_control_config.db_name
         ].collections[access_control_config.collection_name].client
     )
@@ -145,11 +142,10 @@ def getPermission(
     Returns:
         Permission data for the given id.
     """
-    app_config = current_app.config
-    access_control_config = \
-        app_config.foca.security.access_control  # type: ignore[attr-defined]
+    foca_conf = getattr(current_app.config, 'foca')
+    access_control_config = foca_conf.security.access_control
     db_coll_permission: Collection = (
-        app_config.foca.db.dbs[  # type: ignore[attr-defined]
+        foca_conf.db.dbs[
             access_control_config.db_name
         ].collections[access_control_config.collection_name].client
     )
@@ -181,11 +177,10 @@ def deletePermission(
     Returns:
         Delete permission identifier.
     """
-    app_config = current_app.config
-    access_control_config = \
-        app_config.foca.security.access_control  # type: ignore[attr-defined]
+    foca_conf = getattr(current_app.config, 'foca')
+    access_control_config = foca_conf.security.access_control
     db_coll_permission: Collection = (
-        app_config.foca.db.dbs[  # type: ignore[attr-defined]
+        foca_conf.db.dbs[
             access_control_config.db_name
         ].collections[access_control_config.collection_name].client
     )

foca/security/access_control/foca_casbin_adapter/adapter.py

@@ -2,7 +2,7 @@
 
 from casbin import persist
 from casbin.model import Model
-from typing import (List, Optional)
+from typing import (Any, Dict, List, Optional)
 from pymongo import MongoClient
 
 from foca.security.access_control.foca_casbin_adapter.casbin_rule import (
@@ -170,10 +170,10 @@ def remove_filtered_policy(
         if not (1 <= field_index + len(field_values) <= 6):
             return False
 
-        query = {}
+        query: Dict[str, Any] = {}
         for index, value in enumerate(field_values):
             query[f"v{index + field_index}"] = value
 
-        query["ptype"] = ptype  # type: ignore[assignment]
+        query["ptype"] = ptype
         results = self._collection.delete_many(query)
         return results.deleted_count > 0

foca/security/auth.py

@@ -2,18 +2,20 @@
 
 from connexion.exceptions import Unauthorized
 import logging
-from typing import (Dict, Iterable, List, Optional)
+from typing import (Any, cast, Dict, Iterable, List, Optional)
 
 from cryptography.hazmat.primitives import serialization
 from cryptography.hazmat.primitives.asymmetric.rsa import RSAPublicKey
-from flask import current_app, request
+from flask import (current_app, request)
 import jwt
 from jwt.exceptions import InvalidKeyError
 import requests
 from requests.exceptions import ConnectionError
 import json
 from werkzeug.datastructures import ImmutableMultiDict
 
+from foca.models.config import Config
+
 # Get logger instance
 logger = logging.getLogger(__name__)
 
@@ -36,7 +38,8 @@ def validate_token(token: str) -> Dict:
     oidc_config_claim_public_keys: str = 'jwks_uri'
 
     # Fetch security parameters
-    conf = current_app.config.foca.security.auth  # type: ignore[attr-defined]
+    foca_conf = cast(Config, getattr(current_app.config, 'foca'))
+    conf = foca_conf.security.auth
     add_key_to_claims: bool = conf.add_key_to_claims
     allow_expired: bool = conf.allow_expired
     audience: Optional[Iterable[str]] = conf.audience
@@ -245,10 +248,10 @@ def _validate_jwt_public_key(
         validation_options['verify_exp'] = False
 
     # Try public keys one after the other
-    used_key: Dict = {}
+    used_key: Any = {}
     claims = {}
     for key in public_keys.values():
-        used_key = key  # type: ignore[assignment]
+        used_key = key
 
         # Decode JWT and validate via public key
         try:

tests/errors/test_errors.py

@@ -18,6 +18,7 @@
     _subset_nested_dict,
 )
 from foca.models.config import Config
+from foca.factories.flask_app import FocaFlaskAppConfig
 
 EXCEPTION_INSTANCE = Exception()
 INVALID_LOG_FORMAT = 'unknown_log_format'
@@ -103,7 +104,8 @@ def test__exclude_key_nested_dict():
 def test__problem_handler_json():
     """Test problem handler with instance of custom, unlisted error."""
     app = Flask(__name__)
-    setattr(app.config, 'foca', Config())
+    app.config.from_object(FocaFlaskAppConfig)
+    app.config.foca = Config()
     EXPECTED_RESPONSE = app.config.foca.exceptions.mapping[Exception]
     with app.app_context():
         res = _problem_handler_json(UnknownException())
@@ -117,7 +119,8 @@ def test__problem_handler_json():
 def test__problem_handler_json_no_fallback_exception():
     """Test problem handler; unlisted error without fallback."""
     app = Flask(__name__)
-    setattr(app.config, 'foca', Config())
+    app.config.from_object(FocaFlaskAppConfig)
+    app.config.foca = Config()
     del app.config.foca.exceptions.mapping[Exception]
     with app.app_context():
         res = _problem_handler_json(UnknownException())
@@ -131,7 +134,8 @@ def test__problem_handler_json_no_fallback_exception():
 def test__problem_handler_json_with_public_members():
     """Test problem handler with public members."""
     app = Flask(__name__)
-    setattr(app.config, 'foca', Config())
+    app.config.from_object(FocaFlaskAppConfig)
+    app.config.foca = Config()
     app.config.foca.exceptions.public_members = PUBLIC_MEMBERS
     with app.app_context():
         res = _problem_handler_json(UnknownException())
@@ -143,7 +147,8 @@ def test__problem_handler_json_with_public_members():
 def test__problem_handler_json_with_private_members():
     """Test problem handler with private members."""
     app = Flask(__name__)
-    setattr(app.config, 'foca', Config())
+    app.config.from_object(FocaFlaskAppConfig)
+    app.config.foca = Config()
     app.config.foca.exceptions.private_members = PRIVATE_MEMBERS
     with app.app_context():
         res = _problem_handler_json(UnknownException())

tests/factories/test_flask_app.py

@@ -0,0 +1,13 @@
+"""Tests for foca.factories.flask_app."""
+from flask import Flask
+
+from foca.factories.flask_app import create_flask_app
+from foca.models.config import Config
+
+
+def test_create_flask_app():
+    """Test Connexion app creation without config."""
+    flask_app = create_flask_app()
+    assert isinstance(flask_app, Flask)
+    flask_app.config.foca = Config()
+    assert isinstance(flask_app.config.foca, Config)