Merge branch 'dev' into upgrades

Author: uniqueg

.github/workflows/checks.yml

@@ -35,8 +35,7 @@ jobs:
           python-version: ${{ matrix.py-version-img[0] }}
       - name: Install requirements
         run: |
-          pip install -e .
-          pip install -r requirements_dev.txt
+          pip install -e .[dev]
       - name: Lint with flake8
         run: flake8
       - name: Run mypy

foca/models/config.py

@@ -19,7 +19,7 @@
 )
 
 
-def _validate_log_level_choices(level: int) -> int:
+def _validate_log_level_choices(cls, level: int) -> int:
     """Custom validation function for Pydantic to ensure that a valid
     logging level is configured.
 
@@ -32,9 +32,9 @@ def _validate_log_level_choices(level: int) -> int:
     Raises:
         ValueError: Raised if validation fails.
     """
-    choices = [0, 10, 20, 30, 40, 50]
-    if level not in choices:
-        raise ValueError("illegal log level specified")
+    CHOICES = [0, 10, 20, 30, 40, 50]
+    if level not in CHOICES:
+        raise ValueError(f"illegal log level specified: {level}")
     return level
 
 
@@ -593,7 +593,7 @@ def set_abs_path(cls, v):  # pylint: disable=E0213
         absolute path provided.
         """
         # if path is not a list, convert it to single-item list
-        if(isinstance(v, Path)):
+        if (isinstance(v, Path)):
             if not v.is_absolute():
                 return [Path.cwd() / v]
             return [v]
@@ -1181,10 +1181,10 @@ class LogConfig(FOCABaseConfig):
     version: int = 1
     disable_existing_loggers: bool = False
     formatters: Optional[Dict[str, LogFormatterConfig]] = {
-        "standard": LogFormatterConfig(),
+        "standard": LogFormatterConfig(),  # type: ignore
     }
     handlers: Optional[Dict[str, LogHandlerConfig]] = {
-        "console": LogHandlerConfig(),
+        "console": LogHandlerConfig(),  # type: ignore
     }
     root: Optional[LogRootConfig] = LogRootConfig()
 

foca/security/access_control/foca_casbin_adapter/adapter.py

@@ -42,7 +42,9 @@ def __init__(
         self._collection = db[collection]
 
     def load_policy(self, model: CasbinRule):
-        """Implementing add Interface for casbin. Load all policy rules from mongodb
+        """Implementing add Interface for casbin.
+
+        Load all policy rules from MongoDB.
 
         Args:
             model: CasbinRule object.

foca/security/access_control/register_access_control.py

@@ -1,14 +1,16 @@
 """Methods to manage permission management configuration"""
 
 import logging
-from connexion import App
-from connexion.exceptions import Forbidden
-from flask_authz import CasbinEnforcer
+from functools import wraps
 from pkg_resources import resource_filename
+from pathlib import Path
 from typing import (Callable, Optional, Tuple)
-from functools import wraps
+
+from connexion import App
+from connexion.exceptions import Forbidden
 from flask import current_app
 from flask.wrappers import Response
+from flask_authz import CasbinEnforcer
 
 from foca.models.config import (
     DBConfig,
@@ -50,7 +52,7 @@ def register_access_control(
     access_db_conf = DBConfig(
         collections={
             access_control_config.collection_name: CollectionConfig()
-        },
+        } if access_control_config.collection_name is not None else {},
         client=None
     )
 
@@ -113,7 +115,7 @@ def register_permission_specs(
         spec_path = access_control_config.api_specs
 
     spec = SpecConfig(
-        path=spec_path,
+        path=Path(spec_path),
         add_operation_fields={
             "x-openapi-router-controller": (
                 access_control_config.api_controllers
@@ -191,7 +193,9 @@ def check_permissions(
     """
 
     def _decorator_check_permissions(fn):
-        """User access decorator. Used to facilitate optional decorator arguments.
+        """User access decorator.
+
+        Used to facilitate optional decorator arguments.
 
         Args:
             fn: The function to be decorated.
@@ -200,7 +204,7 @@ def _decorator_check_permissions(fn):
             The response returned from the input function.
         """
         @wraps(fn)
-        def _wrapper(*args, **kwargs):
+        def _wrapper(*args, **kwargs) -> Tuple[Response, int]:
             """Wrapper for permissions decorator.
 
             Args:

foca/security/auth.py

@@ -319,7 +319,9 @@ def _get_public_keys(
     public_keys = {}
     for jwk in response.json().get(claim_keys, []):
         try:
-            key = jwt.algorithms.RSAAlgorithm.from_jwk(json.dumps(jwk))
+            key = jwt.algorithms.RSAAlgorithm.from_jwk(  # type:ignore
+                json.dumps(jwk)
+            )
 
             # Ensure key is public
             if not isinstance(key, RSAPublicKey):
@@ -328,7 +330,7 @@ def _get_public_keys(
 
             # Convert to PEM if requested
             if pem:
-                key = key.public_bytes(
+                key = key.public_bytes(  # type: ignore
                     encoding=serialization.Encoding.PEM,
                     format=serialization.PublicFormat.SubjectPublicKeyInfo,
                 ).decode('utf-8').encode('unicode_escape').decode('utf-8')

requirements.txt

@@ -1,17 +1,17 @@
-addict==2.2.1
-celery==5.2.2
-connexion>=2.11.2,<3.0.0
-cryptography==42.0.4
-Flask==2.2.5
-flask-authz==2.5.1
-Flask-Cors==4.0.1
-Flask-PyMongo==2.3.0
-pydantic==1.10.13
-PyJWT==2.4.0
-pymongo==4.7.2
-PyYAML==6.0.1
-requests==2.31.0
-swagger-ui-bundle==0.0.6
-toml==0.10.0
-typing==3.7.4.1
-Werkzeug>=2.2.2,<3.0.0
+addict~=2.2
+celery~=5.2
+connexion~=2.11
+cryptography~=42.0
+Flask~=2.2
+flask-authz~=2.5
+Flask-Cors~=4.0
+Flask-PyMongo~=2.3
+pydantic~=1.10
+PyJWT~=2.4
+pymongo~=4.7
+PyYAML~=6.0
+requests~=2.31
+swagger-ui-bundle~=0.0
+toml~=0.10
+typing~=3.7
+Werkzeug~=2.2

requirements_dev.txt

@@ -1,12 +1,12 @@
-coverage==6.3.2
-flake8==4.0.1
-mongomock==4.0.0
-mypy==0.971
-mypy-extensions==0.4.3
-pylint==2.13.2
-pytest==7.1.1
-python-semantic-release==7.32.2
-types-PyYAML==6.0.12
-types-requests==2.28.11
-types-setuptools==65.3.0
-types-urllib3==1.26.25
+coverage>=6.5
+flake8>=6.1
+mongomock>=4.1
+mypy>=0.991
+mypy-extensions>=0.4.4
+pylint>=3.2
+pytest>=7.4
+python-semantic-release>=7.34,<8.2
+types-PyYAML
+types-requests
+types-setuptools
+types-urllib3

requirements_docs.txt

@@ -1,3 +1,3 @@
-Sphinx==7.2.6
-readthedocs-sphinx-ext==2.2.3
-sphinx-rtd-theme==1.3.0
+Sphinx>=7.2
+readthedocs-sphinx-ext>=2.2
+sphinx-rtd-theme>=1.3

setup.py

@@ -74,13 +74,13 @@
     },
     packages=find_packages(),
     setup_requires=[
-        "setuptools_git==1.2",
-        "twine==3.8.0"
+        "setuptools_git>=1.2",
+        "twine>=3.8.0"
     ],
     install_requires=install_requires,
     extras_require={
-        "docs": docs_require,
         "dev": dev_requires,
+        "docs": docs_require,
     },
     include_package_data=True,
     package_data={

tests/api/controllers/__init__.py

@@ -6,11 +6,11 @@ def listPets():
 
 
 def createPets():
-    return{}
+    return {}
 
 
 def showPetById():
-    return{}
+    return {}
 
 
 def putPetsById():

tests/security/access_control/test_access_control_server.py

@@ -193,8 +193,9 @@ def test_getAllPermissions(self):
             assert res == [data]
 
     def test_getAllPermissions_filters(self):
-        """Test for getting a list of all available permissions; all defined filters
-        specified.
+        """Test for getting a list of all available permissions.
+
+        All defined filters specified.
         """
         app = Flask(__name__)
         base_config = Config(db=MongoConfig(**MONGO_CONFIG))