Add black for code formatting. Remove some linting exclusions. Fix errors.

Author: mfjarvis

.github/workflows/quality-checks.yml

@@ -12,8 +12,26 @@ env:
   LAMBDA_PATH: ${{ github.workspace }}/lambdas
 
 jobs:
-  lint:
-    name: Lint specification and Python projects
+  lint-specification:
+    name: Lint specification
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: actions/setup-node@v5
+        with:
+          node-version: '23.11.0'
+          cache: 'npm'
+
+      - name: Install linting dependencies
+        run: make install-node
+
+      - name: Lint
+        run: make lint
+
+  lint-python:
+    name: Lint Python projects
     runs-on: ubuntu-latest
 
     steps:
@@ -22,23 +40,22 @@ jobs:
       - name: Install poetry
         run: pip install poetry==2.1.4
 
-      # Base linting requires 3.8 due to APIM package dependencies. See root README for details under linting.
-      # Consider upgrading this and poetry deps if we move away from Azure DevOps to using the Proxygen tool.
       - uses: actions/setup-python@v6
         with:
-          python-version: 3.8
+          python-version: 3.11
           cache: 'poetry'
 
-      - uses: actions/setup-node@v5
-        with:
-          node-version: '23.11.0'
-          cache: 'npm'
-
       - name: Install linting dependencies
-        run: make install-node && poetry install --no-root
+        run: poetry install
+        working-directory: quality-checks
 
       - name: Lint
-        run: make lint
+        run: poetry run lint
+        working-directory: quality-checks
+
+      - name: Check formatting
+        run: poetry run format-check
+        working-directory: quality-checks
 
   testcoverage_and_sonarcloud:
     name: Test Coverage and SonarCloud

Makefile

@@ -22,7 +22,6 @@ install: install-node install-python .git/hooks/pre-commit
 #Run the npm linting script (specified in package.json). Used to check the syntax and formatting of files.
 lint:
 	npm run lint
-	find . -name '*.py' -not -path '**/.venv/*' -not -path '**/.terraform/*'| xargs poetry run flake8
 
 #Removes build/ + dist/ directories
 clean:

backend/src/__init__.py

@@ -1 +0,0 @@
-

backend/src/authorisation/authoriser.py

@@ -1,4 +1,5 @@
 """Authoriser class"""
+
 import json
 
 from authorisation.api_operation_code import ApiOperationCode
@@ -8,13 +9,17 @@
 
 class Authoriser:
     """Authoriser class. Used for authorising operations on FHIR vaccinations."""
+
     def __init__(self):
         self._cache_client = redis_client
 
     @staticmethod
-    def _expand_permissions(permissions: list[str]) -> dict[str, list[ApiOperationCode]]:
+    def _expand_permissions(
+        permissions: list[str],
+    ) -> dict[str, list[ApiOperationCode]]:
         """Parses and expands permissions data into a dictionary mapping vaccination types to a list of permitted
-        API operations. The raw string from Redis will be in the form VAC.PERMS e.g. COVID19.CRUDS"""
+        API operations. The raw string from Redis will be in the form VAC.PERMS e.g. COVID19.CRUDS
+        """
         expanded_permissions = {}
 
         for permission in permissions:
@@ -39,7 +44,7 @@ def authorise(
         self,
         supplier_system: str,
         requested_operation: ApiOperationCode,
-        vaccination_types: set[str]
+        vaccination_types: set[str],
     ) -> bool:
         """Checks that the supplier system is permitted to carry out the requested operation on the given vaccination
         type(s)"""
@@ -58,7 +63,7 @@ def filter_permitted_vacc_types(
         self,
         supplier_system: str,
         requested_operation: ApiOperationCode,
-        vaccination_types: set[str]
+        vaccination_types: set[str],
     ) -> set[str]:
         """Returns the set of vaccine types that a given supplier can interact with for a given operation type.
         This is a more permissive form of authorisation e.g. used in search as it will filter out any requested vacc

backend/src/clients.py

@@ -1,9 +1,10 @@
 """Initialise s3, kinesis, lambda and redis clients"""
 
-from boto3 import client as boto3_client
-import os
 import logging
+import os
+
 import redis
+from boto3 import client as boto3_client
 
 REGION_NAME = os.getenv("AWS_REGION", "eu-west-2")
 

backend/src/controller/aws_apig_event_utils.py

@@ -1,4 +1,5 @@
 """Utility module for interacting with the AWS API Gateway event provided to controllers"""
+
 from typing import Optional
 
 from aws_lambda_typing.events import APIGatewayProxyEventV1
@@ -9,11 +10,7 @@
 
 
 def get_path_parameter(event: APIGatewayProxyEventV1, param_name: str) -> str:
-    return dict_utils.get_field(
-        event["pathParameters"],
-        param_name,
-        default=""
-    )
+    return dict_utils.get_field(event["pathParameters"], param_name, default="")
 
 
 def get_supplier_system_header(event: APIGatewayProxyEventV1) -> str:

backend/src/controller/aws_apig_response_utils.py

@@ -1,13 +1,10 @@
 """Utility module providing helper functions for dealing with response formats for AWS API Gateway"""
+
 import json
 from typing import Optional
 
 
-def create_response(
-    status_code: int,
-    body: Optional[dict | str] = None,
-    headers: Optional[dict] = None
-):
+def create_response(status_code: int, body: Optional[dict | str] = None, headers: Optional[dict] = None):
     """Creates response body as per Lambda -> API Gateway proxy integration"""
     if body is not None:
         if isinstance(body, dict):

backend/src/controller/constants.py

@@ -1,5 +1,4 @@
 """FHIR Controller constants"""
 
-
 SUPPLIER_SYSTEM_HEADER_NAME = "SupplierSystem"
 E_TAG_HEADER_NAME = "E-Tag"

backend/src/controller/fhir_api_exception_handler.py

@@ -1,19 +1,25 @@
 """Module for the global FHIR API exception handler"""
+
 import functools
 import uuid
 from typing import Callable, Type
 
 from clients import logger
 from constants import GENERIC_SERVER_ERROR_DIAGNOSTICS_MESSAGE
 from controller.aws_apig_response_utils import create_response
-from models.errors import UnauthorizedVaxError, UnauthorizedError, ResourceNotFoundError, create_operation_outcome, \
-    Severity, Code
-
+from models.errors import (
+    UnauthorizedVaxError,
+    UnauthorizedError,
+    ResourceNotFoundError,
+    create_operation_outcome,
+    Severity,
+    Code,
+)
 
 _CUSTOM_EXCEPTION_TO_STATUS_MAP: dict[Type[Exception], int] = {
     UnauthorizedError: 403,
     UnauthorizedVaxError: 403,
-    ResourceNotFoundError: 404
+    ResourceNotFoundError: 404,
 }
 
 
@@ -39,4 +45,3 @@ def wrapper(*args, **kwargs):
             return create_response(500, server_error)
 
     return wrapper
-

backend/src/controller/fhir_batch_controller.py

@@ -1,7 +1,7 @@
 """Function to send the request directly to lambda (or return appropriate diagnostics if this is not possible)"""
 
-from service.fhir_batch_service import ImmunizationBatchService
 from repository.fhir_batch_repository import ImmunizationBatchRepository
+from service.fhir_batch_service import ImmunizationBatchService
 
 
 def make_batch_controller():
@@ -33,5 +33,9 @@ def send_request_to_dynamo(self, message_body: dict, table: any, is_present: boo
             "DELETE": self.fhir_service.delete_immunization,
         }
         return function_map[operation_requested](
-            immunization=fhir_json, supplier_system=supplier, vax_type=vax_type, table=table, is_present=is_present
+            immunization=fhir_json,
+            supplier_system=supplier,
+            vax_type=vax_type,
+            table=table,
+            is_present=is_present,
         )