Initial refactoring

Author: dlzhry2nhs

backend/src/controller/fhir_api_exception_handler.py

@@ -9,17 +9,25 @@
 from controller.aws_apig_response_utils import create_response
 from models.errors import (
     Code,
+    CustomValidationError,
+    IdentifierDuplicationError,
+    InvalidJsonError,
     ResourceNotFoundError,
     Severity,
     UnauthorizedError,
     UnauthorizedVaxError,
+    UnhandledResponseError,
     create_operation_outcome,
 )
 
 _CUSTOM_EXCEPTION_TO_STATUS_MAP: dict[Type[Exception], int] = {
+    InvalidJsonError: 400,
+    CustomValidationError: 400,
     UnauthorizedError: 403,
     UnauthorizedVaxError: 403,
     ResourceNotFoundError: 404,
+    IdentifierDuplicationError: 422,
+    UnhandledResponseError: 500,
 }
 
 

backend/src/controller/fhir_controller.py

@@ -5,6 +5,7 @@
 import urllib.parse
 import uuid
 from decimal import Decimal
+from json import JSONDecodeError
 from typing import Optional
 
 from aws_lambda_typing.events import APIGatewayProxyEventV1
@@ -19,6 +20,7 @@
 from models.errors import (
     Code,
     IdentifierDuplicationError,
+    InvalidJsonError,
     ParameterException,
     ResourceNotFoundError,
     Severity,
@@ -48,7 +50,8 @@ def make_controller(
 
 
 class FhirController:
-    immunization_id_pattern = r"^[A-Za-z0-9\-.]{1,64}$"
+    _IMMUNIZATION_ID_PATTERN = r"^[A-Za-z0-9\-.]{1,64}$"
+    _API_SERVICE_URL = get_service_url()
 
     def __init__(
         self,
@@ -105,46 +108,22 @@ def get_immunization_by_id(self, aws_event: APIGatewayProxyEventV1) -> dict:
 
         return create_response(200, resource.json(), {E_TAG_HEADER_NAME: version})
 
-    def create_immunization(self, aws_event):
-        if not aws_event.get("headers"):
-            return create_response(
-                403,
-                create_operation_outcome(
-                    resource_id=str(uuid.uuid4()),
-                    severity=Severity.error,
-                    code=Code.forbidden,
-                    diagnostics="Unauthorized request",
-                ),
-            )
-
-        supplier_system = self._identify_supplier_system(aws_event)
+    @fhir_api_exception_handler
+    def create_immunization(self, aws_event: APIGatewayProxyEventV1) -> dict:
+        supplier_system = get_supplier_system_header(aws_event)
 
         try:
-            immunisation = json.loads(aws_event["body"], parse_float=Decimal)
-        except json.decoder.JSONDecodeError as e:
-            return self._create_bad_request(f"Request's body contains malformed JSON: {e}")
-        try:
-            resource = self.fhir_service.create_immunization(immunisation, supplier_system)
-            if "diagnostics" in resource:
-                exp_error = create_operation_outcome(
-                    resource_id=str(uuid.uuid4()),
-                    severity=Severity.error,
-                    code=Code.invariant,
-                    diagnostics=resource["diagnostics"],
-                )
-                return create_response(400, json.dumps(exp_error))
-            else:
-                location = f"{get_service_url()}/Immunization/{resource.id}"
-                version = "1"
-                return create_response(201, None, {"Location": location, "E-Tag": version})
-        except ValidationError as error:
-            return create_response(400, error.to_operation_outcome())
-        except IdentifierDuplicationError as duplicate:
-            return create_response(422, duplicate.to_operation_outcome())
-        except UnhandledResponseError as unhandled_error:
-            return create_response(500, unhandled_error.to_operation_outcome())
-        except UnauthorizedVaxError as unauthorized:
-            return create_response(403, unauthorized.to_operation_outcome())
+            immunisation: dict = json.loads(aws_event["body"], parse_float=Decimal)
+        except JSONDecodeError as e:
+            raise InvalidJsonError(message=str(f"Request's body contains malformed JSON: {e}"))
+
+        created_resource_id = self.fhir_service.create_immunization(immunisation, supplier_system)
+
+        return create_response(
+            status_code=201,
+            body=None,
+            headers={"Location": f"{self._API_SERVICE_URL}/Immunization/{created_resource_id}", "E-Tag": "1"},
+        )
 
     def update_immunization(self, aws_event):
         try:
@@ -178,7 +157,7 @@ def update_immunization(self, aws_event):
                 )
                 return create_response(400, json.dumps(exp_error))
             # Validate the imms id in the path params and body of request - end
-        except json.decoder.JSONDecodeError as e:
+        except JSONDecodeError as e:
             return self._create_bad_request(f"Request's body contains malformed JSON: {e}")
         except Exception as e:
             return self._create_bad_request(f"Request's body contains string: {e}")
@@ -407,7 +386,7 @@ def search_immunizations(self, aws_event: APIGatewayProxyEventV1) -> dict:
         return create_response(200, json.dumps(result_json_dict))
 
     def _validate_id(self, _id: str) -> Optional[dict]:
-        if not re.match(self.immunization_id_pattern, _id):
+        if not re.match(self._IMMUNIZATION_ID_PATTERN, _id):
             msg = "Validation errors: the provided event ID is either missing or not in the expected format."
             return create_operation_outcome(
                 resource_id=str(uuid.uuid4()),

backend/src/create_imms_handler.py

@@ -1,14 +1,10 @@
 import argparse
 import logging
 import pprint
-import uuid
 
-from constants import GENERIC_SERVER_ERROR_DIAGNOSTICS_MESSAGE
-from controller.aws_apig_response_utils import create_response
 from controller.fhir_controller import FhirController, make_controller
 from local_lambda import load_string
 from log_structure import function_info
-from models.errors import Code, Severity, create_operation_outcome
 
 logging.basicConfig(level="INFO")
 logger = logging.getLogger()
@@ -20,17 +16,7 @@ def create_imms_handler(event, _context):
 
 
 def create_immunization(event, controller: FhirController):
-    try:
-        return controller.create_immunization(event)
-    except Exception:  # pylint: disable = broad-exception-caught
-        logger.exception("Unhandled exception")
-        exp_error = create_operation_outcome(
-            resource_id=str(uuid.uuid4()),
-            severity=Severity.error,
-            code=Code.server_error,
-            diagnostics=GENERIC_SERVER_ERROR_DIAGNOSTICS_MESSAGE,
-        )
-        return create_response(500, exp_error)
+    return controller.create_immunization(event)
 
 
 if __name__ == "__main__":

backend/src/models/errors.py

@@ -201,6 +201,21 @@ def to_operation_outcome(self) -> dict:
         )
 
 
+@dataclass
+class InvalidJsonError(RuntimeError):
+    """Raised when client provides an invalid JSON payload"""
+
+    message: str
+
+    def to_operation_outcome(self) -> dict:
+        return create_operation_outcome(
+            resource_id=str(uuid.uuid4()),
+            severity=Severity.error,
+            code=Code.invalid,
+            diagnostics=self.message,
+        )
+
+
 def create_operation_outcome(resource_id: str, severity: Severity, code: Code, diagnostics: str) -> dict:
     """Create an OperationOutcome object. Do not use `fhir.resource` library since it adds unnecessary validations"""
     return {

backend/src/repository/fhir_repository.py

@@ -1,6 +1,5 @@
 import os
 import time
-import uuid
 from dataclasses import dataclass
 from typing import Optional, Tuple
 
@@ -17,6 +16,7 @@
     ResourceNotFoundError,
     UnhandledResponseError,
 )
+from models.utils.generic_utils import get_contained_patient
 from models.utils.validation_utils import (
     check_identifier_system_value,
     get_vaccine_type,
@@ -151,15 +151,22 @@ def get_immunization_by_id_all(self, imms_id: str, imms: dict) -> Optional[dict]
         else:
             return None
 
-    def create_immunization(self, immunization: dict, patient: any, supplier_system: str) -> dict:
-        new_id = str(uuid.uuid4())
-        immunization["id"] = new_id
-        attr = RecordAttributes(immunization, patient)
+    def check_immunization_identifier_exists(self, system: str, unique_id: str) -> bool:
+        """Checks whether an immunization with the given immunization identifier (system + local ID) exists."""
+        response = self.table.query(
+            IndexName="IdentifierGSI",
+            KeyConditionExpression=Key("IdentifierPK").eq(f"{system}#{unique_id}"),
+        )
 
-        query_response = _query_identifier(self.table, "IdentifierGSI", "IdentifierPK", attr.identifier)
+        if "Items" in response and len(response["Items"]) > 0:
+            return True
 
-        if query_response is not None:
-            raise IdentifierDuplicationError(identifier=attr.identifier)
+        return False
+
+    def create_immunization(self, immunization: dict, supplier_system: str) -> str:
+        """Creates a new immunization record returning the unique id if successful."""
+        patient = get_contained_patient(immunization)
+        attr = RecordAttributes(immunization, patient)
 
         response = self.table.put_item(
             Item={
@@ -174,10 +181,10 @@ def create_immunization(self, immunization: dict, patient: any, supplier_system:
             }
         )
 
-        if response["ResponseMetadata"]["HTTPStatusCode"] == 200:
-            return immunization
-        else:
-            raise UnhandledResponseError(message="Non-200 response from dynamodb", response=response)
+        if response["ResponseMetadata"]["HTTPStatusCode"] != 200:
+            raise UnhandledResponseError(message="Non-200 response from dynamodb", response=dict(response))
+
+        return immunization.get("id")
 
     def update_immunization(
         self,

backend/src/service/fhir_service.py

@@ -1,6 +1,7 @@
 import datetime
 import logging
 import os
+import uuid
 from enum import Enum
 from typing import Optional, Union
 from uuid import uuid4
@@ -22,6 +23,7 @@
 from filter import Filter
 from models.errors import (
     CustomValidationError,
+    IdentifierDuplicationError,
     InvalidPatientId,
     MandatoryError,
     ResourceNotFoundError,
@@ -132,26 +134,30 @@ def get_immunization_by_id_all(self, imms_id: str, imms: dict) -> Optional[dict]
         imms_resp = self.immunization_repo.get_immunization_by_id_all(imms_id, imms)
         return imms_resp
 
-    def create_immunization(self, immunization: dict, supplier_system: str) -> dict | Immunization:
+    def create_immunization(self, immunization: dict, supplier_system: str) -> str:
         if immunization.get("id") is not None:
             raise CustomValidationError("id field must not be present for CREATE operation")
 
         try:
             self.validator.validate(immunization)
         except (ValidationError, ValueError, MandatoryError) as error:
             raise CustomValidationError(message=str(error)) from error
-        patient = self._validate_patient(immunization)
-
-        if "diagnostics" in patient:
-            return patient
 
         vaccination_type = get_vaccine_type(immunization)
 
         if not self.authoriser.authorise(supplier_system, ApiOperationCode.CREATE, {vaccination_type}):
             raise UnauthorizedVaxError()
 
-        immunisation = self.immunization_repo.create_immunization(immunization, patient, supplier_system)
-        return Immunization.parse_obj(immunisation)
+        # TODO - consider only using FHIR entities in service layer
+        identifier_system = immunization["identifier"][0]["system"]
+        identifier_value = immunization["identifier"][0]["value"]
+
+        if self.immunization_repo.check_immunization_identifier_exists(identifier_system, identifier_value):
+            raise IdentifierDuplicationError(identifier=f"{identifier_system}#{identifier_value}")
+
+        # Set ID for the requested new record
+        immunization["id"] = str(uuid.uuid4())
+        return self.immunization_repo.create_immunization(immunization, supplier_system)
 
     def update_immunization(
         self,

backend/tests/controller/test_fhir_api_exception_handler.py

@@ -3,7 +3,13 @@
 from unittest.mock import patch
 
 from controller.fhir_api_exception_handler import fhir_api_exception_handler
-from models.errors import ResourceNotFoundError, UnauthorizedError, UnauthorizedVaxError
+from models.errors import (
+    CustomValidationError,
+    InvalidJsonError,
+    ResourceNotFoundError,
+    UnauthorizedError,
+    UnauthorizedVaxError,
+)
 
 
 class TestFhirApiExceptionHandler(unittest.TestCase):
@@ -27,6 +33,8 @@ def dummy_func():
     def test_exception_handler_handles_custom_exception_and_returns_fhir_response(self):
         """Test that custom exceptions are handled by the wrapper and a valid response is returned to the client"""
         test_cases = [
+            (InvalidJsonError("Invalid JSON provided"), 400, "invalid", "Invalid JSON provided"),
+            (CustomValidationError("This field was invalid"), 400, "invariant", "This field was invalid"),
             (UnauthorizedError(), 403, "forbidden", "Unauthorized request"),
             (
                 UnauthorizedVaxError(),