Use entities instead of passing dicts around

Author: dlzhry2nhs

backend/src/repository/fhir_repository.py

@@ -8,6 +8,8 @@
 import simplejson as json
 from boto3.dynamodb.conditions import Attr, Key
 from botocore.config import Config
+from fhir.resources.R4B.fhirtypes import Id
+from fhir.resources.R4B.immunization import Immunization
 from mypy_boto3_dynamodb.service_resource import DynamoDBServiceResource, Table
 from responses import logger
 
@@ -163,17 +165,19 @@ def check_immunization_identifier_exists(self, system: str, unique_id: str) -> b
 
         return False
 
-    def create_immunization(self, immunization: dict, supplier_system: str) -> str:
+    def create_immunization(self, immunization: Immunization, supplier_system: str) -> Id:
         """Creates a new immunization record returning the unique id if successful."""
-        patient = get_contained_patient(immunization)
-        attr = RecordAttributes(immunization, patient)
+        immunization_as_dict = immunization.dict()
+
+        patient = get_contained_patient(immunization_as_dict)
+        attr = RecordAttributes(immunization_as_dict, patient)
 
         response = self.table.put_item(
             Item={
                 "PK": attr.pk,
                 "PatientPK": attr.patient_pk,
                 "PatientSK": attr.patient_sk,
-                "Resource": json.dumps(attr.resource, use_decimal=True),
+                "Resource": immunization.json(use_decimal=True),
                 "IdentifierPK": attr.identifier,
                 "Operation": "CREATE",
                 "Version": 1,
@@ -184,7 +188,7 @@ def create_immunization(self, immunization: dict, supplier_system: str) -> str:
         if response["ResponseMetadata"]["HTTPStatusCode"] != 200:
             raise UnhandledResponseError(message="Non-200 response from dynamodb", response=dict(response))
 
-        return immunization.get("id")
+        return immunization.id
 
     def update_immunization(
         self,

backend/src/service/fhir_service.py

@@ -3,7 +3,7 @@
 import os
 import uuid
 from enum import Enum
-from typing import Optional, Union
+from typing import Optional, Union, cast
 from uuid import uuid4
 
 from fhir.resources.R4B.bundle import (
@@ -14,6 +14,8 @@
     BundleEntrySearch,
     BundleLink,
 )
+from fhir.resources.R4B.fhirtypes import Id
+from fhir.resources.R4B.identifier import Identifier
 from fhir.resources.R4B.immunization import Immunization
 from pydantic import ValidationError
 
@@ -134,7 +136,7 @@ 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) -> str:
+    def create_immunization(self, immunization: dict, supplier_system: str) -> Id:
         if immunization.get("id") is not None:
             raise CustomValidationError("id field must not be present for CREATE operation")
 
@@ -148,15 +150,16 @@ def create_immunization(self, immunization: dict, supplier_system: str) -> str:
         if not self.authoriser.authorise(supplier_system, ApiOperationCode.CREATE, {vaccination_type}):
             raise UnauthorizedVaxError()
 
-        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)
+
+        immunization_fhir_entity = Immunization.parse_obj(immunization)
+        identifier = cast(Identifier, immunization_fhir_entity.identifier[0])
+
+        if self.immunization_repo.check_immunization_identifier_exists(identifier.system, identifier.value):
+            raise IdentifierDuplicationError(identifier=f"{identifier.system}#{identifier.value}")
+
+        return self.immunization_repo.create_immunization(immunization_fhir_entity, supplier_system)
 
     def update_immunization(
         self,

backend/tests/repository/test_fhir_repository.py

@@ -6,6 +6,7 @@
 import botocore.exceptions
 import simplejson as json
 from boto3.dynamodb.conditions import Attr, Key
+from fhir.resources.R4B.immunization import Immunization
 
 from models.errors import (
     IdentifierDuplicationError,
@@ -195,7 +196,7 @@ def setUp(self):
 
     def test_create_immunization(self):
         """it should create Immunization, and return created object unique ID"""
-        imms = create_covid_19_immunization_dict(imms_id=self._MOCK_CREATED_UUID)
+        imms = Immunization.parse_obj(create_covid_19_immunization_dict(imms_id=self._MOCK_CREATED_UUID))
 
         self.table.put_item = MagicMock(return_value={"ResponseMetadata": {"HTTPStatusCode": 200}})
         self.mock_redis_client.hget.return_value = "COVID19"
@@ -208,7 +209,7 @@ def test_create_immunization(self):
                 "PK": f"Immunization#{self._MOCK_CREATED_UUID}",
                 "PatientPK": "Patient#9990548609",
                 "PatientSK": f"COVID19#{self._MOCK_CREATED_UUID}",
-                "Resource": json.dumps(imms),
+                "Resource": imms.json(),
                 "IdentifierPK": "https://supplierABC/identifiers/vacc#ACME-vacc123456",
                 "Operation": "CREATE",
                 "Version": 1,
@@ -225,7 +226,9 @@ def test_create_should_catch_dynamo_error(self):
 
         with self.assertRaises(UnhandledResponseError) as e:
             # When
-            self.repository.create_immunization(create_covid_19_immunization_dict("an-id"), "Test")
+            self.repository.create_immunization(
+                Immunization.parse_obj(create_covid_19_immunization_dict("an-id")), "Test"
+            )
 
         # Then
         self.assertDictEqual(e.exception.response, response)
@@ -251,7 +254,7 @@ def test_create_patient_gsi(self):
         self.table.query = MagicMock(return_value={})
 
         # When
-        _ = self.repository.create_immunization(imms, "Test")
+        _ = self.repository.create_immunization(Immunization.parse_obj(imms), "Test")
 
         # Then
         item = self.table.put_item.call_args.kwargs["Item"]
@@ -268,7 +271,7 @@ def test_create_patient_with_vaccine_type(self):
         self.table.put_item = MagicMock(return_value={"ResponseMetadata": {"HTTPStatusCode": 200}})
 
         # When
-        _ = self.repository.create_immunization(imms, "Test")
+        _ = self.repository.create_immunization(Immunization.parse_obj(imms), "Test")
 
         # Then
         item = self.table.put_item.call_args.kwargs["Item"]
@@ -584,12 +587,12 @@ def setUp(self):
     def test_decimal_on_create(self):
         """it should create Immunization, and preserve decimal value"""
         imms = create_covid_19_immunization_dict(imms_id="an-id")
-        imms["doseQuantity"] = 0.7477
+        imms["doseQuantity"]["value"] = 0.7477
 
         self.table.put_item = MagicMock(return_value={"ResponseMetadata": {"HTTPStatusCode": 200}})
         self.table.query = MagicMock(return_value={})
 
-        res_imms = self.repository.create_immunization(imms, "Test")
+        res_imms = self.repository.create_immunization(Immunization.parse_obj(imms), "Test")
 
         self.assertEqual(res_imms, "an-id")
 
@@ -599,7 +602,7 @@ def test_decimal_on_create(self):
             "PK": ANY,
             "PatientPK": ANY,
             "PatientSK": ANY,
-            "Resource": json.dumps(imms, use_decimal=True),
+            "Resource": Immunization.parse_obj(imms).json(use_decimal=True),
             "IdentifierPK": ANY,
             "Operation": "CREATE",
             "Version": 1,
@@ -612,7 +615,7 @@ def test_decimal_on_create(self):
 
         resource_from_item = json.loads(item_passed_to_put_item["Resource"])
         self.assertEqual(
-            resource_from_item["doseQuantity"],
+            resource_from_item["doseQuantity"]["value"],
             0.7477,
         )
 

backend/tests/service/test_fhir_service.py

@@ -481,7 +481,7 @@ def test_create_immunization(self):
         self.imms_repo.check_immunization_identifier_exists.assert_called_once_with(
             "https://supplierABC/identifiers/vacc", "ACME-vacc123456"
         )
-        self.imms_repo.create_immunization.assert_called_once_with(req_imms, "Test")
+        self.imms_repo.create_immunization.assert_called_once_with(Immunization.parse_obj(req_imms), "Test")
 
         self.validator.validate.assert_called_once_with(req_imms)
         self.assertEqual(self._MOCK_NEW_UUID, created_id)