Fix root issue and add python unit tests

Author: dlzhry2nhs

.github/workflows/run-e2e-automation-tests.yml

@@ -197,7 +197,7 @@ jobs:
           echo "::add-mask::$CODE"
 
           echo "Requesting access token from Apigee..."
-          response=$(curl -s -X POST "https://login.apigee.com/oauth/token" \
+          response=$(curl -s --retry 3 -X POST "https://login.apigee.com/oauth/token" \
             -H "Content-Type: application/x-www-form-urlencoded" \
             -H "Accept: application/json;charset=utf-8" \
             -H "Authorization: Basic $APIGEE_BASIC_AUTH_TOKEN" \

lambdas/backend/src/filter.py

@@ -1,6 +1,6 @@
 """Functions for filtering a FHIR Immunization Resource"""
 
-from common.models.constants import Urls
+from common.models.constants import Constants, Urls
 from common.models.utils.generic_utils import (
     get_contained_patient,
     get_contained_practitioner,
@@ -28,23 +28,34 @@ def create_reference_to_patient_resource(patient_full_url: str, patient: dict) -
     """
     Returns a reference to the given patient which includes the patient nhs number identifier (system and value fields
     only) and a reference to patient full url. "Type" field is set to "Patient".
+
+    Due to validation business rules, it is possible (VED-1073) for a patient to be created without a value for NHS
+    Number or indeed an entry for their identifier.
     """
-    patient_nhs_number_identifier = [x for x in patient["identifier"] if x.get("system") == Urls.NHS_NUMBER][0]
+    patient_nhs_number_identifier: dict | None = None
+
+    for identifier in patient.get("identifier", []):
+        if identifier.get("system", "") == Urls.NHS_NUMBER:
+            patient_nhs_number_identifier = identifier
+            break
+
+    if patient_nhs_number_identifier is None:
+        return {
+            "reference": patient_full_url,
+            "type": Constants.PATIENT_RESOURCE_TYPE,
+        }
 
     return {
         "reference": patient_full_url,
-        "type": "Patient",
-        "identifier": {
-            "system": patient_nhs_number_identifier["system"],
-            "value": patient_nhs_number_identifier["value"],
-        },
+        "type": Constants.PATIENT_RESOURCE_TYPE,
+        "identifier": patient_nhs_number_identifier,
     }
 
 
 def replace_address_postal_codes(imms: dict) -> dict:
     """Replace any postal codes found in contained patient address with 'ZZ99 3CZ'"""
     for resource in imms.get("contained", [{}]):
-        if resource.get("resourceType") == "Patient":
+        if resource.get("resourceType") == Constants.PATIENT_RESOURCE_TYPE:
             for address in resource.get("address", [{}]):
                 if address.get("postalCode") is not None:
                     address["postalCode"] = "ZZ99 3CZ"

lambdas/backend/tests/service/test_fhir_service.py

@@ -288,6 +288,38 @@ def test_get_immunization_by_identifier_when_elements_parameter_provided(self):
             Immunization.construct(**{"resourceType": "Immunization", "id": "1234-some-id", "meta": {"versionId": 1}}),
         )
 
+    def test_get_immunization_by_identifier_returns_patient_created_without_nhs_number(self):
+        """VED-1073 - the contained patient within an Immunization resource MAY be created without an NHS Number as per
+        the business rules. The identifier retrieval should still succeed when this is the case."""
+        mock_resource_no_nhs_number = create_covid_immunization_dict("1234-some-id", omit_nhs_number=True)
+
+        self.mock_redis.hget.return_value = "COVID"
+        self.mock_redis_getter.return_value = self.mock_redis
+        self.authoriser.authorise.return_value = True
+        self.imms_repo.get_immunization_by_identifier.return_value = mock_resource_no_nhs_number, self.mock_resource_meta
+
+        # When
+        result = self.fhir_service.get_immunization_by_identifier(self.test_identifier, self.MOCK_SUPPLIER_NAME, None)
+
+        # Then
+        self.imms_repo.get_immunization_by_identifier.assert_called_once_with(self.test_identifier)
+        self.authoriser.authorise.assert_called_once_with(self.MOCK_SUPPLIER_NAME, ApiOperationCode.SEARCH, {"COVID"})
+
+        self.assertEqual(result.type, "searchset")
+        self.assertEqual(result.total, 1)
+        self.assertEqual(
+            result.link[0],
+            BundleLink.construct(
+                relation="self",
+                url="https://internal-dev.api.service.nhs.uk/immunisation-fhir-api/FHIR/R4/Immunization?identifier=some-"
+                "system|some-value",
+            ),
+        )
+
+        # Search function adds meta to the resource
+        mock_resource_no_nhs_number["meta"] = {"versionId": "1"}
+        self.assertEqual(result.entry[0].resource, Immunization.parse_obj(mock_resource_no_nhs_number))
+
 
 class TestCreateImmunization(TestFhirServiceBase):
     """Tests for FhirService.create_immunization"""

lambdas/backend/tests/test_filter.py

@@ -86,6 +86,38 @@ def test_create_reference_to_patient_resource(self):
             expected_output,
         )
 
+    def test_create_reference_to_patient_resource_when_identifier_missing(self):
+        """Test that create_reference_to_patient_resource creates an appropriate reference without identifier info
+        where the saved patient record does not contain this information"""
+        test_data = deepcopy(self.bundle_patient_resource)
+        del test_data["identifier"]
+
+        patient_uuid = str(uuid4())
+        expected_output = {"reference": patient_uuid, "type": "Patient"}
+
+        self.assertEqual(
+            create_reference_to_patient_resource(patient_uuid, test_data),
+            expected_output,
+        )
+
+    def test_create_reference_to_patient_resource_when_nhs_number_missing(self):
+        """Test that create_reference_to_patient_resource creates an appropriate reference with empty identifier info
+        where the saved patient record does not contain this information"""
+        test_data = deepcopy(self.bundle_patient_resource)
+        del test_data["identifier"][0]["value"]
+
+        patient_uuid = str(uuid4())
+        expected_output = {
+            "reference": patient_uuid,
+            "type": "Patient",
+            "identifier": {"system": "https://fhir.nhs.uk/Id/nhs-number"},
+        }
+
+        self.assertEqual(
+            create_reference_to_patient_resource(patient_uuid, test_data),
+            expected_output,
+        )
+
     def test_add_use_to_identifier(self):
         """Test that a use of "offical" is added to identifier[0] is no use already given"""
         input_data = deepcopy(self.covid_immunization_event)

lambdas/shared/src/common/models/constants.py

@@ -45,8 +45,9 @@ class Constants:
             "address",
         },
     }
-
-    ALLOWED_CONTAINED_RESOURCES = {"Practitioner", "Patient"}
+    PATIENT_RESOURCE_TYPE = "Patient"
+    PRACTITIONER_RESOURCE_TYPE = "Practitioner"
+    ALLOWED_CONTAINED_RESOURCES = {PRACTITIONER_RESOURCE_TYPE, PATIENT_RESOURCE_TYPE}
 
     # As per Personal Demographics Service (PDS) FHIR API, the maximum length of a family name is 35 characters:
     # https://digital.nhs.uk/developer/api-catalogue/personal-demographics-service-fhir#post-/Patient

lambdas/shared/tests/test_common/testing_utils/immunization_utils.py

@@ -18,13 +18,17 @@ def create_covid_immunization_dict(
     nhs_number: str = VALID_NHS_NUMBER,
     occurrence_date_time: str = "2021-02-07T13:28:17+00:00",
     status: str = "completed",
+    omit_nhs_number: bool = False,
 ):
     immunization_json = load_json_data("completed_covid_immunization_event.json")
     immunization_json["id"] = imms_id
 
-    [x for x in immunization_json["contained"] if x.get("resourceType") == "Patient"][0]["identifier"][0]["value"] = (
-        nhs_number
-    )
+    for contained_resource in immunization_json.get("contained", []):
+        if contained_resource.get("resourceType") == "Patient":
+            if omit_nhs_number:
+                del contained_resource["identifier"][0]["value"]
+            else:
+                contained_resource["identifier"][0]["value"] = nhs_number
 
     immunization_json["occurrenceDateTime"] = occurrence_date_time
     immunization_json["status"] = status