VED-1073 Fix unhandled exception when searching record by identifier where pat has no NHS Number (#1229)

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 +1,8 @@
 """Functions for filtering a FHIR Immunization Resource"""
 
-from common.models.constants import Urls
+import copy
+
+from common.models.constants import Constants, Urls
 from common.models.utils.generic_utils import (
     get_contained_patient,
     get_contained_practitioner,
@@ -28,23 +30,34 @@ 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 = copy.deepcopy(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[0].value 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

@@ -2,6 +2,7 @@
 
 from fhir.resources.R4B.immunization import Immunization
 
+from common.models.constants import Constants
 from test_common.testing_utils.generic_utils import load_json_data
 from test_common.testing_utils.values_for_tests import ValidValues
 
@@ -18,13 +19,17 @@ 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") == Constants.PATIENT_RESOURCE_TYPE:
+            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

tests/e2e_automation/features/APITests/search.feature

@@ -201,14 +201,22 @@ Feature: Search the immunization of a patient
     @Delete_cleanUp @vaccine_type_FLU @patient_id_Random  @supplier_name_Postman_Auth
     Scenario: Flu event is created and search post request fetch the only one record matched with identifier
         Given I have created a valid vaccination record
-        When Send a search request with Post method using identifier header for Immunization event created
+        When I send a search request with Post method using identifier parameter for Immunization event created
+        Then The request will be successful with the status code '200'
+        And correct immunization event is returned in the response
+
+    @smoke
+    @Delete_cleanUp @vaccine_type_FLU @patient_id_NullNHS  @supplier_name_Postman_Auth
+    Scenario: Search by Identifier (POST) is successful when patient does not have an NHS Number recorded
+        Given I have created a valid vaccination record
+        When I send a search request with Post method using identifier parameter for Immunization event created
         Then The request will be successful with the status code '200'
         And correct immunization event is returned in the response
 
     @Delete_cleanUp @vaccine_type_FLU @patient_id_Random  @supplier_name_Postman_Auth
     Scenario: Flu event is created and search post request fetch the only one record matched with identifier and _elements
         Given I have created a valid vaccination record
-        When Send a search request with Post method using identifier and _elements header for Immunization event created
+        When I send a search request with Post method using identifier and _elements parameters for Immunization event created
         Then The request will be successful with the status code '200'
         And correct immunization event is returned in the response with only specified elements
 
@@ -217,7 +225,7 @@ Feature: Search the immunization of a patient
     Scenario: Flu event is created and search post request fetch the only one record matched with identifier with correct version id
         Given I have created a valid vaccination record
         And created event is being updated twice
-        When Send a search request with Post method using identifier header for Immunization event created
+        When I send a search request with Post method using identifier parameter for Immunization event created
         Then The request will be successful with the status code '200'
         And correct immunization event is returned in the response
 
@@ -226,13 +234,13 @@ Feature: Search the immunization of a patient
     Scenario: Flu event is created and search post request fetch the only one record matched with identifier and _elements with correct version id
         Given I have created a valid vaccination record
         And created event is being updated twice
-        When Send a search request with Post method using identifier and _elements header for Immunization event created
+        When I send a search request with Post method using identifier and _elements parameters for Immunization event created
         Then The request will be successful with the status code '200'
         And correct immunization event is returned in the response with only specified elements
 
     @smoke
     @vaccine_type_4IN1 @patient_id_Random  @supplier_name_Postman_Auth
     Scenario: Empty search response will be received when no record is found for the given identifier in search request
-        When Send a search request with post method using invalid identifier header for Immunization event created
+        When I send a search request with Post method using an invalid identifier header for Immunization event created
         Then The request will be successful with the status code '200'
         And Empty immunization event is returned in the response

tests/e2e_automation/features/APITests/steps/test_search_steps.py

@@ -20,7 +20,7 @@
 scenarios("APITests/search.feature")
 
 
-@when("Send a search request with Post method using identifier header for Immunization event created")
+@when("I send a search request with Post method using identifier parameter for Immunization event created")
 def send_search_post_request_with_identifier_header(context):
     get_search_post_url_header(context)
     context.request = {
@@ -30,7 +30,9 @@ def send_search_post_request_with_identifier_header(context):
     context.response = http_requests_session.post(context.url, headers=context.headers, data=context.request)
 
 
-@when("Send a search request with Post method using identifier and _elements header for Immunization event created")
+@when(
+    "I send a search request with Post method using identifier and _elements parameters for Immunization event created"
+)
 def send_search_post_request_with_identifier_and_elements_header(context):
     get_search_post_url_header(context)
     context.request = {
@@ -41,7 +43,7 @@ def send_search_post_request_with_identifier_and_elements_header(context):
     context.response = http_requests_session.post(context.url, headers=context.headers, data=context.request)
 
 
-@when("Send a search request with post method using invalid identifier header for Immunization event created")
+@when("I send a search request with Post method using an invalid identifier header for Immunization event created")
 def send_search_post_request_with_invalid_identifier_header(context):
     get_search_post_url_header(context)
     context.request = {"identifier": f"https://www.ieds.england.nhs.uk/|{str(uuid.uuid4())}", "_elements": "meta,id"}

tests/e2e_automation/input/testData.csv

@@ -1,6 +1,6 @@
 id,nhs_number,family_name,given_name,gender,birth_date,address_text,address_line,city,district,state,postal_code,country,start_date,end_date
 ValidNHS,9449309981,test1,test2,unknown,1980-11-01,Validate Obf,"1, obf_2",obf_3,obf_4,obf_5,LS01 1AB,obf_7,2000-01-01,2025-01-01
-NUllNHS,,test1,test2,unknown,1980-11-01,Validate Obf,"1, obf_2",obf_3,obf_4,obf_5,LS01 1AB,obf_7,2000-01-01,2025-01-01
+NullNHS,none,test1,test2,unknown,1980-11-01,Validate Obf,"1, obf_2",obf_3,obf_4,obf_5,LS01 1AB,obf_7,2000-01-01,2025-01-01
 SFlag,9449310475,test1,test2,unknown,1980-11-01,Validate Obf,"1, obf_2",obf_3,obf_4,obf_5,LS01 1AB,obf_7,2000-01-01,2025-01-01
 InvalidInPDS,9449310599,test1,test2,unknown,1980-11-01,Validate Obf,"1, obf_2",obf_3,obf_4,obf_5,LS01 1AB,obf_7,2000-01-01,2025-01-01
 InvalidMOD11Check,1234567890,test1,test2,unknown,1980-11-01,Validate Obf,"1, obf_2",obf_3,obf_4,obf_5,LS01 1AB,obf_7,2000-01-01,2025-01-01
@@ -1006,4 +1006,4 @@ Valid_NHS,9000046696,GLENN,ROWE,male,2005-03-14,Moore 01 Bishop,Essex,City,distr
 Valid_NHS,9734891650,HETTY,DAWKIN,female,2005-03-14,1 GARDEN COURT,EPWORTH,City,district,State,DN9 1GA,UK,2016-06-12,2033-01-01
 Valid_NHS,9734281674,LANDON,EWART,male,2005-03-14,1186 THE MOORS,KIDLINGTON,City,district,State,OX5 2AD,UK,2021-09-29,2033-01-01
 Valid_NHS,9734353055,BETSY,HOPSON,female,2005-03-14,1186 THE MOORS,KIDLINGTON,City,district,State,OX4 4LX,UK,2013-01-28,2033-01-01
-Valid_NHS,9734107720,SARAH,PEILL,female,2005-03-14,1 DELAMERE,WYNYARD,City,district,State,TS22 5GH,UK,2016-11-10,2033-01-01
+Valid_NHS,9734107720,SARAH,PEILL,female,2005-03-14,1 DELAMERE,WYNYARD,City,district,State,TS22 5GH,UK,2016-11-10,2033-01-01