VED-000 Quick test - will close soon

lambdas/backend/src/repository/fhir_repository.py

@@ -5,7 +5,7 @@
 import boto3
 import botocore.exceptions
 import simplejson as json
-from boto3.dynamodb.conditions import Attr, Key
+from boto3.dynamodb.conditions import Attr, ConditionBase, Key
 from botocore.config import Config
 from fhir.resources.R4B.fhirtypes import Id
 from fhir.resources.R4B.identifier import Identifier
@@ -299,39 +299,38 @@ def delete_immunization(self, imms_id: str, supplier_system: str) -> None:
             else:
                 raise error
 
-    def find_immunizations(self, patient_identifier: str, vaccine_types: set) -> list[dict]:
-        condition = Key("PatientPK").eq(_make_patient_pk(patient_identifier))
-        is_not_deleted = Attr("DeletedAt").not_exists() | Attr("DeletedAt").eq("reinstated")
+    def search_immunizations(self, patient_identifier: str, vaccine_types: set) -> list[dict]:
+        """Searches for immunisations by patient identifier (NHS Number) and the vaccination type"""
+        nhs_number_key_condition = Key("PatientPK").eq(_make_patient_pk(patient_identifier))
+        vacc_type_condition = self._build_vacc_type_key_condition(vaccine_types)
+        filter_condition = vacc_type_condition & (Attr("DeletedAt").not_exists() | Attr("DeletedAt").eq("reinstated"))
 
-        ieds_resources = self.get_all_items(condition, is_not_deleted)
+        ieds_resources = self.get_all_items(nhs_number_key_condition, filter_condition)
 
         if not ieds_resources:
             return []
 
-        # Filter the response to contain only the requested vaccine types
-        filtered_ieds_resources = [x for x in ieds_resources if self._vaccine_type(x["PatientSK"]) in vaccine_types]
-
         # Return a list of the FHIR immunization resource JSON items
         final_resources = [
             {
                 **json.loads(item["Resource"]),
                 "meta": {"versionId": int(item.get("Version", 1))},
             }
-            for item in filtered_ieds_resources
+            for item in ieds_resources
         ]
 
         return final_resources
 
-    def get_all_items(self, condition, is_not_deleted):
+    def get_all_items(self, key_condition: ConditionBase, filter_condition: ConditionBase):
         """Query DynamoDB and paginate through all results."""
         all_items = []
         last_evaluated_key = None
 
         while True:
             query_args = {
                 "IndexName": "PatientGSI",
-                "KeyConditionExpression": condition,
-                "FilterExpression": is_not_deleted,
+                "KeyConditionExpression": key_condition,
+                "FilterExpression": filter_condition,
             }
             if last_evaluated_key:
                 query_args["ExclusiveStartKey"] = last_evaluated_key
@@ -349,6 +348,16 @@ def get_all_items(self, condition, is_not_deleted):
 
         return all_items
 
+    @staticmethod
+    def _build_vacc_type_key_condition(vacc_types: set) -> ConditionBase:
+        vacc_type_condition = None
+
+        for vacc_type in vacc_types:
+            key_cond = Attr("PatientSK").begins_with(vacc_type)
+            vacc_type_condition = key_cond if vacc_type_condition is None else vacc_type_condition | key_cond
+
+        return vacc_type_condition
+
     @staticmethod
     def _vaccine_type(patient_sk: str) -> str:
         parsed = [str.strip(s) for s in patient_sk.split("#")]

lambdas/backend/src/service/fhir_service.py

@@ -213,7 +213,7 @@ def search_immunizations(
             raise UnauthorizedVaxError()
 
         # Have to retrieve first and then inspect resource to filter by date
-        all_resources = self.immunization_repo.find_immunizations(nhs_number, permitted_vacc_types)
+        all_resources = self.immunization_repo.search_immunizations(nhs_number, permitted_vacc_types)
         filtered_resources = self._filter_search_results_by_date_and_status(
             immunizations=all_resources, date_from=date_from, date_to=date_to, status=Constants.COMPLETED_STATUS
         )

lambdas/backend/tests/repository/test_fhir_repository.py

@@ -596,13 +596,14 @@ def test_find_immunizations_returns_empty_list_when_not_found(self):
         self.table.query = MagicMock(return_value=dynamo_response)
 
         # When
-        result = self.repository.find_immunizations(nhs_number, vaccine_types={"COVID"})
+        result = self.repository.search_immunizations(nhs_number, vaccine_types={"COVID"})
 
         # Then
         self.table.query.assert_called_once_with(
             IndexName="PatientGSI",
             KeyConditionExpression=Key("PatientPK").eq(_make_patient_pk(nhs_number)),
-            FilterExpression=Attr("DeletedAt").not_exists() | Attr("DeletedAt").eq("reinstated"),
+            FilterExpression=Attr("PatientSK").begins_with("COVID")
+            & (Attr("DeletedAt").not_exists() | Attr("DeletedAt").eq("reinstated")),
         )
         self.assertEqual(result, [])
 
@@ -627,7 +628,7 @@ def test_find_immunizations_returns_resources_including_meta(self):
         self.table.query = MagicMock(return_value=dynamo_response)
 
         # When
-        results = self.repository.find_immunizations("an-id", {"COVID"})
+        results = self.repository.search_immunizations("an-id", {"COVID"})
 
         # Then
         self.assertListEqual(results, [imms1, imms2])
@@ -650,19 +651,19 @@ def test_find_immunizations_filters_any_vacc_types_not_in_the_request(self):
             },
             {
                 "Resource": json.dumps(imms3),
-                "PatientSK": "MMR#some_other_text",
+                "PatientSK": "FLU#some_other_text",
                 "Version": "4",
             },
         ]
 
         dynamo_response = {"ResponseMetadata": {"HTTPStatusCode": 200}, "Items": items}
-        self.table.query = MagicMock(return_value=dynamo_response)
+        self.table.query = MagicMock(side_effect=[dynamo_response])
 
         # When
-        results = self.repository.find_immunizations("an-id", {"COVID", "FLU"})
+        results = self.repository.search_immunizations("an-id", {"COVID", "FLU"})
 
         # Then
-        self.assertListEqual(results, [imms1, imms2])
+        self.assertListEqual(results, [imms1, imms2, imms3])
 
     def test_bad_response_from_dynamo(self):
         """it should throw UnhandledResponse when the response from dynamodb can't be handled"""
@@ -672,7 +673,7 @@ def test_bad_response_from_dynamo(self):
 
         with self.assertRaises(UnhandledResponseError) as e:
             # When
-            self.repository.find_immunizations("an-id", {"COVID"})
+            self.repository.search_immunizations("an-id", {"COVID"})
 
         # Then
         self.assertDictEqual(e.exception.response, response)

lambdas/backend/tests/service/test_fhir_service.py

@@ -752,15 +752,15 @@ def test_search_immunizations_returns_results_as_a_search_bundle(self, mock_uuid
         mock_resource = create_covid_immunization_dict("1234-some-id")
         vaccine_type = "COVID"
         self.authoriser.filter_permitted_vacc_types.return_value = {vaccine_type}
-        self.imms_repo.find_immunizations.return_value = [mock_resource]
+        self.imms_repo.search_immunizations.return_value = [mock_resource]
 
         # When
         result = self.fhir_service.search_immunizations(
             VALID_NHS_NUMBER, {vaccine_type}, self.MOCK_SUPPLIER_SYSTEM_NAME, None, None, None
         )
 
         # Then
-        self.imms_repo.find_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
+        self.imms_repo.search_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
         mock_uuid.assert_called_once()
         self.authoriser.filter_permitted_vacc_types.assert_called_once_with(
             self.MOCK_SUPPLIER_SYSTEM_NAME, ApiOperationCode.SEARCH, {"COVID"}
@@ -797,7 +797,7 @@ def test_search_immunizations_filters_by_date_and_status(self, mock_uuid):
 
         vaccine_type = "COVID"
         self.authoriser.filter_permitted_vacc_types.return_value = {vaccine_type}
-        self.imms_repo.find_immunizations.return_value = [
+        self.imms_repo.search_immunizations.return_value = [
             mock_resource_filtered_date_from,
             mock_resource,
             mock_resource_filtered_date_to,
@@ -815,7 +815,7 @@ def test_search_immunizations_filters_by_date_and_status(self, mock_uuid):
         )
 
         # Then
-        self.imms_repo.find_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
+        self.imms_repo.search_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
         mock_uuid.assert_called_once()
         self.authoriser.filter_permitted_vacc_types.assert_called_once_with(
             self.MOCK_SUPPLIER_SYSTEM_NAME, ApiOperationCode.SEARCH, {"COVID"}
@@ -848,15 +848,15 @@ def test_search_immunizations_adds_include_to_searched_url(self, mock_uuid):
         mock_resource = create_covid_immunization_dict("1234-some-id")
         vaccine_type = "COVID"
         self.authoriser.filter_permitted_vacc_types.return_value = {vaccine_type}
-        self.imms_repo.find_immunizations.return_value = [mock_resource]
+        self.imms_repo.search_immunizations.return_value = [mock_resource]
 
         # When
         result = self.fhir_service.search_immunizations(
             VALID_NHS_NUMBER, {vaccine_type}, self.MOCK_SUPPLIER_SYSTEM_NAME, None, None, "Patient.identifier"
         )
 
         # Then
-        self.imms_repo.find_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
+        self.imms_repo.search_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
         mock_uuid.assert_called_once()
         self.authoriser.filter_permitted_vacc_types.assert_called_once_with(
             self.MOCK_SUPPLIER_SYSTEM_NAME, ApiOperationCode.SEARCH, {"COVID"}
@@ -884,15 +884,15 @@ def test_search_immunizations_returns_empty_bundle_when_no_results_found(self):
         """it should return an empty search bundle when no results are found"""
         vaccine_type = "FLU"
         self.authoriser.filter_permitted_vacc_types.return_value = {vaccine_type}
-        self.imms_repo.find_immunizations.return_value = []
+        self.imms_repo.search_immunizations.return_value = []
 
         # When
         result = self.fhir_service.search_immunizations(
             VALID_NHS_NUMBER, {vaccine_type}, self.MOCK_SUPPLIER_SYSTEM_NAME, None, None, None
         )
 
         # Then
-        self.imms_repo.find_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
+        self.imms_repo.search_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
         self.authoriser.filter_permitted_vacc_types.assert_called_once_with(
             self.MOCK_SUPPLIER_SYSTEM_NAME, ApiOperationCode.SEARCH, {vaccine_type}
         )
@@ -920,7 +920,7 @@ def test_search_immunizations_includes_an_error_outcome_within_results_if_client
         mock_resource = create_covid_immunization_dict("1234-some-id")
         vaccine_type = "COVID"
         self.authoriser.filter_permitted_vacc_types.return_value = {vaccine_type}
-        self.imms_repo.find_immunizations.return_value = [mock_resource]
+        self.imms_repo.search_immunizations.return_value = [mock_resource]
 
         # When
         result = self.fhir_service.search_immunizations(
@@ -929,7 +929,7 @@ def test_search_immunizations_includes_an_error_outcome_within_results_if_client
 
         # Then
         # Does not pass FLU in as client is only permitted to retrieve COVID vaccinations
-        self.imms_repo.find_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
+        self.imms_repo.search_immunizations.assert_called_once_with(VALID_NHS_NUMBER, {vaccine_type})
         mock_uuid.assert_called_once()
         self.authoriser.filter_permitted_vacc_types.assert_called_once_with(
             self.MOCK_SUPPLIER_SYSTEM_NAME, ApiOperationCode.SEARCH, {"COVID", "FLU"}
@@ -969,14 +969,14 @@ def test_search_raises_unauthorised_error_if_no_permissions(self):
         self.authoriser.filter_permitted_vacc_types.assert_called_once_with(
             self.MOCK_SUPPLIER_SYSTEM_NAME, ApiOperationCode.SEARCH, {vaccine_type}
         )
-        self.imms_repo.find_immunizations.assert_not_called()
+        self.imms_repo.search_immunizations.assert_not_called()
 
     def test_search_immunizations_includes_operation_outcome_when_invalid_immunization_targets_provided(self):
         """it should include an OperationOutcome in the bundle when invalid -immunization.target values were provided"""
         mock_resource = create_covid_immunization_dict("1234-some-id")
         vaccine_type = "COVID"
         self.authoriser.filter_permitted_vacc_types.return_value = {vaccine_type}
-        self.imms_repo.find_immunizations.return_value = [mock_resource]
+        self.imms_repo.search_immunizations.return_value = [mock_resource]
 
         result = self.fhir_service.search_immunizations(
             VALID_NHS_NUMBER,

lambdas/backend/tests/service/test_fhir_service_target_disease.py

@@ -47,7 +47,7 @@ def test_make_empty_search_bundle_with_target_disease_not_in_mapping_returns_bun
     def test_search_immunizations_with_target_disease_codes_for_url_echoes_target_disease_in_bundle_link(self):
         """it should include target-disease param in bundle self link when target_disease_codes_for_url is set"""
         self.authoriser.filter_permitted_vacc_types.return_value = {"MMR"}
-        self.imms_repo.find_immunizations.return_value = []
+        self.imms_repo.search_immunizations.return_value = []
 
         result = self.fhir_service.search_immunizations(
             "9000000009",
@@ -70,7 +70,7 @@ def test_search_immunizations_with_target_disease_codes_for_url_echoes_target_di
     def test_search_immunizations_with_invalid_target_diseases_adds_operation_outcomes(self):
         """it should add one OperationOutcome entry per invalid target disease diagnostic"""
         self.authoriser.filter_permitted_vacc_types.return_value = {"MMR"}
-        self.imms_repo.find_immunizations.return_value = []
+        self.imms_repo.search_immunizations.return_value = []
 
         result = self.fhir_service.search_immunizations(
             "9000000009",